bioRxiv Channel: Rutgers University https://biorxiv.org This feed contains articles for bioRxiv Channel "Rutgers University" bioRxiv bioRxiv https://biorxiv.org <![CDATA[ Spectacle: Faster and more accurate chromatin state annotation using spectral learning ]]> https://biorxiv.org/content/10.1101/002725v1?rss=1 Jimin Song Kevin C Chen 2014-02-14 doi:10.1101/002725 Cold Spring Harbor Laboratory Press 2014-02-14 <![CDATA[ Behavioral variation in Drosophila melanogaster: no evidence for common alleles of large- effect at the foraging gene in a population from North Carolina, USA ]]> https://biorxiv.org/content/10.1101/004325v1?rss=1 Thomas Turner Christopher C Giauque Daniel R Schrider Andrew D Kern 2014-04-21 doi:10.1101/004325 Cold Spring Harbor Laboratory Press 2014-04-21 <![CDATA[ Protein folding and binding can emerge as evolutionary spandrels through structural coupling ]]> https://biorxiv.org/content/10.1101/008250v1?rss=1 Michael Manhart Alexandre V Morozov 2014-08-20 doi:10.1101/008250 Cold Spring Harbor Laboratory Press 2014-08-20 <![CDATA[ MDTraj: a modern, open library for the analysis of molecular dynamics trajectories ]]> https://biorxiv.org/content/10.1101/008896v1?rss=1 Robert T McGibbon Kyle A Beauchamp Christian R Schwantes Lee-Ping Wang Carlos X Hernández Matthew P Harrigan Thomas J Lane Jason M Swails Vijay S Pande 2014-09-09 doi:10.1101/008896 Cold Spring Harbor Laboratory Press 2014-09-09 <![CDATA[ Scaling properties of evolutionary paths in a biophysical model of protein adaptation ]]> https://biorxiv.org/content/10.1101/010082v1?rss=1 Michael Manhart Alexandre V. Morozov 2014-10-06 doi:10.1101/010082 Cold Spring Harbor Laboratory Press 2014-10-06 <![CDATA[ A biophysical approach to predicting protein-DNA binding energetics ]]> https://biorxiv.org/content/10.1101/012864v1?rss=1 George Locke Alexandre V Morozov 2014-12-17 doi:10.1101/012864 Cold Spring Harbor Laboratory Press 2014-12-17 <![CDATA[ Some remarks on moments for stochastic chemical kinetics ]]> https://biorxiv.org/content/10.1101/021410v1?rss=1 Eduardo Sontag Abhyudai Singh 2015-06-24 doi:10.1101/021410 Cold Spring Harbor Laboratory Press 2015-06-24 <![CDATA[ S/HIC: Robust identification of soft and hard sweeps using machine learning ]]> https://biorxiv.org/content/10.1101/024547v1?rss=1 Daniel R Schrider Andrew D Kern 2015-08-13 doi:10.1101/024547 Cold Spring Harbor Laboratory Press 2015-08-13 <![CDATA[ Incoherent feedforward motifs as immune change detectors ]]> https://biorxiv.org/content/10.1101/035600v1?rss=1 Eduardo Sontag 2015-12-30 doi:10.1101/035600 Cold Spring Harbor Laboratory Press 2015-12-30 <![CDATA[ fusionDB: assessing microbial diversity and environmental preferences via functional similarity networks ]]> https://biorxiv.org/content/10.1101/035923v1?rss=1 Chengsheng Zhu Yannick Mahlich Yana Bromberg 2016-01-06 doi:10.1101/035923 Cold Spring Harbor Laboratory Press 2016-01-06 <![CDATA[ Computational prediction shines light on type III secretion origins ]]> https://biorxiv.org/content/10.1101/036251v1?rss=1 Tatyana Goldberg Burkhard Rost Yana Bromberg 2016-01-10 doi:10.1101/036251 Cold Spring Harbor Laboratory Press 2016-01-10 <![CDATA[ Epistasis and the dynamics of reversion in molecular evolution ]]> https://biorxiv.org/content/10.1101/042895v1?rss=1 David M McCandlish Premal Shah Joshua B Plotkin 2016-03-09 doi:10.1101/042895 Cold Spring Harbor Laboratory Press 2016-03-09 <![CDATA[ Effects of linked selective sweeps on demographic inference and model selection ]]> https://biorxiv.org/content/10.1101/047019v1?rss=1 Daniel R Schrider Alexander G Shanku Andrew D Kern 2016-04-05 doi:10.1101/047019 Cold Spring Harbor Laboratory Press 2016-04-05 <![CDATA[ Multiplex gene editing by CRISPR-Cpf1 through autonomous processing of a single crRNA array ]]> https://biorxiv.org/content/10.1101/049122v1?rss=1 nView larger version (35K):norg.highwire.dtl.DTLVardef@1f0c15corg.highwire.dtl.DTLVardef@126a6fdorg.highwire.dtl.DTLVardef@9d6a2eorg.highwire.dtl.DTLVardef@a61f75_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1C_FLOATNO Cpf1 mediates processing of pre-crRNA. (a) Schematic of pre-crRNA processing for Cas9 and Cpf1. Cleavage sites indicated with red triangle. (b) In vitro processing of FnCpf1 pre-crRNA transcript (80 nM) with purified AsCpf1 or LbCpf1 protein ([~]320 nM). In the presence of Cpf1 nuclease the pre-crRNA was cleaved in a distinct pattern, indicating cleavage at similar sequence motifs. RNA molecules without Cpf1 DR features where not cleaved by Cpf1 (control RNA). (c) RNAseq analysis of FnCpf1 pre-crRNA cleavage products, as shown in (b). A high fraction of sequence reads smaller than 65nt are cleavage products of spacers flanked by DR sequences.nnC_FIG ]]> Bernd Zetsche Matthias Heidenreich Prarthana Mohanraju Iana Fedorova Jeroen Kneppers Ellen M DeGennaro Nerges Winblad Sourav R Choudhury Omar O Abudayyeh Jonathan S Gootenberg Wen Y Wu David A Scott Konstantin Severinov John van der Oost Feng Zhang 2016-10-01 doi:10.1101/049122 Cold Spring Harbor Laboratory Press 2016-10-01 <![CDATA[ Maximum intrinsic rate of population increase in sharks, rays, and chimaeras: the importance of survival to maturity ]]> https://biorxiv.org/content/10.1101/051482v1?rss=1 Sebastián A. Pardo Holly K. Kindsvater John D. Reynolds Nicholas K. Dulvy 2016-05-05 doi:10.1101/051482 Cold Spring Harbor Laboratory Press 2016-05-05 <![CDATA[ Separating spandrels from phenotypic targets of selection in adaptive molecular evolution ]]> https://biorxiv.org/content/10.1101/051862v1?rss=1 Stevan A Springer Michael Manhart Alexandre V Morozov 2016-05-05 doi:10.1101/051862 Cold Spring Harbor Laboratory Press 2016-05-05 <![CDATA[ Synthesizer: Expediting synthesis studies from context-free data with natural language processing ]]> https://biorxiv.org/content/10.1101/053629v1?rss=1 Lisa Gandy Jordan Gumm Benjamin Fertig Michael J Kennish Sameer Chavan Ann Thessen Luigi Marchionni Xiaoxan Xia Shambhavi Shankrit Elana J Fertig 2016-05-16 doi:10.1101/053629 Cold Spring Harbor Laboratory Press 2016-05-16 <![CDATA[ C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector ]]> https://biorxiv.org/content/10.1101/054742v1?rss=1 Omar O Abudayyeh Jonathan S Gootenberg Silvana Konermann Julia Joung Ian M Slaymaker David BT Cox Sergey Shmakov Kira S Makarova Ekaterina Semenova Leonid Minakhin Konstantin Severinov Aviv Regev Eric S Lander Eugene V Koonin Feng Zhang 2016-05-21 doi:10.1101/054742 Cold Spring Harbor Laboratory Press 2016-05-21 <![CDATA[ Activity flow over resting-state networks shapes cognitive task activations ]]> https://biorxiv.org/content/10.1101/055194v1?rss=1 Michael W Cole Takuya Ito Danielle S Bassett Douglas H Schultz 2016-05-24 doi:10.1101/055194 Cold Spring Harbor Laboratory Press 2016-05-24 <![CDATA[ Inference of epistatic effects and the development of drug resistance in HIV-1 protease ]]> https://biorxiv.org/content/10.1101/063750v1?rss=1 William F Flynn Allan Haldane Bruce E Torbett Ronald M Levy 2016-07-13 doi:10.1101/063750 Cold Spring Harbor Laboratory Press 2016-07-13 <![CDATA[ Generalization of the Ewens sampling formula to arbitrary fitness landscapes ]]> https://biorxiv.org/content/10.1101/065011v1?rss=1 Pavel Khromov Constantin D Malliaris Alexandre V Morozov 2016-07-21 doi:10.1101/065011 Cold Spring Harbor Laboratory Press 2016-07-21 <![CDATA[ Large-scale multivariate activation states of the human brain ]]> https://biorxiv.org/content/10.1101/068221v1?rss=1 Richard H Chen Takuya Ito Kaustubh R Kulkarni Michael W Cole 2016-08-06 doi:10.1101/068221 Cold Spring Harbor Laboratory Press 2016-08-06 <![CDATA[ The Modular Adaptive Ribosome ]]> https://biorxiv.org/content/10.1101/068361v1?rss=1 Anupama Yadav Aparna Radhakrishnan Anshuman Panda Amartya Singh Himanshu Sinha Gyan Bhanot 2016-08-16 doi:10.1101/068361 Cold Spring Harbor Laboratory Press 2016-08-16 <![CDATA[ Empirical validation of directed functional connectivity ]]> https://biorxiv.org/content/10.1101/070979v1?rss=1 Ravi D Mill Anto Bagic Walter Schneider Michael W Cole 2016-08-22 doi:10.1101/070979 Cold Spring Harbor Laboratory Press 2016-08-22 <![CDATA[ Pollinator species traits do not predict either response to agricultural intensification or functional contribution ]]> https://biorxiv.org/content/10.1101/072132v1?rss=1 Ignasi Bartomeus Daniel Cariveau Tina Harrison Rachael Winfree 2016-08-29 doi:10.1101/072132 Cold Spring Harbor Laboratory Press 2016-08-29 <![CDATA[ The tubulin repertoire of C. elegans sensory neurons and its context dependent role in process outgrowth ]]> https://biorxiv.org/content/10.1101/075879v1?rss=1 Dean Lockhead Erich M Schwarz Robert O'Hagan Sebastian Bellotti Michael Krieg Maureen Barr Alexander R Dunn Paul W. Sternberg Miriam B Goodman 2016-09-21 doi:10.1101/075879 Cold Spring Harbor Laboratory Press 2016-09-21 <![CDATA[ Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset ]]> https://biorxiv.org/content/10.1101/077248v1?rss=1 Michael R. Shirts Christoph Klein Jason M. Swails Jian Yin Michael K. Gilson David L. Mobley David A. Case Ellen D. Zhong 2016-09-25 doi:10.1101/077248 Cold Spring Harbor Laboratory Press 2016-09-25 <![CDATA[ Unexpected diversity in socially synchronized rhythms of shorebirds ]]> https://biorxiv.org/content/10.1101/084806v1?rss=1 Bulla, M. Valcu, M. Dokter, A. A. Dondua, A. A. Kosztolanyi, A. Rutten, A. Helm, B. Sandercock, B. K. Casler, B. Ens, B. J. Spiegel, C. S. Hassell, C. J. Kupper, C. Minton, C. Burgas, D. Lank, D. B. Payer, D. C. Loktinov, E. E. Nol, E. Kwon, E. Smith, F. Gates, H. R. Vitnerova, H. Pruter, H. Johnson, J. A. St Clair, J. J. H. Lamarre, J.-F. Rausch, J. Reneerkens, J. Conklin, J. R. Burger, J. Liebezeit, J. Bety, J. Coleman, J. T. Figuerola, J. Hooijmeijer, J. C. E. W. Alves, J. A. Smith, J. A. M. Weidinger, K. Koivula, K. Gosbell, K. Niles, L. Koloski, L 2016-11-01 doi:10.1101/084806 Cold Spring Harbor Laboratory Press 2016-11-01 <![CDATA[ Construction of a high-density American cranberry (Vaccinium macrocarpon Ait.) composite map using genotyping-by-sequencing for multi-pedigree linkage mapping ]]> https://biorxiv.org/content/10.1101/088419v1?rss=1 0.99) between the LGs of the parental maps demonstrates the utility of GBS in cranberry for identifying polymorphic SNP loci that are transferable between pedigrees and populations in future trait-association studies. Furthermore, the high-density of markers anchored within the component maps allowed identification of segregation distortion regions, placement of centromeres on each of the 12 LGs, and anchoring of genomic scaffolds. Collectively, the results represent an important contribution to the current understanding of cranberry genomic structure and to the availability of molecular tools for future genetic research and breeding efforts in cranberry. ]]> Schlautman, B. Covarrubias-Pazaran, G. Diaz-Garcia, L. Iorizzo, M. Polashock, J. Grygleski, E. Vorsa, N. Zalapa, J. 2016-11-17 doi:10.1101/088419 Cold Spring Harbor Laboratory Press 2016-11-17 <![CDATA[ Soft sweeps are the dominant mode of adaptation in the human genome ]]> https://biorxiv.org/content/10.1101/090084v1?rss=1 Schrider, D. R. Kern, A. D. 2016-11-28 doi:10.1101/090084 Cold Spring Harbor Laboratory Press 2016-11-28 <![CDATA[ OpenMM 7: Rapid Development of High Performance Algorithms for Molecular Dynamics ]]> https://biorxiv.org/content/10.1101/091801v1?rss=1 Eastman, P. Swails, J. Chodera, J. D. McGibbon, R. T. Zhao, Y. Beauchamp, K. A. Wang, L.-P. Simmonett, A. C. Harrigan, M. P. Brooks, B. R. Pande, V. S. 2016-12-06 doi:10.1101/091801 Cold Spring Harbor Laboratory Press 2016-12-06 <![CDATA[ Two-zone tumor tolerance can arise from a simple immunological feedforward motif that estimates tumor growth rates ]]> https://biorxiv.org/content/10.1101/095455v1?rss=1 Sontag, E. 2016-12-20 doi:10.1101/095455 Cold Spring Harbor Laboratory Press 2016-12-20 <![CDATA[ Dynamic compensation, parameter identifiability, and equivariances ]]> https://biorxiv.org/content/10.1101/095828v1?rss=1 Sontag, E. 2016-12-21 doi:10.1101/095828 Cold Spring Harbor Laboratory Press 2016-12-21 <![CDATA[ Selectivity matters: rules of thumb for management of plate-sized, sex-changing fish in the live reef food fish trade ]]> https://biorxiv.org/content/10.1101/098624v1?rss=1 Kindsvater, H. Reynolds, J. Sadovy de Mitcheson, Y. Mangel, M. 2017-01-05 doi:10.1101/098624 Cold Spring Harbor Laboratory Press 2017-01-05 <![CDATA[ Structural basis of Mycobacterium tuberculosis transcription and transcription inhibition ]]> https://biorxiv.org/content/10.1101/099606v1?rss=1 Lin, W. Mandal, S. Degen, D. Liu, Y. Ebright, Y. Li, S. Feng, Y. Zhang, Y. Mandal, S. Jiang, Y. Liu, S. Gigliotti, M. Talaue, M. Connell, N. Das, K. Arnold, E. Ebright, R. H. 2017-01-10 doi:10.1101/099606 Cold Spring Harbor Laboratory Press 2017-01-10 <![CDATA[ riboviz: analysis and visualization of ribosome profiling datasets ]]> https://biorxiv.org/content/10.1101/100032v1?rss=1 Carja, O. Xing, T. Plotkin, J. B. Shah, P. 2017-01-12 doi:10.1101/100032 Cold Spring Harbor Laboratory Press 2017-01-12 <![CDATA[ Cognitive task information is transferred between brain regions via resting-state network topology ]]> https://biorxiv.org/content/10.1101/101782v1?rss=1 Ito, T. Kulkarni, K. R. Schultz, D. H. Mill, R. D. Chen, R. H. Solomyak, L. I. Cole, M. W. 2017-01-19 doi:10.1101/101782 Cold Spring Harbor Laboratory Press 2017-01-19 <![CDATA[ Multiple roles of PIWIL1 in mouse neocorticogenesis ]]> https://biorxiv.org/content/10.1101/106070v1?rss=1 Viljetic, B. Diao, L. Liu, J. Krsnik, Z. Wijeratne, S. H. R. Kristopovich, R. Dutre-Clarke, M. Kraushar, M. L. Song, J. Xing, J. Chen, K. Rasin, M.-R. 2017-02-05 doi:10.1101/106070 Cold Spring Harbor Laboratory Press 2017-02-05 <![CDATA[ Free energy calculations suggest a mechanism for Na+/K+-ATPase ion selectivity ]]> https://biorxiv.org/content/10.1101/106724v1?rss=1 Razavi, A. M. Delemotte, L. Berlin, J. R. Carnevale, V. Voelz, V. A. 2017-02-07 doi:10.1101/106724 Cold Spring Harbor Laboratory Press 2017-02-07 <![CDATA[ Antibacterial nucleoside-analog inhibitor of bacterial RNA polymerase: pseudouridimycin ]]> https://biorxiv.org/content/10.1101/106906v1?rss=1 Maffioli, S. Zhang, Y. Degen, D. Carzaniga, T. Del Gatto, G. Serina, S. Monciardini, P. Mazzetti, C. Guglierame, P. Candiani, G. Chiriac, A. I. Facchetti, G. Kaltofen, P. Sahl, H.-G. Deho, G. Donadio, S. Ebright, R. H. 2017-02-08 doi:10.1101/106906 Cold Spring Harbor Laboratory Press 2017-02-08 <![CDATA[ TOWARDS A GLOBAL SUPPORT OF CORE DATA RESOURCES FOR THE LIFE SCIENCES ]]> https://biorxiv.org/content/10.1101/110825v1?rss=1 Anderson, W. Apweiler, R. Bateman, A. Bauer, G. A. Berman, H. Blake, J. A. Blomberg, N. Burley, S. K. Cochrane, G. Di Francesco, V. Donohue, T. Durinx, C. Game, A. Green, E. Gojobori, T. Goodhand, P. Hamosh, A. Hermjakob, H. Kanehisa, M. Kiley, R. McEntyre, J. McKibbin, R. Miyano, S. Pauly, B. Perrimon, N. Ragan, M. A. Richards, G. Teo, Y.-Y. Westerfield, M. Westhof, E. Lasko, P. F. 2017-02-23 doi:10.1101/110825 Cold Spring Harbor Laboratory Press 2017-02-23 <![CDATA[ A toolbox of immunoprecipitation-grade monoclonal antibodies against human transcription factors. ]]> https://biorxiv.org/content/10.1101/116442v1?rss=1 Venkataraman, A. Yang, K. Irrizary, J. Mackiewicz, M. Mita, P. Kuang, Z. Xue, L. Ghosh, D. Liu, S. Ramos, P. Hu, S. Bayron, D. Keegan, S. Saul, R. Colantonio, S. Zhang, H. Pauli Behn, F. Song, G. Albino, E. Asencio, L. Ramos, L. Lugo, L. Morell, G. Rivera, J. Ruiz, K. Almodovar, R. Nazario, L. Murphy, K. Vargas, I. Rivera-Pacheco, Z. Rosa, C. Vargas, M. McDade, J. Clark, B. Yoo, S. Khambadkone, S. de Melo, J. Stevanovic, M. Jiang, L. Li, Y. Yap, W. Jones, B. Tandon, A. Campbell, E. Anderson, S. Myers, R. Boeke, J. Fenyo, D. Whiteley, G. Bader, J 2017-03-14 doi:10.1101/116442 Cold Spring Harbor Laboratory Press 2017-03-14 <![CDATA[ Gene-centric constraint of metabolic models ]]> https://biorxiv.org/content/10.1101/116558v1?rss=1 Fyson, N. Kim, M. K. Lun, D. Colijn, C. 2017-03-14 doi:10.1101/116558 Cold Spring Harbor Laboratory Press 2017-03-14 <![CDATA[ A Note On Dynamical Compensation And Its Relation To Parameter Identifiability ]]> https://biorxiv.org/content/10.1101/123489v1?rss=1 Karin, O. Alon, U. Sontag, E. 2017-04-03 doi:10.1101/123489 Cold Spring Harbor Laboratory Press 2017-04-03 <![CDATA[ Highly sensitive detection of small variants in multi-sample ultra-deep tumor sequencing ]]> https://biorxiv.org/content/10.1101/128587v1?rss=1 Rabadan, R. Marsilio, S. Chiorazzi, N. Pasqualucci, L. Khiabanian, H. 2017-04-19 doi:10.1101/128587 Cold Spring Harbor Laboratory Press 2017-04-19 <![CDATA[ The effect of common inversion polymorphisms In(2L)t and In(3R)Mo on patterns of transcriptional variation in Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/128926v1?rss=1 Lavington, E. Kern, A. D. 2017-04-20 doi:10.1101/128926 Cold Spring Harbor Laboratory Press 2017-04-20 <![CDATA[ Ionic Current Correlations Are Ubiquitous Across Phyla ]]> https://biorxiv.org/content/10.1101/137133v1?rss=1 Tran, T. Unal, C. T. Zaborszky, L. Rotstein, H. G. Kirkwood, A. Golowasch, J. P. 2017-05-12 doi:10.1101/137133 Cold Spring Harbor Laboratory Press 2017-05-12 <![CDATA[ Translation Inhibition And Resource Balance In The Cell-Free Gene Expression System ]]> https://biorxiv.org/content/10.1101/142869v1?rss=1 Nagaraj, V. H. Greene, J. M. Sengupta, A. M. Sontag, E. 2017-05-26 doi:10.1101/142869 Cold Spring Harbor Laboratory Press 2017-05-26 <![CDATA[ Subharmonics And Chaos In Simple Periodically-Forced Biomolecular Models ]]> https://biorxiv.org/content/10.1101/145201v1?rss=1 Nikolaev, E. V. Rahi, S. J. Sontag, E. 2017-06-02 doi:10.1101/145201 Cold Spring Harbor Laboratory Press 2017-06-02 <![CDATA[ Network Connectivity Predicts Cortical Thinning and Cognitive Decline in Early Parkinson’s Disease ]]> https://biorxiv.org/content/10.1101/147611v1?rss=1 Yau, Y. H. C. Zeighami, Y. Baker, T. Larcher, K. Vainik, U. Dadar, M. Fonov, V. Hagmann, P. Griffa, A. Misic, B. Collins, D. L. Dagher, A. 2017-06-08 doi:10.1101/147611 Cold Spring Harbor Laboratory Press 2017-06-08 <![CDATA[ The mechanism of transcription start site selection ]]> https://biorxiv.org/content/10.1101/156877v1?rss=1 Yu, L. Winkelman, J. Pukhrambam, C. Strick, T. Nickels, B. Ebright, R. H. 2017-06-28 doi:10.1101/156877 Cold Spring Harbor Laboratory Press 2017-06-28 <![CDATA[ Supervised machine learning reveals introgressed loci in the genomes of Drosophila simulans and D. sechellia ]]> https://biorxiv.org/content/10.1101/170670v1?rss=1 Schrider, D. Ayroles, J. Matute, D. R. Kern, A. D. 2017-07-31 doi:10.1101/170670 Cold Spring Harbor Laboratory Press 2017-07-31 <![CDATA[ Targeting posttranslational modifications of RioK1 inhibits the progression of colorectal and gastric cancers ]]> https://biorxiv.org/content/10.1101/171058v1?rss=1 Hong, X. Huang, H. Ding, Z. Feng, X. Zhu, Y. Zhuo, H. Hou, J. Cai, W. Hong, X. Song, H. Zhang, Z. 2017-08-01 doi:10.1101/171058 Cold Spring Harbor Laboratory Press 2017-08-01 <![CDATA[ Biophysical determinants of mutational robustness in a viral molecular fitness landscape ]]> https://biorxiv.org/content/10.1101/172197v1?rss=1 Pethe, M. A. Rubenstein, A. B. Zorine, D. Khare, S. D. 2017-08-03 doi:10.1101/172197 Cold Spring Harbor Laboratory Press 2017-08-03 <![CDATA[ N-methyl-bacillithiol, a new metabolite discovered in the Chlorobiaceae, indicates that bacillithiol and derivatives are widely phylogenetically distributed. ]]> https://biorxiv.org/content/10.1101/173617v1?rss=1 Hiras, J. Sharma, S. V. Raman, V. Tinson, R. A. J. Arbach, M. Rodrigues, D. F. Norambuena, J. Hamilton, C. J. Hanson, T. E. 2017-08-08 doi:10.1101/173617 Cold Spring Harbor Laboratory Press 2017-08-08 <![CDATA[ Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum functional genome and evolutionary origin of diatoms ]]> https://biorxiv.org/content/10.1101/176024v1?rss=1 Rastogi, A. Maheswari, U. Dorrell, R. G. Maumus, F. Rocha Jimenez Vieira, F. Kustka, A. McCarthy, J. Allen, A. E. Kersey, P. Bowler, C. Tirichine, L. 2017-08-14 doi:10.1101/176024 Cold Spring Harbor Laboratory Press 2017-08-14 <![CDATA[ Heterogeneity Within the Frontoparietal Control Network and its Relationship to the Default and Dorsal Attention Networks ]]> https://biorxiv.org/content/10.1101/178863v1?rss=1 Dixon, M. L. de la Vega, A. Mills, C. Andrews-Hanna, J. Spreng, R. N. Cole, M. Christoff, K. 2017-08-21 doi:10.1101/178863 Cold Spring Harbor Laboratory Press 2017-08-21 <![CDATA[ MERIT: a Mutation Error Rate Identification Toolkit for Ultra-deep Sequencing Applications ]]> https://biorxiv.org/content/10.1101/184291v1?rss=1 Hadigol, M. Khiabanian, H. 2017-09-04 doi:10.1101/184291 Cold Spring Harbor Laboratory Press 2017-09-04 <![CDATA[ Global connectivity of the frontoparietal cognitive control network is related to depression symptoms in undiagnosed individuals ]]> https://biorxiv.org/content/10.1101/185306v1?rss=1 Schultz, D. H. Ito, T. Solomyak, L. I. Chen, R. H. Mill, R. D. Kulkarni, K. R. Cole, M. W. 2017-09-06 doi:10.1101/185306 Cold Spring Harbor Laboratory Press 2017-09-06 <![CDATA[ Genetic Diversity Turns a New PAGE in Our Understanding of Complex Traits ]]> https://biorxiv.org/content/10.1101/188094v1?rss=1 Wojcik, G. Graff, M. Nishimura, K. K. Tao, R. Haessler, J. Gignoux, C. R. Highland, H. M. Patel, Y. M. Sorokin, E. P. Avery, C. L. Belbin, G. M. Bien, S. A. Cheng, I. Hodonsky, C. J. Huckins, L. M. Jeff, J. Justice, A. E. Kocarnik, J. M. Lim, U. Lin, B. M. Lu, Y. Nelson, S. C. Park, S.-S. L. Preuss, M. H. Richard, M. A. Schurmann, C. Setiawan, V. W. Vahi, K. Vishnu, A. Verbanck, M. Walker, R. Young, K. L. Zubair, N. Ambite, J. L. Boerwinkle, E. Bottinger, E. Bustamante, C. D. Caberto, C. Conomos, M. P. Deelman, E. Do, R. Doheny, K. Fernandez-Rhodes, L. 2017-09-15 doi:10.1101/188094 Cold Spring Harbor Laboratory Press 2017-09-15 <![CDATA[ CA2 Neuronal Activity Controls Hippocampal Oscillations and Social Behavior ]]> https://biorxiv.org/content/10.1101/190504v1?rss=1 Alexander, G. Brown, L. Farris, S. Lustberg, D. Pantazis, C. Gloss, B. Plummer, N. Riddick, N. Moy, S. Jensen, P. Dudek, S. 2017-09-19 doi:10.1101/190504 Cold Spring Harbor Laboratory Press 2017-09-19 <![CDATA[ The Dynamic Landscape of Transcription Initiation in Yeast Mitochondria ]]> https://biorxiv.org/content/10.1101/2019.12.16.877878v1?rss=1 Sohn, B.-K. Basu, U. Lee, S.-W. Cho, H. Shen, J. Deshpande, A. Patel, S. S. Kim, H. 2019-12-17 doi:10.1101/2019.12.16.877878 Cold Spring Harbor Laboratory Press 2019-12-17 <![CDATA[ An exhaustive analysis of single amino acid variants in helical transmembrane proteins ]]> https://biorxiv.org/content/10.1101/2019.12.18.881318v1?rss=1 5% of the population) have, on average, more significant impact on the molecular function of proteins than do rare SAVs (shared by <1% of the population). Here, we investigated the impact of variants in a human population upon helical transmembrane proteins (TMPs). Three main results stood out. Firstly, common SAVs, on average, have stronger effects than rare SAVs for TMPs, and are enriched, in particular, in the membrane helices. Secondly, proteins with seven transmembrane helices (7TM, including GPCRs, i.e. G protein-coupled receptors) are depleted of SAVs in comparison to other proteins, possibly due to increased evolutionary constraints in these important proteins. Thirdly, rare SAVs with strong effect are significantly absent (over common SAVs) in signal peptide regions. ]]> Llorian-Salvador, O. Bernhofer, M. Mahlich, Y. Rost, B. 2019-12-19 doi:10.1101/2019.12.18.881318 Cold Spring Harbor Laboratory Press 2019-12-19 <![CDATA[ XACT-seq comprehensively defines the promoter-position and promoter-sequence determinants for initial-transcription pausing ]]> https://biorxiv.org/content/10.1101/2019.12.21.886044v1?rss=1 Winkelman, J. T. Pukhrambam, C. Vvedenskaya, I. O. Zhang, Y. Taylor, D. M. Shah, P. Ebright, R. H. Nickels, B. E. 2019-12-23 doi:10.1101/2019.12.21.886044 Cold Spring Harbor Laboratory Press 2019-12-23 <![CDATA[ Sequestration of Methane by Symbiotic Deep-Sea Annelids: Ancient and Future Implications of Redefining the Seep Influence ]]> https://biorxiv.org/content/10.1101/2019.12.23.887653v1?rss=1 Goffredi, S. K. Tilic, E. Mullin, S. W. Dawson, K. S. Keller, A. Lee, R. Wu, F. Levin, L. A. Rouse, G. W. Cordes, E. Orphan, V. J. 2019-12-27 doi:10.1101/2019.12.23.887653 Cold Spring Harbor Laboratory Press 2019-12-27 <![CDATA[ Predicting long-term multicategory cause of death in patients with prostate cancer: random forest versus multinomial model ]]> https://biorxiv.org/content/10.1101/2020.01.03.893966v1?rss=1 Wang, J. Deng, F. Zeng, F. Shanahan, A. J. Zhang, L. 2020-01-03 doi:10.1101/2020.01.03.893966 Cold Spring Harbor Laboratory Press 2020-01-03 <![CDATA[ Identifying Sequence Perturbations to an Intrinsically Disordered Protein that Determine Its Phase Separation Behavior ]]> https://biorxiv.org/content/10.1101/2020.01.06.894576v1?rss=1 Schuster, B. Dignon, G. L. Tang, W. S. Kelley, F. Ranganath, A. K. Jahnke, C. N. Simpkins, A. G. Regy, R. M. Hammer, D. A. Good, M. C. Mittal, J. 2020-01-06 doi:10.1101/2020.01.06.894576 Cold Spring Harbor Laboratory Press 2020-01-06 <![CDATA[ Geometric Analysis of Regime Shifts in Coral Reef Communities ]]> https://biorxiv.org/content/10.1101/2020.01.10.899179v1?rss=1 Tekwa, E. W. McManus, L. C. Greiner, A. Colton, M. A. Webster, M. S. Pinsky, M. L. 2020-01-11 doi:10.1101/2020.01.10.899179 Cold Spring Harbor Laboratory Press 2020-01-11 <![CDATA[ Tyrosine-Derived Polycarbonate Nerve Guidance Tubes Elicit Pro-Regenerative Extracellular Matrix Deposition When Used to Bridge Segmental Nerve Defects in Swine ]]> https://biorxiv.org/content/10.1101/2020.01.11.902007v1?rss=1 Burrell, J. C. Bhatnagar, D. Brown, D. P. Murthy, N. S. Dutton, J. Laimo, F. A. Ali, Z. Rosen, J. M. Kaplan, H. M. Kohn, J. Cullen, D. K. 2020-01-11 doi:10.1101/2020.01.11.902007 Cold Spring Harbor Laboratory Press 2020-01-11 <![CDATA[ Modular and distinct PlexinA4/Farp2/Rac1 signaling controls dendrite morphogenesis ]]> https://biorxiv.org/content/10.1101/2020.01.15.908434v1?rss=1 Danelon, V. Goldner, R. Martinez, E. Gokhman, I. Wang, K. Yaron, A. Tran, T. S. 2020-01-16 doi:10.1101/2020.01.15.908434 Cold Spring Harbor Laboratory Press 2020-01-16 <![CDATA[ Design, optimization, and analysis of large DNA and RNA nanostructures through interactive visualization, editing, and molecular simulation ]]> https://biorxiv.org/content/10.1101/2020.01.24.917419v1?rss=1 Poppleton, E. Bohlin, J. Matthies, M. Sharma, S. Zhang, F. Sulc, P. 2020-01-25 doi:10.1101/2020.01.24.917419 Cold Spring Harbor Laboratory Press 2020-01-25 <![CDATA[ The role of humans on Antillean land vertebrate extinctions: new insights from Cuba ]]> https://biorxiv.org/content/10.1101/2020.01.27.922237v1?rss=1 Orihuela, J. Vinola, L. W. Jimenez Vazquez, O. Mychajliw, A. Hernandez de Lara, O. Lorenzo, L. Soto-Centeno, J. A. 2020-01-28 doi:10.1101/2020.01.27.922237 Cold Spring Harbor Laboratory Press 2020-01-28 <![CDATA[ Modeling metabolic variation with single-cell expression data ]]> https://biorxiv.org/content/10.1101/2020.01.28.923680v1?rss=1 Zhang, Y. Kim, M. S. Nguyen, E. Taylor, D. M. 2020-01-29 doi:10.1101/2020.01.28.923680 Cold Spring Harbor Laboratory Press 2020-01-29 <![CDATA[ Microbial trend analysis for common dynamic trend, group comparison and classification in longitudinal microbiome study ]]> https://biorxiv.org/content/10.1101/2020.01.30.926824v1?rss=1 Wang, C. Hu, J. Blaser, M. J. Li, H. 2020-01-31 doi:10.1101/2020.01.30.926824 Cold Spring Harbor Laboratory Press 2020-01-31 <![CDATA[ Bidirectional synaptic plasticity rapidly modifies hippocampal representations independent of correlated activity ]]> https://biorxiv.org/content/10.1101/2020.02.04.934182v1?rss=1 Milstein, A. D. Li, Y. Bittner, K. C. Grienberger, C. Soltesz, I. Magee, J. C. Romani, S. 2020-02-05 doi:10.1101/2020.02.04.934182 Cold Spring Harbor Laboratory Press 2020-02-05 <![CDATA[ Cold-mediated regulation of systemic retinol transport controls adipose tissue browning ]]> https://biorxiv.org/content/10.1101/2020.02.07.938688v1?rss=1 Fenzl, A. Kulterer, O. C. Spirk, K. Mitulovic, G. Marculescu, R. Bilban, M. Baumgartner-Parzer, S. Kautzky-Willer, A. Kenner, L. Plutzky, J. Quadro, L. Kiefer, F. W. 2020-02-07 doi:10.1101/2020.02.07.938688 Cold Spring Harbor Laboratory Press 2020-02-07 <![CDATA[ Inferring Models with Alternative Stable States from Independent Observations ]]> https://biorxiv.org/content/10.1101/2020.02.07.939413v1?rss=1 Tekwa, E. W. Krkosek, M. Pinsky, M. L. 2020-02-09 doi:10.1101/2020.02.07.939413 Cold Spring Harbor Laboratory Press 2020-02-09 <![CDATA[ The architecture of protein synthesis in the developing neocortex at near-atomic resolution reveals Ebp1-mediated neuronal proteostasis at the 60S tunnel exit ]]> https://biorxiv.org/content/10.1101/2020.02.08.939488v1?rss=1 View larger version (59K): org.highwire.dtl.DTLVardef@1231351org.highwire.dtl.DTLVardef@1c940f7org.highwire.dtl.DTLVardef@1c81e2corg.highwire.dtl.DTLVardef@135008b_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Kraushar, M. L. Krupp, F. Turko, P. Ambrozkiewicz, M. C. Sprink, T. Imami, K. Vieira-Vieira, C. H. Schaub, T. Harnett, D. Munster-Wandowski, A. Burger, J. Zinnall, U. Borisova, E. Yamamoto, H. Rasin, M.-R. Beule, D. Landthaler, M. Mielke, T. Tarabykin, V. Vida, I. Selbach, M. Spahn, C. M. T. 2020-02-10 doi:10.1101/2020.02.08.939488 Cold Spring Harbor Laboratory Press 2020-02-10 <![CDATA[ The FUSED LEAVES1/ADHERENT1 Regulatory Module Is Required For Maize Cuticle Development And Organ Separation ]]> https://biorxiv.org/content/10.1101/2020.02.11.943787v1?rss=1 Liu, X. Bourgault, R. Strable, J. Galli, M. Chen, Z. Dong, J. Molina, I. Gallavotti, A. 2020-02-12 doi:10.1101/2020.02.11.943787 Cold Spring Harbor Laboratory Press 2020-02-12 <![CDATA[ Widespread selection against deleterious mutations in the Drosophila genome ]]> https://biorxiv.org/content/10.1101/2020.02.12.946392v1?rss=1 Khromov, P. Morozov, A. V. 2020-02-13 doi:10.1101/2020.02.12.946392 Cold Spring Harbor Laboratory Press 2020-02-13 <![CDATA[ Discovering and exploiting multiple types of DNA methylation from individual bacteria and microbiome using nanopore sequencing ]]> https://biorxiv.org/content/10.1101/2020.02.18.954636v1?rss=1 Tourancheau, A. Mead, E. A. Zhang, X.-s. Fang, G. 2020-02-19 doi:10.1101/2020.02.18.954636 Cold Spring Harbor Laboratory Press 2020-02-19 <![CDATA[ C. elegans nuclear RNAi factor SET-32 deposits the transgenerational heritable histone modification, H3K23me3 ]]> https://biorxiv.org/content/10.1101/2020.02.19.956656v1?rss=1 Schwartz-Orbach, L. Zhang, C. Sidoli, S. Amin, R. Kaur, D. Zhebrun, A. Ni, J. Gu, S. G. 2020-02-20 doi:10.1101/2020.02.19.956656 Cold Spring Harbor Laboratory Press 2020-02-20 <![CDATA[ Biogenic Amine Neurotransmitters Promote Eicosanoid Production And Protein Homeostasis ]]> https://biorxiv.org/content/10.1101/2020.02.25.964189v1?rss=1 Rongo, C. G. Joshi, K. K. Matlack, T. L. Pyonteck, S. Menzel, R. 2020-02-26 doi:10.1101/2020.02.25.964189 Cold Spring Harbor Laboratory Press 2020-02-26 <![CDATA[ Proteomic cellular signatures of kinase inhibitor-induced cardiotoxicity: Mount Sinai DToxS LINCS Center Dataset ]]> https://biorxiv.org/content/10.1101/2020.02.26.966606v1?rss=1 Xiong, Y. Liu, T. Chen, T. Hansen, J. Hu, B. Chen, Y. Jayaraman, G. Schürer, S. Vidovic, D. Goldfarb, J. Sobie, E. A. Birtwistle, M. R. Iyengar, R. Li, H. Azeloglu, E. U. 2020-02-26 doi:10.1101/2020.02.26.966606 Cold Spring Harbor Laboratory Press 2020-02-26 <![CDATA[ Structural basis of transcription-translation coupling ]]> https://biorxiv.org/content/10.1101/2020.03.01.972380v1?rss=1 Wang, C. Molodtsov, V. Firlar, E. Kaelber, J. Blaha, G. Su, M. Ebright, R. H. 2020-03-02 doi:10.1101/2020.03.01.972380 Cold Spring Harbor Laboratory Press 2020-03-02 <![CDATA[ Developmental differentiation in a cytoplasm-dwelling obligate intracellular bacterium ]]> https://biorxiv.org/content/10.1101/2020.03.03.975011v1?rss=1 Giengkam, S. Wongsantichon, J. Atwal, S. Jaiyen, Y. Goh, W. I. Wright, G. Chung, T. Huh, H. Lee, S. Sobota, R. Salje, J. 2020-03-05 doi:10.1101/2020.03.03.975011 Cold Spring Harbor Laboratory Press 2020-03-05 <![CDATA[ Histidine-Triad Hydrolases Provide Resistance to Peptide-Nucleotide Antibiotics ]]> https://biorxiv.org/content/10.1101/2020.03.04.977132v1?rss=1 Yagmurov, E. Tsibulskaya, D. Livenskyi, A. Serebryakova, M. Wolf, Y. I. Borukhov, S. Severinov, K. V. Dubiley, S. 2020-03-05 doi:10.1101/2020.03.04.977132 Cold Spring Harbor Laboratory Press 2020-03-05 <![CDATA[ The anti-tubercular activity of simvastatin is mediated by cholesterol-dependent regulation of autophagy via the AMPK-mTORC1-TFEB axis ]]> https://biorxiv.org/content/10.1101/2020.03.04.977579v1?rss=1 Bruiners, N. Dutta, N. K. Guerrini, V. Salamon, H. Yamaguchi, K. Karakousis, P. Gennaro, M. L. 2020-03-05 doi:10.1101/2020.03.04.977579 Cold Spring Harbor Laboratory Press 2020-03-05 <![CDATA[ mbImpute: an accurate and robust imputation method for microbiome data ]]> https://biorxiv.org/content/10.1101/2020.03.07.982314v1?rss=1 Jiang, R. Li, W. V. Li, J. J. 2020-03-08 doi:10.1101/2020.03.07.982314 Cold Spring Harbor Laboratory Press 2020-03-08 <![CDATA[ Structural Basis for Ca2+-Dependent Activation of a Plant Metacaspase ]]> https://biorxiv.org/content/10.1101/2020.03.09.983940v1?rss=1 Zhu, P. Yu, X.-H. Wang, C. Zhang, Q. Liu, W. McSweeney, S. Shanklin, J. Lam, E. Liu, Q. 2020-03-10 doi:10.1101/2020.03.09.983940 Cold Spring Harbor Laboratory Press 2020-03-10 <![CDATA[ Morphological profiling of tubercule bacilli identifies drug pathways of action ]]> https://biorxiv.org/content/10.1101/2020.03.11.987545v1?rss=1 Smith, T. C. Pullen, K. M. Olson, M. C. McNellis, M. E. Richardson, I. Hu, S. Larkins-Ford, J. Wang, X. Freundlich, J. S. Ando, D. M. Aldridge, B. 2020-03-12 doi:10.1101/2020.03.11.987545 Cold Spring Harbor Laboratory Press 2020-03-12 <![CDATA[ A Piezo1 open state reveals a multi-fenestrated ion permeation pathway ]]> https://biorxiv.org/content/10.1101/2020.03.12.988378v1?rss=1 Jiang, W. Del Rosario, J. S. Botello-Smith, W. M. Zhao, S. Lin, Y.-C. Zhang, H. Lacroix, J. J. Rohacs, T. Luo, Y. L. 2020-03-12 doi:10.1101/2020.03.12.988378 Cold Spring Harbor Laboratory Press 2020-03-12 <![CDATA[ Large-scale Proteomic and Phosphoproteomic Analysis of Maize Seedling Leaves During De-etiolation ]]> https://biorxiv.org/content/10.1101/2020.03.13.977843v1?rss=1 Gao, Z.-f. Shen, Z. Chao, Q. Yan, Z. Ge, X.-L. Lu, T. Zheng, H. Qian, C.-R. Wang, B.-c. 2020-03-14 doi:10.1101/2020.03.13.977843 Cold Spring Harbor Laboratory Press 2020-03-14 <![CDATA[ Connexin 43 hemichannels mediate spatial and temporal disease spread in ALS ]]> https://biorxiv.org/content/10.1101/2020.03.14.990747v1?rss=1 Almad, A. A. Taga, A. Joseph, J. Welsh, C. Patankar, A. Gross, S. K. Richard, J.-P. Pokharel, A. Lillo, M. Dastgheyb, R. Eggan, K. Haughey, N. Contreras, J. E. Maragakis, N. J. 2020-03-15 doi:10.1101/2020.03.14.990747 Cold Spring Harbor Laboratory Press 2020-03-15 <![CDATA[ Quantitative properties of the creation and activation of a cell-intrinsic engram ]]> https://biorxiv.org/content/10.1101/2020.03.17.995258v1?rss=1 > 1). ]]> Gallistel, C. R. Johansson, F. Jirenhed, D.-A. Rasmussen, A. Ricci, M. Hesslow, G. 2020-03-18 doi:10.1101/2020.03.17.995258 Cold Spring Harbor Laboratory Press 2020-03-18 <![CDATA[ Rapid community-driven development of a SARS-CoV-2 tissue simulator ]]> https://biorxiv.org/content/10.1101/2020.04.02.019075v1?rss=1 Wang, Y. Heiland, R. Craig, M. Davis, C. L. Ford Versypt, A. N. Jenner, A. Ozik, J. Collier, N. Cockrell, C. Becker, A. An, G. Glazier, J. A. Narayanan, A. Smith, A. M. Macklin, P. 2020-04-05 doi:10.1101/2020.04.02.019075 Cold Spring Harbor Laboratory Press 2020-04-05 <![CDATA[ Testing the Effect of the Toba Volcanic Eruption on Population Sizes in Worldwide Mammal Species ]]> https://biorxiv.org/content/10.1101/2020.04.06.028050v1?rss=1 Torosin, N. S. Raff, J. S. Hayes, M. G. 2020-04-07 doi:10.1101/2020.04.06.028050 Cold Spring Harbor Laboratory Press 2020-04-07 <![CDATA[ Genetic similarity and facial cues for kin recognition in humans ]]> https://biorxiv.org/content/10.1101/2020.04.06.028134v1?rss=1 Torosin, N. S. Ward, J. Bell, A. V. Knapp, L. A. 2020-04-07 doi:10.1101/2020.04.06.028134 Cold Spring Harbor Laboratory Press 2020-04-07 <![CDATA[ Cell-ECM interactions play distinct and essential roles at multiple stages during the development of the aortic arch arteries ]]> https://biorxiv.org/content/10.1101/2020.04.07.029926v1?rss=1 Warkala, M. Chen, D. Jubran, A. Ramirez, A. Schonning, M. Wang, X. Astrof, S. 2020-04-08 doi:10.1101/2020.04.07.029926 Cold Spring Harbor Laboratory Press 2020-04-08 <![CDATA[ Origin and Evolution of DNA methyltransferases (DNMT) along the tree of life: A multi-genome survey. ]]> https://biorxiv.org/content/10.1101/2020.04.09.033167v1?rss=1 Bhattacharyya, M. De, S. Chakrabarti, S. 2020-04-09 doi:10.1101/2020.04.09.033167 Cold Spring Harbor Laboratory Press 2020-04-09 <![CDATA[ Reorganization of 3D genome structure in the Drosophila melanogaster species group ]]> https://biorxiv.org/content/10.1101/2020.04.09.033753v1?rss=1 Torosin, N. S. Anand, A. Rao Golla, T. Cao, W. Ellison, C. E. 2020-04-10 doi:10.1101/2020.04.09.033753 Cold Spring Harbor Laboratory Press 2020-04-10 <![CDATA[ CREBBP/EP300 mutation is associated with poor outcome in HNSCC and targetable with synthetic cytotoxicity. ]]> https://biorxiv.org/content/10.1101/2020.04.10.028217v1?rss=1 Kumar, M. Molkentine, D. Molkentine, J. Bridges, K. Xie, T. Yang, L. Gao, M. Frederick, M. J. Seth, S. Abdelhakiem, M. Johnson, F. M. Wang, J. Shen, L. Heffernan, T. Sheth, A. Ferris, R. Myers, J. N. Pickering, C. R. Skinner, H. D. 2020-04-11 doi:10.1101/2020.04.10.028217 Cold Spring Harbor Laboratory Press 2020-04-11 <![CDATA[ Impaired HSF1 transactivation drives proteostasis collapse and senescent phenotype of IPF lung fibroblast. ]]> https://biorxiv.org/content/10.1101/2020.04.10.036327v1?rss=1 Cuevas-Mora, K. Roque, W. Sales, D. Ritzenthaler, J. D. Torres-Gonzales, E. Halayko, A. J. Rosas, I. O. Roman, J. Romero, F. 2020-04-11 doi:10.1101/2020.04.10.036327 Cold Spring Harbor Laboratory Press 2020-04-11 <![CDATA[ Cryo-EM structures reveal transcription initiation steps by yeast mitochondrial RNA polymerase ]]> https://biorxiv.org/content/10.1101/2020.04.13.038620v1?rss=1 De Wijngaert, B. Sultana, S. Dharia, C. Vanbuel, H. Shen, J. vasilchuk, D. Martinez, S. E. Kandiah, E. Patel, S. S. Das, K. 2020-04-14 doi:10.1101/2020.04.13.038620 Cold Spring Harbor Laboratory Press 2020-04-14 <![CDATA[ Bio-Node - Bioinformatics in the Cloud ]]> https://biorxiv.org/content/10.1101/2020.04.15.043596v1?rss=1 Spreen, Y. Miller, M. 2020-04-16 doi:10.1101/2020.04.15.043596 Cold Spring Harbor Laboratory Press 2020-04-16 <![CDATA[ Sensory-evoked extracellular vesicle release and targeting ]]> https://biorxiv.org/content/10.1101/2020.04.21.050690v1?rss=1 Wang, J. Nikonorova, I. A. Gu, A. Sternberg, P. W. Barr, M. M. 2020-04-22 doi:10.1101/2020.04.21.050690 Cold Spring Harbor Laboratory Press 2020-04-22 <![CDATA[ Intermittent self-administration of fentanyl induces a multifaceted addiction state associated with persistent changes in the orexin system. ]]> https://biorxiv.org/content/10.1101/2020.04.23.055848v1?rss=1 Fragale, J. E. James, M. H. Aston-Jones, G. 2020-04-25 doi:10.1101/2020.04.23.055848 Cold Spring Harbor Laboratory Press 2020-04-25 <![CDATA[ The dual orexin/hypocretin receptor antagonist suvorexant reduces addiction-like behaviors for the opioid fentanyl ]]> https://biorxiv.org/content/10.1101/2020.04.25.061887v1?rss=1 O'Connor, S. L. Fragale, J. E. James, M. H. Aston-Jones, G. 2020-04-27 doi:10.1101/2020.04.25.061887 Cold Spring Harbor Laboratory Press 2020-04-27 <![CDATA[ Effects of gene by microbiome interactions on behavioral and neurobiological phenotypes in a mouse model for autism spectrum disorder ]]> https://biorxiv.org/content/10.1101/2020.04.29.065821v1?rss=1 Osman, A. Mervosh, N. L. Strat, A. N. Meckel, K. R. Euston, T. J. Zipursky, G. D. Drapeau, E. Buxbaum, J. Breen, M. S. Kiraly, D. D. 2020-04-30 doi:10.1101/2020.04.29.065821 Cold Spring Harbor Laboratory Press 2020-04-30 <![CDATA[ Structural basis of Rgg protein binding to their regulatory pheromones and target DNA promoters ]]> https://biorxiv.org/content/10.1101/2020.04.30.069369v1?rss=1 Capodagli, G. C. Tylor, K. M. Kaelber, J. T. Petrou, V. I. Federle, M. J. Neiditch, M. B. 2020-04-30 doi:10.1101/2020.04.30.069369 Cold Spring Harbor Laboratory Press 2020-04-30 <![CDATA[ DECODING SECOND ORDER ISOMORPHISMS IN THE BRAIN: The case of colors and letters. ]]> https://biorxiv.org/content/10.1101/2020.05.04.076703v1?rss=1 Hanson, S. J. Caglar, L. R. Hanson, C. 2020-05-05 doi:10.1101/2020.05.04.076703 Cold Spring Harbor Laboratory Press 2020-05-05 <![CDATA[ Resolving spatial complexities of hybridization in the context of the gray zone of speciation in North American ratsnakes (Pantherophis obsoletus complex) ]]> https://biorxiv.org/content/10.1101/2020.05.05.079467v1?rss=1 Burbrink, F. Gehara, M. Myers, E. A. 2020-05-07 doi:10.1101/2020.05.05.079467 Cold Spring Harbor Laboratory Press 2020-05-07 <![CDATA[ Transcriptomics, metabolomics and lipidomics of chronically injured alveolar epithelial cells reveals similar features of IPF lung epithelium ]]> https://biorxiv.org/content/10.1101/2020.05.08.084459v1?rss=1 Roque, W. Cuevas-Mora, K. Sales, D. Li, W. V. Rosas, I. O. Romero, F. 2020-05-10 doi:10.1101/2020.05.08.084459 Cold Spring Harbor Laboratory Press 2020-05-10 <![CDATA[ HDAC inhibitors decrease TLR7/9-mediated human plasmacytoid dendritic cell activation by interfering with IRF-7 and NF-қB signaling ]]> https://biorxiv.org/content/10.1101/2020.05.09.085456v1?rss=1 Descalzi-Montoya, D. B. Dai, J. Singh, S. Fitzgerald-Bocarsly, P. 2020-05-09 doi:10.1101/2020.05.09.085456 Cold Spring Harbor Laboratory Press 2020-05-09 <![CDATA[ Gut dysbiosis protects against liver injury in autophagy deficient mice by FXR-FGF15 feedback signaling ]]> https://biorxiv.org/content/10.1101/2020.05.12.090613v1?rss=1 Yan, S. Khambu, B. Chen, X. Dong, Z. Guo, G. Yin, X.-M. 2020-05-14 doi:10.1101/2020.05.12.090613 Cold Spring Harbor Laboratory Press 2020-05-14 <![CDATA[ An RNA dynamic ensemble at atomic resolution ]]> https://biorxiv.org/content/10.1101/2020.05.13.092981v1?rss=1 Shi, H. Rangadurai, A. Abou Assi, H. Roy, R. Case, D. A. Herschlag, D. Yesselman, J. D. Al-Hashimi, H. M. 2020-05-15 doi:10.1101/2020.05.13.092981 Cold Spring Harbor Laboratory Press 2020-05-15 <![CDATA[ Expression changes in immune and epigenetic gene pathways associated with nutritional metabolites in maternal blood from pregnancies resulting in autism and atypical neurodevelopment ]]> https://biorxiv.org/content/10.1101/2020.05.14.096586v1?rss=1 Zhu, Y. Mordaunt, C. E. Durbin-Johnson, B. P. Caudill, M. A. Malysheva, O. V. Miller, J. W. Green, R. James, S. J. Melnyk, S. B. Fallin, M. D. Hertz-Picciotto, I. Schmidt, R. J. LaSalle, J. M. 2020-05-16 doi:10.1101/2020.05.14.096586 Cold Spring Harbor Laboratory Press 2020-05-16 <![CDATA[ Chemical probe-based Nanopore direct RNA sequencing method to selectively assess the pseudouridine and inosine modifications ]]> https://biorxiv.org/content/10.1101/2020.05.19.105338v1?rss=1 View larger version (10K): org.highwire.dtl.DTLVardef@137799aorg.highwire.dtl.DTLVardef@110764aorg.highwire.dtl.DTLVardef@1c61ddaorg.highwire.dtl.DTLVardef@1d1db4d_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Pandian, G. N. Sugiyama, H. Cai, L. Yu, Z. Hidaka, T. Sahayasheela, V. J. Ramasamy, S. 2020-05-20 doi:10.1101/2020.05.19.105338 Cold Spring Harbor Laboratory Press 2020-05-20 <![CDATA[ Mutation of NEKL-4/NEK10 and TTLL genes opposes loss of the CCPP-1 deglutamylase and prevents neuronal ciliary degeneration ]]> https://biorxiv.org/content/10.1101/2020.05.21.108449v1?rss=1 Power, K. M. Akella, J. S. Gu, A. Walsh, J. D. Belotti, S. Morash, M. Zhang, W. Ross, N. Golden, A. Smith, H. E. Barr, M. M. O'Hagan, R. 2020-05-22 doi:10.1101/2020.05.21.108449 Cold Spring Harbor Laboratory Press 2020-05-22 <![CDATA[ Chemogenetic manipulation of microglia inhibits neuroinflammation and neuropathic pain in mice ]]> https://biorxiv.org/content/10.1101/2020.05.21.109538v1?rss=1 Yi, M.-H. Liu, Y. U. Liu, K. Chen, T. Bosco, D. B. Zheng, J. Xie, M. Zhou, L. Qu, W. Wu, L.-J. 2020-05-22 doi:10.1101/2020.05.21.109538 Cold Spring Harbor Laboratory Press 2020-05-22 <![CDATA[ Decreased miR-24-3p potentiates DNA damage responses and increases susceptibility to COPD ]]> https://biorxiv.org/content/10.1101/2020.05.22.108688v1?rss=1 Nouws, J. Wan, F. Finnemore, E. Roque, W. Kim, S. Bazan, I. Li, C.-x. Skold, M. Yan, X. Neumeister, V. Britto, C. J. Bindra, R. Wheelock, A. Gomez-Villalobos, J. Kaminski, N. Lee, P. J. Sauler, M. 2020-05-25 doi:10.1101/2020.05.22.108688 Cold Spring Harbor Laboratory Press 2020-05-25 <![CDATA[ MCH enables synchronized firing in the hippocamposeptal circuit to facilitate spatial memory ]]> https://biorxiv.org/content/10.1101/2020.05.25.114389v1?rss=1 Liu, J.-J. Tsien, R. W. Pang, Z. P. 2020-05-25 doi:10.1101/2020.05.25.114389 Cold Spring Harbor Laboratory Press 2020-05-25 <![CDATA[ Common substructures and sequence characteristics of sandwich-like proteins from 42 different folds ]]> https://biorxiv.org/content/10.1101/2020.05.27.108969v1?rss=1 Kister, A. 2020-05-27 doi:10.1101/2020.05.27.108969 Cold Spring Harbor Laboratory Press 2020-05-27 <![CDATA[ Activating an adaptive immune response from a hydrogel scaffold imparts regenerative wound healing. ]]> https://biorxiv.org/content/10.1101/2020.05.27.117317v1?rss=1 Griffin, D. R. Archang, M. M. Kuan, C. H. Weaver, W. Weinstein, J. S. Feng, A. C. Ruccia, A. Sideris, E. Ragkousis, V. Koh, J. Plikus, M. V. Di Carlo, D. Segura, T. Scumpia, P. O. 2020-05-30 doi:10.1101/2020.05.27.117317 Cold Spring Harbor Laboratory Press 2020-05-30 <![CDATA[ Roadmap to Help Develop Personalized Targeted Treatments for Autism as a Disorder of the Nervous Systems ]]> https://biorxiv.org/content/10.1101/2020.06.01.127597v1?rss=1 Torres, E. B. 2020-06-02 doi:10.1101/2020.06.01.127597 Cold Spring Harbor Laboratory Press 2020-06-02 <![CDATA[ Foxa1/2 downregulates liver differentiation markers and the endoderm and liver gene regulatory network in human stem cells and in a human stable liver cell line ]]> https://biorxiv.org/content/10.1101/2020.06.01.128108v1?rss=1 Warren, I. T. Maloy, M. H. Guiggey, D. Ogoke, O. Groth, T. S. Mon, T. Meamardoost, S. Liu, X. Szeglowski, A. Thompson, R. Chen, P. Paulmurugan, R. Parashurama, N. 2020-06-02 doi:10.1101/2020.06.01.128108 Cold Spring Harbor Laboratory Press 2020-06-02 <![CDATA[ Metabolome shift associated with thermal stress in coral holobionts ]]> https://biorxiv.org/content/10.1101/2020.06.04.134619v1?rss=1 Williams, A. Chiles, E. N. Conetta, D. Pathmanathan, J. S. Cleves, P. A. Putnam, H. M. Su, X. Bhattacharya, D. 2020-06-05 doi:10.1101/2020.06.04.134619 Cold Spring Harbor Laboratory Press 2020-06-05 <![CDATA[ Chaperone-mediated stress-sensing in Mycobacterium tuberculosis enables fast activation and sustained response ]]> https://biorxiv.org/content/10.1101/2020.06.04.135335v1?rss=1 Rao, S. D. Datta, P. Gennaro, M. L. Igoshin, O. A. 2020-06-05 doi:10.1101/2020.06.04.135335 Cold Spring Harbor Laboratory Press 2020-06-05 <![CDATA[ A chromosome-level genome assembly for the Eastern Fence Lizard (Sceloporus undulatus), a reptile model for physiological and evolutionary ecology ]]> https://biorxiv.org/content/10.1101/2020.06.06.138248v1?rss=1 90% of reads mapped for species within 20 million years divergence from S. undulatus, this dropped to 75% reads mapped for species at 35 million years divergence. Finally we use RNAseq and whole genome resequencing data to compare the three assemblies as references, each representing an increased level of sequencing, cost and assembly efforts: Supernova Assembly with data from10X Genomics Chromium library; HiRise Assembly that added data from HiC library; and PBJelly Assembly that added data from PacBio sequencing. We found that the Supernova Assembly contained the full genome and was a suitable reference for RNAseq, but the chromosome-level scaffolds provided by the addition of the HiC data allowed the reference to be used for other whole genome analysis, including synteny and whole genome association mapping analyses. The addition of PacBio data provided negligible gains. Overall, these new genomic resources provide valuable tools for advanced molecular analysis of an organism that has become a model in physiology and evolutionary ecology. ]]> Westfall, A. K. Telemeco, R. S. Grizante, M. B. Waits, D. S. Clark, A. D. Simpson, D. Y. Klabacka, R. L. Sullivan, A. P. Perry, G. H. Sears, M. W. Cox, C. L. Cox, R. M. Gifford, M. E. John-Alder, H. B. Langkilde, T. Angilletta, M. Leache, A. Tollis, M. Kusumi, K. Schwartz, T. S. 2020-06-06 doi:10.1101/2020.06.06.138248 Cold Spring Harbor Laboratory Press 2020-06-06 <![CDATA[ Pandora: 4-D white matter bundle population-based atlasesderived from diffusion MRI fiber tractography ]]> https://biorxiv.org/content/10.1101/2020.06.12.148999v1?rss=1 Hansen, C. B. Yang, Q. Lyu, I. Rheault, F. Kerley, C. Chandio, B. Q. Fadnavis, S. Williams, O. Shafer, A. T. Resnick, S. M. Zald, D. H. Cutting, L. Taylor, W. D. Boyd, B. Garyfallidis, E. Anderson, A. W. Descoteaux, M. Landman, B. A. Schilling, K. 2020-06-13 doi:10.1101/2020.06.12.148999 Cold Spring Harbor Laboratory Press 2020-06-13 <![CDATA[ Conclusive Identification of Senescent T Cells Reveals Their Abundance in Aging Humans ]]> https://biorxiv.org/content/10.1101/2020.06.17.157826v1?rss=1 Martinez Zamudio, R. I. Dewald, H. K. Vasilopoulos, T. Gittens-Williams, L. Fitzgerald-Bocarsly, P. Herbig, U. 2020-06-19 doi:10.1101/2020.06.17.157826 Cold Spring Harbor Laboratory Press 2020-06-19 <![CDATA[ Distinct roles for RAB10 and RAB29 in pathogenic LRRK2-mediated endolysosomal trafficking alterations ]]> https://biorxiv.org/content/10.1101/2020.06.20.163063v1?rss=1 Rivero-Rios, P. Romo-Lozano, M. Fernandez, B. Fdez, E. Hilfiker, S. 2020-06-20 doi:10.1101/2020.06.20.163063 Cold Spring Harbor Laboratory Press 2020-06-20 <![CDATA[ A novel and highly effective mitochondrial uncoupling drug in T-cell leukemia ]]> https://biorxiv.org/content/10.1101/2020.06.23.168005v1?rss=1 da Silva-Diz, V. Cao, B. Lancho, O. Chiles, E. Alasadi, A. Luo, S. Augeri, D. Minuzzo, S. Indraccolo, S. Su, X. Jin, S. Herranz, D. 2020-06-23 doi:10.1101/2020.06.23.168005 Cold Spring Harbor Laboratory Press 2020-06-23 <![CDATA[ Modulation of motor behavior by the mesencephalic locomotor region ]]> https://biorxiv.org/content/10.1101/2020.06.25.172296v1?rss=1 Dautan, D. Kovacs, A. Bayasgalan, T. Diaz-Acevedo, M. A. Pal, B. Mena-Segovia, J. 2020-06-26 doi:10.1101/2020.06.25.172296 Cold Spring Harbor Laboratory Press 2020-06-26 <![CDATA[ Reduced type-A carbohydrate-binding module interactions to cellulose leads to improved endocellulase activity ]]> https://biorxiv.org/content/10.1101/2020.07.02.183293v1?rss=1 Nemmaru, B. Ramirez, N. Farino, C. J. Yarbrough, J. M. Kravhcenko, N. Chundawat, S. P. S. 2020-07-03 doi:10.1101/2020.07.02.183293 Cold Spring Harbor Laboratory Press 2020-07-03 <![CDATA[ Pygmaeomycetaceae, a new root associated family in Mucoromycotina from the pygmy pine plains ]]> https://biorxiv.org/content/10.1101/2020.07.03.187096v1?rss=1 Walsh, E. Luo, J. Khiste, S. Scalera, A. Sajjad, S. Zhang, N. 2020-07-03 doi:10.1101/2020.07.03.187096 Cold Spring Harbor Laboratory Press 2020-07-03 <![CDATA[ The functional relevance of task-state functional connectivity ]]> https://biorxiv.org/content/10.1101/2020.07.06.187245v1?rss=1 Cole, M. W. Ito, T. Cocuzza, C. Sanchez-Romero, R. 2020-07-10 doi:10.1101/2020.07.06.187245 Cold Spring Harbor Laboratory Press 2020-07-10 <![CDATA[ Genetic, textual, and archaeological evidence of the historical global spread of cowpea (Vigna unguiculata Walp) ]]> https://biorxiv.org/content/10.1101/2020.07.08.193995v1?rss=1 Ira A Herniter María Muñoz-Amatriaín Timothy A Close 2020-07-10 doi:10.1101/2020.07.08.193995 Cold Spring Harbor Laboratory Press 2020-07-10 <![CDATA[ GrgA controls Chlamydia trachomatis growth and development by regulating expression of transcription factors Euo and HrcA ]]> https://biorxiv.org/content/10.1101/2020.07.08.194431v1?rss=1 Wurihan Wurihan Yi Zou Alec M. Weber Korri Weldon Yehong Huang Zheng Gong Zhongzi Lou Samantha Sun Chengsheng Zhu Xiang Wu Jizhang Zhou Yaqun Wang Zhao Lai Huizhou Fan 2020-07-08 doi:10.1101/2020.07.08.194431 Cold Spring Harbor Laboratory Press 2020-07-08 <![CDATA[ Reframing Psychiatry for Precision Medicine ]]> https://biorxiv.org/content/10.1101/2020.07.19.210971v1?rss=1 Torres, E. B. 2020-07-21 doi:10.1101/2020.07.19.210971 Cold Spring Harbor Laboratory Press 2020-07-21 <![CDATA[ Species-Specific Responses of Bird Song Output in the Presence of Drones ]]> https://biorxiv.org/content/10.1101/2020.07.19.211045v1?rss=1 Wilson, A. M. Boyle, K. S. Gilmore, J. L. Kiefer, C. J. Walker, M. F. 2020-07-19 doi:10.1101/2020.07.19.211045 Cold Spring Harbor Laboratory Press 2020-07-19 <![CDATA[ A Trypanosoma brucei ORFeome-based Gain-of-Function Library identifies genes that promote survival during melarsoprol treatment ]]> https://biorxiv.org/content/10.1101/2020.07.19.211375v1?rss=1 Carter, M. Gomez, S. Gritz, S. Larson, S. Silva-Herzog, E. Kim, H.-s. Schulz, D. Hovel-Miner, G. A. 2020-07-21 doi:10.1101/2020.07.19.211375 Cold Spring Harbor Laboratory Press 2020-07-21 <![CDATA[ β-Coronaviruses use lysosomal organelles for cellular egress. ]]> https://biorxiv.org/content/10.1101/2020.07.25.192310v1?rss=1 Altan-Bonnet, N. Altan-Bonnet, G. Y. Ghosh, S. Dellibovi-Ragheb, T. Pak, E. Qiu, Q. Fisher, M. Takvorian, P. Bleck, C. Hsu, V. Fehr, A. Perlman, S. Straus, M. Whittaker, G. de Haan, C. A. 2020-07-25 doi:10.1101/2020.07.25.192310 Cold Spring Harbor Laboratory Press 2020-07-25 <![CDATA[ Identification of clinical combination therapies to induce durable responses in kidney cancers ]]> https://biorxiv.org/content/10.1101/2020.07.25.221507v1?rss=1 Thomas, G. V. 2020-07-26 doi:10.1101/2020.07.25.221507 Cold Spring Harbor Laboratory Press 2020-07-26 <![CDATA[ Intersection of structural and functional connectivity of the nucleus basalis of Meynert in Parkinson's disease dementia and Lewy body dementia ]]> https://biorxiv.org/content/10.1101/2020.07.27.221853v1?rss=1 Oswal, A. gratwicke, j. Akram, H. Jahanshahi, M. Zaborszky, L. Brown, P. Hariz, M. Zrinzo, L. Foltynie, T. Litvak, V. 2020-07-28 doi:10.1101/2020.07.27.221853 Cold Spring Harbor Laboratory Press 2020-07-28 <![CDATA[ From plants to ants: Fungal modification of leaf lipids for nutrition and communication in the leaf-cutter ant fungal garden ecosystem ]]> https://biorxiv.org/content/10.1101/2020.07.28.224139v1?rss=1 Khadempour, L. Kyle, J. E. Webb-Robertson, B.-J. M. Nicora, C. D. Smith, F. B. Smith, R. D. Lipton, M. S. Currie, C. R. Baker, E. S. Burnum-Johnson, K. E. 2020-07-29 doi:10.1101/2020.07.28.224139 Cold Spring Harbor Laboratory Press 2020-07-29 <![CDATA[ Protein Phosphatase 2A-B56 maintains the meiotic spindle, kinetochore attachments and cohesion by antagonizing Aurora B Drosophila Oocytes ]]> https://biorxiv.org/content/10.1101/2020.08.01.232512v1?rss=1 Jang, J. K. Gladstein, A. Das, A. Cisco, Z. McKim, K. 2020-08-03 doi:10.1101/2020.08.01.232512 Cold Spring Harbor Laboratory Press 2020-08-03 <![CDATA[ Brain Anatomical Covariation Patterns Linked to Binge Drinking and Age at First Full Drink Prior to 21 Years ]]> https://biorxiv.org/content/10.1101/2020.08.02.232942v1?rss=1 Zhao, Y. Constable, R. T. Hien, D. Chung, T. Potenza, M. 2020-08-04 doi:10.1101/2020.08.02.232942 Cold Spring Harbor Laboratory Press 2020-08-04 <![CDATA[ Deeply sequenced infectious clones of key cassava begomovirus isolates from Cameroon ]]> https://biorxiv.org/content/10.1101/2020.08.10.244335v1?rss=1 Hoyer, J. S. Fondong, V. N. Dallas, M. M. Aimone, C. D. Deppong, D. O. Duffy, S. Hanley-Bowdoin, L. 2020-08-10 doi:10.1101/2020.08.10.244335 Cold Spring Harbor Laboratory Press 2020-08-10 <![CDATA[ Early Classification of Motor Tasks Using Dynamic Functional Connectivity Graphs from EEG ]]> https://biorxiv.org/content/10.1101/2020.08.12.244921v1?rss=1 Shamsi, F. Haddad, A. Najafizadeh, L. 2020-08-12 doi:10.1101/2020.08.12.244921 Cold Spring Harbor Laboratory Press 2020-08-12 <![CDATA[ Whole-brain mapping of monosynaptic inputs to midbrain cholinergic neurons ]]> https://biorxiv.org/content/10.1101/2020.08.14.251546v1?rss=1 Huerta-Ocampo, I. Dautan, D. Gut, N. K. Khan, B. Mena-Segovia, J. 2020-08-15 doi:10.1101/2020.08.14.251546 Cold Spring Harbor Laboratory Press 2020-08-15 <![CDATA[ Electronic cigarettes induce mitochondrial DNA damage and trigger toll-like receptor 9-mediated atherosclerosis ]]> https://biorxiv.org/content/10.1101/2020.08.15.252494v1?rss=1 Li, J. Huynh, D. L. Tang, M.-S. Simborio, H. Huang, J. Kosmider, B. Steinberg, M. B. Le, L. T. T. Pham, K. Liu, C. Wang, H. 2020-08-15 doi:10.1101/2020.08.15.252494 Cold Spring Harbor Laboratory Press 2020-08-15 <![CDATA[ Probing acetylated-α-synuclein monomer-aggregate complexes by NMR elucidates mechanism of fibril seeding ]]> https://biorxiv.org/content/10.1101/2020.08.17.254508v1?rss=1 Yang, X. Wang, B. Hoop, C. L. Williams, J. K. Baum, J. 2020-08-18 doi:10.1101/2020.08.17.254508 Cold Spring Harbor Laboratory Press 2020-08-18 <![CDATA[ Histidine Protonation Controls Structural Heterogeneity in the Cyanobacteriochrome AnPixJg2 ]]> https://biorxiv.org/content/10.1101/2020.08.21.260158v1?rss=1 G. Rao, A. Wiebeler, C. Sen, S. Cerutti, D. S. Schapiro, I. 2020-08-21 doi:10.1101/2020.08.21.260158 Cold Spring Harbor Laboratory Press 2020-08-21 <![CDATA[ Hemodynamic responses link individual differences in informational masking to the vicinity of superior temporal gyrus ]]> https://biorxiv.org/content/10.1101/2020.08.21.261222v1?rss=1 Zhang, M. Alamatsaz, N. Ihlefeld, A. 2020-08-23 doi:10.1101/2020.08.21.261222 Cold Spring Harbor Laboratory Press 2020-08-23 <![CDATA[ pMAT: An Open-Source Software Suite for the Analysis of Fiber Photometry Calcium Imaging ]]> https://biorxiv.org/content/10.1101/2020.08.23.263673v1?rss=1 Bruno, C. A. O'Brien, C. Bryant, S. Mejaes, J. Pizzano, C. Estrin, D. J. Barker, D. J. 2020-08-24 doi:10.1101/2020.08.23.263673 Cold Spring Harbor Laboratory Press 2020-08-24 <![CDATA[ Homeotic Regulation of Olfactory Receptor Choice via NFI-dependent Heterochromatic Silencing and Genomic Compartmentalization ]]> https://biorxiv.org/content/10.1101/2020.08.30.274035v1?rss=1 1000 olfactory receptor (OR) genes is stochastic but, yet, spatially organized in stereotypic anatomical segments, or "zones", along the dorsoventral axis of the mouse olfactory epithelium. We discovered that zonal OR expression is specified by OR chromatin structure and genome architecture during olfactory neuron differentiation. Specifically, across every zone dorsally expressed ORs have higher levels of heterochromatic marks and long-range contacts than ORs expressed ventrally. However, OR heterochromatin levels and frequency of genomic contacts between ORs gradually increase towards ventral zones. Consequently, ORs from dorsal indexes accumulate high H3K9me3/H3K79me3 enrichment and become silenced in ventral zones, while ORs from ventral indexes lack activating long-range genomic interactions and, thus, cannot be chosen in dorsal segments. This process is regulated by NFIA, B, and X gradients along the dorsoventral axis, triple deletion of which causes homeotic transformations on zonal OR expression, heterochromatin formation, and genomic compartmentalization. ]]> Bashkirova, E. Monahan, K. Campbell, C. E. Osinski, J. M. Tan, L. Schieren, I. Barnea, G. Xie, S. Gronostajski, R. M. Lomvardas, S. 2020-08-30 doi:10.1101/2020.08.30.274035 Cold Spring Harbor Laboratory Press 2020-08-30 <![CDATA[ New mechanism of fibronectin fibril assembly revealed by live imaging and super-resolution microscopy. ]]> https://biorxiv.org/content/10.1101/2020.09.09.290130v1?rss=1 Tomer, D. Munshi, S. Alexander, B. French, B. Vedula, P. House, A. Guvendiren, M. Kashina, A. Schwarzbauer, J. Astrof, S. 2020-09-10 doi:10.1101/2020.09.09.290130 Cold Spring Harbor Laboratory Press 2020-09-10 <![CDATA[ Performance and efficiency of machine learning algorithms for analyzing rectangular biomedical data ]]> https://biorxiv.org/content/10.1101/2020.09.13.295592v1?rss=1 Deng, F. Huang, J. Yuan, X. Cheng, C. Zhang, L. 2020-09-14 doi:10.1101/2020.09.13.295592 Cold Spring Harbor Laboratory Press 2020-09-14 <![CDATA[ High yield preparation of outer-membrane protein efflux pumps by in vitro refolding is concentration dependent ]]> https://biorxiv.org/content/10.1101/2020.09.14.296756v1?rss=1 Budiardjo, S. J. Ikujuni, A. P. Firlar, E. Cordova, A. Kaelber, J. Slusky, J. S. G. 2020-09-14 doi:10.1101/2020.09.14.296756 Cold Spring Harbor Laboratory Press 2020-09-14 <![CDATA[ CCP1, a tubulin deglutamylase, increases survival of rodent spinal cord neurons following glutamate-induced excitotoxicity ]]> https://biorxiv.org/content/10.1101/2020.09.16.295279v1?rss=1 Ramadan, Y. H. Gu, A. Ross, N. McEwan, S. A. Barr, M. M. Firestein, B. L. O'Hagan, R. 2020-09-16 doi:10.1101/2020.09.16.295279 Cold Spring Harbor Laboratory Press 2020-09-16 <![CDATA[ Quantifying dispersal variability among nearshore marine populations ]]> https://biorxiv.org/content/10.1101/2020.09.17.299941v1?rss=1 Catalano, K. A. Dedrick, A. G. Stuart, M. R. Puritz, J. B. Montes, H. R. Pinsky, M. L. 2020-09-19 doi:10.1101/2020.09.17.299941 Cold Spring Harbor Laboratory Press 2020-09-19 <![CDATA[ Reporting quality of trend analyses in leading medicine and oncology journals ]]> https://biorxiv.org/content/10.1101/2020.09.18.303701v1?rss=1 Yuan, X. Lin, Y. Wang, Y. Zhang, L. 2020-09-21 doi:10.1101/2020.09.18.303701 Cold Spring Harbor Laboratory Press 2020-09-21 <![CDATA[ Steady state evoked potential (SSEP) responses in the primary and secondary somatosensory cortices of anesthetized cats: nonlinearity characterized by harmonic and intermodulation frequencies ]]> https://biorxiv.org/content/10.1101/2020.09.22.307652v1?rss=1 Kawashima, Y. Li, R. Chen, S. C.-Y. Vickery, R. M. Morley, J. W. Tsuchiya, N. 2020-09-22 doi:10.1101/2020.09.22.307652 Cold Spring Harbor Laboratory Press 2020-09-22 <![CDATA[ Phage-shock-protein (Psp) Envelope Stress Response: Evolutionary History and Discovery of Novel Players ]]> https://biorxiv.org/content/10.1101/2020.09.24.301986v1?rss=1 Ravi, J. Anantharaman, V. Chen, S. Z. Datta, P. Aravind, L. Gennaro, M. L. 2020-09-25 doi:10.1101/2020.09.24.301986 Cold Spring Harbor Laboratory Press 2020-09-25 <![CDATA[ A chromosome-level genome assembly for the Pacific oyster (Crassostrea gigas) ]]> https://biorxiv.org/content/10.1101/2020.09.25.313494v1?rss=1 Penaloza, C. Gutierrez, A. P. Eory, L. Wang, S. Guo, X. Archibald, A. L. Bean, T. P. Houston, R. D. 2020-09-25 doi:10.1101/2020.09.25.313494 Cold Spring Harbor Laboratory Press 2020-09-25 <![CDATA[ ACP-MHCNN: An Accurate Multi-Headed Deep-Convolutional Neural Network to Predict Anticancer peptides ]]> https://biorxiv.org/content/10.1101/2020.09.25.313668v1?rss=1 Ahmed, S. Muhammod, R. Adilina, S. Khan, Z. H. Shatabda, S. Dehzangi, A. 2020-09-28 doi:10.1101/2020.09.25.313668 Cold Spring Harbor Laboratory Press 2020-09-28 <![CDATA[ A cis-regulatory atlas in maize at single-cell resolution ]]> https://biorxiv.org/content/10.1101/2020.09.27.315499v1?rss=1 Marand, A. P. Chen, Z. Gallavotti, A. Schmitz, R. J. 2020-09-28 doi:10.1101/2020.09.27.315499 Cold Spring Harbor Laboratory Press 2020-09-28 <![CDATA[ Measuring effects of trainee professional development on research productivity: A cross-institutional meta-analysis ]]> https://biorxiv.org/content/10.1101/2020.09.28.316422v1?rss=1 Brandt, P. Sturzenegger Varvayanis, S. Baas, T. Bolgioni-Smith, A. Alder, J. Petrie, K. A. Dominguez, I. Brown, A. M. Stayart, C. A. Singh, H. Van Wart, A. Chow, C. S. Mathur, A. Schreiber, B. M. Fruman, D. A. Bowden, B. Holmquist, C. E. Arneman, D. Hall, J. D. Hyman, L. E. Gould, K. Chalkley, R. Brennwald, P. Layton, R. 2020-09-28 doi:10.1101/2020.09.28.316422 Cold Spring Harbor Laboratory Press 2020-09-28 <![CDATA[ An improved experimental pipeline for preparing circular ssDNA viruses for next-generation sequencing ]]> https://biorxiv.org/content/10.1101/2020.09.30.321224v1?rss=1 Aimone, C. D. Hoyer, J. S. Dye, A. E. Deppong, D. O. Duffy, S. Carbone, I. Hanley-Bowdoin, L. 2020-10-01 doi:10.1101/2020.09.30.321224 Cold Spring Harbor Laboratory Press 2020-10-01 <![CDATA[ Human hypertrophic cardiomyopathy mutation R712L suppresses the working stroke of cardiac myosin and can be rescued by omecamtiv mecarbil ]]> https://biorxiv.org/content/10.1101/2020.10.02.323782v1?rss=1 Snoberger, A. Barua, B. Atherton, J. L. Shuman, H. Forgacs, E. Goldman, Y. E. Winkelmann, D. A. Ostap, E. M. 2020-10-02 doi:10.1101/2020.10.02.323782 Cold Spring Harbor Laboratory Press 2020-10-02 <![CDATA[ Adenosine modulates extracellular glutamate levels via adenosine A2A receptors in the delayed-ethanol induced headache. ]]> https://biorxiv.org/content/10.1101/2020.10.02.324517v1?rss=1 Fried, N. T. Maxwell, C. R. Hoek, J. B. Elliott, M. B. Oshinsky, M. L. 2020-10-04 doi:10.1101/2020.10.02.324517 Cold Spring Harbor Laboratory Press 2020-10-04 <![CDATA[ Developing Human Pluripotent Stem Cell-Based Cerebral Organoids with a Controllable Microglia Ratio for Modeling Brain Development and Pathology ]]> https://biorxiv.org/content/10.1101/2020.10.09.331710v1?rss=1 Xu, R. Boreland, A. J. Li, X. Erickson, C. Jin, M. Atkins, C. Pang, Z. Daniels, B. P. Jiang, P. 2020-10-12 doi:10.1101/2020.10.09.331710 Cold Spring Harbor Laboratory Press 2020-10-12 <![CDATA[ Metaproteogenomic profiling of chemosynthetic microbial biofilms reveals metabolic flexibility during colonization of a shallow-water gas vent ]]> https://biorxiv.org/content/10.1101/2020.10.15.340729v1?rss=1 Patwardhan, S. Smedile, F. Giovannelli, D. Vetriani, C. 2020-10-15 doi:10.1101/2020.10.15.340729 Cold Spring Harbor Laboratory Press 2020-10-15 <![CDATA[ Evolutionary and phylogenetic insights from a nuclear genome sequence of the extinct, giant subfossil koala lemur Megaladapis edwardsi ]]> https://biorxiv.org/content/10.1101/2020.10.16.342907v1?rss=1 10 kg survived a relatively recent wave of extinction on the island. From morphological and isotopic analyses of skeletal subfossil remains we can reconstruct some of the biology and behavioral ecology of giant lemurs (primates; up to ~160 kg), elephant birds (up to ~860 kg), and other extraordinary Malagasy megafauna that survived well into the past millennium. Yet much about the evolutionary biology of these now extinct species remains unknown, along with persistent phylogenetic uncertainty in some cases. Thankfully, despite the challenges of DNA preservation in tropical and sub-tropical environments, technical advances have enabled the recovery of ancient DNA from some Malagasy subfossil specimens. Here we present a nuclear genome sequence (~2X coverage) for one of the largest extinct lemurs, the koala lemur Megaladapis edwardsi (~85kg). To support the testing of key phylogenetic and evolutionary hypotheses we also generated new high-coverage complete nuclear genomes for two extant lemur species, Eulemur rufifrons and Lepilemur mustelinus, and we aligned these sequences with previously published genomes for three other extant lemur species and 47 non-lemur vertebrates. Our phylogenetic results confirm that Megaladapis is most closely related to the extant Lemuridae (typified in our analysis by E. rufifrons) to the exclusion of L. mustelinus, which contradicts morphology-based phylogenies. Our evolutionary analyses identified significant convergent evolution between M. edwardsi and extant folivorous primates (colobine monkeys) and ungulate herbivores (horses) in genes encoding protein products that function in the biodegradation of plant toxins and nutrient absorption. These results suggest that koala lemurs were highly adapted to a leaf-based diet, which may also explain their convergent craniodental morphology with the small-bodied folivore Lepilemur. ]]> Marciniak, S. Mughal, M. R. Godfrey, L. R. Bankoff, R. J. Randrianatoandro, H. Crowley, B. E. Bergey, C. M. Muldoon, K. M. Randrianasy, J. Raharivololona, B. M. Schuster, S. C. Malhi, R. S. Yoder, A. D. Louis, E. E. Kistler, L. Perry, G. H. 2020-10-17 doi:10.1101/2020.10.16.342907 Cold Spring Harbor Laboratory Press 2020-10-17 <![CDATA[ Single-cell Sequencing Reveals Brain/Spinal Cord Oligodendrocyte Precursor Heterogeneity and Requirement for mTOR in Cholesterol Biosynthesis and Myelin Maintenance ]]> https://biorxiv.org/content/10.1101/2020.10.22.349209v1?rss=1 Khandker, L. Jeffries, M. A. Chang, Y.-J. Mather, M. L. Bourne, J. N. Tafreshi, A. K. Bozdagi-Gunal, O. Macklin, W. B. Wood, T. L. 2020-10-22 doi:10.1101/2020.10.22.349209 Cold Spring Harbor Laboratory Press 2020-10-22 <![CDATA[ Bayesian inference: The comprehensive approach to analyzing single-molecule experiments ]]> https://biorxiv.org/content/10.1101/2020.10.23.353110v1?rss=1 Kinz-Thompson, C. D. Ray, K. K. Gonzalez, R. L. 2020-10-25 doi:10.1101/2020.10.23.353110 Cold Spring Harbor Laboratory Press 2020-10-25 <![CDATA[ Purinergic P2Y1 and P2Y2/4 receptors elicit distinct Ca2+ signaling patterns in hepatocytes via differential feedback regulation by Protein Kinase C ]]> https://biorxiv.org/content/10.1101/2020.10.29.360784v1?rss=1 Corrca-Velloso, J. C. Bartlett, P. J. Brumer, R. Gaspers, L. Ulrich, H. Thomas, A. P. 2020-10-30 doi:10.1101/2020.10.29.360784 Cold Spring Harbor Laboratory Press 2020-10-30 <![CDATA[ Metabolomic investigation of the pseudouridimycin producer, a prolific streptomycete ]]> https://biorxiv.org/content/10.1101/2020.11.05.369249v1?rss=1 Iorio, M. Davatgarbenam, S. Serina, S. Criscenzo, P. Zdouc, M. M. Simone, M. Maffioli, S. I. Ebright, R. H. Donadio, S. Sosio, M. 2020-11-05 doi:10.1101/2020.11.05.369249 Cold Spring Harbor Laboratory Press 2020-11-05 <![CDATA[ Mayaro Virus Infection Elicits an Innate Immune Response and Represses Autophagy in Anopheles stephensi ]]> https://biorxiv.org/content/10.1101/2020.11.15.383596v1?rss=1 Henderson, C. A. Brustolin, M. Hegde, S. Hughes, G. Rasgon, J. L. 2020-11-15 doi:10.1101/2020.11.15.383596 Cold Spring Harbor Laboratory Press 2020-11-15 <![CDATA[ Alternating handedness motifs in proteins classify structure and cofactor binding ]]> https://biorxiv.org/content/10.1101/2020.11.17.367490v1?rss=1 Rizwan, S. Pike, D. Poudel, S. Nanda, V. 2020-11-20 doi:10.1101/2020.11.17.367490 Cold Spring Harbor Laboratory Press 2020-11-20 <![CDATA[ Fibrillar α-synuclein induces neurotoxic astrocyte activation via RIP kinase signaling and NF-κB ]]> https://biorxiv.org/content/10.1101/2020.11.17.387175v1?rss=1 Chou, T.-W. Chang, N. P. Krishnagiri, M. Patel, A. P. Atkins, C. Daniels, B. P. 2020-11-17 doi:10.1101/2020.11.17.387175 Cold Spring Harbor Laboratory Press 2020-11-17 <![CDATA[ AI-Driven Multiscale Simulations Illuminate Mechanisms of SARS-CoV-2 Spike Dynamics ]]> https://biorxiv.org/content/10.1101/2020.11.19.390187v1?rss=1 Casalino, L. Dommer, A. C. Gaieb, Z. Barros, E. P. Sztain, T. Ahn, S.-H. Trifan, A. Brace, A. Ma, H. Lee, H. Turilli, M. Bogetti, A. Khalid, S. Chong, L. Simmerling, C. Hardy, D. Maia, J. Phillips, J. Kurth, T. Stern, A. Huang, L. McCalpain, J. Tatineni, M. Gibbs, T. Stone, J. E. Jha, S. Ramanathan, A. Amaro, R. E. 2020-11-20 doi:10.1101/2020.11.19.390187 Cold Spring Harbor Laboratory Press 2020-11-20 <![CDATA[ Crystal structure of prototype foamy virus (PFV) protease-reverse transcriptase fusion (PR-RT) reveals conformational plasticity: implications for function ]]> https://biorxiv.org/content/10.1101/2020.11.23.395087v1?rss=1 Harrison, J. J. E. K. Tuske, S. Das, K. Ruiz, F. X. Bauman, J. D. Boyer, P. DeStefano, J. J. Hughes, S. H. Arnold, E. 2020-11-24 doi:10.1101/2020.11.23.395087 Cold Spring Harbor Laboratory Press 2020-11-24 <![CDATA[ Immunogenetic response to a malaria-like parasite in a wild primate ]]> https://biorxiv.org/content/10.1101/2020.11.24.396317v1?rss=1 Trujillo, A. E. Bergey, C. M. 2020-11-24 doi:10.1101/2020.11.24.396317 Cold Spring Harbor Laboratory Press 2020-11-24 <![CDATA[ yama , a mutant allele of Mov10l1, disrupts retrotransposon silencing and piRNA biogenesis ]]> https://biorxiv.org/content/10.1101/2020.11.26.399659v1?rss=1 Guan, Y. Jain, D. Keeney, S. Wang, P. J. 2020-11-26 doi:10.1101/2020.11.26.399659 Cold Spring Harbor Laboratory Press 2020-11-26 <![CDATA[ A selective projection from the subthalamic nucleus to parvalbumin-expressing interneurons of the striatum ]]> https://biorxiv.org/content/10.1101/2020.11.26.400242v1?rss=1 Kondabolu, K. Doig, N. M. Ayeko, O. Kahn, B. Torres, A. Calvigioni, D. Meletis, K. Magill, P. J. Koos, T. 2020-11-26 doi:10.1101/2020.11.26.400242 Cold Spring Harbor Laboratory Press 2020-11-26 <![CDATA[ Neuroprotective mechanisms of red clover and soy isoflavones in Parkinson's disease models ]]> https://biorxiv.org/content/10.1101/2020.12.01.391268v1?rss=1 View larger version (40K): org.highwire.dtl.DTLVardef@14446dcorg.highwire.dtl.DTLVardef@1884a7borg.highwire.dtl.DTLVardef@d1ebaborg.highwire.dtl.DTLVardef@1c744b1_HPS_FORMAT_FIGEXP M_FIG The isoflavone-rich extracts red clover and soy and the individual isoflavones daidzein and equol protect neuronal cultures against environmental and genetic triggers of Parkinsons disease, and rescue motor deficits in rats exposed to the neurotoxin 6-OHDA. C_FIG ]]> de Rus Jacquet, A. Ambaw, A. Tambe, M. A. Timmers, M. Ma, S. Y. Wu, Q.-L. Simon, J. E. McCabe, G. P. Lila, M. A. Shi, R. Rochet, J.-C. 2020-12-02 doi:10.1101/2020.12.01.391268 Cold Spring Harbor Laboratory Press 2020-12-02 <![CDATA[ Differential effects of antiseptic mouth rinses on SARS-CoV-2 infectivity in vitro ]]> https://biorxiv.org/content/10.1101/2020.12.01.405662v1?rss=1 Xu, C. Wang, A. Hoskin, E. R. Cugini, C. Markowitz, K. Chang, T. L. Fine, D. H. 2020-12-01 doi:10.1101/2020.12.01.405662 Cold Spring Harbor Laboratory Press 2020-12-01 <![CDATA[ Evolution of the SARS-CoV-2 proteome in three dimensions (3D) during the first six months of the COVID-19 pandemic ]]> https://biorxiv.org/content/10.1101/2020.12.01.406637v1?rss=1 48,000 viral proteome sequences showed how each one of the 29 viral study proteins have undergone amino acid changes. Structural models computed for every unique sequence variant revealed that most substitutions map to protein surfaces and boundary layers with a minority affecting hydrophobic cores. Conservative changes were observed more frequently in cores versus boundary layers/surfaces. Active sites and protein-protein interfaces showed modest numbers of substitutions. Energetics calculations showed that the impact of substitutions on the thermodynamic stability of the proteome follows a universal bi-Gaussian distribution. Detailed results are presented for six drug discovery targets and four structural proteins comprising the virion, highlighting substitutions with the potential to impact protein structure, enzyme activity, and functional interfaces. Characterizing the evolution of the virus in three dimensions provides testable insights into viral protein function and should aid in structure-based drug discovery efforts as well as the prospective identification of amino acid substitutions with potential for drug resistance. ]]> Lubin, J. H. Zardecki, C. Dolan, E. M. Lu, C. Shen, Z. Dutta, S. Westbrook, J. D. Hudson, B. P. Goodsell, D. S. Williams, J. K. Voigt, M. Sarma, V. Xie, L. Venkatachalam, T. Arnold, S. Alfaro Alvarado, L. H. Catalfano, K. Khan, A. McCarthy, E. Staggers, S. Tinsley, B. Trudeau, A. Singh, J. Whitmore, L. Zheng, H. Benedek, M. Currier, J. Dresel, M. Duvvuru, A. Dyszel, B. Fingar, E. Hennen, E. M. Kirsch, M. Khan, A. A. Labrie-Cleary, C. Laporte, S. Lenkeit, E. Martin, K. Orellana, M. Ortiz-Alvarez de la Campa, M. Paredes, I. Wheeler, B. Rupert, A. Sam, A 2020-12-01 doi:10.1101/2020.12.01.406637 Cold Spring Harbor Laboratory Press 2020-12-01 <![CDATA[ Quantifying bacterial evolution in the wild: a birthday problem for Campylobacter lineages ]]> https://biorxiv.org/content/10.1101/2020.12.02.407999v1?rss=1 Calland, J. K. Pascoe, B. Bayliss, S. C. Mourkas, E. Berthenet, E. Thorpe, H. A. Hitchings, M. D. Feil, E. J. Blaser, M. J. Falush, D. Sheppard, S. K. 2020-12-03 doi:10.1101/2020.12.02.407999 Cold Spring Harbor Laboratory Press 2020-12-03 <![CDATA[ Unusual predominance of maintenance DNA methylation in Spirodela polyrhiza ]]> https://biorxiv.org/content/10.1101/2020.12.03.410332v1?rss=1 Harkess, A. E. Bewick, A. Lu, Z. Fourounjian, P. Messing, J. Michael, T. Schmitz, R. J. Meyers, B. C. 2020-12-03 doi:10.1101/2020.12.03.410332 Cold Spring Harbor Laboratory Press 2020-12-03 <![CDATA[ Circular RNA profiling reveals abundant and diverse circRNAs of SARS-CoV-2, SARS-CoV and MERS-CoV origin ]]> https://biorxiv.org/content/10.1101/2020.12.07.415422v1?rss=1 Yang, S. Zhou, H. Cruz-Cosme, R. Liu, M. Niu, X. Xu, J. Li, Y. Xiao, L. Wang, Q. Zhu, H. Tang, Q. 2020-12-08 doi:10.1101/2020.12.07.415422 Cold Spring Harbor Laboratory Press 2020-12-08 <![CDATA[ Joint Modeling of Zero-inflated Longitudinal Proportions and Time-to-event Data with Application to a Gut Microbiome Study ]]> https://biorxiv.org/content/10.1101/2020.12.10.419945v1?rss=1 Hu, J. Wang, C. Blaser, M. J. Li, H. 2020-12-11 doi:10.1101/2020.12.10.419945 Cold Spring Harbor Laboratory Press 2020-12-11 <![CDATA[ Enhancing Task fMRI Preprocessing via Individualized Model-Based Filtering of Intrinsic Activity Dynamics ]]> https://biorxiv.org/content/10.1101/2020.12.10.420273v1?rss=1 Singh, M. F. Wang, A. Cole, M. Ching, S. Braver, T. S. 2020-12-11 doi:10.1101/2020.12.10.420273 Cold Spring Harbor Laboratory Press 2020-12-11 <![CDATA[ A diencephalic circuit for opioid analgesia but not positive reinforcement ]]> https://biorxiv.org/content/10.1101/2020.12.15.422931v1?rss=1 Waung, M. W. Maanum, K. A. Driscoll, J. R. O'Brien, C. Bryant, S. Mansourian, K. Morales, M. Barker, D. J. Margolis, E. B. 2020-12-15 doi:10.1101/2020.12.15.422931 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ Activity flow underlying abnormalities in brain activations and cognition in schizophrenia ]]> https://biorxiv.org/content/10.1101/2020.12.16.423109v1?rss=1 Hearne, L. J. Mill, R. D. Keane, B. P. Repovs, G. Anticevic, A. Cole, M. W. 2020-12-18 doi:10.1101/2020.12.16.423109 Cold Spring Harbor Laboratory Press 2020-12-18 <![CDATA[ Improved microbial community characterization of 16S rRNA via metagenome hybridization capture enrichment ]]> https://biorxiv.org/content/10.1101/2020.12.18.423101v1?rss=1 400-fold) and decrease analysis time to obtain consistent community assessments. Furthermore, our study reveals that bioinformatic methods used to analyze sequencing data may have a greater influence on estimates of community composition than library preparation method used, likely in part to the extent and curation of the reference databases considered. ]]> Beaudry, M. S. Wang, J. Kieran, T. Thomas, J. Bayona-Vasquez, N. J. Gao, B. Devault, A. Brunelle, B. Lu, K. Wang, J.-S. Rhodes, O. E. Glenn, T. C. 2020-12-19 doi:10.1101/2020.12.18.423101 Cold Spring Harbor Laboratory Press 2020-12-19 <![CDATA[ Effect of land use, habitat suitability, and hurricanes on the population connectivity of an endemic insular bat ]]> https://biorxiv.org/content/10.1101/2020.12.18.423522v1?rss=1 Calderon-Acevedo, C. A. Rodriguez-Duran, A. Soto-Centeno, J. A. 2020-12-21 doi:10.1101/2020.12.18.423522 Cold Spring Harbor Laboratory Press 2020-12-21 <![CDATA[ Quantifying shifts in natural selection on codon usagebetween protein regions: A population genetics approach ]]> https://biorxiv.org/content/10.1101/2020.12.18.423529v1?rss=1 Cope, A. L. Gilchrist, M. A. 2020-12-20 doi:10.1101/2020.12.18.423529 Cold Spring Harbor Laboratory Press 2020-12-20 <![CDATA[ Narratives: fMRI data for evaluating models of naturalistic language comprehension ]]> https://biorxiv.org/content/10.1101/2020.12.23.424091v1?rss=1 Nastase, S. A. Liu, Y.-F. Hillman, H. Zadbood, A. Hasenfratz, L. Keshavarzian, N. Chen, J. Honey, C. J. Yeshurun, Y. Regev, M. Nguyen, M. Chang, C. H. C. Baldassano, C. Lositsky, O. Simony, E. Chow, M. A. Leong, Y. C. Brooks, P. P. Micciche, E. Choe, G. Goldstein, A. Vanderwal, T. Halchenko, Y. O. Norman, K. A. Hasson, U. 2020-12-23 doi:10.1101/2020.12.23.424091 Cold Spring Harbor Laboratory Press 2020-12-23 <![CDATA[ Shedding Light on Microbial Dark Matter with A Universal Language of Life ]]> https://biorxiv.org/content/10.1101/2020.12.23.424215v1?rss=1 Hoarfrost, A. Aptekmann, A. Farfanuk, G. Bromberg, Y. 2020-12-24 doi:10.1101/2020.12.23.424215 Cold Spring Harbor Laboratory Press 2020-12-24 <![CDATA[ Constructing neural network models from brain data reveals representational transformations underlying adaptive behavior ]]> https://biorxiv.org/content/10.1101/2020.12.24.424353v1?rss=1 Ito, T. Yang, G. R. Laurent, P. Schultz, D. H. Cole, M. W. 2020-12-24 doi:10.1101/2020.12.24.424353 Cold Spring Harbor Laboratory Press 2020-12-24 <![CDATA[ A quantitative model predicts how m6A reshapes the kinetic landscape of nucleic acid hybridization and conformational transitions ]]> https://biorxiv.org/content/10.1101/2020.12.25.424401v1?rss=1 Liu, B. Shi, H. Rangadurai, A. Nussbaumer, F. Chu, C.-C. Erharter, K. A. Case, D. A. Kreutz, C. Al-Hashimi, H. M. 2020-12-26 doi:10.1101/2020.12.25.424401 Cold Spring Harbor Laboratory Press 2020-12-26 <![CDATA[ ComEB protein is dispensable for transformation but must be translated for optimal synthesis of ComEC ]]> https://biorxiv.org/content/10.1101/2020.12.30.424838v1?rss=1 De Santis, M. Hahn, J. Dubnau, D. 2020-12-30 doi:10.1101/2020.12.30.424838 Cold Spring Harbor Laboratory Press 2020-12-30 <![CDATA[ The gastrin-releasing peptide regulates stress-enhanced fear and dopamine signaling ]]> https://biorxiv.org/content/10.1101/2020.12.31.424996v1?rss=1 Morishita, Y. Fuentes, I. Favate, J. Zushida, K. Nishi, A. Hevi, C. Goldsmith, N. Buyske, S. Sillivan, S. E. Miller, C. A. Kandel, E. R. Uchida, S. Shah, P. Shumyatsky, G. P. 2021-01-01 doi:10.1101/2020.12.31.424996 Cold Spring Harbor Laboratory Press 2021-01-01 <![CDATA[ EdU incorporation to assess cell proliferation and drug susceptibility for the brain-eating amoeba, Naegleria fowleri ]]> https://biorxiv.org/content/10.1101/2021.01.07.425827v1?rss=1 97%. Until recently, few advances have been made in the discovery of new drugs for N. fowleri and one drawback is the lack of validated tools and methods to enhance drug discovery and diagnostics research. In this study we aimed to validate alternative methods to assess cell proliferation that are commonly used for other cell types and develop a novel drug screening assay to evaluate drug efficacy on N. fowleri replication. EdU (5-ethynyl-2'-deoxyuridine) is a pyrimidine analog of thymidine that can be used as a quantitative endpoint for cell proliferation. EdU incorporation is detected via a copper catalyzed click reaction with an Alexa Fluor linked azide. EdU incorporation in replicating N. fowleri was validated using fluorescence microscopy and quantitative methods for assessing EdU incorporation were developed by using an imaging flow cytometer. Currently used PAM therapeutics inhibited N. fowleri replication and EdU incorporation in vitro. EdA (5'ethynyl-2'-deoxyadenosine), an adenine analog, also was incorporated by N. fowleri, but was more cytotoxic than EdU. In summary, EdU incorporation could be used as a complimentary method for drug discovery for these neglected pathogens. ]]> Troth, E. V. Kyle, D. E. 2021-01-08 doi:10.1101/2021.01.07.425827 Cold Spring Harbor Laboratory Press 2021-01-08 <![CDATA[ Aurora kinase A is essential for meiosis in mouse oocytes ]]> https://biorxiv.org/content/10.1101/2021.01.08.425851v1?rss=1 Blengini, C. S. Ibrahimian, P. Vaskovicova, M. Drutovic, D. Solc, P. Schindler, K. 2021-01-08 doi:10.1101/2021.01.08.425851 Cold Spring Harbor Laboratory Press 2021-01-08 <![CDATA[ Molecular Dynamics Analysis of a Flexible Loop at the Binding Interface of the SARS-CoV-2 Spike Protein Receptor-Binding Domain ]]> https://biorxiv.org/content/10.1101/2021.01.08.425965v1?rss=1 Williams, J. K. Wang, B. Sam, A. Hoop, C. L. Case, D. A. Baum, J. 2021-01-11 doi:10.1101/2021.01.08.425965 Cold Spring Harbor Laboratory Press 2021-01-11 <![CDATA[ Synaptojanin1 deficiency upregulates basal level autophagosome formation in astrocytes ]]> https://biorxiv.org/content/10.1101/2021.01.08.425969v1?rss=1 Pan, P.-Y. Zhu, J. Rizvi, A. Zhu, X. Tanaka, H. Dreyfus, C. F. 2021-01-08 doi:10.1101/2021.01.08.425969 Cold Spring Harbor Laboratory Press 2021-01-08 <![CDATA[ Protoporphyrin-IX nanostructures modulate their protein aggregation ability via differential oxidation and protein binding ]]> https://biorxiv.org/content/10.1101/2021.01.11.426224v1?rss=1 Maitra, D. Pinsky, B. M. Soherwardy, A. Zheng, H. Banerjee, R. Omary, B. 2021-01-11 doi:10.1101/2021.01.11.426224 Cold Spring Harbor Laboratory Press 2021-01-11 <![CDATA[ The landscape of transcriptional and translational changes over 22 years of bacterial adaptation ]]> https://biorxiv.org/content/10.1101/2021.01.12.426406v1?rss=1 Favate, J. S. Liang, S. Yadavalli, S. S. Shah, P. 2021-01-13 doi:10.1101/2021.01.12.426406 Cold Spring Harbor Laboratory Press 2021-01-13 <![CDATA[ Near-atomic resolution Cryo-EM structure of Mayaro virus identifies key structural determinants of alphavirus particle formation ]]> https://biorxiv.org/content/10.1101/2021.01.14.425226v1?rss=1 Chmielewski, D. Kaelber, J. Jin, J. Weaver, S. C. Auguste, A. J. Chiu, W. 2021-01-14 doi:10.1101/2021.01.14.425226 Cold Spring Harbor Laboratory Press 2021-01-14 <![CDATA[ Frequency preference response in covalent modification cycles under substrate sequestration conditions ]]> https://biorxiv.org/content/10.1101/2021.01.14.426711v1?rss=1 Reves Szemere, J. Rotstein, H. G. Ventura, A. C. 2021-01-16 doi:10.1101/2021.01.14.426711 Cold Spring Harbor Laboratory Press 2021-01-16 <![CDATA[ CAR-NK Cells Effectively Target the D614 and G614 SARS-CoV-2-infected Cells ]]> https://biorxiv.org/content/10.1101/2021.01.14.426742v1?rss=1 Ma, M. Badeti, S. Chen, C.-H. Pinter, A. Jiang, Q. Shi, L. Zhou, R. Xu, H. Li, Q. Gause, W. Liu, D. 2021-01-15 doi:10.1101/2021.01.14.426742 Cold Spring Harbor Laboratory Press 2021-01-15 <![CDATA[ Free energy and kinetics of cAMP permeation through connexin26 hemichannel with and without voltage ]]> https://biorxiv.org/content/10.1101/2021.01.18.427208v1?rss=1 Jiang, W. Lin, Y.-C. Botello-Smith, W. M. Contreras, J. E. Harris, A. Maragliano, L. Luo, Y. 2021-01-19 doi:10.1101/2021.01.18.427208 Cold Spring Harbor Laboratory Press 2021-01-19 <![CDATA[ γδ intraepithelial lymphocytes facilitate pathological epithelial cell shedding via CD103-mediated granzyme release. ]]> https://biorxiv.org/content/10.1101/2021.01.20.427150v1?rss=1 Hu, M. D. Golovchenko, N. B. Kelly, T. J. Agos, J. Zeglinski, M. R. Bonder, E. M. Granville, D. J. Watson, A. J. M. Edelblum, K. L. 2021-01-21 doi:10.1101/2021.01.20.427150 Cold Spring Harbor Laboratory Press 2021-01-21 <![CDATA[ Developmental and behavioral phenotypes in a new mouse model of DDX3X syndrome ]]> https://biorxiv.org/content/10.1101/2021.01.22.427482v1?rss=1 Boitnott, A. Ung, D. Garcia-Forn, M. Niblo, K. Mendonca, D. Flores, M. Maxwell, S. Ellegood, J. Qiu, L. R. Grice, D. E. Lerch, J. P. Rasin, M.-R. Buxbaum, J. D. Drapeau, E. De Rubeis, S. 2021-01-23 doi:10.1101/2021.01.22.427482 Cold Spring Harbor Laboratory Press 2021-01-23 <![CDATA[ The human brain's intrinsic network architecture is organized to represent diverse cognitive task information ]]> https://biorxiv.org/content/10.1101/2021.01.25.428141v1?rss=1 Schultz, D. H. Ito, T. Cole, M. W. 2021-01-25 doi:10.1101/2021.01.25.428141 Cold Spring Harbor Laboratory Press 2021-01-25 <![CDATA[ Causal emergence of task information from dynamic network interactions in the human brain ]]> https://biorxiv.org/content/10.1101/2021.01.26.428276v1?rss=1 Mill, R. D. Hamilton, J. L. Winfield, E. C. Lalta, N. Chen, R. H. Cole, M. W. 2021-01-27 doi:10.1101/2021.01.26.428276 Cold Spring Harbor Laboratory Press 2021-01-27 <![CDATA[ Voluntary alcohol consumption disrupts coupling of prefrontal cortical activity to arousal ]]> https://biorxiv.org/content/10.1101/2021.02.01.429229v1?rss=1 Sipe, G. O. Linares-Garcia, I. Nguyen, M. Vazey, E. Huda, R. 2021-02-02 doi:10.1101/2021.02.01.429229 Cold Spring Harbor Laboratory Press 2021-02-02 <![CDATA[ Understanding of the 2-oxoglutarate dehydrogenase and 2-oxoadipate dehydrogenase assembly with the E2o core relevant to a hybrid complex formation ]]> https://biorxiv.org/content/10.1101/2021.02.03.429618v1?rss=1 Zhang, X. Jordan, F. Nemeria, N. S. 2021-02-03 doi:10.1101/2021.02.03.429618 Cold Spring Harbor Laboratory Press 2021-02-03 <![CDATA[ Low doses of the organic insecticide spinosad trigger lysosomal defects, ROS driven lipid dysregulation and neurodegeneration in flies ]]> https://biorxiv.org/content/10.1101/2021.02.03.429672v1?rss=1 Martelli, F. Zuo, Z. Wang, J. Wong, C.-O. Karagas, N. E. Roessner, U. Rupasinghe, T. Venkatachalam, K. Perry, T. Batterham, P. Bellen, H. J. 2021-02-04 doi:10.1101/2021.02.03.429672 Cold Spring Harbor Laboratory Press 2021-02-04 <![CDATA[ Evolution and connectivity influence the persistence and recovery of coral reefs under climate change in the Caribbean, Southwest Pacific, and Coral Triangle ]]> https://biorxiv.org/content/10.1101/2021.02.04.429453v1?rss=1 McManus, L. C. Forrest, D. L. Tekwa, E. W. Schindler, D. E. Colton, M. A. Webster, M. M. Essington, T. E. Palumbi, S. R. Mumby, P. J. Pinsky, M. L. 2021-02-05 doi:10.1101/2021.02.04.429453 Cold Spring Harbor Laboratory Press 2021-02-05 <![CDATA[ Sensory cilia act as a specialized venue for regulated EV biogenesis and signaling ]]> https://biorxiv.org/content/10.1101/2021.02.04.429799v1?rss=1 Wang, J. Nikonorova, I. A. Silva, M. S. Walsh, J. D. Tilton, P. E. Gu, A. Barr, M. M. 2021-02-04 doi:10.1101/2021.02.04.429799 Cold Spring Harbor Laboratory Press 2021-02-04 <![CDATA[ Multi-omic characterization of the thermal stress phenome in the stony coral Montipora capitata ]]> https://biorxiv.org/content/10.1101/2021.02.05.429981v1?rss=1 Pathmanathan, J. Williams, A. Stephens, T. G. Su, X. Chiles, E. N. Conetta, D. Putnam, H. M. Bhattacharya, D. 2021-02-07 doi:10.1101/2021.02.05.429981 Cold Spring Harbor Laboratory Press 2021-02-07 <![CDATA[ Chronic paternal morphine exposure increases sensitivity to morphine-derived antinociception ]]> https://biorxiv.org/content/10.1101/2021.02.07.430143v1?rss=1 Toussaint, A. B. Foster, W. Jones, J. M. Kaufmann, S. Wachira, M. Hughes, R. Bongiovanni, A. R. Famularo, S. T. Dunham, B. P. Schwark, R. Fried, N. T. Wimmer, M. Abdus-Saboor, I. 2021-02-08 doi:10.1101/2021.02.07.430143 Cold Spring Harbor Laboratory Press 2021-02-08 <![CDATA[ The UCR Minicore: a valuable resource for cowpea research and breeding ]]> https://biorxiv.org/content/10.1101/2021.02.09.430326v1?rss=1 Munoz-Amatriain, M. Lo, S. Herniter, I. A. Boukar, O. Fatokun, C. Carvalho, M. Castro, I. Guo, Y.-N. Huynh, B.-L. Roberts, P. A. Carnide, V. Close, T. J. 2021-02-11 doi:10.1101/2021.02.09.430326 Cold Spring Harbor Laboratory Press 2021-02-11 <![CDATA[ Similar neural and perceptual masking effects of low-power optogenetic stimulation in primate V1 ]]> https://biorxiv.org/content/10.1101/2021.02.16.431182v1?rss=1 Chen, S. C.-Y. Benvenuti, G. Chen, Y. Kumar, S. Ramakrishnan, C. Deisseroth, K. Geisler, W. S. Seidemann, E. 2021-02-17 doi:10.1101/2021.02.16.431182 Cold Spring Harbor Laboratory Press 2021-02-17 <![CDATA[ Phase transitions may explain why SARS-CoV-2 spreads so fast and why new variants are spreading faster ]]> https://biorxiv.org/content/10.1101/2021.02.16.431437v1?rss=1 Phillips, J. C. Moret, M. Zebende, G. F. Chow, C. C. 2021-02-17 doi:10.1101/2021.02.16.431437 Cold Spring Harbor Laboratory Press 2021-02-17 <![CDATA[ A large-scale transcriptome-wide association study (TWAS) of ten blood cell phenotypes reveals complexities of TWAS fine-mapping ]]> https://biorxiv.org/content/10.1101/2021.02.23.432444v1?rss=1 Tapia, A. L. Rowland, B. T. Rosen, J. D. Preuss, M. Young, K. Graff, M. Choquet, H. Couper, D. J. Buyske, S. Bien, S. A. Jorgenson, E. Kooperberg, C. Loos, R. J. F. Morrison, A. C. North, K. E. Yu, B. Reiner, A. P. Li, Y. Raffield, L. M. 2021-02-23 doi:10.1101/2021.02.23.432444 Cold Spring Harbor Laboratory Press 2021-02-23 <![CDATA[ PredictProtein - Predicting Protein Structure and Function for 29 Years ]]> https://biorxiv.org/content/10.1101/2021.02.23.432527v1?rss=1 Bernhofer, M. Dallago, C. Karl, T. Satagopam, V. Heinzinger, M. Littmann, M. Olenyi, T. Qiu, J. Schuetze, K. Yachdav, G. Ashkenazy, H. Ben-Tal, N. Bromberg, Y. Goldberg, T. Kajan, L. O'Donoghue, S. Sander, C. Schafferhans, A. Schlessinger, A. Vriend, G. Mirdita, M. Gawron, P. Gu, W. Jarosz, Y. Trefois, C. Steinegger, M. Schneider, R. Rost, B. 2021-02-24 doi:10.1101/2021.02.23.432527 Cold Spring Harbor Laboratory Press 2021-02-24 <![CDATA[ Neutralizing IFNL3 Autoantibodies in Severe COVID-19 Identified Using Molecular Indexing of Proteins by Self-Assembly ]]> https://biorxiv.org/content/10.1101/2021.03.02.432977v1?rss=1 View larger version (25K): org.highwire.dtl.DTLVardef@a3c55aorg.highwire.dtl.DTLVardef@1f1c840org.highwire.dtl.DTLVardef@920bc7org.highwire.dtl.DTLVardef@43633e_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Credle, J. J. Gunn, J. Sangkhapreecha, P. Monaco, D. R. Zheng, X. A. Tsai, H.-J. Wilbon, A. Morgenlander, W. R. Dong, Y. Jayaraman, S. Tosi, L. Parekkadan, B. Baer, A. N. Roederer, M. Bloch, E. M. Tobian, A. A. R. Zyskind, I. Silverberg, J. I. Rosenberg, A. Z. Cox, A. L. Lloyd, T. Mammen, A. L. Larman, H. B. 2021-03-03 doi:10.1101/2021.03.02.432977 Cold Spring Harbor Laboratory Press 2021-03-03 <![CDATA[ Optimal Time Lags from Causal Prediction Model Help Stratify and Forecast Nervous System Pathology ]]> https://biorxiv.org/content/10.1101/2021.03.05.434171v1?rss=1 Bermperidis, T. Rai, R. Torres, E. B. 2021-03-09 doi:10.1101/2021.03.05.434171 Cold Spring Harbor Laboratory Press 2021-03-09 <![CDATA[ The CATP-8/P5A-type ATPase functions in multiple pathways during neuronal patterning ]]> https://biorxiv.org/content/10.1101/2021.03.10.434729v1?rss=1 Tang, L. Trivedi, M. Freund, J. Salazar, C. Ramirez-Suarez, N. Lee, G. Rahman, M. Wang, Y. Grant, B. Bülow, H. E. 2021-03-10 doi:10.1101/2021.03.10.434729 Cold Spring Harbor Laboratory Press 2021-03-10 <![CDATA[ Value signals in orbitofrontal cortex predict economic decisions on a trial-to-trial basis ]]> https://biorxiv.org/content/10.1101/2021.03.11.434452v1?rss=1 McGinty, V. B. Lupkin, S. M. 2021-03-12 doi:10.1101/2021.03.11.434452 Cold Spring Harbor Laboratory Press 2021-03-12 <![CDATA[ Massively parallel reporter perturbation assay uncovers temporal regulatory architecture during neural differentiation ]]> https://biorxiv.org/content/10.1101/2021.03.12.435197v1?rss=1 Kreimer, A. Ashuach, T. Inoue, F. Khodaverdian, A. Yosef, N. Ahituv, N. 2021-03-12 doi:10.1101/2021.03.12.435197 Cold Spring Harbor Laboratory Press 2021-03-12 <![CDATA[ Design and proof-of-concept for targeted phage-based COVID-19 vaccination strategies with a streamlined cold-free supply chain ]]> https://biorxiv.org/content/10.1101/2021.03.15.435496v1?rss=1 Staquicini, D. I. Tang, F. H. F. Markosian, C. Yao, V. J. Staquicini, F. I. Dodero Rojas, E. Contessoto, V. G. Davis, D. O'Brien, P. Habib, N. Smith, T. L. Bruiners, N. Sidman, R. L. Gennaro, M. L. Lattime, E. C. Libutti, S. K. Whitford, P. C. Burley, S. K. Onuchic, J. N. Arap, W. Pasqualini, R. 2021-03-16 doi:10.1101/2021.03.15.435496 Cold Spring Harbor Laboratory Press 2021-03-16 <![CDATA[ Curtobacterium glycinis sp. nov. from Glycine max, Curtobacterium gossypii sp. nov. from Gossypium hirsutum and Curtobacterium oryzae sp. nov. from Oryza sativa, three new Curtobacterium species and endophytes from agricultural crops ]]> https://biorxiv.org/content/10.1101/2021.03.18.434777v1?rss=1 Seaton, S. Lemaire, J. Inderbitzin, P. Knight-Connoni, V. White, J. F. Trujillo, M. E. 2021-03-18 doi:10.1101/2021.03.18.434777 Cold Spring Harbor Laboratory Press 2021-03-18 <![CDATA[ Population diversity of cassava mosaic begomoviruses increases over the course of serial vegetative propagation ]]> https://biorxiv.org/content/10.1101/2021.03.22.436436v1?rss=1 Aimone, C. D. Lavington, E. Hoyer, J. S. Deppong, D. O. Mickelson-Young, L. Jacobson, A. Kennedy, G. G. Carbone, I. Hanley-Bowdoin, L. Duffy, S. 2021-03-22 doi:10.1101/2021.03.22.436436 Cold Spring Harbor Laboratory Press 2021-03-22 <![CDATA[ Computational Structure Prediction Provides a Plausible Mechanism for Electron Transfer by the Outer Membrane Protein Cyc2 from Acidithiobacillus ferrooxidans ]]> https://biorxiv.org/content/10.1101/2021.03.22.436458v1?rss=1 Jiang, V. Khare, S. D. Banta, S. 2021-03-22 doi:10.1101/2021.03.22.436458 Cold Spring Harbor Laboratory Press 2021-03-22 <![CDATA[ Isolation and Purification of Lipoarabinomannan from Urine of Adults with Active Tuberculosis ]]> https://biorxiv.org/content/10.1101/2021.03.24.436904v1?rss=1 Cantera, J. L. Rashid, A. Lillis, L. Peck, R. Drain, P. K. Pinter, A. Kawasaki, M. Moreau, E. Boyle, D. S. 2021-03-25 doi:10.1101/2021.03.24.436904 Cold Spring Harbor Laboratory Press 2021-03-25 <![CDATA[ Dynamic distortion of the orientation representational space after learning in the mouse primary visual cortex ]]> https://biorxiv.org/content/10.1101/2021.03.25.437032v1?rss=1 Corbo, J. McClure, J. P. Erkat, O. B. Polack, P.-O. 2021-03-26 doi:10.1101/2021.03.25.437032 Cold Spring Harbor Laboratory Press 2021-03-26 <![CDATA[ Massively parallel, computationally-guided design of a pro-enzyme ]]> https://biorxiv.org/content/10.1101/2021.03.25.437042v1?rss=1 Yachnin, B. J. Azouz, L. R. White, R. E. Minetti, C. A. S. A. Remeta, D. P. Tan, V. M. Drake, J. M. Khare, S. D. 2021-03-26 doi:10.1101/2021.03.25.437042 Cold Spring Harbor Laboratory Press 2021-03-26 <![CDATA[ High Throughput Virtual Screening and Validation of a SARS-CoV-2 Main Protease Non-Covalent Inhibitor ]]> https://biorxiv.org/content/10.1101/2021.03.27.437323v1?rss=1 Clyde, A. Galanie, S. Kneller, D. W. Ma, H. Babuji, Y. Blaiszik, B. Brace, A. Brettin, T. Chard, K. Chard, R. Coates, L. Foster, I. Hauner, D. Kertesz, V. Kumar, N. Lee, H. Li, Z. Merzky, A. Schmidt, J. G. Tan, L. Titov, M. Trifan, A. Turilli, M. Van Dam, H. Chennubhotla, S. C. Jha, S. Kovalevsky, A. Ramanathan, A. Head, M. Stevens, R. 2021-03-27 doi:10.1101/2021.03.27.437323 Cold Spring Harbor Laboratory Press 2021-03-27 <![CDATA[ Transcription initiation at a consensus bacterial promoter proceeds via a "bind-unwind-load-and-lock" mechanism ]]> https://biorxiv.org/content/10.1101/2021.03.28.437135v1?rss=1 Mazumder, A. Ebright, R. H. Kapanidis, A. 2021-03-28 doi:10.1101/2021.03.28.437135 Cold Spring Harbor Laboratory Press 2021-03-28 <![CDATA[ Invertebrate methylomes provide insight into mechanisms of environmental tolerance and reveal methodological biases ]]> https://biorxiv.org/content/10.1101/2021.03.29.437539v1?rss=1 Trigg, S. A. Venkataraman, Y. R. Gavery, M. Roberts, S. B. Bhattacharya, D. Downey-Wall, A. Eirin-Lopez, J. M. Johnson, K. M. Lotterhos, K. E. Puritz, J. B. Putnam, H. M. 2021-03-30 doi:10.1101/2021.03.29.437539 Cold Spring Harbor Laboratory Press 2021-03-30 <![CDATA[ Acitretin mitigates uroporphyrin-induced bone defects in congenital erythropoietic porphyria models ]]> https://biorxiv.org/content/10.1101/2021.03.30.437658v1?rss=1 Bragazzi Cunha, J. Elenbaas, J. S. Maitra, D. Kuo, N. Azuero-Dajud, R. Ferguson, A. C. Griffin, M. S. Lentz, S. I. Shavit, J. A. Omary, B. 2021-03-30 doi:10.1101/2021.03.30.437658 Cold Spring Harbor Laboratory Press 2021-03-30 <![CDATA[ Latent functional connectivity underlying multiple brain states ]]> https://biorxiv.org/content/10.1101/2021.04.05.438534v1?rss=1 McCormick, E. M. Arnemann, K. L. Ito, T. Hanson, S. J. Cole, M. W. 2021-04-06 doi:10.1101/2021.04.05.438534 Cold Spring Harbor Laboratory Press 2021-04-06 <![CDATA[ Interspecies recombination has driven the macroevolution of cassava mosaic begomoviruses ]]> https://biorxiv.org/content/10.1101/2021.04.05.438541v1?rss=1 Crespo-Bellido, A. Hoyer, J. S. Dubey, D. Jeannot, R. B. Duffy, S. 2021-04-06 doi:10.1101/2021.04.05.438541 Cold Spring Harbor Laboratory Press 2021-04-06 <![CDATA[ Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli ]]> https://biorxiv.org/content/10.1101/2021.04.06.438613v1?rss=1 Skalenko, K. S. Li, L. Zhang, Y. Vvedenskaya, I. O. Winkelman, J. T. Cope, A. Taylor, D. M. Shah, P. Ebright, R. H. Kinney, J. B. Zhang, Y. Nickels, B. E. 2021-04-07 doi:10.1101/2021.04.06.438613 Cold Spring Harbor Laboratory Press 2021-04-07 <![CDATA[ YTHDC2 Is Essential for Pachytene Progression and Prevents Aberrant Microtubule-Driven Telomere Clustering in Male Meiosis ]]> https://biorxiv.org/content/10.1101/2021.04.12.439470v1?rss=1 Liu, R. Kasowitz, S. D. Homolka, D. Leu, N. A. Shaked, J. T. Ruthel, G. Jain, D. Keeney, S. Luo, M. Wang, J. 2021-04-12 doi:10.1101/2021.04.12.439470 Cold Spring Harbor Laboratory Press 2021-04-12 <![CDATA[ Auditory processing remains sensitive to environmental experience during adolescence ]]> https://biorxiv.org/content/10.1101/2021.04.12.439537v1?rss=1 View larger version (18K): org.highwire.dtl.DTLVardef@50b787org.highwire.dtl.DTLVardef@1410662org.highwire.dtl.DTLVardef@a0fa6org.highwire.dtl.DTLVardef@897b1c_HPS_FORMAT_FIGEXP M_FIG Summary of experimental design and main findings. C_FIG ]]> Anbuhl, K. L. Yao, J. D. Hotz, R. A. Mowery, T. M. Sanes, D. H. 2021-04-14 doi:10.1101/2021.04.12.439537 Cold Spring Harbor Laboratory Press 2021-04-14 <![CDATA[ Germline testing data validate inferences of mutational status for variants detected from tumor-only sequencing ]]> https://biorxiv.org/content/10.1101/2021.04.14.439855v1?rss=1 75% of all detected variants, with a sensitivity of 65%, specificity of 88%, and overall accuracy of 86% for pathogenic variants. False omission rate was 3%, signifying minimal error in misclassifying true PGV. A higher portion of PGV in known hereditary tumor suppressors were found to be retained with LOH in the tumor specimens (72%) compared to variants of uncertain significance (58%). ConclusionsTumor-only sequencing provides sufficient power to distinguish germline and somatic variants and infer LOH. Although accurate detection of PGV from tumor-only data is possible, analyzing sequencing data in the context of specimens tumor cell content allows systematic exclusion of somatic variants, and suggests a balance between type 1 and 2 errors for identification of patients with candidate PGV for standard germline testing. Our approach, implemented in a user-friendly bioinformatics application, facilities objective analysis of tumor-only data in clinical settings. HighlightsO_LIMost pathogenic germline variants in cancer predisposition genes can be identified by analyzing tumor-only sequencing data. C_LIO_LIInformation-theoretic gene-independent analysis of common sequencing data accurately infers germline vs. somatic status. C_LIO_LIA reasonable statistical balance can be established between sensitivity and specificity demonstrating clinical utility. C_LIO_LIPathogenic germline variants are more often detected with loss of heterozygosity vs. germline variants of uncertain significance. C_LI ]]> Jalloul, N. Gomy, I. Stokes, S. M. Gusev, A. Johnson, B. E. Lindmen, N. Macconaill, L. Ganesan, S. Garber, J. E. Khiabanian, H. 2021-04-15 doi:10.1101/2021.04.14.439855 Cold Spring Harbor Laboratory Press 2021-04-15 <![CDATA[ Genomic analysis reveals the influence of climate change and currents on adaptation in an estuarine species ]]> https://biorxiv.org/content/10.1101/2021.04.16.440152v1?rss=1 Li, A. Dai, H. Guo, X. Zhang, Z. Zhang, K. Wang, C. Wang, W. Chen, H. Li, X. Zheng, H. Zhang, G. Li, L. 2021-04-18 doi:10.1101/2021.04.16.440152 Cold Spring Harbor Laboratory Press 2021-04-18 <![CDATA[ Redefining replication in multi-ancestry genome-wide association studies ]]> https://biorxiv.org/content/10.1101/2021.04.20.440612v1?rss=1 Smith, S. P. Shahamatdar, S. Cheng, W. Zhang, S. Paik, J. Graff, M. Haiman, C. A. Matise, T. C. North, K. E. Peters, U. Kenny, E. Gignoux, C. R. Wojcik, G. L. Crawford, L. Ramachandran, S. 2021-04-20 doi:10.1101/2021.04.20.440612 Cold Spring Harbor Laboratory Press 2021-04-20 <![CDATA[ Continuous multiplexed population representations of task context in the mouse primary visual cortex ]]> https://biorxiv.org/content/10.1101/2021.04.20.440666v1?rss=1 Hajnal, M. A. Tran, D. Einstein, M. Martelo, M. V. Safaryan, K. Polack, P.-O. Golshani, P. Orban, G. 2021-04-20 doi:10.1101/2021.04.20.440666 Cold Spring Harbor Laboratory Press 2021-04-20 <![CDATA[ Chemogenetic stimulation of a retinal circuit activates brain noradrenergic neurons, prevents apoptosis, and suppresses depression-like behaviors ]]> https://biorxiv.org/content/10.1101/2021.04.20.440684v1?rss=1 Bowrey, H. E. James, M. H. Omrani, M. Mohammdkhani, A. Aston-Jones, G. 2021-04-21 doi:10.1101/2021.04.20.440684 Cold Spring Harbor Laboratory Press 2021-04-21 <![CDATA[ Informational masking vs. crowding - A mid-level trade-off between auditory and visual processing ]]> https://biorxiv.org/content/10.1101/2021.04.21.440826v1?rss=1 Zhang, M. Denison, R. N. Pelli, D. G. Le, T. T. C. Ihlefeld, A. 2021-04-22 doi:10.1101/2021.04.21.440826 Cold Spring Harbor Laboratory Press 2021-04-22 <![CDATA[ Extracellular vesicle molecular signatures characterize metastatic dynamicity in ovarian cancer ]]> https://biorxiv.org/content/10.1101/2021.04.22.440951v1?rss=1 Gonda, A. Zhao, N. Shah, J. V. Siebert, J. N. Gunda, S. Inan, B. Kwon, M. Libutti, S. K. Moghe, P. V. Francis, N. L. Ganapathy, V. 2021-04-22 doi:10.1101/2021.04.22.440951 Cold Spring Harbor Laboratory Press 2021-04-22 <![CDATA[ Neural circuits for dynamics-based segmentation of time series ]]> https://biorxiv.org/content/10.1101/2021.04.23.441218v1?rss=1 Tesileanu, T. Golkar, S. Nasiri, S. Sengupta, A. M. Chklovskii, D. B. 2021-04-24 doi:10.1101/2021.04.23.441218 Cold Spring Harbor Laboratory Press 2021-04-24 <![CDATA[ Using Stakeholder Insights to Enhance Engagement in PhD Professional Development ]]> https://biorxiv.org/content/10.1101/2021.04.28.440824v1?rss=1 Ramadoss, D. Bolgioni, A. F. Layton, R. L. Alder, J. L. Lundsteen, N. Stayart, C. A. Yellin, J. B. Smart, C. L. Varvayanis, S. S. 2021-04-29 doi:10.1101/2021.04.28.440824 Cold Spring Harbor Laboratory Press 2021-04-29 <![CDATA[ The Hypoxia Response Pathway Promotes PEP Carboxykinase Expression And Gluconeogenesis ]]> https://biorxiv.org/content/10.1101/2021.05.04.442650v1?rss=1 Vora, M. Pyonteck, S. M. Matlack, T. L. Prashar, A. Kane, N. S. Shah, P. Rongo, C. 2021-05-04 doi:10.1101/2021.05.04.442650 Cold Spring Harbor Laboratory Press 2021-05-04 <![CDATA[ Ssl2/TFIIH Function in Transcription Start Site Scanning by RNA Polymerase II in Saccharomyces cerevisiae ]]> https://biorxiv.org/content/10.1101/2021.05.05.442816v1?rss=1 Zhao, T. Vvedenskaya, I. O. Lai, W. K. M. Basu, S. Pugh, B. F. Nickels, B. E. Kaplan, C. D. 2021-05-05 doi:10.1101/2021.05.05.442816 Cold Spring Harbor Laboratory Press 2021-05-05 <![CDATA[ Structural and mechanistic basis of RNA extension in reiterative transcription initiation: RNA slippingwithout DNA scrunching ]]> https://biorxiv.org/content/10.1101/2021.05.08.443277v1?rss=1 Liu, Y. Winkelman, J. T. Yu, L. Pukhrambam, C. Zhang, Y. Nickels, B. E. Ebright, R. H. 2021-05-09 doi:10.1101/2021.05.08.443277 Cold Spring Harbor Laboratory Press 2021-05-09 <![CDATA[ A burst of transposon expression accompanies the activation of Y chromosome fertility genes during Drosophila spermatogenesis ]]> https://biorxiv.org/content/10.1101/2021.05.10.443472v1?rss=1 Lawlor, M. A. Cao, W. Ellison, C. E. 2021-05-10 doi:10.1101/2021.05.10.443472 Cold Spring Harbor Laboratory Press 2021-05-10 <![CDATA[ mRNA-decapping associated DcpS enzyme controls critical steps of neuronal development ]]> https://biorxiv.org/content/10.1101/2021.05.10.443481v1?rss=1 Salamon, I. Palsule, G. Luo, X. Roque, A. Tucai, S. Khosla, I. Volk, N. Liu, W. Cui, H. Dal Pozzo, V. Zalamea, P. Jiao, X. DArcangelo, G. Hart, R. P. Rasin, M.-R. Kiledjian, M. 2021-05-11 doi:10.1101/2021.05.10.443481 Cold Spring Harbor Laboratory Press 2021-05-11 <![CDATA[ Pseudomonas arenae sp. nov., Pseudomonas glycinis sp. nov. and Pseudomonas harudinis sp. nov., three novel bacterial species and plant endophytes ]]> https://biorxiv.org/content/10.1101/2021.05.13.444027v1?rss=1 Seaton, S. Lemaire, J. Inderbitzin, P. Knight-Connoni, V. White, J. F. Trujillo, M. E. 2021-05-15 doi:10.1101/2021.05.13.444027 Cold Spring Harbor Laboratory Press 2021-05-15 <![CDATA[ Understanding Microbeads Stacking in Deformable Nano-Sieve for Efficient Plasma Separation and Blood Cell Retrieval ]]> https://biorxiv.org/content/10.1101/2021.05.13.444053v1?rss=1 Chen, X. Zhang, S. Gan, Y. Liu, R. Wang, R. Du, K. 2021-05-14 doi:10.1101/2021.05.13.444053 Cold Spring Harbor Laboratory Press 2021-05-14 <![CDATA[ riboviz 2: A flexible and robust ribosome profiling data analysis and visualization workflow ]]> https://biorxiv.org/content/10.1101/2021.05.14.443910v1?rss=1 Cope, A. L. Anderson, F. Favate, J. Jackson, M. Mok, A. Kurowska, A. MacKenzie, E. Shivakumar, V. Tilton, P. Winterbourne, S. M. Xue, S. Kavoussanakis, K. Lareau, L. F. Shah, P. Wallace, E. W. 2021-05-17 doi:10.1101/2021.05.14.443910 Cold Spring Harbor Laboratory Press 2021-05-17 <![CDATA[ Fiberoptic Probe For Hemodynamic Spectroscopy in Freely Moving Mice Shows Cerebrovascular Dysregulation In Alzheimers and Glioma Models ]]> https://biorxiv.org/content/10.1101/2021.05.17.444224v1?rss=1 Gareau, D. S. Snuderl, M. Thomas, C. Bayin, N. S. Placantonakis, D. Zou, J. Yaroslavsky, A. Dietz, M. P. Jacques, S. L. Strickland, S. Krueger, J. G. Ahn, H. J. 2021-05-18 doi:10.1101/2021.05.17.444224 Cold Spring Harbor Laboratory Press 2021-05-18 <![CDATA[ Higher concentrations of bacterial enveloped virus Phi6 can protect the virus from environmental decay ]]> https://biorxiv.org/content/10.1101/2021.05.17.444592v1?rss=1 Bangiyev, R. Chudaev, M. Schaffner, D. W. Goldman, E. 2021-05-18 doi:10.1101/2021.05.17.444592 Cold Spring Harbor Laboratory Press 2021-05-18 <![CDATA[ Aggregation state of Mycobacterium tuberculosis impacts host immunity and augments pulmonary disease pathology ]]> https://biorxiv.org/content/10.1101/2021.05.19.444830v1?rss=1 Kolloli, A. Kumar, R. Singh, P. Narang, A. Kaplan, G. Sigal, A. Subbian, S. 2021-05-19 doi:10.1101/2021.05.19.444830 Cold Spring Harbor Laboratory Press 2021-05-19 <![CDATA[ Decoding the effects of synonymous variants ]]> https://biorxiv.org/content/10.1101/2021.05.20.445019v1?rss=1 Zeng, Z. Aptekmann, A. A. Bromberg, Y. 2021-05-22 doi:10.1101/2021.05.20.445019 Cold Spring Harbor Laboratory Press 2021-05-22 <![CDATA[ Pollinator habitat plantings benefit wild, native bees, but do not necessarily favor rare species ]]> https://biorxiv.org/content/10.1101/2021.05.24.445524v1?rss=1 Cariveau, D. P. Roswell, M. Harrison, T. Genung, M. A. Gibbs, J. Winfree, R. 2021-05-26 doi:10.1101/2021.05.24.445524 Cold Spring Harbor Laboratory Press 2021-05-26 <![CDATA[ Secreted Proteases Control the Timing of Aggregative Community Formation in Vibrio cholerae ]]> https://biorxiv.org/content/10.1101/2021.05.25.445717v1?rss=1 Jemielita, M. Mashruwala, A. A. Valastyan, J. S. Wingreen, N. Bassler, B. 2021-05-26 doi:10.1101/2021.05.25.445717 Cold Spring Harbor Laboratory Press 2021-05-26 <![CDATA[ Tannic Acid Inhibits α-Synuclein Amyloid Fibril Formation via Binding to the Monomer N-terminal Domain ]]> https://biorxiv.org/content/10.1101/2021.05.26.445860v1?rss=1 Stoeber, J. Williams, J. K. Moghe, P. V. Baum, J. 2021-05-26 doi:10.1101/2021.05.26.445860 Cold Spring Harbor Laboratory Press 2021-05-26 <![CDATA[ Tightly constrained genome reduction and relaxation of purifying selection during secondary plastid endosymbiosis ]]> https://biorxiv.org/content/10.1101/2021.05.27.446077v1?rss=1 uthanumallian, k. Iha, C. Repetti, S. I. Chan, C. X. Bhattacharya, D. Duchene, S. Verbruggen, H. 2021-05-29 doi:10.1101/2021.05.27.446077 Cold Spring Harbor Laboratory Press 2021-05-29 <![CDATA[ Amphiphilic proteins coassemble into multiphasic condensates and act as biomolecular surfactants ]]> https://biorxiv.org/content/10.1101/2021.05.28.446223v1?rss=1 Kelley, F. M. Favetta, B. Regy, R. M. Mittal, J. Schuster, B. S. 2021-05-29 doi:10.1101/2021.05.28.446223 Cold Spring Harbor Laboratory Press 2021-05-29 <![CDATA[ More than just oil droplets in water: surface tension and viscosity of protein condensates quantified by micropipette aspiration ]]> https://biorxiv.org/content/10.1101/2021.05.28.446248v1?rss=1 Wang, H. Kelley, F. M. Milovanovic, D. Schuster, B. S. Shi, Z. 2021-05-29 doi:10.1101/2021.05.28.446248 Cold Spring Harbor Laboratory Press 2021-05-29 <![CDATA[ Immune dynamics in a time of covid ]]> https://biorxiv.org/content/10.1101/2021.06.01.446677v1?rss=1 Shinbrot, T. 2021-06-02 doi:10.1101/2021.06.01.446677 Cold Spring Harbor Laboratory Press 2021-06-02 <![CDATA[ Drivers of Transcriptional Variance in Human Intestinal Epithelial Organoids ]]> https://biorxiv.org/content/10.1101/2021.06.02.446644v1?rss=1 Criss, Z. K. Bhasin, N. Di Rienzi, S. C. Rajan, A. Deans-Fielder, K. Swaminathan, G. Kamyabi, N. Zeng, X.-L. Chakravarti, D. Estrella, C. Yu, X. Patil, K. Fleet, J. C. Verzi, M. P. Christakos, S. Helmrath, M. A. Arimura, S. DePinho, R. A. Britton, R. Maresso, A. Grande-Allen, J. Blutt, S. E. Crawford, S. E. Estes, M. K. Ramani, S. Shroyer, N. F. 2021-06-03 doi:10.1101/2021.06.02.446644 Cold Spring Harbor Laboratory Press 2021-06-03 <![CDATA[ PALB2 maintains redox and mitochondrial homeostasis in the brain and cooperates with ATG7 to suppress p53 dependent neurodegeneration ]]> https://biorxiv.org/content/10.1101/2021.06.07.447248v1?rss=1 Huo, Y. Sawant, A. Tan, Y. Mahdi, A. H. Li, T. Ma, H. Bhatt, V. Yan, R. Coleman, J. Dreyfus, C. F. Guo, J. Y. Mouradian, M. M. White, E. Xia, B. 2021-06-07 doi:10.1101/2021.06.07.447248 Cold Spring Harbor Laboratory Press 2021-06-07 <![CDATA[ Rat anterior cingulate cortex continuously signals decision variables in a patchforaging task ]]> https://biorxiv.org/content/10.1101/2021.06.07.447464v1?rss=1 Kane, G. A. James, M. H. Shenhav, A. Daw, N. D. Cohen, J. D. Aston-Jones, G. 2021-06-08 doi:10.1101/2021.06.07.447464 Cold Spring Harbor Laboratory Press 2021-06-08 <![CDATA[ ZFC3H1 and U1-70K promote the nuclear retention of mRNAs with 5' splice site motif within nuclear speckles ]]> https://biorxiv.org/content/10.1101/2021.06.08.447610v1?rss=1 Lee, E. S. Smith, H. W. Wolf, E. J. Guvenek, A. Emili, A. Tian, B. Palazzo, A. F. 2021-06-10 doi:10.1101/2021.06.08.447610 Cold Spring Harbor Laboratory Press 2021-06-10 <![CDATA[ Optimized Splitting of RNA Sequencing Data by Species ]]> https://biorxiv.org/content/10.1101/2021.06.09.447735v1?rss=1 97% accuracy across a range of species ratios. Alignment-independent methods, such as Convolutional Neural Networks, which extract the conserved patterns of sequences from two species, classify RNA sequencing reads with over 85% accuracy. Importantly, both methods perform well with different ratios of human and mouse reads. Our evaluation identifies valuable and effective strategies to dissect species composition of RNA sequencing data from mixed populations. ]]> Song, X. Gao, H. Y. Herrup, K. Hart, R. P. 2021-06-10 doi:10.1101/2021.06.09.447735 Cold Spring Harbor Laboratory Press 2021-06-10 <![CDATA[ Reduced Hippocampal Inhibition and Enhanced Autism-Epilepsy Comorbidity in Mice Lacking Neuropilin 2 ]]> https://biorxiv.org/content/10.1101/2021.06.11.448071v1?rss=1 Eisenberg, C. Subramanian, D. Afrasiabi, M. Ziobro, P. DeLucia, J. Hirschberg, P. R. Shiflett, M. W. Santhakumar, V. Tran, T. S. 2021-06-11 doi:10.1101/2021.06.11.448071 Cold Spring Harbor Laboratory Press 2021-06-11 <![CDATA[ Tools, strains, and strategies to effectively conduct anaerobic and aerobic transcriptional reporter screens and assays in Staphylococcus aureus ]]> https://biorxiv.org/content/10.1101/2021.06.11.448164v1?rss=1 Price, E. E. Rudra, P. Norambuena, J. Roman-Rodriguez, F. Boyd, J. M. 2021-06-13 doi:10.1101/2021.06.11.448164 Cold Spring Harbor Laboratory Press 2021-06-13 <![CDATA[ The voltage and spiking responses of subthreshold resonant neurons to structured and fluctuating inputs: resonance, loss of resonance and variability ]]> https://biorxiv.org/content/10.1101/2021.06.14.448368v1?rss=1 Pena, R. F. Rotstein, H. G. 2021-06-15 doi:10.1101/2021.06.14.448368 Cold Spring Harbor Laboratory Press 2021-06-15 <![CDATA[ Oscillations and variability in neuronal systems: interplay of autonomous transient dynamics and fast deterministic fluctuations ]]> https://biorxiv.org/content/10.1101/2021.06.14.448371v1?rss=1 Pena, R. F. Rotstein, H. G. 2021-06-15 doi:10.1101/2021.06.14.448371 Cold Spring Harbor Laboratory Press 2021-06-15 <![CDATA[ Behavioral and nociceptor states of inflammatory painacross timescales in 2D and 3D ]]> https://biorxiv.org/content/10.1101/2021.06.16.448689v1?rss=1 Bohic, M. Pattison, L. A. Jhumka, Z. A. Rossi, H. Thackray, J. K. Ricci, M. Foster, W. Arnold, J. Mossazghi, N. Yttri, E. A. Tischfield, M. A. Smith, E. S. J. Abdus-Saboor, I. Abraira, V. E. 2021-06-17 doi:10.1101/2021.06.16.448689 Cold Spring Harbor Laboratory Press 2021-06-17 <![CDATA[ A Unified Model for Entrainment by Circadian Clocks: Dynamic Circadian Integrated Response Characteristic (dCiRC) ]]> https://biorxiv.org/content/10.1101/2021.06.16.448692v1?rss=1 An, Z. Piccoli, B. Merrow, M. Lee, K. 2021-06-17 doi:10.1101/2021.06.16.448692 Cold Spring Harbor Laboratory Press 2021-06-17 <![CDATA[ Emergence of border-ownership by large-scale consistency and long-range interactions: Neuro-computational model to reflect global configurations ]]> https://biorxiv.org/content/10.1101/2021.06.17.448869v1?rss=1 Kogo, N. Froyen, V. 2021-06-21 doi:10.1101/2021.06.17.448869 Cold Spring Harbor Laboratory Press 2021-06-21 <![CDATA[ An evolutionarily conserved odontode gene regulatory network underlies head armor formation in suckermouth armored catfish ]]> https://biorxiv.org/content/10.1101/2021.06.21.449322v1?rss=1 Mori, S. Nakamura, T. 2021-06-22 doi:10.1101/2021.06.21.449322 Cold Spring Harbor Laboratory Press 2021-06-22 <![CDATA[ Familial Danish dementia young Knock-in rats expressing humanized APP and human Aβ show impaired pre and postsynaptic glutamatergic transmission ]]> https://biorxiv.org/content/10.1101/2021.06.24.449787v1?rss=1 Yin, T. Yao, W. Norris, K. A. D'Adamio, L. 2021-06-24 doi:10.1101/2021.06.24.449787 Cold Spring Harbor Laboratory Press 2021-06-24 <![CDATA[ Xrn1 is a deNADding Enzyme Modulating Mitochondrial NAD Levels ]]> https://biorxiv.org/content/10.1101/2021.06.25.449970v1?rss=1 Sharma, S. Yang, J. Grudzien Nogalska, E. Kiledjian, M. 2021-06-25 doi:10.1101/2021.06.25.449970 Cold Spring Harbor Laboratory Press 2021-06-25 <![CDATA[ New intranasal and injectable gene therapy for healthy life extension ]]> https://biorxiv.org/content/10.1101/2021.06.26.449305v1?rss=1 Zhu, H. Jaijyan, D. K. Selariu, A. Cruz-cosme, R. Tong, M. Yang, S. Church, G. Kekich, D. Sadoshima, J. Tang, Q. Parrish, E. 2021-06-26 doi:10.1101/2021.06.26.449305 Cold Spring Harbor Laboratory Press 2021-06-26 <![CDATA[ Flying in the Face of Adversity: A Drosophila-based Virtual CURE Provides Semester-long Authentic Research Opportunity to the Flipped Classroom. ]]> https://biorxiv.org/content/10.1101/2021.06.28.450232v1?rss=1 Waddell, E. A. Ruiz-Whalen, D. O'Reilly, A. M. Fried, N. T. 2021-06-30 doi:10.1101/2021.06.28.450232 Cold Spring Harbor Laboratory Press 2021-06-30 <![CDATA[ Cherry-picking information: humans actively sample evidence to support prior beliefs ]]> https://biorxiv.org/content/10.1101/2021.06.29.450332v1?rss=1 Kaanders, P. Sepulveda, P. Folke, T. Ortoleva, P. De Martino, B. 2021-06-30 doi:10.1101/2021.06.29.450332 Cold Spring Harbor Laboratory Press 2021-06-30 <![CDATA[ Designed architectural proteins that tune DNA looping in bacteria ]]> https://biorxiv.org/content/10.1101/2021.06.30.450240v1?rss=1 Tse, D. H. Becker, N. A. Young, R. T. Olson, W. K. Peters, J. P. Schwab, T. L. Clark, K. J. Maher, L. J. 2021-06-30 doi:10.1101/2021.06.30.450240 Cold Spring Harbor Laboratory Press 2021-06-30 <![CDATA[ TMEM120A/TACAN inhibits mechanically activated Piezo2 channels ]]> https://biorxiv.org/content/10.1101/2021.06.30.450616v1?rss=1 Del Rosario, J. S. Gabrielle, M. Yudin, Y. Rohacs, T. 2021-06-30 doi:10.1101/2021.06.30.450616 Cold Spring Harbor Laboratory Press 2021-06-30 <![CDATA[ Economic costs of biological invasions in the United States ]]> https://biorxiv.org/content/10.1101/2021.07.02.450757v1?rss=1 Fantle-Lepczyk, J. Haubrock, P. J. Cuthbert, R. N. Kramer, A. M. Turbelin, A. J. Crystal-Ornelas, R. Diagne, C. Courchamp, F. 2021-07-04 doi:10.1101/2021.07.02.450757 Cold Spring Harbor Laboratory Press 2021-07-04 <![CDATA[ Towards a Neurometric-based Construct Validity of Trust ]]> https://biorxiv.org/content/10.1101/2021.07.04.451074v1?rss=1 Chen, P.-H. A. Fareri, D. Guroglu, B. Delgado, M. R. Chang, L. J. 2021-07-05 doi:10.1101/2021.07.04.451074 Cold Spring Harbor Laboratory Press 2021-07-05 <![CDATA[ Dietary Exposure to Antibiotic Residues Facilitates Metabolic Disorder by Altering the Gut Microbiota and Bile Acid Composition ]]> https://biorxiv.org/content/10.1101/2021.07.06.451284v1?rss=1 Chen, R.-A. Wu, W.-K. Panyod, S. Liu, P.-Y. Chuang, H.-L. Chen, Y.-H. Lyu, Q. Hsu, H.-C. Lin, T.-L. Shen, T.-C. D. Yang, Y.-T. Zou, H.-B. Huang, H.-S. Lin, Y.-E. Chen, C.-C. Ho, C.-T. Lai, H.-C. Wu, M.-S. Hsu, C.-C. Sheen, L.-Y. 2021-07-06 doi:10.1101/2021.07.06.451284 Cold Spring Harbor Laboratory Press 2021-07-06 <![CDATA[ The methamphetamine-induced RNA targetome of hnRNP H in Hnrnph1 mutants showing reduced dopamine release and behavior ]]> https://biorxiv.org/content/10.1101/2021.07.06.451358v1?rss=1 Ruan, Q. T. Rieger, M. A. Lynch, W. B. Cox, J. W. Beierle, J. A. Yao, E. J. Kandola, A. Chen, M. M. Kelliher, J. C. Babbs, R. K. Ash, P. E. A. Wolozin, B. Szumlinski, K. K. Johnson, W. E. Dougherty, J. Bryant, C. D. 2021-07-07 doi:10.1101/2021.07.06.451358 Cold Spring Harbor Laboratory Press 2021-07-07 <![CDATA[ Mapping circuit dynamics during function and dysfunction ]]> https://biorxiv.org/content/10.1101/2021.07.06.451370v1?rss=1 Gorur-Shandilya, S. Cronin, E. M. Schneider, A. C. Haddad, S. A. Rosenbaum, P. Bucher, D. Nadim, F. Marder, E. 2021-07-07 doi:10.1101/2021.07.06.451370 Cold Spring Harbor Laboratory Press 2021-07-07 <![CDATA[ SPE-51, a sperm secreted protein with an Immunoglobulin-like domain, is required for sperm-egg fusion in C. elegans ]]> https://biorxiv.org/content/10.1101/2021.07.07.451548v1?rss=1 Mei, X. Druzhinina, M. Dharia, S. Krauchunas, A. R. Ni, J. Singaravelu, G. Gu, S. G. Shakes, D. C. Grant, B. D. Singson, A. W. 2021-07-08 doi:10.1101/2021.07.07.451548 Cold Spring Harbor Laboratory Press 2021-07-08 <![CDATA[ The EGF-motif containing protein SPE-36 is a secreted protein required for sperm function at fertilization in C. elegans ]]> https://biorxiv.org/content/10.1101/2021.07.07.451551v1?rss=1 Krauchunas, A. R. Marcello, M. R. Looper, A. Mei, X. Putiri, E. Singaravelu, G. Ahmed, I. I. Singson, A. 2021-07-08 doi:10.1101/2021.07.07.451551 Cold Spring Harbor Laboratory Press 2021-07-08 <![CDATA[ Rapid sequence evolution is associated with genetic incompatibilities in the plastid Clp complex ]]> https://biorxiv.org/content/10.1101/2021.07.13.452280v1?rss=1 Abdel-Ghany, S. E. LaManna, L. M. Svab, Z. Harroun, H. E. Maliga, P. Sloan, D. B. 2021-07-14 doi:10.1101/2021.07.13.452280 Cold Spring Harbor Laboratory Press 2021-07-14 <![CDATA[ Novel Class of Psychedelic Iboga Alkaloids Disrupts Opioid Addiction States ]]> https://biorxiv.org/content/10.1101/2021.07.22.453441v1?rss=1 Havel, V. Kruegel, A. C. Bechand, B. McIntosh, S. Stallings, L. Hodges, A. Wulf, M. G. Nelson, M. Hunkele, A. Ansonoff, M. Pintar, J. E. Hwu, C. Abi-Gerges, N. Zaidi, S. A. Katritch, V. Yang, M. Javitch, J. A. Majumdar, S. Hemby, S. E. Sames, D. 2021-07-23 doi:10.1101/2021.07.22.453441 Cold Spring Harbor Laboratory Press 2021-07-23 <![CDATA[ CRISPR-Cas Controls Cryptic Prophages ]]> https://biorxiv.org/content/10.1101/2021.07.28.454074v1?rss=1 Song, S. Wood, T. K. 2021-07-28 doi:10.1101/2021.07.28.454074 Cold Spring Harbor Laboratory Press 2021-07-28 <![CDATA[ Precision Autism: Genomic Stratification of Disorders Making Up the Broad Spectrum May Demystify its "Epidemic Rates" ]]> https://biorxiv.org/content/10.1101/2021.07.28.454081v1?rss=1 Torres, E. B. 2021-07-29 doi:10.1101/2021.07.28.454081 Cold Spring Harbor Laboratory Press 2021-07-29 <![CDATA[ ADAD2 regulates heterochromatin in meiotic and post-meiotic male germ cells via translation of MDC1 ]]> https://biorxiv.org/content/10.1101/2021.07.29.454317v1?rss=1 Chukrallah, L. G. Badrinath, A. Vittor, G. G. Snyder, E. M. 2021-07-29 doi:10.1101/2021.07.29.454317 Cold Spring Harbor Laboratory Press 2021-07-29 <![CDATA[ Multiplexed action-outcome representation by striatal striosome-matrix compartments detected with a novel cost-benefit foraging task ]]> https://biorxiv.org/content/10.1101/2021.08.17.456542v1?rss=1 Bloem, B. Huda, R. Amemori, K.-i. Abate, A. Krishna, G. Wilson, A. Carter, C. W. Sur, M. Graybiel, A. M. 2021-08-18 doi:10.1101/2021.08.17.456542 Cold Spring Harbor Laboratory Press 2021-08-18 <![CDATA[ Immersion in Modified Reality: Sensitivity to the Slope (α) of the Amplitude Spectrum is Dependent on the α of Recently Viewed Environments ]]> https://biorxiv.org/content/10.1101/2021.08.19.456985v1?rss=1 Richard, B. Shafto, P. 2021-08-19 doi:10.1101/2021.08.19.456985 Cold Spring Harbor Laboratory Press 2021-08-19 <![CDATA[ A gene-based capture assay for surveying patterns of genetic diversity and insecticide resistance in a worldwide group of invasive mosquitoes ]]> https://biorxiv.org/content/10.1101/2021.08.24.457535v1?rss=1 Aardema, M. L. Campana, M. G. Wagner, N. E. Ferreira, F. C. Fonseca, D. M. 2021-08-24 doi:10.1101/2021.08.24.457535 Cold Spring Harbor Laboratory Press 2021-08-24 <![CDATA[ The growth and expansion of meningeal lymphatic networks are affected in craniosynostosis ]]> https://biorxiv.org/content/10.1101/2021.08.27.457986v1?rss=1 Ang, P. Matrongolo, M. Tischfield, M. 2021-08-28 doi:10.1101/2021.08.27.457986 Cold Spring Harbor Laboratory Press 2021-08-28 <![CDATA[ Apropos of Universal Epitope Discovery for COVID-19 Vaccines: A Framework for Targeted Phage Display-Based Delivery and Integration of New Evaluation Tools ]]> https://biorxiv.org/content/10.1101/2021.08.30.458222v1?rss=1 Markosian, C. Staquicini, D. I. Dogra, P. Dodero-Rojas, E. Tang, F. H. F. Smith, T. L. Contessoto, V. G. Libutti, S. K. Wang, Z. Cristini, V. Whitford, P. C. Burley, S. K. Onuchic, J. N. Pasqualini, R. Arap, W. 2021-08-31 doi:10.1101/2021.08.30.458222 Cold Spring Harbor Laboratory Press 2021-08-31 <![CDATA[ Breast tumor IGF-1R regulates cell adhesion and metastasis: Alignment of mouse single cell and human breast cancer transcriptomics ]]> https://biorxiv.org/content/10.1101/2021.08.31.458283v1?rss=1 Obr, A. E. Chang, Y.-J. Ciliento, V. Lemenze, A. Maingrette, K. Bulatowicz, J. J. Shang, Q. Gallagher, E. LeRoith, D. Wood, T. L. 2021-09-01 doi:10.1101/2021.08.31.458283 Cold Spring Harbor Laboratory Press 2021-09-01 <![CDATA[ Novel genome assemblies and Evolutionary Dynamics of North American Anopheles mosquitoes ]]> https://biorxiv.org/content/10.1101/2021.08.31.458407v1?rss=1 Henderson, C. A. Kemirembe, K. Mckeand, S. Bergey, C. M. Rasgon, J. L. 2021-08-31 doi:10.1101/2021.08.31.458407 Cold Spring Harbor Laboratory Press 2021-08-31 <![CDATA[ High-altitude adaptation and incipient speciation in geladas ]]> https://biorxiv.org/content/10.1101/2021.09.01.458582v1?rss=1 Chiou, K. L. Janiak, M. C. Schneider-Crease, I. Sen, S. Ayele, F. Chuma, I. S. Knauf, S. Lemma, A. Signore, A. V. D'Ippolito, A. M. Abebe, B. Haile, A. A. Kebede, F. Fashing, P. J. Nguyen, N. McCann, C. Houck, M. L. Wall, J. D. Burrell, A. S. Bergey, C. M. Rogers, J. Phillips-Conroy, J. E. Jolly, C. J. Melin, A. D. Storz, J. F. Lu, A. Beehner, J. C. Bergman, T. J. Snyder-Mackler, N. 2021-09-01 doi:10.1101/2021.09.01.458582 Cold Spring Harbor Laboratory Press 2021-09-01 <![CDATA[ Prey identity affects fitness of a generalist consumer in a brown food web ]]> https://biorxiv.org/content/10.1101/2021.09.02.458769v1?rss=1 Khadempour, L. Rivas Quijano, L. terHorst, C. 2021-09-04 doi:10.1101/2021.09.02.458769 Cold Spring Harbor Laboratory Press 2021-09-04 <![CDATA[ Contiguously-hydrophobic sequences are functionally significant throughout the human exome ]]> https://biorxiv.org/content/10.1101/2021.09.02.458776v1?rss=1 Lohia, R. Hansen, M. E. Brannigan, G. H. 2021-09-04 doi:10.1101/2021.09.02.458776 Cold Spring Harbor Laboratory Press 2021-09-04 <![CDATA[ Relationship Between Inter-individual Variation in Circadian Rhythm and Sociality: A case Study Using Halictid Bees ]]> https://biorxiv.org/content/10.1101/2021.09.03.458748v1?rss=1 Melendez Cartagena, S. Ortiz-Alvarado, C. A. Ordonez, P. Cordero-Martinez, C. S. Ambrose, A. F. Roman Lizasoain, L. A. Santos Vega, M. A. Velez Velez, A. V. Acevedo-Gonzalez, J. P. Gibbs, J. Petanidou, T. Tscheulin, T. Barthell, J. T. Gonzalez, V. H. Giray, T. Agosto-Rivera, J. L. 2021-09-06 doi:10.1101/2021.09.03.458748 Cold Spring Harbor Laboratory Press 2021-09-06 <![CDATA[ CluSem: Accurate Clustering-based Ensemble Methodto Predict Motor Imagery Tasks from Multi-channelEEG Data ]]> https://biorxiv.org/content/10.1101/2021.09.05.458710v1?rss=1 Miah, M. O. Muhammod, R. Al Mamun, K. A. Farid, D. M. Kumar, S. Sharma, A. Dehzangi, A. 2021-09-06 doi:10.1101/2021.09.05.458710 Cold Spring Harbor Laboratory Press 2021-09-06 <![CDATA[ Mechanistic insight into light-dependent recognition of Timeless by Drosophila cryptochrome ]]> https://biorxiv.org/content/10.1101/2021.09.10.459772v1?rss=1 Lin, C. Schneps, C. M. Chandrasekaran, S. Ganguly, A. Crane, B. R. 2021-09-10 doi:10.1101/2021.09.10.459772 Cold Spring Harbor Laboratory Press 2021-09-10 <![CDATA[ Temporal filters in response to presynaptic spike trains: Interplay of cellular, synaptic and short-term plasticity time scales ]]> https://biorxiv.org/content/10.1101/2021.09.16.460719v1?rss=1 Mondal, Y. Pena, R. F. O. Rotstein, H. G. 2021-09-19 doi:10.1101/2021.09.16.460719 Cold Spring Harbor Laboratory Press 2021-09-19 <![CDATA[ Identification of touch neurons underlying dopaminergic pleasurable touch and sexual receptivity ]]> https://biorxiv.org/content/10.1101/2021.09.22.461355v1?rss=1 Middleton, L. Schaffler, M. Succi, I. Foster, W. Gradwell, M. Bohic, M. Ejoh, L. Abraira, V. Abdus-Saboor, I. 2021-09-22 doi:10.1101/2021.09.22.461355 Cold Spring Harbor Laboratory Press 2021-09-22 <![CDATA[ Tracking extracellular vesicle (EV) cargo as a platform for studying EVomics, signaling, and targeting in vivo ]]> https://biorxiv.org/content/10.1101/2021.09.23.461577v1?rss=1 Nikonorova, I. A. Wang, J. Cope, A. L. Tilton, P. E. Power, K. M. Walsh, J. D. Akella, J. S. Krauchunas, A. R. Shah, P. R. Barr, M. M. 2021-09-23 doi:10.1101/2021.09.23.461577 Cold Spring Harbor Laboratory Press 2021-09-23 <![CDATA[ Chromosome-scale genome assembly of the brown anole (Anolis sagrei), a model species for evolution and ecology ]]> https://biorxiv.org/content/10.1101/2021.09.28.462146v1?rss=1 Geneva, A. J. Park, S. Bock, D. de Mello, P. Sarigol, F. Tollis, M. Donihue, C. Reynolds, R. G. Feiner, N. Rasys, A. Lauderdale, J. Minchey, S. G. Alcala, A. J. Infante, C. Kolbe, J. J. Schluter, D. Menke, D. B. Losos, J. B. 2021-09-30 doi:10.1101/2021.09.28.462146 Cold Spring Harbor Laboratory Press 2021-09-30 <![CDATA[ Characterizing Genetic Mechanisms Involved in Measuring Day-length in Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/2021.09.29.462474v1?rss=1 Khaira, H. Lee, K. 2021-10-01 doi:10.1101/2021.09.29.462474 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ Bile Acid Regulates the Colonization and Dissemination of Candida albicans from the Gastrointestinal Tract by Controlling Host Defense System and Microbiota ]]> https://biorxiv.org/content/10.1101/2021.09.29.462497v1?rss=1 Thangamani, S. Monasky, R. Lee, J. K. Antharam, V. HogenEsch, H. Hazbun, T. R. Yan Jin, Y. Gu, H. Guo, G. L. 2021-09-30 doi:10.1101/2021.09.29.462497 Cold Spring Harbor Laboratory Press 2021-09-30 <![CDATA[ Bioorthogonal Functionalization of Material Surfaces with Bioactive Molecules ]]> https://biorxiv.org/content/10.1101/2021.10.01.462811v1?rss=1 Hast, K. Jia, Z. Baci, M. Aggarwal, T. Izgu, E. C. 2021-10-01 doi:10.1101/2021.10.01.462811 Cold Spring Harbor Laboratory Press 2021-10-01 <![CDATA[ Cryo-EM Structure of the Pol Polyprotein Provides Insights into HIV Maturation ]]> https://biorxiv.org/content/10.1101/2021.10.03.462959v1?rss=1 Harrison, J. J. E. K. Passos, D. O. Bruhn, J. F. Bauman, J. D. Tuberty, L. DeStefano, J. J. Ruiz, F. X. Lyumkis, D. Arnold, E. 2021-10-04 doi:10.1101/2021.10.03.462959 Cold Spring Harbor Laboratory Press 2021-10-04 <![CDATA[ Slow TCA flux implies low ATP production in tumors ]]> https://biorxiv.org/content/10.1101/2021.10.04.463108v1?rss=1 Bartman, C. R. Shen, Y. Lee, W. D. TeSlaa, T. Jankowski, C. S. R. Wang, L. Yang, L. Roichman, A. Bhatt, V. Lan, T. Hu, Z. S. Xing, X. Lu, W. Guo, J. Y. Rabinowitz, J. D. 2021-10-04 doi:10.1101/2021.10.04.463108 Cold Spring Harbor Laboratory Press 2021-10-04 <![CDATA[ Power dynamics of theta oscillations during goal-directed navigation in freely moving humans: A mobile EEG-virtual reality T-maze study ]]> https://biorxiv.org/content/10.1101/2021.10.05.463245v1?rss=1 Lin, M.-h. Liran, O. Bauer, N. K. Baker, T. E. 2021-10-07 doi:10.1101/2021.10.05.463245 Cold Spring Harbor Laboratory Press 2021-10-07 <![CDATA[ Processive translocation of cohesive and non-cohesive cohesin in vivo ]]> https://biorxiv.org/content/10.1101/2021.10.07.463478v1?rss=1 Gartenberg, M. R. Borrie, M. S. 2021-10-07 doi:10.1101/2021.10.07.463478 Cold Spring Harbor Laboratory Press 2021-10-07 <![CDATA[ Supercharged Cellulases Show Reduced Non-Productive Binding, But Enhanced Activity, on Pretreated Lignocellulosic Biomass ]]> https://biorxiv.org/content/10.1101/2021.10.17.464688v1?rss=1 Nemmaru, B. Douglass, J. Yarbrough, J. M. De Chellis, A. Shankar, S. Thokkadam, A. Wang, A. Chundawat, S. P. S. 2021-10-17 doi:10.1101/2021.10.17.464688 Cold Spring Harbor Laboratory Press 2021-10-17 <![CDATA[ Uncovering the Genetic Architecture of Broad Antisocial Behavior through a Genome-Wide Association Study Meta-analysis. ]]> https://biorxiv.org/content/10.1101/2021.10.19.462578v1?rss=1 Tielbeek, J. J. Uffelmann, E. Williams, B. S. Colodro-Conde, L. Gagnon, E. Mallard, T. T. Levitt, B. E. Jansen, P. R. Johansson, A. Sallis, H. M. Pistis, G. Saunders, G. R. Allegrini, A. G. Rimfeld, K. Konte, B. Klein, M. Hartmann, A. M. Salvatore, J. E. Nolte, I. M. Demontis, D. Malmberg, A. Burt, S. A. Savage, J. E. Sugden, K. Poulton, R. Harris, K. M. Vrieze, S. McGue, M. Iacono, W. G. Mota, N. R. Mill, J. Viana, J. F. Mitchell, B. L. Morosoli, J. J. Andlauer, T. F. M. Ouellet-Morin, I. Tremblay, R. E. Cote, S. M. Gouin, J.-P. Brendgen, M. R. Dionne, 2021-10-20 doi:10.1101/2021.10.19.462578 Cold Spring Harbor Laboratory Press 2021-10-20 <![CDATA[ Severe fever with thrombocytopenia syndrome virus and parthenogenetic Asian longhorned tick Haemaphysalis longicornis (Acari: Ixodidae) ]]> https://biorxiv.org/content/10.1101/2021.10.20.465214v1?rss=1 Zheng, A. Zhang, Z. Zhang, G. Zhan, X. Z. Zhang, X. Zhao, C. Cheng, C. Li, H. Yu, T. Lawrence, K. L. Sun, J. Yang, Z. Ye, L. Chu, H. C. Wang, Y. W. Han, X. Jia, Y. Fan, S. Kanuka, H. Tanaka, T. Jenkins, C. Gedye, K. Chandra, S. Price, D. C. Liu, Q. Choi, Y. K. 2021-10-21 doi:10.1101/2021.10.20.465214 Cold Spring Harbor Laboratory Press 2021-10-21 <![CDATA[ Offline memory replay in recurrent neuronal networks emerges from constraints on online dynamics ]]> https://biorxiv.org/content/10.1101/2021.10.27.466186v1?rss=1 Milstein, A. D. Tran, S. Ng, G. Soltesz, I. 2021-10-28 doi:10.1101/2021.10.27.466186 Cold Spring Harbor Laboratory Press 2021-10-28 <![CDATA[ Intragenomic variation in mutation biases causes underestimation of selection on synonymous codon usage ]]> https://biorxiv.org/content/10.1101/2021.10.29.466462v1?rss=1 Cope, A. L. Shah, P. 2021-11-01 doi:10.1101/2021.10.29.466462 Cold Spring Harbor Laboratory Press 2021-11-01 <![CDATA[ Spatiotemporal patterns of urban mosquitoes are modulated by socioeconomic status and environmental traits in the United States ]]> https://biorxiv.org/content/10.1101/2021.10.30.466623v1?rss=1 Yitbarek, S. Chen, K. Celestin, M. McCary, M. 2021-11-02 doi:10.1101/2021.10.30.466623 Cold Spring Harbor Laboratory Press 2021-11-02 <![CDATA[ Towards a general framework for modeling large-scale biophysical neuronal networks: a full-scale computational model of the rat dentate gyrus ]]> https://biorxiv.org/content/10.1101/2021.11.02.466940v1?rss=1 Raikov, I. G. Milstein, A. D. Moolchand, P. Szabo, G. G. Schneider, C. J. Hadjiabadi, D. H. Chatzikalymniou, A. P. Soltesz, I. 2021-11-04 doi:10.1101/2021.11.02.466940 Cold Spring Harbor Laboratory Press 2021-11-04 <![CDATA[ Discovery of imidazole-based inhibitors of P. falciparum cGMP-dependent protein kinase ]]> https://biorxiv.org/content/10.1101/2021.11.05.467463v1?rss=1 Yadav, R. R. de Souza, M. L. Gonzalez, M. L. Mahmood, S. U. Eck, T. Kreiss, T. Aylor, S. O. Roth, A. Lee, P. Pybus, B. S. Colussi, D. J. Childers, W. E. Gordon, J. Siekierka, J. J. Bhanot, P. Rotella, D. P. 2021-11-05 doi:10.1101/2021.11.05.467463 Cold Spring Harbor Laboratory Press 2021-11-05 <![CDATA[ Antioxidants green tea extract and nordihydroguaiaretic acid confer species and strain specific lifespan and health effects in Caenorhabditis nematodes ]]> https://biorxiv.org/content/10.1101/2021.11.09.464847v1?rss=1 Banse, S. A. Sedore, C. A. Johnson, E. Coleman-Hulbert, A. L. Onken, B. Hall, D. Jackson, E. G. Huynh, P. Foulger, A. C. Guo, S. Garrett, T. Xue, J. Inman, D. Morshead, M. L. Plummer, W. T. Chen, E. Bhaumik, D. Chen, M. K. Harinath, G. Chamoli, M. Quinn, R. P. Falkowski, R. Edgar, D. Schmidt, M. O. Lucanic, M. Guo, M. Driscoll, M. Lithgow, G. J. Phillips, P. C. 2021-11-10 doi:10.1101/2021.11.09.464847 Cold Spring Harbor Laboratory Press 2021-11-10 <![CDATA[ Quantitative analysis of transcription start site selection in Saccharomyces cerevisiae determines contributions of DNA sequence and RNA Polymerase II activity ]]> https://biorxiv.org/content/10.1101/2021.11.09.467992v1?rss=1 Zhu, Y. Vvedenskaya, I. O. Nickels, B. E. Kaplan, C. D. 2021-11-10 doi:10.1101/2021.11.09.467992 Cold Spring Harbor Laboratory Press 2021-11-10 <![CDATA[ Preclinical studies for plant-based oral enzyme replacement therapy (Oral-ERT) in Pompe disease knockout mice with transgenic tobacco seeds expressing human GAA (tobrhGAA) ]]> https://biorxiv.org/content/10.1101/2021.11.11.468227v1?rss=1 Martiniuk, F. Martiniuk, J. Mack, A. Voronin, G. Miller, S. Reimer, D. Rossi, N. Bird, L. Gupta, R. Nigro, M. Saleh, S. Meinke, P. Schoser, B. Wu, F. Tchou-Wong, K. M. Kambitsis, A. Arvanitopoulos, J. Arvanitopoulos, E. 2021-11-12 doi:10.1101/2021.11.11.468227 Cold Spring Harbor Laboratory Press 2021-11-12 <![CDATA[ #COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol ]]> https://biorxiv.org/content/10.1101/2021.11.12.468428v1?rss=1 Dommer, A. Casalino, L. Kearns, F. Rosenfeld, M. Wauer, N. Ahn, S.-H. Russo, J. Oliveira, S. Morris, C. Bogetti, A. Trifan, A. Brace, A. Sztain, T. Clyde, A. Ma, H. Chennubhotla, C. Lee, H. Turilli, M. Khalid, S. Tamayo-Mendoza, T. Welborn, M. Christiansen, A. Smith, D. G. A. Qiao, Z. Sirumalla, S. K. O'Connor, M. Manby, F. Anandkumar, A. Hardy, D. Phillips, J. Stern, A. Romero, J. Clark, D. Dorrell, M. Maiden, T. Huang, L. McCalpin, J. Woods, C. Gray, A. Williams, M. Barker, B. Rajapaksha, H. Pitts, R. Gibbs, T. Stone, J. Zuckerman, D. Muholland, 2021-11-15 doi:10.1101/2021.11.12.468428 Cold Spring Harbor Laboratory Press 2021-11-15 <![CDATA[ Semaphorin signaling restricts neuronal regeneration in C. elegans ]]> https://biorxiv.org/content/10.1101/2021.11.13.468479v1?rss=1 Harreguy, M. B. Shah, E. Tanvir, Z. Simprevil, B. Tran, T. S. Haspel, G. 2021-11-14 doi:10.1101/2021.11.13.468479 Cold Spring Harbor Laboratory Press 2021-11-14 <![CDATA[ Zika virus-induced TNF-α signaling dysregulates expression of neurologic genes associated with psychiatric disorders ]]> https://biorxiv.org/content/10.1101/2021.11.15.468744v1?rss=1 Kung, P.-L. Chou, T.-W. Lindman, M. Chang, N. P. Buckley, B. D. Atkins, C. Daniels, B. P. 2021-11-18 doi:10.1101/2021.11.15.468744 Cold Spring Harbor Laboratory Press 2021-11-18 <![CDATA[ Bacterial LomR Induces the Vibriophage VP882 VqmA-Directed Quorum-Sensing Lysogeny-Lysis Transition ]]> https://biorxiv.org/content/10.1101/2021.11.15.468771v1?rss=1 Sun, J. S. Mashruwala, A. A. Fei, C. Bassler, B. 2021-11-16 doi:10.1101/2021.11.15.468771 Cold Spring Harbor Laboratory Press 2021-11-16 <![CDATA[ Ploidy variation and its implications for reproduction and population dynamics in two sympatric Hawaiian coral species ]]> https://biorxiv.org/content/10.1101/2021.11.21.469467v1?rss=1 Stephens, T. G. Strand, E. L. Mohamed, A. R. Williams, A. Chiles, E. N. Su, X. Bhattacharya, D. Putnam, H. M. 2021-11-22 doi:10.1101/2021.11.21.469467 Cold Spring Harbor Laboratory Press 2021-11-22 <![CDATA[ Cholinergic control of striatal GABAergic microcircuits ]]> https://biorxiv.org/content/10.1101/2021.11.22.469580v1?rss=1 Kocaturk, S. Shah, F. Guven, E. B. Tepper, J. M. Assous, M. 2021-11-23 doi:10.1101/2021.11.22.469580 Cold Spring Harbor Laboratory Press 2021-11-23 <![CDATA[ Rapid multilocus adaptation of clonal cabbage leaf curl virus populations to Arabidopsis thaliana ]]> https://biorxiv.org/content/10.1101/2021.11.29.468282v1?rss=1 Hoyer, J. S. Wilkins, O. W. Munshi, A. Wiese, E. Dubey, D. Renard, S. Mortensen, K. R. H. Dye, A. E. Carbone, I. Duffy, S. Ascencio-Ibanez, J. T. 2021-12-01 doi:10.1101/2021.11.29.468282 Cold Spring Harbor Laboratory Press 2021-12-01 <![CDATA[ The evolution of neurosensation drives the gain and loss of phenotypic plasticity ]]> https://biorxiv.org/content/10.1101/2021.11.29.470389v1?rss=1 Chen, E. Y. Adams, D. K. 2021-11-29 doi:10.1101/2021.11.29.470389 Cold Spring Harbor Laboratory Press 2021-11-29 <![CDATA[ Genomic architecture controls spatial structuring in Amazonian birds ]]> https://biorxiv.org/content/10.1101/2021.12.01.470789v1?rss=1 Thom, G. Moreira, L. R. Batista, R. Gehara, M. Aleixo, A. Smith, B. T. 2021-12-02 doi:10.1101/2021.12.01.470789 Cold Spring Harbor Laboratory Press 2021-12-02 <![CDATA[ Analyses of the Autism-associated Neuroligin-3 R451C Mutation in Human Neurons Reveals a Gain-of-Function Synaptic Mechanism ]]> https://biorxiv.org/content/10.1101/2021.12.07.471501v1?rss=1 Wang, L. Mirabella, V. R. Dai, R. Su, X. Xu, R. Jadali, A. Bernabucci, M. Singh, I. Chen, Y. Tian, J. Jiang, P. Kwan, K. Pak, C. LIU, C. Comoletti, D. Hart, R. P. Chen, C. Sudhof, T. C. Pang, Z. P. 2021-12-09 doi:10.1101/2021.12.07.471501 Cold Spring Harbor Laboratory Press 2021-12-09 <![CDATA[ Scalable Adaptive Protein Ensemble Refinement Integrating Flexible Fitting ]]> https://biorxiv.org/content/10.1101/2021.12.07.471672v1?rss=1 Sarkar, D. Lee, H. Vant, J. W. Turilli, M. Jha, S. Singharoy, A. 2021-12-09 doi:10.1101/2021.12.07.471672 Cold Spring Harbor Laboratory Press 2021-12-09 <![CDATA[ The Gulf Coast tick, Amblyomma maculatum (Ixodida: Ixodidae) and spotted fever group Rickettsia in the highly urbanized northeastern US ]]> https://biorxiv.org/content/10.1101/2021.12.08.471803v1?rss=1 Bajwa, W. I. Tsynman, L. Egizi, A. M. Tokarz, R. Maestas, L. P. Fonseca, D. M. 2021-12-10 doi:10.1101/2021.12.08.471803 Cold Spring Harbor Laboratory Press 2021-12-10 <![CDATA[ Multiple genes in cis mediate the effects of a single chromatin accessibility variant on aberrant synaptic development and function in human neurons ]]> https://biorxiv.org/content/10.1101/2021.12.11.472229v1?rss=1 Zhang, S. Zhang, H. Forrest, M. Zhou, Y. Bagchi, V. A. Kozlova, A. Santos, M. D. Piguel, N. Dionisio, L. E. Sanders, A. R. Pang, Z. P. He, X. Penzes, P. Duan, J. 2021-12-12 doi:10.1101/2021.12.11.472229 Cold Spring Harbor Laboratory Press 2021-12-12 <![CDATA[ Structural models of SARS-CoV-2 Omicron variant in complex with ACE2 receptor or antibodies suggest altered binding interfaces ]]> https://biorxiv.org/content/10.1101/2021.12.12.472313v1?rss=1 Lubin, J. H. Markosian, C. Balamurugan, D. Pasqualini, R. Arap, W. Burley, S. K. Khare, S. D. 2021-12-13 doi:10.1101/2021.12.12.472313 Cold Spring Harbor Laboratory Press 2021-12-13 <![CDATA[ Loss of Activity-Induced Mitochondrial ATP Production Underlies the Synaptic Defects in a Drosophila model of ALS ]]> https://biorxiv.org/content/10.1101/2021.12.14.472444v1?rss=1 Karagas, N. E. Tan, K. L. Bellen, H. J. Venkatachalam, K. Wong, C.-O. 2021-12-16 doi:10.1101/2021.12.14.472444 Cold Spring Harbor Laboratory Press 2021-12-16 <![CDATA[ Unconstrained coevolution of bacterial size and the latent period of plastic phage ]]> https://biorxiv.org/content/10.1101/2021.12.19.473366v1?rss=1 Bonachela, J. A. Choua, M. Heath, M. H. 2021-12-19 doi:10.1101/2021.12.19.473366 Cold Spring Harbor Laboratory Press 2021-12-19 <![CDATA[ Novel regimens of bedaquiline-pyrazinamide combined with moxifloxacin, rifabutin, delamanid and/or OPC-167832 in murine tuberculosis models ]]> https://biorxiv.org/content/10.1101/2021.12.21.473769v1?rss=1 Nuermberger, E. Tasneen, R. Garcia, A. Converse, P. J. Zimmerman, M. D. Dartois, V. A. Kurbatova, E. V. Vernon, A. Carr, W. Stout, J. E. Dooley, K. E. 2021-12-23 doi:10.1101/2021.12.21.473769 Cold Spring Harbor Laboratory Press 2021-12-23 <![CDATA[ Type I Interferon Signaling Drives Microglial Dysfunction and Senescence in Human iPSC Models of Down Syndrome and Alzheimers Disease ]]> https://biorxiv.org/content/10.1101/2021.12.22.473858v1?rss=1 Jin, M. Xu, R. Alam, M. M. Ma, Z. Zhu, S. Wang, L. Martini, A. C. Bernabucci, M. Xie, P. Kwan, K. Pang, Z. P. Head, E. Liu, Y. Hart, R. P. Jiang, P. 2021-12-23 doi:10.1101/2021.12.22.473858 Cold Spring Harbor Laboratory Press 2021-12-23 <![CDATA[ Structural Evolution of the Ancient Enzyme, Dissimilatory Sulfite Reductase ]]> https://biorxiv.org/content/10.1101/2021.12.28.474277v1?rss=1 Colman, D. R. Labesse, G. Swapna, G. V. T. Stefanakis, J. Montelione, G. T. Boyd, E. S. Royer, C. A. 2021-12-28 doi:10.1101/2021.12.28.474277 Cold Spring Harbor Laboratory Press 2021-12-28 <![CDATA[ Introducing a New Bond-Forming Activity in an Archaeal DNA Polymerase by Structure-Guided Enzyme Redesign ]]> https://biorxiv.org/content/10.1101/2021.12.28.474375v1?rss=1 Aggarwal, T. Hansen, W. A. Hong, J. Ganguly, A. York, D. M. Khare, S. D. Izgu, E. C. 2021-12-29 doi:10.1101/2021.12.28.474375 Cold Spring Harbor Laboratory Press 2021-12-29 <![CDATA[ Normal Reproductive function in male mice lacking pituitary kisspeptin receptor. ]]> https://biorxiv.org/content/10.1101/2021.12.30.474587v1?rss=1 Ma, Y. Awe, O. Radovick, S. Yang, X. Divall, S. Wolfe, A. Wu, S. 2022-01-01 doi:10.1101/2021.12.30.474587 Cold Spring Harbor Laboratory Press 2022-01-01 <![CDATA[ INFLUENCE OF RAT CENTRAL THALAMIC NEURONS ON FORAGING BEHAVIOR IN A HAZARDOUS ENVIRONMENT ]]> https://biorxiv.org/content/10.1101/2021.12.31.474632v1?rss=1 Herzallah, M. Amir, A. Pare, D. 2022-01-01 doi:10.1101/2021.12.31.474632 Cold Spring Harbor Laboratory Press 2022-01-01 <![CDATA[ Hippocampal Volume, Neurite Density and Trace Eye-Blink Conditioning in Young Children ]]> https://biorxiv.org/content/10.1101/2022.01.03.474711v1?rss=1 Vieites, V. Ralph, Y. Reeb-Sutherland, B. Dick, A. S. Mattfeld, A. T. Pruden, S. M. 2022-01-04 doi:10.1101/2022.01.03.474711 Cold Spring Harbor Laboratory Press 2022-01-04 <![CDATA[ Real-time dynamic single-molecule protein sequencing on an integrated semiconductor device ]]> https://biorxiv.org/content/10.1101/2022.01.04.475002v1?rss=1 Reed, B. D. Meyer, M. J. Abramzon, V. Ad, O. Adcock, P. Ahmad, F. R. Alppay, G. Ball, J. A. Beach, J. Belhachemi, D. Bellofiore, A. Bellow, M. Felipe Beltran, J. Betta, A. Wadud Bhuiya, M. Blacklock, K. Boer, R. Boisvert, D. Brault, N. D. Buxbaum, A. Caprio, S. Choi, C. Christian, T. D. Clancy, R. Clark, J. Connolly, T. Fink Croce, K. Cullen, R. Davey, M. Davidson, J. Elshenawy, M. M. Ferrigno, M. Frier, D. Gudipati, S. Hamill, S. He, Z. Hosali, S. Huang, H. Huang, L. Kabiri, A. Kriger, G. Lathrop, B. Li, A. Lim, P. Liu, S. Luo, F. Lv, C. Ma, X. 2022-01-05 doi:10.1101/2022.01.04.475002 Cold Spring Harbor Laboratory Press 2022-01-05 <![CDATA[ Loss-of-function of OTUD7A in the schizophrenia-associated 15q13.3 deletion impairs synapse development and function in human neurons ]]> https://biorxiv.org/content/10.1101/2022.01.06.473910v1?rss=1 Kozlova, A. Zhang, S. Kotlar, A. V. Jamison, B. Zhang, H. Shi, S. Forrest, M. P. McDaid, J. Cutler, D. J. Epstein, M. P. Zwick, M. E. Pang, Z. P. Sanders, A. R. Warren, S. T. Gejman, P. V. Mulle, J. G. Duan, J. 2022-01-07 doi:10.1101/2022.01.06.473910 Cold Spring Harbor Laboratory Press 2022-01-07 <![CDATA[ Comprehensive analysis of disease pathology in immunocompetent and immunocompromised hamster models of SARS-CoV-2 infection ]]> https://biorxiv.org/content/10.1101/2022.01.07.475406v1?rss=1 Ramasamy, S. Kolloli, A. Kumar, R. Hussain, S. Soteropoulos, P. Chang, T. Subbian, S. 2022-01-08 doi:10.1101/2022.01.07.475406 Cold Spring Harbor Laboratory Press 2022-01-08 <![CDATA[ Seasonal variability in carbon:234thorium ratios of suspended and sinking particles in coastal Antarctic waters: Field data and modeling synthesis ]]> https://biorxiv.org/content/10.1101/2022.01.07.475468v1?rss=1 Stukel, M. R. Schofield, O. M. E. Ducklow, H. W. 2022-01-10 doi:10.1101/2022.01.07.475468 Cold Spring Harbor Laboratory Press 2022-01-10 <![CDATA[ Glutamine is required for M1-like polarization in response to Mycobacterium tuberculosis infection ]]> https://biorxiv.org/content/10.1101/2022.01.11.475775v1?rss=1 Shi, L. Jiang, Q. Qiu, Y. Kurland, I. J. Drlica, K. Subbian, S. Tyagi, S. 2022-01-11 doi:10.1101/2022.01.11.475775 Cold Spring Harbor Laboratory Press 2022-01-11 <![CDATA[ MicroRNA Detection in Biological Media Using a Split Aptamer Platform ]]> https://biorxiv.org/content/10.1101/2022.01.17.476684v1?rss=1 Wang, L. Hast, K. Aggarwal, T. Baci, M. Hong, J. Izgu, E. C. 2022-01-18 doi:10.1101/2022.01.17.476684 Cold Spring Harbor Laboratory Press 2022-01-18 <![CDATA[ Selective inhibition of goal-directed actions in the mesencephalic locomotor region ]]> https://biorxiv.org/content/10.1101/2022.01.18.476772v1?rss=1 Gut, N. K. Yilmaz, D. Kondabolu, K. Huerta-Ocampo, I. Mena-Segovia, J. 2022-01-20 doi:10.1101/2022.01.18.476772 Cold Spring Harbor Laboratory Press 2022-01-20 <![CDATA[ Caulobacter requires anionic sphingolipids and deactivation of fur to lose lipid A ]]> https://biorxiv.org/content/10.1101/2022.01.20.477143v1?rss=1 Zik, J. J. Yoon, S. H. Guan, Z. Skidmore, G. S. Gudoor, R. R. Davies, K. M. Deutschbauer, A. M. Goodlett, D. R. Klein, E. A. Ryan, K. R. 2022-01-21 doi:10.1101/2022.01.20.477143 Cold Spring Harbor Laboratory Press 2022-01-21 <![CDATA[ The amyloid precursor protein modulates the position and length of the axon initial segment offering a new perspective on Alzheimer's disease genetics ]]> https://biorxiv.org/content/10.1101/2022.01.23.477413v1?rss=1 Ma, F. Xu, J. Liu, Y. Popova, D. Youssef, M. Hart, R. P. Herrup, K. 2022-01-24 doi:10.1101/2022.01.23.477413 Cold Spring Harbor Laboratory Press 2022-01-24 <![CDATA[ Structural and mechanistic basis of σ-dependent transcriptional pausing ]]> https://biorxiv.org/content/10.1101/2022.01.24.477500v1?rss=1 Pukhrambam, C. Molodtsov, V. Kooshkbaghi, M. Tareen, A. Vu, H. Skalenko, K. S. Su, M. Zhou, Y. Winkelman, J. T. Kinney, J. B. Ebright, R. H. Nickels, B. E. 2022-01-25 doi:10.1101/2022.01.24.477500 Cold Spring Harbor Laboratory Press 2022-01-25 <![CDATA[ Target-dependent siRNA suppression distinguishes self from non-self endogenous siRNAs in C. elegans germline ]]> https://biorxiv.org/content/10.1101/2022.01.25.477739v1?rss=1 Gajic, Z. Kaur, D. Gu, S. G. 2022-01-26 doi:10.1101/2022.01.25.477739 Cold Spring Harbor Laboratory Press 2022-01-26 <![CDATA[ The P132H mutation in the main protease of Omicron SARS-CoV-2 decreases thermal stability without compromising catalysis or small-molecule drug inhibition ]]> https://biorxiv.org/content/10.1101/2022.01.26.477774v1?rss=1 Sacco, M. D. Hu, Y. Gongora, M. V. Meilleur, F. Kemp, M. T. Zhang, X. Wang, J. Chen, Y. 2022-01-27 doi:10.1101/2022.01.26.477774 Cold Spring Harbor Laboratory Press 2022-01-27 <![CDATA[ ARZIMM: A Novel Analytic Platform for the Inference of Microbial Interactions and Community Stability from Longitudinal Microbiome Study ]]> https://biorxiv.org/content/10.1101/2022.01.26.477892v1?rss=1 Li, H. He, L. wang, c. Hu, J. Gao, z. Falcone, E. Holland, S. Blaser, M. 2022-01-28 doi:10.1101/2022.01.26.477892 Cold Spring Harbor Laboratory Press 2022-01-28 <![CDATA[ Sensing Echoes: Temporal misalignment as the Earliest Marker of Neurodevelopmental Derail ]]> https://biorxiv.org/content/10.1101/2022.01.27.478048v1?rss=1 Torres, E. B. Bermperidis, T. Varkey, H. Vero, J. London, E. Phan, H. Kittler, P. Gordon, A. Schafer, S. Gage, F. H. Sejnowski, T. 2022-01-28 doi:10.1101/2022.01.27.478048 Cold Spring Harbor Laboratory Press 2022-01-28 <![CDATA[ Stable Potassium Isotopes (41K/39K) Track Transcellular and Paracellular Potassium Transport in Biological Systems ]]> https://biorxiv.org/content/10.1101/2022.01.31.478485v1?rss=1 Higgins, J. A. Santiago-Ramos, D. Gili, S. Spetea, C. Kanoski, S. Ha, D. McDonough, A. A. Youn, J. H. 2022-02-01 doi:10.1101/2022.01.31.478485 Cold Spring Harbor Laboratory Press 2022-02-01 <![CDATA[ Extinction Risk of Sonoran Desert Annuals Following Potential Changes in Precipitation Regimes ]]> https://biorxiv.org/content/10.1101/2022.02.02.478887v1?rss=1 Cuello, W. S. Schreiber, S. J. Gremer, J. R. Venable, L. Trimmer, P. C. Sih, A. 2022-02-04 doi:10.1101/2022.02.02.478887 Cold Spring Harbor Laboratory Press 2022-02-04 <![CDATA[ KMT2C deficiency promotes APOBEC mutagenesis and genomic instability in multiple cancers ]]> https://biorxiv.org/content/10.1101/2022.02.04.478993v1?rss=1 Hu, X. Biswas, A. De, S. 2022-02-04 doi:10.1101/2022.02.04.478993 Cold Spring Harbor Laboratory Press 2022-02-04 <![CDATA[ Transcriptional response of individual Hawaiian Culex quinquefasciatus mosquitoes to the avian malaria parasite Plasmodium relictum ]]> https://biorxiv.org/content/10.1101/2022.02.10.479890v1?rss=1 Ferreira, F. C. Videvall, E. Seidl, C. M. Wagner, N. E. Kilpatrick, A. M. Fleischer, R. C. Fonseca, D. M. 2022-02-10 doi:10.1101/2022.02.10.479890 Cold Spring Harbor Laboratory Press 2022-02-10 <![CDATA[ Biogeography and Validation of species limits in Caribbean Red Bats (Vespertilionidae: Lasiurus) ]]> https://biorxiv.org/content/10.1101/2022.02.11.479705v1?rss=1 Soto-Centeno, J. A. Calderon-Acevedo, C. A. 2022-02-12 doi:10.1101/2022.02.11.479705 Cold Spring Harbor Laboratory Press 2022-02-12 <![CDATA[ Environmental contributions to the evolution of trait differences in Geum triflorum: implications for restoration ]]> https://biorxiv.org/content/10.1101/2022.02.11.480132v1?rss=1 Volk, K. Braasch, J. Ahlering, M. Hamilton, J. 2022-02-12 doi:10.1101/2022.02.11.480132 Cold Spring Harbor Laboratory Press 2022-02-12 <![CDATA[ A Ferroptosis-mediated regulation of the biogenesis of the oxidative phosphorylation system ]]> https://biorxiv.org/content/10.1101/2022.02.17.480976v1?rss=1 Murari, A. Rhooms, S.-k. Hossain, K. Liu, T. Li, H. Goparaju, N. S. Osei, C. Owusu-Ansah, E. 2022-02-19 doi:10.1101/2022.02.17.480976 Cold Spring Harbor Laboratory Press 2022-02-19 <![CDATA[ Distributed network processes account for the majority of variance in localized visual category selectivity ]]> https://biorxiv.org/content/10.1101/2022.02.19.481103v1?rss=1 Cocuzza, C. V. Sanchez-Romero, R. Ito, T. Mill, R. D. Keane, B. P. Cole, M. W. 2022-02-22 doi:10.1101/2022.02.19.481103 Cold Spring Harbor Laboratory Press 2022-02-22 <![CDATA[ Monkeys exhibit human-like gaze biases in economic decisions ]]> https://biorxiv.org/content/10.1101/2022.02.24.481847v1?rss=1 Lupkin, S. M. McGinty, V. B. 2022-02-26 doi:10.1101/2022.02.24.481847 Cold Spring Harbor Laboratory Press 2022-02-26 <![CDATA[ Cryo-EM structures of Doravirine and Rilpivirine with HIV-1 Reverse Transcriptase/DNA Aptamer: Nonnucleoside Inhibitor Resistance by E138K and M184I Mutations ]]> https://biorxiv.org/content/10.1101/2022.02.27.482155v1?rss=1 Singh, A. K. De Wijngaert, B. Bijnens, M. Uyttersprot, K. Nguyen, H. Martinez, S. E. Schols, D. Herdewijn, P. Pannecouque, C. Arnold, E. Das, K. 2022-02-27 doi:10.1101/2022.02.27.482155 Cold Spring Harbor Laboratory Press 2022-02-27 <![CDATA[ A cadherin mutation in Celsr3 linked to Tourette Disorder affects dendritic patterning and excitability of cholinergic interneurons ]]> https://biorxiv.org/content/10.1101/2022.03.06.483205v1?rss=1 Poppi, L. A. Ho-Nguyen, K. Wu, J. Matrongolo, M. Thackray, J. K. Nasello, C. Shi, A. Ricci, M. McGinnis, J. Carayannopoulos, N. L. Cheedalla, N. Schaper, S. Daut, C. Hernandez, J. Heiman, G. A. Tischfield, J. A. Tischfield, M. A. 2022-03-07 doi:10.1101/2022.03.06.483205 Cold Spring Harbor Laboratory Press 2022-03-07 <![CDATA[ Remodeled Connexin 43 hemichannels alter cardiac excitability and promote arrhythmias ]]> https://biorxiv.org/content/10.1101/2022.03.08.483464v1?rss=1 Lillo, M. A. Munoz, M. F. Gaul-Muller, K. Shirokova, N. Xie, L.-h. Fraidenraich, D. Contreras, J. E. 2022-03-10 doi:10.1101/2022.03.08.483464 Cold Spring Harbor Laboratory Press 2022-03-10 <![CDATA[ Identifying transcription factor-DNA interactions using machine learning ]]> https://biorxiv.org/content/10.1101/2022.03.10.483780v1?rss=1 Bang, S. Galli, M. Crisp, P. A. Gallavotti, A. Schmitz, R. J. 2022-03-12 doi:10.1101/2022.03.10.483780 Cold Spring Harbor Laboratory Press 2022-03-12 <![CDATA[ Hepatocyte-specific loss of LAP2α reduces hepatic steatosis in male mice by enhancing LMNA-mediated transcriptional regulation ]]> https://biorxiv.org/content/10.1101/2022.03.18.484917v1?rss=1 Upadhyay, K. K. Choi, E.-Y. K. Foisner, R. Omary, M. B. Brady, G. F. 2022-03-19 doi:10.1101/2022.03.18.484917 Cold Spring Harbor Laboratory Press 2022-03-19 <![CDATA[ Triple Notch/Tgfβ/FoxO1 blockade converts multiple intestinal sub-lineages into β-like cells and lowers glycemia in diabetic animals ]]> https://biorxiv.org/content/10.1101/2022.03.21.484748v1?rss=1 Du, W. Wang, J. Kuo, T. Wang, L. McKimpson, W. Son, J. Watanabe, H. Kitamoto, T. Yunkyoung, L. Ratner, L. McCune, K. Chen, Y.-W. Grubbs, B. Thornton, M. Fan, J. Sultana, N. Diaz, B. Balasubramanian, I. Gao, N. Belvedere, S. Accili, D. 2022-03-21 doi:10.1101/2022.03.21.484748 Cold Spring Harbor Laboratory Press 2022-03-21 <![CDATA[ Polypyrimidine Tract-Binding Protein 1 (PTBP1) regulates CD4 T cell Activation independent of its role in proliferation ]]> https://biorxiv.org/content/10.1101/2022.03.21.485057v1?rss=1 Narayanan, B. Prado De Maio, D. La Porta, J. Voskoboynik, Y. Matus-Nicodemos, R. Summers, S. Ganapathi, U. Valentin-Acevedo, A. Covey, L. R. 2022-03-21 doi:10.1101/2022.03.21.485057 Cold Spring Harbor Laboratory Press 2022-03-21 <![CDATA[ A novel oral GyrB/ParE dual binding inhibitor effective against multidrug resistant Neisseria gonorrhoeae and other high-threat pathogens ]]> https://biorxiv.org/content/10.1101/2022.03.23.485573v1?rss=1 Park, S. Russo, R. Westfall, L. Shrestha, R. Zimmerman, M. Dartois, V. A. Kurepina, N. Kreiswith, B. Singleton, E. LI, S.-G. Mittal, N. Ahn, Y.-M. Bilotta, j. Connolly, K. L. Jerse, A. E. Freundlich, J. S. Perlin, D. S. 2022-03-24 doi:10.1101/2022.03.23.485573 Cold Spring Harbor Laboratory Press 2022-03-24 <![CDATA[ Suboptimal foraging decisions and involvement of the ventral tegmental area in human opioid addiction ]]> https://biorxiv.org/content/10.1101/2022.03.24.485654v1?rss=1 Raio, C. M. Biernacki, K. Kapoor, A. Wengler, K. Bonagura, D. Xue, J. Constantino, S. M. Horga, G. Konova, A. B. 2022-03-27 doi:10.1101/2022.03.24.485654 Cold Spring Harbor Laboratory Press 2022-03-27 <![CDATA[ Structural basis of transcription antitermination by Q{lambda}: NusA induces refolding of Q{lambda} to form nozzle for RNA polymerase exit channel ]]> https://biorxiv.org/content/10.1101/2022.03.25.485794v1?rss=1 Yin, Z. Bird, J. G. Kaelber, J. T. Nickels, B. E. Ebright, R. H. 2022-03-26 doi:10.1101/2022.03.25.485794 Cold Spring Harbor Laboratory Press 2022-03-26 <![CDATA[ S51 family peptidases provide resistance to peptidyl-nucleotide antibiotic McC ]]> https://biorxiv.org/content/10.1101/2022.03.27.485901v1?rss=1 Yagmurov, E. Gilep, K. Serebryakova, M. Wolf, Y. I. Dubiley, S. Severinov, K. V. 2022-03-27 doi:10.1101/2022.03.27.485901 Cold Spring Harbor Laboratory Press 2022-03-27 <![CDATA[ CD169-mediated restrictive SARS-CoV-2 infection of macrophages induces pro-inflammatory responses ]]> https://biorxiv.org/content/10.1101/2022.03.29.486190v1?rss=1 Gummuluru, S. Jalloh, S. Olejnik, J. Berrigan, J. Nisa, A. Suder, E. L. Akiyama, H. Lei, M. Tyagi, S. Bushkin, Y. Muhlberger, E. 2022-03-29 doi:10.1101/2022.03.29.486190 Cold Spring Harbor Laboratory Press 2022-03-29 <![CDATA[ Microtubule-Connexin-43 regulation suppresses arrhythmias and fibrosis in Duchenne muscular dystrophy mice. ]]> https://biorxiv.org/content/10.1101/2022.03.29.486276v1?rss=1 Himelman, E. Nouet, J. Lillo, M. Chong, A. Wehrens, X. Rodney, G. Xie, L. Shirokova, N. Contreras, J. E. Fraidenraich, D. 2022-03-29 doi:10.1101/2022.03.29.486276 Cold Spring Harbor Laboratory Press 2022-03-29 <![CDATA[ A paracrine circuit of IL-1b/IL-1R1 between myeloid and tumor cells drives glioblastoma progression ]]> https://biorxiv.org/content/10.1101/2022.04.03.486888v1?rss=1 View larger version (66K): org.highwire.dtl.DTLVardef@1c99e57org.highwire.dtl.DTLVardef@1ba9d24org.highwire.dtl.DTLVardef@a2c418org.highwire.dtl.DTLVardef@1f8091c_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Chen, Z. Giotti, B. Kaluzova, M. Herting, C. Pinero, G. vallcorba, m. p. Cristea, S. Ross, J. L. Ackley, J. Maximov, V. Szulzewsky, F. Marquez-Ropero, M. Angione, A. Nichols, N. Tsankkova, N. Michor, F. Shayakhmetov, D. M. Gutmann, D. H. Tsankov, A. M. Hambardzumyan, D. 2022-04-05 doi:10.1101/2022.04.03.486888 Cold Spring Harbor Laboratory Press 2022-04-05 <![CDATA[ Functional Contribution of Cancer-Associated Fibroblasts in Glioblastoma ]]> https://biorxiv.org/content/10.1101/2022.04.07.487495v1?rss=1 Galbo, P. M. Liu, Y. Peng, M. Wei, Y. Madsen, A. T. Graff, S. Montagna, C. Segall, J. E. Sidoli, S. Zang, X. Zheng, D. 2022-04-08 doi:10.1101/2022.04.07.487495 Cold Spring Harbor Laboratory Press 2022-04-08 <![CDATA[ Design of a Minimal di-Nickel Hydrogenase Peptide ]]> https://biorxiv.org/content/10.1101/2022.04.09.487740v1?rss=1 Mancini, J. A. Pike, D. H. Poudel, S. Timm, J. Tyryshkin, A. M. Siess, J. Molinaro, P. McCann, J. J. Waldie, K. M. Koder, R. L. Falkowski, P. G. Nanda, V. 2022-04-10 doi:10.1101/2022.04.09.487740 Cold Spring Harbor Laboratory Press 2022-04-10 <![CDATA[ Whole-genome duplication in an algal symbiont serendipitously confers thermal tolerance to corals ]]> https://biorxiv.org/content/10.1101/2022.04.10.487810v1?rss=1 Dougan, K. E. Bellantuono, A. J. Kahlke, T. Abbriano, R. M. Chen, Y. Shah, S. Granados-Cifuentes, C. van Oppen, M. J. H. Bhattacharya, D. Suggett, D. J. Chan, C. X. Rodriguez-Lanetty, M. 2022-04-11 doi:10.1101/2022.04.10.487810 Cold Spring Harbor Laboratory Press 2022-04-11 <![CDATA[ Performance of novel antibodies for lipoarabinomannan to develop diagnostic tests for Mycobacterium tuberculosis ]]> https://biorxiv.org/content/10.1101/2022.04.12.488063v1?rss=1 Cantera, J. L. Lillis, L. M. Peck, R. B. Moreau, E. Schouten, J. A. Davis, P. Drain, P. K. Andama, A. Pinter, A. Kawasaki, M. Kallenius, G. Sundling, C. Dobos, K. M. Flores, D. Chatterjee, D. Murphy, E. Halas, O. R. Boyle, D. S. 2022-04-12 doi:10.1101/2022.04.12.488063 Cold Spring Harbor Laboratory Press 2022-04-12 <![CDATA[ Multiple waves of viral invasions in Symbiodiniaceae algal genomes ]]> https://biorxiv.org/content/10.1101/2022.04.12.488082v1?rss=1 Benites, L. F. d. A. Stephens, T. G. Bhattacharya, D. 2022-04-13 doi:10.1101/2022.04.12.488082 Cold Spring Harbor Laboratory Press 2022-04-13 <![CDATA[ Landscape change and alien invasions drive shifts in native lady beetle communities over a century ]]> https://biorxiv.org/content/10.1101/2022.04.21.489069v1?rss=1 Perry, K. I. Bahlai, C. I. Assal, T. J. Riley, C. B. Turo, K. J. Taylor, L. Radl, J. Delgado de la flor, Y. A. Sivakoff, F. S. Gardiner, M. M. 2022-04-22 doi:10.1101/2022.04.21.489069 Cold Spring Harbor Laboratory Press 2022-04-22 <![CDATA[ Gene Transfer based Phylogenetics: Analytical Expressions and Additivity via Birth/Death Theory ]]> https://biorxiv.org/content/10.1101/2022.04.21.489106v1?rss=1 Katriel, G. Mahanaymi, U. Koutschan, C. Zeilberger, D. Steel, M. Snir, S. 2022-04-22 doi:10.1101/2022.04.21.489106 Cold Spring Harbor Laboratory Press 2022-04-22 <![CDATA[ Toward Interpretable Digital Biomarkers of Walking and Reaching in Parkinson's Disease ]]> https://biorxiv.org/content/10.1101/2022.04.23.489070v1?rss=1 Ryu, J. Torres, E. B. 2022-04-25 doi:10.1101/2022.04.23.489070 Cold Spring Harbor Laboratory Press 2022-04-25 <![CDATA[ Great-tailed Grackles (Quiscalus mexicanus) as a tolerant host of avian malaria parasites ]]> https://biorxiv.org/content/10.1101/2022.04.25.489425v1?rss=1 Pacheco, M. A. Ferreira, F. C. Logan, C. J. McCune, K. B. MacPherson, M. P. Albino Miranda, S. Santiago-Alarcon, D. Escalante, A. A. 2022-04-25 doi:10.1101/2022.04.25.489425 Cold Spring Harbor Laboratory Press 2022-04-25 <![CDATA[ p75NTR prevents the onset of cerebellar granule cell migration via RhoA activation ]]> https://biorxiv.org/content/10.1101/2022.04.26.489604v1?rss=1 Zanin, J. P. Friedman, W. J. 2022-04-26 doi:10.1101/2022.04.26.489604 Cold Spring Harbor Laboratory Press 2022-04-26 <![CDATA[ The antibiotic phazolicin displays a dual mode of uptake in Gram-negative bacteria ]]> https://biorxiv.org/content/10.1101/2022.04.27.489825v1?rss=1 Travin, D. Y. Vigouroux, A. Inaba-Inoue, S. Qu, F. Jouan, R. Lachat, J. Sutormin, D. Dubiley, S. Beis, K. MORERA, S. Severinov, K. V. Mergaert, P. 2022-04-28 doi:10.1101/2022.04.27.489825 Cold Spring Harbor Laboratory Press 2022-04-28 <![CDATA[ Experimental Guidance for Discovering Genetic Networks through Iterative Hypothesis Reduction on Time Series ]]> https://biorxiv.org/content/10.1101/2022.04.28.489981v1?rss=1 Cummins, B. Motta, F. C. Moseley, R. C. Deckard, A. Campione, S. Gedeon, T. Mischaikow, K. Haase, S. B. 2022-04-30 doi:10.1101/2022.04.28.489981 Cold Spring Harbor Laboratory Press 2022-04-30 <![CDATA[ Two Competing Guilds as a Core Microbiome Signature for Chronic Diseases ]]> https://biorxiv.org/content/10.1101/2022.05.02.490290v1?rss=1 Wu, G. Xu, T. Zhao, N. Lam, Y. Y. Ding, X. Wei, D. Fan, J. Shi, Y. Li, X. Li, M. Ji, S. Wang, X. Fu, H. Zhang, F. Peng, Y. Shi, Y. Zhang, C. Zhao, L. 2022-05-02 doi:10.1101/2022.05.02.490290 Cold Spring Harbor Laboratory Press 2022-05-02 <![CDATA[ Identification of a novel deFADding activity in 5' to 3' exoribonucleases ]]> https://biorxiv.org/content/10.1101/2022.05.10.491372v1?rss=1 Sharma, S. Yang, J. Doamekpor, S. K. Grudizen-Nogalska, E. Tong, L. Kiledjian, M. 2022-05-10 doi:10.1101/2022.05.10.491372 Cold Spring Harbor Laboratory Press 2022-05-10 <![CDATA[ Category representations in the primary visual cortex support orientation discrimination ]]> https://biorxiv.org/content/10.1101/2022.05.13.491867v1?rss=1 Corbo, J. Erkat, O. B. McClure, J. P. Khdour, H. Y. Polack, P.-O. 2022-05-15 doi:10.1101/2022.05.13.491867 Cold Spring Harbor Laboratory Press 2022-05-15 <![CDATA[ Identification by cryoEM of a densovirus causing mass mortality in mass-reared larval darkling beetles (Zophobas morio) ]]> https://biorxiv.org/content/10.1101/2022.05.14.491968v1?rss=1 Penzes, J. J. Kaelber, J. T. 2022-05-15 doi:10.1101/2022.05.14.491968 Cold Spring Harbor Laboratory Press 2022-05-15 <![CDATA[ The L1 Cell Adhesion Molecule Constrains Dendritic Spine Density through Ankyrin Binding in Pyramidal Neurons of the Mouse Cerebral Cortex ]]> https://biorxiv.org/content/10.1101/2022.05.16.492130v1?rss=1 Murphy, K. E. Wade, S. D. Sperringer, J. E. Mohan, V. Duncan, B. W. Pak, Y. Lutz, D. Schachner, M. Maness, P. F. 2022-05-16 doi:10.1101/2022.05.16.492130 Cold Spring Harbor Laboratory Press 2022-05-16 <![CDATA[ MFGE8 links absorption of dietary fatty acids with catabolism of enterocyte lipid stores through HNF4 γ- dependent transcription of CES enzymes ]]> https://biorxiv.org/content/10.1101/2022.05.16.492147v1?rss=1 Datta, R. Gholampour, M. A. Yang, C. D. Volk, R. Lin, S. Podolsky, M. J. Arnold, T. Rieder, F. Zaro, B. W. Verzi, M. Lehner, R. Abumrad, N. Lizama, C. O. Atabai, K. 2022-05-18 doi:10.1101/2022.05.16.492147 Cold Spring Harbor Laboratory Press 2022-05-18 <![CDATA[ Assessing PDB Macromolecular Crystal Structure Confidence at the Individual Amino Acid Residue Level ]]> https://biorxiv.org/content/10.1101/2022.05.17.492280v1?rss=1 100 million individual amino acid residues occurring within [~]150,000 PDB MX structures was analyzed in detail. The Real-Space-Correlation-Coefficient (RSCC) calculated using the 3D atomic coordinates for each residue and experimental electron density enables outlier detection of unreliable atomic coordinates (particularly important for poorly-resolved sidechain atoms) and ready evaluation of local structure quality by PDB users. For human protein MX structures in PDB, comparisons of per-residue RSCC experimental-agreement metric with AlphaFold2 computed structure model confidence (pLDDT-predicted local distance difference test) document (i) that RSCC values and pLDDT scores are correlated (median correlation coefficient[~]0.41), and (ii) that experimentally-determined MX structures (3.5 [A] resolution or better) are more reliable than AlphaFold2 computed structure models and should be used preferentially whenever possible. ]]> Shao, C. Burley, S. K. Wang, S. 2022-05-17 doi:10.1101/2022.05.17.492280 Cold Spring Harbor Laboratory Press 2022-05-17 <![CDATA[ Analysis of the Drosophila Ajuba LIM protein defines functions for distinct LIM domains ]]> https://biorxiv.org/content/10.1101/2022.05.18.492446v1?rss=1 Rauskolb, C. Han, A. Kirichenko, E. Ibar, C. Irvine, K. 2022-05-18 doi:10.1101/2022.05.18.492446 Cold Spring Harbor Laboratory Press 2022-05-18 <![CDATA[ Inhibitory interneurons within the deep dorsal horn integrate convergent sensory input to regulate motor performance ]]> https://biorxiv.org/content/10.1101/2022.05.21.492933v1?rss=1 Ozeri-Engelhard, N. Gradwell, M. A. Laflamme, O. D. Upadhyay, A. Aoki, A. Shrier, T. Gandhi, M. Gonzalez, M. Eisdorfer, J. T. Abbas- Zadeh, G. Yusuf, N. Katz, J. Haas, M. Akay, T. Abraira, V. E. 2022-05-21 doi:10.1101/2022.05.21.492933 Cold Spring Harbor Laboratory Press 2022-05-21 <![CDATA[ Enhancing the anti-tumor efficacy of Bispecific T cell engagers via cell surface glycocalyx editing ]]> https://biorxiv.org/content/10.1101/2022.05.22.492978v1?rss=1 Yang, Z. Grande, G. Hou, Y. Wang, C. Shi, Y. Lerner, R. A. Wu, P. 2022-05-23 doi:10.1101/2022.05.22.492978 Cold Spring Harbor Laboratory Press 2022-05-23 <![CDATA[ Identification of novel basil downy mildew resistance genes using de novo comparative transcriptomics ]]> https://biorxiv.org/content/10.1101/2022.05.23.491563v1?rss=1 Allen, K. S. DeIulio, G. A. Pyne, R. Maman, J. Guo, L. Wick, R. L. Simon, J. Gershenson, A. Ma, L.-J. 2022-05-24 doi:10.1101/2022.05.23.491563 Cold Spring Harbor Laboratory Press 2022-05-24 <![CDATA[ Alcohol reverses the effects of KCNJ6 (GIRK2) noncoding variants on excitability of human glutamatergic neurons ]]> https://biorxiv.org/content/10.1101/2022.05.24.493086v1?rss=1 Popova, D. Gameiro-Ros, I. Youssef, M. M. Zalamea, P. Morris, A. D. Prytkova, I. Jadali, A. Kwan, K. Y. Kamarajan, C. Salvatore, J. E. Edenberg, H. J. Xuei, X. Chorlian, D. B. Porjesz, B. Kuperman, S. Dick, D. M. Goate, A. Tischfield, J. A. Pang, Z. P. Slesinger, P. A. Hart, R. P. 2022-05-24 doi:10.1101/2022.05.24.493086 Cold Spring Harbor Laboratory Press 2022-05-24 <![CDATA[ High frequency DBS-like optogenetic stimulation of nucleus accumbens dopamine D2 receptor-containing neurons attenuates cocaine reinstatement in male rats ]]> https://biorxiv.org/content/10.1101/2022.05.26.493617v1?rss=1 Swinford-Jackson, S. E. Huffman, P. J. Knouse, M. C. Thomas, A. S. Mankame, S. Worobey, S. J. Sarmiento, M. Coleman, A. Pierce, R. C. 2022-05-28 doi:10.1101/2022.05.26.493617 Cold Spring Harbor Laboratory Press 2022-05-28 <![CDATA[ Biochemical and structural insights into SARS-CoV-2 polyprotein processing by Mpro ]]> https://biorxiv.org/content/10.1101/2022.05.27.493767v1?rss=1 Yadav, R. Courouble, V. V. Dey, S. K. Harrison, J. J. E. K. Timm, J. Hopkins, J. B. Slack, R. L. Sarafianos, S. G. Ruiz, F. X. Griffin, P. R. Arnold, E. 2022-05-30 doi:10.1101/2022.05.27.493767 Cold Spring Harbor Laboratory Press 2022-05-30 <![CDATA[ Development of the Intestinal Microbiome in Cystic Fibrosis in Early Life ]]> https://biorxiv.org/content/10.1101/2022.05.27.493808v1?rss=1 Price, C. E. Hampton, T. H. Valls, R. Barrack, K. O'Toole, G. Madan, J. C. Coker, M. 2022-05-30 doi:10.1101/2022.05.27.493808 Cold Spring Harbor Laboratory Press 2022-05-30 <![CDATA[ Causal effects of prefrontal transcranial magnetic stimulation on dopamine-mediated reinforcement learning in healthy adults ]]> https://biorxiv.org/content/10.1101/2022.06.03.494692v1?rss=1 Biernacki, K. Myers, C. Cole, S. Cavanagh, J. F. Baker, T. E. 2022-06-05 doi:10.1101/2022.06.03.494692 Cold Spring Harbor Laboratory Press 2022-06-05 <![CDATA[ Saturated cell lysing is critical for high sensitivity microbiome analysis ]]> https://biorxiv.org/content/10.1101/2022.06.04.494821v1?rss=1 Wang, Y. Zhao, C. Lam, Y. Y. Zhao, L. Wu, G. 2022-06-04 doi:10.1101/2022.06.04.494821 Cold Spring Harbor Laboratory Press 2022-06-04 <![CDATA[ Structural mechanism of leaflet-specific phospholipid modulation of a pentameric ligand-gated ion channel ]]> https://biorxiv.org/content/10.1101/2022.06.07.494883v1?rss=1 Petroff, J. T. Dietzen, N. M. Santiago-McRae, E. Deng, B. Washington, M. S. Chen, L. J. Moreland, K. T. Deng, Z. Rau, M. Fitzpatrick, J. A. Yuan, P. Joseph, T. T. Henin, J. Brannigan, G. Cheng, W. W. 2022-06-09 doi:10.1101/2022.06.07.494883 Cold Spring Harbor Laboratory Press 2022-06-09 <![CDATA[ β-catenin obstructs γδ T cell immunosurveillance in colon cancer through loss of BTNL expression ]]> https://biorxiv.org/content/10.1101/2022.06.10.495115v1?rss=1 Suzuki, T. Kilbey, A. Ridgway, R. A. Hayman, H. Byrne, R. Casa Rodriguez, N. Georgakopoulou, A. Chen, L. Verzi, M. Gay, D. M. Vzquez, E. G. Belnoue-Davis, H. L. Gilroy, K. Kostner, A. H. Kersten, C. Thuwajit, C. Andersen, D. Wiesheu, R. Jandke, A. Roberts, N. Blyth, K. Roseweir, A. Leedham, S. J. Dunne, P. D. Edwards, J. Hayday, A. Sansom, O. J. Coffelt, S. B. 2022-06-12 doi:10.1101/2022.06.10.495115 Cold Spring Harbor Laboratory Press 2022-06-12 <![CDATA[ Robustness and reproducibility of simple and complex synthetic logic circuit designs using a DBTL loop ]]> https://biorxiv.org/content/10.1101/2022.06.10.495560v1?rss=1 Cummins, B. Vrana, J. Moseley, R. C. Eramian, H. Deckard, A. Fontanarrosa, P. Bryce, D. Weston, M. Zheng, G. Nowak, J. Motta, F. C. Eslami, M. Johnson, K. L. Goldman, R. P. Myers, C. J. Johnson, T. Vaughn, M. W. Gaffney, N. Urrutia, J. Gopaulakrishnan, S. Biggers, V. Higa, T. Mosqueda, L. Gameiro, M. Gedeon, T. Mischaikow, K. Beal, J. Bartley, B. Mitchell, T. Nguyen, T. T. Roehner, N. Haase, S. B. 2022-06-11 doi:10.1101/2022.06.10.495560 Cold Spring Harbor Laboratory Press 2022-06-11 <![CDATA[ Computational Prediction of Synthetic Circuit Function Across Growth Conditions ]]> https://biorxiv.org/content/10.1101/2022.06.13.495701v1?rss=1 Cummins, B. Moseley, R. C. Deckard, A. Weston, M. Zheng, G. Bryce, D. Nowak, J. Gameiro, M. Gedeon, T. Mischaikow, K. Beal, J. Johnson, T. Vaughn, M. Gaffney, N. I. Gopaulakrishnan, S. Urrutia, J. Goldman, R. P. Bartley, B. Nguyen, T. T. Roehner, N. Mitchell, T. Vrana, J. D. Clowers, K. J. Maheshri, N. Becker, D. Mikhalev, E. Biggers, V. Higa, T. Mosqueda, L. Haase, S. B. 2022-06-13 doi:10.1101/2022.06.13.495701 Cold Spring Harbor Laboratory Press 2022-06-13 <![CDATA[ Understanding the Dynamics of Fluid-Structure Interaction with an Air Deflected Microfluidic Chip (ADMC) ]]> https://biorxiv.org/content/10.1101/2022.06.14.496157v1?rss=1 ten Pas, C. Du, K. Wang, R.-Q. Pan, L. Xu, S. 2022-06-17 doi:10.1101/2022.06.14.496157 Cold Spring Harbor Laboratory Press 2022-06-17 <![CDATA[ Mutagenesis and structural modeling implicate RME-8 IWN domains as conformational control points ]]> https://biorxiv.org/content/10.1101/2022.06.16.496522v1?rss=1 Norris, A. McManus, C. Ying, R. Wang, S. Grant, B. D. 2022-06-17 doi:10.1101/2022.06.16.496522 Cold Spring Harbor Laboratory Press 2022-06-17 <![CDATA[ GCN2 eIF2 kinase promotes prostate cancer by maintaining amino acid homeostasis ]]> https://biorxiv.org/content/10.1101/2022.06.17.496598v1?rss=1 Cordova, R. Misra, J. Amin, P. H. Klunk, A. J. Damayanti, N. P. Carlson, K. R. Elmendorf, A. J. Hyeong-Geug, K. Mirek, E. T. Miller, M. J. Dong, X. C. Cheng, L. Anthony, T. G. Pili, R. Wek, R. C. Staschke, K. A. 2022-06-18 doi:10.1101/2022.06.17.496598 Cold Spring Harbor Laboratory Press 2022-06-18 <![CDATA[ Functional Redundancy of the Posterior Hippocampi, but not Anterior Hippocampi or Left Frontal Cortex, is Disrupted in Pathological Brain Aging ]]> https://biorxiv.org/content/10.1101/2022.06.18.496543v1?rss=1 Blujus, J. Cole, M. W. Festa, E. K. Buka, S. L. Salloway, S. P. Heindel, W. C. Oh, H. ADNI, 2022-06-20 doi:10.1101/2022.06.18.496543 Cold Spring Harbor Laboratory Press 2022-06-20 <![CDATA[ Membrane curvature governs the distribution of Piezo1 in cellulo ]]> https://biorxiv.org/content/10.1101/2022.06.22.497259v1?rss=1 Yang, S. Arnold, S. Li, B. Wang, H. Wang, M. Cox, C. D. Shi, Z. 2022-06-25 doi:10.1101/2022.06.22.497259 Cold Spring Harbor Laboratory Press 2022-06-25 <![CDATA[ Activity-Based Imaging of Lipid Environments Targeted by Peroxynitrite in Biomimetic Vesicles and Live Cells ]]> https://biorxiv.org/content/10.1101/2022.06.22.497268v1?rss=1 Gutierrez, B. Erguven, H. Stone, M. R. L. Aggarwal, T. Izgu, E. C. 2022-06-23 doi:10.1101/2022.06.22.497268 Cold Spring Harbor Laboratory Press 2022-06-23 <![CDATA[ Chromosomal assembly of the flat oyster (Ostrea edulis L.) genome as a new genetic ressource for aquaculture ]]> https://biorxiv.org/content/10.1101/2022.06.26.497643v1?rss=1 Boutet, I. Monteiro, H. J. A. Takeuchi, T. Baudry, L. Bonnivard, E. Billoud, B. Farhat, S. Gonzales-Haraya, R. Salaun, B. Andersen, A. Toullec, J.-Y. Lallier, F. Flot, J.-F. Guiglielmoni, N. Guo, X. Cui, L. Allam, B. Pales-Espinoza, E. Hemmer, J. Marbouty, M. Koszul, R. Tanguy, A. 2022-06-28 doi:10.1101/2022.06.26.497643 Cold Spring Harbor Laboratory Press 2022-06-28 <![CDATA[ Thalamocortical contribution to cognitive task activity ]]> https://biorxiv.org/content/10.1101/2022.06.28.497905v1?rss=1 Sorenson, E. Shine, J. M. Cole, M. W. Hwang, K. 2022-07-01 doi:10.1101/2022.06.28.497905 Cold Spring Harbor Laboratory Press 2022-07-01 <![CDATA[ Denoising sparse microbial signals from single-cell sequencing of mammalian host tissues ]]> https://biorxiv.org/content/10.1101/2022.06.29.498176v1?rss=1 Ghaddar, B. Blaser, M. J. De, S. 2022-06-30 doi:10.1101/2022.06.29.498176 Cold Spring Harbor Laboratory Press 2022-06-30 <![CDATA[ Development of amidase-dependent pyrazinoic acid prodrugs with activity against pyrazinamide resistant Mycobacterium tuberculosis ]]> https://biorxiv.org/content/10.1101/2022.07.05.496887v1?rss=1 Levine, C. Jadhav, R. Yan, P. Tsotetsi, K. Wang, X. Awasthi, D. Grady, C. Shelke, A. Daher, S. S. Richmann, T. Shrestha, R. Sukheja, P. Patel, J. Barnett, P. R. Dikdan, R. J. Kim, T. Russo, R. Hanna, J. Zimmerman, M. Dartois, V. Freundlich, J. Alland, D. Kumar, P. 2022-07-05 doi:10.1101/2022.07.05.496887 Cold Spring Harbor Laboratory Press 2022-07-05 <![CDATA[ TLR4 signaling in presence of HIV-induced activation enhances programmed death ligand-1 expression on human plasmacytoid dendritic cells and modulates their function ]]> https://biorxiv.org/content/10.1101/2022.07.05.498853v1?rss=1 Patel, M. Singh, S. Davidow, A. Dai, J. Fitzgerald-Bocarsly, P. 2022-07-05 doi:10.1101/2022.07.05.498853 Cold Spring Harbor Laboratory Press 2022-07-05 <![CDATA[ Telomere dysfunction impairs intestinal differentiation andpredisposes to diet-induced colitis ]]> https://biorxiv.org/content/10.1101/2022.07.14.499988v1?rss=1 Engevik, M. Guo, L. Song, W.-S. Chronowski, C. Akhanov, V. Bosquez, N. Engevik, A. Oezguen, N. Coarfa, C. Putluri, N. Catic, A. Baur, J. Finegold, M. Shroyer, N. Gu, J. Ferraris, R. Halliday, J. Herman, C. Colla, S. Dierick, H. Jang, C. Sahin, E. 2022-07-15 doi:10.1101/2022.07.14.499988 Cold Spring Harbor Laboratory Press 2022-07-15 <![CDATA[ A comprehensive update to the Mycobacterium tuberculosis H37Rv reference genome ]]> https://biorxiv.org/content/10.1101/2022.07.15.500236v1?rss=1 Chitale, P. Lemenze, A. D. Fogarty, E. C. Shah, A. Grady, C. A. Odom-Mabey, A. R. Johnson, W. E. Yang, J. H. Eren, A. M. Brosch, R. Kumar, P. Alland, D. 2022-07-16 doi:10.1101/2022.07.15.500236 Cold Spring Harbor Laboratory Press 2022-07-16 <![CDATA[ Improved Cladocopium goreaui genome assembly reveals features of a facultative coral symbiont and the complex evolutionary history of dinoflagellate genes ]]> https://biorxiv.org/content/10.1101/2022.07.19.500725v1?rss=1 Chen, Y. Shah, S. Dougan, K. E. van Oppen, M. J. H. Bhattacharya, D. Chan, C. X. 2022-07-20 doi:10.1101/2022.07.19.500725 Cold Spring Harbor Laboratory Press 2022-07-20 <![CDATA[ Maf Family Transcription Factors are Required for Nutrient Uptake in the Neonatal Gut ]]> https://biorxiv.org/content/10.1101/2022.07.26.501624v1?rss=1 Bara, A. M. Chen, L. Ma, C. Underwood, J. Moreci, R. S. Sumigray, K. Sun, T. Diao, Y. Verzi, M. Lechler, T. 2022-07-28 doi:10.1101/2022.07.26.501624 Cold Spring Harbor Laboratory Press 2022-07-28 <![CDATA[ Honey Bees Get Map Coordinates from the Dance ]]> https://biorxiv.org/content/10.1101/2022.07.27.501756v1?rss=1 Wang, Z. Chen, X. Becker, F. Walter, S. Greggers, U. Werner, M. Gallistel, C. R. Menzel, R. 2022-07-28 doi:10.1101/2022.07.27.501756 Cold Spring Harbor Laboratory Press 2022-07-28 <![CDATA[ Large vesicle extrusion from C. elegans neurons requires phagocytic interaction via the ARF-6 and CED-1/DRAPER pathways ]]> https://biorxiv.org/content/10.1101/2022.07.31.502194v1?rss=1 Wang, Y. Arnold, M. L. Smart, A. J. Wang, G. Morera, A. Nguyen, K. C. Schweinsberg, P. J. Bai, G. Cooper, J. Hall, D. H. Driscoll, M. Grant, B. 2022-08-01 doi:10.1101/2022.07.31.502194 Cold Spring Harbor Laboratory Press 2022-08-01 <![CDATA[ The Effects of CdSe/ZnS Quantum Dots on the Photosynthesis Rate of the Chlorella Vulgaris Beads ]]> https://biorxiv.org/content/10.1101/2022.08.01.500842v1?rss=1 Dissanayake, W. Hailstone, R. Bao, M. Wang, R.-Q. Yong, X. Du, K. 2022-08-03 doi:10.1101/2022.08.01.500842 Cold Spring Harbor Laboratory Press 2022-08-03 <![CDATA[ Intermediate Filaments Associate with Aggresome-like Structures and Influence Rate of Cellular Expulsion of Neuronal Disease Aggregates ]]> https://biorxiv.org/content/10.1101/2022.08.03.501714v1?rss=1 Arnold, M. L. Cooper, J. F. Androwski, R. Ardeshna, S. Melentijevic, I. Smart, A. J. Guasp, R. J. Nguyen, K. C. Bai, G. Hall, D. H. Grant, B. D. Driscoll, M. 2022-08-05 doi:10.1101/2022.08.03.501714 Cold Spring Harbor Laboratory Press 2022-08-05 <![CDATA[ Predicting Clinical Outcomes in Infants With Cystic Fibrosis From Stool Microbiota using Random Forest Algorithms ]]> https://biorxiv.org/content/10.1101/2022.08.06.503028v1?rss=1 Valls, R. Hampton, T. H. Price, C. E. Barrack, K. O'Toole, G. Coker, M. Madan, J. C. 2022-08-08 doi:10.1101/2022.08.06.503028 Cold Spring Harbor Laboratory Press 2022-08-08 <![CDATA[ A yeast-based system to study SARS-CoV-2 Mpro structure and to identify nirmatrelvir resistant mutations ]]> https://biorxiv.org/content/10.1101/2022.08.06.503039v1?rss=1 Ou, J. Lewandowski, E. Hu, Y. Lipinski, A. Morgan, R. Jacobs, L. Zhang, X. Bikowitz, M. Langlais, P. Tan, H. Wang, J. Chen, Y. Choy, J. S. 2022-08-08 doi:10.1101/2022.08.06.503039 Cold Spring Harbor Laboratory Press 2022-08-08 <![CDATA[ The effects of ethnoracial-related stressors during pregnancy on the developing offspring brain. ]]> https://biorxiv.org/content/10.1101/2022.08.08.503168v1?rss=1 Spann, M. N. Alleyne, K. Holland, C. M. Davids, A. Pierre-Louis, A. Bang, C. Oyeneye, V. Kiflom, R. Shea, E. Cheng, B. Peterson, B. S. Monk, C. Scheinost, D. 2022-08-11 doi:10.1101/2022.08.08.503168 Cold Spring Harbor Laboratory Press 2022-08-11 <![CDATA[ The cognitive basis of intracranial self-stimulation of midbrain dopamine neurons ]]> https://biorxiv.org/content/10.1101/2022.08.11.503670v1?rss=1 Millard, S. J. Hoang, I. B. Greer, Z. O'Connor, S. L. Wassum, K. M. James, M. H. Barker, D. J. Sharpe, M. J. 2022-08-14 doi:10.1101/2022.08.11.503670 Cold Spring Harbor Laboratory Press 2022-08-14 <![CDATA[ A Neural Index Reflecting the Amount of Cognitive Resources Available during Memory Encoding: A Model-based Approach ]]> https://biorxiv.org/content/10.1101/2022.08.16.504058v1?rss=1 Ma, S. Popov, V. Zhang, Q. 2022-08-16 doi:10.1101/2022.08.16.504058 Cold Spring Harbor Laboratory Press 2022-08-16 <![CDATA[ Robust total X-ray scattering workflow to study correlated motion of proteins in crystals ]]> https://biorxiv.org/content/10.1101/2022.08.22.504832v1?rss=1 Meisburger, S. P. Case, D. A. Ando, N. 2022-08-22 doi:10.1101/2022.08.22.504832 Cold Spring Harbor Laboratory Press 2022-08-22 <![CDATA[ A neural signature of reward ]]> https://biorxiv.org/content/10.1101/2022.08.23.504939v1?rss=1 Chang, L. J. Li, X. Nguyen, K. Ranger, M. S. Begunova, Y. Chen, P.-H. A. Castrellon, j. Samanez-Larkin, G. R. Zald, D. Fareri, D. Delgado, M. Tomova, L. 2022-08-24 doi:10.1101/2022.08.23.504939 Cold Spring Harbor Laboratory Press 2022-08-24 <![CDATA[ Short-term high fat diet feeding of mice suppresses catecholamine-stimulated Ca2+ signalling in hepatocytes and intact liver. ]]> https://biorxiv.org/content/10.1101/2022.08.28.505514v1?rss=1 Brumer, R. P. Correa-Velloso, J. C. Thomas, S. J. Sandiford, O. A. Thomas, A. P. Bartlett, P. J. 2022-08-28 doi:10.1101/2022.08.28.505514 Cold Spring Harbor Laboratory Press 2022-08-28 <![CDATA[ FAVOR: Functional Annotation of Variants Online Resource and Annotator for Variation across the Human Genome ]]> https://biorxiv.org/content/10.1101/2022.08.28.505582v1?rss=1 Zhou, H. Arapoglou, T. Li, X. Li, Z. Zheng, X. Moore, J. E. Asok, A. Kumar, S. Blue, E. E. Buyske, S. Cox, N. Felsenfeld, A. Gerstein, M. Kenny, E. Li, B. Matise, T. Philippakis, A. Rehm, H. Sofia, H. J. Neale, B. Snyder, G. Weng, Z. Sunyaev, S. Lin, X. 2022-08-29 doi:10.1101/2022.08.28.505582 Cold Spring Harbor Laboratory Press 2022-08-29 <![CDATA[ A second unveiling: haplotig masking of the eastern oyster genome improves population-level inference ]]> https://biorxiv.org/content/10.1101/2022.08.29.505626v1?rss=1 Puritz, J. B. Guo, X. Hare, M. P. He, Y. Hillier, L. Liu, M. Lotterhos, K. E. Minx, P. Modak, T. Proestou, D. Rice, E. S. Tomlison, C. Warren, W. C. Witkop, E. Zhao, H. Gomez-Chiarri, M. 2022-08-29 doi:10.1101/2022.08.29.505626 Cold Spring Harbor Laboratory Press 2022-08-29 <![CDATA[ Nucleotide and structural polymorphisms of the eastern oyster genome paint a mosaic of divergence, selection, and human impacts ]]> https://biorxiv.org/content/10.1101/2022.08.29.505629v1?rss=1 Puritz, J. B. Zhao, H. Guo, X. Hare, M. P. He, Y. LaPeyre, J. Lotterhos, K. E. Lundgren, K. M. Modak, T. Proestou, D. A. Rawson, P. Fernandez Robledo, J. A. Witkop, E. Weedop, K. B. Gomez-Chiarri, M. 2022-09-01 doi:10.1101/2022.08.29.505629 Cold Spring Harbor Laboratory Press 2022-09-01 <![CDATA[ Structural basis of Rho-dependent transcription termination ]]> https://biorxiv.org/content/10.1101/2022.08.29.505764v1?rss=1 Molodtsov, V. Wang, C. Firlar, E. Kaelber, J. T. Ebright, R. H. 2022-08-29 doi:10.1101/2022.08.29.505764 Cold Spring Harbor Laboratory Press 2022-08-29 <![CDATA[ Outcome of Crash Course Training on Protein Structure Prediction with Artificial Intelligence ]]> https://biorxiv.org/content/10.1101/2022.09.01.506222v1?rss=1 Balamurugan, D. Dougherty, M. Lubin, J. Arias, P. Chang, J. Dalenberg, K. Kholodovych, V. Zelzion, E. Khare, S. von Oehsen, J. B. Zwick, M. E. Burley, S. K. 2022-09-03 doi:10.1101/2022.09.01.506222 Cold Spring Harbor Laboratory Press 2022-09-03 <![CDATA[ The combination of morphogenic regulators BABY BOOM and GRF-GIF improves maize transformation efficiency ]]> https://biorxiv.org/content/10.1101/2022.09.02.506370v1?rss=1 Chen, Z. Debernardi, J. M. Dubcovsky, J. Gallavotti, A. 2022-09-02 doi:10.1101/2022.09.02.506370 Cold Spring Harbor Laboratory Press 2022-09-02 <![CDATA[ Tracking N-and C-termini of C. elegans polycystin-1 reveals their distinct targeting requirements and functions in cilia and extracellular vesicles ]]> https://biorxiv.org/content/10.1101/2022.09.07.504996v1?rss=1 Walsh, J. D. Wang, J. DeHart, M. T. Nikonorova, I. Srinivasan, J. Barr, M. M. 2022-09-08 doi:10.1101/2022.09.07.504996 Cold Spring Harbor Laboratory Press 2022-09-08 <![CDATA[ Myalgic Encephalomyelitis/Chronic Fatigue Syndrome and fibromyalgia are indistinguishable by their cerebrospinal fluid proteomes ]]> https://biorxiv.org/content/10.1101/2022.09.14.506792v1?rss=1 Schutzer, S. E. Liu, T. Tsai, C.-F. Petyuk, V. A. Schepmoes, A. Wang, Y.-T. Weitz, K. Bergquist, J. Smith, R. Natelson, B. 2022-09-17 doi:10.1101/2022.09.14.506792 Cold Spring Harbor Laboratory Press 2022-09-17 <![CDATA[ Visual-motor integration deficits in 3q29 deletion syndrome ]]> https://biorxiv.org/content/10.1101/2022.09.15.508134v1?rss=1 Pollak, R. M. Burrell, T. L. Cubells, J. F. Klaiman, C. Murphy, M. M. Saulnier, C. A. Walker, E. F. White, S. P. Mulle, J. G. 2022-09-17 doi:10.1101/2022.09.15.508134 Cold Spring Harbor Laboratory Press 2022-09-17 <![CDATA[ Cells in the Polyaneuploid Cancer Cell (PACC) state have increased metastatic potential ]]> https://biorxiv.org/content/10.1101/2022.09.16.508155v1?rss=1 Mallin, M. M. Kim, N. Choudhury, M. I. Lee, S. J. An, S. S. Sun, S. X. Konstantopoulos, K. Pienta, K. J. Amend, S. R. 2022-09-19 doi:10.1101/2022.09.16.508155 Cold Spring Harbor Laboratory Press 2022-09-19 <![CDATA[ Dysregulation of mTOR Signaling Mediates Common Neurite and Migration Defects in Both Idiopathic and 16p11.2 Deletion Autism Neural Precursor Cells ]]> https://biorxiv.org/content/10.1101/2022.09.17.508382v1?rss=1 Prem, S. Dev, B. Peng, C. Mehta, M. Alibutud, R. Connacher, R. J. St. Thomas, M. Zhou, X. Matteson, P. Xing, J. Millonig, J. DiCicco-Bloom, E. 2022-09-20 doi:10.1101/2022.09.17.508382 Cold Spring Harbor Laboratory Press 2022-09-20 <![CDATA[ Guild-level microbiome signature associated with COVID-19 severity and prognosis ]]> https://biorxiv.org/content/10.1101/2022.09.18.508418v1?rss=1 Guo, M. Wu, G. Tan, Y. Li, Y. Jin, X. Qi, W. Guo, X. Zhang, C. Zhu, Z. Zhao, L. 2022-09-19 doi:10.1101/2022.09.18.508418 Cold Spring Harbor Laboratory Press 2022-09-19 <![CDATA[ The logic of recurrent circuits in the primary visual cortex ]]> https://biorxiv.org/content/10.1101/2022.09.20.508739v1?rss=1 Oldenburg, I. A. Hendricks, W. D. Handy, G. Shamardani, K. Bounds, H. A. Doiron, B. Adesnik, H. 2022-09-22 doi:10.1101/2022.09.20.508739 Cold Spring Harbor Laboratory Press 2022-09-22 <![CDATA[ Identification and structural modeling of the chlamydial RNA polymerase omega subunit ]]> https://biorxiv.org/content/10.1101/2022.09.22.509108v1?rss=1 Cheng, A. Wu, D. Ghatak, A. Wang, C. Feng, D. Fondell, J. D. Ebright, R. H. Fan, H. 2022-09-23 doi:10.1101/2022.09.22.509108 Cold Spring Harbor Laboratory Press 2022-09-23 <![CDATA[ A helminth mimic of TGF-β, TGM, enhances regenerative cutaneous wound healing and modulates immune cell recruitment and activation ]]> https://biorxiv.org/content/10.1101/2022.09.24.509317v1?rss=1 Lothstein, K. E. Chen, F. Mishra, P. Smyth, D. J. Wu, W. Lemenze, A. Kumamoto, Y. Maizels, R. M. Gause, W. C. 2022-09-25 doi:10.1101/2022.09.24.509317 Cold Spring Harbor Laboratory Press 2022-09-25 <![CDATA[ A Multivariate Approach to Understanding the Genetic Overlap between Externalizing Phenotypes and Substance Use Disorders ]]> https://biorxiv.org/content/10.1101/2022.09.27.509777v1?rss=1 .87) and similarly genetically correlated with external criteria, suggesting they did not represent meaningfully distinct dimensions. Results from this study can be used to inform future efforts to characterize genetic liability for broad externalizing as well as specific externalizing phenotypes. ]]> Poore, H. E. Hatoum, A. Mallard, T. T. Sanchez-Roige, S. Waldman, I. D. Palmer, A. A. Harden, K. P. Barr, P. B. Dick, D. M. 2022-09-28 doi:10.1101/2022.09.27.509777 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ Twist1 and balanced retinoic acid signaling act to suppress cortical folding in mice ]]> https://biorxiv.org/content/10.1101/2022.09.27.509818v1?rss=1 Ho-Nguyen, K.-T. Jain, M. Matrongolo, M. J. Ang, P. S. Schaper, S. Tischfield, M. A. 2022-09-28 doi:10.1101/2022.09.27.509818 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ Synapsing with oligodendrocyte precursor cells stop sensory axons regenerating into the spinal cord ]]> https://biorxiv.org/content/10.1101/2022.09.28.509944v1?rss=1 Kim, H. Skuba, A. Xia, J. Han, S. B. Zhai, J. Yoo, R. Hu, H. Kang, S. H. Son, Y.-J. 2022-09-30 doi:10.1101/2022.09.28.509944 Cold Spring Harbor Laboratory Press 2022-09-30 <![CDATA[ Entropic control of the free energy landscape of an archetypal biomolecular machine ]]> https://biorxiv.org/content/10.1101/2022.10.03.510626v1?rss=1 Ray, K. K. Kinz-Thompson, C. D. Fei, J. Wang, B. Lin, Q. Gonzalez, R. L. 2022-10-05 doi:10.1101/2022.10.03.510626 Cold Spring Harbor Laboratory Press 2022-10-05 <![CDATA[ Origin and dynamics of Mycobacterium tuberculosis subpopulations that predictably generate drug tolerance and resistance ]]> https://biorxiv.org/content/10.1101/2022.10.05.511058v1?rss=1 Alland, D. Sebastian, J. Thomas, A. Levine, C. Shrestha, R. Levy, S. Safi, H. Pentakota, S. R. Kumar, P. 2022-10-06 doi:10.1101/2022.10.05.511058 Cold Spring Harbor Laboratory Press 2022-10-06 <![CDATA[ Improving polygenic risk prediction in admixed populations by explicitly modeling ancestral-specific effects via GAUDI ]]> https://biorxiv.org/content/10.1101/2022.10.06.511219v1?rss=1 Sun, Q. Rowland, B. T. Chen, J. Mikhaylova, A. V. Avery, C. Peters, U. Lundin, J. Matise, T. Buyske, S. Tao, R. Mathias, R. A. Reiner, A. P. Auer, P. L. Cox, N. J. Kooperberg, C. Thornton, T. Raffield, L. M. Li, Y. 2022-10-08 doi:10.1101/2022.10.06.511219 Cold Spring Harbor Laboratory Press 2022-10-08 <![CDATA[ A novel pH-sensitive reporter reveals the cocaine-regulated trafficking of dopamine transporters in neuronal processes ]]> https://biorxiv.org/content/10.1101/2022.10.12.511970v1?rss=1 Saenz, J. Yao, O. Aggarwal, M. Zhou, X. Barker, D. J. DiCicco-Bloom, E. Pan, P.-Y. 2022-10-13 doi:10.1101/2022.10.12.511970 Cold Spring Harbor Laboratory Press 2022-10-13 <![CDATA[ TCID50 Measurements of anti-viral efficacy on metal printed masks and plastic surfaces ]]> https://biorxiv.org/content/10.1101/2022.10.13.512105v1?rss=1 Bilynsky, C. S. Taylor, K. Anand, M. Wayne, E. C. 2022-10-14 doi:10.1101/2022.10.13.512105 Cold Spring Harbor Laboratory Press 2022-10-14 <![CDATA[ A Transducing Bacteriophage Infecting Staphylococcus epidermidis Contributes to the Expansion of aNovel Siphovirus Genus and Implies Genus is Inappropriate for Phage Therapy ]]> https://biorxiv.org/content/10.1101/2022.10.13.512176v1?rss=1 Andrews, T. Hoyer, J. S. Ficken, K. Fey, P. D. Duffy, S. Boyd, J. 2022-10-14 doi:10.1101/2022.10.13.512176 Cold Spring Harbor Laboratory Press 2022-10-14 <![CDATA[ Synaptojanin1 regulates lysosomal functions in ventral midbrain neurons ]]> https://biorxiv.org/content/10.1101/2022.10.14.512269v1?rss=1 Zhu, X. Prakash, S. S. McAuliffe, G. Pan, P.-Y. 2022-10-14 doi:10.1101/2022.10.14.512269 Cold Spring Harbor Laboratory Press 2022-10-14 <![CDATA[ The Halo Library, a Tool for Rapid Identification of Ligand Binding Sites on Proteins Using Crystallographic Fragment Screening ]]> https://biorxiv.org/content/10.1101/2022.10.17.512577v1?rss=1 300 Da). Previous studies from our lab and others have shown that fragments containing halogen atoms have a higher binding occurrence compared to non-halogenated fragments. Specifically, we showed that 4-halopyrazoles hold potential for predicting the likelihood of success of a XCFS campaign. Here, we designed the Halo Library containing 46 halogenated fragments (including the "universal fragment" 4-bromopyrazole). The basis of fragment selection was presence of (at least) one halogen atom, and binding to or inhibitory activity against (at least) two targets in literature. The library was screened against crystals of HIV-1 reverse transcriptase with drug rilpivirine, yielding an overall hit rate of 26%. Two new binding sites were discovered in addition to previously reported sites, and several hot spots were identified (i.e., sites with multiple fragment hits). This small library may thus provide a convenient tool for assessing feasibility of a target for XCFS, mapping hot spots and cryptic sites, as well as finding fragment binders that can be useful for developing drug leads. ]]> Chopra, A. Bauman, J. D. Ruiz, F. X. Arnold, E. 2022-10-17 doi:10.1101/2022.10.17.512577 Cold Spring Harbor Laboratory Press 2022-10-17 <![CDATA[ Structural and molecular biology of Acheta domesticus segmented densovirus, the first parvovirus to harbor a bipartite genome ]]> https://biorxiv.org/content/10.1101/2022.10.20.513106v1?rss=1 Penzes, J. J. Pham, H. T. Chipman, P. Smith, E. W. McKenna, R. Tijssen, P. 2022-10-21 doi:10.1101/2022.10.20.513106 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Career Self-Efficacy Disparities in Underrepresented Biomedical Scientist Trainees ]]> https://biorxiv.org/content/10.1101/2022.10.21.512368v1?rss=1 Chatterjee, D. Jacob, G. A. Sturzenegger Varvayanis, S. Wefes, I. Chalkley, R. Nogueira, A. T. Fuhrmann, C. Varadarajan, J. Hubbard, N. M. Gaines, C. H. Layton, R. L. Chaudhary, S. 2022-10-21 doi:10.1101/2022.10.21.512368 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ The cellular Notch1 Protein Promotes KSHV reactivation in an Rta-dependent manner. ]]> https://biorxiv.org/content/10.1101/2022.10.21.513206v1?rss=1 100 RBP-Jk DNA motifs, we show that none of the four isoforms of activated Notch can productively reactivate the virus from latency in a highly quantitative trans-complementing reporter virus system. Nevertheless, Notch contributed positively to reactivation because broad inhibition of Notch1-4 with gamma secretase inhibitor (GSI) or expression of dominant negative mastermind-like1 (dnMAML1) coactivators severely reduced production of infectious KSHV from Vero cells. Reduction of KSHV production is associated with gene specific reduction of viral transcription in both Vero and PEL cells. Specific inhibition of Notch1 by siRNA partially reduces production of infectious KSHV, and NICD1 forms promoter-specific complexes with viral DNA during reactivation. We conclude that constitutive Notch activity is required for robust production of infectious KSHV, and our results implicate activated Notch1 as a pro-viral member of a MAML1/RBP-Jk/DNA complex during viral reactivation. ImportanceKaposis sarcoma-associated herpesvirus (KSHV) manipulates the host cell oncogenic Notch signaling pathway for viral reactivation from latency and cell pathogenesis. KSHV reactivation requires that the viral protein Rta functionally interacts with RBP-Jk, the DNA binding component of the Notch pathway, and with promoter DNA to drive transcription of productive cycle genes. We show that the Notch pathway is constitutively active during KSHV reactivation and is essential for robust production of infectious virus progeny. Inhibiting Notch during reactivation reduces expression of specific viral genes yet does not affect growth of the host cells. Although Notch cannot reactivate KSHV alone, the requisite expression of Rta reveals a previously unappreciated role for Notch in reactivation. We propose that activated Notch cooperates with Rta in a promoter-specific manner that is partially programmed by Rtas ability to redistribute RBP-Jk DNA binding to the virus during reactivation. ]]> DeCotiis-Mauro, J. Han, S. M. Mello, H. Goyeneche, C. Marchesini-Tovar, G. Jin, L. Bellofatto, V. Lukac, D. M. 2022-10-22 doi:10.1101/2022.10.21.513206 Cold Spring Harbor Laboratory Press 2022-10-22 <![CDATA[ Matters Arising: Re-examining the correlations between codon usage and dihedral bond angles using a population genetics model ]]> https://biorxiv.org/content/10.1101/2022.10.26.513858v1?rss=1 Akeju, O. Cope, A. L. 2022-10-27 doi:10.1101/2022.10.26.513858 Cold Spring Harbor Laboratory Press 2022-10-27 <![CDATA[ Equalizing epigenetically imprinted centromeres in early mammalian embryos ]]> https://biorxiv.org/content/10.1101/2022.10.27.514094v1?rss=1 Manske, G. Jorgensen, K. Ma, B. Aboelenain, M. Tower, C. Chakraborty, S. Ranjan, R. Das, A. Lampson, M. A. Black, B. E. Schindler, K. Chen, X. Hammoud, S. S. 2022-10-28 doi:10.1101/2022.10.27.514094 Cold Spring Harbor Laboratory Press 2022-10-28 <![CDATA[ Mice lacking Ptprd exhibit deficits in goal-directed behavior and female-specific impairments in sensorimotor gating ]]> https://biorxiv.org/content/10.1101/2022.10.28.514214v1?rss=1 Ho, E. Welch, A. Knowles, J. Dulawa, S. C. 2022-10-28 doi:10.1101/2022.10.28.514214 Cold Spring Harbor Laboratory Press 2022-10-28 <![CDATA[ The mesodermal source of fibronectin is required for heart morphogenesis and cardiac outflow tract elongation by regulating cell shape, polarity, and mechanotransduction in the second heart field. ]]> https://biorxiv.org/content/10.1101/2022.10.28.514299v1?rss=1 Arriagada, C. Astrof, S. 2022-10-31 doi:10.1101/2022.10.28.514299 Cold Spring Harbor Laboratory Press 2022-10-31 <![CDATA[ Development and validation of an fMRI-informed EEG model of reward-related ventral striatum activation ]]> https://biorxiv.org/content/10.1101/2022.11.01.514407v1?rss=1 Singer, N. Poker, G. Dunsky, N. Nemni, S. Doron, M. Baker, T. Dagher, A. Zatorre, R. Hendler, T. 2022-11-03 doi:10.1101/2022.11.01.514407 Cold Spring Harbor Laboratory Press 2022-11-03 <![CDATA[ mEnrich-seq: Methylation-guided enrichment sequencing of bacterial taxa of interest from microbiome ]]> https://biorxiv.org/content/10.1101/2022.11.07.515285v1?rss=1 Cao, L. Kong, Y. Fan, Y. Ni, M. Tourancheau, A. Ksiezarek, M. Mead, E. A. Koo, T. Gitman, M. R. Zhang, X.-S. Fang, G. 2022-11-08 doi:10.1101/2022.11.07.515285 Cold Spring Harbor Laboratory Press 2022-11-08 <![CDATA[ Two RNA binding proteins, ADAD2 and RNF17, interact to form novel meiotic germ cell granules required for male fertility ]]> https://biorxiv.org/content/10.1101/2022.11.11.516086v1?rss=1 Chukrallah, L. G. Potgieter, S. M. Snyder, E. 2022-11-12 doi:10.1101/2022.11.11.516086 Cold Spring Harbor Laboratory Press 2022-11-12 <![CDATA[ The tissue-specific autophagic response to nutrient deprivation ]]> https://biorxiv.org/content/10.1101/2022.11.12.516287v1?rss=1 Yang, Y. J. Grosso Jasutkar, H. Griffey, C. J. Kim, K. Melia, T. Dephoure, N. Yamamoto, A. 2022-11-15 doi:10.1101/2022.11.12.516287 Cold Spring Harbor Laboratory Press 2022-11-15 <![CDATA[ Application of a Latent Trait Modeling Method for Missing Data Across Datasets: Guidance on Appropriate Factor Structure ]]> https://biorxiv.org/content/10.1101/2022.11.14.516488v1?rss=1 bartlett, c. Gorham, T. J. Knapp, E. A. Kress, A. M. Klamer, B. Buyske, S. Lau, B. Petrill, S. A. 2022-11-16 doi:10.1101/2022.11.14.516488 Cold Spring Harbor Laboratory Press 2022-11-16 <![CDATA[ Initiation of fibronectin fibrillogenesis is an enzyme-dependent process ]]> https://biorxiv.org/content/10.1101/2022.11.16.516843v1?rss=1 Melamed, S. Zaffryar-Eilot, S. Nadjar-Boger, E. Aviram, R. Zhao, H. Yaseen-Badarne, W. Kalev-Altman, R. Sela-Donenfeld, D. Lewinson, O. Astrof, S. Hasson, P. Wolfenson, H. 2022-11-17 doi:10.1101/2022.11.16.516843 Cold Spring Harbor Laboratory Press 2022-11-17 <![CDATA[ A meiotic midbody structure in mouse oocytes acts as a barrier for nascent translation to ensure developmental competence ]]> https://biorxiv.org/content/10.1101/2022.11.17.516899v1?rss=1 Jung, G. I. Londono-Vasquez, D. Park, S. Skop, A. Balboula, A. Schindler, K. 2022-11-17 doi:10.1101/2022.11.17.516899 Cold Spring Harbor Laboratory Press 2022-11-17 <![CDATA[ Rab11 is essential to pancreas morphogenesis, lumen formation and endocrine mass. ]]> https://biorxiv.org/content/10.1101/2022.11.17.516976v1?rss=1 Barlow, H. R. Htike, Y. Fassetta, L. Ahuja, N. Bierschenk, T. Azizoglu, D. B. Flores, J. Gao, N. Marciano, D. Cleaver, O. 2022-11-18 doi:10.1101/2022.11.17.516976 Cold Spring Harbor Laboratory Press 2022-11-18 <![CDATA[ Computational structure prediction methods enable the systematic identification of oncogenic mutations ]]> https://biorxiv.org/content/10.1101/2022.11.18.517015v1?rss=1 Fu, X. Reglero, C. Swamy, V. Loh, J. W. Khiabanian, H. Albero, R. Forouhar, F. Al Quraishi, M. Ferrando, A. A. Rabadan, R. 2022-11-20 doi:10.1101/2022.11.18.517015 Cold Spring Harbor Laboratory Press 2022-11-20 <![CDATA[ Human endometrial KISS1R inhibits stromal cell decidualization in a manner associated with a reduction in ESR1 levels ]]> https://biorxiv.org/content/10.1101/2022.11.20.517219v1?rss=1 Schaefer, J. Chadchan, S. George, A. Roan, N. Bhattacharya, M. Kommagaini, R. Babwah, A. 2022-11-20 doi:10.1101/2022.11.20.517219 Cold Spring Harbor Laboratory Press 2022-11-20 <![CDATA[ Lipid nanodisc scaffold and size alters the structure of a pentameric ligand-gated ion channel ]]> https://biorxiv.org/content/10.1101/2022.11.20.517256v1?rss=1 Dalal, V. Arcario, M. J. Petroff, J. T. Dietzen, N. M. Rau, M. J. Fitzpatrick, J. A. J. Brannigan, G. Cheng, W. W. L. 2022-11-20 doi:10.1101/2022.11.20.517256 Cold Spring Harbor Laboratory Press 2022-11-20 <![CDATA[ The Drosophila Dopamine 2-like receptor D2R (Dop2R) is required in the Blood Brain Barrier for male courtship ]]> https://biorxiv.org/content/10.1101/2022.11.22.516688v1?rss=1 Love, C. R. Gautam, S. Lama, C. Le, N. H. Dauwalder, B. 2022-11-23 doi:10.1101/2022.11.22.516688 Cold Spring Harbor Laboratory Press 2022-11-23 <![CDATA[ Large-scale signal and noise correlations configure multi-task coding in human brain networks ]]> https://biorxiv.org/content/10.1101/2022.11.23.517699v1?rss=1 Ito, T. Murray, J. D. 2022-11-24 doi:10.1101/2022.11.23.517699 Cold Spring Harbor Laboratory Press 2022-11-24 <![CDATA[ The role of the thalamus in human reinforcement learning ]]> https://biorxiv.org/content/10.1101/2022.11.23.517731v1?rss=1 Collomb-Clerc, A. Gueguen, M. C. Minotti, L. Kahane, P. Navarro, V. Bartolomei, F. Carron, R. Regis, J. Chabardes, S. Palminteri, S. Bastin, J. 2022-11-24 doi:10.1101/2022.11.23.517731 Cold Spring Harbor Laboratory Press 2022-11-24 <![CDATA[ , a prion-form of Cut4/ Apc1, enforces non-Mendelian inheritance of heterochromatin silencing defect in Fission Yeast ]]> https://biorxiv.org/content/10.1101/2022.11.26.517888v1?rss=1 Srivastava, S. Dubey, R. N. Shukla, P. Singh, J. 2022-11-26 doi:10.1101/2022.11.26.517888 Cold Spring Harbor Laboratory Press 2022-11-26 <![CDATA[ Competition between myosin II and βH-Spectrin regulates cytoskeletal tension ]]> https://biorxiv.org/content/10.1101/2022.12.01.518662v1?rss=1 Ibar, C. Chinthalapudi, K. Heissler, S. Irvine, K. D. 2022-12-01 doi:10.1101/2022.12.01.518662 Cold Spring Harbor Laboratory Press 2022-12-01 <![CDATA[ The E2 SUMO-conjugating enzyme UBE2I coordinates the oocyte and zygotic transcriptional programs ]]> https://biorxiv.org/content/10.1101/2022.12.06.519314v1?rss=1 Briley, S. M. Ahmed, A. A. Jiang, P. Hartig, S. M. Schindler, K. Pangas, S. 2022-12-06 doi:10.1101/2022.12.06.519314 Cold Spring Harbor Laboratory Press 2022-12-06 <![CDATA[ Development of a heat-killed fbp1 mutant strain as a therapeutic agent to treat invasive Cryptococcus infection ]]> https://biorxiv.org/content/10.1101/2022.12.06.519380v1?rss=1 Wang, Y. Wang, K. Rivera, A. Xue, C. 2022-12-09 doi:10.1101/2022.12.06.519380 Cold Spring Harbor Laboratory Press 2022-12-09 <![CDATA[ Computing absolute binding affinities by Streamlined Alchemical Free Energy Perturbation ]]> https://biorxiv.org/content/10.1101/2022.12.09.519809v1?rss=1 Santiago-McRae, E. Ebrahimi, M. Sandberg, J. W. Brannigan, G. Henin, J. 2022-12-10 doi:10.1101/2022.12.09.519809 Cold Spring Harbor Laboratory Press 2022-12-10 <![CDATA[ Fibroblast Growth Factor 5 (FGF5) and Its Missense Mutant FGF5-Y174H Underlying Trichomegaly: A Molecular Dynamics Simulation Investigation ]]> https://biorxiv.org/content/10.1101/2022.12.10.519912v1?rss=1 Hoang, S. H. 2022-12-13 doi:10.1101/2022.12.10.519912 Cold Spring Harbor Laboratory Press 2022-12-13 <![CDATA[ Inhibition of early-acting autophagy genes in C. elegans neurons improves protein homeostasis, promotes exopher production, and extends lifespan via the ATG-16.2 WD40 domain ]]> https://biorxiv.org/content/10.1101/2022.12.12.520171v1?rss=1 Yang, Y. Arnold, M. L. Choy, E. H. Lange, C. M. Poon, K. Broussalian, M. Sun, L.-H. Moreno, T. M. Singh, A. Driscoll, M. Kumsta, C. Hansen, M. 2022-12-14 doi:10.1101/2022.12.12.520171 Cold Spring Harbor Laboratory Press 2022-12-14 <![CDATA[ Characterizing habit learning in the human brain at the individual and group levels: a multi-modal MRI study ]]> https://biorxiv.org/content/10.1101/2022.12.12.520188v1?rss=1 Gera, R. Bar Or, M. Tavor, I. Roll, D. Cockburn, J. Barak, S. Tricomi, E. O'Doherty, J. P. Schonberg, T. 2022-12-13 doi:10.1101/2022.12.12.520188 Cold Spring Harbor Laboratory Press 2022-12-13 <![CDATA[ A MTA2-SATB2 chromatin complex restrains colonic plasticity toward small intestine by retaining HNF4A at colonic chromatin ]]> https://biorxiv.org/content/10.1101/2022.12.15.520587v1?rss=1 Gu, W. Huang, X. Singh, P. N. P. Lan, Y. Gomez-Salinero, J. M. Rafii, S. Verzi, M. Shivdasani, R. Zhou, Q. 2022-12-16 doi:10.1101/2022.12.15.520587 Cold Spring Harbor Laboratory Press 2022-12-16 <![CDATA[ The first fossil replete ant worker establishes living food storage in the Eocene ]]> https://biorxiv.org/content/10.1101/2022.12.15.520604v1?rss=1 Sawh, I. Bae, E. Camilo, L. Lanan, M. Lucky, A. Menezes, H. M. Fiorentino, G. Sosiak, C. Khadempour, L. Barden, P. 2022-12-18 doi:10.1101/2022.12.15.520604 Cold Spring Harbor Laboratory Press 2022-12-18 <![CDATA[ Improved humoral immunity and protection against influenza virus infection with a 3D porous biomaterial vaccine ]]> https://biorxiv.org/content/10.1101/2022.12.16.520784v1?rss=1 Miwa, H. Antao, O. Q. Kelly-Scumpia, K. M. Baghdasarian, S. Mayer, D. P. Shang, L. Sanchez, G. M. Archang, M. M. Scumpia, P. O. Weinstein, J. S. Di Carlo, D. 2022-12-17 doi:10.1101/2022.12.16.520784 Cold Spring Harbor Laboratory Press 2022-12-17 <![CDATA[ Automated Workflow for Instant Labeling and Real-Time Monitoring of Monoclonal Antibody N-Glycosylation ]]> https://biorxiv.org/content/10.1101/2022.12.22.521623v1?rss=1 View larger version (37K): org.highwire.dtl.DTLVardef@16cf139org.highwire.dtl.DTLVardef@150db0borg.highwire.dtl.DTLVardef@15cbe36org.highwire.dtl.DTLVardef@1cbdf6a_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Gyorgypal, A. Potter, O. Chaturvedi, A. Powers, D. N. Chundawat, S. 2022-12-22 doi:10.1101/2022.12.22.521623 Cold Spring Harbor Laboratory Press 2022-12-22 <![CDATA[ Conserved NIMA kinases regulate multiple steps of endocytic trafficking ]]> https://biorxiv.org/content/10.1101/2022.12.22.521653v1?rss=1 Joseph, B. B. Naslavsky, N. Binti, S. Conquest, S. Robison, L. Bai, G. Grant, B. D. Caplan, S. Fay, D. 2022-12-22 doi:10.1101/2022.12.22.521653 Cold Spring Harbor Laboratory Press 2022-12-22 <![CDATA[ Predicting alcohol-related memory problems in older adults: A machine learning study with multi-domain features ]]> https://biorxiv.org/content/10.1101/2022.12.30.522330v1?rss=1 Kamarajan, C. Pandey, A. K. Chorlian, D. B. Meyers, J. L. Kinreich, S. Pandey, G. Subbie Saenz de Viteri, S. Zhang, J. Kuang, W. Barr, P. B. Aliev, F. Anokhin, A. P. Plawecki, M. H. Kuperman, S. Almasy, L. Merikangas, A. Brislin, S. J. Bauer, L. Hesselbrock, V. Chan, G. Kramer, J. Lai, D. Hartz, S. Bierut, L. J. McCutcheon, V. V. Bucholz, K. K. Dick, D. M. Schuckit, M. A. Edenberg, H. J. Porjesz, B. 2023-01-02 doi:10.1101/2022.12.30.522330 Cold Spring Harbor Laboratory Press 2023-01-02 <![CDATA[ The Physical Basis of Osmosis ]]> https://biorxiv.org/content/10.1101/2023.01.02.522450v1?rss=1 Manning, G. S. Kay, A. R. 2023-01-04 doi:10.1101/2023.01.02.522450 Cold Spring Harbor Laboratory Press 2023-01-04 <![CDATA[ Tet-dependent 5-hydroxymethyl-Cytosine modification of mRNA regulates the axon guidance genes robo2 and slit in Drosophila ]]> https://biorxiv.org/content/10.1101/2023.01.03.522592v1?rss=1 Singh, B. N. Tran, H. Kramer, J. Kirishenko, E. Changela, N. Wang, F. Feng, Y. Kumar, D. Tu, M. Liang, S. Lan, J. Bizet, M. Fuks, F. Steward, R. 2023-01-07 doi:10.1101/2023.01.03.522592 Cold Spring Harbor Laboratory Press 2023-01-07 <![CDATA[ Behavioral and Neuroanatomical Investigation of Attention Deficit Hyperactivity Disorder Pathogenesis in Juvenile Spontaneously Hypertensive Rats ]]> https://biorxiv.org/content/10.1101/2023.01.04.522787v1?rss=1 Aydin, A. G. Adiguzel, E. 2023-01-04 doi:10.1101/2023.01.04.522787 Cold Spring Harbor Laboratory Press 2023-01-04 <![CDATA[ Temporal Dynamics of Activity in Default Mode Network Suggests a Role in Top-down processing ]]> https://biorxiv.org/content/10.1101/2023.01.08.523152v1?rss=1 Mastrovito, D. Hanson, S. Hanson, C. 2023-01-08 doi:10.1101/2023.01.08.523152 Cold Spring Harbor Laboratory Press 2023-01-08 <![CDATA[ Developmental hearing loss-induced perceptual deficits are rescued by cortical expression of GABAB receptors ]]> https://biorxiv.org/content/10.1101/2023.01.10.523440v1?rss=1 Masri, S. Fair, R. Mowery, T. M. Sanes, D. H. 2023-01-10 doi:10.1101/2023.01.10.523440 Cold Spring Harbor Laboratory Press 2023-01-10 <![CDATA[ A Network Pharmacology Approach to Elucidate the Anti-inflammatory Effects of Ellagic Acid ]]> https://biorxiv.org/content/10.1101/2023.01.10.523505v1?rss=1 Hoang, S. H. 2023-01-12 doi:10.1101/2023.01.10.523505 Cold Spring Harbor Laboratory Press 2023-01-12 <![CDATA[ TGFB1 Induces Fetal Reprogramming and Enhances Intestinal Regeneration ]]> https://biorxiv.org/content/10.1101/2023.01.13.523825v1?rss=1 View larger version (54K): org.highwire.dtl.DTLVardef@147f3b7org.highwire.dtl.DTLVardef@d1a64dorg.highwire.dtl.DTLVardef@1fd0dc0org.highwire.dtl.DTLVardef@91f7d8_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Chen, L. Dupre, A. Qiu, X. Pellon-Cardenas, O. Walton, K. D. Wang, J. Perekatt, A. O. Hu, W. Spence, J. R. Verzi, M. P. 2023-01-13 doi:10.1101/2023.01.13.523825 Cold Spring Harbor Laboratory Press 2023-01-13 <![CDATA[ Integrated ACMG approved genes and ICD codes for the translational research and precision medicine ]]> https://biorxiv.org/content/10.1101/2023.01.14.524076v1?rss=1 Wable, R. Nair, A. S. Pappu, A. Pierre-Louis, W. Abdelhalim, H. Patel, K. Mendhe, D. Bolla, S. Mittal, S. Ahmed, Z. 2023-01-17 doi:10.1101/2023.01.14.524076 Cold Spring Harbor Laboratory Press 2023-01-17 <![CDATA[ Defining the contribution of microRNA-specific slicing Argonautes in animals ]]> https://biorxiv.org/content/10.1101/2023.01.19.524781v1?rss=1 Pal, A. Vasudevan, V. Houle, F. Lantin, M. Maniates, K. A. Quevillon Huberdeau, M. Abbott, A. Simard, M. J. 2023-01-20 doi:10.1101/2023.01.19.524781 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ Gene expression of macaques infected with malaria species of zoonotic concern ]]> https://biorxiv.org/content/10.1101/2023.01.19.524806v1?rss=1 Bergey, C. M. Trujillo, A. E. 2023-01-20 doi:10.1101/2023.01.19.524806 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ Low frequency optogenetic deep brain stimulation of nucleus accumbens dopamine D1 or D2 receptor-containing neurons attenuates cocaine seeking selectively in male rats in part by reversing synaptic plasticity deficits ]]> https://biorxiv.org/content/10.1101/2023.01.23.524956v1?rss=1 100 Hz). In preclinical models, 160 Hz stimulation of the nucleus accumbens in rodents prevents relapse of drug seeking. However, the ability of varied frequencies of accumbens DBS to attenuate drug seeking, and the neuronal subtype specificity of this effect, is unclear. MethodsThe present study examined the effect of DBS in the nucleus accumbens on neuronal plasticity and cocaine-primed reinstatement of cocaine seeking behavior in rats. ResultsElectrical DBS of the accumbens shell attenuated cocaine primed reinstatement across a range of frequencies in male rats, including as low as 12 Hz. The majority of nucleus accumbens neurons are medium spiny neurons (MSNs), which can be differentiated in terms of projections and effects on cocaine-related behaviors by expression of dopamine D1 receptors (D1DRs) or D2DRs. In slice electrophysiology experiments, 12 Hz electrical stimulation evoked long term potentiation (LTP) in eYFP labeled D1DR-MSNs and D2DR-MSNs from cocaine naive male and female rats. However, in rats that self-administered cocaine and underwent extinction training, a paradigm identical to our reinstatement experiments, electrical DBS only elicited LTP in D2DR-MSNs from male rats; this effect was replicated by optical stimulation in rats expressing Cre-dependent ChR2 in D2DR-MSNs. Low-frequency optogenetic-DBS in D1DR-containing or D2DR-containing neurons attenuated cocaine-primed reinstatement of cocaine seeking in male but not female rats. ConclusionsThese results suggest that administering DBS in the nucleus accumbens shell at lower frequencies effectively, but sex-specifically, suppresses cocaine craving, perhaps in part by reversing synaptic plasticity deficits selectively in D2DR-MSNs. ]]> Swinford-Jackson, S. E. Rich, M. T. Huffman, P. J. Knouse, M. C. Thomas, A. S. Mankame, S. Worobey, S. J. Pierce, R. C. 2023-01-23 doi:10.1101/2023.01.23.524956 Cold Spring Harbor Laboratory Press 2023-01-23 <![CDATA[ Atypical cognitive training-induced learning and brain plasticity and their relation to insistence on sameness in children with autism ]]> https://biorxiv.org/content/10.1101/2023.01.25.525594v1?rss=1 Liu, J. Chang, H. Abrams, D. A. Kang, J. B. Chen, L. Rosenberg-Lee, M. Menon, V. 2023-01-26 doi:10.1101/2023.01.25.525594 Cold Spring Harbor Laboratory Press 2023-01-26 <![CDATA[ Cross-species transcriptomic analysis identifies mitochondrial dysregulation as a functional consequence of the schizophrenia-associated 3q29 deletion ]]> https://biorxiv.org/content/10.1101/2023.01.27.525748v1?rss=1 40). Understanding the impact of the 3q29 deletion (3q29Del) on the developing CNS may therefore lead to insights about the pathobiology of schizophrenia. To gain clues about the molecular and cellular perturbations caused by the 3q29 deletion, we interrogated transcriptomic effects in two experimental model systems with complementary advantages: isogenic human forebrain cortical organoids and isocortex from the 3q29Del mouse model. We first created isogenic lines by engineering the full 3q29Del into an induced pluripotent stem cell line from a neurotypical individual. We profiled transcriptomes from isogenic cortical organoids that were aged for 2 months and 12 months, as well as day p7 perinatal mouse isocortex, all at single cell resolution. Differential expression analysis by genotype in each cell-type cluster revealed that more than half of the differentially expressed genes identified in mouse cortex were also differentially expressed in human cortical organoids, and strong correlations were observed in mouse-human differential gene expression across most major cell-types. We systematically filtered differentially expressed genes to identify changes occurring in both model systems. Pathway analysis on this filtered gene set implicated dysregulation of mitochondrial function and energy metabolism, although the direction of the effect was dependent on developmental timepoint. Transcriptomic changes were validated at the protein level by analysis of oxidative phosphorylation protein complexes in mouse brain tissue. Assays of mitochondrial function in human heterologous cells further confirmed robust mitochondrial dysregulation in 3q29Del cells, and these effects are partially recapitulated by ablation of the 3q29Del gene PAK2. Taken together these data indicate that metabolic disruption is associated with 3q29Del and is conserved across species. These results converge with data from other rare SCZ-associated variants as well as idiopathic schizophrenia, suggesting that mitochondrial dysfunction may be a significant but overlooked contributing factor to the development of psychotic disorders. This cross-species scRNA-seq analysis of the SCZ-associated 3q29 deletion reveals that this copy number variant may produce early and persistent changes in cellular metabolism that are relevant to human neurodevelopment. ]]> Purcell, R. H. Sefik, E. Werner, E. King, A. T. Mosley, T. J. Merritt-Garza, M. E. Chopra, P. McEachin, Z. T. Karne, S. Raj, N. Tilahun, K. Robinette, M. Warren, S. T. Wen, Z. Faundez, V. Sloan, S. A. Bassell, G. J. Mulle, J. G. 2023-01-28 doi:10.1101/2023.01.27.525748 Cold Spring Harbor Laboratory Press 2023-01-28 <![CDATA[ A comprehensive survey of coronaviral main protease active site diversity in 3D: Identifying and analyzing drug discovery targets in search of broad specificity inhibitors for the next coronavirus pandemic ]]> https://biorxiv.org/content/10.1101/2023.01.30.526101v1?rss=1 Lubin, J. H. Martinusen, S. G. Zardecki, C. Olivas, C. Bacorn, M. Balogun, M. Slaton, E. W. Wu, A. W. Sakeer, S. Hudson, B. P. Denard, C. Burley, S. K. Khare, S. D. 2023-01-31 doi:10.1101/2023.01.30.526101 Cold Spring Harbor Laboratory Press 2023-01-31 <![CDATA[ Physical contacts between sparse biofilms promote plasmid transfer and generate functional novelty ]]> https://biorxiv.org/content/10.1101/2023.02.01.526699v1?rss=1 Ramoneda, J. Ma, Y. Schmidt, J. Manhart, M. Angst, D. C. Johnson, D. R. 2023-02-01 doi:10.1101/2023.02.01.526699 Cold Spring Harbor Laboratory Press 2023-02-01 <![CDATA[ Imaging Architecture of Granulomas Induced by Mycobacterium tuberculosis Infections with Single-Molecule FISH ]]> https://biorxiv.org/content/10.1101/2023.02.02.526702v1?rss=1 Kumar, R. Kolloli, A. Subbian, S. Kaushal, D. Shi, L. Tyagi, S. 2023-02-03 doi:10.1101/2023.02.02.526702 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Distinct Aurora B pools at the inner centromere and kinetochore have different contributions to meiotic and mitotic chromosome segregation ]]> https://biorxiv.org/content/10.1101/2023.02.05.527197v1?rss=1 Cairo, G. Greiwe, C. Jung, G. I. Blengini, C. Schindler, K. Lacefield, S. 2023-02-05 doi:10.1101/2023.02.05.527197 Cold Spring Harbor Laboratory Press 2023-02-05 <![CDATA[ A SARS-CoV-2 vaccine designed for manufacturability results in unexpected potency and non-waning humoral response ]]> https://biorxiv.org/content/10.1101/2023.02.06.527376v1?rss=1 Campbell, E. Dobkin, J. Osorio, L. Ramasamy, S. Kumar, R. SantAngelo, D. B. Subbian, S. Denzin, L. K. Anderson, S. 2023-02-07 doi:10.1101/2023.02.06.527376 Cold Spring Harbor Laboratory Press 2023-02-07 <![CDATA[ Characterization of microsatellite markers for the duckweed Spirodela polyrhiza and Lemna minor tested on samples from Europe or the United States of America. ]]> https://biorxiv.org/content/10.1101/2023.02.15.528655v1?rss=1 Kerestetter, J. E. Reid, A. L. Armstrong, J. T. Zallek, T. A. Hobble, T. T. Turcotte, M. M. 2023-02-15 doi:10.1101/2023.02.15.528655 Cold Spring Harbor Laboratory Press 2023-02-15 <![CDATA[ Linking genotypic and phenotypic changes in the LTEE using metabolomics ]]> https://biorxiv.org/content/10.1101/2023.02.15.528756v1?rss=1 Favate, J. S. Skalenko, K. S. Chiles, E. Su, X. Yadavalli, S. S. Shah, P. 2023-02-16 doi:10.1101/2023.02.15.528756 Cold Spring Harbor Laboratory Press 2023-02-16 <![CDATA[ 3D Microcapsules for Human Bone Marrow Derived Mesenchymal Stem Cell Biomanufacturing in a Vertical-Wheel Bioreactor ]]> https://biorxiv.org/content/10.1101/2023.02.16.528656v1?rss=1 Teryek, M. Jadhav, P. Bento, R. Parekkadan, B. 2023-02-16 doi:10.1101/2023.02.16.528656 Cold Spring Harbor Laboratory Press 2023-02-16 <![CDATA[ Prediction and Design of Protease Enzyme Specificity Using a Structure-Aware Graph Convolutional Network ]]> https://biorxiv.org/content/10.1101/2023.02.16.528728v1?rss=1 Lu, C. Lubin, J. H. Sarma, V. S. Stentz, S. Z. Wang, G. Wang, S. Khare, S. D. 2023-02-16 doi:10.1101/2023.02.16.528728 Cold Spring Harbor Laboratory Press 2023-02-16 <![CDATA[ Citizenship status and career self-efficacy: An intersectional study of biomedical trainees in the United States ]]> https://biorxiv.org/content/10.1101/2023.02.19.526477v1?rss=1 Chatterjee, D. Nogueira, A. T. Wefes, I. Chalkley, R. Sturzenegger Varvayanis, S. Fuhrmann, C. N. Varadarajan, J. Jacob, G. A. Gaines, C. H. Hubbard, N. M. Chaudhary, S. Layton, R. L. 2023-02-21 doi:10.1101/2023.02.19.526477 Cold Spring Harbor Laboratory Press 2023-02-21 <![CDATA[ Evolutionary changes in germ granule mRNA content are driven by multiple mechanisms in Drosophila ]]> https://biorxiv.org/content/10.1101/2023.02.21.529147v1?rss=1 Doyle, D. A. Burian, F. N. Aharoni, B. Klinder, A. J. Menzel, M. M. Nifras, G. C. C. Shabazz-Henry, A. L. Ulrich Palma, B. Hidalgo, G. A. Sottolano, C. J. Ortega, B. M. Niepielko, M. G. 2023-02-21 doi:10.1101/2023.02.21.529147 Cold Spring Harbor Laboratory Press 2023-02-21 <![CDATA[ Active zone protein SYD-2/Liprin-α acts downstream of LRK-1/LRRK2 to regulate polarized trafficking of synaptic vesicle precursors through clathrin adaptor protein complexes ]]> https://biorxiv.org/content/10.1101/2023.02.26.530068v1?rss=1 Nadiminti, S. S. P. Dixit, S. B. Ratnakaran, N. Hegde, S. Swords, S. Grant, B. D. Koushika, S. P. 2023-02-26 doi:10.1101/2023.02.26.530068 Cold Spring Harbor Laboratory Press 2023-02-26 <![CDATA[ Genetic influences vary by age and sex: Trajectories of the association of cholinergic system variants and theta band event related oscillations ]]> https://biorxiv.org/content/10.1101/2023.02.27.530318v1?rss=1 Chorlian, D. B. Meyers, J. L. Manz, N. Zhang, J. Kamarajan, C. Pandey, A. Wang, J.-C. Plawecki, M. Edenberg, H. Goate, A. Tischfield, J. Porjesz, B. 2023-02-28 doi:10.1101/2023.02.27.530318 Cold Spring Harbor Laboratory Press 2023-02-28 <![CDATA[ A Conserved Requirement for RME-8/DNAJC13 in Neuronal Autolysosome Reformation ]]> https://biorxiv.org/content/10.1101/2023.02.27.530319v1?rss=1 Swords, S. B. Jia, N. Norris, A. Modi, J. Cai, Q. Grant, B. D. 2023-02-28 doi:10.1101/2023.02.27.530319 Cold Spring Harbor Laboratory Press 2023-02-28 <![CDATA[ Identification of novel buffering mechanisms in aortic arch artery development and congenital heart disease. ]]> https://biorxiv.org/content/10.1101/2023.03.02.530833v1?rss=1 Ramirez, A. Degenhardt, K. Astrof, S. 2023-03-02 doi:10.1101/2023.03.02.530833 Cold Spring Harbor Laboratory Press 2023-03-02 <![CDATA[ Expanding the molecular language of protein liquid-liquid phase separation ]]> https://biorxiv.org/content/10.1101/2023.03.02.530853v1?rss=1 Rekhi, S. Garcia, C. G. Barai, M. Rizuan, A. Schuster, B. S. Kiick, K. L. Mittal, J. 2023-03-03 doi:10.1101/2023.03.02.530853 Cold Spring Harbor Laboratory Press 2023-03-03 <![CDATA[ Feature selection followed by a residuals-based normalization simplifies and improves single-cell gene expression analysis ]]> https://biorxiv.org/content/10.1101/2023.03.02.530891v1?rss=1 Singh, A. Khiabanian, H. 2023-03-03 doi:10.1101/2023.03.02.530891 Cold Spring Harbor Laboratory Press 2023-03-03 <![CDATA[ Requirement of GrgA for Chlamydia infectious progeny production ]]> https://biorxiv.org/content/10.1101/2023.03.09.531986v1?rss=1 Lu, B. Wang, Y. Wurihan, W. Yeung, S. Fondell, J. Wu, X. Fan, H. 2023-03-10 doi:10.1101/2023.03.09.531986 Cold Spring Harbor Laboratory Press 2023-03-10 <![CDATA[ B12-dependent virioplankton demonstrate interseasonal dynamics and associate with a diversity of pelagic bacterioplankton ]]> https://biorxiv.org/content/10.1101/2023.03.13.532061v1?rss=1 Wu, L.-Y. Piedade, G. J. Moore, R. M. Harrison, A. O. Martins, A. M. Bidle, K. D. Polson, S. W. Sakowski, E. Nissimov, J. I. Dums, J. T. Ferrell, B. D. Wommack, K. E. 2023-03-14 doi:10.1101/2023.03.13.532061 Cold Spring Harbor Laboratory Press 2023-03-14 <![CDATA[ SMAD4: A Critical Regulator of Cardiac Neural Crest Cell Fate and Vascular Smooth Muscle Differentiation ]]> https://biorxiv.org/content/10.1101/2023.03.14.532676v1?rss=1 Alexander, B. Zhao, H. Astrof, S. 2023-03-15 doi:10.1101/2023.03.14.532676 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ Opposing, spatially-determined epigenetic forces impose restrictions on stochastic olfactory receptor choice ]]> https://biorxiv.org/content/10.1101/2023.03.15.532726v1?rss=1 Bashkirova, E. Klimpert, N. Pourmorady, A. Monahan, K. Campbell, C. Osinski, J. Tan, L. Schieren, I. Stecky, R. Barnea, G. Xie, X. S. Abdus-Saboor, I. Shykind, B. Marlin, B. J. Gronostajski, R. Fleischmann, A. Lomvardas, S. 2023-03-15 doi:10.1101/2023.03.15.532726 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ Predatory Bacteria can Reduce Pseudomonas aeruginosa Induced Corneal Perforation and Proliferation in a Rabbit Keratitis Model ]]> https://biorxiv.org/content/10.1101/2023.03.15.532777v1?rss=1 Romanowski, E. G. Stella, N. A. Brazile, B. L. Lathrop, K. L. Franks, J. M. Sigal, I. A. Kim, T. Elsayed, M. Kadouri, D. E. Shanks, R. M. Q. 2023-03-15 doi:10.1101/2023.03.15.532777 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ Guidelines for Evaluating the Comparability of Down-Sampled GWAS Summary Statistics ]]> https://biorxiv.org/content/10.1101/2023.03.21.533641v1?rss=1 Williams, C. M. Poore, H. Tanksley, P. T. Kweon, H. Courchesne-Krak, N. S. Londono-Correa, D. Mallard, T. T. Barr, P. Koellinger, P. D. Waldman, I. Sanchez-Roige, S. Harden, K. P. Palmer, A. A. Dick, D. D. Linner, R. K. 2023-03-24 doi:10.1101/2023.03.21.533641 Cold Spring Harbor Laboratory Press 2023-03-24 <![CDATA[ Upregulated GIRK2 counteracts ethanol-induced changes in excitability and respiration in human neurons ]]> https://biorxiv.org/content/10.1101/2023.03.22.533236v1?rss=1 Prytkova, I. A. Liu, Y. Fernando, M. B. Gameiro-Ros, I. Popova, D. Kamarajan, C. Xuei, X. Chorlian, D. B. Edenberg, H. J. Tischfield, J. A. Porjesz, B. Pang, Z. P. Hart, R. P. Goate, A. M. Slesinger, P. A. 2023-03-23 doi:10.1101/2023.03.22.533236 Cold Spring Harbor Laboratory Press 2023-03-23 <![CDATA[ Total RNA sequencing reveals gene expression and microbial alterations shared by oral pre-malignant lesions and cancer. ]]> https://biorxiv.org/content/10.1101/2023.03.24.534064v1?rss=1 View larger version (27K): org.highwire.dtl.DTLVardef@86cf7org.highwire.dtl.DTLVardef@129e6d1org.highwire.dtl.DTLVardef@1f0ae31org.highwire.dtl.DTLVardef@3c4d67_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Khan, M. M. Frustino, J. Villa, A. Nguyen, B.-C. Woo, S.-B. Johnson, W. E. Varelas, X. Kukuruzinska, M. Monti, S. 2023-03-24 doi:10.1101/2023.03.24.534064 Cold Spring Harbor Laboratory Press 2023-03-24 <![CDATA[ Massive genome reduction occurred prior to the origin of coral algal symbionts ]]> https://biorxiv.org/content/10.1101/2023.03.24.534093v1?rss=1 Shah, S. Dougan, K. E. Chen, Y. Lo, R. Laird, G. Fortuin, M. D. A. Rai, S. K. Murigneux, V. Bellantuono, A. J. Rodriguez-Lanetty, M. Bhattacharya, D. Chan, C. X. 2023-03-25 doi:10.1101/2023.03.24.534093 Cold Spring Harbor Laboratory Press 2023-03-25 <![CDATA[ Therapeutic targeting of ACLY in T-ALL in vivo ]]> https://biorxiv.org/content/10.1101/2023.03.27.534395v1?rss=1 da Silva-Diz, V. Singh, A. Lancho, O. Aleksandrova, M. Mandleywala, K. Nunes, P. R. Khatun, J. Kim, O. Chiles, E. Su, X. Khiabanian, H. Wellen, K. Herranz, D. 2023-03-28 doi:10.1101/2023.03.27.534395 Cold Spring Harbor Laboratory Press 2023-03-28 <![CDATA[ Cultured Mesenchymal Cells from Nasal Turbinate as a Cellular Model of the Neurodevelopmental Component of Schizophrenia Etiology ]]> https://biorxiv.org/content/10.1101/2023.03.28.534295v1?rss=1 Tung, V. S. K. Mathews, F. Boruk, M. Suppa, G. Foronjy, R. Pato, M. Pato, C. Knowles, J. A. Evgrafov, O. V. 2023-03-29 doi:10.1101/2023.03.28.534295 Cold Spring Harbor Laboratory Press 2023-03-29 <![CDATA[ Intraspecies genomic divergence of coral algal symbionts shaped by gene duplication ]]> https://biorxiv.org/content/10.1101/2023.03.28.534646v1?rss=1 Shah, S. Dougan, K. E. Chen, Y. Bhattacharya, D. Chan, C. X. 2023-03-29 doi:10.1101/2023.03.28.534646 Cold Spring Harbor Laboratory Press 2023-03-29 <![CDATA[ Untangling the mechanisms of pulmonary hypertension-induced right ventricular stiffening in a large animal model ]]> https://biorxiv.org/content/10.1101/2023.04.03.535491v1?rss=1 Kakaletsis, S. Malinowski, M. Mathur, M. Sugerman, G. P. Luci, J. J. Snider, C. Jazwiec, T. Bersi, M. R. Timek, T. A. Rausch, M. K. 2023-04-06 doi:10.1101/2023.04.03.535491 Cold Spring Harbor Laboratory Press 2023-04-06 <![CDATA[ METTL3 is essential for small intestinal epithelial proliferation via regulation of growth factor signaling including KRAS ]]> https://biorxiv.org/content/10.1101/2023.04.06.535853v1?rss=1 Danan, C. H. Naughton, K. E. Hayer, K. E. Vellapan, S. McMillan, E. A. Zhou, Y. Matsuda, R. Nettleford, S. K. Katada, K. Parham, L. R. Ma, X. Chowdhury, A. Wilkins, B. J. Shah, P. Weitzman, M. D. Hamilton, K. E. 2023-04-06 doi:10.1101/2023.04.06.535853 Cold Spring Harbor Laboratory Press 2023-04-06 <![CDATA[ Reply to Barton et al: signatures of natural selection during the Black Death ]]> https://biorxiv.org/content/10.1101/2023.04.06.535944v1?rss=1 Vilgalys, T. P. Klunk, J. Demeure, C. E. Cheng, X. Shiratori, M. Madej, J. Beau, R. Elli, D. Patino, M. I. Redfern, R. DeWitte, S. N. Gamble, J. Boldsen, J. L. Carmichael, A. Varlik, N. Eaton, K. Grenier, J.-C. Golding, G. B. Devault, A. Rouillard, J.-M. Yotova, V. Sindeaux, R. Ye, C. J. Bikaran, M. Dumaine, A. Brinkworth, J. F. Missiakas, D. Rouleau, G. A. Steinrücken, M. Pizarro-Cerda, J. Poinar, H. Barreiro, L. B. 2023-04-07 doi:10.1101/2023.04.06.535944 Cold Spring Harbor Laboratory Press 2023-04-07 <![CDATA[ Ticks (Acari: Ixodida) on synanthropic small and medium-sized mammals in areas of the northeastern United States infested with the Asian longhorned tick, Haemaphysalis longicornis ]]> https://biorxiv.org/content/10.1101/2023.04.07.536052v1?rss=1 Ferreira, F. C. Gonzalez, J. Milholland, M. T. Tung, G. A. Fonseca, D. M. 2023-04-08 doi:10.1101/2023.04.07.536052 Cold Spring Harbor Laboratory Press 2023-04-08 <![CDATA[ Decoupling of evolutionary changes in mRNA and protein levels ]]> https://biorxiv.org/content/10.1101/2023.04.08.536110v1?rss=1 Jiang, D. Cope, A. L. Zhang, J. Pennell, M. 2023-04-08 doi:10.1101/2023.04.08.536110 Cold Spring Harbor Laboratory Press 2023-04-08 <![CDATA[ ME-Bayes SL: Enhanced Bayesian Polygenic Risk Prediction Leveraging Information across Multiple Ancestry Groups ]]> https://biorxiv.org/content/10.1101/2023.04.12.536510v1?rss=1 Jin, J. Zhan, J. Zhang, J. Zhao, R. O'Connell, J. Jiang, Y. 23andMe Research Team, Buyske, S. Gignoux, C. R. Haiman, C. A. Kenny, E. Kooperberg, C. North, K. E. Koelsch, B. L. Wojcik, G. L. Zhang, H. Chatterjee, N. 2023-04-13 doi:10.1101/2023.04.12.536510 Cold Spring Harbor Laboratory Press 2023-04-13 <![CDATA[ Building the Next Generation Workforce: Why We Need Science Policy Training at the Undergraduate Level ]]> https://biorxiv.org/content/10.1101/2023.04.15.537026v1?rss=1 Bogard, G. Saybolt, E. Castro-Faix, M. Bankston, A. 2023-04-17 doi:10.1101/2023.04.15.537026 Cold Spring Harbor Laboratory Press 2023-04-17 <![CDATA[ Molecular physiology of Antarctic diatom natural assemblages reveals multiple strategies contributing to their ecological success ]]> https://biorxiv.org/content/10.1101/2023.04.19.537459v1?rss=1 Moreno, C. M. Bernish, M. Meyer, M. G. Li, Z. Waite, N. Cohen, N. R. Schofield, O. Marchetti, A. 2023-04-20 doi:10.1101/2023.04.19.537459 Cold Spring Harbor Laboratory Press 2023-04-20 <![CDATA[ Saracatinib synergizes with enzalutamide to downregulate androgen receptor activity in castration resistant prostate cancer ]]> https://biorxiv.org/content/10.1101/2023.04.22.537922v1?rss=1 White, R. E. Bannister, M. Day, A. Bergom, H. E. Tan, V. M. Hwang, J. Nguyen, H. D. Drake, J. 2023-04-25 doi:10.1101/2023.04.22.537922 Cold Spring Harbor Laboratory Press 2023-04-25 <![CDATA[ Protective effects of polyphenol-rich extracts against neurotoxicity elicited by paraquat or rotenone in cellular models of Parkinson's disease ]]> https://biorxiv.org/content/10.1101/2023.04.26.538474v1?rss=1 Tambe, M. A. Jacquet, A. d. R. Strathearn, K. E. Yousef, G. G. Grace, M. H. Ferruzzi, M. G. Wu, Q. Simon, J. E. Lila, M. A. Rochet, J.-C. 2023-04-27 doi:10.1101/2023.04.26.538474 Cold Spring Harbor Laboratory Press 2023-04-27 <![CDATA[ Tet Controls Axon Guidance in Early Brain Development through Glutamatergic Signaling ]]> https://biorxiv.org/content/10.1101/2023.05.02.539069v1?rss=1 Tran, H. Le, L. Singh, B. N. Kramer, J. Steward, R. 2023-05-02 doi:10.1101/2023.05.02.539069 Cold Spring Harbor Laboratory Press 2023-05-02 <![CDATA[ Single-cell Mayo Map (scMayoMap): an easy-to-use tool for cell type annotation in single-cell RNA-sequencing data analysis ]]> https://biorxiv.org/content/10.1101/2023.05.03.538463v1?rss=1 Yang, L. Ng, Y. E. Sun, H. Li, Y. Lucas, C. C. S. LeBrasseur, N. K. Chen, J. Zhang, X. 2023-05-04 doi:10.1101/2023.05.03.538463 Cold Spring Harbor Laboratory Press 2023-05-04 <![CDATA[ Broad-Spectrum Heavily Mutated Monoclonal Antibody Isolated from COVID-19 Convalescent Vaccinee with Capacity to Neutralize SARS-CoV2 Variants Ranging from B.1 to BQ.1.1 ]]> https://biorxiv.org/content/10.1101/2023.05.04.539267v1?rss=1 View larger version (45K): org.highwire.dtl.DTLVardef@f7dab8org.highwire.dtl.DTLVardef@388861org.highwire.dtl.DTLVardef@181a7c7org.highwire.dtl.DTLVardef@12e02cb_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG In briefChoudhary et al. have isolated and characterized Acovimab, a broadly neutralizing RBM-specific human monoclonal antibody with a relatively high level of somatic hypermutation, which potently neutralizes SARS-CoV2 variants ranging from WuhanB.1 to OmicronBQ.1.1, but not the XBB.1.5 variant. Acovimab also possesses strong synergistic neutralizing activity against some Omicron variants when combined with Sotrovimab. Polyclonal plasma antibodies from COVID-19 vaccinees who had recovered from SARS-CoV2 infection were shown to possess low neutralizing titers of antibodies against conserved RBD targets of CoV2 variants including XBB.1.5, which also synergistically neutralize with Sotrovimab against this variant. SummaryThe increasing prevalence of the highly antibody-evasive Omicron sublineages increases the risk of breakthrough infections and leaves high-risk and vulnerable immunocompromised individuals with no effective options for prophylactic or therapeutic antibody treatments. Here, we report a heavily mutated anti-RBD monoclonal antibody, Acovimab, directed against a site in the receptor-binding motif (RBM) region of the CoV2 receptor-binding domain (RBD), that possesses very broad and highly potent neutralizing activity against CoV2 variants, including many Omicron variants. This antibody is derived from the IGHV1-58*01 germline sequence and possesses a relatively high level of mutation (15.5% of the VH aa sequence), which is unusual for anti-RBD antibodies. Neutralizing activity was very potent (IC50s range of 1-9 ng/ml) for early Omicron subvariants that possess an unmutated F486 residue and is retained but less potent (IC50s of 200-650 ng/ml) for more resistant Omicron subvariants which contain the F486V mutation (BA4/5, BA4.6, and BQ1.1), but is lost for the later ultra-resistant variants that contain F486S (XBB) or F486P (XBB.1.5) mutations. Based on these specificities, it is predicted that Acovimab by itself should protect against CoV2 infections other than those caused by the XBB/XBB.1.5 family. Acovimab also shows strong synergy in neutralization when combined with Sotrovimab, which neutralizes all Omicron variants, including XBB.1.5. Plasma from subjects with hybrid immunity (induced by vaccination + infection) possessed low levels of XBB.1.5 RBM-targeting plasma-neutralizing antibodies, and these also neutralized synergistically when combined with Sotrovimab. These results suggest potentially novel immunotherapeutic options for treating most of the CoV2 variants responsible for current infections. ]]> Choudhary, A. K. Calianese, D. Honnen, W. Kolloli, A. Dikdan, R. J. Jaijyan, D. Song, G. Capozzola, T. Akkaraju, V. Mattappallil, A. Rosania, A. Khan, S. Lerman, M. Afzal, N. Subbian, S. Chou, T. C. Andrabi, R. Burton, D. Pinter, A. 2023-05-04 doi:10.1101/2023.05.04.539267 Cold Spring Harbor Laboratory Press 2023-05-04 <![CDATA[ Calcium-triggered DNA-mediated membrane fusion in synthetic cells ]]> https://biorxiv.org/content/10.1101/2023.05.06.539684v1?rss=1 Hsu, Y.-Y. Chen, S. J. Bernal-Chanchavac, J. Moghimianavval, H. Stephanopoulos, N. Liu, A. P. 2023-05-06 doi:10.1101/2023.05.06.539684 Cold Spring Harbor Laboratory Press 2023-05-06 <![CDATA[ Whole Transcriptome and Functional Analyses Identify Novel Genes Involved in Meiosis and Fertility in Drosophila melanogaster ]]> https://biorxiv.org/content/10.1101/2023.05.12.540472v1?rss=1 Sun, S. Defosse, T. Boyd, A. Sop, J. Verderose, F. Surray, D. Aziz, M. Howland, M. Wu, S. Changela, N. Jang, J. Schindler, K. Xing, J. McKim, K. 2023-05-14 doi:10.1101/2023.05.12.540472 Cold Spring Harbor Laboratory Press 2023-05-14 <![CDATA[ Guild-level response of the gut microbiota to isocaloric time-restricted feeding in high-fat diet-fed mice ]]> https://biorxiv.org/content/10.1101/2023.05.23.541832v1?rss=1 Ghosh, S. Li, Y. Yang, X. Wu, G. Zhang, C. Zhao, L. 2023-05-23 doi:10.1101/2023.05.23.541832 Cold Spring Harbor Laboratory Press 2023-05-23 <![CDATA[ Host subversion of bacterial metallophore usage drives copper intoxication ]]> https://biorxiv.org/content/10.1101/2023.05.30.542972v1?rss=1 Hossain, S. Morey, J. R. Neville, S. L. Ganio, K. Radin, J. N. Norambuena, J. Boyd, J. M. McDevitt, C. A. Kehl-Fie, T. E. 2023-05-31 doi:10.1101/2023.05.30.542972 Cold Spring Harbor Laboratory Press 2023-05-31 <![CDATA[ Capture Efficiency Of Long-Adapter Single-Strand Oligonucleotide Probe Libraries ]]> https://biorxiv.org/content/10.1101/2023.06.02.543477v1?rss=1 Chkaiban, L. Tosi, L. Parekkadan, B. 2023-06-06 doi:10.1101/2023.06.02.543477 Cold Spring Harbor Laboratory Press 2023-06-06 <![CDATA[ Heterogeneity of foam cell biogenesis across diseases ]]> https://biorxiv.org/content/10.1101/2023.06.08.542766v1?rss=1 Guerrini, V. Prideaux, B. Khan, R. Subbian, S. Wang, Y. Sadimin, E. Pawar, S. Ukey, R. Singer, E. A. Xue, C. Gennaro, M. L. 2023-06-08 doi:10.1101/2023.06.08.542766 Cold Spring Harbor Laboratory Press 2023-06-08 <![CDATA[ Quorum-sensing agr system of Staphylococcus aureus primes gene expression for protection from lethal oxidative stress ]]> https://biorxiv.org/content/10.1101/2023.06.08.544038v1?rss=1 Shopsin, B. Podkowik, M. Perault, A. I. Putzel, G. Pountain, A. Kim, J. DuMont, A. Zwack, E. Ulrich, R. J. Karagounis, T. K. Zhou, C. Haag, A. F. Shenderovich, J. Wasserman, G. A. Kwon, J. Chen, J. Richardson, A. R. Weiser, J. N. Nowosad, C. R. Lun, D. S. Zhao, X. Parker, D. Pironti, A. Drlica, K. N. Yanai, I. Torres, V. J. 2023-06-08 doi:10.1101/2023.06.08.544038 Cold Spring Harbor Laboratory Press 2023-06-08 <![CDATA[ Neurobehavioural Correlates of Obesity are Largely Heritable ]]> https://biorxiv.org/content/10.1101/204917v1?rss=1 Vainik, U. Baker, T. B. Alanis, J. C. G. Dadar, M. Michaud, A. Misic, B. Zeighami, Y. Zhang, Y. Collins, D. L. Dagher, A. 2017-10-18 doi:10.1101/204917 Cold Spring Harbor Laboratory Press 2017-10-18 <![CDATA[ Mapping the human brain’s cortical-subcortical functional network organization ]]> https://biorxiv.org/content/10.1101/206292v1?rss=1 Spronk, M. Ji, J. L. Kulkarni, K. Repovs, G. Anticevic, A. Cole, M. W. 2017-10-19 doi:10.1101/206292 Cold Spring Harbor Laboratory Press 2017-10-19 <![CDATA[ spe-43 is required for sperm activation in C. elegans ]]> https://biorxiv.org/content/10.1101/206441v1?rss=1 Krauchunas, A. R. Mendez, E. Ni, J. Z. Druzhinina, M. Mulia, A. Parry, J. Gu, S. G. Stanfield, G. M. Singson, A. 2017-10-19 doi:10.1101/206441 Cold Spring Harbor Laboratory Press 2017-10-19 <![CDATA[ Machine Learning for Population Genetics: A New Paradigm ]]> https://biorxiv.org/content/10.1101/206482v1?rss=1 Schrider, D. R. Kern, A. D. 2017-10-20 doi:10.1101/206482 Cold Spring Harbor Laboratory Press 2017-10-20 <![CDATA[ Conserved patterns of somatic mutations in human peripheral blood cells ]]> https://biorxiv.org/content/10.1101/208066v1?rss=1 Liggett, L. A. Sharma, A. De, S. DeGregori, J. 2017-10-25 doi:10.1101/208066 Cold Spring Harbor Laboratory Press 2017-10-25 <![CDATA[ Voltage-dependent inward currents in smooth muscle cells of skeletal muscle arterioles ]]> https://biorxiv.org/content/10.1101/211540v1?rss=1 Ulyanova, A. V. Shirokov, R. E. 2017-11-01 doi:10.1101/211540 Cold Spring Harbor Laboratory Press 2017-11-01 <![CDATA[ Identifying Crohns disease signal from variome analysis ]]> https://biorxiv.org/content/10.1101/216432v1?rss=1 Wang, Y. Astrakhan, Y. Petersen, B.-S. Schreiber, S. Franke, A. Bromberg, Y. 2017-11-08 doi:10.1101/216432 Cold Spring Harbor Laboratory Press 2017-11-08 <![CDATA[ Correlated disasters and need-based transfers: The limits of risk pooling systems in simulated ecologies ]]> https://biorxiv.org/content/10.1101/230607v1?rss=1 Campenni, M. Cronk, L. Aktipis, A. 2017-12-07 doi:10.1101/230607 Cold Spring Harbor Laboratory Press 2017-12-07 <![CDATA[ A mathematical approach to differentiate spontaneous and induced evolution to drug resistance during cancer treatment ]]> https://biorxiv.org/content/10.1101/235150v1?rss=1 Greene, J. M. Gevertz, J. L. Sontag, E. D. 2017-12-15 doi:10.1101/235150 Cold Spring Harbor Laboratory Press 2017-12-15 <![CDATA[ Structural basis of transcription inhibition by fidaxomicin (lipiarmycin A3) ]]> https://biorxiv.org/content/10.1101/237123v1?rss=1 Lin, W. Das, K. Degen, D. Mazumder, A. Duchi, D. Wang, D. Ebright, Y. W. Ebright, R. Y. Sineva, E. Gigliotti, M. Srivastava, A. Mandal, S. Jiang, Y. Liu, Y. Yin, R. Zhang, Z. Eng, E. Thomas, D. Donadio, S. Zhang, H. Zhang, C. Kapanidis, A. Ebright, R. H. 2017-12-20 doi:10.1101/237123 Cold Spring Harbor Laboratory Press 2017-12-20 <![CDATA[ “CapZyme-Seq” comprehensively defines promoter-sequence determinants for RNA 5’ capping with NAD+ ]]> https://biorxiv.org/content/10.1101/239426v1?rss=1 Vvedenskaya, I. O. Bird, J. G. Zhang, Y. Zhang, Y. Jiao, X. Barvik, I. Krasny, L. Kiledjian, M. Taylor, D. M. Ebright, R. H. Nickels, B. E. 2017-12-24 doi:10.1101/239426 Cold Spring Harbor Laboratory Press 2017-12-24 <![CDATA[ Cell adhesion and fluid flow jointly initiate genotype spatial distribution in biofilms ]]> https://biorxiv.org/content/10.1101/243055v1?rss=1 Martinez-Garcia, R. Nadell, C. D. Hartmann, R. Drescher, K. Bonachela, J. A. 2018-01-24 doi:10.1101/243055 Cold Spring Harbor Laboratory Press 2018-01-24 <![CDATA[ TuBA: Tunable Biclustering Algorithm Reveals Clinically Relevant Tumor Transcriptional Profiles in Breast Cancer ]]> https://biorxiv.org/content/10.1101/245712v1?rss=1 Singh, A. Bhanot, G. Khiabanian, H. 2018-01-25 doi:10.1101/245712 Cold Spring Harbor Laboratory Press 2018-01-25 <![CDATA[ Chemogenetic Manipulations of Ventral Tegmental Area Dopamine Neurons Reveal Multifaceted Roles in Cocaine Abuse ]]> https://biorxiv.org/content/10.1101/246595v1?rss=1 Mahler, S. V. Brodnik, Z. D. Cox, B. M. Buchta, W. C. Bentzley, B. S. Cope, Z. A. Lin, E. C. Riedy, M. D. Scofield, M. D. Messinger, J. Riegel, A. C. Espana, R. A. Aston-Jones, G. 2018-02-26 doi:10.1101/246595 Cold Spring Harbor Laboratory Press 2018-02-26 <![CDATA[ Caenorhabditis elegans heterochromatin factor SET-32 plays an essential role in transgenerational establishment of nuclear RNAi-mediated epigenetic silencing ]]> https://biorxiv.org/content/10.1101/255562v1?rss=1 Kalinava, N. Ni, J. Gajic, Z. Ushakov, H. Gu, S. 2018-01-29 doi:10.1101/255562 Cold Spring Harbor Laboratory Press 2018-01-29 <![CDATA[ Maturation Trajectories of Cortical Resting-State Networks Depend on the Mediating Frequency Band ]]> https://biorxiv.org/content/10.1101/264416v1?rss=1 Khan, S. Hashmi, J. Mamashli, F. Michmizos, K. Kitzbichler, M. Bharadwaj, H. Bekhti, Y. Ganesan, S. Garel, K. A. Whitfield-Gabrieli, S. Gollub, R. Kong, J. Vaina, L. M. Rana, K. Stufflebeam, S. Hamalainen, M. Kenet, T. 2018-02-13 doi:10.1101/264416 Cold Spring Harbor Laboratory Press 2018-02-13 <![CDATA[ Functional equivalence of genome sequencing analysis pipelines enables harmonized variant calling across human genetics projects ]]> https://biorxiv.org/content/10.1101/269316v1?rss=1 Regier, A. A. Farjoun, Y. Larson, D. Krasheninina, O. Kang, H. M. Howrigan, D. P. Chen, B.-J. Kher, M. Banks, E. Ames, D. C. English, A. C. Li, H. The NHLBI Trans-Omics for Precision Medicine (TOPMed) Program, Abecasis, G. R. Salerno, W. Zody, M. C. Neale, B. M. Hall, I. M. 2018-02-22 doi:10.1101/269316 Cold Spring Harbor Laboratory Press 2018-02-22 <![CDATA[ Yeast heterochromatin regulators Sir2 and Sir3 act directly at euchromatic DNA replication origins ]]> https://biorxiv.org/content/10.1101/271304v1?rss=1 Hoggard, T. Chang, F. Perry, K. R. Subramanian, S. Kenworthy, J. Chueng, J. Shor, E. Cosgrove, M. Boeke, J. Fox, C. A. Weinreich, M. 2018-02-24 doi:10.1101/271304 Cold Spring Harbor Laboratory Press 2018-02-24 <![CDATA[ Stimulus-responsive self-assembly of enzymatic fractal structures by computational design ]]> https://biorxiv.org/content/10.1101/274183v1?rss=1 Hernandez, N. Hansen, W. Zhu, D. Shea, M. Khalid, M. Manichev, V. Putnis, M. Chen, M. Dodge, A. Yang, L. Banal, M. Gustaffson, T. Feldman, L. Lee, S.-H. Wackett, L. Dai, W. Khare, S. 2018-03-01 doi:10.1101/274183 Cold Spring Harbor Laboratory Press 2018-03-01 <![CDATA[ The RNA polymerase clamp interconverts dynamically among three states and is stabilized in a partly closed state by ppGpp ]]> https://biorxiv.org/content/10.1101/278838v1?rss=1 Duchi, D. Mazumder, A. Malinen, A. M. Ebright, R. Kapanidis, A. 2018-03-08 doi:10.1101/278838 Cold Spring Harbor Laboratory Press 2018-03-08 <![CDATA[ Serotonin signaling in hippocampus during initial cocaine abstinence drives persistent drug seeking ]]> https://biorxiv.org/content/10.1101/279729v1?rss=1 Kohtz, A. S. Aston-Jones, G. 2018-03-10 doi:10.1101/279729 Cold Spring Harbor Laboratory Press 2018-03-10 <![CDATA[ Multisensory expectations shape olfactory input to the brain ]]> https://biorxiv.org/content/10.1101/283242v1?rss=1 Czarnecki, L. Moberly, A. Fast, C. Turkel, D. McGann, J. 2018-03-19 doi:10.1101/283242 Cold Spring Harbor Laboratory Press 2018-03-19 <![CDATA[ Ecological and evolutionary consequences of viral plasticity ]]> https://biorxiv.org/content/10.1101/289116v1?rss=1 Choua, M. Bonachela, J. 2018-03-27 doi:10.1101/289116 Cold Spring Harbor Laboratory Press 2018-03-27 <![CDATA[ Task activations produce spurious but systematic inflation of task functional connectivity estimates ]]> https://biorxiv.org/content/10.1101/292045v1?rss=1 Cole, M. W. Ito, T. Schultz, D. Mill, R. Chen, R. Cocuzza, C. 2018-03-30 doi:10.1101/292045 Cold Spring Harbor Laboratory Press 2018-03-30 <![CDATA[ Active presynaptic ribosomes in mammalian brain nerve terminals, and increased transmitter release after protein synthesis inhibition ]]> https://biorxiv.org/content/10.1101/295543v1?rss=1 Scarnati, M. S. Kataria, R. Biswas, M. Paradiso, K. G. 2018-04-05 doi:10.1101/295543 Cold Spring Harbor Laboratory Press 2018-04-05 <![CDATA[ Positive Cardiac Inotrope, Omecamtiv Mecarbil, Activates Muscle Despite Suppressing the Myosin Working Stroke ]]> https://biorxiv.org/content/10.1101/298141v1?rss=1 Woody, M. S. Greenberg, M. J. Barua, B. Winkelmann, D. A. Goldman, Y. E. Ostap, E. M. 2018-04-11 doi:10.1101/298141 Cold Spring Harbor Laboratory Press 2018-04-11 <![CDATA[ Helicase Promotes Replication Re-initiation from an RNA Transcript ]]> https://biorxiv.org/content/10.1101/310235v1?rss=1 Sun, B. Singh, A. Sultana, S. Inman, J. Patel, S. Wang, M. 2018-04-28 doi:10.1101/310235 Cold Spring Harbor Laboratory Press 2018-04-28 <![CDATA[ A role for GrgA in regulation of σ28-dependent transcription in the obligate intracellular bacterial pathogen Chlamydia trachomatis ]]> https://biorxiv.org/content/10.1101/322701v1?rss=1 Desai, M. Wurihan, W. Di, R. Fondell, J. D. Nickels, B. Bao, X. Fan, H. 2018-05-15 doi:10.1101/322701 Cold Spring Harbor Laboratory Press 2018-05-15 <![CDATA[ RefCell: Multi-dimensional analysis of image-based high-throughput screens based on ‘typical cells’ ]]> https://biorxiv.org/content/10.1101/325415v1?rss=1 Shen, Y. Kubben, N. Candia, J. Morozov, A. V. Misteli, T. Losert, W. 2018-05-18 doi:10.1101/325415 Cold Spring Harbor Laboratory Press 2018-05-18 <![CDATA[ A whole-brain and cross-diagnostic perspective on functional brain network dysfunction ]]> https://biorxiv.org/content/10.1101/326728v1?rss=1 Spronk, M. Kulkarni, K. Ji, J. L. Keane, B. Anticevic, A. Cole, M. W. 2018-05-21 doi:10.1101/326728 Cold Spring Harbor Laboratory Press 2018-05-21 <![CDATA[ Addiction associated N40D mu-opioid receptor variant modulates synaptic function in human neurons ]]> https://biorxiv.org/content/10.1101/328898v1?rss=1 Halikere, A. Popova, D. Hamod, A. Swerdel, M. S. Moore, J. C. Tischfield, J. A. Hart, R. P. Pang, Z. 2018-05-23 doi:10.1101/328898 Cold Spring Harbor Laboratory Press 2018-05-23 <![CDATA[ Immunobiochemical reconstruction of influenza lung infection - Melanoma skin cancer interactions ]]> https://biorxiv.org/content/10.1101/331546v1?rss=1 Nikolaev, E. V. Zloza, A. Sontag, E. 2018-05-25 doi:10.1101/331546 Cold Spring Harbor Laboratory Press 2018-05-25 <![CDATA[ Structural insights on TRPV5 gating by endogenous modulators ]]> https://biorxiv.org/content/10.1101/338798v1?rss=1 Hughes, T. E. T. Pumroy, R. A. Fluck, E. C. Huynh, K. W. Samanta, A. Molugu, S. Zhou, Z. H. Moiseenkova-Bell, V. Y. 2018-06-05 doi:10.1101/338798 Cold Spring Harbor Laboratory Press 2018-06-05 <![CDATA[ Manifold-tiling Localized Receptive Fields are Optimal in Similarity-preserving Neural Networks ]]> https://biorxiv.org/content/10.1101/338947v1?rss=1 Sengupta, A. Tepper, M. Pehlevan, C. Genkin, A. Chklovskii, D. 2018-06-04 doi:10.1101/338947 Cold Spring Harbor Laboratory Press 2018-06-04 <![CDATA[ Vesicular delivery of the antifungal antibiotics of Lysobacter enzymogenes C3 ]]> https://biorxiv.org/content/10.1101/344838v1?rss=1 Meers, P. Liu, C. Chen, R. Bartos, W. Davis, J. Dziedzic, N. Orciuolo, J. Kutyla, S. Pozo, M. J. Mithrananda, D. Panzera, D. Wang, S. 2018-06-12 doi:10.1101/344838 Cold Spring Harbor Laboratory Press 2018-06-12 <![CDATA[ Towards a universal structural and energetic model for prokaryotic promoters ]]> https://biorxiv.org/content/10.1101/348854v1?rss=1 Mishra, A. Siwach, P. Misra, P. Jayaram, B. Bansal, M. Olson, W. K. Thayer, K. Beveridge, D. L. 2018-06-15 doi:10.1101/348854 Cold Spring Harbor Laboratory Press 2018-06-15 <![CDATA[ 14-3-3 recruits keratin intermediate filaments to mechanically sensitive cell-cell contacts ]]> https://biorxiv.org/content/10.1101/349092v1?rss=1 Mariani, R. A. Paranjpe, S. Dobrowolski, R. Weber, G. F. 2018-06-16 doi:10.1101/349092 Cold Spring Harbor Laboratory Press 2018-06-16 <![CDATA[ Orexin-1 receptor signaling in ventral pallidum mediates demand for the opioid remifentanil ]]> https://biorxiv.org/content/10.1101/353896v1?rss=1 Mohammdkhani, A. Pantazis, C. B. Bowrey, H. E. James, M. H. Aston-Jones, G. 2018-06-29 doi:10.1101/353896 Cold Spring Harbor Laboratory Press 2018-06-29 <![CDATA[ Knockdown of butyrylcholinesterase but not inhibition by chlorpyrifos alters early differentiation mechanisms in human neural stem cells ]]> https://biorxiv.org/content/10.1101/354308v1?rss=1 Teithof, A. K. Richardson, J. R. Hart, R. P. 2018-06-28 doi:10.1101/354308 Cold Spring Harbor Laboratory Press 2018-06-28 <![CDATA[ Posttranscriptional regulation of intestinal epithelial cell repair by RNA binding protein IMP1 ]]> https://biorxiv.org/content/10.1101/368050v1?rss=1 Chatterji, P. Whelan, K. A. Andres, S. F. Samper, F. C. Simon, L. A. Mizuno, R. Lundsmith, E. T. Lee, D. S. M. Liang, S. Wijeratne, H. R. S. Marti, S. Chau, L. Williams, P. A. Giroux, V. Wilkins, B. J. Wu, G. D. Shah, P. Tartaglia, G. G. Hamilton, K. E. 2018-07-12 doi:10.1101/368050 Cold Spring Harbor Laboratory Press 2018-07-12 <![CDATA[ Fluoxetine effects on behavior and adult hippocampal neurogenesis in female C57BL/6J mice across the estrous cycle ]]> https://biorxiv.org/content/10.1101/368449v1?rss=1 Yohn, C. N. Shifman, S. Garino, A. Diethorn, E. Bokka, L. Ashamalla, S. A. Samuels, B. A. 2018-07-13 doi:10.1101/368449 Cold Spring Harbor Laboratory Press 2018-07-13 <![CDATA[ A novel virtual plus-maze for studying electrophysiological correlates of spatial reorientation ]]> https://biorxiv.org/content/10.1101/369207v1?rss=1 Torok, A. Kobor, A. Honbolygo, F. Baker, T. 2018-07-13 doi:10.1101/369207 Cold Spring Harbor Laboratory Press 2018-07-13 <![CDATA[ Backward evolution from gene network dynamics ]]> https://biorxiv.org/content/10.1101/369371v1?rss=1 Belete, M. K. Charlebois, D. A. Balazsi, G. 2018-07-14 doi:10.1101/369371 Cold Spring Harbor Laboratory Press 2018-07-14 <![CDATA[ Scedar: a scalable Python package for single-cell RNA-seq exploratory data analysis ]]> https://biorxiv.org/content/10.1101/375196v1?rss=1 Zhang, Y. Taylor, D. M. 2018-07-23 doi:10.1101/375196 Cold Spring Harbor Laboratory Press 2018-07-23 <![CDATA[ Extracellular matrix regulates morphogenesis and function of ciliated sensory organs in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/376152v1?rss=1 Barr, M. M. De Vore, D. M. Knobel, K. M. Nguyen, K. C. Q. Hall, D. H. 2018-07-24 doi:10.1101/376152 Cold Spring Harbor Laboratory Press 2018-07-24 <![CDATA[ Structural basis of ECF-sigma-factor-dependent transcription initiation. ]]> https://biorxiv.org/content/10.1101/381020v1?rss=1 Lin, W. Mandal, S. Degen, D. Cho, M. Feng, Y. Das, K. Ebright, R. H. 2018-07-31 doi:10.1101/381020 Cold Spring Harbor Laboratory Press 2018-07-31 <![CDATA[ Mitochondrial RNA capping: highly efficient 5’-RNA capping with NAD+ and NADH by yeast and human mitochondrial RNA polymerase ]]> https://biorxiv.org/content/10.1101/381160v1?rss=1 Bird, J. G. Basu, U. Kuster, D. Ramachandran, A. Grudzien-Nogalska, E. Kiledjian, M. Temiakov, D. Patel, S. S. Ebright, R. H. Nickels, B. E. 2018-07-31 doi:10.1101/381160 Cold Spring Harbor Laboratory Press 2018-07-31 <![CDATA[ Cell type-specific structural plasticity of the ciliary transition zone in C. elegans ]]> https://biorxiv.org/content/10.1101/382689v1?rss=1 Akella, J. S. Silva, M. S. Morsci, N. S. Nguyen, K. C. Q. Rice, W. Hall, D. H. Barr, M. M. 2018-08-01 doi:10.1101/382689 Cold Spring Harbor Laboratory Press 2018-08-01 <![CDATA[ Kingdom-wide comparison reveals conserved diurnal gene expression in Archaeplastida ]]> https://biorxiv.org/content/10.1101/387316v1?rss=1 Ferrari, C. Proost, S. Janowski, M. Becker, J. Nikoloski, Z. Bhattacharya, D. Price, D. Tohge, T. Bar-Even, A. Fernie, A. Stitt, M. Mutwil, M. 2018-08-15 doi:10.1101/387316 Cold Spring Harbor Laboratory Press 2018-08-15 <![CDATA[ Cholinergic Midbrain Afferents Modulate Striatal Circuits and Shape Encoding of Action Control ]]> https://biorxiv.org/content/10.1101/388223v1?rss=1 Dautan, D. Huerta-Ocampo, I. Valencia, M. Kondabolu, K. Gerdjikov, T. V. Mena-Segovia, J. 2018-08-08 doi:10.1101/388223 Cold Spring Harbor Laboratory Press 2018-08-08 <![CDATA[ ATM is activated by ATP depletion and modulates mitochondrial function through NRF1 ]]> https://biorxiv.org/content/10.1101/414490v1?rss=1 Chow, H.-M. Cheng, A. Song, X. Swerdel, M. R. Hart, R. P. Herrup, K. 2018-09-11 doi:10.1101/414490 Cold Spring Harbor Laboratory Press 2018-09-11 <![CDATA[ Optimization of Dose Schedules for Chemotherapy of Early Colon Cancer Determined by High Performance Computer Simulations ]]> https://biorxiv.org/content/10.1101/420232v1?rss=1 Cockrell, C. Axelrod, D. 2018-09-17 doi:10.1101/420232 Cold Spring Harbor Laboratory Press 2018-09-17 <![CDATA[ The Lineage-Specific Transcription Factor CDX2 Navigates Dynamic Chromatin to Control Distinct Stages of Intestine Development ]]> https://biorxiv.org/content/10.1101/425827v1?rss=1 Kumar, N. Tsai, Y.-H. Chen, L. Zhou, A. Banerjee, K. J. Saxena, M. Huang, S. Xing, J. Shivdasani, R. A. Spence, J. R. Verzi, M. 2018-09-24 doi:10.1101/425827 Cold Spring Harbor Laboratory Press 2018-09-24 <![CDATA[ Male and female bees show large differences in floral preference ]]> https://biorxiv.org/content/10.1101/432518v1?rss=1 Roswell, M. Dushoff, J. Winfree, R. 2018-10-03 doi:10.1101/432518 Cold Spring Harbor Laboratory Press 2018-10-03 <![CDATA[ GrgA as a potential target of selective antichlamydials ]]> https://biorxiv.org/content/10.1101/437285v1?rss=1 Zhang, H. Vellappan, S. Tang, M. M. Bao, X. Fan, H. 2018-10-07 doi:10.1101/437285 Cold Spring Harbor Laboratory Press 2018-10-07 <![CDATA[ An intrinsic neural eye tracker in primary visual cortex ]]> https://biorxiv.org/content/10.1101/443507v1?rss=1 Morris, A. P. Krekelberg, B. 2018-10-15 doi:10.1101/443507 Cold Spring Harbor Laboratory Press 2018-10-15 <![CDATA[ Pluripotent Stem Cell-derived Cerebral Organoids Reveal Human Oligodendrogenesis with Dorsal and Ventral Origins ]]> https://biorxiv.org/content/10.1101/460907v1?rss=1 Kim, H. Xu, R. Ragunathan, P. Dunaevsky, A. Liu, Y. Dreyfus, C. Jiang, P. 2018-11-04 doi:10.1101/460907 Cold Spring Harbor Laboratory Press 2018-11-04 <![CDATA[ Cannabinoid 1-Receptor regulation of deep and distributed subcellular processes enables neurite outgrowth ]]> https://biorxiv.org/content/10.1101/462200v1?rss=1 Hansen, J. Yadaw, A. S. Siddiq, M. M. Tolentino, R. Rabinovitch, V. Liu, T. Li, H. Goldfarb, J. Iyenagar, R. 2018-11-05 doi:10.1101/462200 Cold Spring Harbor Laboratory Press 2018-11-05 <![CDATA[ Reversing Abnormal Neural Development by Inhibiting OLIG2 in Down Syndrome Human iPSC Brain Organoids and Neuronal Mouse Chimeras ]]> https://biorxiv.org/content/10.1101/462739v1?rss=1 Xu, R. Brawner, A. Li, S. Kim, H. Xue, H. Pang, Z. Kim, W.-Y. Hart, R. Liu, Y. Jiang, P. 2018-11-05 doi:10.1101/462739 Cold Spring Harbor Laboratory Press 2018-11-05 <![CDATA[ Long-distance dispersal, ice sheet dynamics, and mountaintop isolation underlie the genetic structure of glacier ice worms ]]> https://biorxiv.org/content/10.1101/463521v1?rss=1 1,500 km) areas of unsuitable habitat. In this study, we analyzed genome-scale sequence data for most of the known ice worm range. We found clear support for divergence between populations along the Pacific Coast and the inland flanks of the Coast Mountains (mean FST = 0.60), likely precipitated by episodic ice sheet expansion and contraction during the Pleistocene. We also found support for LDD of ice worms from Alaska to Vancouver Island, perhaps mediated by migrating birds. Our results highlight the power of genomic data for disentangling complex biogeographic patterns, including the presence of LDD. ]]> Hotaling, S. Shain, D. H. Lang, S. A. Bagley, R. K. M., L. Weisrock, D. W. Kelley, J. L. 2018-11-08 doi:10.1101/463521 Cold Spring Harbor Laboratory Press 2018-11-08 <![CDATA[ The orexin-1 receptor antagonist SB-334867 reduces motivation, but not inhibitory control, in a rat stop signal task ]]> https://biorxiv.org/content/10.1101/467308v1?rss=1 Wiskerke, J. James, M. H. Aston-Jones, G. 2018-11-09 doi:10.1101/467308 Cold Spring Harbor Laboratory Press 2018-11-09 <![CDATA[ Unbiased genome-scale identification of cis-regulatory modules in the human genome by GRAMc ]]> https://biorxiv.org/content/10.1101/468405v1?rss=1 Guay, C. L. Nam, J. 2018-11-12 doi:10.1101/468405 Cold Spring Harbor Laboratory Press 2018-11-12 <![CDATA[ Genomic signatures of evolutionary rescue in bats surviving white-nose syndrome ]]> https://biorxiv.org/content/10.1101/470294v1?rss=1 Gignoux-Wolfsohn, S. A. Pinsky, M. Kerwin, K. Herzog, C. Hall, M. Bennett, A. Fefferman, N. Maslo, B. 2018-11-15 doi:10.1101/470294 Cold Spring Harbor Laboratory Press 2018-11-15 <![CDATA[ Structural and biochemical studies define Nudt12 as a new class of RNA deNADding enzyme in mammalian cells ]]> https://biorxiv.org/content/10.1101/474478v1?rss=1 Grudzien-Nogalska, E. Wu, Y. Jiao, X. Cui, H. Hart, R. P. Tong, L. Kiledjian, M. 2018-11-20 doi:10.1101/474478 Cold Spring Harbor Laboratory Press 2018-11-20 <![CDATA[ Mathematical Details on a Cancer Resistance Model ]]> https://biorxiv.org/content/10.1101/475533v1?rss=1 Greene, J. Sanchez-Tapia, C. Sontag, E. 2018-11-22 doi:10.1101/475533 Cold Spring Harbor Laboratory Press 2018-11-22 <![CDATA[ Realtime 2-5A kinetics suggests interferons β and {lambda} evade global arrest of translation by RNase L ]]> https://biorxiv.org/content/10.1101/476341v1?rss=1 Chitrakar, A. Rath, S. Donovan, J. Demarest, K. Li, Y. Rao Sridhar, R. Weiss, S. Kotenko, S. Wingreen, N. Korennykh, A. 2018-11-26 doi:10.1101/476341 Cold Spring Harbor Laboratory Press 2018-11-26 <![CDATA[ Dynamic properties of internal noise probed by modulating binocular rivalry ]]> https://biorxiv.org/content/10.1101/480988v1?rss=1 Baker, D. Richard, B. 2018-11-29 doi:10.1101/480988 Cold Spring Harbor Laboratory Press 2018-11-29 <![CDATA[ A novel photoactivatable tool for intermediate filament disruption indicates a role for keratin filaments in early embryogenesis ]]> https://biorxiv.org/content/10.1101/484246v1?rss=1 Sanghvi-Shah, R. Paranjpe, S. Baek, J. Dobrowolski, R. Weber, G. 2018-11-30 doi:10.1101/484246 Cold Spring Harbor Laboratory Press 2018-11-30 <![CDATA[ Dentate Gyrus Activin Signaling Mediates the Antidepressant Treatment Response ]]> https://biorxiv.org/content/10.1101/491613v1?rss=1 Gergues, M. M. Yohn, C. N. Levinstein, M. R. Samuels, B. A. 2018-12-10 doi:10.1101/491613 Cold Spring Harbor Laboratory Press 2018-12-10 <![CDATA[ One-dimensional sliding assists σ70-dependent promoter binding by Escherichia coli RNA polymerase ]]> https://biorxiv.org/content/10.1101/494534v1?rss=1 300 s). We estimate a lower bound for the "diffusion facilitation threshold" - the RNAP concentration at which three-dimensional search and one-dimensional sliding contribute equally to promoter binding - of 0.2 M RNAP. The results suggest facilitated diffusion occurs in promoter search by RNAP, even at the relatively high, 0.2-0.6 M, concentrations of RNAP in cells.nnSignificance statementThe flow of genetic information from DNA to RNA is of central importance to living systems, and it can only start after an RNA polymerase (RNAP) has found a promoter site. But how does this enzyme find promoter sites on DNA in the first place? In recent years, debate on this topic has favored a promoter search mechanism that is dominated by three-dimensional diffusion of RNAP, rather than by one-dimensional sliding of RNAP on DNA. Here, we designed an improved single-molecule assay that unambiguously revealed extensive one-dimensional sliding of RNAP on DNA. Our results imply that, at the RNAP concentrations in living cells, the promoter-search process is facilitated by one-dimensional sliding on DNA. ]]> Heller, I. Marchetti, M. Mazumder, A. Chakraborty, A. Malinowska, A. M. Roos, W. H. Ebright, R. H. Peterman, E. J. G. Wuite, G. J. L. 2018-12-13 doi:10.1101/494534 Cold Spring Harbor Laboratory Press 2018-12-13 <![CDATA[ Analysis of whole genome-transcriptomic organization in brain to identify genes associated with alcoholism ]]> https://biorxiv.org/content/10.1101/500439v1?rss=1 Kapoor, M. Wang, J.-C. Farris, S. P. Liu, Y. McClintick, J. Gupta, I. Meyers, J. L. Bertelsen, S. Chao, M. Nurnberger, J. Tischfield, J. Harari, O. Zeran, L. Hesselbroc, V. Bauer, L. Raj, T. Porjesz, B. Agrawal, A. Foroud, T. Edenberg, H. Mayfield, R. D. Goate, A. 2018-12-19 doi:10.1101/500439 Cold Spring Harbor Laboratory Press 2018-12-19 <![CDATA[ Convergent Allostery in Ribonucleotide Reductase ]]> https://biorxiv.org/content/10.1101/504290v1?rss=1 Thomas, W. C. Brooks, F. P. Burnim, A. A. Bacik, J.-P. Stubbe, J. Kaelber, J. T. Chen, J. Z. Ando, N. 2018-12-21 doi:10.1101/504290 Cold Spring Harbor Laboratory Press 2018-12-21 <![CDATA[ The effect of ocean warming on black sea bass (Centropristis striata) aerobic scope and hypoxia tolerance ]]> https://biorxiv.org/content/10.1101/507368v1?rss=1 Slesinger, E. Andres, A. Young, R. Seibel, B. Saba, V. Phelan, B. Rosendale, J. Wieczorek, D. Saba, G. 2018-12-27 doi:10.1101/507368 Cold Spring Harbor Laboratory Press 2018-12-27 <![CDATA[ A tRNA modification balances carbon and nitrogen metabolism by regulating phosphate homeostasis, to couple metabolism to cell cycle progression. ]]> https://biorxiv.org/content/10.1101/507707v1?rss=1 Gupta, R. Walvekar, A. Liang, S. Rashida, Z. Shah, P. Laxman, S. 2018-12-28 doi:10.1101/507707 Cold Spring Harbor Laboratory Press 2018-12-28 <![CDATA[ Mapping and characterization of structural variation in 17,795 deeply sequenced human genomes ]]> https://biorxiv.org/content/10.1101/508515v1?rss=1 Abel, H. J. Larson, D. E. Chiang, C. Das, I. Kanchi, K. L. Layer, R. M. Neale, B. M. Salerno, W. J. Reeves, C. Buyske, S. NHGRI Centers for Common Disease Genomics, Matise, T. C. Muzny, D. M. Zody, M. C. Lander, E. S. Dutcher, S. K. Stitziel, N. O. Hall, I. M. 2018-12-31 doi:10.1101/508515 Cold Spring Harbor Laboratory Press 2018-12-31 <![CDATA[ Coupled fast and slow feedbacks lead to continual evolution: A general modeling approach ]]> https://biorxiv.org/content/10.1101/513416v1?rss=1 Wortel, M. T. Peters, H. Stenseth, N. C. 2019-01-07 doi:10.1101/513416 Cold Spring Harbor Laboratory Press 2019-01-07 <![CDATA[ Allele-Specific Expression and High-Throughput Reporter Assay Reveal Functional Variants in Human Brains with Alcohol Use Disorders ]]> https://biorxiv.org/content/10.1101/514992v1?rss=1 Rao, X. Thapa, K. S. Chen, A. B. Lin, H. Gao, H. Reiter, J. L. Hargreaves, K. A. Ipe, J. Lai, D. Xuei, X. Gu, H. Kapoor, M. Farris, S. P. Tischfield, J. Foroud, T. Goate, A. M. Skaar, T. C. Mayfield, R. D. Edenberg, H. J. Liu, Y. 2019-01-09 doi:10.1101/514992 Cold Spring Harbor Laboratory Press 2019-01-09 <![CDATA[ A brainstem-central amygdala circuit underlies defensive responses to learned threats ]]> https://biorxiv.org/content/10.1101/519249v1?rss=1 Gu, Y. Vazey, E. M. Aston-Jones, G. Lin, L. LeDoux, J. E. Sears, R. M. 2019-01-13 doi:10.1101/519249 Cold Spring Harbor Laboratory Press 2019-01-13 <![CDATA[ Persistent effects of the orexin-1 receptor antagonist SB-334867 on motivation for the fast acting opioid remifentanil ]]> https://biorxiv.org/content/10.1101/521633v1?rss=1 Mohammadkhani, A. James, M. Aston-Jones, G. 2019-01-17 doi:10.1101/521633 Cold Spring Harbor Laboratory Press 2019-01-17 <![CDATA[ PIK3CA in KrasG12D/Trp53R172H Tumor Cells Promotes Immune Evasion by Limiting Infiltration of T Cells in a Model of Pancreatic Cancer ]]> https://biorxiv.org/content/10.1101/521831v1?rss=1 Sivaram, N. McLaughlin, P. A. Han, H. V. Petrenko, O. Jiang, Y.-P. Ballou, L. M. Pham, K. Liu, C. Van der Velden, A. W. M. Lin, R. Z. 2019-01-15 doi:10.1101/521831 Cold Spring Harbor Laboratory Press 2019-01-15 <![CDATA[ Molecular mechanism of TRPV2 channel modulation by cannabidiol ]]> https://biorxiv.org/content/10.1101/521880v1?rss=1 Pumroy, R. A. Samanta, A. Liu, Y. Hughes, T. E. T. Zhao, S. Yudin, Y. Huynh, K. W. Zhou, Z. H. Rohacs, T. Han, S. Moiseenkova-Bell, V. Y. 2019-01-16 doi:10.1101/521880 Cold Spring Harbor Laboratory Press 2019-01-16 <![CDATA[ The genomes of polyextremophilic Cyanidiales contain 1% horizontally transferred genes with diverse adaptive functions ]]> https://biorxiv.org/content/10.1101/526111v1?rss=1 Rossoni, A. W. Price, D. C. Seger, M. Lyska, D. Lammers, P. Bhattacharya, D. Weber, A. P. M. 2019-01-23 doi:10.1101/526111 Cold Spring Harbor Laboratory Press 2019-01-23 <![CDATA[ Anhedonia following mild traumatic brain injury in rats: A behavioral economic analysis of positive and negative reinforcement ]]> https://biorxiv.org/content/10.1101/527895v1?rss=1 Avcu, P. Fortress, A. M. Fragale, J. E. Spiegler, K. Pang, K. 2019-01-23 doi:10.1101/527895 Cold Spring Harbor Laboratory Press 2019-01-23 <![CDATA[ Pure tones modulate the representation of orientation and direction in the primary visual cortex ]]> https://biorxiv.org/content/10.1101/531194v1?rss=1 McClure, J. P. Polack, P.-O. 2019-01-26 doi:10.1101/531194 Cold Spring Harbor Laboratory Press 2019-01-26 <![CDATA[ The Role of Orexin-1 Receptor Signaling in Demand for the Opioid Fentanyl ]]> https://biorxiv.org/content/10.1101/533059v1?rss=1 Fragale, J. E. Pantazis, C. B. James, M. H. Aston-Jones, G. 2019-01-31 doi:10.1101/533059 Cold Spring Harbor Laboratory Press 2019-01-31 <![CDATA[ Drug-like Fragments Inhibit agr-Mediated Virulence Expression in Staphylococcus aureus ]]> https://biorxiv.org/content/10.1101/538173v1?rss=1 Bezar, I. F. Mashruwala, A. A. Boyd, J. M. Stock, A. M. 2019-02-01 doi:10.1101/538173 Cold Spring Harbor Laboratory Press 2019-02-01 <![CDATA[ The number of lateral hypothalamus orexin/hypocretin neurons contributes to individual differences in cocaine demand ]]> https://biorxiv.org/content/10.1101/547836v1?rss=1 Pantazis, C. James, M. H. Bentzley, B. S. Aston-Jones, G. 2019-02-12 doi:10.1101/547836 Cold Spring Harbor Laboratory Press 2019-02-12 <![CDATA[ Social Instability is an Effective Chronic Stress Paradigm for both Male and Female Mice ]]> https://biorxiv.org/content/10.1101/550525v1?rss=1 Yohn, C. N. Ashamalla, S. A. Bokka, L. Gergues, M. M. Garino, A. Samuels, B. A. 2019-02-14 doi:10.1101/550525 Cold Spring Harbor Laboratory Press 2019-02-14 <![CDATA[ A Quasi Birth-and-Death Model For Tumor Recurrence ]]> https://biorxiv.org/content/10.1101/551770v1?rss=1 M. Santana, L. Bhanot, G. Ganesan, S. 2019-02-15 doi:10.1101/551770 Cold Spring Harbor Laboratory Press 2019-02-15 <![CDATA[ H2A.Z-dependent and -independent recruitment of metabolic enzymes to chromatin required for histone modifications ]]> https://biorxiv.org/content/10.1101/553297v1?rss=1 Choi, S. Jeon, Y. H. Yang, Z. He, M. Shin, H. Pfleger, J. Sayed, D. Astrof, S. Abdellatif, M. 2019-02-18 doi:10.1101/553297 Cold Spring Harbor Laboratory Press 2019-02-18 <![CDATA[ Interaction of NPC2 protein with Lysobisphosphatidic Acid is required for normal endolysosomal cholesterol trafficking ]]> https://biorxiv.org/content/10.1101/559849v1?rss=1 McCauliff, L. A. Langan, A. Li, R. Ilnytska, O. Bose, D. Kahn, P. C. Storch, J. 2019-02-24 doi:10.1101/559849 Cold Spring Harbor Laboratory Press 2019-02-24 <![CDATA[ Task-evoked activity quenches neural correlations and variability in large-scale brain systems ]]> https://biorxiv.org/content/10.1101/560730v1?rss=1 Ito, T. Brincat, S. L. Siegel, M. Mill, R. D. He, B. J. Miller, E. K. Rotstein, H. G. Cole, M. W. 2019-02-25 doi:10.1101/560730 Cold Spring Harbor Laboratory Press 2019-02-25 <![CDATA[ Identification of new MmpL3 inhibitors by untargeted and targeted mutant screens defines MmpL3 domains with differential resistance ]]> https://biorxiv.org/content/10.1101/564245v1?rss=1 Williams, J. T. Haiderer, E. R. Coulson, G. B. Conner, K. N. Ellsworth, E. Chen, C. Dick, T. Abramovitch, R. B. 2019-02-28 doi:10.1101/564245 Cold Spring Harbor Laboratory Press 2019-02-28 <![CDATA[ Corticotropin-Releasing Hormone Signaling in the Oval Bed Nucleus of the Stria Terminalis Mediates Chronic Stress-Induced Negative Valence Behaviors Associated with Anxiety ]]> https://biorxiv.org/content/10.1101/572966v1?rss=1 Hu, P. Maita, I. Kwok, C. Gu, E. Gergues, M. Liu, J. Pang, Z. Swaab, D. F. Lucassen, P. J. Roepke, T. A. Samuels, B. A. 2019-03-09 doi:10.1101/572966 Cold Spring Harbor Laboratory Press 2019-03-09 <![CDATA[ fuNTRp: Identifying protein positions for variation driven functional tuning ]]> https://biorxiv.org/content/10.1101/578757v1?rss=1 Miller, M. Vitale, D. Rost, B. Bromberg, Y. 2019-03-16 doi:10.1101/578757 Cold Spring Harbor Laboratory Press 2019-03-16 <![CDATA[ Inferring biophysical models of evolution from genome-wide patterns of codon usage ]]> https://biorxiv.org/content/10.1101/578815v1?rss=1 Kion-Crosby, W. B. Manhart, M. Morozov, A. V. 2019-03-16 doi:10.1101/578815 Cold Spring Harbor Laboratory Press 2019-03-16 <![CDATA[ Chronic corticosterone administration induces negative valence and impairs positive valence behaviors in mice ]]> https://biorxiv.org/content/10.1101/593632v1?rss=1 Dieterich, A. Srivastava, P. Sharif, A. Stech, K. Samuels, B. A. 2019-03-30 doi:10.1101/593632 Cold Spring Harbor Laboratory Press 2019-03-30 <![CDATA[ Detection of Spacer Precursors Formed In Vivo During Primed CRISPR Adaptation ]]> https://biorxiv.org/content/10.1101/594259v1?rss=1 Shiriaeva, A. A. Savitskaya, E. Datsenko, K. A. Vvedenskaya, I. O. Fedorova, I. Morozova, N. Metlitskaya, A. Sabantsev, A. Nickels, B. E. Severinov, K. Semenova, E. 2019-03-30 doi:10.1101/594259 Cold Spring Harbor Laboratory Press 2019-03-30 <![CDATA[ Xenotransplantation of Human PSC-derived Microglia Creates a Chimeric Mouse Brain Model that Recapitulates Features of Adult Human Microglia ]]> https://biorxiv.org/content/10.1101/594721v1?rss=1 Xu, R. Boreland, A. Posyton, A. Kwan, K. Hart, R. P. Jiang, P. 2019-03-31 doi:10.1101/594721 Cold Spring Harbor Laboratory Press 2019-03-31 <![CDATA[ A new immunotherapeutic concept for pancreatic cancer using childhood vaccine recall antigens and Listeria ]]> https://biorxiv.org/content/10.1101/600106v1?rss=1 Selvanesan, B. C. Chandra, D. Quispe-Tintaya, W. Jahangir, A. Patel, A. Meena, K. Alberto Alves Da Silva, R. Libutti, S. K. Yuan, Z. Beck, A. Tesfa, L. Koba, W. Chuy, J. McAuliffe, J. C. Jafari, R. Entenberg, D. Wang, Y. Condeelis, J. Gravekamp, C. 2019-04-05 doi:10.1101/600106 Cold Spring Harbor Laboratory Press 2019-04-05 <![CDATA[ A Porcine Model of Peripheral Nerve Injury Enabling Ultra-Long Regenerative Distances: Surgical Approach, Recovery Kinetics, and Clinical Relevance ]]> https://biorxiv.org/content/10.1101/610147v1?rss=1 Burrell, J. C. Browne, K. D. Dutton, J. L. Das, S. Brown, D. P. Laimo, F. A. Roberts, S. Petrov, D. Ali, Z. Ledebur, H. C. Rosen, J. M. Kaplan, H. M. Wolf, J. A. Smith, D. H. Chen, H. I. Cullen, D. K. 2019-04-16 doi:10.1101/610147 Cold Spring Harbor Laboratory Press 2019-04-16 <![CDATA[ HNF4 factors control chromatin accessibility and are redundantly required for maturation of the fetal intestine ]]> https://biorxiv.org/content/10.1101/610428v1?rss=1 Chen, L. Toke, N. H. Luo, S. Vasoya, R. P. Aita, R. Parthasarathy, A. Tsai, Y.-H. Spence, J. R. Verzi, M. P. 2019-04-15 doi:10.1101/610428 Cold Spring Harbor Laboratory Press 2019-04-15 <![CDATA[ Simultaneous ribosome profiling of human host cells infected with Toxoplasma gondii ]]> https://biorxiv.org/content/10.1101/619916v1?rss=1 Holmes, M. J. Shah, P. Wek, R. C. Sullivan, W. J. 2019-04-26 doi:10.1101/619916 Cold Spring Harbor Laboratory Press 2019-04-26 <![CDATA[ Increased Dynamics of α-Synuclein Fibrils by β-Synuclein Leads to Reduced Seeding and Cytotoxicity ]]> https://biorxiv.org/content/10.1101/620401v1?rss=1 Yang, X. Williams, J. Yan, R. Mouradian, M. M. Baum, J. 2019-04-26 doi:10.1101/620401 Cold Spring Harbor Laboratory Press 2019-04-26 <![CDATA[ Targeting RET Kinase in Neuroendocrine Prostate Cancer ]]> https://biorxiv.org/content/10.1101/622415v1?rss=1 VanDeusen, H. Ramroop, J. R. Morel, K. L. Sheahan, A. V. Sychev, Z. Lau, N. A. Cheng, L. C. Tan, V. Li, Z. Petersen, A. Lee, J. K. Wook Park, J. Yang, R. Coleman, I. Witte, O. N. Morrissey, C. Corey, E. Nelson, P. S. Ellis, L. Drake, J. M. 2019-04-29 doi:10.1101/622415 Cold Spring Harbor Laboratory Press 2019-04-29 <![CDATA[ All-FIT: Allele-Frequency-based Imputation of Tumor Purity from High-Depth Sequencing Data ]]> https://biorxiv.org/content/10.1101/625376v1?rss=1 Loh, J. W. Guccione, C. Di Clemente, F. Riedlinger, G. Ganesan, S. Khiabanian, H. 2019-05-02 doi:10.1101/625376 Cold Spring Harbor Laboratory Press 2019-05-02 <![CDATA[ Organohalide-respiring Desulfoluna species isolated from marine environments ]]> https://biorxiv.org/content/10.1101/630186v1?rss=1 Peng, P. Goris, T. Lu, Y. Nijsse, B. Burrichter, A. Schleheck, D. Koehorst, J. J. Liu, J. Sipkema, D. Damste, J. S. S. Stams, A. J. M. Haggblom, M. M. Smidt, H. Atashgahi, S. 2019-05-07 doi:10.1101/630186 Cold Spring Harbor Laboratory Press 2019-05-07 <![CDATA[ Transcranial alternating current stimulation reduces BOLD adaptation and increases functional connectivity ]]> https://biorxiv.org/content/10.1101/630368v1?rss=1 Kar, K. Ito, T. Cole, M. W. Krekelberg, B. 2019-05-08 doi:10.1101/630368 Cold Spring Harbor Laboratory Press 2019-05-08 <![CDATA[ Global ecotypes in the ubiquitous marine clade SAR86 ]]> https://biorxiv.org/content/10.1101/635185v1?rss=1 Hoarfrost, A. Nayfach, S. Ladau, J. Yooseph, S. Arnosti, C. Dupont, C. L. Pollard, K. 2019-05-10 doi:10.1101/635185 Cold Spring Harbor Laboratory Press 2019-05-10 <![CDATA[ Lysosomal enzyme tripeptidyl peptidase 1 plays a role in degradation of beta amyloid fibrils ]]> https://biorxiv.org/content/10.1101/639682v1?rss=1 Cruz, D. L. El-Banna, M. Majumdar, A. Sleat, D. E. Muldowney, M. Lobel, P. Maxfield, F. R. 2019-05-16 doi:10.1101/639682 Cold Spring Harbor Laboratory Press 2019-05-16 <![CDATA[ An omnidirectional visualization model of personalized gene regulatory networks ]]> https://biorxiv.org/content/10.1101/644070v1?rss=1 Chen, C. Jiang, L. Wang, M. Wang, Y. Shen, B. Liu, Z. Wang, Z. Hou, W. Berceli, S. Wu, R. 2019-05-21 doi:10.1101/644070 Cold Spring Harbor Laboratory Press 2019-05-21 <![CDATA[ Overt attention towards appetitive cues enhances their subjective value, independent of orbitofrontal cortex activity ]]> https://biorxiv.org/content/10.1101/648931v1?rss=1 McGinty, V. B. 2019-05-24 doi:10.1101/648931 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ Structural basis of Q-dependent antitermination ]]> https://biorxiv.org/content/10.1101/651190v1?rss=1 Yin, Z. Kaelber, J. Ebright, R. H. 2019-05-27 doi:10.1101/651190 Cold Spring Harbor Laboratory Press 2019-05-27 <![CDATA[ Multi-ethnic genome-wide association study of decomposed cardioelectric phenotypes illustrates strategies to identify and characterize evidence of shared genetic effects for complex traits ]]> https://biorxiv.org/content/10.1101/654012v1?rss=1 Baldassari, A. R. Avery, C. L. Highland, H. M. Arking, D. R. Buyske, S. Darbar, D. Gondalia, R. Graff, M. R. Guo, X. R. Heckbert, S. R. Hindorff, L. A. Hodonsky, C. J. Ida Chen, Y.-D. Kaplan, R. C. Peters, U. Post, W. Reiner, A. P. Shohet, R. V. Sotoodehnia, N. Tao, R. Taylor, K. D. Yao, J. D. Kenny, E. D. Lin, H. J. Soliman, E. Z. Whitsel, E. A. North, K. E. Kooperberg, C. Rotters, j. Seyerle, A. A. 2019-05-31 doi:10.1101/654012 Cold Spring Harbor Laboratory Press 2019-05-31 <![CDATA[ Tissue Engineered Axon Tracts Serve as Living Scaffolds to Accelerate Axonal Regeneration and Functional Recovery Following Peripheral Nerve Injury in Rats ]]> https://biorxiv.org/content/10.1101/654723v1?rss=1 Katiyar, K. Struzyna, L. A. Morand, J. P. Burrell, J. C. Clements, B. Laimo, F. A. Browne, K. D. Kohn, J. Ali, Z. Ledebur, H. C. Smith, D. H. Cullen, D. K. 2019-05-31 doi:10.1101/654723 Cold Spring Harbor Laboratory Press 2019-05-31 <![CDATA[ AimB is a small protein regulator of cell size and MreB assembly ]]> https://biorxiv.org/content/10.1101/655720v1?rss=1 Werner, J. N. Shi, H. Hsin, J. Huang, K. Gitai, Z. Klein, E. A. 2019-05-31 doi:10.1101/655720 Cold Spring Harbor Laboratory Press 2019-05-31 <![CDATA[ Neuropilin 2 signaling mediates corticostriatal transmission, spine maintenance, and goal-directed learning in mice ]]> https://biorxiv.org/content/10.1101/659342v1?rss=1 Assous, M. Martinez, E. Eisenberg, C. Kosc, A. Varghese, K. Espinoza, D. Bhimani, S. Shah, F. Tepper, J. Shiflett, M. W. Tran, T. S. 2019-06-03 doi:10.1101/659342 Cold Spring Harbor Laboratory Press 2019-06-03 <![CDATA[ Strategies for Integrating Single-Cell RNA Sequencing Results With Multiple Species ]]> https://biorxiv.org/content/10.1101/671115v1?rss=1 Hart, R. P. 2019-06-14 doi:10.1101/671115 Cold Spring Harbor Laboratory Press 2019-06-14 <![CDATA[ Spatiotemporal patterns of transcranial electrical stimulation can strengthen the metamemory of individual episodic memories in humans ]]> https://biorxiv.org/content/10.1101/672378v1?rss=1 Pilly, P. K. Skorheim, S. W. Hubbard, R. J. Ketz, N. A. Roach, S. M. Jones, A. P. Robert, B. Bryant, N. B. Lerner, I. Hartholt, A. Mullins, T. S. Choe, J. Clark, V. P. Howard, M. D. 2019-06-15 doi:10.1101/672378 Cold Spring Harbor Laboratory Press 2019-06-15 <![CDATA[ NemaLife: A structured microfluidic culture device optimized for aging studies in crawling C. elegans ]]> https://biorxiv.org/content/10.1101/675827v1?rss=1 Rahman, M. Edwards, H. Birze, N. Gabrilska, R. Rumbaugh, K. P. Blawzdziewicz, J. Szewczyk, N. Driscoll, M. Vanapalli, S. A. 2019-06-19 doi:10.1101/675827 Cold Spring Harbor Laboratory Press 2019-06-19 <![CDATA[ Predicting dysfunctional age-related task activations from resting-state network alterations ]]> https://biorxiv.org/content/10.1101/678086v1?rss=1 Mill, R. D. Gordon, B. A. Balota, D. A. Zacks, J. M. Cole, M. W. 2019-06-21 doi:10.1101/678086 Cold Spring Harbor Laboratory Press 2019-06-21 <![CDATA[ Individualized Dynamic Brain Models: Estimation and Validation with Resting-State fMRI ]]> https://biorxiv.org/content/10.1101/678243v1?rss=1 Singh, M. Braver, T. Cole, M. Ching, S. 2019-06-21 doi:10.1101/678243 Cold Spring Harbor Laboratory Press 2019-06-21 <![CDATA[ Evidence that inconsistent gene prediction can mislead analysis of algal genomes ]]> https://biorxiv.org/content/10.1101/690040v1?rss=1 Chen, Y. Stephens, T. G. Bhattacharya, D. Gonzalez-Pech, R. A. Chan, C. X. 2019-07-02 doi:10.1101/690040 Cold Spring Harbor Laboratory Press 2019-07-02 <![CDATA[ Estimating and testing the microbial causal mediation effect with high-dimensional and compositional microbiome data ]]> https://biorxiv.org/content/10.1101/692152v1?rss=1 Wang, C. Hu, J. Blaser, M. J. Li, H. 2019-07-04 doi:10.1101/692152 Cold Spring Harbor Laboratory Press 2019-07-04 <![CDATA[ Colicin E1 Fragments Potentiate Antibiotics by Plugging TolC ]]> https://biorxiv.org/content/10.1101/692251v1?rss=1 Budiardjo, S. J. Deay, J. J. Calkins, A. L. Wimalasena, V. K. Montezano, D. Biteen, J. S. Slusky, J. S. G. 2019-07-04 doi:10.1101/692251 Cold Spring Harbor Laboratory Press 2019-07-04 <![CDATA[ Competitive dewetting underlies site-specific binding of general anesthetics to GABA(A) receptors ]]> https://biorxiv.org/content/10.1101/694612v1?rss=1 Murlidaran, S. Henin, J. Brannigan, G. 2019-07-08 doi:10.1101/694612 Cold Spring Harbor Laboratory Press 2019-07-08 <![CDATA[ Mathematical models of protease-based enzymatic biosensors ]]> https://biorxiv.org/content/10.1101/695320v1?rss=1 Agrawal, D. K. Khare, S. Sontag, E. D. 2019-07-08 doi:10.1101/695320 Cold Spring Harbor Laboratory Press 2019-07-08 <![CDATA[ Sugar-phosphate metabolism regulates stationary phase entry and stalk elongation in Caulobacter crescentus ]]> https://biorxiv.org/content/10.1101/700559v1?rss=1 de Young, K. D. Stankeviciute, G. Klein, E. A. 2019-07-14 doi:10.1101/700559 Cold Spring Harbor Laboratory Press 2019-07-14 <![CDATA[ Polarella glacialis genomes encode tandem repeats of single-exon genes with functions critical to adaptation of dinoflagellates ]]> https://biorxiv.org/content/10.1101/704437v1?rss=1 50,000 high-quality genes. About 68% of the genome is repetitive sequence; long terminal repeats likely contribute to intra-species structural divergence and distinct genome sizes (3.0 and 2.7 Gbp). Of all genes, [~]40% are encoded unidirectionally, [~]25% comprised of single exons. Multi-genome comparison unveiled genes specific to P. glacialis and a common, putatively bacterial, origin of ice-binding domains in cold-adapted dinoflagellates. Our results elucidate how selection acts within the context of a complex genome structure to facilitate local adaptation. Since most dinoflagellate genes are constitutively expressed, Polarella glacialis has enhanced transcriptional responses via unidirectional, tandem duplication of single-exon genes that encode functions critical to survival in cold, low-light environments. ]]> Stephens, T. G. Gonzalez-Pech, R. A. Cheng, Y. Mohamed, A. R. Bhattacharya, D. Ragan, M. A. Chan, C. X. 2019-07-16 doi:10.1101/704437 Cold Spring Harbor Laboratory Press 2019-07-16 <![CDATA[ Beyond the Motor Cortex: Theta Burst Stimulation of the Anterior Midcingulate Cortex ]]> https://biorxiv.org/content/10.1101/707802v1?rss=1 Baker, T. E. Lin, M.-H. E. Parikh, S. E. Bauer, N. E. Cocuzza, C. E. 2019-07-19 doi:10.1101/707802 Cold Spring Harbor Laboratory Press 2019-07-19 <![CDATA[ Ribosomal stalk proteins RPLP1 and RPLP2 promote biogenesis of flaviviral and cellular multi-pass transmembrane proteins ]]> https://biorxiv.org/content/10.1101/713016v1?rss=1 Campos, R. K. Wijeratne, S. Shah, P. Garcia-Blanco, M. A. Bradrick, S. S. 2019-07-24 doi:10.1101/713016 Cold Spring Harbor Laboratory Press 2019-07-24 <![CDATA[ A ciliary BBSome-ARL-6-PDE6D pathway trafficks RAB-28, a negative regulator of extracellular vesicle biogenesis ]]> https://biorxiv.org/content/10.1101/715730v1?rss=1 Akella, J. S. Carter, S. P. Rizvi, F. Nguyen, K. C. Q. Tsiropoulou, S. Moran, A. L. Silva, M. Kennedy, B. N. Hall, D. H. Barr, M. M. Blacque, O. E. 2019-07-25 doi:10.1101/715730 Cold Spring Harbor Laboratory Press 2019-07-25 <![CDATA[ Phase variation in Mycobacterium tuberculosis glpK produces transiently heritable drug tolerance ]]> https://biorxiv.org/content/10.1101/717272v1?rss=1 Safi, H. Gopal, P. Lingaraju, S. Ma, S. Levine, C. Dartois, V. Yee, M. Li, L. Blanc, L. Liang, H.-P. H. Husain, S. Hoque, M. Soteropoulos, P. Rustad, T. Sherman, D. Dick, T. Alland, D. 2019-07-28 doi:10.1101/717272 Cold Spring Harbor Laboratory Press 2019-07-28 <![CDATA[ Hidden Aspects of the Research-ADOS are Bound to Affect Autism Science ]]> https://biorxiv.org/content/10.1101/717827v1?rss=1 Torres, E. B. Rai, R. B. Mistry, S. B. Gupta, B. 2019-07-28 doi:10.1101/717827 Cold Spring Harbor Laboratory Press 2019-07-28 <![CDATA[ SirT7 auto-ADP-ribosylation regulates glucose starvation response through macroH2A1.1 ]]> https://biorxiv.org/content/10.1101/719559v1?rss=1 Simonet, N. G. Thackray, J. K. Vazquez, B. N. Ianni, A. Espinosa-Alcantud, M. Morales-Sanfrutos, J. Hurtado-Bages, S. Sabido, E. Buschbeck, M. Tischfield, J. de la Torre, C. Esteller, M. Braun, T. Olivella, M. Serrano, L. Vaquero, A. 2019-08-05 doi:10.1101/719559 Cold Spring Harbor Laboratory Press 2019-08-05 <![CDATA[ Direct Binding of Phosphatidylglycerol at Specific Sites Modulates Desensitization of a Pentameric Ligand-Gated Ion Channel ]]> https://biorxiv.org/content/10.1101/722512v1?rss=1 Tong, A. Petroff, J. T. Hsu, F.-F. Schmidpeter, P. A. Nimigean, C. M. Sharp, L. Brannigan, G. Cheng, W. W. 2019-08-07 doi:10.1101/722512 Cold Spring Harbor Laboratory Press 2019-08-07 <![CDATA[ The interplay between molten globule intermediates and heme disassociation characterizes human hemoglobin disassembly ]]> https://biorxiv.org/content/10.1101/726216v1?rss=1 Samuel, P. P. White, M. A. Ou, W. C. Case, D. A. Phillips, G. N. Olson, J. S. 2019-08-07 doi:10.1101/726216 Cold Spring Harbor Laboratory Press 2019-08-07 <![CDATA[ Post-Transcriptional Bone Morphogenetic Protein 2 (BMP2) Gene Regulation in Aorta ]]> https://biorxiv.org/content/10.1101/735852v1?rss=1 Shah, T. A. Tang, Y. Yurkow, E. J. Rogers, M. B. 2019-08-15 doi:10.1101/735852 Cold Spring Harbor Laboratory Press 2019-08-15 <![CDATA[ Quantitative trait loci (QTL) underlying phenotypic variation in bioethanol-related processes in Neurospora crassa. ]]> https://biorxiv.org/content/10.1101/736470v1?rss=1 Waters, J. C. Jhaveri, D. Biffinger, J. C. Lee, K. 2019-08-15 doi:10.1101/736470 Cold Spring Harbor Laboratory Press 2019-08-15 <![CDATA[ Protein-protein docking using learned three-dimensional representations ]]> https://biorxiv.org/content/10.1101/738690v1?rss=1 Derevyanko, G. Lamoureux, G. 2019-08-19 doi:10.1101/738690 Cold Spring Harbor Laboratory Press 2019-08-19 <![CDATA[ Dual RNA-seq provides insight into the biology of the neglected intracellular human pathogen Orientia tsutsugamushi ]]> https://biorxiv.org/content/10.1101/743641v1?rss=1 Mika-Gospodorz, B. Giengkam, S. Westermann, A. Wongsantichon, J. Kion-Crosby, W. B. Chuenklin, S. Wang, L. C. Sunyakumthorn, P. Sobota, R. Subbian, S. Vogel, J. Barquist, L. Salje, J. 2019-08-24 doi:10.1101/743641 Cold Spring Harbor Laboratory Press 2019-08-24 <![CDATA[ Demonstrating and disrupting well-learned habits ]]> https://biorxiv.org/content/10.1101/745356v1?rss=1 Ceceli, A. O. Myers, C. E. Tricomi, E. 2019-08-24 doi:10.1101/745356 Cold Spring Harbor Laboratory Press 2019-08-24 <![CDATA[ VAMP8 contributes to TRIM6-mediated type-I interferon antiviral response during West Nile virus infection ]]> https://biorxiv.org/content/10.1101/749853v1?rss=1 Van Tol, S. Atkins, C. Bharaj, P. Johnson, K. N. Hage, A. Freiberg, A. N. Rajsbaum, R. 2019-08-28 doi:10.1101/749853 Cold Spring Harbor Laboratory Press 2019-08-28 <![CDATA[ Control of clathrin-mediated endocytosis by NIMA family kinases ]]> https://biorxiv.org/content/10.1101/757427v1?rss=1 Joseph, B. B. Wang, Y. Lazetic, V. Edeen, P. Grant, B. Fay, D. S. 2019-09-04 doi:10.1101/757427 Cold Spring Harbor Laboratory Press 2019-09-04 <![CDATA[ Spatiotemporal dynamics of RNA virus diversity in a phyllosphere microbial community ]]> https://biorxiv.org/content/10.1101/772475v1?rss=1 Bono, L. M. Orton, R. J. Peredo, E. L. Morrison, H. G. Sistrom, M. J. Simmons, S. Turner, P. 2019-09-18 doi:10.1101/772475 Cold Spring Harbor Laboratory Press 2019-09-18 <![CDATA[ Enhanced maturation of fast-spiking interneurons driven by mTOR activation ]]> https://biorxiv.org/content/10.1101/777714v1?rss=1 Chu, J. Fitzgerald, M. L. Sehgal, N. Manley, W. Fitzgerald, S. Naung, H. Goldberg, E. M. Anderson, S. A. 2019-09-20 doi:10.1101/777714 Cold Spring Harbor Laboratory Press 2019-09-20 <![CDATA[ Structure-Based Discovery of a Novel Small-Molecule Inhibitor of Methicillin-Resistant S. aureus ]]> https://biorxiv.org/content/10.1101/781971v1?rss=1 Lu, M. Liu, J. Kozhaya, L. 2019-10-01 doi:10.1101/781971 Cold Spring Harbor Laboratory Press 2019-10-01 <![CDATA[ Structural rearrangements drive extensive genome divergence between symbiotic and free-living Symbiodinium ]]> https://biorxiv.org/content/10.1101/783902v1?rss=1 Gonzalez-Pech, R. A. Stephens, T. G. Chen, Y. Mohamed, A. R. Cheng, Y. Burt, D. W. Bhattacharya, D. Ragan, M. A. Chan, C. X. 2019-09-26 doi:10.1101/783902 Cold Spring Harbor Laboratory Press 2019-09-26 <![CDATA[ Clickable methionine as a universal probe for labelling intracellular bacteria ]]> https://biorxiv.org/content/10.1101/784371v1?rss=1 Atwal, S. Giengkam, S. Jaiyen, Y. Feaga, h. Dworkin, J. Salje, J. 2019-09-26 doi:10.1101/784371 Cold Spring Harbor Laboratory Press 2019-09-26 <![CDATA[ Regulatory Feedbacks on Receptor and Non-receptor Synthesis for Robust Signaling ]]> https://biorxiv.org/content/10.1101/791509v1?rss=1 Lander, A. D. Nie, Q. Sanchez-Tapia, C. H. Simonyan, A. Wan, F. Y. M. 2019-10-03 doi:10.1101/791509 Cold Spring Harbor Laboratory Press 2019-10-03 <![CDATA[ Paulinella micropora KR01 holobiont genome assembly for studying primary plastid evolution ]]> https://biorxiv.org/content/10.1101/794941v1?rss=1 1 billion years ago, therefore relatively little can be learned about plastid integration during the initial stages of primary endosymbiosis by studying these highly derived species. Here we focused on a unique model for endosymbiosis research, the photosynthetic amoeba Paulinella micropora KR01 (Rhizaria) that underwent a more recent independent primary endosymbiosis about 124 Mya. A total of 149 Gbp of PacBio and 19 Gbp of Illumina data were used to generate the draft assembly that comprises 7,048 contigs with N50=143,028 bp and a total length of 707 Mbp. Genome GC-content was 44% with 76% repetitive sequences. We predicted 32,358 genes that contain 73% of the complete, conserved genes in the BUSCO database. The mean intron length was 882 bp, which is significantly greater than in other Rhizaria (86[~]184 bp). Symbiotic bacteria from the culture were isolated and completed genomes were generated from three species (Mesorhizobium amorphae Pch-S, Methylibium petroeiphilum Pch-M, Polaromonas sp. Pch-P) with one draft genome (Pimelobacter simplex Pch-N). Our holobiont data establish P. micropora KR01 as a model for studying plastid integration and the role of bacterial symbionts in Paulinella biology. ]]> Lhee, D. Lee, J. Cho, C. H. Ha, J.-S. Jeong, S. E. Jeon, C. O. Zelzion, U. Price, D. C. Chan, Y.-F. Gabr, A. Bhattacharya, D. Yoon, H. S. 2019-10-07 doi:10.1101/794941 Cold Spring Harbor Laboratory Press 2019-10-07 <![CDATA[ Genomes of Symbiodiniaceae reveal extensive sequence divergence but conserved functions at family and genus levels ]]> https://biorxiv.org/content/10.1101/800482v1?rss=1 Gonzalez-Pech, R. A. Chen, Y. Stephens, T. G. Shah, S. Mohamed, A. R. Lagorce, R. Bhattacharya, D. Ragan, M. A. Chan, C. X. 2019-10-10 doi:10.1101/800482 Cold Spring Harbor Laboratory Press 2019-10-10 <![CDATA[ Collagen I weakly interacts with the β-sheets of β2-microglobulin and enhances conformational exchange to induce amyloid formation ]]> https://biorxiv.org/content/10.1101/801522v1?rss=1 Hoop, C. L. Zhu, J. Bhattacharya, S. Tobita, C. A. Radford, S. E. Baum, J. 2019-10-11 doi:10.1101/801522 Cold Spring Harbor Laboratory Press 2019-10-11 <![CDATA[ Diffuse X-ray Scattering from Correlated Motions in a Protein Crystal ]]> https://biorxiv.org/content/10.1101/805424v1?rss=1 Meisburger, S. P. Case, D. A. Ando, N. 2019-10-17 doi:10.1101/805424 Cold Spring Harbor Laboratory Press 2019-10-17 <![CDATA[ Intracellular Neutralization of Ricin Toxin by Single Domain Antibodies Targeting the Active Site Pocket ]]> https://biorxiv.org/content/10.1101/805754v1?rss=1 Rudolph, M. J. Czajka, T. J. Davis, S. Nguyen, C. M. T. Li, X.-p. Tumer, N. Vance, D. J. MANTIS, N. J. 2019-10-15 doi:10.1101/805754 Cold Spring Harbor Laboratory Press 2019-10-15 <![CDATA[ Promoter scanning during transcription initiation in Saccharomyces cerevisiae: Pol II in the \"shooting gallery\" ]]> https://biorxiv.org/content/10.1101/810127v1?rss=1 Qiu, C. Jin, H. Vvedenskaya, I. Llenas, J. A. Zhao, T. Malik, I. Schwartz, S. L. Cui, P. Cabart, P. Han, K. H. Metz, R. P. Johnson, C. D. Sze, S.-H. Pugh, B. F. Nickels, B. E. Kaplan, C. D. 2019-10-22 doi:10.1101/810127 Cold Spring Harbor Laboratory Press 2019-10-22 <![CDATA[ The influence of relationship closeness on default-mode network connectivity during social interactions ]]> https://biorxiv.org/content/10.1101/815274v1?rss=1 Fareri, D. S. Smith, D. V. Delgado, M. R. 2019-10-22 doi:10.1101/815274 Cold Spring Harbor Laboratory Press 2019-10-22 <![CDATA[ Closing and opening of the RNA polymerase trigger loop ]]> https://biorxiv.org/content/10.1101/817080v1?rss=1 Mazumder, A. Lin, M. Kapanidis, A. Ebright, R. H. 2019-10-24 doi:10.1101/817080 Cold Spring Harbor Laboratory Press 2019-10-24 <![CDATA[ Coordination among neighbors improves the efficacy of Zika control despite economic costs ]]> https://biorxiv.org/content/10.1101/819490v1?rss=1 Lemanski, N. J. Schwab, S. R. Fonseca, D. M. Fefferman, N. H. 2019-10-25 doi:10.1101/819490 Cold Spring Harbor Laboratory Press 2019-10-25 <![CDATA[ Flexible coordinator and switcher hubs for adaptive task control ]]> https://biorxiv.org/content/10.1101/822213v1?rss=1 Cocuzza, C. V. Ito, T. Schultz, D. H. Bassett, D. S. Cole, M. W. 2019-10-29 doi:10.1101/822213 Cold Spring Harbor Laboratory Press 2019-10-29 <![CDATA[ Sparse epistatic patterns in the evolution of terpene synthases ]]> https://biorxiv.org/content/10.1101/822544v1?rss=1 Ballal, A. Laurendon, C. Salmon, M. Vardakou, M. Cheema, J. O'Maille, P. E. Morozov, A. V. 2019-10-29 doi:10.1101/822544 Cold Spring Harbor Laboratory Press 2019-10-29 <![CDATA[ Protein thermal stability does not correlate with cellular half-life: Global observations and a case study of tripeptidyl-peptidase 1 ]]> https://biorxiv.org/content/10.1101/828509v1?rss=1 Collier, A. M. Nemtsova, Y. Kuber, N. Banach-Petrosky, W. Modak, A. Sleat, D. E. Nanda, V. Lobel, P. 2019-11-11 doi:10.1101/828509 Cold Spring Harbor Laboratory Press 2019-11-11 <![CDATA[ Combining multiple functional connectivity methods to improve causal inferences ]]> https://biorxiv.org/content/10.1101/841890v1?rss=1 Sanchez-Romero, R. Cole, M. W. 2019-11-14 doi:10.1101/841890 Cold Spring Harbor Laboratory Press 2019-11-14 <![CDATA[ A synthetic approach reveals a highly sensitive maize auxin response circuit ]]> https://biorxiv.org/content/10.1101/844100v1?rss=1 Ramos Baez, R. Buckley, Y. Yu, H. Chen, Z. Gallavotti, A. Nemhauser, J. Moss, B. L. 2019-11-19 doi:10.1101/844100 Cold Spring Harbor Laboratory Press 2019-11-19 <![CDATA[ Preparing for the 3D data deluge: real time structural search at the scale of the PDB and beyond ]]> https://biorxiv.org/content/10.1101/845123v1?rss=1 Guzenko, D. Burley, S. K. Duarte, J. M. 2019-11-16 doi:10.1101/845123 Cold Spring Harbor Laboratory Press 2019-11-16 <![CDATA[ Nova proteins direct synaptic integration of somatostatin interneurons through activity-dependent alternative splicing ]]> https://biorxiv.org/content/10.1101/845230v1?rss=1 Fishell, G. Wamsley, B. Ibrahim, L. A. Yusuf, N. Fisher, E. Jaglin, X. H. Xu, Q. Gao, L. Khodadadi-Jamayran, A. Favuzzi, E. Yuan, Y. Darnell, R. Dimidschstein, J. 2019-11-16 doi:10.1101/845230 Cold Spring Harbor Laboratory Press 2019-11-16 <![CDATA[ Peripheral Nerve Repair Using Tissue Engineered Living Scaffolds Comprised of Stretch-Grown Aligned Axonal Tracts Promotes Survival of Spinal Cord Motor Neurons ]]> https://biorxiv.org/content/10.1101/847988v1?rss=1 Maggiore, J. C. Burrell, J. C. Browne, K. D. Katiyar, K. C. Laimo, F. A. Ali, Z. Kaplan, H. M. Rosen, J. M. Cullen, D. K. 2019-11-20 doi:10.1101/847988 Cold Spring Harbor Laboratory Press 2019-11-20 <![CDATA[ RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription ]]> https://biorxiv.org/content/10.1101/855544v1?rss=1 Li, L. Molodtsov, V. Lin, W. Ebright, R. H. Zhang, Y. 2019-11-26 doi:10.1101/855544 Cold Spring Harbor Laboratory Press 2019-11-26 <![CDATA[ Deletion of mouse Setd4 promotes the recovery of hematopoietic failure. ]]> https://biorxiv.org/content/10.1101/860239v1?rss=1 Feng, X. Lu, H. Yue, J. Shettigar, M. Liu, J. Denzin, L. K. Shen, Z. 2019-11-29 doi:10.1101/860239 Cold Spring Harbor Laboratory Press 2019-11-29 <![CDATA[ Aurora B and C kinases regulate prophase exit and chromosome segregation during spermatogenesis ]]> https://biorxiv.org/content/10.1101/868836v1?rss=1 Wellard, S. R. Schindler, K. Jordan, P. 2019-12-11 doi:10.1101/868836 Cold Spring Harbor Laboratory Press 2019-12-11 <![CDATA[ MixMir: microRNA motif discovery from gene expression data using mixed linear models ]]> https://biorxiv.org/content/10.1101/004010v1?rss=1 LIYANG Diao Antoine Marcais Scott Norton Kevin C. Chen 2014-04-09 doi:10.1101/004010 Cold Spring Harbor Laboratory Press 2014-04-09 <![CDATA[ Fast Bayesian Inference of Copy Number Variants using Hidden Markov Models with Wavelet Compression ]]> https://biorxiv.org/content/10.1101/023705v1?rss=1 John Wiedenhoeft Eric Brugel Alexander Schliep 2015-07-31 doi:10.1101/023705 Cold Spring Harbor Laboratory Press 2015-07-31 <![CDATA[ Limiting the Development of Anti-Cancer Drug Resistance in a Spatial Model of Micrometastases ]]> https://biorxiv.org/content/10.1101/042408v1?rss=1 Ami B Shah Katarzyna A Rejniak Jana L Gevertz 2016-03-04 doi:10.1101/042408 Cold Spring Harbor Laboratory Press 2016-03-04 <![CDATA[ Clusterflock: A Flocking Algorithm for Isolating Congruent Phylogenomic Datasets ]]> https://biorxiv.org/content/10.1101/045773v1?rss=1 Apurva Narechania Richard H Baker Rob DeSalle Barun Mathema Barry Kreiswirth Sergios-Orestis Kolokotronis Paul J Planet 2016-03-25 doi:10.1101/045773 Cold Spring Harbor Laboratory Press 2016-03-25 <![CDATA[ discoal: flexible coalescent simulations with selection ]]> https://biorxiv.org/content/10.1101/063453v1?rss=1 Andrew D. Kern Daniel Schrider 2016-07-12 doi:10.1101/063453 Cold Spring Harbor Laboratory Press 2016-07-12 <![CDATA[ Exact calculation of the joint allele frequency spectrum for generalized isolation with migration models ]]> https://biorxiv.org/content/10.1101/065003v1?rss=1 Andrew Kern Jody Hey 2016-07-21 doi:10.1101/065003 Cold Spring Harbor Laboratory Press 2016-07-21 <![CDATA[ Scale-Free Exponents of Resting State are Biomarkers of Neuro-Typical and Atypical Brain Activity ]]> https://biorxiv.org/content/10.1101/068841v1?rss=1 2.0) causing a dramatic change in network structure including a loss of global connectivity, an increasing minimum dominating node set, and a shift towards increasing connectivity growth compared to node growth. Is this SFN shift identifiable in atypical brain activity? The Pareto Distribution (P(D)[~]D{wedge}-{beta}) on the hub Degree (D) is a signature of scale-free networks. During resting-state, we assess Degree exponents across a large range of neurotypical and atypical subjects. We use graph complexity theory to provide a predictive theory of the brain network structure. Results.We show that neurotypical resting-state fMRI brain activity possess scale-free Pareto exponents (1.8 se .01) in a single individual scanned over 66 days as well as in 60 different individuals (1.8 se .02). We also show that 60 individuals with Autistic Spectrum Disorder, and 60 individuals with Schizophrenia have significantly higher (>2.0) scale-free exponents (2.4 se .03, 2.3 se .04), indicating more fractionated and less controllable dynamics in the brain networks revealed in resting state. Finally we show that the exponent values vary with phenotypic measures of atypical disease severity indicating that the global topology of the network itself can provide specific diagnostic biomarkers for atypical brain activity. ]]> Stephen Jose Hanson Dana Mastrovito Catherine Hanson Joe Ramsey Clark Glymour 2016-08-10 doi:10.1101/068841 Cold Spring Harbor Laboratory Press 2016-08-10 <![CDATA[ 3-5 Hz membrane potential oscillations decrease the gain of neurons in visual cortex ]]> https://biorxiv.org/content/10.1101/069252v1?rss=1 Michael C Einstein Pierre-Olivier Polack Peyman Golshani 2016-08-11 doi:10.1101/069252 Cold Spring Harbor Laboratory Press 2016-08-11 <![CDATA[ UNC-5 (UNC5) Regulates the Length and Number of Processes that Caenorhabditis elegans Neurons Can Develop ]]> https://biorxiv.org/content/10.1101/083436v1?rss=1 Limerick, G. Tang, X. Lee, W. S. Mohamed, A. Al-Aamiri, A. Wadsworth, W. G. 2016-10-25 doi:10.1101/083436 Cold Spring Harbor Laboratory Press 2016-10-25 <![CDATA[ Natural diversity of the malaria vector Anopheles gambiae ]]> https://biorxiv.org/content/10.1101/096289v1?rss=1 Miles, A. Harding, N. J. Botta, G. Clarkson, C. Antao, T. Kozak, K. Schrider, D. Kern, A. Redmond, S. Sharakhov, I. Pearson, R. Bergey, C. Fontaine, M. Troco, A. Diabate, A. Costantini, C. Rohatgi, K. Elissa, N. Coulibaly, B. Dinis, J. Midega, J. Mbogo, C. Mawejje, H. Stalker, J. Rockett, K. Drury, E. Mead, D. Jeffreys, A. Hubbart, C. Rowlands, K. Isaacs, A. Jyothi, D. Malangone, C. Vauterin, P. Jeffrey, B. Wright, I. Hart, L. Kluczynski, K. Cornelius, V. MacInnis, B. Henrichs, C. Giacomantonio, R. Ayala, D. Bejon, P. Besansky, N. Burt, A. Caputo, 2016-12-22 doi:10.1101/096289 Cold Spring Harbor Laboratory Press 2016-12-22 <![CDATA[ pals-22, A Member Of An Expanded C. elegans Gene Family, Controls Silencing Of Repetitive DNA ]]> https://biorxiv.org/content/10.1101/145094v1?rss=1 Leyva-Diaz, E. Stefanakis, N. Carrera, I. Glenwinkel, L. Wang, G. Driscoll, M. Hobert, O. 2017-06-02 doi:10.1101/145094 Cold Spring Harbor Laboratory Press 2017-06-02 <![CDATA[ GWAS of epigenetic ageing rates in blood reveals a critical role for TERT ]]> https://biorxiv.org/content/10.1101/157776v1?rss=1 Lu, A. T. Xue, L. Salfati, E. L. Chen, B. H. Ferrucci, L. Levy, D. Joehanes, R. Murabito, J. M. Kiel, D. P. Tsai, P.-C. Yet, I. Bell, J. T. Mangino, M. Tanaka, T. McRae, A. Marioni, R. E. Visscher, P. M. Wray, N. R. Deary, I. J. Levine, M. E. Quach, A. Assimes, T. L. Tsao, P. S. Absher, D. Stewart, J. D. Li, Y. Reiner, A. P. Hou, L. Baccarelli, A. A. Whitsel, E. A. Aviv, A. Cardona, A. Day, F. R. Perry, J. R. B. Ong, K. K. Raj, K. Lunetta, K. L. Horvath, S. 2017-06-30 doi:10.1101/157776 Cold Spring Harbor Laboratory Press 2017-06-30 <![CDATA[ A systems approach to the characterization and classification of T-cell responses ]]> https://biorxiv.org/content/10.1101/175620v1?rss=1 Yamamoto, S. Whalen, E. Chujo, D. Nattamai, D. Baldwin, N. O'Brien, K. Nguyen, Q.-A. Gersuk, V. Anguiano, E. Yang, J. Kwok, W. W. Banchereau, J. Ueno, H. Chaussabel, D. 2017-08-13 doi:10.1101/175620 Cold Spring Harbor Laboratory Press 2017-08-13 <![CDATA[ A computational framework for detecting signatures of accelerated somatic evolution in cancer genomes ]]> https://biorxiv.org/content/10.1101/177261v1?rss=1 Smith, K. S. Ghosh, D. Pollard, K. S. De, S. 2017-08-16 doi:10.1101/177261 Cold Spring Harbor Laboratory Press 2017-08-16 <![CDATA[ ATRX, DAXX or MEN1 mutant pancreatic neuroendocrine tumors are a distinct alpha-cell signature subgroup ]]> https://biorxiv.org/content/10.1101/195214v1?rss=1 Chan, C. Laddha, S. Lewis, P. Koletsky, M. Robzyk, K. Da Silva, E. Torres, P. Untch, B. Bose, P. Chan, T. Klimstra, D. Allis, C. D. Tang, L. 2017-09-28 doi:10.1101/195214 Cold Spring Harbor Laboratory Press 2017-09-28 <![CDATA[ RhoGAP RGA-8 supports morphogenesis in C. elegans by polarizing epithelia through CDC-42 ]]> https://biorxiv.org/content/10.1101/2019.12.15.877332v1?rss=1 Raduwan, H. Sasidharan, S. Cordova Burgos, L. Wallace, A. Soto, M. C. 2019-12-16 doi:10.1101/2019.12.15.877332 Cold Spring Harbor Laboratory Press 2019-12-16 <![CDATA[ Enhancing generating and collecting efficiency of single particle upconverting luminescence at low-level power excitation ]]> https://biorxiv.org/content/10.1101/2019.12.17.879858v1?rss=1 2.5 MW/cm2). However, such particles are inadequate for in-vitro live-cell imaging and single-particle tracking since high excitation power can cause photodamage. Here, we compared UCNPs luminescence intensities with different dopants concentrations and presented a more efficient ([~]7x) UCNPs at low excitation power by increasing the concentrations of Yb3+ and Tm3+ dopants (NaYF4: 60% Yb3+, 8% Tm3+) and adding a core-shell structure. ]]> Ma, C. Shan, C. Park, K. Mok, A. T. Yang, X. 2019-12-18 doi:10.1101/2019.12.17.879858 Cold Spring Harbor Laboratory Press 2019-12-18 <![CDATA[ Semilunar Granule Cells Maintain Distinct Dendritic Morphology and Inhibition through Postnatal Development and Receive Heightened Inhibition in Adolescence ]]> https://biorxiv.org/content/10.1101/2019.12.17.880005v1?rss=1 120, corresponding with human infancy, adolescence, and adulthood, we examined the somatodendritic morphology and inhibitory regulation in SGCs and GCs to determine the cell-type specific features. Unsupervised cluster analysis confirmed that morphological features reliably distinguish SGCs from GCs irrespective of animal age. SGCs maintain higher spontaneous inhibitory postsynaptic current (sIPSC) frequency than GCs from infancy through adulthood. Although sIPSC frequency in SGCs was particularly enhanced during adolescence, sIPSC amplitude and cumulative charge transfer declined from infancy to adulthood and were not different between GCs and SGCs. Extrasynaptic GABA current amplitude peaked in adolescence in both cell types and was significantly greater in SGCs than in GCs only during adolescence. Although GC input resistance was higher than in SGCs during infancy and adolescence, input resistance decreased with developmental age in GCs while it progressively increased in SGCs. Consequently, GCs input resistance was significantly lower than SGCs in adults. The data delineate the structural features that can reliably distinguish GCs from SGCs through development. The results reveal developmental differences in passive membrane properties and steady state inhibition between GCs and SGCs which could confound their use in classifying the cell types. ]]> Gupta, A. Subramanian, D. Proddutur, A. Chang, Y.-J. Guevarra, J. Shah, Y. Elgammal, F. S. Santhakumar, V. 2019-12-19 doi:10.1101/2019.12.17.880005 Cold Spring Harbor Laboratory Press 2019-12-19 <![CDATA[ Crowdsourcing digital health measures to predict Parkinson's disease severity: the Parkinson's Disease Digital Biomarker DREAM Challenge ]]> https://biorxiv.org/content/10.1101/2020.01.13.904722v1?rss=1 Sieberts, S. K. Schaff, J. Duda, M. Pataki, B. A. Sun, M. Snyder, P. Daneault, J.-F. Parisi, F. Costante, G. Rubin, U. Banda, P. Chae, Y. Neto, E. C. Dorsey, R. Aydın, Z. Chen, A. Elo, L. L. Espino, C. Glaab, E. Goan, E. Golabchi, F. N. Görmez, Y. Jaakkola, M. K. Jonnagaddala, J. KLEn, R. Li, D. McDaniel, C. Perrin, D. Rad, N. M. Rainaldi, E. Sapienza, S. Schwab, P. Shokhirev, N. Venäläinen, M. S. Vergara-Diaz, G. Zhang, Y. Parkinson's Disease Digital Biomarker Challenge Consortium, Wang, Y. Guan, Y. Brunner, D. Bonato, P. Mangravite, L. M. Omberg 2020-01-16 doi:10.1101/2020.01.13.904722 Cold Spring Harbor Laboratory Press 2020-01-16 <![CDATA[ Dynamin-like proteins are essential for vesicle biogenesis in Mycobacterium tuberculosis. ]]> https://biorxiv.org/content/10.1101/2020.01.14.906362v1?rss=1 Gupta, S. Palacios, A. Khataokar, A. Weinrick, B. Lavin, J. L. Sampedro, L. Gil, D. Anguita, J. Menendez, M. C. Garcia, M. J. Dogra, N. Neiditch, M. B. Prados-Rosales, R. Rodriguez, G. M. 2020-01-15 doi:10.1101/2020.01.14.906362 Cold Spring Harbor Laboratory Press 2020-01-15 <![CDATA[ Super-resolution visualization of distinct stalled and broken replication fork structures ]]> https://biorxiv.org/content/10.1101/2020.01.19.912014v1?rss=1 Whelan, D. R. Lee, W. T. C. Marks, F. Kong, Y. T. Yin, Y. Rothenberg, E. 2020-01-20 doi:10.1101/2020.01.19.912014 Cold Spring Harbor Laboratory Press 2020-01-20 <![CDATA[ A real-time search strategy for finding urban disease vector infestations ]]> https://biorxiv.org/content/10.1101/2020.01.20.911974v1?rss=1 Billig Rose, E. Roy, J. A. Castillo-Neyra, R. Ross, M. E. Condori-Pino, C. Peterson, J. K. Naquira-Velarde, C. Levy, M. Z. 2020-01-24 doi:10.1101/2020.01.20.911974 Cold Spring Harbor Laboratory Press 2020-01-24 <![CDATA[ Inhibition and Crystal Structure of the Human DHTKD1-Thiamin Diphosphate Complex ]]> https://biorxiv.org/content/10.1101/2020.01.20.913012v1?rss=1 Leandro, J. Khamrui, S. Wang, H. Suebsuwong, C. Nemeria, N. S. Huynh, K. Moustakim, M. Secor, C. Wang, M. Dodatko, T. Stauffer, B. Wilson, C. G. Yu, C. Arkin, M. R. Jordan, F. Sanchez, R. DeVita, R. J. Lazarus, M. B. Houten, S. M. 2020-01-21 doi:10.1101/2020.01.20.913012 Cold Spring Harbor Laboratory Press 2020-01-21 <![CDATA[ Diversity increases the stability of ecosystems. ]]> https://biorxiv.org/content/10.1101/2020.01.23.916536v1?rss=1 Makse, H. A. Arese Lucini, F. Morone, F. Tomassone, M. S. 2020-01-23 doi:10.1101/2020.01.23.916536 Cold Spring Harbor Laboratory Press 2020-01-23 <![CDATA[ PGC1/PPAR Drive Cardiomyocyte Maturation through Regulation of Yap1 and SF3B2 ]]> https://biorxiv.org/content/10.1101/2020.02.06.937797v1?rss=1 Murphy, S. Miyamoto, M. Kervadec, A. Kannan, S. Tampakakis, E. Kambhampati, S. Lin, B. L. Paek, S. Andersen, P. Lee, D.-I. Zhu, R. An, S. S. Kass, D. A. Uosaki, H. Colas, A. R. Kwon, C. 2020-02-07 doi:10.1101/2020.02.06.937797 Cold Spring Harbor Laboratory Press 2020-02-07 <![CDATA[ Depletion of glycosaminoglycans decreases contact stiffness of single collagen I fibrils in aqueous solution ]]> https://biorxiv.org/content/10.1101/2020.02.07.935932v1?rss=1 Roth, J. A. Hoop, C. Williams, J. Hayes, R. Baum, J. 2020-02-07 doi:10.1101/2020.02.07.935932 Cold Spring Harbor Laboratory Press 2020-02-07 <![CDATA[ Snow Microbiome Functional Analyses Reveal Novel Microbial Metabolism of Complex Organic Compounds ]]> https://biorxiv.org/content/10.1101/2020.02.07.938555v1?rss=1 Zhu, C. Miller, M. Lusskin, N. Bergk Pinto, B. Maccario, L. Haggblom, M. Vogel, T. Larose, C. Bromberg, Y. 2020-02-07 doi:10.1101/2020.02.07.938555 Cold Spring Harbor Laboratory Press 2020-02-07 <![CDATA[ A novel voltage clamp/dye uptake assay reveals saturable transport of molecules through CALHM1 and connexin channels. ]]> https://biorxiv.org/content/10.1101/2020.02.15.950923v1?rss=1 Gaete, P. S. Lillo, M. A. Lopez, W. Liu, Y. Harris, A. L. Contreras, J. E. 2020-02-15 doi:10.1101/2020.02.15.950923 Cold Spring Harbor Laboratory Press 2020-02-15 <![CDATA[ The Drosophila TART transposon manipulates the piRNA pathway as a counter-defense strategy to limit host silencing ]]> https://biorxiv.org/content/10.1101/2020.02.20.957324v1?rss=1 Ellison, C. Kagda, M. S. Cao, W. 2020-02-20 doi:10.1101/2020.02.20.957324 Cold Spring Harbor Laboratory Press 2020-02-20 <![CDATA[ Staphylococcal DNA repair confers tolerance of the bactericidal activity of both neutrophils and antibiotics ]]> https://biorxiv.org/content/10.1101/2020.02.23.961458v1?rss=1 Ha, K. P. Clarke, R. S. Brittan, J. L. Rowley, J. E. Mavridou, D. Clarke, T. B. Nobbs, A. H. Edwards, A. M. 2020-02-25 doi:10.1101/2020.02.23.961458 Cold Spring Harbor Laboratory Press 2020-02-25 <![CDATA[ Auto-inhibitory regulation of DNA binding by the C-terminal tails of the mitochondrial transcription factors Mtf1 and TFB2M ]]> https://biorxiv.org/content/10.1101/2020.03.06.980961v1?rss=1 Basu, U. Mishra, N. Farooqui, M. Shen, J. Johnson, L. C. Patel, S. S. 2020-03-08 doi:10.1101/2020.03.06.980961 Cold Spring Harbor Laboratory Press 2020-03-08 <![CDATA[ Structure and function of virion RNA polymerase of crAss-like phage ]]> https://biorxiv.org/content/10.1101/2020.03.07.982082v1?rss=1 Drobysheva, A. V. Panafidina, S. A. Kolesnik, M. V. Klimuk, E. I. Minakhin, L. Yakunina, M. V. Borukhov, S. Nilsson, E. Holmfeldt, K. Yutin, N. Makarova, K. S. Koonin, E. V. Severinov, K. V. Leiman, P. G. Sokolova, M. L. 2020-03-08 doi:10.1101/2020.03.07.982082 Cold Spring Harbor Laboratory Press 2020-03-08 <![CDATA[ Small Molecule Targeting IRES Domain Inhibits Enterovirus 71 Replication via an Allosteric Mechanism that Stabilizes a Ternary Complex ]]> https://biorxiv.org/content/10.1101/2020.03.10.981167v1?rss=1 Davila-Calderon, J. Patwardhan, N. N. Chiu, L.-Y. Sugarman, A. L. Cai, Z. Penutmutchu, S. R. Li, M.-L. Brewer, G. Hargrove, A. E. Tolbert, B. S. 2020-03-11 doi:10.1101/2020.03.10.981167 Cold Spring Harbor Laboratory Press 2020-03-11 <![CDATA[ Subventricular zone adult mouse neural stem cells and human glioblastoma stem cells require insulin receptor for self-renewal ]]> https://biorxiv.org/content/10.1101/2020.03.10.985598v1?rss=1 Chidambaram, S. Rothbard, D. Deshpande, K. Cajuste, Y. Fiser, A. Snyder, K. Farjardo, E. Tapinos, N. Wood, T. L. Levison, S. W. 2020-03-11 doi:10.1101/2020.03.10.985598 Cold Spring Harbor Laboratory Press 2020-03-11 <![CDATA[ Investigation of fascin1, a marker of mature dendritic cells, reveals a New role for IL-6 signaling in chemotaxis. ]]> https://biorxiv.org/content/10.1101/2020.03.19.979104v1?rss=1 Matsumura, F. Polz, R. Singh, S. Scheller, J. Yamashiro, S. 2020-03-20 doi:10.1101/2020.03.19.979104 Cold Spring Harbor Laboratory Press 2020-03-20 <![CDATA[ Click-chemistry enabled directed evolution of glycosynthases for bespoke glycans synthesis ]]> https://biorxiv.org/content/10.1101/2020.03.23.001982v1?rss=1 106 mutants) expressed in E. coli to identify several novel mutants with increased activity for {beta}-fucosyl-azide activated donor sugars towards desired acceptor sugars, demonstrating the broader applicability of this methodology. ]]> Agrawal, A. Bandi, C. K. Burgin, T. Woo, Y. Mayes, H. B. Chundawat, S. P. S. 2020-03-25 doi:10.1101/2020.03.23.001982 Cold Spring Harbor Laboratory Press 2020-03-25 <![CDATA[ Alterations in retrotransposition, synaptic connectivity, and myelination implicated by transcriptomic changes following maternal immune activation in non-human primates ]]> https://biorxiv.org/content/10.1101/2020.03.31.019190v1?rss=1 Page, N. F. Gandal, M. Estes, M. Cameron, S. Buth, J. Parhami, S. Ramaswami, G. Murray, K. Amaral, D. Van de Water, J. Schumann, C. M. Carter, C. S. Bauman, M. D. McAllister, A. K. Geschwind, D. H. 2020-04-01 doi:10.1101/2020.03.31.019190 Cold Spring Harbor Laboratory Press 2020-04-01 <![CDATA[ A Novel Model of Pancreatic Cancer Dormancy Reveals Mechanistic Insights and a Dormancy Gene Signature with Human Relevance ]]> https://biorxiv.org/content/10.1101/2020.04.13.037374v1?rss=1 Dudgeon, C. Harris, C. R. Chen, Y. Ghaddar, B. Sharma, A. Shah, M. M. Roberts, A. Casabianca, A. Collisson, E. Balachandran, V. Vertino, P. De, S. Carpizo, D. R. 2020-04-13 doi:10.1101/2020.04.13.037374 Cold Spring Harbor Laboratory Press 2020-04-13 <![CDATA[ TRIP6 is required for tension at adherens junctions ]]> https://biorxiv.org/content/10.1101/2020.04.19.049569v1?rss=1 Venkatramanan, S. Ibar Valenzuela, M. C. Irvine, K. 2020-04-20 doi:10.1101/2020.04.19.049569 Cold Spring Harbor Laboratory Press 2020-04-20 <![CDATA[ Disease-associated mutations in TRPM3 render the channel overactive via two distinct mechanisms ]]> https://biorxiv.org/content/10.1101/2020.04.20.052167v1?rss=1 Zhao, S. Yudin, Y. Rohacs, T. 2020-04-22 doi:10.1101/2020.04.20.052167 Cold Spring Harbor Laboratory Press 2020-04-22 <![CDATA[ Cellular expression and functional roles of all 26 neurotransmitter GPCRs in the C. elegans egg-laying circuit ]]> https://biorxiv.org/content/10.1101/2020.04.23.037242v1?rss=1 Fernandez, R. W. Wei, K. Wang, E. Y. Mikalauskaite, D. Olson, A. Pepper, J. Christie, N. Kim, S. Koelle, M. R. 2020-04-24 doi:10.1101/2020.04.23.037242 Cold Spring Harbor Laboratory Press 2020-04-24 <![CDATA[ A Circuit Mechanism Underlying Suppression of Circadian Signals by Homeostatic Sleep Drive ]]> https://biorxiv.org/content/10.1101/2020.04.29.068627v1?rss=1 King, A. N. Schwarz, J. E. Hsu, C. T. Barber, A. F. Sehgal, A. 2020-04-30 doi:10.1101/2020.04.29.068627 Cold Spring Harbor Laboratory Press 2020-04-30 <![CDATA[ Regulation of dopamine-dependent transcription and cocaine action by Gadd45b ]]> https://biorxiv.org/content/10.1101/2020.05.01.072926v1?rss=1 Zipperly, M. E. Sultan, F. A. Graham, G.-E. Brane, A. C. Simpkins, N. A. Ianov, L. Day, J. J. 2020-05-03 doi:10.1101/2020.05.01.072926 Cold Spring Harbor Laboratory Press 2020-05-03 <![CDATA[ One gene, multiple ecological strategies: a biofilm regulator is a capacitor for sustainable diversity ]]> https://biorxiv.org/content/10.1101/2020.05.02.074534v1?rss=1 20,000 generations with Burkholderia cenocepacia populations grown in a model of the biofilm life cycle and identified parallel mutations in one gene, rpfR, that is a conserved central regulator. Because RpfR has multiple sensor and catalytic domains, different mutations can produce different ecological strategies that can coexist and even increase net growth. This study demonstrates that a single gene may coordinate complex life histories in biofilm-dwelling bacteria and that selection in defined environments can reshape niche breadth by single mutations. ]]> Mhatre, E. R. Snyder, D. J. Sileo, E. Turner, C. B. Buskirk, S. W. Fernandez, N. L. Neiditch, M. B. Waters, C. M. Cooper, V. S. 2020-05-03 doi:10.1101/2020.05.02.074534 Cold Spring Harbor Laboratory Press 2020-05-03 <![CDATA[ Cryo-Electron Microscopy Visualization of a Large Insertion in the 5S ribosomal RNA of the Extremely Halophilic Archaeon Halococcus morrhuae. ]]> https://biorxiv.org/content/10.1101/2020.05.05.079889v1?rss=1 Tirumalai, M. R. Kaelber, J. T. Park, D. R. Tran, Q. Fox, G. E. 2020-05-06 doi:10.1101/2020.05.05.079889 Cold Spring Harbor Laboratory Press 2020-05-06 <![CDATA[ Carbohydrate binding domains facilitate efficient oligosaccharides synthesis by enhancing mutant catalytic domain transglycosylation activity ]]> https://biorxiv.org/content/10.1101/2020.05.06.081356v1?rss=1 140-fold over CDs alone. Dynamic intra-domain interactions that facilitate this poorly understood reaction mechanism were further revealed by small-angle X-ray scattering structural analysis along with detailed mutagenesis studies to shed light on our current limited understanding of similar transglycosylation-type reaction mechanisms. In summary, our study provides a novel strategy for engineering similar CBM-based CAZyme chimeras for synthesis of bespoke oligosaccharides using simple activated sugar monomers. ]]> Bandi, C. K. Goncalves, A. Pingali, S. V. Chundawat, S. P. S. 2020-05-08 doi:10.1101/2020.05.06.081356 Cold Spring Harbor Laboratory Press 2020-05-08 <![CDATA[ Perinatal IL-1-induced Inflammation Suppresses Tbr2+ Intermediate Progenitor Cell Proliferation in the Developing Hippocampus accompanied by Long-Term Behavioral Deficits ]]> https://biorxiv.org/content/10.1101/2020.05.08.084129v1?rss=1 Veerasammy, S. Van Steenwinckel, J. Le-Charpentier, T. Seo, J. H. Fleiss, B. Gressens, P. Levison, S. W. 2020-05-10 doi:10.1101/2020.05.08.084129 Cold Spring Harbor Laboratory Press 2020-05-10 <![CDATA[ Multiscale Characterization of Complex Binding Interactions of Cellulolytic Enzymes Highlights Limitations of Classical Approaches ]]> https://biorxiv.org/content/10.1101/2020.05.08.084152v1?rss=1 Chundawat, S. P. S. Nemmaru, B. Hackl, M. Brady, S. K. Hilton, M. A. Johnson, M. M. Chang, S. Lang, M. J. Huh, H. Lee, S.-H. Yarbrough, J. M. Lopez, C. A. Gnanakaran, S. 2020-05-10 doi:10.1101/2020.05.08.084152 Cold Spring Harbor Laboratory Press 2020-05-10 <![CDATA[ Comparison of analytical methods for rapid & reliable quantification of plant-based carbohydrates for the quintessential bioenergy educator ]]> https://biorxiv.org/content/10.1101/2020.05.21.106468v1?rss=1 Chundawat, S. P. S. 2020-05-23 doi:10.1101/2020.05.21.106468 Cold Spring Harbor Laboratory Press 2020-05-23 <![CDATA[ Polymorphic mobile element insertions contribute to gene expression and alternative splicing in human tissues ]]> https://biorxiv.org/content/10.1101/2020.05.23.111310v1?rss=1 Cao, X. Zhang, Y. Payer, L. M. Lords, H. Steranka, J. P. Burns, K. H. Xing, J. 2020-05-25 doi:10.1101/2020.05.23.111310 Cold Spring Harbor Laboratory Press 2020-05-25 <![CDATA[ The Autonomic Nervous System Differentiates Between Levels of Motor Intent and Hand Dominance ]]> https://biorxiv.org/content/10.1101/2020.06.01.128140v1?rss=1 Ryu, J. Torres, E. B. 2020-06-02 doi:10.1101/2020.06.01.128140 Cold Spring Harbor Laboratory Press 2020-06-02 <![CDATA[ CB1 receptor signaling modulates amygdalar plasticity during context-cocaine memory reconsolidation to promote subsequent cocaine seeking ]]> https://biorxiv.org/content/10.1101/2020.06.02.130419v1?rss=1 Higginbotham, J. A. Wang, R. Richardson, B. D. Shiina, H. Tan, S. M. Presker, M. A. Rossi, D. J. Fuchs, R. A. 2020-06-03 doi:10.1101/2020.06.02.130419 Cold Spring Harbor Laboratory Press 2020-06-03 <![CDATA[ Chromosome-directed oocyte spindle assembly depends HP1 and the Chromosomal Passenger Complex ]]> https://biorxiv.org/content/10.1101/2020.06.03.132142v1?rss=1 Wang, L.-I. Defosse, T. Battaglia, R. Wagner, V. McKim, K. 2020-06-03 doi:10.1101/2020.06.03.132142 Cold Spring Harbor Laboratory Press 2020-06-03 <![CDATA[ Outcomes of the 2019 EMDataResource model challenge: validation of cryo-EM models at near-atomic resolution ]]> https://biorxiv.org/content/10.1101/2020.06.12.147033v1?rss=1 Lawson, C. L. Kryshtafovych, A. Adams, P. D. Afonine, P. Baker, M. L. Barad, B. A. Bond, P. Burnley, T. Cao, R. Cheng, J. Chojnowski, G. Cowtan, K. Dill, K. A. DiMaio, F. Farrell, D. Fraser, J. S. Herzik, M. A. Hoh, S. W. Hou, J. Hung, L.-W. Igaev, M. Joseph, A. P. Kihara, D. Kumar, D. Mittal, S. Monastyrskyy, B. Olek, M. Palmer, C. Patwardhan, A. Perez, A. Pfab, J. Pintilie, G. D. Richardson, J. S. Rosenthal, P. B. Sarkar, D. Schaefer, L. U. Schmid, M. F. Schroeder, G. F. Shekhar, M. Si, D. Singharoy, A. Terashi, G. Terwilliger, T. C. Vaiana, A. Wan 2020-06-15 doi:10.1101/2020.06.12.147033 Cold Spring Harbor Laboratory Press 2020-06-15 <![CDATA[ CK2 inhibits TIMELESS nuclear export and modulates CLOCK transcriptional activity to regulate circadian rhythms ]]> https://biorxiv.org/content/10.1101/2020.06.12.148825v1?rss=1 Cai, Y. D. Xue, Y. Truong, C. Del-Carmen Li, J. Ochoa, C. Vanselow, J. T. Murphy, K. A. Li, Y. H. Liu, X. Kunimoto, B. L. Zheng, H. Zhao, C. Zhang, Y. Schlosser, A. Chiu, J. C. 2020-06-13 doi:10.1101/2020.06.12.148825 Cold Spring Harbor Laboratory Press 2020-06-13 <![CDATA[ REDCRAFT: A Computational Platform Using Residual Dipolar Coupling NMR Data for Determining Structures of Perdeuterated Proteins Without NOEs ]]> https://biorxiv.org/content/10.1101/2020.06.17.156638v1?rss=1 3) that cannot be collected from larger proteins. Here we present the latest version of the REDCRAFT software package designed for structure determination of proteins from RDC data alone. We have demonstrated the success of REDCRAFT in structure determination of proteins ranging in size from 50 to 145 residues using experimentally collected data and large proteins (145 to 573 residues) using simulated RDC data that can be collected from perdeuterated proteins. Finally, we demonstrate the accuracy of structure determination of REDCRAFT from RDCs alone in application to the structurally novel PF.2048 protein. The RDC-based structure of PF.2048 exhibited 1.0 [A] of BB-RMSD with respect to the NOE-based structure by only using a small amount of backbone RDCs ([~]3 restraints per residue) compared to what is required by other approaches. Author SummaryResidual Dipolar Couplings have the potential to reduce the cost and the time needed to characterize protein structures. In addition, RDC data have been demonstrated to concurrently elucidate structure of proteins, perform assignment of resonances, and be used in characterization of the internal dynamics of proteins. Given all the advantages associated with the study of proteins from RDC data, based on the statistics provided by the Protein Databank (PDB), surprisingly the only 124 proteins (out of nearly 150,000 proteins) have utilized RDCs as part of their structure determination. Even a smaller subset of these proteins (approximately 7) have utilized RDCs as the primary source of data for structure determination. The impeding factor in the use of RDCs is the challenging computational and analytical aspects of this source of data. In this report, we demonstrate the success of the REDCRAFT software package in structure determination of proteins using RDC data that can be collected from small and large proteins in a routine fashion. REDCRAFT accomplishes the challenging task of structure determination from RDCs by introducing a unique search and optimization technique that is both robust and computationally tractable. Structure determination from routinely collectable RDC data using REDCRAFT can lead to faster and cheaper study of larger and more complex proteins by NMR spectroscopy in solution state. ]]> Cole, C. A. Daigham, N. S. Liu, G. Montelione, G. T. Valafar, H. 2020-06-17 doi:10.1101/2020.06.17.156638 Cold Spring Harbor Laboratory Press 2020-06-17 <![CDATA[ Pericytes Directly Communicate with Emerging Endothelial Cells During Vasculogenesis ]]> https://biorxiv.org/content/10.1101/2020.07.01.180752v1?rss=1 Payne, L. B. Tewari, B. Dunkenberger, L. Bond, S. Savelli, A. Darden, J. Zhao, H. Powell, M. Oestreich, K. Sontheimer, H. Dal-Pra, S. Chappell, J. C. 2020-07-02 doi:10.1101/2020.07.01.180752 Cold Spring Harbor Laboratory Press 2020-07-02 <![CDATA[ NAD+ Redox Imbalance in the Heart Exacerbates Diabetic Cardiomyopathy ]]> https://biorxiv.org/content/10.1101/2020.07.03.183111v1?rss=1 Chiao, Y. A. Chakraborty, A. Light, C. Tian, R. Sadoshima, J. Shi, X. Gu, H. Lee, C. F. 2020-07-04 doi:10.1101/2020.07.03.183111 Cold Spring Harbor Laboratory Press 2020-07-04 <![CDATA[ MDA5 is an essential vita-PAMP sensor necessary for host resistance against Aspergillus fumigatus ]]> https://biorxiv.org/content/10.1101/2020.07.06.182154v1?rss=1 Wang, X. Caffrey-Carr, A. K. Liu, K.-w. Espinosa, V. Croteau, W. Dhingra, S. Rivera, A. Cramer, R. A. Obar, J. J. 2020-07-06 doi:10.1101/2020.07.06.182154 Cold Spring Harbor Laboratory Press 2020-07-06 <![CDATA[ Synthetic promoter based azide biosensor toolkit to advance chemical-biology ]]> https://biorxiv.org/content/10.1101/2020.07.08.193060v1?rss=1 Chandra Kanth Bandi Kyle S. Skalenko Ayushi Agrawal Neelan Sivaneri Margaux Thiry Shishir P.S. Chundawat 2020-07-09 doi:10.1101/2020.07.08.193060 Cold Spring Harbor Laboratory Press 2020-07-09 <![CDATA[ Reference data based insights expand understanding of human metabolomes ]]> https://biorxiv.org/content/10.1101/2020.07.08.194159v1?rss=1 Julia M Gauglitz Wout Bittremieux Candace L Williams Kelly C Weldon Morgan W Panitchpakdi Francesca Di Ottavio Christine M Aceves Elizabeth Brown Nicole C Sikora Alan K. Jarmusch Cameron Martino Anupriya Tripathi Erfan Sayyari Justin Shaffer Roxana Coras Fernando Vargas Lindsay DeRight Goldasich Tara Schwartz MacKenzie Bryant Gregory Humphrey Abigail J. Johnson Katharina Spengler Pedro Belda-Ferre Edgar Diaz Daniel McDonald Qiyun Zhu Dominic S. Nguyen Emmanuel O. Elijah Mingxun Wang Clarisse Marotz Kate E. Sprecher Daniela Vargas-Robles Dana Withrow Gail Ackerm 2020-07-11 doi:10.1101/2020.07.08.194159 Cold Spring Harbor Laboratory Press 2020-07-11 <![CDATA[ Zinc shapes the folding landscape of p53 and establishes a new pathway for reactivating structurally diverse p53 mutants ]]> https://biorxiv.org/content/10.1101/2020.07.23.217695v1?rss=1 Blanden, A. R. Yu, X. Blayney, A. J. Demas, C. Ha, J.-H. Liu, Y. Withers, T. Carpizo, D. R. Loh, S. N. 2020-07-23 doi:10.1101/2020.07.23.217695 Cold Spring Harbor Laboratory Press 2020-07-23 <![CDATA[ Benchmarking challenging small variants with linked and long reads ]]> https://biorxiv.org/content/10.1101/2020.07.24.212712v1?rss=1 Wagner, J. Olson, N. D. Harris, L. Khan, Z. Farek, J. Mahmoud, M. Stankovic, A. Kovacevic, V. Wenger, A. M. Rowell, W. J. Xiao, C. Yoo, B. Miller, N. Rosenfeld, J. A. Ni, B. Zarate, S. Kirsche, M. Aganezov, S. Schatz, M. Narzisi, G. Byrska-Bishop, M. Clarke, W. Evani, U. S. Markello, C. Shafin, K. Zhou, X. Sidow, A. Bansal, V. Martinez Barrio, A. Fiddes, I. T. Fungtammasan, A. Chin, C.-S. Sedlazeck, F. J. Carroll, A. Salit, M. Zook, J. M. Genome in a Bottle Consortium, 2020-07-25 doi:10.1101/2020.07.24.212712 Cold Spring Harbor Laboratory Press 2020-07-25 <![CDATA[ Pharmacological inhibition of an epigenetic regulator during the formation of extinction memory reveals sensory cortical and subcortical codes for the specificity of salient cues. ]]> https://biorxiv.org/content/10.1101/2020.07.31.230524v1?rss=1 Rotondo, E. K. Bieszczad, K. M. 2020-07-31 doi:10.1101/2020.07.31.230524 Cold Spring Harbor Laboratory Press 2020-07-31 <![CDATA[ Exosome-mediated hematopoietic rejuvenation in a humanized mouse model indicate potential for cancer immunotherapy ]]> https://biorxiv.org/content/10.1101/2020.08.02.233015v1?rss=1 Rameshwar, P. 2020-08-03 doi:10.1101/2020.08.02.233015 Cold Spring Harbor Laboratory Press 2020-08-03 <![CDATA[ Brain Network Mechanisms of Visual Shape Completion ]]> https://biorxiv.org/content/10.1101/2020.08.03.233403v1?rss=1 Keane, B. P. Barch, D. M. Mill, R. Silverstein, S. M. Krekelberg, B. Cole, M. W. 2020-08-04 doi:10.1101/2020.08.03.233403 Cold Spring Harbor Laboratory Press 2020-08-04 <![CDATA[ Predation by Bdellovibrio bacteriovorus transforms the landscape and community assembly of bacterial biofilms ]]> https://biorxiv.org/content/10.1101/2020.08.03.235101v1?rss=1 Wucher, B. Elsayed, M. Kadouri, D. Nadell, C. D. 2020-08-03 doi:10.1101/2020.08.03.235101 Cold Spring Harbor Laboratory Press 2020-08-03 <![CDATA[ Efficacy of Targeting SARS-CoV-2 by CAR-NK Cells ]]> https://biorxiv.org/content/10.1101/2020.08.11.247320v1?rss=1 Ma, M. T. Badeti, S. Geng, K. Liu, D. 2020-08-12 doi:10.1101/2020.08.11.247320 Cold Spring Harbor Laboratory Press 2020-08-12 <![CDATA[ Multi-environment phenotyping of C. elegans for robust evaluation of physical performance ]]> https://biorxiv.org/content/10.1101/2020.08.17.253583v1?rss=1 Hewitt, J. E. Laranjeiro, R. Norouzi, M. Ellwood, R. Antebi, A. Szewczyk, N. J. Driscoll, M. Vanapalli, S. A. 2020-08-17 doi:10.1101/2020.08.17.253583 Cold Spring Harbor Laboratory Press 2020-08-17 <![CDATA[ TNFα reduces inhibitory transmission in young Trem2R47H Sporadic Alzheimer rats before observable Aβ and brain pathology ]]> https://biorxiv.org/content/10.1101/2020.08.20.256099v1?rss=1 Ren, S. Breuillaud, L. Yao, W. Yin, T. Norris, K. A. Zehntner, S. P. D'Adamio, L. 2020-08-20 doi:10.1101/2020.08.20.256099 Cold Spring Harbor Laboratory Press 2020-08-20 <![CDATA[ Integrated Collection of Stem Cell Bank data, a data portal for standardized stem cell information ]]> https://biorxiv.org/content/10.1101/2020.08.26.263830v1?rss=1 16,000 cell lines from four major data resources in Europe, Japan, and the United States. ICSCB is automatically updated to provide the latest cell line information, and its integrative search helps users collect cell line information for over 1,000 diseases including many rare diseases worldwide, which has been a formidable task, thereby distinguishing itself from other database search portals. ]]> Chen, Y. Sakurai, K. Maeda, S. Masui, T. Okano, H. Dewender, J. Seltmann, S. Kurtz, A. Masuya, H. Nakamura, Y. Sheldon, M. Schneider, J. Stacey, G. Panina, Y. Fujibuchi, W. 2020-08-27 doi:10.1101/2020.08.26.263830 Cold Spring Harbor Laboratory Press 2020-08-27 <![CDATA[ Autophagy Compensates for Lkb1 Loss to Maintain Adult Mice Homeostasis and Survival ]]> https://biorxiv.org/content/10.1101/2020.08.26.268003v1?rss=1 Guo, J. Y. Khayati, K. Bhatt, V. Hu, Z. S. Fahumy, S. Luo, X. 2020-08-26 doi:10.1101/2020.08.26.268003 Cold Spring Harbor Laboratory Press 2020-08-26 <![CDATA[ Branching and extinction in evolutionary public goods games ]]> https://biorxiv.org/content/10.1101/2020.08.30.274399v1?rss=1 Johnson, B. Altrock, P. M. Kimmel, G. J. 2020-08-31 doi:10.1101/2020.08.30.274399 Cold Spring Harbor Laboratory Press 2020-08-31 <![CDATA[ Optimal CD4T Cell Priming in Lymph Nodes Requires Repertoire Scanning by CD301b+ Migratory cDC2 Cells ]]> https://biorxiv.org/content/10.1101/2020.08.31.276410v1?rss=1 View larger version (49K): org.highwire.dtl.DTLVardef@118d9b7org.highwire.dtl.DTLVardef@7daf2eorg.highwire.dtl.DTLVardef@17808c0org.highwire.dtl.DTLVardef@186780e_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LINewly homed polyclonal CD4T cells are temporarily retained in the reactive lymph nodes. C_LIO_LIDepletion of CD301b+ DCs results in shorter dwell time of CD4T cells in the draining lymph node and delayed priming of antigen-specific clones. C_LIO_LIThe transient retention of polyclonal CD4T cells in the draining lymph node requires MHCII expression on CD301b+ DCs but not cognate antigen. C_LIO_LICD301b+ DCs are required for robust expansion of rare antigen-specific CD4T cell clones and their skewing toward Th2 cells. C_LI ]]> Tatsumi, N. Codrington, A. L. Kumamoto, Y. 2020-08-31 doi:10.1101/2020.08.31.276410 Cold Spring Harbor Laboratory Press 2020-08-31 <![CDATA[ Disulfiram inhibits M. tuberculosis growth by altering methionine pool, redox status and host-immune response ]]> https://biorxiv.org/content/10.1101/2020.09.01.277368v1?rss=1 Chaudhary, D. Marzuki, M. Lee, A. Bouzeyen, R. Singh, A. Gosain, T. P. Kidwai, S. Grady, C. Tsotetsi, K. Chawla, K. Shihui, F. Lum, J. Gupta, S. K. Agarwal, N. Tsenova, L. Kumar, Y. Lee, B. Kumar, P. Thakur, K. G. Singh, R. Singhal, A. 2020-09-01 doi:10.1101/2020.09.01.277368 Cold Spring Harbor Laboratory Press 2020-09-01 <![CDATA[ A Spatiotemporal Molecular Switch Governs Plant Asymmetric Cell Division ]]> https://biorxiv.org/content/10.1101/2020.09.05.284380v1?rss=1 Guo, X. Park, C. H. Wang, Z.-y. Nickels, B. E. Dong, J. 2020-09-08 doi:10.1101/2020.09.05.284380 Cold Spring Harbor Laboratory Press 2020-09-08 <![CDATA[ Development of a method for revertable CRISPR/Cas9-based mutagenesis in cell culture ]]> https://biorxiv.org/content/10.1101/2020.09.07.286187v1?rss=1 Walsh, J. Eggenschwiler, J. 2020-09-07 doi:10.1101/2020.09.07.286187 Cold Spring Harbor Laboratory Press 2020-09-07 <![CDATA[ Optogenetic activation of CA1 pyramidal neurons in vivo induces hypersynchronous and low voltage fast seizures ]]> https://biorxiv.org/content/10.1101/2020.09.08.288605v1?rss=1 Huynh, T. D. Ashraf, O. Craig, H. Larmeu, L. Barker, B. Stepheson, C. Murcia, D. Howard, B. Sun, H. 2020-09-09 doi:10.1101/2020.09.08.288605 Cold Spring Harbor Laboratory Press 2020-09-09 <![CDATA[ Xpert MTB/XDR: A ten-color reflex assay suitable for point of care settings to detect isoniazid-, fluoroquinolone-, and second line injectable drug-resistance directly from Mycobacterium tuberculosis positive sputum. ]]> https://biorxiv.org/content/10.1101/2020.09.08.288787v1?rss=1 Cao, Y. Parmar, H. Gaur, R. Raghunath, S. Lieu, D. Via, N. Battagalia, S. Cirillo, D. M. Denkinger, C. Georghiou, S. B. Kwiatkowski, R. Persing, D. Alland, D. Chakravorty, S. 2020-09-09 doi:10.1101/2020.09.08.288787 Cold Spring Harbor Laboratory Press 2020-09-09 <![CDATA[ Real-time structural motif searching in proteins using an inverted index strategy ]]> https://biorxiv.org/content/10.1101/2020.09.11.293977v1?rss=1 160,000 PDB structures with unmatched speed. The efficiency of the inverted index method depends critically on identifying the small number of structures containing the query motif and ignoring most of the structures that are irrelevant. Our approach (implemented at motif.rcsb.org) enables real-time retrieval and superposition of structural motifs, either extracted from a reference structure or uploaded by the user. Herein, we describe the method and present five case studies that exemplify its efficacy and speed for analyzing 3D structures of both proteins and nucleic acids. Author summaryThe Protein Data Bank (PDB) provides open access to more than 160,000 three-dimensional structures of proteins, nucleic acids, and biological complexes. Similarities between PDB structures give valuable functional and evolutionary insights but such resemblance may not be evident at sequence or global structure level. Throughout the database, there are recurring structural motifs - groups of modest numbers of residues in proximity that, for example, support catalytic activity. Identification of common structural motifs can unveil subtle similarities between proteins and serve as fingerprints for configurations such as the His-Asp-Ser catalytic triad found in serine proteases or the zinc coordination site found in Zinc Finger DNA-binding domains. We present a highly efficient yet flexible strategy that allows users for the first time to search for arbitrary structural motifs across the entire PDB archive in real-time. Our approach scales favorably with the increasing number and complexity of deposited structures, and, also, has the potential to be adapted for other applications in a macromolecular context. ]]> Bittrich, S. Burley, S. K. Rose, A. S. 2020-09-12 doi:10.1101/2020.09.11.293977 Cold Spring Harbor Laboratory Press 2020-09-12 <![CDATA[ scLink: Inferring Sparse Gene Co-expression Networks from Single-cell Expression Data ]]> https://biorxiv.org/content/10.1101/2020.09.19.304956v1?rss=1 Li, W. V. Li, Y. 2020-09-20 doi:10.1101/2020.09.19.304956 Cold Spring Harbor Laboratory Press 2020-09-20 <![CDATA[ A common binding motif in the ET domain of BRD3 forms polymorphic structural interfaces with host and viral proteins ]]> https://biorxiv.org/content/10.1101/2020.09.21.306696v1?rss=1 Aiyer, S. Swapna, G. V. T. Liu, G. Ma, L.-C. Hao, J. Chalmers, G. Jacobs, B. Montelione, G. T. Roth, M. J. 2020-09-21 doi:10.1101/2020.09.21.306696 Cold Spring Harbor Laboratory Press 2020-09-21 <![CDATA[ Monocyte-derived alveolar macrophages mediate resistance to migrating helminths through depletion of arginine availability ]]> https://biorxiv.org/content/10.1101/2020.10.02.322388v1?rss=1 Chen, F. El Naccache, D. W. Ponessa, J. Lemenze, A. Espinosa, V. Wu, W. Lothstein, K. Jin, L. Rivera, A. Siracusa, M. Gause, W. 2020-10-02 doi:10.1101/2020.10.02.322388 Cold Spring Harbor Laboratory Press 2020-10-02 <![CDATA[ Transcriptomic signatures of sex-specific nicotine sensitization and imprinting of self-administration in rats inform GWAS findings on human addiction phenotypes ]]> https://biorxiv.org/content/10.1101/2020.10.05.327155v1?rss=1 Kozlova, A. Butler, R. R. Zhang, S. Ujas, T. Zhang, H. Steidl, S. Sanders, A. R. Pang, Z. P. Vezina, P. Duan, J. 2020-10-06 doi:10.1101/2020.10.05.327155 Cold Spring Harbor Laboratory Press 2020-10-06 <![CDATA[ RNA polymerase clamp conformational dynamics: long-lived states and modulation by crowding, cations, and nonspecific DNA binding ]]> https://biorxiv.org/content/10.1101/2020.10.06.327965v1?rss=1 1.0 s) and can switch between these long-lived states and the previously observed short-lived states. In addition, we find that clamp motions are increased in the presence of molecular crowding, are unchanged in the presence of elevated monovalent-cation concentrations, and are reduced in the presence of elevated divalent-cation concentrations. Finally, we find that RNAP bound to non-specific DNA predominantly exhibits a closed clamp conformation. Our results raise the possibility of additional regulatory checkpoints that could affect clamp dynamics and consequently could affect transcription and transcriptional regulation. ]]> Mazumder, A. Wang, A. Uhm, H. Ebright, R. H. Kapanidis, A. N. 2020-10-06 doi:10.1101/2020.10.06.327965 Cold Spring Harbor Laboratory Press 2020-10-06 <![CDATA[ Acyclovir Improves the Efficacy of Chemoradiation in Nasopharyngeal Cancer Containing the Epstein Barr Virus Genome ]]> https://biorxiv.org/content/10.1101/2020.10.18.343236v1?rss=1 Thandoni, A. Zloza, A. Schiff, D. Rao, M. Lo, K.-w. Haffty, B. G. Kim, S. Jhawar, S. R. 2020-10-18 doi:10.1101/2020.10.18.343236 Cold Spring Harbor Laboratory Press 2020-10-18 <![CDATA[ Drosophila clock cells use multiple mechanisms to transmit time-of-day signals in the brain ]]> https://biorxiv.org/content/10.1101/2020.10.26.353631v1?rss=1 Barber, A. F. Fong, S. Y. Kolesnik, A. Fetchko, M. Sehgal, A. 2020-10-26 doi:10.1101/2020.10.26.353631 Cold Spring Harbor Laboratory Press 2020-10-26 <![CDATA[ Cross-Platform Validation of Neurotransmitter Release Impairments in Schizophrenia Patient-Derived NRXN1-Mutant Neurons ]]> https://biorxiv.org/content/10.1101/2020.11.03.366617v1?rss=1 Pak, C. Danko, T. Mirabella, V. R. Wang, J. Zhang, X. Ward, T. Grieder, S. Vangipuram, M. Huang, Y.-W. A. Liu, Y. Jin, K. Dexheimer, P. Bardes, E. Mitelpunkt, A. Ma, J. McLachlan, M. Moore, J. C. Urban, A. E. Dage, J. L. Swanson, B. J. Aronow, B. J. Pang, Z. P. Levinson, D. F. Wernig, M. Sudhof, T. C. 2020-11-03 doi:10.1101/2020.11.03.366617 Cold Spring Harbor Laboratory Press 2020-11-03 <![CDATA[ Human brain organoids reveal accelerated development of cortical neuron classes as a shared feature of autism risk genes ]]> https://biorxiv.org/content/10.1101/2020.11.10.376509v1?rss=1 Paulsen, B. Velasco, S. Kedaigle, A. J. Pigoni, M. Quadrato, G. Deo, A. Adiconis, X. Uzquiano, A. Kim, K. Simmons, S. K. Tsafou, K. Albanese, A. Sartore, R. Abbate, C. Tucewicz, A. Smith, S. Chung, K. Lage, K. Regev, A. Levin, J. Z. Arlotta, P. 2020-11-12 doi:10.1101/2020.11.10.376509 Cold Spring Harbor Laboratory Press 2020-11-12 <![CDATA[ Spaceflight Affects Neuronal Morphology and Alters Transcellular Degradation of Neuronal Debris in Adult Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/2020.11.10.377143v1?rss=1 Laranjeiro, R. Harinath, G. Pollard, A. K. Gaffney, C. J. Deane, C. S. Vanapalli, S. A. Etheridge, T. Szewczyk, N. J. Driscoll, M. 2020-11-10 doi:10.1101/2020.11.10.377143 Cold Spring Harbor Laboratory Press 2020-11-10 <![CDATA[ Loss of CDC50A function drives Aβ/p3 production via increased β/α-secretase processing of APP ]]> https://biorxiv.org/content/10.1101/2020.11.12.379636v1?rss=1 Tambini, M. D. D'Adamio, L. 2020-11-12 doi:10.1101/2020.11.12.379636 Cold Spring Harbor Laboratory Press 2020-11-12 <![CDATA[ Cellular and molecular mechanisms of frontal bone development in spotted gar (Lepisosteus oculatus) ]]> https://biorxiv.org/content/10.1101/2020.11.16.383802v1?rss=1 Enny, A. Thompson, A. W. Racicot, B. Braasch, I. Nakamura, T. 2020-11-17 doi:10.1101/2020.11.16.383802 Cold Spring Harbor Laboratory Press 2020-11-17 <![CDATA[ The ChiS family DNA-binding domain contains a cryptic helix-turn-helix variant ]]> https://biorxiv.org/content/10.1101/2020.11.18.389122v1?rss=1 Klancher, C. A. Minasov, G. Podicheti, R. Rusch, D. B. Dalia, T. N. Satchell, K. J. Neiditch, M. B. Dalia, A. B. 2020-11-18 doi:10.1101/2020.11.18.389122 Cold Spring Harbor Laboratory Press 2020-11-18 <![CDATA[ The polypyrimidine tract binding protein, PTBP1, regulates selenium homeostasis via the Selenoprotein P 3' untranslated region ]]> https://biorxiv.org/content/10.1101/2020.11.23.394817v1?rss=1 Shetty, S. P. Kiledjian, N. T. Copeland, P. R. 2020-11-23 doi:10.1101/2020.11.23.394817 Cold Spring Harbor Laboratory Press 2020-11-23 <![CDATA[ Deep immune profiling reveals targetable mechanisms of immune evasion in checkpoint blockade-refractory glioblastoma ]]> https://biorxiv.org/content/10.1101/2020.12.01.404939v1?rss=1 View larger version (39K): org.highwire.dtl.DTLVardef@bdd0e4org.highwire.dtl.DTLVardef@1dd335forg.highwire.dtl.DTLVardef@157bfa6org.highwire.dtl.DTLVardef@1e76151_HPS_FORMAT_FIGEXP M_FIG C_FIG In BriefIn mice and humans, tumors that were sensitive to checkpoint blockade had consistent immunological features. A mouse model of glioma that is refractory to checkpoint blockade was sensitized by increasing antigen presentation through a variety of approaches. ]]> Simonds, E. F. Lu, E. D. Liu, E. V. Tamaki, W. Rancan, C. Stultz, J. Sinha, M. McHenry, L. K. Nasholm, N. M. Chuntova, P. Sundstrom, A. Genoud, V. Shahani, S. A. Wang, L. D. brown, c. Walker, P. R. Swartling, F. J. Fong, L. Okada, H. Weiss, W. A. Hellstrom, M. 2020-12-02 doi:10.1101/2020.12.01.404939 Cold Spring Harbor Laboratory Press 2020-12-02 <![CDATA[ Biliverdin reductase bridges focal adhesion kinase to Src to modulate synaptic signaling ]]> https://biorxiv.org/content/10.1101/2020.12.01.405720v1?rss=1 Vasavda, C. Semenza, E. R. Liew, J. Kothari, R. Dhindsa, R. S. Shanmukha, S. Ricco, C. Tokhunts, R. Snowman, A. M. Albacarys, L. K. Paul, B. D. Snyder, S. H. 2020-12-02 doi:10.1101/2020.12.01.405720 Cold Spring Harbor Laboratory Press 2020-12-02 <![CDATA[ PipeMaster: inferring population divergence and demographic history with approximate Bayesian computation and supervised machine-learning in R ]]> https://biorxiv.org/content/10.1101/2020.12.04.410670v1?rss=1 Gehara, M. Mazzochinni, G. G. Burbrink, F. T. 2020-12-06 doi:10.1101/2020.12.04.410670 Cold Spring Harbor Laboratory Press 2020-12-06 <![CDATA[ Reduced Liver-Specific PGC1a Increases Susceptibility for Short-Term Diet-induced Weight Gain in Male Mice ]]> https://biorxiv.org/content/10.1101/2020.12.04.412460v1?rss=1 Morris, E. M. Noland, R. D. Ponte, M. E. Montonye, M. L. Christianson, J. A. Stanford, J. A. Miles, J. M. Hayes, M. R. Thyfault, J. P. 2020-12-06 doi:10.1101/2020.12.04.412460 Cold Spring Harbor Laboratory Press 2020-12-06 <![CDATA[ Amilorides inhibit SARS-CoV-2 replication in vitro by targeting RNA structures ]]> https://biorxiv.org/content/10.1101/2020.12.05.409821v1?rss=1 Zafferani, M. Haddad, C. Luo, L. Davila-Calderon, J. Yuan-Chiu, L. Shema Mugisha, C. Monaghan, A. G. Kennedy, A. A. Yesselman, J. D. Gifford, R. R. Tai, A. W. Kutluay, S. B. Li, M.-L. Brewer, G. Tolbert, B. S. Hargrove, A. E. 2020-12-06 doi:10.1101/2020.12.05.409821 Cold Spring Harbor Laboratory Press 2020-12-06 <![CDATA[ Structure of Human BCCIP and Implications for Binding and Modification of Partner Proteins ]]> https://biorxiv.org/content/10.1101/2020.12.08.416925v1?rss=1 Choi, W. S. Liu, B. Shen, Z. Yang, W. 2020-12-09 doi:10.1101/2020.12.08.416925 Cold Spring Harbor Laboratory Press 2020-12-09 <![CDATA[ Moderately Inducing Autophagy Reduces Tertiary Brain Injury After Perinatal Hypoxia-Ischemia ]]> https://biorxiv.org/content/10.1101/2020.12.09.418186v1?rss=1 Kim, B. H. Jeziorek, M. Hur, K. D. Dobrowolkski, R. Levison, S. W. 2020-12-10 doi:10.1101/2020.12.09.418186 Cold Spring Harbor Laboratory Press 2020-12-10 <![CDATA[ Oligodendrocyte progenitor proliferation is disinhibited following traumatic brain injury in LIF heterozygous mice ]]> https://biorxiv.org/content/10.1101/2020.12.09.418343v1?rss=1 Frondelli, M. J. Mather, M. L. Levison, S. W. 2020-12-09 doi:10.1101/2020.12.09.418343 Cold Spring Harbor Laboratory Press 2020-12-09 <![CDATA[ Efficient target cleavage by Type V Cas12a effector programmed with split CRISPR RNA ]]> https://biorxiv.org/content/10.1101/2020.12.21.423781v1?rss=1 Tkach, R. Nikitchina, N. Shebanov, N. Mekler, V. Ulashchik, E. Sharko, O. Shmanai, V. Tarassov, I. Severinov, K. Entelis, N. Mazunin, I. 2020-12-21 doi:10.1101/2020.12.21.423781 Cold Spring Harbor Laboratory Press 2020-12-21 <![CDATA[ Three neurotransmitters regulate diverse inhibitory and excitatory Parvalbumin interneuron circuits in the dorsal horn ]]> https://biorxiv.org/content/10.1101/2020.12.23.424233v1?rss=1 Gradwell, M. A. Boyle, K. A. Browne, T. J. Dickie, A. C. Bell, A. M. Leonardo, J. Peralta Reyes, F. S. Smith, K. M. Callister, R. J. Dayas, C. V. Hughes, D. I. Graham, B. A. 2020-12-24 doi:10.1101/2020.12.23.424233 Cold Spring Harbor Laboratory Press 2020-12-24 <![CDATA[ Digging behavior discrimination test to probe burrowing and exploratory digging in male and female mice ]]> https://biorxiv.org/content/10.1101/2020.12.29.424478v1?rss=1 Pond, H. L. Heller, A. T. Gural, B. M. McKissick, O. P. Wilkinson, M. K. Manzini, C. 2020-12-30 doi:10.1101/2020.12.29.424478 Cold Spring Harbor Laboratory Press 2020-12-30 <![CDATA[ Spontaneous thought and microstate activity modulation by social imitation ]]> https://biorxiv.org/content/10.1101/2021.01.15.426876v1?rss=1 Tomescu, M. I. Papasteri, C. C. Sofonea, A. Boldasu, R. Kebets, V. Poalelungi, C. Podina, I. R. Nedelcea, C. I. Berceanu, A. I. Carcea, I. 2021-01-18 doi:10.1101/2021.01.15.426876 Cold Spring Harbor Laboratory Press 2021-01-18 <![CDATA[ APOBEC3A drives acquired resistance to targeted therapies in non-small cell lung cancer ]]> https://biorxiv.org/content/10.1101/2021.01.20.426852v1?rss=1 Isozaki, H. Abbasi, A. Nikpour, N. Langenbucher, A. Su, W. Stanzione, M. Frisco-Cabanos, H. Siddiqui, F. M. Phan, N. Jalili, P. Oh, S. Timonina, D. Bilton, S. Gomez-Caraballo, M. Archibald, H. L. Nangia, V. Dionne, K. Riley, A. Lawlor, M. Banwait, M. K. Cobb, R. G. Zou, L. Dyson, N. J. Ott, C. J. Benes, C. Getz, G. Chan, C. Shaw, A. T. Lin, J. J. Sequist, L. V. Piotrowska, Z. Engelman, J. A. Lee, J. J.-K. Maruvka, Y. Buisson, R. Lawrence, M. S. Hata, A. N. 2021-01-21 doi:10.1101/2021.01.20.426852 Cold Spring Harbor Laboratory Press 2021-01-21 <![CDATA[ Hyperoxia Inhibits the Growth of Mouse Forebrain Oligodendrocyte Progenitors ]]> https://biorxiv.org/content/10.1101/2021.01.20.427261v1?rss=1 Moore, L. M. McLane, L. E. Wahl, S. E. Ornelas, I. Wood, T. L. Canoll, P. D. Levison, S. W. 2021-01-21 doi:10.1101/2021.01.20.427261 Cold Spring Harbor Laboratory Press 2021-01-21 <![CDATA[ Adenosine metabolized from extracellular ATP promotes type 2 immunity through triggering A2BAR signaling on intestinal epithelial cells ]]> https://biorxiv.org/content/10.1101/2021.01.24.428000v1?rss=1 El-Naccache, d. w. chen, f. palma, m. lemenze, a. Wu, w. mishra, p. eltzshig, h. robson, s. c. Di Virgilio, f. Hasko, G. gause, w. 2021-01-26 doi:10.1101/2021.01.24.428000 Cold Spring Harbor Laboratory Press 2021-01-26 <![CDATA[ AGES: An auxin-inducible, GAL4-compatible, gene expression system for Drosophila ]]> https://biorxiv.org/content/10.1101/2021.01.26.428209v1?rss=1 McClure, C. D. Hassan, A. Duggal, A. Ying Sia, C. Southall, T. D. 2021-01-26 doi:10.1101/2021.01.26.428209 Cold Spring Harbor Laboratory Press 2021-01-26 <![CDATA[ Glioblastoma remodeling of neural circuits in the human brain decreases survival ]]> https://biorxiv.org/content/10.1101/2021.02.18.431915v1?rss=1 Krishna, S. Choudhury, A. Seo, K. Ni, L. Kakaizada, S. Lee, A. Aabedi, A. Cao, C. Sudharshan, R. Egladyous, A. Almeida, N. Venkatesh, H. Findlay, A. Nagarajan, S. Raleigh, D. Brang, D. Monje, M. Hervey-Jumper, S. 2021-02-19 doi:10.1101/2021.02.18.431915 Cold Spring Harbor Laboratory Press 2021-02-19 <![CDATA[ A Comparison of Cell-Based and Cell-Cultured as Appropriate Common or Usual Names to Label Products Made from the Cells of Fish. ]]> https://biorxiv.org/content/10.1101/2021.02.26.433119v1?rss=1 Hallman, W. K. Hallman, W. K. 2021-03-02 doi:10.1101/2021.02.26.433119 Cold Spring Harbor Laboratory Press 2021-03-02 <![CDATA[ Mechanisms of transforming DNA uptake to the periplasm of Bacillus subtilis ]]> https://biorxiv.org/content/10.1101/2021.03.09.434615v1?rss=1 Hahn, J. De Santis, M. Dubnau, D. 2021-03-09 doi:10.1101/2021.03.09.434615 Cold Spring Harbor Laboratory Press 2021-03-09 <![CDATA[ 3'-Sulfated Lewis A is a Biomarker for Metaplastic and Oncogenic Transformation of Several Gastrointestinal Epithelia ]]> https://biorxiv.org/content/10.1101/2021.03.17.435789v1?rss=1 Brown, J. W. Das, K. K. Kalas, V. Das, K. Mills, J. C. 2021-03-17 doi:10.1101/2021.03.17.435789 Cold Spring Harbor Laboratory Press 2021-03-17 <![CDATA[ MAAPER: model-based analysis of alternative polyadenylation using 3' end-linked reads ]]> https://biorxiv.org/content/10.1101/2021.03.21.436343v1?rss=1 Li, W. V. Zheng, D. Wang, R. Tian, B. 2021-03-22 doi:10.1101/2021.03.21.436343 Cold Spring Harbor Laboratory Press 2021-03-22 <![CDATA[ TCF-1 in CD8 T cells separates GVHD from GVL ]]> https://biorxiv.org/content/10.1101/2021.03.22.436494v1?rss=1 Harris, R. Mammadli, M. May, A. Yang, Q. Fung, I. T. H. Sen, J. M. Karimi, M. 2021-03-23 doi:10.1101/2021.03.22.436494 Cold Spring Harbor Laboratory Press 2021-03-23 <![CDATA[ Structural basis for HCMV Pentamer recognition by antibodies and neuropilin 2 ]]> https://biorxiv.org/content/10.1101/2021.03.25.436804v1?rss=1 Wrapp, D. Ye, X. Ku, Z. Su, H. Jones, H. G. Wang, N. Mishra, A. K. Freed, D. C. Li, F. Tang, A. Li, L. Jaijyan, D. K. Zhu, H. Wang, D. Fu, T.-M. Zhang, N. An, Z. McLellan, J. S. 2021-03-25 doi:10.1101/2021.03.25.436804 Cold Spring Harbor Laboratory Press 2021-03-25 <![CDATA[ An integrative skeletal and paleogenomic analysis of prehistoric stature variation suggests relatively reduced health for early European farmers ]]> https://biorxiv.org/content/10.1101/2021.03.31.437881v1?rss=1 Marciniak, S. Bergey, C. Silva, A. M. Hałuszko, A. Furmanek, M. Veselka, B. Veleminsky, P. Vercellotti, G. Wahl, J. Zarina, G. Longhi, C. Kolar, J. Garrido-Pena, R. Flores-Fernandez, R. Herrero-Corral, A. M. Simalcsik, A. Müller, W. Sheridan, A. Miliauskiene, Z. Jankauskas, R. Moiseyev, V. Köhler, K. Kiraly, A. Gamarra, B. Cheronet, O. Szeverenyi, V. Kiss, V. Szeniczey, T. Kiss, K. Zoffmann, Z. K. Koos, J. Hellebrandt, M. Domboroczki, L. Virag, C. Novak, M. Reich, D. E. Hajdu, T. von Cramon-Taubadel, N. Pinhasi, R. Perry, G. H. 2021-03-31 doi:10.1101/2021.03.31.437881 Cold Spring Harbor Laboratory Press 2021-03-31 <![CDATA[ Memory specific to temporal features of sound is formed by cue-selective enhancements in temporal coding enabled by inhibition of an epigenetic regulator ]]> https://biorxiv.org/content/10.1101/2021.03.31.437889v1?rss=1 Rotondo, E. K. Bieszczad, K. M. 2021-03-31 doi:10.1101/2021.03.31.437889 Cold Spring Harbor Laboratory Press 2021-03-31 <![CDATA[ Long-Term Persistence of Plasmids Targeted by CRISPR Interference in Bacterial Populations ]]> https://biorxiv.org/content/10.1101/2021.04.03.438301v1?rss=1 Mamontov, V. Martynov, A. Morozova, N. Bukatin, A. Staroverov, D. B. Lukyanov, K. A. Ispolatov, Y. Semenova, E. Severinov, K. 2021-04-03 doi:10.1101/2021.04.03.438301 Cold Spring Harbor Laboratory Press 2021-04-03 <![CDATA[ The RNA-binding protein RBP42 regulates cellular energy metabolism in mammalian-infective Trypanosoma brucei ]]> https://biorxiv.org/content/10.1101/2021.04.14.439849v1?rss=1 Das, A. Liu, T. Li, H. Husain, S. 2021-04-14 doi:10.1101/2021.04.14.439849 Cold Spring Harbor Laboratory Press 2021-04-14 <![CDATA[ Integrative molecular and clinical profiling of acral melanoma identifies LZTR1 as a key tumor promoter and therapeutic target ]]> https://biorxiv.org/content/10.1101/2021.04.20.440286v1?rss=1 Farshidfar, F. Peng, C. Levovitz, C. Knight, J. Bacchiocchi, A. Su, J. Rhrissorrakrai, K. Yin, M. Sznol, M. Ariyan, S. Clune, J. Olino, K. Parida, L. Nikolaus, J. Zhang, M. Zhao, S. Wang, Y. Huang, G. Wan, M. Li, X. Cao, J. Yan, Q. Chen, X. Newman, A. M. Halaban, R. M. 2021-04-21 doi:10.1101/2021.04.20.440286 Cold Spring Harbor Laboratory Press 2021-04-21 <![CDATA[ Robust IgM responses following vaccination are associated with prevention of Mycobacterium tuberculosis infection in macaques ]]> https://biorxiv.org/content/10.1101/2021.05.06.442979v1?rss=1 Irvine, E. B. O'Neil, A. Darrah, P. A. Shin, S. Choudhary, A. Li, W. Honnen, W. Mehra, S. Kaushal, D. Gideon, H. P. Flynn, J. L. Roederer, M. Seder, R. A. Pinter, A. Fortune, S. Alter, G. 2021-05-06 doi:10.1101/2021.05.06.442979 Cold Spring Harbor Laboratory Press 2021-05-06 <![CDATA[ Site-specific epigenetic marks in Trypanosoma brucei transcription termination, antigenic variation, and proliferation ]]> https://biorxiv.org/content/10.1101/2021.05.13.444086v1?rss=1 Kim, H.-S. 2021-05-15 doi:10.1101/2021.05.13.444086 Cold Spring Harbor Laboratory Press 2021-05-15 <![CDATA[ Differential Activity-Dependent Scaling of Synaptic Inhibition and Parvalbumin Interneuron Recruitment in Dentate Projection Neuron Subtypes ]]> https://biorxiv.org/content/10.1101/2021.05.18.444756v1?rss=1 Afrasiabi, M. GUPTA, A. - Xu, H. Swietek, B. Santhakumar, V. 2021-05-20 doi:10.1101/2021.05.18.444756 Cold Spring Harbor Laboratory Press 2021-05-20 <![CDATA[ Lateral Preoptic Area Neurons Signal Cocaine Self-Administration Behaviors ]]> https://biorxiv.org/content/10.1101/2021.05.29.446307v1?rss=1 Coffey, K. R. Venkat, V. West, M. Barker, D. 2021-05-30 doi:10.1101/2021.05.29.446307 Cold Spring Harbor Laboratory Press 2021-05-30 <![CDATA[ Sequential delay and probability discounting tasks in mice reveal anchoring effects partially attributable to decision noise ]]> https://biorxiv.org/content/10.1101/2021.06.08.447620v1?rss=1 Rojas, G. R. Curry-Pochy, L. S. Chen, C. S. Heller, A. T. Grissom, N. M. 2021-06-09 doi:10.1101/2021.06.08.447620 Cold Spring Harbor Laboratory Press 2021-06-09 <![CDATA[ High-affinity, neutralizing antibodies to SARS-CoV-2 can be made in the absence of T follicular helper cells ]]> https://biorxiv.org/content/10.1101/2021.06.10.447982v1?rss=1 Chen, J. S. Chow, R. D. Song, E. Mao, T. Israelow, B. Kamath, K. Bozekowski, J. Haynes, W. A. Filler, R. B. Menasche, B. L. Wei, J. Alfajaro, M. M. Song, W. Peng, L. Carter, L. Weinstein, J. S. Gowthaman, U. Chen, S. Craft, J. Shon, J. C. Iwasaki, A. Wilen, C. B. Eisenbarth, S. C. 2021-06-11 doi:10.1101/2021.06.10.447982 Cold Spring Harbor Laboratory Press 2021-06-11 <![CDATA[ Cross-species metabolomic analysis of DDT and Alzheimer's disease-associated tau toxicity ]]> https://biorxiv.org/content/10.1101/2021.06.14.448355v1?rss=1 Kalia, V. Niedzwiecki, M. M. Bradner, J. M. Lau, F. K. Bucher, M. L. Manz, K. E. Coates Fuentes, Z. Pennell, K. D. Picard, M. Walker, D. I. Hu, W. T. Jones, D. P. Miller, G. W. 2021-06-15 doi:10.1101/2021.06.14.448355 Cold Spring Harbor Laboratory Press 2021-06-15 <![CDATA[ Characterization of novel competitive inhibitors of P. falciparum cGMP-dependent protein kinase ]]> https://biorxiv.org/content/10.1101/2021.06.24.449800v1?rss=1 Eck, T. Laureano de Souza, M. Bheemanoboina, R. R. Y. Chakrasali, R. Kreiss, T. Siekierka, J. J. Rotella, D. P. Bhanot, P. Goodey, N. M. 2021-06-24 doi:10.1101/2021.06.24.449800 Cold Spring Harbor Laboratory Press 2021-06-24 <![CDATA[ Contrasting a reference cranberry genome to a crop wild relative provides insights into adaptation, domestication, and breeding ]]> https://biorxiv.org/content/10.1101/2021.06.27.450096v1?rss=1 Kawash, J. Colt, K. Hartwick, N. T. Abramson, B. W. Vorsa, N. polashock, J. J. Michael, T. P. 2021-06-28 doi:10.1101/2021.06.27.450096 Cold Spring Harbor Laboratory Press 2021-06-28 <![CDATA[ Cyp26b1 restrains murine heart valve growth during development ]]> https://biorxiv.org/content/10.1101/2021.07.05.450958v1?rss=1 Ahuja, N. Hiltabildle, M. S. Rajasekhar, H. Daniel, E. Barlow, H. R. Voss, S. Cleaver, O. Maynard, C. 2021-07-05 doi:10.1101/2021.07.05.450958 Cold Spring Harbor Laboratory Press 2021-07-05 <![CDATA[ A complete reference genome improves analysis of human genetic variation ]]> https://biorxiv.org/content/10.1101/2021.07.12.452063v1?rss=1 Aganezov, S. Yan, S. M. Soto, D. C. Kirsche, M. Zarate, S. Avdeyev, P. Taylor, D. J. Shafin, K. Shumate, A. Xiao, C. Wagner, J. McDaniel, J. Olson, N. D. Sauria, M. E. G. Vollger, M. R. Rhie, A. Meredith, M. Martin, S. Lee, J. Koren, S. Rosenfeld, J. Paten, B. Layer, R. Chin, C.-S. Sedlazeck, F. J. Hansen, N. F. Miller, D. E. Phillippy, A. M. Miga, K. H. McCoy, R. C. Dennis, M. Y. Zook, J. M. Schatz, M. C. 2021-07-13 doi:10.1101/2021.07.12.452063 Cold Spring Harbor Laboratory Press 2021-07-13 <![CDATA[ Antagonists targeting eEF2 kinase rescue multiple aspects of pathophysiology in Alzheimer's disease model mice ]]> https://biorxiv.org/content/10.1101/2021.07.15.452522v1?rss=1 Kasica, N. P. Zhou, X. Wang, X. Yang, W. P. Zimmermann, H. R. Holland, C. E. Koscielniak, E. Wu, H. Cox, A. O. Lee, J. Ryazanov, A. G. Furdui, C. M. Ma, T. 2021-07-15 doi:10.1101/2021.07.15.452522 Cold Spring Harbor Laboratory Press 2021-07-15 <![CDATA[ A transmissible γδ intraepithelial lymphocyte hyperproliferative phenotype is associated with the intestinal microbiota and confers protection against acute infection. ]]> https://biorxiv.org/content/10.1101/2021.07.22.453366v1?rss=1 Jia, L. Wu, G. Alonso, S. Zhao, C. Lemenze, A. Lam, Y. Y. Zhao, L. Edelblum, K. L. 2021-07-23 doi:10.1101/2021.07.22.453366 Cold Spring Harbor Laboratory Press 2021-07-23 <![CDATA[ A Data-Dependent Acquisition Ladder for Ultrasensitive (Neuro)Proteomics ]]> https://biorxiv.org/content/10.1101/2021.08.03.454943v1?rss=1 Choi, S. B. Munoz-LLancao, P. Manzini, M. C. Nemes, P. 2021-08-04 doi:10.1101/2021.08.03.454943 Cold Spring Harbor Laboratory Press 2021-08-04 <![CDATA[ mebipred: identifying metal-binding potential in protein sequences. ]]> https://biorxiv.org/content/10.1101/2021.08.12.456141v1?rss=1 Aptekmann, A. A. Buongiorno, J. Giovannelli, D. Glamoclija, M. Ferreiro, D. U. Bromberg, Y. 2021-08-13 doi:10.1101/2021.08.12.456141 Cold Spring Harbor Laboratory Press 2021-08-13 <![CDATA[ Long-term effects of moderate concussive brain injury during adolescence on synaptic and tonic GABA currents in dentate projection neurons. ]]> https://biorxiv.org/content/10.1101/2021.08.15.456415v1?rss=1 GUPTA, A. - Proddutur, A. Elgammal, F. S. Santhakumar, V. 2021-08-15 doi:10.1101/2021.08.15.456415 Cold Spring Harbor Laboratory Press 2021-08-15 <![CDATA[ Impact of Erg11 amino acid substitutions identified in Candida auris clade III isolates on triazole drug susceptibility ]]> https://biorxiv.org/content/10.1101/2021.08.16.456589v1?rss=1 Williamson, B. Wilk, A. Guerrero, K. D. Mikulski, T. D. Elias, T. N. Sawh, I. Cancino-Prado, G. Gardam, D. Heath, C. H. Govender, N. P. Perlin, D. S. Kordalewska, M. Healey, K. R. 2021-08-17 doi:10.1101/2021.08.16.456589 Cold Spring Harbor Laboratory Press 2021-08-17 <![CDATA[ Perinatal Inflammation Disturbs Secondary Germinal Zone Neurogenesis and Gliogenesis Producing Deficits in Sociability ]]> https://biorxiv.org/content/10.1101/2021.08.18.456694v1?rss=1 Velloso, F. J. Wadhwa, A. Kumari, E. Carcea, I. Gunal, O. B. Levison, S. W. 2021-08-19 doi:10.1101/2021.08.18.456694 Cold Spring Harbor Laboratory Press 2021-08-19 <![CDATA[ LRRK2 causes centrosomal deficits via phosphorylated Rab10 and RILPL1 at centriolar subdistal appendages ]]> https://biorxiv.org/content/10.1101/2021.08.23.457380v1?rss=1 Ordonez, A. J. L. Fernandez, B. Fasiczka, R. Naaldijk, Y. Fdez, E. Blanca Ramirez, M. Phan, S. Boassa, D. Hilfiker, S. 2021-08-24 doi:10.1101/2021.08.23.457380 Cold Spring Harbor Laboratory Press 2021-08-24 <![CDATA[ Coordinated drift of receptive fields during noisy representation learning ]]> https://biorxiv.org/content/10.1101/2021.08.30.458264v1?rss=1 Qin, S. Farashahi, S. Lipshutz, D. Sengupta, A. M. Chklovskii, D. B. Pehlevan, C. 2021-09-01 doi:10.1101/2021.08.30.458264 Cold Spring Harbor Laboratory Press 2021-09-01 <![CDATA[ Template strand deoxyuridine promoter recognition by a viral RNA polymerase ]]> https://biorxiv.org/content/10.1101/2021.08.30.458274v1?rss=1 Fraser, A. Sokolova, M. L. Drobysheva, A. V. Gordeeva, J. V. Borukhov, S. Artamonova, T. O. AlphaFold team, Severinov, K. V. Leiman, P. G. 2021-08-31 doi:10.1101/2021.08.30.458274 Cold Spring Harbor Laboratory Press 2021-08-31 <![CDATA[ Dopamine biases sensitivity to personal goals and social influence in self-control over everyday desires ]]> https://biorxiv.org/content/10.1101/2021.09.10.459829v1?rss=1 Castrellon, J. J. Young, J. S. Dang, L. C. Smith, C. T. Cowan, R. L. Zald, D. H. Samanez-Larkin, G. R. 2021-09-11 doi:10.1101/2021.09.10.459829 Cold Spring Harbor Laboratory Press 2021-09-11 <![CDATA[ Molecular and cellular adaptations in hippocampal parvalbumin neurons mediate behavioral responses to chronic social stress ]]> https://biorxiv.org/content/10.1101/2021.09.14.459024v1?rss=1 Bhatti, D. L. Medrihan, L. Chen, M. X. Jin, J. McCabe, K. Wang, W. Azevedo, E. P. Ledo, J. H. Kim, Y. 2021-09-15 doi:10.1101/2021.09.14.459024 Cold Spring Harbor Laboratory Press 2021-09-15 <![CDATA[ Development of a novel, pan-variant aerosol intervention for COVID-19 ]]> https://biorxiv.org/content/10.1101/2021.09.14.459961v1?rss=1 Shoemaker, R. H. Panettieri, R. A. Libutti, S. K. Hochster, H. S. Watts, N. R. Wingfield, P. T. Starkl, P. M. Pimenov, L. Gawish, R. Hladik, A. Knapp, S. Boring, D. White, J. M. Lawrence, Q. Boone, J. Marshall, J. D. Matthews, R. L. Cholewa, B. D. Richig, J. W. Chen, B. T. McCormick, D. L. Gugensberger, R. Holler, S. Penninger, J. M. Wirnsberger, G. 2021-09-14 doi:10.1101/2021.09.14.459961 Cold Spring Harbor Laboratory Press 2021-09-14 <![CDATA[ Circumscribing laser cuts attenuate seizure propagation in a mouse model of focal epilepsy ]]> https://biorxiv.org/content/10.1101/2021.09.17.460788v1?rss=1 Lieberman, S. Rivera, D. A. Morton, R. Hingorani, A. Southard, T. L. Johnson, L. Reukauf, J. Radwanski, R. E. Zhao, M. Nishimura, N. Bracko, O. Schwartz, T. H. Schaffer, C. B. 2021-09-20 doi:10.1101/2021.09.17.460788 Cold Spring Harbor Laboratory Press 2021-09-20 <![CDATA[ Acoustic Force Spectroscopy Reveals Subtle Differences in Cellulose Unbinding Behavior of Carbohydrate-Binding Modules ]]> https://biorxiv.org/content/10.1101/2021.09.20.461102v1?rss=1 15pN). Significance StatementCellulases are multi-modular enzymes produced by numerous microbes that catalyze cellulose hydrolysis into glucose. These enzymes play an important role in global carbon cycling as well as cellulosic biofuels production. CBMs are essential components of cellulolytic enzymes involved in facilitating hydrolysis of polysaccharides by tethered catalytic domains (CD). The subtle interplay between CBM binding and CD activity is poorly understood particularly for heterogeneous reactions at solid-liquid interfaces. Here, we report a highly multiplexed single-molecule force spectroscopy method to study CBM dissociation from cellulose to infer the molecular mechanism governing substrate recognition and dissociation. This approach can be broadly applied to study multivalent protein-polysaccharide binding interactions relevant to other carbohydrates such as starch, chitin, or hyaluronan to engineer efficient biocatalysts. ]]> Hackl, M. Contrada, E. V. Ash, J. E. Kulkarni, A. Yoon, J. Cho, H.-Y. Lee, K.-B. Yarbrough, J. M. Chundawat, S. P. S. 2021-09-20 doi:10.1101/2021.09.20.461102 Cold Spring Harbor Laboratory Press 2021-09-20 <![CDATA[ RIG-I uses its intrinsically disordered CARDs-Helicase linker in RNA proofreading functions ]]> https://biorxiv.org/content/10.1101/2021.09.23.461459v1?rss=1 Patel, S. S. 2021-09-23 doi:10.1101/2021.09.23.461459 Cold Spring Harbor Laboratory Press 2021-09-23 <![CDATA[ Neuronal glucose metabolism sets cholinergic tone and controls thermo-regulated signaling at the neuromuscular junction ]]> https://biorxiv.org/content/10.1101/2021.09.28.462124v1?rss=1 Tang, Y. Zong, H. Kwon, H. Qiu, Y. Pessin, J. B. Wu, L. Buddo, K. A. Boykov, I. Schmidt, C. Lin, C.-T. Neufer, P. D. Schwartz, G. J. Kurland, I. J. Pessin, J. E. 2021-09-30 doi:10.1101/2021.09.28.462124 Cold Spring Harbor Laboratory Press 2021-09-30 <![CDATA[ The In Vivo Source of Type I and Type III IFNs is Pathogen Dependent ]]> https://biorxiv.org/content/10.1101/2021.10.05.463160v1?rss=1 Sandoval, M. J. Tseng, H.-C. Risman, H. P. Smirnov, S. Li, Q. Lin, J.-D. Rivera, A. Durbin, R. K. Kotenko, S. V. Durbin, J. 2021-10-05 doi:10.1101/2021.10.05.463160 Cold Spring Harbor Laboratory Press 2021-10-05 <![CDATA[ Engineered natural killer cells impede the immunometabolic CD73-adenosine axis in solid tumors ]]> https://biorxiv.org/content/10.1101/2021.10.05.463201v1?rss=1 Chambers, A. M. Lupo, K. B. Wang, J. Cao, J. Toregrosa-Allen, S. Elzey, B. Pine, S. Jalal, S. Utturkar, S. Atallah Lanman, N. Bernal-Crespo, V. Matosevic, S. 2021-10-05 doi:10.1101/2021.10.05.463201 Cold Spring Harbor Laboratory Press 2021-10-05 <![CDATA[ Neural networks implicated in autobiographical memory training ]]> https://biorxiv.org/content/10.1101/2021.10.05.463255v1?rss=1 Cirneci, D. Onu, M. Papasteri, C. C. Georgescu, D. P. Poalelungi, C. Sofonea, A. Puscasu, N. Podina, I. R. Berceanu, A. I. Carcea, I. 2021-10-07 doi:10.1101/2021.10.05.463255 Cold Spring Harbor Laboratory Press 2021-10-07 <![CDATA[ Polyunsaturated fatty acids inhibit a pentameric ligand-gated ion channel through one of two binding sites ]]> https://biorxiv.org/content/10.1101/2021.10.08.463634v1?rss=1 Dietzen, N. M. Arcario, M. J. Chen, L. J. Petroff, J. T. Krishnan, K. Brannigan, G. Covey, D. F. Cheng, W. W. 2021-10-08 doi:10.1101/2021.10.08.463634 Cold Spring Harbor Laboratory Press 2021-10-08 <![CDATA[ scINSIGHT for interpreting single-cell gene expression from biologically heterogeneous data ]]> https://biorxiv.org/content/10.1101/2021.10.13.464306v1?rss=1 Qian, K. Fu, S. Li, H. Li, W. V. 2021-10-13 doi:10.1101/2021.10.13.464306 Cold Spring Harbor Laboratory Press 2021-10-13 <![CDATA[ Interaction Between Transcribing RNA Polymerase and Topoisomerase I Prevents R-loop Formation in E. coli ]]> https://biorxiv.org/content/10.1101/2021.10.26.465782v1?rss=1 Sutormin, D. Galivondzhyan, A. Musharova, O. Travin, D. Y. Rusanova, A. Obraztsova, K. Borukhov, S. Severinov, K. 2021-10-26 doi:10.1101/2021.10.26.465782 Cold Spring Harbor Laboratory Press 2021-10-26 <![CDATA[ The expression of essential selenoproteins during zebrafish development requires SECIS binding protein 2-like ]]> https://biorxiv.org/content/10.1101/2021.11.01.466845v1?rss=1 Kiledjian, N. T. Shah, R. Vetick, M. B. Copeland, P. R. 2021-11-02 doi:10.1101/2021.11.01.466845 Cold Spring Harbor Laboratory Press 2021-11-02 <![CDATA[ Creatine utilization as a sole nitrogen source in Pseudomonas putida KT2440 is transcriptionally regulated by CahR ]]> https://biorxiv.org/content/10.1101/2021.11.02.466972v1?rss=1 Hinkel, L. A. Willsey, G. G. Lenahan, S. M. Eckstrom, K. Schutz, K. C. Wargo, M. J. 2021-11-02 doi:10.1101/2021.11.02.466972 Cold Spring Harbor Laboratory Press 2021-11-02 <![CDATA[ Host-associated phages disperse across the extraterrestrial analogue Antarctica ]]> https://biorxiv.org/content/10.1101/2021.11.09.467789v1?rss=1 Rahlff, J. Bornemann, T. L. V. Lopatina, A. Severinov, K. Probst, A. J. 2021-11-09 doi:10.1101/2021.11.09.467789 Cold Spring Harbor Laboratory Press 2021-11-09 <![CDATA[ tRNA anticodon cleavage by target-activated CRISPR-Cas13a effector ]]> https://biorxiv.org/content/10.1101/2021.11.10.468108v1?rss=1 Jain, I. Kolesnik, M. Minakhin, L. Morozova, N. Shiriaeva, A. Kirillov, A. Medvedeva, S. Kuznedelov, K. Borukhov, S. Makarova, K. S. Koonin, E. V. Severinov, K. Semenova, E. 2021-11-10 doi:10.1101/2021.11.10.468108 Cold Spring Harbor Laboratory Press 2021-11-10 <![CDATA[ An Integrated Process Analytical Platform for Automated Monitoring of Monoclonal Antibody N-linked Glycosylation ]]> https://biorxiv.org/content/10.1101/2021.11.14.468439v1?rss=1 View larger version (22K): org.highwire.dtl.DTLVardef@1fbb698org.highwire.dtl.DTLVardef@90da13org.highwire.dtl.DTLVardef@1dd45e5org.highwire.dtl.DTLVardef@17fadd_HPS_FORMAT_FIGEXP M_FIG N-GLYcanyzer is an automated PAT toolkit for rapid sample processing for mAb N-linked glycans analysis to enable advanced biologics manufacturing C_FIG ]]> Gyorgypal, A. Chundawat, S. P. S. 2021-11-14 doi:10.1101/2021.11.14.468439 Cold Spring Harbor Laboratory Press 2021-11-14 <![CDATA[ Mitochondrial dysfunction promotes alternative gasdermin D-mediated inflammatory cell death and susceptibility to infection ]]> https://biorxiv.org/content/10.1101/2021.11.18.469014v1?rss=1 Weindel, C. G. Zhao, X. Martinez, E. Bell, S. L. Vail, K. J. Coleman, A. K. VanPortfliet, J. J. Zhao, B. Mabry, C. Li, P. West, P. Karpac, J. Patrick, K. L. Watson, R. O. 2021-11-19 doi:10.1101/2021.11.18.469014 Cold Spring Harbor Laboratory Press 2021-11-19 <![CDATA[ Transposon Extermination Reveals Their Adaptive Fitness Contribution ]]> https://biorxiv.org/content/10.1101/2021.11.29.470382v1?rss=1 Cranz-Mileva, S. Reilly, E. Chalhoub, N. Patel, R. Atanassova, T. Cao, W. Ellison, C. Zaratiegui, M. 2021-11-30 doi:10.1101/2021.11.29.470382 Cold Spring Harbor Laboratory Press 2021-11-30 <![CDATA[ Deciphering the Molecular Mechanism of HCV Protease Inhibitor Fluorination as a General Approach to Avoid Drug Resistance ]]> https://biorxiv.org/content/10.1101/2021.11.30.470632v1?rss=1 Zephyr, J. Rao, D. N. Vo, S. V. Henes, M. Kosovrasti, K. Matthew, A. N. Hedger, A. K. Timm, J. Chan, E. T. Ali, A. Yilmaz, N. K. Schiffer, C. A. 2021-11-30 doi:10.1101/2021.11.30.470632 Cold Spring Harbor Laboratory Press 2021-11-30 <![CDATA[ Human KIR+CD8+ T cells target pathogenic T cells in Celiac disease and are active in autoimmune diseases and COVID-19 ]]> https://biorxiv.org/content/10.1101/2021.12.23.473930v1?rss=1 Li, J. Zaslavsky, M. E. Su, Y. Sikora, M. van Unen, V. Christophersen, A. Chiou, S.-H. Chen, L. Li, J. Ji, X. Wilhelmy, J. McSween, A. Palanski, B. A. Mallajosyula, V. Dhondalay, G. Bhamidipati, K. Pai, J. Kipp, L. Dunn, J. Hauser, S. Oksenberg, J. Satpathy, A. Robinson, W. Steinmetz, L. Khosla, C. Utz, P. Sollid, L. M. Heath, J. Fernandez-Becker, N. Nadeau, K. Saligrama, N. Davis, M. 2021-12-25 doi:10.1101/2021.12.23.473930 Cold Spring Harbor Laboratory Press 2021-12-25 <![CDATA[ Structure determination of protein-peptide complexes from NMR chemical shift data using MELD. ]]> https://biorxiv.org/content/10.1101/2021.12.31.474671v1?rss=1 Mondal, A. Swapna, G. V. T. Hao, J. Ma, L. Roth, M. J. Montelione, G. T. Perez, A. 2022-01-02 doi:10.1101/2021.12.31.474671 Cold Spring Harbor Laboratory Press 2022-01-02 <![CDATA[ mTORC2 loss in oligodendrocyte progenitor cells results in regional hypomyelination in the central nervous system ]]> https://biorxiv.org/content/10.1101/2022.01.04.474811v1?rss=1 Dahl, K. D. Hathaway, H. A. Almeida, A. R. Bourne, J. Brown, T. L. Finseth, L. T. Wood, T. L. Macklin, W. B. 2022-01-04 doi:10.1101/2022.01.04.474811 Cold Spring Harbor Laboratory Press 2022-01-04 <![CDATA[ Serine 1283 in extracellular matrix glycoprotein Reelin is crucial for Reelin's function in brain development ]]> https://biorxiv.org/content/10.1101/2022.01.06.474241v1?rss=1 Kleene, R. Loers, G. Sharaf, A. Wang, S. Kataria, H. Anstoetz, M. Hermans-Borgmeyer, I. Schachner, M. 2022-01-06 doi:10.1101/2022.01.06.474241 Cold Spring Harbor Laboratory Press 2022-01-06 <![CDATA[ The coupling between healthspan and lifespan in Caenorhabditis depends on complex interactions between compound intervention and genetic background ]]> https://biorxiv.org/content/10.1101/2022.01.15.476462v1?rss=1 Banse, S. A. Jackson, E. G. Sedore, C. A. Onken, B. Hall, D. Coleman-Hulbert, A. L. Huynh, P. Garrett, T. Johnson, E. Harinath, G. Inman, D. Guo, S. Morshead, M. Xue, J. Falkowski, R. Chen, E. Herrera, C. Kirsch, A. J. Perez, V. I. Guo, M. Lithgow, G. J. Driscoll, M. Phillips, P. C. 2022-01-17 doi:10.1101/2022.01.15.476462 Cold Spring Harbor Laboratory Press 2022-01-17 <![CDATA[ Rethinking Statistical Learning as a Dynamic Stochastic Process, from The Motor Systems Perspective ]]> https://biorxiv.org/content/10.1101/2022.01.18.476831v1?rss=1 Vaskevich, A. Torres, E. B. 2022-01-19 doi:10.1101/2022.01.18.476831 Cold Spring Harbor Laboratory Press 2022-01-19 <![CDATA[ Initial assessment of the spatial learning, reversal, and sequencing task capabilities of knock-in rats with humanizing mutations in the Ass-coding region of App ]]> https://biorxiv.org/content/10.1101/2022.01.24.477482v1?rss=1 D'Adamio, L. Pham, H. Yin, T. 2022-01-24 doi:10.1101/2022.01.24.477482 Cold Spring Harbor Laboratory Press 2022-01-24 <![CDATA[ Federated analysis in COINSTAC reveals functional network connectivity and spectral links to smoking and alcohol consumption in nearly 2,000 adolescent brains ]]> https://biorxiv.org/content/10.1101/2022.02.02.478847v1?rss=1 Gazula, H. Rootes-Murdy, K. Holla, B. Basodi, S. Zhang, Z. Verner, E. Kelly, R. Murthy, P. Chakrabarti, A. Basu, D. Bhagyalakshmi, S. Lenin, R. Lourembam, R. Kalyanram, K. Kartik, K. Kalyanaraman, K. Ghattu, K. Kuriyan, R. Kurpad, S. S. Barker, G. Bharath, R. D. Desrivieres, S. Purushottam, M. Orfanos, D. P. Sharma, E. Hickman, M. Toledano, M. Vaidya, N. Banaschewski, T. Bokde, A. L. W. Flor, H. Grigis, A. Garavan, H. Gowland, P. Heinz, A. Bruhl, R. Martinot, J.-L. Martinot, M.-L. P. Artiges, E. Nees, F. Paus, T. Poustka, L. Frohner, J. H. Robinson, L 2022-02-04 doi:10.1101/2022.02.02.478847 Cold Spring Harbor Laboratory Press 2022-02-04 <![CDATA[ Salp blooms increase carbon export 5-fold in the Southern Ocean ]]> https://biorxiv.org/content/10.1101/2022.02.07.479467v1?rss=1 Decima, M. Stukel, M. R. Nodder, S. Gutierrez, A. Selph, K. Lopes dos Santos, A. Safi, K. Kelly, T. Deans, F. Morales, S. E. Baltar, F. Latasa, M. Maxim, G. Pinkerton, M. 2022-02-08 doi:10.1101/2022.02.07.479467 Cold Spring Harbor Laboratory Press 2022-02-08 <![CDATA[ The OncoLoop network-based precision oncology framework ]]> https://biorxiv.org/content/10.1101/2022.02.11.479456v1?rss=1 Vasciaveo, A. Zou, M. Arriaga, J. M. Geraldes de Almeida, F. Douglass, E. F. Shibata, M. Rodriguez-Calero, A. de Brot, S. Mitrofanova, A. Chua, C. W. Karan, C. Realubit, R. Pampou, S. Y. Kim, J. Y. Corey, E. Alvarez, M. Rubin, M. A. Shen, M. M. Califano, A. Abate-Shen, C. 2022-02-14 doi:10.1101/2022.02.11.479456 Cold Spring Harbor Laboratory Press 2022-02-14 <![CDATA[ Loss of Neurodevelopmental Gene CASK Disrupts Neural Connectivity in Human Cortical Excitatory Neurons ]]> https://biorxiv.org/content/10.1101/2022.02.14.480404v1?rss=1 McSweeney, D. Gabriel, R. Jin, K. Pang, Z. P. Aronow, B. J. Pak, C. 2022-02-15 doi:10.1101/2022.02.14.480404 Cold Spring Harbor Laboratory Press 2022-02-15 <![CDATA[ Dynamic Interrogation of Stochastic Transcriptome Trajectories Using Disease Associated Genes Reveals Distinct Origins of Neurological and Neuropsychiatric Disorders ]]> https://biorxiv.org/content/10.1101/2022.02.26.482124v1?rss=1 Bermperidis, T. Schafer, S. Gage, F. H. Sejnowski, T. Torres, E. B. 2022-02-27 doi:10.1101/2022.02.26.482124 Cold Spring Harbor Laboratory Press 2022-02-27 <![CDATA[ Gut microbiota-derived tryptamine impairs insulin sensitivity ]]> https://biorxiv.org/content/10.1101/2022.03.05.483098v1?rss=1 Zhai, L. Xiao, H. Lin, C. Lam, Y. Y. Wong, H. L. X. Gong, M. Wu, G. Deng, Y. Ning, Z. Huang, C. Zhang, Y. Zhuang, M. Chao, Y. Zhang, E. L. Zhao, L. Zhang, C. Fang, X. Jia, W. Zhao, L. Bian, Z.-x. 2022-03-05 doi:10.1101/2022.03.05.483098 Cold Spring Harbor Laboratory Press 2022-03-05 <![CDATA[ Vocalization categorization behavior explained by a feature-based auditory categorization model ]]> https://biorxiv.org/content/10.1101/2022.03.09.483596v1?rss=1 Kar, M. Pernia, M. Williams, K. Parida, S. Schneider, N. A. McAndrew, M. Kumbam, I. Sadagopan, S. 2022-03-10 doi:10.1101/2022.03.09.483596 Cold Spring Harbor Laboratory Press 2022-03-10 <![CDATA[ Evaluating spatial and network properties of NMDA-dependent neuronal connectivity in mixed cortical cultures ]]> https://biorxiv.org/content/10.1101/2022.03.10.483856v1?rss=1 Rojvirat, C. P. Berlin, J. R. Nguyen, T. D. 2022-03-13 doi:10.1101/2022.03.10.483856 Cold Spring Harbor Laboratory Press 2022-03-13 <![CDATA[ Development of ONT-cappable-seq to unravel the transcriptional landscape of Pseudomonas phages ]]> https://biorxiv.org/content/10.1101/2022.03.18.484859v1?rss=1 Putzeys, L. Boon, M. Lammens, E.-M. Kuznedelov, K. Severinov, K. Lavigne, R. 2022-03-19 doi:10.1101/2022.03.18.484859 Cold Spring Harbor Laboratory Press 2022-03-19 <![CDATA[ The little skate genome and the evolutionary emergence of wing-like fin appendages ]]> https://biorxiv.org/content/10.1101/2022.03.21.485123v1?rss=1 Marletaz, F. de la Calle-Mustienes, E. Acemel, R. D. Nakamura, T. Paliou, C. Naranjo, S. Martinez-Garcia, P. M. Cases, I. Sleight, V. A. Hirschberger, C. Marcet-Houben, M. Navon, D. Andrescavage, A. Skvortsova, K. Duckett, P. E. Gonzalez-Rajal, A. Bogdanovic, O. Gibcus, J. H. Yang, L. Gallardo-Fuentes, L. Sospedra, I. Lopez-Rios, J. Darbellay, F. Visel, A. Dekker, J. Shubin, N. Gabaldon, T. Tena, J. J. Lupianez, D. G. Rokhsar, D. S. Gomez-Skarmeta, J. L. 2022-03-22 doi:10.1101/2022.03.21.485123 Cold Spring Harbor Laboratory Press 2022-03-22 <![CDATA[ Cells with Stochastically Increased Methyltransferase to Restriction Endonuclease Ratio Provide an Entry for Bacteriophage into Protected Cell Population ]]> https://biorxiv.org/content/10.1101/2022.03.28.486079v1?rss=1 Kirillov, A. Morozova, N. Polinovaskaya, V. Smirnov, S. Khodorkovskii, M. Zeng, L. Ispolatov, Y. Severinov, K. 2022-03-28 doi:10.1101/2022.03.28.486079 Cold Spring Harbor Laboratory Press 2022-03-28 <![CDATA[ Pain as a Trigger for Epigenetic Modifications in Limbic Circuitry ]]> https://biorxiv.org/content/10.1101/2022.03.29.486268v1?rss=1 Bryant, S. Balouek-Thomert, J.-A. Geiger, L. T. Barker, D. J. Pena, C. J. 2022-03-30 doi:10.1101/2022.03.29.486268 Cold Spring Harbor Laboratory Press 2022-03-30 <![CDATA[ Moxifloxacin-mediated killing of Mycobacterium tuberculosis involves respiratory downshift, reductive stress, and ROS accumulation ]]> https://biorxiv.org/content/10.1101/2022.04.04.486929v1?rss=1 Shee, S. Singh, S. Tripathi, A. Thakur, C. Kumar, A. T. Das, M. Yadav, V. Kohli, S. Rajmani, R. S. Chandra, N. Chakrapani, H. drlica, K. Singh, A. 2022-04-04 doi:10.1101/2022.04.04.486929 Cold Spring Harbor Laboratory Press 2022-04-04 <![CDATA[ Cell-free mutant analysis combined with structure prediction of a lasso peptide biosynthetic protein B2 ]]> https://biorxiv.org/content/10.1101/2022.04.06.487251v1?rss=1 Alfi, A. Popov, A. Kumar, A. Zhang, K. Y. J. Dubiley, S. Severinov, K. Tagami, S. 2022-04-06 doi:10.1101/2022.04.06.487251 Cold Spring Harbor Laboratory Press 2022-04-06 <![CDATA[ Reconstructing physical cell interaction networks from single-cell data using Neighbor-seq ]]> https://biorxiv.org/content/10.1101/2022.04.15.488517v1?rss=1 Ghaddar, B. De, S. 2022-04-16 doi:10.1101/2022.04.15.488517 Cold Spring Harbor Laboratory Press 2022-04-16 <![CDATA[ Elevator mechanism dynamics in a sodium-coupled dicarboxylate transporter ]]> https://biorxiv.org/content/10.1101/2022.05.01.490196v1?rss=1 Kinz-Thompson, C. D. Lopez Redondo, M. Mulligan, C. Sauer, D. B. Marden, J. J. Song, J. Tajkhorshid, E. Hunt, J. F. Stokes, D. L. Mindell, J. A. Wang, D.-N. Gonzalez, R. L. 2022-05-01 doi:10.1101/2022.05.01.490196 Cold Spring Harbor Laboratory Press 2022-05-01 <![CDATA[ Microbial population dynamics decouple nutrient affinity from environmental concentration ]]> https://biorxiv.org/content/10.1101/2022.05.04.490627v1?rss=1 Fink, J. W. Held, N. A. Manhart, M. 2022-05-04 doi:10.1101/2022.05.04.490627 Cold Spring Harbor Laboratory Press 2022-05-04 <![CDATA[ Adsorption of Pulmonary and Exogeneous Surfactants on SARS-CoV-2 Spike Protein ]]> https://biorxiv.org/content/10.1101/2022.05.04.490631v1?rss=1 Santo, K. P. Neimark, A. V. 2022-05-04 doi:10.1101/2022.05.04.490631 Cold Spring Harbor Laboratory Press 2022-05-04 <![CDATA[ Nav1.1 in mammalian sensory neurons is required for normal motor behaviors ]]> https://biorxiv.org/content/10.1101/2022.05.05.490851v1?rss=1 Griffith, T. Espino, C. M. Lewis, C. M. Ortiz, S. Dalal, M. S. Wells, K. M. O'Neil, D. A. Wilkinson, K. A. 2022-05-06 doi:10.1101/2022.05.05.490851 Cold Spring Harbor Laboratory Press 2022-05-06 <![CDATA[ Replicative Instability Drives Cancer Progression ]]> https://biorxiv.org/content/10.1101/2022.05.06.490945v1?rss=1 Morris, B. B. Smith, J. P. Zhang, Q. Jiang, Z. Hampton, O. A. Churchman, M. L. Arnold, S. M. Owen, D. H. Gray, J. E. Dillon, P. M. Soliman, H. H. Stover, D. G. Colman, H. Chakravarti, A. Shain, K. H. Silva, A. S. Villano, J. L. Vogelbaum, M. A. Borges, V. F. Akerley, W. L. Gentzler, R. D. Hall, R. D. Matsen, C. B. Ulrich, C. M. Post, A. R. Nix, D. A. Singer, E. A. Larner, J. M. Stukenberg, T. Jones, D. R. Mayo, M. W. 2022-05-06 doi:10.1101/2022.05.06.490945 Cold Spring Harbor Laboratory Press 2022-05-06 <![CDATA[ Developmentally determined intersectional genetic strategies to dissect adult somatosensory circuit function ]]> https://biorxiv.org/content/10.1101/2022.05.16.492127v1?rss=1 Bohic, M. Upadhyay, A. Keating, J. R. Simon, R. Briones, B. Azadegan, C. Romanienko, P. J. Stuber, G. D. Abraira, V. E. 2022-05-17 doi:10.1101/2022.05.16.492127 Cold Spring Harbor Laboratory Press 2022-05-17 <![CDATA[ Wnt signalling, cell fate determination and anteroposterior polarity of the skate gill arch skeleton ]]> https://biorxiv.org/content/10.1101/2022.05.19.492618v1?rss=1 Rees, J. M. Sleight, V. A. Clark, S. Nakamura, T. Gillis, J. A. 2022-05-20 doi:10.1101/2022.05.19.492618 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ A therapeutically targetable NOTCH1-SIRT1-KAT7 axis in T-cell Leukemia ]]> https://biorxiv.org/content/10.1101/2022.05.21.492944v1?rss=1 Lancho, O. Singh, A. da Silva-Diz, V. Tottone, L. Renck Nunes, P. Aleksandrova, M. Khatun, J. Luo, S. Zhao, C. Zheng, H. Chiles, E. Zuo, Z. Rocha, P. P. Su, X. Khiabanian, H. Herranz, D. 2022-05-22 doi:10.1101/2022.05.21.492944 Cold Spring Harbor Laboratory Press 2022-05-22 <![CDATA[ Structure-based discovery of selective histone deacetylase (HDAC) 3 and 4 inhibitors ]]> https://biorxiv.org/content/10.1101/2022.05.31.494169v1?rss=1 Agarwal, R. Pattarawat, P. Duff, M. R. Wang, H.-C. R. Baudry, J. Smith, J. 2022-05-31 doi:10.1101/2022.05.31.494169 Cold Spring Harbor Laboratory Press 2022-05-31 <![CDATA[ Pathobionts from chemically disrupted gut microbiota induce insulin-dependent diabetes in mice ]]> https://biorxiv.org/content/10.1101/2022.06.05.494898v1?rss=1 Yang, X. Wang, Z. Niu, J. Zhai, R. Xue, X. Wu, G. Gong, M. Zhao, L. Zhang, C. 2022-06-06 doi:10.1101/2022.06.05.494898 Cold Spring Harbor Laboratory Press 2022-06-06 <![CDATA[ Computational and functional characterization of the PI(4,5)P2 binding site of the TRPM3 ion channel ]]> https://biorxiv.org/content/10.1101/2022.06.05.494899v1?rss=1 Zhao, S. Carnevale, V. Gianti, E. Rohacs, T. 2022-06-07 doi:10.1101/2022.06.05.494899 Cold Spring Harbor Laboratory Press 2022-06-07 <![CDATA[ A Development-Inspired Niche for Homeostatic Human Mini-Intestines ]]> https://biorxiv.org/content/10.1101/2022.06.12.495827v1?rss=1 Childs, C. J. Holloway, E. M. Sweet, C. W. Tsai, Y.-H. Wu, A. Wu, J. Cardenas, O. P. Capeling, M. M. Eiken, M. Zwick, R. Palikuqi, B. Trentesaux, C. Zhang, C. Glass, I. Loebel, C. Yu, Q. Camp, G. Sexton, J. Z. Klein, O. D. Verzi, M. P. Spence, J. J. 2022-06-12 doi:10.1101/2022.06.12.495827 Cold Spring Harbor Laboratory Press 2022-06-12 <![CDATA[ Early-Life Stress Impairs Perception and Neural Encoding of Rapid Signals in the Auditory Pathway ]]> https://biorxiv.org/content/10.1101/2022.06.14.496208v1?rss=1 Ye, Y. Mattingly, M. M. Sunthimer, M. J. Gay, J. D. Rosen, M. J. 2022-06-17 doi:10.1101/2022.06.14.496208 Cold Spring Harbor Laboratory Press 2022-06-17 <![CDATA[ Dopamine in the Dorsal Bed Nucleus of Stria Terminalis signals Pavlovian sign-tracking and reward violations ]]> https://biorxiv.org/content/10.1101/2022.06.21.497039v1?rss=1 Gyawali, U. Martin, D. A. Sun, F. Li, Y. Calu, D. J. 2022-06-22 doi:10.1101/2022.06.21.497039 Cold Spring Harbor Laboratory Press 2022-06-22 <![CDATA[ Aromatase Inhibitor Induced Musculoskeletal Inflammation is Observed Independent of Oophorectomy in a Novel Mouse Model ]]> https://biorxiv.org/content/10.1101/2022.06.22.497263v1?rss=1 Young, N. A. Hampton, J. Sharma, J. Jablonski, K. DeVries, A. C. Bratasz, A. Wu, L.-C. Lustberg, M. Reinbolt, R. Jarjour, W. N. 2022-06-26 doi:10.1101/2022.06.22.497263 Cold Spring Harbor Laboratory Press 2022-06-26 <![CDATA[ Early life tolerance depends on a subset of specialized dendritic cells and is reinforced by the skin microbiota ]]> https://biorxiv.org/content/10.1101/2022.06.23.497363v1?rss=1 Weckel, A. A. Dhariwala, M. O. Ly, K. Ojewumi, O. T. Riggs, J. B. Gonzalez, J. R. Dwyer, L. R. Okoro, J. N. Leech, J. M. Bacino, M. S. Cho, G. D. merana, G. Anandasabapathy, N. Kumamoto, Y. O. Scharschmidt, T. C. 2022-06-26 doi:10.1101/2022.06.23.497363 Cold Spring Harbor Laboratory Press 2022-06-26 <![CDATA[ Naturally occurring mutations of SARS-CoV-2 main protease confer drug resistance to nirmatrelvir ]]> https://biorxiv.org/content/10.1101/2022.06.28.497978v1?rss=1 10-fold increase). X-ray crystal structures were determined for seven representative mutants with and/or without GC-376/nirmatrelvir. Viral growth assay showed that Mpro mutants with reduced enzymatic activity led to attenuated viral replication. Overall, our study identified several drug resistant hot spots that warrant close monitoring for possible clinical evidence of Paxlovid resistance. One Sentence SummaryPaxlovid resistant SARS-CoV-2 viruses with mutations in the main protease have been identified from clinical isolates. ]]> Hu, Y. Lewandowski, E. M. Tan, H. Morgan, R. T. Zhang, X. Jacobs, L. M. Butler, S. G. Mongora, M. V. Choy, J. S. Chen, Y. Wang, J. 2022-06-28 doi:10.1101/2022.06.28.497978 Cold Spring Harbor Laboratory Press 2022-06-28 <![CDATA[ Escape From Oncogene-Induced Senescence is Controlled by POU2F2 and Memorized by Chromatin Scars ]]> https://biorxiv.org/content/10.1101/2022.06.29.497942v1?rss=1 Martinez-Zamudio, R. I. Stefa, A. Nabuco, J. A. Vasilopoulos, T. Simpson, M. Dore, G. Roux, P.-F. Galan, M. A. Chokshi, R. J. Bischof, O. Herbig, U. 2022-07-02 doi:10.1101/2022.06.29.497942 Cold Spring Harbor Laboratory Press 2022-07-02 <![CDATA[ Cystathionine β-synthase gene inactivation dysregulates major urinary protein biogenesis and impairs sexual signaling in mice ]]> https://biorxiv.org/content/10.1101/2022.07.10.499408v1?rss=1 Bretes, E. Wroblewski, J. Wyszczelska-Rokiel, M. Jakubowski, H. 2022-07-11 doi:10.1101/2022.07.10.499408 Cold Spring Harbor Laboratory Press 2022-07-11 <![CDATA[ Breakdown of cooperative architecture in dual species biofilms and the spatial ecology of predation ]]> https://biorxiv.org/content/10.1101/2022.07.22.501146v1?rss=1 Wucher, B. R. Elsayed, M. Kadouri, D. E. Nadell, C. D. 2022-07-22 doi:10.1101/2022.07.22.501146 Cold Spring Harbor Laboratory Press 2022-07-22 <![CDATA[ Pharmacodynamic model of the dynamic response of Pseudomonas aeruginosa biofilms to drug treatments ]]> https://biorxiv.org/content/10.1101/2022.07.29.501971v1?rss=1 Roychowdhury, S. Roth, C. M. 2022-07-31 doi:10.1101/2022.07.29.501971 Cold Spring Harbor Laboratory Press 2022-07-31 <![CDATA[ The efficiency of Grignard Pure™ to inactivate airborne SARS-CoV-2 surrogate ]]> https://biorxiv.org/content/10.1101/2022.08.19.504307v1?rss=1 Desai, G. Ramachandran, G. Goldman, E. Galione, A. Lal, A. Choueiri, T. K. Fay, A. Jordan, W. Schaffner, D. W. Caravanos, J. Grignard, E. Mainelis, G. 2022-08-23 doi:10.1101/2022.08.19.504307 Cold Spring Harbor Laboratory Press 2022-08-23 <![CDATA[ Single cell transcriptomic profiling of human brain organoids reveals developmental timing- and cell-type-specific vulnerabilities induced by NRXN1 CNVs in schizophrenia ]]> https://biorxiv.org/content/10.1101/2022.08.24.505165v1?rss=1 Pak, C. Sebastian, R. Jin, K. Pavon, N. Bansal, R. Potter, A. Song, Y. Babu, J. Gabriel, R. Sun, Y. Aronow, B. J. 2022-08-25 doi:10.1101/2022.08.24.505165 Cold Spring Harbor Laboratory Press 2022-08-25 <![CDATA[ Special Nuclear Layer Contacts Among Starburst Amacrine Cells in the Mouse Retina ]]> https://biorxiv.org/content/10.1101/2022.08.28.504668v1?rss=1 Mu, S. Turner, N. L. Silversmith, W. M. Jordan, C. S. Kemnitz, N. Sorek, M. David, C. Jones, D. L. Bland, D. Moore, M. Sterling, A. R. Seung, H. S. the Eyewirers, 2022-08-31 doi:10.1101/2022.08.28.504668 Cold Spring Harbor Laboratory Press 2022-08-31 <![CDATA[ Duplicated zebrafish (Danio rerio) inositol phosphatases inpp5ka and inpp5kb diverged in expression pattern and function ]]> https://biorxiv.org/content/10.1101/2022.08.31.506059v1?rss=1 Shukla, D. Gural, B. M. Cauley, E. S. Roberts, L. E. Karas, B. F. Cavallo, L. Turkalj, L. Moody, S. A. Swan, L. E. Manzini, M. C. 2022-09-02 doi:10.1101/2022.08.31.506059 Cold Spring Harbor Laboratory Press 2022-09-02 <![CDATA[ Multivariable Graphical User Interface for Simulation of Tethered Particle Motion ]]> https://biorxiv.org/content/10.1101/2022.08.31.506066v1?rss=1 Ramdin, K. Hackl, M. Chundawat, S. P. S. 2022-09-03 doi:10.1101/2022.08.31.506066 Cold Spring Harbor Laboratory Press 2022-09-03 <![CDATA[ Yeast mtDNA transcription initiation in single nucleotide addition steps ]]> https://biorxiv.org/content/10.1101/2022.09.27.509796v1?rss=1 Goovaerts, Q. Shen, J. De Wijngaert, B. Basu, U. Patel, S. S. Das, K. 2022-09-28 doi:10.1101/2022.09.27.509796 Cold Spring Harbor Laboratory Press 2022-09-28 <![CDATA[ Evaluating sickness-induced anxiety versus lethargy at the behavioral and neuronal activity level ]]> https://biorxiv.org/content/10.1101/2022.10.03.510687v1?rss=1 Lanovoi, H. T. Oyama, R. Carcea, I. 2022-10-04 doi:10.1101/2022.10.03.510687 Cold Spring Harbor Laboratory Press 2022-10-04 <![CDATA[ Inhibition of the SARS-CoV-2 helicase at single-nucleotide resolution. ]]> https://biorxiv.org/content/10.1101/2022.10.07.511351v1?rss=1 Marx, S. K. Mickolajczyk, K. J. Craig, J. M. Thomas, C. A. Pfeffer, A. M. Abell, S. J. Carrasco, J. D. Franzi, M. C. Huang, J. R. Kim, H. C. Brinkerhoff, H. D. Kapoor, T. M. Gundlach, J. H. Laszlo, A. H. 2022-10-08 doi:10.1101/2022.10.07.511351 Cold Spring Harbor Laboratory Press 2022-10-08 <![CDATA[ The glyoxylate shunt protein ICL-1 protects from mitochondrial superoxide stress through activation of the mitochondrial unfolded protein response. ]]> https://biorxiv.org/content/10.1101/2022.10.10.511563v1?rss=1 Wang, G. Laranjeiro, R. LeValley, S. Van Raamsdonk, J. Driscoll, M. 2022-10-10 doi:10.1101/2022.10.10.511563 Cold Spring Harbor Laboratory Press 2022-10-10 <![CDATA[ Removal of pomt1 in zebrafish leads to loss of α-dystroglycan glycosylation and dystroglycanopathy phenotypes ]]> https://biorxiv.org/content/10.1101/2022.10.15.512359v1?rss=1 Karas, B. F. Terez, K. R. Battula, N. Gural, B. M. Flannery, K. P. Aboussleman, G. Mubin, N. Manzini, C. 2022-10-15 doi:10.1101/2022.10.15.512359 Cold Spring Harbor Laboratory Press 2022-10-15 <![CDATA[ Census: accurate, automated, deep, fast, and hierarchical scRNA-seq cell-type annotation ]]> https://biorxiv.org/content/10.1101/2022.10.19.512926v1?rss=1 Ghaddar, B. De, S. 2022-10-21 doi:10.1101/2022.10.19.512926 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ The BRCA1 isoform, BRCA1-IRIS, operates independently of the full-length BRCA1 in the Fanconi anemia pathway ]]> https://biorxiv.org/content/10.1101/2022.11.02.514969v1?rss=1 Li, A. G. Chan, B. C. Murphy, E. C. He, Y. Ors, M. Kong, Q. Cantor, S. B. Brugge, J. S. Brown, M. Livingston, D. M. 2022-11-04 doi:10.1101/2022.11.02.514969 Cold Spring Harbor Laboratory Press 2022-11-04 <![CDATA[ Inhibition of extracellular vesicle-encapsulated miRNA produced by estrogen-mediated upregulation of cellular processing suppresses target organ inflammation in a humanized model of systemic lupus erythematosus ]]> https://biorxiv.org/content/10.1101/2022.11.03.514940v1?rss=1 Young, N. A. Schwarz, E. Mesa, R. A. Jablonski, K. Wu, L.-C. Roberson, E. D. O. Jarjour, W. 2022-11-04 doi:10.1101/2022.11.03.514940 Cold Spring Harbor Laboratory Press 2022-11-04 <![CDATA[ The N-terminal domain of the human mitochondrial helicase Twinkle has DNA binding activity crucial for supporting processive DNA synthesis by Polymerase γ ]]> https://biorxiv.org/content/10.1101/2022.11.10.516034v1?rss=1 Johnson, L. C. Singh, A. Patel, S. S. 2022-11-10 doi:10.1101/2022.11.10.516034 Cold Spring Harbor Laboratory Press 2022-11-10 <![CDATA[ MSP1 encodes an essential RNA-binding PPR factor required for nad1 maturation and complex I biogenesis in Arabidopsis mitochondria ]]> https://biorxiv.org/content/10.1101/2022.11.12.516219v1?rss=1 Best, C. Mizrahi, R. Edris, R. Tang, H. Zer, H. Colas des Francs-Small, C. Finkel, O. M. Zhu, H. Small, I. D. Ostersetzer, O. 2022-11-13 doi:10.1101/2022.11.12.516219 Cold Spring Harbor Laboratory Press 2022-11-13 <![CDATA[ Bone Marrow- and Umbilical Cord-Derived Mesenchymal Stem Cell Secretome Alters Gene Expression and Upregulates Motility of Human Endometrial Stromal Cells ]]> https://biorxiv.org/content/10.1101/2022.11.12.516251v1?rss=1 Zhao, Q. Larios, K. Naaldijk, Y. Sherman, L. Chemerinski, A. Okereke, K. Rameshwar, P. Lemenze, A. Douglas, N. C. Morelli, S. S. 2022-11-14 doi:10.1101/2022.11.12.516251 Cold Spring Harbor Laboratory Press 2022-11-14 <![CDATA[ Investigations into hydrogen sulfide-induced suppression of neuronal activity in vivo and calcium dysregulation in vitro ]]> https://biorxiv.org/content/10.1101/2022.11.14.516514v1?rss=1 5 ppm dysregulated SCO patterns in a dose-dependent manner. Inhibitors of NMDA and AMPA receptors magnified H2S-induced SCO suppression. Inhibitors of L-type voltage gated Ca2+ channels (VGCC) and transient receptor potential (TRP) channels prevented H2S-induced SCO suppression. Inhibitors of T-type VGCC, ryanodine receptors, and sodium channels had no measurable influence on H2S-induced SCO suppression. Exposures to >5 ppm sulfide also suppressed neuronal electrical activity in PCN measured by multi-electrode array (MEA), an effect alleviated by pretreatment with the nonselective TRP inhibitor 2-APB. The TRP inhibitor also reduced PCN cell death from sulfide exposure. These results improve our understanding of the role of different Ca2+ channels in acute H2S-induced neurotoxicity and identify TRP channel modulators as novel structures with potential therapeutic benefits. ]]> Kim, D.-S. Pessah, I. N. Santana, C. M. Purnell, B. Li, R. Buchanan, G. F. Rumbeiha, W. K. 2022-11-16 doi:10.1101/2022.11.14.516514 Cold Spring Harbor Laboratory Press 2022-11-16 <![CDATA[ Effort Foraging Task reveals positive correlation between individual differences in the cost of cognitive and physical effort in humans and relationship to self-reported motivation and affect ]]> https://biorxiv.org/content/10.1101/2022.11.21.517394v1?rss=1 Bustamante, L. A. Oshinowo, T. Lee, J. R. Tong, E. Burton, A. R. Shenhav, A. S. Cohen, J. D. Daw, N. D. 2022-11-22 doi:10.1101/2022.11.21.517394 Cold Spring Harbor Laboratory Press 2022-11-22 <![CDATA[ Rethinking bacterial relationships in light of their molecular abilities ]]> https://biorxiv.org/content/10.1101/2022.11.28.518265v1?rss=1 Mahlich, Y. Zhu, C. Chung, H. Velaga, P. K. de Paolis Kaluza, M. C. Radivojac, P. Friedberg, I. Bromberg, Y. 2022-11-29 doi:10.1101/2022.11.28.518265 Cold Spring Harbor Laboratory Press 2022-11-29 <![CDATA[ Machine learning assisted ligand binding energy prediction for in silico generated glycosyl hydrolase enzyme combinatorial mutant library ]]> https://biorxiv.org/content/10.1101/2022.11.29.518414v1?rss=1 Guranovic, I. Kumar, M. Bandi, C. K. Chundawat, S. P. S. 2022-12-02 doi:10.1101/2022.11.29.518414 Cold Spring Harbor Laboratory Press 2022-12-02 <![CDATA[ Tail-tape-fused virion and non-virion RNA polymerases of a thermophilic virus with an extremely long tail ]]> https://biorxiv.org/content/10.1101/2022.12.01.518664v1?rss=1 Chaban, A. Minakhin, L. Goldobina, E. Bae, B. Hao, Y. Borukhov, S. Putzeys, L. Boon, M. Lavigne, R. Makarova, K. S. Koonin, E. V. Nair, S. K. Tagami, S. Severinov, K. Sokolova, M. L. 2022-12-01 doi:10.1101/2022.12.01.518664 Cold Spring Harbor Laboratory Press 2022-12-01 <![CDATA[ Endometrial adhesion G protein-coupled receptors are dynamically expressed across the menstrual cycle and expression is altered by ovarian stimulation ]]> https://biorxiv.org/content/10.1101/2022.12.04.519044v1?rss=1 Kalakota, N. R. Lemenze, A. George, L. Zhao, Q. Wu, T. Morelli, S. S. Douglas, N. C. Babwah, A. V. 2022-12-05 doi:10.1101/2022.12.04.519044 Cold Spring Harbor Laboratory Press 2022-12-05 <![CDATA[ ModelCIF: An extension of PDBx/mmCIF data representation for computed structure models ]]> https://biorxiv.org/content/10.1101/2022.12.06.518550v1?rss=1 Vallat, B. Tauriello, G. Bienert, S. Haas, J. Webb, B. M. Zidek, A. Zheng, W. Peisach, E. Piehl, D. W. Anishchanka, I. Sillitoe, I. Tolchard, J. Varadi, M. Baker, D. Orengo, C. Zhang, Y. Hoch, J. Kurisu, G. Patwardhan, A. Velankar, S. Burley, S. K. Sali, A. Schwede, T. Berman, H. M. Westbrook, J. D. 2022-12-09 doi:10.1101/2022.12.06.518550 Cold Spring Harbor Laboratory Press 2022-12-09 <![CDATA[ Effects of DNA extraction, DNA integrity, and laboratory on the precision of qPCR-based telomere length measurement - a multi-lab impartial study ]]> https://biorxiv.org/content/10.1101/2022.12.14.520438v1?rss=1 Lin, J. Verhulst, S. Fernandez Alonso, C. Dagnall, C. Gadalla, S. Hastings, W. Lai, T.-P. Zheng, Y.-L. Wang, Y. Shalev, I. Epel, E. Drury, S. 2022-12-14 doi:10.1101/2022.12.14.520438 Cold Spring Harbor Laboratory Press 2022-12-14 <![CDATA[ The Radiogenomic and Spatiogenomic Landscapes of Glioblastoma, and Their Relationship to Oncogenic Drivers ]]> https://biorxiv.org/content/10.1101/2022.12.15.517767v1?rss=1 Fathi Kazerooni, A. Akbari, H. Hu, X. Bommineni, V. Grigoriadis, D. Toorens, E. Sako, C. Mamourian, E. Ballinger, D. Sussman, R. Singh, A. Verginadis, I. I. Dahmane, N. Koumenis, C. Binder, Z. A. Bagley, S. J. Mohan, S. Hatzigeorgiou, A. O'Rourke, D. M. Ganguly, T. De, S. Bakas, S. Nasrallah, M. P. Davatzikos, C. 2022-12-18 doi:10.1101/2022.12.15.517767 Cold Spring Harbor Laboratory Press 2022-12-18 <![CDATA[ Microbiome features differentiating unsupervised-stratification based clusters of patients with abnormal glycometabolism ]]> https://biorxiv.org/content/10.1101/2022.12.19.521148v1?rss=1 Xu, T. Wang, X. Chen, Y. Li, H. Zhao, L. Ding, X. Zhang, C. 2022-12-20 doi:10.1101/2022.12.19.521148 Cold Spring Harbor Laboratory Press 2022-12-20 <![CDATA[ Efficient delivery of FMR1 across the blood brain barrier using 2 AAVphp construct in adult FMR1 KO mice demonstrates the 3 feasibility of gene therapy for fragile X syndrome ]]> https://biorxiv.org/content/10.1101/2022.12.22.520936v1?rss=1 Chadman, K. K. Adayev, T. Udayan, A. Ahmed, R. Dai, C.-L. Goodman, J. H. Meeker, H. Dolzhanskaya, N. Velinov, M. 2022-12-23 doi:10.1101/2022.12.22.520936 Cold Spring Harbor Laboratory Press 2022-12-23 <![CDATA[ Obtaining Increased Functional Proteomics Insights from Thermal Proteome Profiling through Optimized Melt Shift Calculation and Statistical Analysis ]]> https://biorxiv.org/content/10.1101/2022.12.30.522131v1?rss=1 McCracken, N. A. Liu, H. Runnebohm, A. M. Wijeratne, H. S. Wijeratne, A. B. Staschke, K. A. Mosley, A. L. 2022-12-30 doi:10.1101/2022.12.30.522131 Cold Spring Harbor Laboratory Press 2022-12-30 <![CDATA[ Engineering and characterization of carbohydrate-binding modules to enable real-time imaging of cellulose fibrils biosynthesis in plant protoplasts ]]> https://biorxiv.org/content/10.1101/2023.01.02.522519v1?rss=1 Jayachandran, D. Smith, P. Irfan, M. Sun, J. Yarborough, J. M. Bomble, Y. J. Lam, E. Chundawat, S. P. S. 2023-01-03 doi:10.1101/2023.01.02.522519 Cold Spring Harbor Laboratory Press 2023-01-03 <![CDATA[ Comparison of gene set scoring methods for reproducible evaluation of multiple tuberculosis gene signatures ]]> https://biorxiv.org/content/10.1101/2023.01.19.520627v1?rss=1 Wang, X. Vanvalkenburg, A. Odom-Mabey, A. R. Ellner, J. J. Hochberg, N. S. Salgame, P. Patil, P. Johnson, W. E. 2023-01-20 doi:10.1101/2023.01.19.520627 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ Structural insights into regulation of TRPM7 divalent cation uptake by the small GTPase ARL15 ]]> https://biorxiv.org/content/10.1101/2023.01.19.524765v1?rss=1 Mahbub, L. Kozlov, G. Zong, P. Tetteh, S. Nethramangalath, T. Knorn, C. Jiang, J. Shahsavan, A. Lee, E. Yue, L. Runnels, L. Gehring, K. 2023-01-20 doi:10.1101/2023.01.19.524765 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ Dasatinib Resensitizes MAPK Inhibitor Efficacy in Standard-of-Care Relapsed Melanomas ]]> https://biorxiv.org/content/10.1101/2023.01.20.524923v1?rss=1 Rebecca, V. W. Xiao, M. Kossenkov, A. Godok, T. Brown, G. S. Fingerman, D. Alicea, G. M. Wei, M. Ji, H. Bravo, J. Chen, Y. Fane, M. E. Villanueva, J. Nathanson, K. L. Liu, Q. Gopal, Y. N. V. Daies, M. A. Herlyn, M. 2023-01-21 doi:10.1101/2023.01.20.524923 Cold Spring Harbor Laboratory Press 2023-01-21 <![CDATA[ RIPK3 promotes brain region-specific interferon signaling and restriction of tick-borne flavivirus infection ]]> https://biorxiv.org/content/10.1101/2023.01.23.525284v1?rss=1 Lindman, M. Angel, J. P. Estevez, I. Chang, N. P. Chou, T.-W. McCourt, M. Atkins, C. Daniels, B. P. 2023-01-24 doi:10.1101/2023.01.23.525284 Cold Spring Harbor Laboratory Press 2023-01-24 <![CDATA[ Investigating variant and expression of CVD genes associated phenotypes among high-risk Heart Failure patients ]]> https://biorxiv.org/content/10.1101/2023.01.24.525457v1?rss=1 Ahmed, Z. Zeeshan, S. Persaud, N. Liang, B. T. 2023-01-25 doi:10.1101/2023.01.24.525457 Cold Spring Harbor Laboratory Press 2023-01-25 <![CDATA[ Oriented Display of Cello-Oligosaccharides for Pull-down Binding Assays to Distinguish Binding Preferences of Glycan Binding Proteins ]]> https://biorxiv.org/content/10.1101/2023.01.26.525732v1?rss=1 Hackl, M. Power, Z. Chundawat, S. P. S. 2023-01-26 doi:10.1101/2023.01.26.525732 Cold Spring Harbor Laboratory Press 2023-01-26 <![CDATA[ CALCIUM-DEPENDENT PROTEIN KINASE32 regulates cellulose biosynthesis through post-translational modification of cellulose synthase ]]> https://biorxiv.org/content/10.1101/2023.02.01.526621v1?rss=1 Xin, X. Wei, D. Lei, L. Zheng, H. Wallace, I. S. Li, S. Gu, Y. 2023-02-02 doi:10.1101/2023.02.01.526621 Cold Spring Harbor Laboratory Press 2023-02-02 <![CDATA[ Ketogenic diet promotes tumor ferroptosis but induces relative corticosterone deficiency that accelerates cachexia ]]> https://biorxiv.org/content/10.1101/2023.02.17.528937v1?rss=1 View larger version (24K): org.highwire.dtl.DTLVardef@613bb6org.highwire.dtl.DTLVardef@19746a4org.highwire.dtl.DTLVardef@9ef652org.highwire.dtl.DTLVardef@3db934_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIKetogenic diet delays tumor growth but accelerates cancer cachexia and shortens survival C_LIO_LIIn the tumor, accumulation of lipid peroxidation products results in saturation of the GSH detoxifying pathway and ferroptotic death of cancer cells C_LIO_LIIn the host organism, systemic redox state imbalance causes NADPH depletion, GDF-15 elevations, and relative corticosterone deficiency C_LIO_LIDexamethasone coadministration with ketogenic diet delays onset of cancer cachexia by improving food intake, glucose homeostasis and utilization of nutritional substrates C_LI ]]> Ferrer, M. Mourikis, N. Davidson, E. E. Kleeman, S. O. Zaccaria, M. Habel, J. Rubino, R. Flint, T. R. Connell, C. M. Lukey, M. White, E. P. Coll, A. P. Venkitaraman, A. R. Janowitz, T. 2023-02-18 doi:10.1101/2023.02.17.528937 Cold Spring Harbor Laboratory Press 2023-02-18 <![CDATA[ Enterovirus Evolution Reveals the Mechanism of an RNA-Targeted Antiviral and Determinants of Viral Replication ]]> https://biorxiv.org/content/10.1101/2023.02.20.529064v1?rss=1 Davila-Calderon, J. Li, M.-L. Penumutchu, S. Haddad, C. Malcolm, L. Hargrove, A. E. Brewer, G. Tolbert, B. S. 2023-02-20 doi:10.1101/2023.02.20.529064 Cold Spring Harbor Laboratory Press 2023-02-20 <![CDATA[ Chemogenetic activation of corticotropin-releasing factor-expressing neurons in the anterior bed nucleus of the stria terminalis reduces effortful motivation behaviors ]]> https://biorxiv.org/content/10.1101/2023.02.23.529717v1?rss=1 Maita, I. Bazer, A. Chae, K. Parida, A. Mirza, M. Sucher, J. Phan, M. Liu, T. Hu, P. Soni, R. Roepke, T. A. Samuels, B. A. 2023-02-23 doi:10.1101/2023.02.23.529717 Cold Spring Harbor Laboratory Press 2023-02-23 <![CDATA[ Phage T3 overcomes the BREX defence through SAM cleavage and inhibition of SAM synthesis ]]> https://biorxiv.org/content/10.1101/2023.02.27.530186v1?rss=1 Andriianov, A. Triguis, S. Drobiazko, A. Sierro, N. Ivanov, N. V. Selmer, M. Severinov, K. Isaev, A. 2023-02-27 doi:10.1101/2023.02.27.530186 Cold Spring Harbor Laboratory Press 2023-02-27 <![CDATA[ Syndapin Regulates the RAP-1 GTPase to Control Endocytic Recycling via RHO-1 and Non-Muscle Myosin II ]]> https://biorxiv.org/content/10.1101/2023.02.27.530328v1?rss=1 Rodriguez-Polanco, W. R. Norris, A. Velasco, A. B. Gleason, A. Grant, B. 2023-02-28 doi:10.1101/2023.02.27.530328 Cold Spring Harbor Laboratory Press 2023-02-28 <![CDATA[ Cell-Type Specific Connectivity of Whisker-Related Sensory and Motor Cortical Input to Dorsal Striatum ]]> https://biorxiv.org/content/10.1101/2023.03.06.531405v1?rss=1 Sanabria, B. D. Baskar, S. S. Yonk, A. J. Lee, C. R. Margolis, D. J. 2023-03-06 doi:10.1101/2023.03.06.531405 Cold Spring Harbor Laboratory Press 2023-03-06 <![CDATA[ Transcription Factor Dynamics in Cross-Regulation of Plant Hormone Signaling Pathways ]]> https://biorxiv.org/content/10.1101/2023.03.07.531630v1?rss=1 Yin, L. Zander, M. Huang, S.-s. C. Xie, M. Song, L. Saldierna Guzman, J. P. Hann, E. Shanbhag, B. K. Ng, S. Jain, S. Janssen, B. J. Clark, N. M. Walley, J. Beddoe, T. Bar-Joseph, Z. Lewsey, M. G. Ecker, J. R. 2023-03-09 doi:10.1101/2023.03.07.531630 Cold Spring Harbor Laboratory Press 2023-03-09 <![CDATA[ A Dynamic population of prophase CENP-C is required for meiotic chromosome segregation ]]> https://biorxiv.org/content/10.1101/2023.03.13.532437v1?rss=1 Fellmeth, J. Sturm, H. Jang, J. K. Changela, N. Parikh, A. Persaud, M. McKim, K. S. 2023-03-13 doi:10.1101/2023.03.13.532437 Cold Spring Harbor Laboratory Press 2023-03-13 <![CDATA[ Hierarchy and networks in the transcriptional response of Mycobacterium abscessus to antibiotics ]]> https://biorxiv.org/content/10.1101/2023.03.16.533064v1?rss=1 100 genes, a few of which are known determinants of drug resistance. The function of the vast majority of genes within the regulon is unknown, but some conceivably encode additional mechanisms of resistance. Furthermore, the hierarchy of gene expression within the regulon, if any, is poorly understood. In the present work we have identified 56 WhiB7 binding sites using chromatin immunoprecipitation sequencing (CHIP-Seq) which accounts for the WhiB7-dependent upregulation of 70 genes, and find that M. abscessus WhiB7 functions exclusively as a transcriptional activator at promoters recognized by {sigma}A/{sigma}B We have investigated the role of 18 WhiB7 regulated genes in drug resistance and demonstrated the role of MAB_1409c and MAB_4324c in aminoglycoside resistance. Further, we identify a {sigma}H-dependent pathway in aminoglycoside and tigecycline resistance which is induced upon drug exposure and is further activated by WhiB7 demonstrating the existence of a crosstalk between components of the WhiB7-dependent and -independent circuits. Abstract ImportanceThe induction of multiple genes that confer resistance to structurally diverse ribosome-targeting antibiotics is funneled through the induction of a single transcriptional activator, WhiB7, by antibiotic-stalled ribosomes. This poses a severe restriction in M. abscessus therapy as treatment with one ribosome-targeting antibiotic confers resistance to all other ribosome-targeting antibiotics. Here we uncover the intricacies of the WhiB7 regulatory circuit, identify three previously unknown determinants of aminoglycoside resistance and unveil a communication between WhiB7 dependent and independent components. This not only expands our understanding of the antibiotic resistance potential of M. abscessus but can also inform the development of much needed therapeutic options. ]]> Hurst-Hess, K. R. McManaman, C. Yang, Y. Gupta, S. N. Ghosh, P. 2023-03-17 doi:10.1101/2023.03.16.533064 Cold Spring Harbor Laboratory Press 2023-03-17 <![CDATA[ Three-dimensional reconstructions of mechanosensory end organs suggest a unifying mechanism underlying dynamic, light touch ]]> https://biorxiv.org/content/10.1101/2023.03.17.533188v1?rss=1 Handler, A. Zhang, Q. Pang, S. Nguyen, T. M. Iskols, M. Nolan-Tamariz, M. Cattel, S. Plumb, R. Sanchez, B. Ashjian, K. Shotland, A. Brown, B. Kabeer, M. Turecek, J. Rankin, G. Xiang, W. Pavarino, E. C. Africawala, N. Santiago, C. Lee, W.-C. A. Xu, C. S. Ginty, D. D. 2023-03-18 doi:10.1101/2023.03.17.533188 Cold Spring Harbor Laboratory Press 2023-03-18 <![CDATA[ Depletion of bleomycin hydrolase (Blmh) downregulates histone demethylase Phf8, impairs mTOR signaling/autophagy, accelerates amyloid beta accumulation, and induces neurological deficits in mice ]]> https://biorxiv.org/content/10.1101/2023.03.20.533511v1?rss=1 Witucki, L. Borowczyk, K. Suszynska-Zajczyk, J. Warzych, E. Pawlak, P. Jakubowski, H. 2023-03-21 doi:10.1101/2023.03.20.533511 Cold Spring Harbor Laboratory Press 2023-03-21 <![CDATA[ Homocysteine Metabolites Inhibit Autophagy and Elevate Amyloid Beta by Impairing Phf8/H4K20me1-dependent Epigenetic Regulation of mTOR in Cystathionine Beta-Synthase-Deficient Mice ]]> https://biorxiv.org/content/10.1101/2023.03.22.533769v1?rss=1 H4K20me1->mTOR->autophagy pathway thereby increasing A{beta} accumulation. ]]> Witucki, L. Jakubowski, H. 2023-03-22 doi:10.1101/2023.03.22.533769 Cold Spring Harbor Laboratory Press 2023-03-22 <![CDATA[ Site-specific Effector Protein Functionalization to Create Bead-based Avidity Model Systems ]]> https://biorxiv.org/content/10.1101/2023.03.27.534459v1?rss=1 Hackl, M. Jayachandran, D. Ramdin, K. Zhong, T. Chundawat, S. P. S. 2023-03-27 doi:10.1101/2023.03.27.534459 Cold Spring Harbor Laboratory Press 2023-03-27 <![CDATA[ Plant cellulose synthase membrane protein isolation directly from Pichia pastoris protoplasts, liposome reconstitution, and its enzymatic characterization ]]> https://biorxiv.org/content/10.1101/2023.03.29.534738v1?rss=1 Jayachandran, D. Banerjee, S. Chundawat, S. P. S. 2023-03-30 doi:10.1101/2023.03.29.534738 Cold Spring Harbor Laboratory Press 2023-03-30 <![CDATA[ Isolation of Actinomyces cricetomyis sp. nov from orocervicofacial abscesses of African giant pouched rats (Cricetomys ansorgei) ]]> https://biorxiv.org/content/10.1101/2023.04.04.535624v1?rss=1 Franklin-Guild, R. J. Labitt, R. N. McQueary, H. C. Llanos-Soto, S. Mitchell, P. K. Tallmadge, R. L. Anderson, R. R. Flint, J. F. Ophir, A. G. Thachil, A. Singh, B. Goodman, L. B. 2023-04-04 doi:10.1101/2023.04.04.535624 Cold Spring Harbor Laboratory Press 2023-04-04 <![CDATA[ Interferon epsilon restricts Zika virus infection in the female reproductive tract ]]> https://biorxiv.org/content/10.1101/2023.04.06.535968v1?rss=1 Xu, C. Wang, A. Ebraham, L. Sullivan, L. Tasker, C. Pizutelli, V. Couret, J. Hernandez, C. Deb, P. Q. Fritzky, L. Subbian, S. Gao, N. Lo, Y. Salvatore, M. Rivera, A. Lemenze, A. Fitzgerald-Bocarsly, P. Tyagi, S. Lu, W. Beaulieu, A. Chang, T. L. 2023-04-07 doi:10.1101/2023.04.06.535968 Cold Spring Harbor Laboratory Press 2023-04-07 <![CDATA[ A potential patient stratification biomarker for Parkinson's disease based on LRRK2 kinase-mediated centrosomal alterations in peripheral blood-derived cells ]]> https://biorxiv.org/content/10.1101/2023.04.11.536367v1?rss=1 Naaldijk, Y. Fernandez, B. Fasiczka, R. Fdez, E. Leghay, C. Croitoru, I. Kwok, J. B. Boulesnane, Y. Vizeneux, A. Mutez, E. Calvez, C. Destee, A. Taymans, J.-M. Vinagre Aragon, A. Bergareche Yarza, A. Padmanabhan, S. Delgado, M. Alcalay, R. N. Chatterton, Z. Dzamko, N. Halliday, G. Ruiz-Martinez, J. Chartier-Harlin, M.-C. Hilfiker, S. 2023-04-12 doi:10.1101/2023.04.11.536367 Cold Spring Harbor Laboratory Press 2023-04-12 <![CDATA[ Temporal Effects of Galactose and Manganese Supplementation on Monoclonal Antibody N-Linked Glycosylation in Fed-Batch and Perfusion Bioreactor Operation ]]> https://biorxiv.org/content/10.1101/2023.04.15.535602v1?rss=1 Gyorgypal, A. Fratz-Berilla, E. Kohnhorst, C. Powers, D. N. Chundawat, S. P. S. 2023-04-15 doi:10.1101/2023.04.15.535602 Cold Spring Harbor Laboratory Press 2023-04-15 <![CDATA[ Learning induces unique transcriptional landscapes in the auditory cortex ]]> https://biorxiv.org/content/10.1101/2023.04.15.536914v1?rss=1 Graham, G.-E. Chimenti, M. S. Knudtson, K. Grenard, D. N. Co, L. Sumner, M. Tchou, T. Bieszczad, K. M. 2023-04-15 doi:10.1101/2023.04.15.536914 Cold Spring Harbor Laboratory Press 2023-04-15 <![CDATA[ Amyloplast sedimentation repolarizes LAZYs to achieve gravity sensing in plants ]]> https://biorxiv.org/content/10.1101/2023.04.17.537121v1?rss=1 Chen, J. Yu, R. Li, N. Deng, Z. Zhang, X. Zhao, Y. Qu, C. Yuan, Y. Pan, Z. Zhou, Y. Li, K. Wang, J. Chen, Z. Wang, X. Wang, X. Dong, J. Deng, X. W. Chen, H. 2023-04-18 doi:10.1101/2023.04.17.537121 Cold Spring Harbor Laboratory Press 2023-04-18 <![CDATA[ The soluble guanylyl cyclase pathway is inhibited to evade androgen deprivation-induced senescence and enable progression to castration resistance ]]> https://biorxiv.org/content/10.1101/2023.05.03.537252v1?rss=1 Rai, P. Zhang, L. Troccoli, C. I. Mateo-Victoriano, B. Misiara, L. Jackson, E. N. Shu, P. Plastini, T. M. Tao, W. Kwon, D. Chen, X. Sharma, J. Jorda, M. Gulley, J. L. Bilusic, M. Lockhart, A. C. Beuve, A. 2023-05-03 doi:10.1101/2023.05.03.537252 Cold Spring Harbor Laboratory Press 2023-05-03 <![CDATA[ Enhancing Collaborative Neuroimaging Research: Introducing COINSTAC Vaults for Federated Analysis and Reproducibility ]]> https://biorxiv.org/content/10.1101/2023.05.08.539852v1?rss=1 Panta, S. Martin, D. Basodi, S. Rootes-Murdy, K. Prae, P. T Baker, B. Kelly, R. Romero, J. Plis, S. Calhoun, V. Bockholt, J. Sarwate, A. B Esper Franco, N. R Franco, A. Gazula, H. Turner, J. 2023-05-08 doi:10.1101/2023.05.08.539852 Cold Spring Harbor Laboratory Press 2023-05-08 <![CDATA[ Klf9 plays a critical role in GR dependent metabolic adaptations in cardiomyocytes ]]> https://biorxiv.org/content/10.1101/2023.05.08.539871v1?rss=1 Thakkar, C. Alikunju, S. Rizvi, W. Abbas, A. Sayed, D. 2023-05-09 doi:10.1101/2023.05.08.539871 Cold Spring Harbor Laboratory Press 2023-05-09 <![CDATA[ Selenoprotein synthesis is not induced by hepatotoxic drugs ]]> https://biorxiv.org/content/10.1101/2023.05.12.540527v1?rss=1 Shetty, S. P. He, D. Copeland, P. R. 2023-05-14 doi:10.1101/2023.05.12.540527 Cold Spring Harbor Laboratory Press 2023-05-14 <![CDATA[ Formation of a stable RNase Y-RicT (YaaT) complex requires RicA (YmcA) and RicF (YlbF) ]]> https://biorxiv.org/content/10.1101/2023.05.22.541740v1?rss=1 Dubnau, E. DeSantis, M. DUBNAU, D. 2023-05-23 doi:10.1101/2023.05.22.541740 Cold Spring Harbor Laboratory Press 2023-05-23 <![CDATA[ Long-read genome assemblies for the study of chromosome expansion: Drosophila kikkawai Drosophila takahashii, Drosophila bipectinata, and Drosophila ananassae ]]> https://biorxiv.org/content/10.1101/2023.05.22.541758v1?rss=1 18 Mb. Here, we present chromosome-level long read genome assemblies for four Drosophila species with expanded F Elements ranging in size from 2.3 Mb to 20.5 Mb. Each Muller Element is present as a single scaffold in each assembly. These assemblies will enable new insights into the evolutionary causes and consequences of chromosome size expansion. ]]> Leung, W. Torosin, N. Cao, W. Reed, L. K. Arrigo, C. Elgin, S. C. R. Ellison, C. E. 2023-05-24 doi:10.1101/2023.05.22.541758 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ Identification of an anti-CRISPR protein that inhibits the CRISPR-Cas type I-B system in Clostridioides difficile ]]> https://biorxiv.org/content/10.1101/2023.05.22.541795v1?rss=1 Muzyukina, P. Shkaruta, A. Guzman, N. M. Andreani, J. Borges, A. L. Bondy-Denomy, J. Maikova, A. Semenova, E. Severinov, K. SOUTOURINA, O. 2023-05-22 doi:10.1101/2023.05.22.541795 Cold Spring Harbor Laboratory Press 2023-05-22 <![CDATA[ A bioinformatics tool for identifying intratumoral microbes from the ORIEN dataset ]]> https://biorxiv.org/content/10.1101/2023.05.24.541982v1?rss=1 Wang, C. Ma, A. McNutt, M. E. Hoyd, R. Wheeler, C. E. Robinson, L. A. Chan, C. H. F. Zakharia, Y. Dodd, R. D. Ulrich, C. M. Hardikar, S. Churchman, M. L. Tarhini, A. A. Singer, E. A. Ikeguchi, A. P. McCarter, M. D. Denko, N. Tinoco, G. Husain, M. Jin, N. Osman, A. E. G. Eljilany, I. Tan, A. C. Coleman,, S. S. Denko, L. Riedlinger, G. Schneider, B. P. Spakowicz, D. Ma, Q. 2023-05-24 doi:10.1101/2023.05.24.541982 Cold Spring Harbor Laboratory Press 2023-05-24 <![CDATA[ Ribosomal protein control of hematopoietic stem cell transformation through direct, non-canonical regulation of metabolism ]]> https://biorxiv.org/content/10.1101/2023.05.31.543132v1?rss=1 Harris, B. Singh, D. K. Verma, M. Fahl, S. P. Rhodes, M. Sprinkle, S. R. Wang, M. Zhang, Y. Perrigoue, J. Kessel, R. Peri, S. West, J. Giricz, O. Boultwood, J. Pellagatti, A. Ramesh, K. Montangna, C. Pradhan, K. Tyner, J. Kennedy, B. K. Holinstat, M. Steidl, U. Sykes, S. Verma, A. Wiest, D. L. 2023-06-01 doi:10.1101/2023.05.31.543132 Cold Spring Harbor Laboratory Press 2023-06-01 <![CDATA[ Calretinin-expressing islet cells: a source of pre- and post-synaptic inhibition of non-peptidergic nociceptor input to the mouse spinal cord ]]> https://biorxiv.org/content/10.1101/2023.06.01.543241v1?rss=1 Davis, O. C. Dickie, A. C. Mustapa, M. B. Boyle, K. A. Browne, T. J. Gradwell, M. A. Smith, K. M. Polgar, E. Bell, A. M. Kokai, E. Watanabe, M. Wildner, H. Zeilhofer, H. U. Ginty, D. D. Callister, R. J. Graham, B. A. Todd, A. J. Hughes, D. I. 2023-06-05 doi:10.1101/2023.06.01.543241 Cold Spring Harbor Laboratory Press 2023-06-05 <![CDATA[ Single-molecule studies reveal the off-pathway elemental pause state as a target of streptolydigin inhibition of RNA polymerase and its dramatic enhancement by Gre factors ]]> https://biorxiv.org/content/10.1101/2023.06.05.542125v1?rss=1 Arseniev, A. Panfilov, M. Pobegalov, G. Potyseva, A. Pavlinova, P. Yakunina, M. Lee, J. Borukhov, S. Severinov, K. Khodorkovskii, M. 2023-06-05 doi:10.1101/2023.06.05.542125 Cold Spring Harbor Laboratory Press 2023-06-05 <![CDATA[ Shu complex SWS1-SWSAP1 is required for mouse meiotic recombination in concert with the BRCA2 C terminus ]]> https://biorxiv.org/content/10.1101/238196v1?rss=1 Abreu, C. M. Prakash, R. Romanienko, P. J. Roig, I. Keeney, S. Jasin, M. 2017-12-22 doi:10.1101/238196 Cold Spring Harbor Laboratory Press 2017-12-22 <![CDATA[ Tension-dependent regulation of mammalian Hippo signaling through LIMD1 ]]> https://biorxiv.org/content/10.1101/238394v1?rss=1 Ibar, C. Kirichenko, E. Keepers, B. Enners, E. Fleisch, K. Irvine, K. 2017-12-22 doi:10.1101/238394 Cold Spring Harbor Laboratory Press 2017-12-22 <![CDATA[ diploS/HIC: an updated approach to classifying selective sweeps ]]> https://biorxiv.org/content/10.1101/267229v1?rss=1 Kern, A. D. Schrider, D. R. 2018-02-18 doi:10.1101/267229 Cold Spring Harbor Laboratory Press 2018-02-18 <![CDATA[ An epigenetic biomarker of aging for lifespan and healthspan ]]> https://biorxiv.org/content/10.1101/276162v1?rss=1 Levine, M. E. Lu, A. T. Quach, A. Chen, B. Assimes, T. L. Bandinelli, S. Hou, L. Baccarelli, A. A. Stewart, J. D. Li, Y. Whitsel, E. A. Wilson, J. G. Reiner, A. P. Aviv, A. Lohman, K. Liu, Y. Ferrucci, L. Horvath, S. 2018-03-05 doi:10.1101/276162 Cold Spring Harbor Laboratory Press 2018-03-05 <![CDATA[ Developmentally regulated transcription and silencing cycle of nuclear RNAi-targeted LTR retrotransposons in Caenorhabditis elegans ]]> https://biorxiv.org/content/10.1101/303230v1?rss=1 Gu, S. G. Ni, J. Z. Kalinava, N. Mendoza, S. G. 2018-04-17 doi:10.1101/303230 Cold Spring Harbor Laboratory Press 2018-04-17 <![CDATA[ The RhoGAP myosin 9/HUM-7 integrates membrane signals to modulate Rho/RHO-1 during embryonic morphogenesis in C. elegans ]]> https://biorxiv.org/content/10.1101/325274v1?rss=1 Wallace, A. G. Raduwan, H. Carlet, J. Soto, M. C. 2018-05-17 doi:10.1101/325274 Cold Spring Harbor Laboratory Press 2018-05-17 <![CDATA[ Grape polyphenols reduce gut-localized reactive oxygen species associated with the development of metabolic syndrome in mice. ]]> https://biorxiv.org/content/10.1101/331348v1?rss=1 Kuhn, P. Kalariya, H. M. Poulev, A. Ribnicky, D. M. Jaja-Chimedza, A. Roopchand, D. Raskin, I. 2018-05-25 doi:10.1101/331348 Cold Spring Harbor Laboratory Press 2018-05-25 <![CDATA[ Enterobacter cloacae complex ST171 Isolates Expressing KPC-4 Carbapenemase Recovered from Canine Patients in Ohio, USA ]]> https://biorxiv.org/content/10.1101/337428v1?rss=1 Daniels, J. B. Wittum, T. E. Chen, L. Kreiswirth, B. N. Grooters, S. V. Mathys, D. A. Mollenkopf, D. F. 2018-06-04 doi:10.1101/337428 Cold Spring Harbor Laboratory Press 2018-06-04 <![CDATA[ Increased number and activity of a lateral subpopulation of hypothalamic orexin/hypocretin neurons underlies the expression of an addicted state in rats ]]> https://biorxiv.org/content/10.1101/356220v1?rss=1 James, M. Stopper, C. M. Zimmer, B. A. Koll, N. E. Bowrey, H. E. Aston-Jones, G. 2018-06-27 doi:10.1101/356220 Cold Spring Harbor Laboratory Press 2018-06-27 <![CDATA[ Demand elasticity predicts addiction endophenotypes and the therapeutic efficacy of an orexin/hypocretin-1 receptor antagonist in rats ]]> https://biorxiv.org/content/10.1101/356709v1?rss=1 James, M. H. Bowrey, H. E. Stopper, C. M. Aston-Jones, G. 2018-06-29 doi:10.1101/356709 Cold Spring Harbor Laboratory Press 2018-06-29 <![CDATA[ Activation of lateral hypothalamic group III mGluRs suppresses drug-seeking following abstinence and cocaine-associated increases in excitatory drive to orexin/hypocretin cells ]]> https://biorxiv.org/content/10.1101/360081v1?rss=1 Yeoh, J. W. James, M. H. Adams, C. D. Bains, J. S. Sakurai, T. Aston-Jones, G. Graham, B. A. Dayas, C. V. 2018-07-03 doi:10.1101/360081 Cold Spring Harbor Laboratory Press 2018-07-03 <![CDATA[ Repeated Measures Regression In Laboratory, Clincal And Enviromental Research - Different Between/Within Subject Slopes And Common Misconceptions ]]> https://biorxiv.org/content/10.1101/374124v1?rss=1 Hoover, D. R. Shi, Q. Anastos, K. 2018-07-25 doi:10.1101/374124 Cold Spring Harbor Laboratory Press 2018-07-25 <![CDATA[ Did a novel virus contribute to late blight epidemics? ]]> https://biorxiv.org/content/10.1101/383653v1?rss=1 Cai, G. Meyers, K. Fry, W. E. Hillman, B. I. 2018-08-02 doi:10.1101/383653 Cold Spring Harbor Laboratory Press 2018-08-02 <![CDATA[ Existing host range mutations constrain further emergence of RNA viruses ]]> https://biorxiv.org/content/10.1101/394080v1?rss=1 Zhao, L. Seth Pasricha, M. Stemate, D. Crespo-Bellido, A. Gagnon, J. Duffy, S. 2018-08-17 doi:10.1101/394080 Cold Spring Harbor Laboratory Press 2018-08-17 <![CDATA[ Gαq sensitizes TRPM8 to inhibition by PI(4,5)P2 depletion upon receptor activation ]]> https://biorxiv.org/content/10.1101/410878v1?rss=1 Liu, L. Yudin, Y. Kang, C. Shirokova, N. Rohacs, T. 2018-09-06 doi:10.1101/410878 Cold Spring Harbor Laboratory Press 2018-09-06 <![CDATA[ SIX1 cooperates with RUNX1 and SMAD4 in cell fate commitment of Müllerian duct epithelium ]]> https://biorxiv.org/content/10.1101/427351v1?rss=1 Terakawa, j. Serna, V. A. Nair, D. Sato, S. Kawakami, K. Radovick, S. Maire, P. Kurita, T. 2018-09-25 doi:10.1101/427351 Cold Spring Harbor Laboratory Press 2018-09-25 <![CDATA[ The G protein-biased PZM21 and TRV130 act as partial agonists of μ-opioid receptors signaling to ion channel targets ]]> https://biorxiv.org/content/10.1101/445536v1?rss=1 Yudin, Y. Rohacs, T. 2018-10-17 doi:10.1101/445536 Cold Spring Harbor Laboratory Press 2018-10-17 <![CDATA[ Opposing Influence of Sensory and Motor Cortex on Striatal Circuitry and Choice Behavior ]]> https://biorxiv.org/content/10.1101/446708v1?rss=1 Lee, C. R. Yonk, A. J. Wiskerke, J. Paradiso, K. G. Tepper, J. M. Margolis, D. J. 2018-10-23 doi:10.1101/446708 Cold Spring Harbor Laboratory Press 2018-10-23 <![CDATA[ Optogenetic and transcriptomic interrogation of enhanced muscle function in the paralyzed mouse whisker pad ]]> https://biorxiv.org/content/10.1101/473298v1?rss=1 Vajtay, T. J. Bandi, A. Upadhyay, A. Swerdel, M. R. Hart, R. P. Lee, C. R. Margolis, D. J. 2018-11-19 doi:10.1101/473298 Cold Spring Harbor Laboratory Press 2018-11-19 <![CDATA[ C. elegans models of Marfan and Marfan-like Syndromes reveal trafficking defects of the type II TGFβ receptor as a potential novel disease mechanism ]]> https://biorxiv.org/content/10.1101/486381v1?rss=1 Lin, J. Vora, M. Kane, N. S. Gleason, R. J. Padgett, R. W. 2018-12-03 doi:10.1101/486381 Cold Spring Harbor Laboratory Press 2018-12-03 <![CDATA[ Molecular epidemiology of carbapenem-resistant Enterobacter cloacae complex infections uncovers high frequency of non-carbapenemase-producers in five tertiary care hospitals from Colombia ]]> https://biorxiv.org/content/10.1101/494807v1?rss=1 Cienfuegos-Gallet, A. Ocampo, A. M. Chavda, K. Chen, L. Kreiswirth, B. N. Jimenez, J. N. 2018-12-12 doi:10.1101/494807 Cold Spring Harbor Laboratory Press 2018-12-12 <![CDATA[ In vitro activity of the new β-lactamase inhibitors relebactam and vaborbactam in combination with β-lactams against Mycobacterium abscessus complex clinical isolates ]]> https://biorxiv.org/content/10.1101/499830v1?rss=1 Kaushik, A. Ammerman, N. C. Lee, J. Martins, O. Kreiswirth, B. N. Lamichhane, G. Parrish, N. M. Nuermberger, E. 2018-12-19 doi:10.1101/499830 Cold Spring Harbor Laboratory Press 2018-12-19 <![CDATA[ The antiparasitic drug atovaquone inhibits arbovirus replication through the depletion of intracellular nucleotides. ]]> https://biorxiv.org/content/10.1101/507152v1?rss=1 Cifuentes Kottkamp, A. De Jesus, E. Grande, R. Brown, J. K. Jacobs, A. R. Lim, J. K. Stapleford, K. 2018-12-27 doi:10.1101/507152 Cold Spring Harbor Laboratory Press 2018-12-27 <![CDATA[ The MHC class-II HLA-DR receptor mediates bat influenza A-like H17N10 virus entry into mammalian cells ]]> https://biorxiv.org/content/10.1101/507467v1?rss=1 Giotis, E. S. Carnell, G. Young, E. F. Ghanny, S. Soteropoulos, P. Barclay, W. S. Skinner, M. A. Temperton, N. 2019-01-04 doi:10.1101/507467 Cold Spring Harbor Laboratory Press 2019-01-04 <![CDATA[ Phosphoinositides regulate the TRPV1 channel via two functionally distinct binding sites ]]> https://biorxiv.org/content/10.1101/558874v1?rss=1 Yazici, A. T. Gianti, E. Kasimova, M. A. Carnevale, V. Rohacs, T. 2019-02-22 doi:10.1101/558874 Cold Spring Harbor Laboratory Press 2019-02-22 <![CDATA[ TCF4 induces enzalutamide resistance via neuroendocrine differentiation in prostate cancer ]]> https://biorxiv.org/content/10.1101/560821v1?rss=1 lee, G. T. Kim, W. T. Kwon, Y. S. Palapattu, G. Kim, W.-J. Kim, I. Y. 2019-02-25 doi:10.1101/560821 Cold Spring Harbor Laboratory Press 2019-02-25 <![CDATA[ Cohesin and microtubule dependent mechanisms regulate sister centromere fusion during meiosis I ]]> https://biorxiv.org/content/10.1101/571067v1?rss=1 McKim, K. S. Wang, L.-I. Das, A. 2019-03-07 doi:10.1101/571067 Cold Spring Harbor Laboratory Press 2019-03-07 <![CDATA[ Ethanolamine regulates CqsR quorum-sensing signaling in Vibrio cholerae ]]> https://biorxiv.org/content/10.1101/589390v1?rss=1 Ng, W.-L. Watve, S. Barrasso, K. Jung, S. A. Davis, K. J. Hawver, L. A. Khataokar, A. Palaganas, R. G. Neiditch, M. B. Perez, L. J. 2019-03-26 doi:10.1101/589390 Cold Spring Harbor Laboratory Press 2019-03-26 <![CDATA[ Identification of pathogen genomic differences that impact human immune response and disease during Cryptococcus neoformans infection ]]> https://biorxiv.org/content/10.1101/592212v1?rss=1 Gerstein, A. C. Jackson, K. M. McDonald, T. R. Wang, Y. Lueck, B. D. Bohjanen, S. Smith, K. D. Akampurira, A. Meya, D. B. Xue, C. Boulware, D. R. Nielsen, K. 2019-03-28 doi:10.1101/592212 Cold Spring Harbor Laboratory Press 2019-03-28 <![CDATA[ Function and clinical relevance of RHAMM isoforms in pancreatic tumor progression ]]> https://biorxiv.org/content/10.1101/598334v1?rss=1 Choi, S. Wang, D. Chen, X. Tang, L. H. Verma, A. Chen, Z. Kim, B. J. Selesner, L. Robzyk, K. Zhang, G. Pang, S. Han, T. Chan, C. S. Fahey, T. J. Elemento, O. Du, Y.-C. N. 2019-04-08 doi:10.1101/598334 Cold Spring Harbor Laboratory Press 2019-04-08 <![CDATA[ Precise memory is predicted by learning-induced sensory system neurophysiological plasticity ]]> https://biorxiv.org/content/10.1101/600866v1?rss=1 Rotondo, E. K. Bieszczad, K. M. 2019-04-06 doi:10.1101/600866 Cold Spring Harbor Laboratory Press 2019-04-06 <![CDATA[ A spatiotemporal ventricular myocyte model incorporating mitochondrial calcium cycling ]]> https://biorxiv.org/content/10.1101/604926v1?rss=1 Song, Z. Xie, L. Weiss, J. N. Qu, Z. 2019-04-10 doi:10.1101/604926 Cold Spring Harbor Laboratory Press 2019-04-10 <![CDATA[ AP-1 Imprints a Reversible Transcriptional Program of Senescent Cells ]]> https://biorxiv.org/content/10.1101/633594v1?rss=1 Martinez Zamudio, R. I. Roux, P.-F. Freitas, J. A. Robinson, L. Dore, G. Sun, B. Gil, J. Herbig, U. Bischof, O. 2019-05-09 doi:10.1101/633594 Cold Spring Harbor Laboratory Press 2019-05-09 <![CDATA[ Swim exercise in C. elegans extends neuromuscular and intestinal healthspan, enhances learning ability, and protects against neurodegeneration ]]> https://biorxiv.org/content/10.1101/633776v1?rss=1 Laranjeiro, R. Harinath, G. Hewitt, J. E. Hartman, J. H. Royal, M. A. Meyer, J. N. Vanapalli, S. A. Driscoll, M. 2019-05-09 doi:10.1101/633776 Cold Spring Harbor Laboratory Press 2019-05-09 <![CDATA[ Insertional oncogenesis by HPV70 revealed by multiple genomic analyses in a clinically HPV-negative cervical cancer ]]> https://biorxiv.org/content/10.1101/634857v1?rss=1 Van Arsdale, A. Patterson, N. E. Maggi, E. C. Agoni, L. Van Doorslaer, K. Harmon, B. Nevadunsky, N. Kuo, D. Y. S. Einstein, M. H. Lenz, J. Montagna, C. 2019-05-10 doi:10.1101/634857 Cold Spring Harbor Laboratory Press 2019-05-10 <![CDATA[ Exploring the Mechanism of Olfactory Recognition at the Initial Stage by Modeling the Emission Spectrum of Electron Transfer ]]> https://biorxiv.org/content/10.1101/641738v1?rss=1 Liu, S. Fu, R. Li, G. 2019-05-17 doi:10.1101/641738 Cold Spring Harbor Laboratory Press 2019-05-17 <![CDATA[ The evolutionary origins and diversity of the neuromuscular system of paired appendages in batoids ]]> https://biorxiv.org/content/10.1101/644062v1?rss=1 Turner, N. Mikalauskaite, D. Barone, K. Flaherty, K. Senevirathne, G. Adachi, N. Shubin, N. Nakamura, T. 2019-05-21 doi:10.1101/644062 Cold Spring Harbor Laboratory Press 2019-05-21 <![CDATA[ A robust benchmark for germline structural variant detection ]]> https://biorxiv.org/content/10.1101/664623v1?rss=1 98.7 %. We demonstrate the utility of the benchmark set by showing it reliably identifies both false negatives and false positives in high-quality SV callsets from short-, linked-, and long-read sequencing and optical mapping. ]]> Zook, J. M. Hansen, N. F. Olson, N. D. Chapman, L. M. Mullikin, J. C. Xiao, C. Sherry, S. Koren, S. Phillippy, A. M. Boutros, P. C. Ebrahim, S. M. Huang, V. Rouette, A. Alexander, N. Mason, C. C. Hajirasouliha, I. C. Ricketts, C. C. Lee, J. Tearle, R. Fiddes, I. T. Barrio, A. M. Wala, J. Carroll, A. Ghaffari, N. C. Rodriguez, O. L. Bashir, A. Jackman, S. Farrell, J. J. Wenger, A. M. Alkan, C. Soylev, A. Schatz, M. C. Garg, S. Church, G. Marschall, T. Chen, K. Fan, X. English, A. C. Rosenfeld, J. D. Zhou, W. Mills, R. E. Sage, J. M. Davis, J. R. Kaiser 2019-06-09 doi:10.1101/664623 Cold Spring Harbor Laboratory Press 2019-06-09 <![CDATA[ Single molecule mechanics resolves the earliest events in force generation by cardiac myosin ]]> https://biorxiv.org/content/10.1101/683623v1?rss=1 Woody, M. Capitanio, M. Winkelmann, D. Ostap, E. M. Goldman, Y. E. 2019-06-27 doi:10.1101/683623 Cold Spring Harbor Laboratory Press 2019-06-27 <![CDATA[ A comprehensive genealogy of the replication associated protein of CRESS DNA viruses reveals a single origin of intron-containing Rep ]]> https://biorxiv.org/content/10.1101/687855v1?rss=1 Zhao, L. Lavington, E. Duffy, S. 2019-07-01 doi:10.1101/687855 Cold Spring Harbor Laboratory Press 2019-07-01 <![CDATA[ Non-genetic intra-tumor heterogeneity is a major predictor of phenotypic heterogeneity and ongoing evolutionary dynamics in lung tumors ]]> https://biorxiv.org/content/10.1101/698845v1?rss=1 Sharma, A. Merritt, E. Cruz, A. Jiang, C. Sarkodie, H. Zhou, Z. Malhotra, J. Riedlinger, G. M. De, S. 2019-07-11 doi:10.1101/698845 Cold Spring Harbor Laboratory Press 2019-07-11 <![CDATA[ Phazolicin - a Novel Thiazole/Oxazole-Modified Peptide Inhibiting the Bacterial Ribosome in a Species-Specific Way. ]]> https://biorxiv.org/content/10.1101/705970v1?rss=1 Travin, D. Y. Watson, Z. L. Metelev, M. Ward, F. R. Osterman, I. A. Khven, I. M. Khabibullina, N. F. Serebryakova, M. Mergaert, P. Polikanov, Y. S. Cate, J. H. D. Severinov, K. 2019-07-18 doi:10.1101/705970 Cold Spring Harbor Laboratory Press 2019-07-18 <![CDATA[ Dynamic Reorganization of the Frontal Parietal Network During Cognitive Control and Episodic Memory ]]> https://biorxiv.org/content/10.1101/709220v1?rss=1 Ray, K. Ragland, J. D. MacDonald, A. Gold, J. Silverstain, S. Barch, D. Carter, C. S. 2019-07-22 doi:10.1101/709220 Cold Spring Harbor Laboratory Press 2019-07-22 <![CDATA[ Gi-Coupled Receptor Activation Potentiates Piezo2 Currents via Gβγ ]]> https://biorxiv.org/content/10.1101/722637v1?rss=1 Del Rosario, J. S. Yudin, Y. Su, S. Hartle, C. Mirshahi, T. Rohacs, T. 2019-08-02 doi:10.1101/722637 Cold Spring Harbor Laboratory Press 2019-08-02 <![CDATA[ Targeting EZH2 Increases Therapeutic Efficacy of Check-Point Blockade in Models of Prostate Cancer ]]> https://biorxiv.org/content/10.1101/730135v1?rss=1 Sheahan, A. V. Morel, K. L. Burkhart, D. L. Baca, S. C. Labbe, D. P. Roehle, K. Heckler, M. Calagua, C. Ye, H. Galbo, P. Panja, S. Mitrofanova, A. Hamid, A. A. Kibel, A. S. Choudhury, A. D. Pomerantz, M. M. Freedman, M. L. Sweeney, C. J. Dougan, S. K. Sowalsky, A. Loda, M. Olson, B. M. Ellis, L. 2019-08-08 doi:10.1101/730135 Cold Spring Harbor Laboratory Press 2019-08-08 <![CDATA[ Distinct and shared contributions of diagnosis and symptom domains to cognitive performance in severe mental illness ]]> https://biorxiv.org/content/10.1101/731265v1?rss=1 Service, S. K. Munoz Umanes, M. Vargas Upegui, C. Castano Ramirez, M. Agudelo Arango, L. G. Diaz-Zuluaga, A. M. Melo Esepjo, J. Lopez, M. C. Palacio, J. D. Sanchez Ruiz, S. Valencia, J. Teshiba, T. Espinoza, A. Olde Loohuis, L. Brodey, B. Sabatti, C. Moore, T. Port, A. Escobar, J. I. Reus, V. I. Lopez Jaramillo, C. Gur, R. Bearden, C. E. Freimer, N. B. 2019-08-10 doi:10.1101/731265 Cold Spring Harbor Laboratory Press 2019-08-10 <![CDATA[ Post-transcriptional regulation of aortic calcification in KLOTHO deficient mice: impact of miR-145 and miR-378 ]]> https://biorxiv.org/content/10.1101/736330v1?rss=1 Tang, Y. Shah, T. A. Garsetti, D. E. Rogers, M. B. 2019-08-15 doi:10.1101/736330 Cold Spring Harbor Laboratory Press 2019-08-15 <![CDATA[ Distinct cellular mediators drive the Janus Faces of Toll-like Receptor 4 regulation of network excitability which impacts working memory performance after brain Injury ]]> https://biorxiv.org/content/10.1101/750869v1?rss=1 Korgaonkar, A. A. Li, Y. Guevarra, J. Pang, K. C. Santhakumar, V. 2019-09-02 doi:10.1101/750869 Cold Spring Harbor Laboratory Press 2019-09-02 <![CDATA[ Automated Lifespan Determination Across Caenorhabditis Strains and Species Reveals Assay-Specific Effects of Chemical Interventions ]]> https://biorxiv.org/content/10.1101/757302v1?rss=1 Banse, S. A. Lucanic, M. Sedore, C. A. Coleman-Hulbert, A. L. Plummer, W. T. Chen, E. Kish, J. L. Hall, D. Onken, B. Presley, M. P. Jones, E. G. Blue, B. W. Garrett, T. Abbott, M. Xue, J. Guo, S. Johnson, E. Foulger, A. C. Chamoli, M. Falkowski, R. Melentijevic, I. Harinath, G. Huynh, P. Patel, S. Edgar, D. Jarrett, C. M. Guo, M. Kapahi, P. Lithgow, G. J. Driscoll, M. Phillips, P. C. 2019-09-14 doi:10.1101/757302 Cold Spring Harbor Laboratory Press 2019-09-14 <![CDATA[ Evaluation of IL-1 blockade as a host-directed therapy for tuberculosis in mice and macaques ]]> https://biorxiv.org/content/10.1101/792390v1?rss=1 Winchell, C. G. M. Mishra, B. B. Phuah, J. Y. Saqib, M. Nelson, S. J. Maiello, P. Causgrove, C. M. Ameel, C. L. Stein, B. Borish, H. J. White, A. G. Klein, E. C. Zimmerman, M. D. Dartois, V. Lin, P. L. Sassetti, C. M. Flynn, J. L. 2019-10-03 doi:10.1101/792390 Cold Spring Harbor Laboratory Press 2019-10-03 <![CDATA[ Overlapping and distinct roles of CDPK family members in the pre-erythrocytic cycle of the rodent malaria parasite, Plasmodium berghei ]]> https://biorxiv.org/content/10.1101/797886v1?rss=1 Govindasamy, K. Bhanot, P. 2019-10-08 doi:10.1101/797886 Cold Spring Harbor Laboratory Press 2019-10-08 <![CDATA[ A Shh/Gli-driven three-node timer motif controls temporal identity and fate of neural stem cells ]]> https://biorxiv.org/content/10.1101/809418v1?rss=1 Dias, J. M. Alekseenko, Z. Jeggari, A. Boareto, M. Vollmer, J. Kozhevnikova, M. Wang, H. Matise, M. P. Alexeyenko, A. Iber, D. Ericson, J. 2019-10-17 doi:10.1101/809418 Cold Spring Harbor Laboratory Press 2019-10-17 <![CDATA[ Short-wavelength violet light (420nm) stimulates melanopsin-dependent acute alertness responses in zebrafish ]]> https://biorxiv.org/content/10.1101/825257v1?rss=1 Contreras, J. E. Lisse, T. S. Bouzidi, C. Cavanaugh, A. M. Matynia, A. Rieger, S. 2019-10-31 doi:10.1101/825257 Cold Spring Harbor Laboratory Press 2019-10-31 <![CDATA[ dSNE: a visualization approach for use with decentralized data ]]> https://biorxiv.org/content/10.1101/826974v1?rss=1 Saha, D. K. Calhoun, V. D. DU, Y. FU, Z. Panta, S. R. Plis, S. M. 2019-11-12 doi:10.1101/826974 Cold Spring Harbor Laboratory Press 2019-11-12 <![CDATA[ Allele-specific open chromatin in human iPSC neurons elucidates functional non-coding disease variants ]]> https://biorxiv.org/content/10.1101/827048v1?rss=1 Zhang, S. Zhang, H. Qiao, M. Zhou, Y. Zhao, S. Kozlova, A. Shi, J. Sanders, A. R. Wang, G. Sengupta, S. West, S. Streit, M. Cowan, C. A. Chen, M. Pang, Z. Gejman, P. V. He, X. Duan, J. 2019-11-01 doi:10.1101/827048 Cold Spring Harbor Laboratory Press 2019-11-01 <![CDATA[ The Manifold Actions of Signaling Peptides on Subcellular Dynamics of a Receptor Specify Stomatal Cell Fate ]]> https://biorxiv.org/content/10.1101/836437v1?rss=1 Qi, X. Maes, M. Zeng, S. Torii, K. U. 2019-11-09 doi:10.1101/836437 Cold Spring Harbor Laboratory Press 2019-11-09 <![CDATA[ Whole Genome Sequencing and Assembly of the Asian Honey Bee Apis dorsata ]]> https://biorxiv.org/content/10.1101/840207v1?rss=1 Oppenheim, S. Cao, X. Rueppel, O. Chantawannakul, P. Krongdang, S. Phokasem, P. DeSalle, R. Goodwin, S. Xing, J. Rosenfeld, J. A. 2019-11-13 doi:10.1101/840207 Cold Spring Harbor Laboratory Press 2019-11-13 <![CDATA[ Family permutation profiling identifies a dynamic protein domain as functionally tolerant to increased conformational entropy ]]> https://biorxiv.org/content/10.1101/840603v1?rss=1 Atkinson, J. T. Jones, A. M. Nanda, V. Silberg, J. J. 2019-11-14 doi:10.1101/840603 Cold Spring Harbor Laboratory Press 2019-11-14 <![CDATA[ Divergent Energy Expenditure Impacts Mouse Metabolic Adaptation to Acute High-Fat/High-Sucrose Diet Producing Sexually Dimorphic Weight Gain Patterns ]]> https://biorxiv.org/content/10.1101/840702v1?rss=1 View larger version (35K): org.highwire.dtl.DTLVardef@39eb69org.highwire.dtl.DTLVardef@8e564forg.highwire.dtl.DTLVardef@c46714org.highwire.dtl.DTLVardef@4b5898_HPS_FORMAT_FIGEXP M_FIG Legend: Male and female mice housed at 30{degrees}C had lower energy expenditure (EE) & energy intake (EI), while having greater energy balance (EB), during 7-day high-fat/high-sucrose (HFHS) feeding compared to male and female mice, respectively, housed at 20{degrees}C. However, female mice had lower EB compared to males at both housing temperature. Female mice housed at 30{degrees}C gained less weight than 30{degrees}C males but gained the same relative amount of fat mass during acute HFHS feeding. Interestingly, 20{degrees}C females gained the same amount of weight as 20{degrees}C males but gained primarily fat-free mass, while the males gained the same proportion of fat as 30{degrees}C males and females. C_FIG ]]> Morris, E. M. M. Noland, R. D. Allen, J. A. McCoin, C. S. Xia, Q. Koestler, D. C. Shook, R. P. Lighton, J. R. B. Christianson, J. A. Thyfault, J. P. 2019-11-13 doi:10.1101/840702 Cold Spring Harbor Laboratory Press 2019-11-13 <![CDATA[ Cellular Fitness Phenotype of Cancer Target Genes in Repurposing Cancer Therapeutics ]]> https://biorxiv.org/content/10.1101/840975v1?rss=1 George, B. Mukundan, P. P. Paul, A. M. Leitzel, K. Ali, S. M. Sandiford, O. Lipton, A. Rameshwar, P. Hortobagyi, G. N. Pillai, R. M. Kumar, R. 2019-11-15 doi:10.1101/840975 Cold Spring Harbor Laboratory Press 2019-11-15 <![CDATA[ A Trypanosoma brucei ORFeome-based Gain-of-Function Library reveals novel genes associated with melarsoprol resistance ]]> https://biorxiv.org/content/10.1101/849042v1?rss=1 Carter, M. Kim, H.-S. Gomez, S. Gritz, S. Larson, S. Schulz, D. Hovel-Miner, G. 2019-11-20 doi:10.1101/849042 Cold Spring Harbor Laboratory Press 2019-11-20 <![CDATA[ BRI2-mediated regulation of TREM2 processing in microglia and its potential implications for Alzheimer's disease and related dementias ]]> https://biorxiv.org/content/10.1101/2023.06.14.544924v1?rss=1 Yin, T. D'Adamio, L. 2023-06-14 doi:10.1101/2023.06.14.544924 Cold Spring Harbor Laboratory Press 2023-06-14 <![CDATA[ An aptamer-mediated base editing platform for simultaneous knock-in and multiple gene knockout for allogeneic CAR-T cells generation ]]> https://biorxiv.org/content/10.1101/2023.06.20.545315v1?rss=1 Porreca, I. Blassberg, R. Joubert, B. Harbottle, J. Mielczarek, O. Stombaugh, J. Hemphill, K. Sumner, J. Pazeraitis, D. Touza, J. L. Francesatto, M. Selmi, T. Collantes, J. C. Strezoska, Z. Taylor, B. Jin, S. Wiggins, C. M. van Brabant Smith, A. Lambourne, J. J. 2023-06-21 doi:10.1101/2023.06.20.545315 Cold Spring Harbor Laboratory Press 2023-06-21 <![CDATA[ Predicting the impact of rare variants on RNA splicing in CAGI6 ]]> https://biorxiv.org/content/10.1101/2023.06.20.545093v1?rss=1 Lord, J. Jaramillo Oquendo, C. Wai, H. A. Douglas, A. G. L. Bunyan, D. J. Wang, Y. Hu, Z. Zeng, Z. Danis, D. Katsonis, P. Williams, A. Lichtarge, O. Chang, Y. Bagnall, R. D. Mount, S. M. Matthiasardottir, B. Lin, C. van Overeem Hansen, T. Leman, R. Martins, A. Houdayer, C. Krieger, S. Bakolitsa, C. Peng, Y. Kamandula, A. Radivojac, P. Baralle, D. 2023-06-22 doi:10.1101/2023.06.20.545093 Cold Spring Harbor Laboratory Press 2023-06-22 <![CDATA[ In-vivo whole-cortex estimation of excitation-inhibition ratio indexes cortical maturation and cognitive ability in youth ]]> https://biorxiv.org/content/10.1101/2023.06.22.546023v1?rss=1 Zhang, S. Larsen, B. Sydnor, V. J. Zeng, T. An, L. Yan, X. Kong, R. Kong, X. Gur, R. C. Gur, R. E. Moore, T. M. Wolf, D. H. Holmes, A. J. Xie, Y. Zhou, J. H. Fortier, M. V. Tan, A. P. Gluckman, P. Chong, Y. S. Meaney, M. Deco, G. Satterthwaite, T. D. Yeo, B. T. T. 2023-06-22 doi:10.1101/2023.06.22.546023 Cold Spring Harbor Laboratory Press 2023-06-22 <![CDATA[ Developmental exposure to the Parkinson's disease-associated organochlorine pesticide dieldrin alters dopamine neurotransmission in α-synuclein pre-formed fibril (PFF)-injected mice ]]> https://biorxiv.org/content/10.1101/2023.06.21.545967v1?rss=1 View larger version (24K): org.highwire.dtl.DTLVardef@d679deorg.highwire.dtl.DTLVardef@db0d70org.highwire.dtl.DTLVardef@14f368dorg.highwire.dtl.DTLVardef@1868894_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Boyd, S. L. Kuhn, N. C. Patterson, J. R. Stoll, A. C. Zimmerman, S. A. Kolanowski, M. R. Neubecker, J. J. Luk, K. C. Ramsson, E. S. Sortwell, C. E. Bernstein, A. I. 2023-06-24 doi:10.1101/2023.06.21.545967 Cold Spring Harbor Laboratory Press 2023-06-24 <![CDATA[ Life on the edge: a new toolbox for population-level climate change vulnerability assessments ]]> https://biorxiv.org/content/10.1101/2023.06.23.543988v1?rss=1 Barratt, C. D. Onstein, R. E. Pinsky, M. L. Steinfartz, S. Kuehl, H. S. Forester, B. R. Razgour, O. 2023-06-24 doi:10.1101/2023.06.23.543988 Cold Spring Harbor Laboratory Press 2023-06-24 <![CDATA[ Early Deficits in Dentate Circuit and Behavioral Pattern Separation after Concussive Brain Injury ]]> https://biorxiv.org/content/10.1101/2023.06.22.546120v1?rss=1 Corrubia, L. Huang, A. Nguyen, S. Shiflett, M. W. Jones, M. Ewell, L. Santhakumar, V. 2023-06-25 doi:10.1101/2023.06.22.546120 Cold Spring Harbor Laboratory Press 2023-06-25 <![CDATA[ Single cell transcriptomics unveiled that early life BDE-99 exposure reprogrammed the gut-liver axis to promote a pro-inflammatory metabolic signature in male mice at late adulthood ]]> https://biorxiv.org/content/10.1101/2023.06.22.546158v1?rss=1 Lim, J. J. Goedkin, M. Jin, Y. Gu, H. Cui, J. Y. 2023-06-25 doi:10.1101/2023.06.22.546158 Cold Spring Harbor Laboratory Press 2023-06-25 <![CDATA[ Homocysteine Metabolites Impair the Phf8/H4K20me1/mTOR/Autophagy Pathway by Upregulating the Expression of PHF8-targeting miR-22-3p and miR-1229-3p in Human Vascular Endothelial Cells ]]> https://biorxiv.org/content/10.1101/2023.06.27.546759v1?rss=1 Witucki, L. Jakubowski, H. 2023-06-27 doi:10.1101/2023.06.27.546759 Cold Spring Harbor Laboratory Press 2023-06-27 <![CDATA[ Piroplasm parasites (Apicomplexa: Piroplasmida) in northeastern populations of the invasive Asian longhorned tick, Haemaphysalis longicornis Neumann (Ixodida: Ixodidae), in the United States ]]> https://biorxiv.org/content/10.1101/2023.06.26.546593v1?rss=1 Herb, H. E. Ferreira, F. C. Gonzalez, J. Fonseca, D. M. 2023-06-28 doi:10.1101/2023.06.26.546593 Cold Spring Harbor Laboratory Press 2023-06-28 <![CDATA[ Genome-wide transcriptome analysis reveals the diversity and function of long non-coding RNAs in dinoflagellates ]]> https://biorxiv.org/content/10.1101/2023.06.27.546665v1?rss=1 Chen, Y. Dougan, K. E. Nguyen, Q. Bhattacharya, D. Chan, C. X. 2023-06-29 doi:10.1101/2023.06.27.546665 Cold Spring Harbor Laboratory Press 2023-06-29 <![CDATA[ Neural representation dynamics reveal computational principles of cognitive task learning ]]> https://biorxiv.org/content/10.1101/2023.06.27.546751v1?rss=1 Mill, R. D. Cole, M. W. 2023-06-29 doi:10.1101/2023.06.27.546751 Cold Spring Harbor Laboratory Press 2023-06-29 <![CDATA[ Electrophysiology of human iPSC-derived vascular smooth muscle cells and cell autonomous consequences of Cantu Syndrome mutations ]]> https://biorxiv.org/content/10.1101/2023.06.29.547088v1?rss=1 Hanson, A. McClenaghan, C. Weng, K.-C. Colijn, S. Stratman, A. N. Halabi, C. M. Grange, D. K. Silva, J. R. Nichols, C. G. 2023-07-01 doi:10.1101/2023.06.29.547088 Cold Spring Harbor Laboratory Press 2023-07-01 <![CDATA[ Postsynaptic frequency filters shaped by the interplay of synaptic short-term plasticity and cellular time scales ]]> https://biorxiv.org/content/10.1101/2023.07.02.547439v1?rss=1 Mondal, Y. Villanueva Benito, G. Pena, R. F. Rotstein, H. G. 2023-07-03 doi:10.1101/2023.07.02.547439 Cold Spring Harbor Laboratory Press 2023-07-03 <![CDATA[ ASD mutation of Katnal2 impairs ependymal ciliary motion and causes hydrocephalus ]]> https://biorxiv.org/content/10.1101/2023.07.03.547302v1?rss=1 Qiu, S. Cao, H. Xue, Y. Zhao, W. Xie, S. Wu, N. Song, M. Pan, Y.-H. Baas, P. W. Ma, J. Yuan, X.-B. 2023-07-03 doi:10.1101/2023.07.03.547302 Cold Spring Harbor Laboratory Press 2023-07-03 <![CDATA[ The Cellular Underpinnings of the Human Cortical Connectome ]]> https://biorxiv.org/content/10.1101/2023.07.05.547828v1?rss=1 Zhang, X.-H. Anderson, K. M. Dong, H.-M. Chopra, S. Dhamala, E. Emani, P. S. Margulies, D. Holmes, A. J. 2023-07-06 doi:10.1101/2023.07.05.547828 Cold Spring Harbor Laboratory Press 2023-07-06 <![CDATA[ Neural Correlates of Perceptual Similarity Masking in Primate V1 ]]> https://biorxiv.org/content/10.1101/2023.07.06.547970v1?rss=1 Chen, S. C.-Y. Chen, Y. Geisler, W. S. Seidemann, E. 2023-07-10 doi:10.1101/2023.07.06.547970 Cold Spring Harbor Laboratory Press 2023-07-10 <![CDATA[ Multiple embryonic sources converge to form the pectoral girdle skeleton in zebrafish ]]> https://biorxiv.org/content/10.1101/2023.07.14.548949v1?rss=1 Kuroda, S. Lalonde, R. L. Mansour, T. A. Mosimann, C. Nakamura, T. 2023-07-14 doi:10.1101/2023.07.14.548949 Cold Spring Harbor Laboratory Press 2023-07-14 <![CDATA[ Ebola Virus VP35 Interacts Non-Covalently with Ubiquitin Chains to Promote Viral Replication Creating New Therapeutic Opportunities ]]> https://biorxiv.org/content/10.1101/2023.07.14.549057v1?rss=1 Rodriguez-Salazar, C. A. van Tol, S. Mailhot, O. Galdino, G. T. Borges Teruel, N. F. Zhang, L. Warren, A. N. Gonzalez-Orozco, M. Freiberg, A. N. Najmanovich, R. J. Giraldo, M. I. Rajsbaum, R. 2023-07-15 doi:10.1101/2023.07.14.549057 Cold Spring Harbor Laboratory Press 2023-07-15 <![CDATA[ Distinct ossification trade-offs illuminate the shoulder girdle reconfiguration at the water-to-land transition. ]]> https://biorxiv.org/content/10.1101/2023.07.17.547998v1?rss=1 Wei, J. Wood, T. W. P. Flaherty, K. Enny, A. Andrescavage, A. Brazer, D. Navon, D. Stewart, T. A. Cohen, H. Shanabag, A. Kuroda, S. Braasch, I. Nakamura, T. 2023-07-17 doi:10.1101/2023.07.17.547998 Cold Spring Harbor Laboratory Press 2023-07-17 <![CDATA[ Ethanol Drives Evolution of Hsp90-Dependent Robustness by Redundancy in Yeast Domestication ]]> https://biorxiv.org/content/10.1101/2023.07.21.547572v1?rss=1 Patel, D. Amiji, H. Shropshire, W. Condic, N. Ozirmak Lermi, N. Sabha, Y. John, B. Hanson, B. Karras, G. I. 2023-07-21 doi:10.1101/2023.07.21.547572 Cold Spring Harbor Laboratory Press 2023-07-21 <![CDATA[ A paradigm for ethanol consumption in head-fixed mice during prefrontal cortical two-photon calcium imaging ]]> https://biorxiv.org/content/10.1101/2023.07.20.549846v1?rss=1 1000) to explore how acute ethanol affects their activity. Drinking modulated activity rates in a subset of neurons on slow (minutes) and fast (seconds) time scales but the majority of neurons were unaffected. Moreover, ethanol intake did not significantly affect network level interactions in the PFC as assessed through inter-neuronal pairwise correlations. By establishing a method for binge-like drinking in head-fixed mice, we lay the groundwork for leveraging advanced microscopy technologies to study alcohol-induced neuroadaptations in PFC and other brain circuits. HighlightsO_LIC57BL/6J mice voluntarily consume ethanol to binge-like levels during head-fixation, with females consuming more ethanol than males. C_LIO_LIMice show differences in frontloading and licking behavior for head-fixed ethanol and sucrose consumption. C_LIO_LIHead-fixed paradigm enables two-photon calcium imaging in the anterior cingulate cortex subdivision of the prefrontal cortex. C_LIO_LIAcute ethanol increases and decreases single neuron activity at fast (seconds) and slow (minutes) time scales but does not alter pairwise correlations between neurons. C_LI ]]> Kalelkar, A. Sipe, G. O. Castro E Costa, A. R. Lorenzo, I. M. Nguyen, M. Linares-Garcia, I. Vazey, E. Huda, R. 2023-07-22 doi:10.1101/2023.07.20.549846 Cold Spring Harbor Laboratory Press 2023-07-22 <![CDATA[ Neuronal DAMPs exacerbate neurodegeneration via astrocytic RIPK3 signaling ]]> https://biorxiv.org/content/10.1101/2023.07.21.550097v1?rss=1 Chang, N. P. DaPrano, E. M. Evans, W. R. Nissenbaum, M. McCourt, M. Alzate, D. Lindman, M. Chou, T.-W. Atkins, C. Kusnecov, A. W. Huda, R. Daniels, B. P. 2023-07-24 doi:10.1101/2023.07.21.550097 Cold Spring Harbor Laboratory Press 2023-07-24 <![CDATA[ Propionyl-CoA carboxylase subunit B modulates PIK3CA-regulated immune-surveillance in a pancreatic cancer mouse model ]]> https://biorxiv.org/content/10.1101/2023.07.24.550301v1?rss=1 Han, H. V. Efem, R. Rosati, B. Maimouni, S. Lu, K. Jiang, Y.-P. Zong, W.-X. Lin, R. Z. 2023-07-26 doi:10.1101/2023.07.24.550301 Cold Spring Harbor Laboratory Press 2023-07-26 <![CDATA[ Benchmarking DNA Isolation Methods for Marine Metagenomics Studies ]]> https://biorxiv.org/content/10.1101/2023.07.25.550485v1?rss=1 Isaev, A. Demkina, A. Slonova, D. Mamontov, V. Konovalova, O. Yurikova, D. Rogozhin, V. Belova, V. Korostin, D. Sutormin, D. Severinov, K. V. 2023-07-26 doi:10.1101/2023.07.25.550485 Cold Spring Harbor Laboratory Press 2023-07-26 <![CDATA[ Region-specific reversal of epidermal planar polarity in the fancy rosette mouse ]]> https://biorxiv.org/content/10.1101/2023.07.27.550849v1?rss=1 Cetera, M. Sharan, R. Hayward-Lara, G. Phillips, B. Biswas, A. Halley, M. Beall, E. vonHoldt, B. Devenport, D. 2023-07-28 doi:10.1101/2023.07.27.550849 Cold Spring Harbor Laboratory Press 2023-07-28 <![CDATA[ USING SMALL MOLECULES TO TURN AN RNA APTAMER INTO SENSORS FOR INORGANIC TARGETS WITHOUT IN VITRO SELECTION ]]> https://biorxiv.org/content/10.1101/2023.07.29.551132v1?rss=1 Aggarwal, T. Wang, L. Gutierrez, B. Erguven, H. Guven, H. Izgu, E. C. 2023-07-30 doi:10.1101/2023.07.29.551132 Cold Spring Harbor Laboratory Press 2023-07-30 <![CDATA[ Irregularity of instantaneous gamma frequency in the motor control network characterize visuomotor and proprioceptive information processing ]]> https://biorxiv.org/content/10.1101/2023.07.28.551050v1?rss=1 Ryu, J. Choi, J.-W. Niketeghad, S. Torres, E. B. Pouratian, N. 2023-07-31 doi:10.1101/2023.07.28.551050 Cold Spring Harbor Laboratory Press 2023-07-31 <![CDATA[ Blueberry and cranberry pangenomes as a resource for future genetic studies and breeding efforts ]]> https://biorxiv.org/content/10.1101/2023.07.31.551392v1?rss=1 Yocca, A. E. Platts, A. Alger, E. Teresi, S. Mengist, M. F. Benevenuto, J. Felipe V. Ferrao, L. Jacobs, M. Babinski, M. Magallanes-Lundback, M. Bayer, P. Golicz, A. Humann, J. L. Main, D. Espley, R. V. Chagne, D. Albert, N. W. Montanari, S. Vorsa, N. Polashock, J. Diaz-Garcia, L. Zalapa, J. Bassil, N. V. Munoz, P. R. Iorizzo, M. Edger, P. P. 2023-08-02 doi:10.1101/2023.07.31.551392 Cold Spring Harbor Laboratory Press 2023-08-02 <![CDATA[ Requirement of GrgA for Chlamydia infectious progeny production, optimal growth, and efficient plasmid maintenance ]]> https://biorxiv.org/content/10.1101/2023.08.02.551707v1?rss=1 Lu, B. Wang, Y. Wurihan, W. Cheng, A. Yeung, S. Fondell, J. D. Lai, Z. Wan, D. wu, x. Li, V. W. Fan, H. 2023-08-02 doi:10.1101/2023.08.02.551707 Cold Spring Harbor Laboratory Press 2023-08-02 <![CDATA[ Muscle-restricted Nox4 knockout partially corrects muscle contractility following spinal cord injury in mice ]]> https://biorxiv.org/content/10.1101/2023.08.04.551985v1?rss=1 Toro, C. A. De Gasperi, R. Aslan, A. Johnson, N. Siddiq, M. M. Chow, C. Zhao, W. Harlow, L. Graham, Z. A. Liu, X.-H. Sadoshima, J. Iyengar, R. Cardozo, C. P. 2023-08-04 doi:10.1101/2023.08.04.551985 Cold Spring Harbor Laboratory Press 2023-08-04 <![CDATA[ The genomes and epigenomes of aquatic plants (Lemnaceae) promote triploid hybridization and clonal reproduction ]]> https://biorxiv.org/content/10.1101/2023.08.02.551673v1?rss=1 Ernst, E. Abramson, B. Acosta, K. Hoang, P. T. Mateo-Elizalde, C. Schubert, V. Pasaribu, B. Hartwick, N. Colt, K. Aylward, A. J. Ramu, U. Birchler, J. A. Schubert, I. Lam, E. Michael, T. P. Martienssen, R. A. 2023-08-05 doi:10.1101/2023.08.02.551673 Cold Spring Harbor Laboratory Press 2023-08-05 <![CDATA[ Structural basis of archaeal FttA-dependent transcription termination ]]> https://biorxiv.org/content/10.1101/2023.08.09.552649v1?rss=1 Wang, C. Molodtsov, V. Sanders, T. J. Marshall, C. J. Firlar, E. Kaelber, J. T. Santangelo, T. J. Ebright, R. H. 2023-08-10 doi:10.1101/2023.08.09.552649 Cold Spring Harbor Laboratory Press 2023-08-10 <![CDATA[ Neural Domains Associated with Substance Use Disorders: A Systematic Review of Neuroimaging Studies ]]> https://biorxiv.org/content/10.1101/2023.08.11.552870v1?rss=1 Hinojosa, C. A. Sitar, S. I. Zhao, J. C. Barbosa, J. D. Hien, D. A. Welsh, J. W. Fani, N. van Rooij, S. J. H. 2023-08-14 doi:10.1101/2023.08.11.552870 Cold Spring Harbor Laboratory Press 2023-08-14 <![CDATA[ Increasing the accuracy of single-molecule data analysis using tMAVEN ]]> https://biorxiv.org/content/10.1101/2023.08.15.553409v1?rss=1 Verma, A. R. Ray, K. K. Bodick, M. E. Kinz-Thompson, C. D. Gonzalez, R. L. 2023-08-17 doi:10.1101/2023.08.15.553409 Cold Spring Harbor Laboratory Press 2023-08-17 <![CDATA[ Using network control theory to study the dynamics of the structural connectome ]]> https://biorxiv.org/content/10.1101/2023.08.23.554519v1?rss=1 Parkes, L. Kim, J. Z. Stiso, J. Brynildsen, J. K. Cieslak, M. Covitz, S. Gur, R. E. Gur, R. C. Pasqualetti, F. Shinohara, R. T. Zhou, D. Satterthwaite, T. D. Bassett, D. S. 2023-08-24 doi:10.1101/2023.08.23.554519 Cold Spring Harbor Laboratory Press 2023-08-24 <![CDATA[ Long-term breast cancer response to CDK4/6 inhibition defined by TP53-mediated geroconversion ]]> https://biorxiv.org/content/10.1101/2023.08.25.554716v1?rss=1 Kudo, R. Safonov, A. da Silva, E. M. Li, Q. Shao, H. Will, M. Fushimi, A. Nakshatri, H. Reis-Filho, J. S. Goel, S. Koff, A. Weigelt, B. Khan, Q. J. Razavi, P. Chandarlapaty, S. 2023-08-27 doi:10.1101/2023.08.25.554716 Cold Spring Harbor Laboratory Press 2023-08-27 <![CDATA[ Loss of the polarity protein Par3 promotes dendritic spine neoteny and enhances learning and memory ]]> https://biorxiv.org/content/10.1101/2023.08.30.555530v1?rss=1 Voglewede, M. M. Ozsen, E. N. Ivak, N. Bernabucci, M. Sun, M. Pang, Z. P. Zhang, H. 2023-09-01 doi:10.1101/2023.08.30.555530 Cold Spring Harbor Laboratory Press 2023-09-01 <![CDATA[ Extracellular Histone Promotes Calcium Phosphate-Dependent Calcification in Mouse Vascular Smooth Muscle Cells ]]> https://biorxiv.org/content/10.1101/2023.08.31.555403v1?rss=1 View larger version (19K): org.highwire.dtl.DTLVardef@19c3239org.highwire.dtl.DTLVardef@1a563fdorg.highwire.dtl.DTLVardef@1479cd1org.highwire.dtl.DTLVardef@886219_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Hoshino, T. Kharaghani, D. Kohno, S. 2023-09-01 doi:10.1101/2023.08.31.555403 Cold Spring Harbor Laboratory Press 2023-09-01 <![CDATA[ Dysregulation of γδ intraepithelial lymphocytes precedes Crohn's disease-like ileitis ]]> https://biorxiv.org/content/10.1101/2023.08.31.555710v1?rss=1 Xu, W. Golovchenko, N. B. Fong, A. Achi, S. Bucar, E. B. Vidmar, K. J. Zhang, L. Frey, M. R. Prinz, I. Pizarro, T. T. Kollias, G. Edelblum, K. L. 2023-09-03 doi:10.1101/2023.08.31.555710 Cold Spring Harbor Laboratory Press 2023-09-03 <![CDATA[ Recording neural reward signals in the real-world using mobile-EEG and augmented reality ]]> https://biorxiv.org/content/10.1101/2023.08.31.555757v1?rss=1 Stringfellow, J. S. Liran, O. Lin, M.-H. Baker, T. E. 2023-09-03 doi:10.1101/2023.08.31.555757 Cold Spring Harbor Laboratory Press 2023-09-03 <![CDATA[ Interference Requirements of Type III CRISPR-Cas Systems from Thermus thermophilus ]]> https://biorxiv.org/content/10.1101/2023.09.03.556089v1?rss=1 Karneyeva, K. Kolesnik, M. Livenskyi, A. Zgoda, V. Zubarev, V. Trofimova, A. Artamonova, D. Ispolatov, Y. Severinov, K. 2023-09-03 doi:10.1101/2023.09.03.556089 Cold Spring Harbor Laboratory Press 2023-09-03 <![CDATA[ KAT2 paralogs prevent dsRNA accumulation and interferon signaling to maintain intestinal stem cells ]]> https://biorxiv.org/content/10.1101/2023.09.04.556156v1?rss=1 Nguyen, M.-U. T. Potgieter, S. Huang, W. Pfeffer, J. Woo, S. Zhao, C. Lawlor, M. Yang, R. Halstead, A. Dent, S. Saenz, J. Zheng, H. Yuan, Z.-F. Sidoli, S. Ellison, C. E. Verzi, M. 2023-09-05 doi:10.1101/2023.09.04.556156 Cold Spring Harbor Laboratory Press 2023-09-05 <![CDATA[ The tumor microbiome reacts to hypoxia and can influence response to radiation treatment in colorectal cancer ]]> https://biorxiv.org/content/10.1101/2023.09.01.555936v1?rss=1 Benej, M. Hoyd, R. Kreamer, M. Wheeler, C. E. Grencewicz, D. J. Choueiry, F. Chan, C. H. Zakharia, Y. Ma, Q. Dodd, R. D. Ulrich, C. M. Hardikar, S. Churchman, M. L. Tarhini, A. A. Robinson, L. A. Singer, E. A. Ikeguchi, A. P. McCarter, M. D. Tinoco, G. Husain, M. Jin, N. Tan, A. C. Osman, A. E. G. Eljilany, I. Riedlinger, G. Schneider, B. P. Benejova, K. Kery, M. Papandreou, I. Zhu, J. Denko, N. Spakowicz, D. 2023-09-06 doi:10.1101/2023.09.01.555936 Cold Spring Harbor Laboratory Press 2023-09-06 <![CDATA[ Deep Learning for Protein Peptide bindingPrediction: Incorporating Sequence, Structural andLanguage Model Features ]]> https://biorxiv.org/content/10.1101/2023.09.02.556055v1?rss=1 Chandra, A. Sharma, A. Dehzangi, I. Tsunoda, T. Sattar, A. 2023-09-06 doi:10.1101/2023.09.02.556055 Cold Spring Harbor Laboratory Press 2023-09-06 <![CDATA[ Dietary Pyruvate Targets Cytosolic Phospholipase A2 to Mitigate Inflammation and Obesity in Mice ]]> https://biorxiv.org/content/10.1101/2023.09.07.556702v1?rss=1 Hasan, S. Ghani, N. Zhao, X. Good, J. Huang, A. Wrona, H. L. Liu, J. Liu, C. 2023-09-08 doi:10.1101/2023.09.07.556702 Cold Spring Harbor Laboratory Press 2023-09-08 <![CDATA[ Discovering biomarkers associated and predicting cardiovascular disease with high accuracy using a novel nexus of machine learning techniques for precision medicine ]]> https://biorxiv.org/content/10.1101/2023.09.08.553995v1?rss=1 Degroat, W. Abdelhalim, H. Patel, K. Mendhe, D. Zeeshan, S. Ahmed, Z. 2023-09-11 doi:10.1101/2023.09.08.553995 Cold Spring Harbor Laboratory Press 2023-09-11 <![CDATA[ Supercharging carbohydrate-binding module alone enhances endocellulase thermostability, binding, and activity on cellulosic biomass ]]> https://biorxiv.org/content/10.1101/2023.09.09.557007v1?rss=1 DeChellis, A. Nemmaru, B. Sammond, D. Douglas, J. Patil, N. Reste, O. Chundawat, S. P. S. 2023-09-12 doi:10.1101/2023.09.09.557007 Cold Spring Harbor Laboratory Press 2023-09-12 <![CDATA[ Neurotransmitter signaling specifies sweat gland stem cell fate through SLN-mediated intracellular calcium regulation ]]> https://biorxiv.org/content/10.1101/2023.09.10.557066v1?rss=1 Remark, J. Tong, J. Lin, M. J. Concepcion, A. R. Mareedu, S. Babu, G. J. Feske, S. Lu, C. P.-j. 2023-09-13 doi:10.1101/2023.09.10.557066 Cold Spring Harbor Laboratory Press 2023-09-13 <![CDATA[ SOX4-SMARCA4 complex promotes glycolysis-dependent TNBC cell growth through transcriptional regulation of Hexokinase 2 ]]> https://biorxiv.org/content/10.1101/2023.09.10.557071v1?rss=1 Khanna, P. Mehta, R. Mehta, G. A. Gatza, M. L. 2023-09-13 doi:10.1101/2023.09.10.557071 Cold Spring Harbor Laboratory Press 2023-09-13 <![CDATA[ The Dynamics of Synthesis and Localization of Jumbo Phage RNA Polymerases inside Infected Cells ]]> https://biorxiv.org/content/10.1101/2023.09.14.557509v1?rss=1 Antonova, D. Belousova, V. V. Zhivkoplias, E. Sobinina, M. Artamonova, T. Vishnyakov, I. E. Kurdyumova, I. Arseniev, A. Morozova, N. Severinov, K. Khodorkovskii, M. Yakunina, M. 2023-09-14 doi:10.1101/2023.09.14.557509 Cold Spring Harbor Laboratory Press 2023-09-14 <![CDATA[ Regularized partial correlation provides reliable functional connectivity estimates while correcting for widespread confounding ]]> https://biorxiv.org/content/10.1101/2023.09.16.558065v1?rss=1 Peterson, K. L. Sanchez-Romero, R. Mill, R. D. Cole, M. W. 2023-09-17 doi:10.1101/2023.09.16.558065 Cold Spring Harbor Laboratory Press 2023-09-17 <![CDATA[ Intra-ocular Predation of Fluoroquinolone-Resistant Pseudomonas aeruginosa and Serratia marcescens by the Predatory Bacteria ]]> https://biorxiv.org/content/10.1101/2023.09.17.558130v1?rss=1 Romanowski, E. G. Brothers, K. M. Calvario, R. C. Stella, N. A. Kim, T. Elsayed, M. Kadouri, D. E. Shanks, R. M. Q. 2023-09-17 doi:10.1101/2023.09.17.558130 Cold Spring Harbor Laboratory Press 2023-09-17 <![CDATA[ Oscillatory correlates of threat imminence during virtual navigation ]]> https://biorxiv.org/content/10.1101/2023.09.18.558288v1?rss=1 Karpov, G. Lin, M.-H. Headley, D. B. Baker, T. E. 2023-09-18 doi:10.1101/2023.09.18.558288 Cold Spring Harbor Laboratory Press 2023-09-18 <![CDATA[ Engineered transcription-associated Cas9 targeting in eukaryotic cells ]]> https://biorxiv.org/content/10.1101/2023.09.18.558319v1?rss=1 Goldberg, G. W. Kogenaru, M. Keegan, S. Haase, M. A. B. Kagermazova, L. Arias, M. A. Onyebeke, K. Adams, S. Fenyo, D. Noyes, M. B. Boeke, J. D. 2023-09-18 doi:10.1101/2023.09.18.558319 Cold Spring Harbor Laboratory Press 2023-09-18 <![CDATA[ The NS1 protein of influenza B virus binds 5'-triphosphorylated dsRNA to suppress RIG-I activation and the antiviral innate immune response ]]> https://biorxiv.org/content/10.1101/2023.09.25.559316v1?rss=1 Woltz, R. Schweibenz, B. Tsutakawa, S. E. Zhao, C. Ma, L.-C. Shurina, B. Hura, G. L. John, R. Vorobiev, S. Gurla, S. Solotchi, M. Tainer, J. A. Krug, R. M. Patel, S. S. Montelione, G. T. 2023-09-25 doi:10.1101/2023.09.25.559316 Cold Spring Harbor Laboratory Press 2023-09-25 <![CDATA[ Quantifying nutrient colimitation of microbial growth ]]> https://biorxiv.org/content/10.1101/2023.09.27.559472v1?rss=1 Held, N. A. Krishna, A. Crippa, D. Dragan, A. Manhart, M. 2023-09-27 doi:10.1101/2023.09.27.559472 Cold Spring Harbor Laboratory Press 2023-09-27 <![CDATA[ Piezo1 agonist restores meningeal lymphatic vessels, drainage, and brain-CSF perfusion in craniosynostosis and aged mice ]]> https://biorxiv.org/content/10.1101/2023.09.27.559761v1?rss=1 Matrongolo, M. J. Ang, P. S. Wu, J. Jain, A. Thackray, J. K. Reddy, A. Sung, C. C. Barbet, G. Hong, Y.-K. Tischfield, M. 2023-09-27 doi:10.1101/2023.09.27.559761 Cold Spring Harbor Laboratory Press 2023-09-27 <![CDATA[ Determining the effects of temperature on the evolution of bacterial tRNA pools ]]> https://biorxiv.org/content/10.1101/2023.09.26.559538v1?rss=1 Jain, V. Cope, A. L. 2023-09-28 doi:10.1101/2023.09.26.559538 Cold Spring Harbor Laboratory Press 2023-09-28 <![CDATA[ Analysis of nasopharyngeal microbiome patterns in Zambian infants with fatal acute febrile illness ]]> https://biorxiv.org/content/10.1101/2023.09.27.559805v1?rss=1 Odom, A. R. McClintock, J. Gill, C. J. Pieciak, R. Ismail, A. MacLeod, W. B. Johnson, W. E. Lapidot, R. 2023-09-28 doi:10.1101/2023.09.27.559805 Cold Spring Harbor Laboratory Press 2023-09-28 <![CDATA[ Best practices for perturbation MPRA--a computational evaluation framework of sequence design strategies ]]> https://biorxiv.org/content/10.1101/2023.09.27.559768v1?rss=1 Liu, J. Ashuach, T. Inoue, F. Ahituv, N. Yosef, N. Kreimer, A. 2023-09-29 doi:10.1101/2023.09.27.559768 Cold Spring Harbor Laboratory Press 2023-09-29 <![CDATA[ Simulating Interclonal Interactions in Diffuse Large B-Cell Lymphoma ]]> https://biorxiv.org/content/10.1101/2023.09.28.559950v1?rss=1 Ganesh, S. R. Roth, C. Parekkadan, B. 2023-09-29 doi:10.1101/2023.09.28.559950 Cold Spring Harbor Laboratory Press 2023-09-29 <![CDATA[ Distinct functions of EHMT1 and EHMT2 in cancer chemotherapy and immunotherapy ]]> https://biorxiv.org/content/10.1101/2023.10.03.560719v1?rss=1 Kang, Z. Fu, P. Ma, H. Li, T. Lu, K. Liu, J. Ginjala, V. Romanienko, P. Feng, Z. Guan, M. Ganesan, S. Xia, B. 2023-10-04 doi:10.1101/2023.10.03.560719 Cold Spring Harbor Laboratory Press 2023-10-04 <![CDATA[ YlaN is an iron(II) binding protein that functions to relieve Fur-mediated repression of gene expression in Staphylococcus aureus ]]> https://biorxiv.org/content/10.1101/2023.10.03.560778v1?rss=1 Boyd, J. M. esquilin-lebron, K. M. Campbell, C. J. Ryan Kaler, K. M. Norambuena, J. Foley, M. E. Stephens, T. G. Rios, G. Mereddy, G. Zheng, V. Bovermann, H. Kim, J. Kulczyk, A. W. Yang, J. H. Greco, T. M. Cristea, I. M. Carabetta, V. J. Beavers, W. N. Bhattacharya, D. Skaar, E. P. Parker, D. Carroll, R. K. Stemmler, T. L. 2023-10-04 doi:10.1101/2023.10.03.560778 Cold Spring Harbor Laboratory Press 2023-10-04 <![CDATA[ CED-5/CED-12 (DOCK/ELMO) can promote and inhibit F-actin formation via distinct motifs that target different GTPases ]]> https://biorxiv.org/content/10.1101/2023.10.04.560868v1?rss=1 Venkatachalam, T. Mannimala, S. Soto, M. C. 2023-10-05 doi:10.1101/2023.10.04.560868 Cold Spring Harbor Laboratory Press 2023-10-05 <![CDATA[ Differential processing of delay versus uncertainty in male but not female 16p11.2 hemideletion mice ]]> https://biorxiv.org/content/10.1101/2023.10.04.560951v1?rss=1 Rojas, G. R. Heller, A. T. Grissom, N. M. 2023-10-06 doi:10.1101/2023.10.04.560951 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ G6PD Maintains Redox Homeostasis and Biosynthesis in LKB1-Deficient KRAS-Driven Lung Cancer ]]> https://biorxiv.org/content/10.1101/2023.10.06.561131v1?rss=1 Lan, T. Arastu, S. Wang, S. Lam, J. Wang, W. Bhatt, V. Lopes, E. C. Hu, Z. S. Sun, M. Luo, X. Ghergurovich, J. M. Li, C. Su, X. Rabinowitz, J. D. White, E. Guo, J. Y. 2023-10-09 doi:10.1101/2023.10.06.561131 Cold Spring Harbor Laboratory Press 2023-10-09 <![CDATA[ Shifts in attention drive context-dependent subspace encoding in anterior cingulate cortex during decision making ]]> https://biorxiv.org/content/10.1101/2023.10.10.561737v1?rss=1 Hajnal, M. A. Tran, D. Szabo, Z. Albert, A. Safaryan, K. Einstein, M. Martelo, M. V. Polack, P.-O. Golshani, P. Orban, G. 2023-10-10 doi:10.1101/2023.10.10.561737 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ A Hard Sphere Model for Single File Water Transport Across Biological Membranes ]]> https://biorxiv.org/content/10.1101/2023.10.11.561951v1?rss=1 Manning, G. S. 2023-10-12 doi:10.1101/2023.10.11.561951 Cold Spring Harbor Laboratory Press 2023-10-12 <![CDATA[ Arrayed in vivo barcoding for multiplexed sequence verification of plasmid DNA and demultiplexing of pooled libraries ]]> https://biorxiv.org/content/10.1101/2023.10.13.562064v1?rss=1 45,000 plasmids and show that the method can be used to transform error-containing dispersed plasmid pools into sequence-perfect arrays or well-balanced pools. In vivo barcoding does not require any specialized equipment beyond a low-overhead Oxford Nanopore sequencer, enabling most labs to flexibly process hundreds to thousands of plasmids in parallel. ]]> Li, W. Miller, D. Liu, X. Tosi, L. Chkaiban, L. Mei, H. Hung, P.-H. Parekkadan, B. Sherlock, G. Levy, S. F. 2023-10-13 doi:10.1101/2023.10.13.562064 Cold Spring Harbor Laboratory Press 2023-10-13 <![CDATA[ KatG catalase deficiency confers bedaquiline hyper-susceptibility to isoniazid resistant Mycobacterium tuberculosis ]]> https://biorxiv.org/content/10.1101/2023.10.17.562707v1?rss=1 Ofori-Anyinam, N. Hamblin, M. Coldren, M. L. Li, B. Mereddy, G. Shaikh, M. Shah, A. Ranu, N. Lu, S. Blainey, P. C. Ma, S. Collins, J. J. Yang, J. H. 2023-10-17 doi:10.1101/2023.10.17.562707 Cold Spring Harbor Laboratory Press 2023-10-17 <![CDATA[ Scale-dependent hierarchical resolution: applications to atomic resolution and model validation in cryoEM ]]> https://biorxiv.org/content/10.1101/2023.10.17.562748v1?rss=1 Ray, K. K. Kinz-Thompson, C. D. 2023-10-19 doi:10.1101/2023.10.17.562748 Cold Spring Harbor Laboratory Press 2023-10-19 <![CDATA[ Yes1-mediated Cul9 phosphorylation promotes the metabolic reprogramming in gastric cancer ]]> https://biorxiv.org/content/10.1101/2023.10.18.562906v1?rss=1 Wu, Y. Zhang, H. Zhang, S. Wang, M. Wang, H. Huang, H. Hong, X. Zhang, Z. Li, Y. 2023-10-20 doi:10.1101/2023.10.18.562906 Cold Spring Harbor Laboratory Press 2023-10-20 <![CDATA[ Characterizing the Cellulose Binding Interactions of Type-A Carbohydrate-Binding Modules using Acoustic Force Spectroscopy ]]> https://biorxiv.org/content/10.1101/2023.10.18.563009v1?rss=1 Ganesan, G. Hackl, M. Chundawat, S. P. S. 2023-10-21 doi:10.1101/2023.10.18.563009 Cold Spring Harbor Laboratory Press 2023-10-21 <![CDATA[ ZNF91 is an endogenous repressor of the molecular phenotype associated with X-linked dystonia-parkinsonism (XDP) ]]> https://biorxiv.org/content/10.1101/2023.10.20.563263v1?rss=1 Rosenkrantz, J. L. Raghib, S. Brandorff, J. E. Kapadia, A. Vaine, C. A. Bragg, D. C. Farmiloe, G. Jacobs, F. L. 2023-10-23 doi:10.1101/2023.10.20.563263 Cold Spring Harbor Laboratory Press 2023-10-23 <![CDATA[ Neurocognitive Dynamics of Preparatory and Adaptive Cognitive Control: Insights from Mass-Univariate and Multivariate Pattern Analysis of EEG data ]]> https://biorxiv.org/content/10.1101/2023.10.23.563561v1?rss=1 Garcia Alanis, J. C. Güth, M. R. Chavanon, M.-L. Peper, M. 2023-10-23 doi:10.1101/2023.10.23.563561 Cold Spring Harbor Laboratory Press 2023-10-23 <![CDATA[ Platelet proteo-transcriptomic profiling validates mediators of thrombosis and proteostasis in patients with myeloproliferative neoplasms ]]> https://biorxiv.org/content/10.1101/2023.10.23.563619v1?rss=1 View larger version (20K): org.highwire.dtl.DTLVardef@1cb6290org.highwire.dtl.DTLVardef@1b3ec3eorg.highwire.dtl.DTLVardef@15b0c8eorg.highwire.dtl.DTLVardef@9575b2_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Kelliher, S. Gamba, S. Weiss, L. Shen, Z. Marchetti, M. Schieppati, F. Scaife, C. Madden, S. Bennett, K. Fortune, A. Maung, S. Fay, M. Ni Ainle, F. Maguire, P. Falanga, A. Kevane, B. Krishnan, A. 2023-10-25 doi:10.1101/2023.10.23.563619 Cold Spring Harbor Laboratory Press 2023-10-25 <![CDATA[ Dysregulated neuroimmune interactions and sustained type I interferon signaling after human immunodeficiency virus type 1 infection of human iPSC derived microglia and cerebral organoids ]]> https://biorxiv.org/content/10.1101/2023.10.25.563950v1?rss=1 Boreland, A. J. Stillitano, A. C. Lin, H. Abbo, Y. Hart, R. P. Jiang, P. Pang, Z. P. Rabson, A. B. 2023-10-25 doi:10.1101/2023.10.25.563950 Cold Spring Harbor Laboratory Press 2023-10-25 <![CDATA[ PDB NextGen Archive: Centralising Access to Integrated Annotations and Enriched Structural Information by the Worldwide Protein Data Bank ]]> https://biorxiv.org/content/10.1101/2023.10.24.563739v1?rss=1 Choudhary, P. Feng, Z. Berrisford, J. Chao, H. Ikegawa, Y. Peisach, E. Piehl, D. W. Smith, J. Tanweer, A. Varadi, M. Westbrook, J. D. Young, J. Y. Patwardhan, A. Morris, K. L. Hoch, J. C. Kurisu, G. Velankar, S. Burley, S. K. 2023-10-27 doi:10.1101/2023.10.24.563739 Cold Spring Harbor Laboratory Press 2023-10-27 <![CDATA[ Plexin-B1 and Plexin-B2 play non-redundant roles in GABAergic synapse formation ]]> https://biorxiv.org/content/10.1101/2023.10.27.564428v1?rss=1 Adel, S. Pranske, Z. J. Kowalski, T. F. Kanzler, N. Ray, R. Carmona, C. Paradis, S. 2023-10-27 doi:10.1101/2023.10.27.564428 Cold Spring Harbor Laboratory Press 2023-10-27 <![CDATA[ Fatty acid metabolism in neutrophils promotes lung damage and bacterial replication during tuberculosis. ]]> https://biorxiv.org/content/10.1101/2023.10.25.563909v1?rss=1 Mishra, B. B. Sankar, P. Ramos, R. B. Corro, J. Saqib, M. Nafiz, T. N. Bhargavi, G. Ojha, A. K. Cai, Y. Subbian, S. 2023-10-29 doi:10.1101/2023.10.25.563909 Cold Spring Harbor Laboratory Press 2023-10-29 <![CDATA[ Metabolic and behavioral alterations associated with viral vector-mediated toxicity in the paraventricular hypothalamic nucleus ]]> https://biorxiv.org/content/10.1101/2023.10.26.564009v1?rss=1 Savani, R. Park, E. Busannagari, N. Lu, Y. Kwon, H. Wang, L. Pang, Z. P. 2023-10-30 doi:10.1101/2023.10.26.564009 Cold Spring Harbor Laboratory Press 2023-10-30 <![CDATA[ Rapid activation of IL-2 receptor signaling by CD301b+DC-derived IL-2 dictates the outcome of helper T cell differentiation ]]> https://biorxiv.org/content/10.1101/2023.10.26.564276v1?rss=1 Tatsumi, N. El-Fenej, J. Davila-Pagan, A. Kumamoto, Y. 2023-10-31 doi:10.1101/2023.10.26.564276 Cold Spring Harbor Laboratory Press 2023-10-31 <![CDATA[ Queuosine biosynthetic enzyme, QueE moonlights as a cell division regulator ]]> https://biorxiv.org/content/10.1101/2023.10.31.565030v1?rss=1 Adeleye, S. A. Yadavalli, S. S. 2023-11-01 doi:10.1101/2023.10.31.565030 Cold Spring Harbor Laboratory Press 2023-11-01 <![CDATA[ Using behavioral biomarkers to redefine epochs of spontaneous recovery following spinal cord injury ]]> https://biorxiv.org/content/10.1101/2023.10.31.564826v1?rss=1 Eisdorfer, J. T. Thackray, J. Theis, T. Vivinetto, A. Ricci, M. T. Lin, S. Oputa, O. Martinez, A. M. Nacht, H. D. Tschang, M. Mahmood, M. Tucker, A. Pusuloori, S. Zmoyro, L. Abraira Lab Computational Group, Popovich, P. Ferguson, A. R. McTigue, D. Tysseling, V. M. Dulin, J. Hollis, E. Datta, S. R. Abraira, V. E. G. 2023-11-02 doi:10.1101/2023.10.31.564826 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ Ciliary intrinsic mechanisms regulate dynamic ciliary extracellular vesicle release from sensory neurons ]]> https://biorxiv.org/content/10.1101/2023.11.01.565151v1?rss=1 Wang, J. Saul, J. Nikonorova, I. A. Cruz, C. N. Power, K. M. Nguyen, K. C. Hall, D. H. Barr, M. M. 2023-11-03 doi:10.1101/2023.11.01.565151 Cold Spring Harbor Laboratory Press 2023-11-03 <![CDATA[ Structural basis of RfaH-mediated transcription-translation coupling ]]> https://biorxiv.org/content/10.1101/2023.11.05.565726v1?rss=1 Molodtsov, V. Wang, C. Kaelber, J. T. Blaha, G. Ebright, R. H. 2023-11-06 doi:10.1101/2023.11.05.565726 Cold Spring Harbor Laboratory Press 2023-11-06 <![CDATA[ Targeting phosphoRab-RILPL Interactions as a Strategy to Downregulate Pathogenic LRRK2 in Parkinson's Disease ]]> https://biorxiv.org/content/10.1101/2023.11.06.565863v1?rss=1 Alexander, K. Naaldijk, Y. Fasiczka, R. Brahmia, B. Chen, T. Hilfiker, S. Kennedy, E. J. 2023-11-06 doi:10.1101/2023.11.06.565863 Cold Spring Harbor Laboratory Press 2023-11-06 <![CDATA[ Spatial organization of bacterial sphingolipid synthesis enzymes ]]> https://biorxiv.org/content/10.1101/2023.11.08.566215v1?rss=1 Uchendu, C. G. Klein, E. A. 2023-11-08 doi:10.1101/2023.11.08.566215 Cold Spring Harbor Laboratory Press 2023-11-08 <![CDATA[ Phylogeographic analysis of Begomovirus coat and replication-associated proteins ]]> https://biorxiv.org/content/10.1101/2023.11.08.565637v1?rss=1 Crespo-Bellido, A. Hoyer, J. S. Burgos-Amengual, Y. Duffy, S. 2023-11-09 doi:10.1101/2023.11.08.565637 Cold Spring Harbor Laboratory Press 2023-11-09 <![CDATA[ Dynamic RNA Polymerase II Recruitment Drives Differentiation of the Intestine under the direction of HNF4 ]]> https://biorxiv.org/content/10.1101/2023.11.08.566322v1?rss=1 Vemuri, K. Kumar, S. Chen, L. Verzi, M. P. 2023-11-10 doi:10.1101/2023.11.08.566322 Cold Spring Harbor Laboratory Press 2023-11-10 <![CDATA[ Genetic, transcriptomic, histological, and biochemical analysis of progressive supranuclear palsy implicates glial activation and novel risk genes ]]> https://biorxiv.org/content/10.1101/2023.11.09.565552v1?rss=1 Farrell, K. Humphrey, J. Chang, T. Zhao, Y. Leung, Y. Y. Kuksa, P. P. Patil, V. Lee, W.-P. Kuzma, A. B. Valladares, O. Cantwell, L. B. Wang, H. Ravi, A. De Sanctis, C. Han, N. Christie, T. D. Whitney, K. Krassner, M. M. Walsh, H. Kim, S. Dangoor, D. Iida, M. A. Casella, A. Walker, R. H. Nirenberg, M. J. Renton, A. E. Babrowicz, B. Coppola, G. Raj, T. Hoglinger, G. U. Golbe, L. I. Morris, H. R. Hardy, J. Revesz, T. Warner, T. T. Jaunmuktane, Z. Mok, K. Y. Rademakers, R. Dickson, D. W. Ross, O. A. Wang, L.-S. Goate, A. Schellenberg, G. Geschwind, D. H. 2023-11-13 doi:10.1101/2023.11.09.565552 Cold Spring Harbor Laboratory Press 2023-11-13 <![CDATA[ Functional brain networks are associated with both sex and gender in children ]]> https://biorxiv.org/content/10.1101/2023.11.12.566592v1?rss=1 Dhamala, E. Bassett, D. Yeo, B. T. T. Holmes, A. 2023-11-15 doi:10.1101/2023.11.12.566592 Cold Spring Harbor Laboratory Press 2023-11-15 <![CDATA[ The mechanism of mRNA activation ]]> https://biorxiv.org/content/10.1101/2023.11.15.567265v1?rss=1 Gentry, R. C. Ide, N. A. Comunale, V. M. Hartwick, E. W. Kinz-Thompson, C. D. Gonzalez, R. L. 2023-11-15 doi:10.1101/2023.11.15.567265 Cold Spring Harbor Laboratory Press 2023-11-15 <![CDATA[ Mechanical force of uterine occupation enables large vesicle extrusion from proteostressed maternal neurons ]]> https://biorxiv.org/content/10.1101/2023.11.13.565361v1?rss=1 Wang, G. Guasp, R. Salam, S. Chuang, E. Morera, A. Smart, A. J. Jimenez, D. Shekhar, S. Melentijevic, I. Nguyen, K. C. Hall, D. H. Grant, B. D. Driscoll, M. 2023-11-16 doi:10.1101/2023.11.13.565361 Cold Spring Harbor Laboratory Press 2023-11-16 <![CDATA[ Precision data-driven modeling of cortical dynamics reveals idiosyncratic mechanisms of canonical oscillations ]]> https://biorxiv.org/content/10.1101/2023.11.14.567088v1?rss=1 Singh, M. F. Braver, T. S. Cole, M. Ching, S. 2023-11-16 doi:10.1101/2023.11.14.567088 Cold Spring Harbor Laboratory Press 2023-11-16 <![CDATA[ Hot springs viruses at Yellowstone National Park have ancient origins and are adapted to their thermophilic hosts. ]]> https://biorxiv.org/content/10.1101/2023.11.15.567249v1?rss=1 Benites, L. F. Stephens, T. G. Van Etten, J. James, T. Christian, W. C. Barry, K. Grigoriev, I. V. McDermott, T. R. Bhattacharya, D. 2023-11-17 doi:10.1101/2023.11.15.567249 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ Cell-specific alpha-tubulin TBA-6 and pan-ciliary IFT cargo RAB-28 generate a non-canonical transition zone ]]> https://biorxiv.org/content/10.1101/2023.11.16.567340v1?rss=1 Akella, J. S. Silva, M. S. Nguyen, K. C. Q. Hall, D. H. Barr, M. M. 2023-11-17 doi:10.1101/2023.11.16.567340 Cold Spring Harbor Laboratory Press 2023-11-17 <![CDATA[ A shared spatial topography links the functional connectome correlates of cocaine use disorder and dopamine D2/3 receptor densities ]]> https://biorxiv.org/content/10.1101/2023.11.17.567591v1?rss=1 Ricard, J. A. Labache, L. Segal, A. Dhamala, E. Cocuzza, C. V. Jones, G. Yip, S. Chopra, S. Holmes, A. J. 2023-11-20 doi:10.1101/2023.11.17.567591 Cold Spring Harbor Laboratory Press 2023-11-20 <![CDATA[ Functional and antigenic characterization of SARS-CoV-2 spike fusion peptide by deep mutational scanning ]]> https://biorxiv.org/content/10.1101/2023.11.28.569051v1?rss=1 Lei, R. Qing, E. Odle, A. Yuan, M. Tan, T. J. C. So, N. Ouyang, W. O. Wilson, I. A. Gallagher, T. Perlman, S. Wu, N. C. Wong, L. Y. R. 2023-11-29 doi:10.1101/2023.11.28.569051 Cold Spring Harbor Laboratory Press 2023-11-29 <![CDATA[ Analysis of the Cross-Study Replicability of Tuberculosis Gene Signatures Using 49 Curated Transcriptomic Datasets ]]> https://biorxiv.org/content/10.1101/2023.12.01.569442v1?rss=1 Wang, X. Harper, K. Sinha, P. Johnson, W. E. Patil, P. 2023-12-01 doi:10.1101/2023.12.01.569442 Cold Spring Harbor Laboratory Press 2023-12-01 <![CDATA[ Inferring Disease Progressive Stages in Single-Cell Transcriptomics Using Weakly-Supervised Deep Learning Approach ]]> https://biorxiv.org/content/10.1101/2023.12.01.569595v1?rss=1 Wehbe, F. Yuen, S. Tanaka, Y. Kim, Y.-S. Adams, L. 2023-12-01 doi:10.1101/2023.12.01.569595 Cold Spring Harbor Laboratory Press 2023-12-01 <![CDATA[ Design of SARS-CoV-2 papain-like protease inhibitor with antiviral efficacy in a mouse model ]]> https://biorxiv.org/content/10.1101/2023.12.01.569653v1?rss=1 Tan, B. Zhang, X. Ansari, A. Jadhav, P. Tan, H. Li, K. Chopra, A. Ford, A. Chi, X. Figueras, F. R. Arnold, E. Deng, X. Wang, J. 2023-12-03 doi:10.1101/2023.12.01.569653 Cold Spring Harbor Laboratory Press 2023-12-03 <![CDATA[ MARK1 regulates dendritic spine morphogenesis and cognitive functions in vivo ]]> https://biorxiv.org/content/10.1101/2023.12.03.569757v1?rss=1 Kelly-Castro, E. C. Shear, R. Dindigal, A. H. Bhagwat, M. Zhang, H. 2023-12-05 doi:10.1101/2023.12.03.569757 Cold Spring Harbor Laboratory Press 2023-12-05 <![CDATA[ The Effect of Pseudoknot Base Pairing on Cotranscriptional Structural Switching of the Fluoride Riboswitch ]]> https://biorxiv.org/content/10.1101/2023.12.05.570056v1?rss=1 Hertz, L. M. White, E. N. Kuznedelov, K. Cheng, L. Yu, A. M. Kakkaramadam, R. Severinov, K. Chen, A. Lucks, J. B. 2023-12-05 doi:10.1101/2023.12.05.570056 Cold Spring Harbor Laboratory Press 2023-12-05 <![CDATA[ Hyper-specialized bamboo lemurs possess a reduced suite of xenobiotic-metabolizing cytochrome P450 genes. ]]> https://biorxiv.org/content/10.1101/2023.12.06.570463v1?rss=1 Chaney, M. E. Bergey, C. M. Tosi, A. J. 2023-12-08 doi:10.1101/2023.12.06.570463 Cold Spring Harbor Laboratory Press 2023-12-08 <![CDATA[ Characterization of Streptococcus uberis Cas9 (SuCas9) - a Type II-A Ortholog Functional in Human Cells ]]> https://biorxiv.org/content/10.1101/2023.12.11.571105v1?rss=1 Selkova, P. Vasileva, A. Arseniev, A. Abramova, M. Musharova, O. Malysheva, P. Khodorkovskii, M. Severinov, K. 2023-12-11 doi:10.1101/2023.12.11.571105 Cold Spring Harbor Laboratory Press 2023-12-11 <![CDATA[ Chewing Through Challenges: Exploring the Evolutionary Pathways to Wood-Feeding in Insects ]]> https://biorxiv.org/content/10.1101/2023.12.27.573094v1?rss=1 Beza-Beza, C. F. Wiegmann, B. M. Ware, J. A. Petersen, M. Gunter, N. Cole, M. E. Schwarz, M. Bertone, M. A. Young, D. Mikaelyan, A. 2023-12-28 doi:10.1101/2023.12.27.573094 Cold Spring Harbor Laboratory Press 2023-12-28 <![CDATA[ Reprogramming neuroblastoma by diet-enhanced polyamine depletion ]]> https://biorxiv.org/content/10.1101/2024.01.07.573662v1?rss=1 View larger version (64K): org.highwire.dtl.DTLVardef@1fdbaecorg.highwire.dtl.DTLVardef@fb03f4org.highwire.dtl.DTLVardef@1c0afa7org.highwire.dtl.DTLVardef@14c384f_HPS_FORMAT_FIGEXP M_FIG C_FIG Highlights- Extra-tumoral conversion of arginine feeds tumor ornithine via uptake from circulation in MYCN-neuroblastoma. - A proline and arginine free diet enhances pharmacological polyamine depletion via reduced ornithine substrate availability. - Polyamine depletion disrupts oncogenic translation to induce a pro-differentiation proteome causing neuroblast differentiation and prolonged survival in the TH-MYCN mouse model. - Genes of specific cellular programs have evolved codon usage preferences that enable coherent translational rewiring in response to metabolic stress, such as polyamine depletion. ]]> Cherkaoui, S. Yang, L. McBride, M. J. Turn, C. Lu, W. Eigenmann, C. Allen, G. E. Panasenko, O. O. Zhang, L. Vu, A. Liu, K. Li, Y. Gandhi, O. H. Surrey, L. Wierer, M. White, E. Rabinowitz, J. D. Hogarty, M. D. Morscher, R. J. 2024-01-08 doi:10.1101/2024.01.07.573662 Cold Spring Harbor Laboratory Press 2024-01-08 <![CDATA[ Identification of candidate genes controlling red seed coat color in cowpea (Vigna unguiculata Walp) ]]> https://biorxiv.org/content/10.1101/2024.01.08.574663v1?rss=1 Herniter, I. A. Munoz-Amatriain, M. Lo, S. Guo, Y.-N. Lonardi, S. Close, T. J. 2024-01-08 doi:10.1101/2024.01.08.574663 Cold Spring Harbor Laboratory Press 2024-01-08 <![CDATA[ SAFE-OPT: A Bayesian optimization algorithm for learning optimal deep brain stimulation parameters with safety constraints ]]> https://biorxiv.org/content/10.1101/2024.02.13.580142v1?rss=1 Cole, E. R. Connolly, M. Ghetiya, M. Sendi, M. Kashlan, A. Eggers, T. Gross, R. E. 2024-02-16 doi:10.1101/2024.02.13.580142 Cold Spring Harbor Laboratory Press 2024-02-16 <![CDATA[ Revealing nanoscale structure and interfaces of protein and polymer condensates via cryo-electron microscopy ]]> https://biorxiv.org/content/10.1101/2024.02.15.577400v1?rss=1 RIZVI, A. Favetta, B. Jaber, N. Lee, Y.-k. Jiang, J. Idris, N. Schuster, B. S. Dai, W. Patterson, J. P. 2024-02-16 doi:10.1101/2024.02.15.577400 Cold Spring Harbor Laboratory Press 2024-02-16 <![CDATA[ Tissue Tension and Strain as Indicators of Suction-mediated Cutaneous DNA Transfection: A Parametric Study ]]> https://biorxiv.org/content/10.1101/2024.02.15.580412v1?rss=1 Jhumur, N. C. Lallow, E. O. Nachtigal, C. Yeo, D. Kwon, I. Park, Y. K. Roberts, C. C. Zahn, J. D. Shreiber, D. I. Shan, J. W. Singer, J. P. Maslow, J. N. Lin, H. 2024-02-16 doi:10.1101/2024.02.15.580412 Cold Spring Harbor Laboratory Press 2024-02-16 <![CDATA[ Striatal Dopamine Can Enhance Learning, Both Fast and Slow, and Also Make it Cheaper ]]> https://biorxiv.org/content/10.1101/2024.02.14.580392v1?rss=1 Westbrook, A. van den Bosch, R. Hofmans, L. Papadopetraki, D. Maatta, J. I. Collins, A. G. E. Frank, M. J. Cools, R. 2024-02-17 doi:10.1101/2024.02.14.580392 Cold Spring Harbor Laboratory Press 2024-02-17 <![CDATA[ Local Delivery of Soluble Fractalkine (CX3CL1) Peptide Restore Ribbon Synapses After Noise-Induced Cochlear Synaptopathy ]]> https://biorxiv.org/content/10.1101/2024.02.20.581182v1?rss=1 Manickam, V. N. Maity, S. Murali, S. V. Gawande, D. Y. Stothert, A. R. Batalkina, L. V. Cardona, A. Kaur, T. 2024-02-23 doi:10.1101/2024.02.20.581182 Cold Spring Harbor Laboratory Press 2024-02-23 <![CDATA[ The Dorsal Column Nuclei Scales Mechanical Allodynia During Neuropathic Pain ]]> https://biorxiv.org/content/10.1101/2024.02.20.581208v1?rss=1 Upadhyay, A. Gradwell, M. A. Vajtay, T. J. Conner, J. Sayal, A. A. Azadegan, C. Patel, K. R. Thackray, J. K. Bohic, M. Imai, F. Ogundare, S. O. Yoshida, Y. Abdus-Saboor, I. Azim, E. Abraira, V. E. G. 2024-02-23 doi:10.1101/2024.02.20.581208 Cold Spring Harbor Laboratory Press 2024-02-23 <![CDATA[ Genetic polymorphisms of Leukocyte Immunoglobulin-Like Receptor B3 (LILRB3) gene in African American kidney transplant recipients are associated with post-transplant graft failure ]]> https://biorxiv.org/content/10.1101/2024.02.21.581383v1?rss=1 Sun, Z. Yi, Z. Wei, C. Wang, W. Cravedi, P. Tedla, F. Ward, S. C. Azeloglu, E. Schrider, D. R. Li, Y. Ali, S. Ren, T. Liu, S. Liang, D. Fu, J. Liu, T. Li, H. Xi, C. Vy, T. H. Mosoyan, G. Sun, Q. Kumar, A. Zhang, Z. Farouk, S. Campbell, K. Ochando, J. Lee, K. Coca, S. Xiang, J. Connolly, P. Gallon, L. Colvin, R. Menon, M. Nadkarni, G. He, J. C. Kraft, M. Jiang, X. Zhang, X. Zhang, W. Chen, S.-h. Heeger, P. Zhang, W. 2024-02-23 doi:10.1101/2024.02.21.581383 Cold Spring Harbor Laboratory Press 2024-02-23 <![CDATA[ RIPK3 coordinates RHIM domain-dependent inflammatory transcription in neurons ]]> https://biorxiv.org/content/10.1101/2024.02.29.582857v1?rss=1 Kofman, S. B. Chu, L. H. Ames, J. M. Chavarria, S. D. Lichauco, K. Daniels, B. P. Oberst, A. 2024-03-02 doi:10.1101/2024.02.29.582857 Cold Spring Harbor Laboratory Press 2024-03-02 <![CDATA[ Phosphatidic acid is an endogenous negative regulator of PIEZO2 channels and mechanical sensitivity ]]> https://biorxiv.org/content/10.1101/2024.03.01.582964v1?rss=1 Gabrielle, M. Yudin, Y. Wang, Y. Su, X. Rohacs, T. 2024-03-02 doi:10.1101/2024.03.01.582964 Cold Spring Harbor Laboratory Press 2024-03-02 <![CDATA[ Large-scale single-cell profiling of stem cells uncovers redundant regulators of shoot development and yield trait variation ]]> https://biorxiv.org/content/10.1101/2024.03.04.583414v1?rss=1 Xu, X. Passalacqua, M. Rice, B. Demesa-Arevalo, E. Kojima, M. Takebayashi, Y. Harris, B. Sakakibara, H. Gallavotti, A. Gillis, J. Jackson, D. 2024-03-06 doi:10.1101/2024.03.04.583414 Cold Spring Harbor Laboratory Press 2024-03-06 <![CDATA[ Off-target depletion of plasma tryptophan by allosteric inhibitors of BCKDK ]]> https://biorxiv.org/content/10.1101/2024.03.05.582974v1?rss=1 Bowman, C. E. Neinast, M. D. Jang, C. Patel, J. Blair, M. C. Mirek, E. T. Jonsson, W. O. Chu, Q. Merlo, L. Mandik-Nayak, L. Anthony, T. G. Rabinowitz, J. D. Arany, Z. 2024-03-11 doi:10.1101/2024.03.05.582974 Cold Spring Harbor Laboratory Press 2024-03-11 <![CDATA[ Pharmacological inhibition of macrophage triglyceride biosynthesis pathways does not improve Mycobacterium tuberculosis control in infected mice ]]> https://biorxiv.org/content/10.1101/2024.03.06.583745v1?rss=1 Castillo, J. R. Guerrini, V. Quijada, D. Karanika, S. Neupane, P. Harris, H. Garcia, A. Shenkoya, B. Yilma, A. Bailey, H. Khan, R. Gopalakrishnan, M. Gennaro, M. L. Karakousis, P. C. 2024-03-11 doi:10.1101/2024.03.06.583745 Cold Spring Harbor Laboratory Press 2024-03-11 <![CDATA[ Smad4 Loss in the Mouse Intestinal Epithelium Alleviates the Pathological Fibrotic Response to Injury in the Colon ]]> https://biorxiv.org/content/10.1101/2024.03.08.578000v1?rss=1 Hashemi, Z. Hui, T. Wu, A. Matouba, D. Zokowski, S. Nejati, S. Lim, C. Bruzzese, J. Seabold, K. Mills, C. Lin, C. Wrath, K. Wang, H. Wang, H. Verzi, M. P. Perekatt, A. 2024-03-12 doi:10.1101/2024.03.08.578000 Cold Spring Harbor Laboratory Press 2024-03-12 <![CDATA[ In vitro and in vivo validation of cwlM and pbpB essentiality for viability and resistance to imipenem in Mycobacterium abscessus ]]> https://biorxiv.org/content/10.1101/2024.03.08.584109v1?rss=1 Nuermberger, E. L. Lee, J. I. Li, S.-Y. Rifat, D. Kurepina, N. Chen, L. Kreiswirth, B. N. 2024-03-09 doi:10.1101/2024.03.08.584109 Cold Spring Harbor Laboratory Press 2024-03-09 <![CDATA[ A Trisomy 21-linked Hematopoietic Gene Variant in Microglia Confers Resilience in Human iPSC Models of Alzheimers Disease ]]> https://biorxiv.org/content/10.1101/2024.03.12.584646v1?rss=1 Jin, M. Ma, Z. Dang, R. Zhang, H. Xue, H. Pascual, J. Finkbeiner, S. Head, E. Liu, Y. Jiang, P. 2024-03-14 doi:10.1101/2024.03.12.584646 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ Stem rot affects the structure of rhizosphere microbiome in Berseem Clover (Trifolium alexandrinum) ]]> https://biorxiv.org/content/10.1101/2024.03.13.584667v1?rss=1 Mukhtar, S. Ahmad, Z. Khan, N. John, M. Aiysha, D. 2024-03-14 doi:10.1101/2024.03.13.584667 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ Structures of transcription-translation coupling complexes at each stage of the translation cycle ]]> https://biorxiv.org/content/10.1101/2024.03.13.584796v1?rss=1 Zhang, J. Lu, G. Zhou, W. Yang, M. Li, L. Shao, H. Zhou, X. Chen, C. Gao, Y. Ebright, R. H. Lin, J. Wang, C. 2024-03-14 doi:10.1101/2024.03.13.584796 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ Meiosis-specific functions of kinetochore protein SPC105R required for chromosome segregation in Drosophila oocytes ]]> https://biorxiv.org/content/10.1101/2024.03.14.585003v1?rss=1 Joshi, J. N. Changela, N. Mahal, L. Defosse, T. McKim, J. K. Wang, L.-I. Das, A. Shapiro, J. G. McKim, K. 2024-03-14 doi:10.1101/2024.03.14.585003 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ Scaled and Efficient Derivation of Loss of Function Alleles in Risk Genes for Neurodevelopmental and Psychiatric Disorders in Human iPSC ]]> https://biorxiv.org/content/10.1101/2024.03.18.585542v1?rss=1 Zhang, H. Peyton, L. L. McCarroll, A. G. Guerrerro, S. D. d. L. Zhang, S. Gowda, P. Sirkin, D. J. M. El Achwah, M. Duhe, A. Wood, W. G. Jamison, B. Tracy, G. Pollak, R. Hart, R. P. Pato, C. N. Mulle, J. G. Sanders, A. R. Pang, Z. P. Duan, J. 2024-03-19 doi:10.1101/2024.03.18.585542 Cold Spring Harbor Laboratory Press 2024-03-19 <![CDATA[ Role of Posterior Medial Thalamus in the Modulation of Striatal Circuitry and Choice Behavior ]]> https://biorxiv.org/content/10.1101/2024.03.21.586152v1?rss=1 Yonk, A. J. Linares-Garcia, I. Pasternak, L. Juliani, S. E. Gradwell, M. A. George, A. J. Margolis, D. J. 2024-03-27 doi:10.1101/2024.03.21.586152 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ EVOLUTIONARY CO-OPTION OF AN ANCESTRAL CLOACAL REGULATORY LANDSCAPE DURING THE EMERGENCE OF DIGITS AND GENITALS ]]> https://biorxiv.org/content/10.1101/2024.03.24.586442v1?rss=1 Hintermann, A. Bolt, C. C. Hawkins, M. B. Valentin, G. Lopez-Delisle, L. Gitto, S. Gomez, P. B. Mascrez, B. Mansour, T. A. Nakamura, T. Harris, M. P. Shubin, N. H. Duboule, D. 2024-03-27 doi:10.1101/2024.03.24.586442 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Dorsolateral septum GLP-1R neurons regulate feeding via lateral hypothalamic projections ]]> https://biorxiv.org/content/10.1101/2024.03.26.586855v1?rss=1 Lu, Y. Wang, L. Luo, F. Savani, R. Rossi, M. A. Pang, Z. P. 2024-03-27 doi:10.1101/2024.03.26.586855 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Spatio-temporal requirements of Aurora kinase A in mouse oocytes meiotic spindle building ]]> https://biorxiv.org/content/10.1101/2024.04.01.587547v1?rss=1 Blengini, C. S. Vaskovicova, M. Schier, J. Drutovic, D. Schindler, K. 2024-04-01 doi:10.1101/2024.04.01.587547 Cold Spring Harbor Laboratory Press 2024-04-01 <![CDATA[ Distal Protein-Protein Interactions Contribute to SARS-CoV-2 Main Protease Substrate Binding and Nirmatrelvir Resistance ]]> https://biorxiv.org/content/10.1101/2024.04.01.587566v1?rss=1 Lewandowski, E. M. Zhang, X. Tan, H. Jaskolka-Brown, A. Kohaal, N. Frazier, A. Madsen, J. J. Jacobs, L. M. C. Wang, J. Chen, Y. 2024-04-02 doi:10.1101/2024.04.01.587566 Cold Spring Harbor Laboratory Press 2024-04-02 <![CDATA[ Elevating levels of the endocannabinoid 2-arachidonoylglycerol blunts opioid reward but not analgesia ]]> https://biorxiv.org/content/10.1101/2024.04.02.585967v1?rss=1 Martinez-Rivera, A. Fetcho, R. Birmingham, L. Jiu, J. X. Yang, R. Foord, C. Scala-Chavez, D. Mekawy, N. Pleil, K. E. Pickel, V. M. Liston, C. Castorena, C. M. Levitz, J. Pan, Y.-X. Briand, L. A. Rajadhyaksha, A. M. Lee, F. S. 2024-04-02 doi:10.1101/2024.04.02.585967 Cold Spring Harbor Laboratory Press 2024-04-02 <![CDATA[ Functional activation of dorsal striatum astrocytes improves movement deficits in hemi-parkinsonian mice ]]> https://biorxiv.org/content/10.1101/2024.04.02.587694v1?rss=1 Evans, W. R. Baskar, S. S. Castro E Costa, A. R. Ravoori, S. Arigbe, A. Huda, R. 2024-04-02 doi:10.1101/2024.04.02.587694 Cold Spring Harbor Laboratory Press 2024-04-02 <![CDATA[ Orbitofrontal high-gamma reflects spike-dissociable value and decision mechanisms ]]> https://biorxiv.org/content/10.1101/2024.04.02.587758v1?rss=1 Sharma, D. Lupkin, S. M. McGinty, V. B. 2024-04-02 doi:10.1101/2024.04.02.587758 Cold Spring Harbor Laboratory Press 2024-04-02 <![CDATA[ Contributions of the Dachsous intracellular domain to Dachsous-Fat signaling ]]> https://biorxiv.org/content/10.1101/2024.04.03.587940v1?rss=1 Tripathi, B. K. Irvine, K. D. 2024-04-03 doi:10.1101/2024.04.03.587940 Cold Spring Harbor Laboratory Press 2024-04-03 <![CDATA[ Embryonic motor neuron programming factors reactivate immature gene expression and suppress ALS pathologies in postnatal motor neurons ]]> https://biorxiv.org/content/10.1101/2024.04.03.587963v1?rss=1 Lowry, E. R. Patel, T. Costa, J. A. Chang, E. Tariq, S. Melikyan, H. Davis, I. M. Aziz, S. Dermentzaki, G. Lotti, F. Wichterle, H. 2024-04-05 doi:10.1101/2024.04.03.587963 Cold Spring Harbor Laboratory Press 2024-04-05 <![CDATA[ PAK6 rescues pathogenic LRRK2-mediated ciliogenesis and centrosomal cohesion defects in a mutation-specific manner ]]> https://biorxiv.org/content/10.1101/2024.04.11.589075v1?rss=1 Iannotta, L. Fasiczka, R. Favetta, G. Zhao, Y. Giusto, E. Dall'Ara, E. Wei, J. Ho, F. Ciriani, C. Cogo, S. Tessari, I. Iaccarino, C. Liberelle, M. Bubacco, L. Taymans, J.-M. Manzoni, C. Kortholt, A. Civiero, L. Hilfiker, S. Lu, M. Greggio, E. 2024-04-14 doi:10.1101/2024.04.11.589075 Cold Spring Harbor Laboratory Press 2024-04-14 <![CDATA[ The longitudinal behavioral effects of acute exposure to galactic cosmic radiation in female C57BL/6J mice: implications for deep space missions, female crews, and potential antioxidant countermeasures ]]> https://biorxiv.org/content/10.1101/2024.04.12.588768v1?rss=1 Yun, S. Kiffer, F. C. Guzman, C. S. Soler, I. Bancroft, G. L. Haas, H. A. Shi, R. Patel, R. A. Lara-Jimenez, J. A. Kumar, P. L. Tran, F. H. Ahn, K. J. Rong, Y. Luitel, K. Shay, J. W. Eisch, A. J. 2024-04-15 doi:10.1101/2024.04.12.588768 Cold Spring Harbor Laboratory Press 2024-04-15 <![CDATA[ Affective Symptoms in Pregnancy are Associated with the Vaginal Microbiome ]]> https://biorxiv.org/content/10.1101/2024.04.12.589254v1?rss=1 Scheible, K. Beblavy, R. Sohn, M. B. Qiu, X. Gill, A. L. Narvaez miranda, J. Brunner, J. Miller, R. K. Barrett, E. S. O'Connor, T. G. Gill, S. 2024-04-12 doi:10.1101/2024.04.12.589254 Cold Spring Harbor Laboratory Press 2024-04-12 <![CDATA[ Molecular basis of foreign DNA recognition by BREX anti-phage immunity system ]]> https://biorxiv.org/content/10.1101/2024.04.12.589305v1?rss=1 Drobiazko, A. Adams, M. Skutel, M. Kristina, P. Matlashov, M. Maxwell, K. L. Blower, T. R. Severinov, K. Ghilarov, D. Isaev, A. 2024-04-12 doi:10.1101/2024.04.12.589305 Cold Spring Harbor Laboratory Press 2024-04-12 <![CDATA[ Atp1a2 and Kcnj9 are candidate genes underlying oxycodone behavioral sensitivity and withdrawal in C57BL/6 substrains ]]> https://biorxiv.org/content/10.1101/2024.04.16.589731v1?rss=1 Goldberg, L. R. Baskin, B. M. Adla, Y. Beierle, J. A. Kelliher, J. C. Yao, E. J. Kirkpatrick, S. L. Reed, E. R. Jenkins, D. F. Luong, A. M. Luttik, K. P. Scotellaro, J. A. Drescher, T. A. Crotts, S. B. Yazdani, N. Ferris, M. T. R. Johnson, W. E. Mulligan, M. K. Bryant, C. D. 2024-04-17 doi:10.1101/2024.04.16.589731 Cold Spring Harbor Laboratory Press 2024-04-17 <![CDATA[ Functional diversities within neurons and astrocytes in the adult rat auditory cortex revealed by single-nucleus RNA sequencing. ]]> https://biorxiv.org/content/10.1101/2024.04.16.589831v1?rss=1 Aydin, A. G. Lemenze, A. Bieszczad, K. M. 2024-04-20 doi:10.1101/2024.04.16.589831 Cold Spring Harbor Laboratory Press 2024-04-20 <![CDATA[ Polycystins recruit cargo to distinct ciliary extracellular vesicle subtypes ]]> https://biorxiv.org/content/10.1101/2024.04.17.588758v1?rss=1 Nikonorova, I. A. desRanleau, E. Jacobs, K. C. Saul, J. Walsh, J. D. Wang, J. Barr, M. M. 2024-04-18 doi:10.1101/2024.04.17.588758 Cold Spring Harbor Laboratory Press 2024-04-18 <![CDATA[ Prophage-encoded methyltransferase drives adaptation of community-acquired methicillin-resistant Staphylococcus aureus ]]> https://biorxiv.org/content/10.1101/2024.04.17.589803v1?rss=1 View larger version (26K): org.highwire.dtl.DTLVardef@b97d6forg.highwire.dtl.DTLVardef@1da30f1org.highwire.dtl.DTLVardef@1c34311org.highwire.dtl.DTLVardef@6834df_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Ulrich, R. J. Podkowik, M. Tierce, R. Irnov, I. Putzel, G. Samhadaneh, N. Lacey, K. A. Boff, D. Morales, S. M. Makita, S. Karagounis, T. K. Zwack, E. E. Zhou, C. Kim, R. Drlica, K. Pironti, A. van Bakel, H. Torres, V. J. Shopsin, B. 2024-04-17 doi:10.1101/2024.04.17.589803 Cold Spring Harbor Laboratory Press 2024-04-17 <![CDATA[ A conserved germline-specific Dsn1 alternative splice isoform supports oocyte and embryo development ]]> https://biorxiv.org/content/10.1101/2024.04.17.589883v1?rss=1 Ly, J. Blengini, C. S. Cady, S. Schindler, K. Cheeseman, I. M. 2024-04-18 doi:10.1101/2024.04.17.589883 Cold Spring Harbor Laboratory Press 2024-04-18 <![CDATA[ ProLLM: Protein Chain-of-Thoughts Enhanced LLM for Protein-Protein Interaction Prediction ]]> https://biorxiv.org/content/10.1101/2024.04.18.590025v1?rss=1 Jin, M. Haochen, X. Wang, Z. Kang, B. Ye, R. Zhou, K. Du, M. Zhang, Y. 2024-04-21 doi:10.1101/2024.04.18.590025 Cold Spring Harbor Laboratory Press 2024-04-21 <![CDATA[ Specific oncogene activation of the cell of origin in mucosal melanoma ]]> https://biorxiv.org/content/10.1101/2024.04.22.590595v1?rss=1 Babu, S. Chen, J. Robitschek, E. Baron, C. S. McConnell, A. Wu, C. Dedeilia, A. Sade-Feldman, M. Modhurima, R. Manos, M. P. Chen, K. Y. Cox, A. M. Ludwig, C. G. Yang, J. Kellis, M. Buchbinder, E. I. Hacohen, N. Boland, G. M. Abraham, B. J. Liu, D. Zon, L. I. Insco, M. L. 2024-04-26 doi:10.1101/2024.04.22.590595 Cold Spring Harbor Laboratory Press 2024-04-26 <![CDATA[ Sex differences in the functional network underpinnings of psychotic-like experiences in children ]]> https://biorxiv.org/content/10.1101/2024.04.22.590660v1?rss=1 Dhamala, E. Chopra, S. Ooi, L. Q. R. Rubio, J. M. Yeo, B. T. T. Malhotra, A. K. Holmes, A. J. 2024-04-23 doi:10.1101/2024.04.22.590660 Cold Spring Harbor Laboratory Press 2024-04-23 <![CDATA[ Imaging the large-scale and cellular cortical response to focal traumatic brain injury in mouse neocortex ]]> https://biorxiv.org/content/10.1101/2024.04.24.590835v1?rss=1 Bibineyshvili, Y. Vajtay, T. J. Salsabilian, S. Fliss, N. Suvarnakar, A. Fang, J. Teng, S. Alder, J. Najafizadeh, L. Margolis, D. J. 2024-04-25 doi:10.1101/2024.04.24.590835 Cold Spring Harbor Laboratory Press 2024-04-25 <![CDATA[ A dynamic compositional equilibrium governs mRNA recognition by eIF3 ]]> https://biorxiv.org/content/10.1101/2024.04.25.581977v1?rss=1 Ide, N. A. Gentry, R. C. Rudbach, M. A. Yoo, K. Velez, P. K. Communale, V. M. Hartwick, E. W. Kinz-Thompson, C. D. Gonzalez, R. L. Aitken, C. E. 2024-04-26 doi:10.1101/2024.04.25.581977 Cold Spring Harbor Laboratory Press 2024-04-26 <![CDATA[ APOE3-R136S mutation confers resilience against tau pathology via cGAS-STING-IFN inhibition ]]> https://biorxiv.org/content/10.1101/2024.04.25.591140v1?rss=1 Naguib, S. A. Torres, E. R. Lopez-Lee, C. Fan, L. Bhagwat, M. Norman, K. Lee, S.-I. Zhu, J. Ye, P. Wong, M. Y. Patel, T. Mok, S.-A. Luo, W. Sinha, S. Zhao, M. Gong, S. Gan, L. 2024-04-28 doi:10.1101/2024.04.25.591140 Cold Spring Harbor Laboratory Press 2024-04-28 <![CDATA[ A Conserved Inhibitory Interdomain Interaction Regulates DNA-binding Activities of Hybrid Two-component Systems in Bacteroides ]]> https://biorxiv.org/content/10.1101/2024.04.25.591157v1?rss=1 Gao, R. Wu, T. Stock, A. M. 2024-04-26 doi:10.1101/2024.04.25.591157 Cold Spring Harbor Laboratory Press 2024-04-26 <![CDATA[ Developmental origins of Parkinson's disease risk: perinatal exposure to the organochlorine pesticide dieldrin leads to sex-specific DNA modifications in critical neurodevelopmental pathways in the mouse midbrain ]]> https://biorxiv.org/content/10.1101/2024.04.26.590998v1?rss=1 Kochmanski, J. Virani, M. Kuhn, N. C. Boyd, S. L. Becker, K. Adams, M. Bernstein, A. I. 2024-04-29 doi:10.1101/2024.04.26.590998 Cold Spring Harbor Laboratory Press 2024-04-29 <![CDATA[ RIPK3 promotes neuronal survival by suppressing excitatory neurotransmission during CNS viral infection ]]> https://biorxiv.org/content/10.1101/2024.04.26.591333v1?rss=1 Estevez, I. Buckley, B. D. Panzera, N. Lindman, M. Chou, T.-W. McCourt, M. Vaglio, B. J. Atkins, C. Firestein, B. L. Daniels, B. P. 2024-04-28 doi:10.1101/2024.04.26.591333 Cold Spring Harbor Laboratory Press 2024-04-28 <![CDATA[ Mechanisms Of Meristem Maintenance By Maize Transcriptional Corepressors ]]> https://biorxiv.org/content/10.1101/2024.04.26.591374v1?rss=1 Gregory, J. Liu, X. Chen, Z. Gallardo, C. Punskovsky, J. Koslow, G. Galli, M. Gallavotti, A. 2024-04-29 doi:10.1101/2024.04.26.591374 Cold Spring Harbor Laboratory Press 2024-04-29 <![CDATA[ Design principles to tailor Hsp104 therapeutics ]]> https://biorxiv.org/content/10.1101/2024.04.26.591398v1?rss=1 View larger version (31K): org.highwire.dtl.DTLVardef@1520616org.highwire.dtl.DTLVardef@db3f5org.highwire.dtl.DTLVardef@1a1ae5eorg.highwire.dtl.DTLVardef@1beab7e_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Lin, J. Carman, P. J. Gambogi, C. W. Kendsersky, N. M. Chuang, E. Gates, S. N. Yokom, A. L. Rizo, A. N. Southworth, D. R. Shorter, J. 2024-04-28 doi:10.1101/2024.04.26.591398 Cold Spring Harbor Laboratory Press 2024-04-28 <![CDATA[ Genetic modification of the shikimate pathway to reduce lignin content in switchgrass (Panicum virgatum L.) significantly impacts plant microbiomes ]]> https://biorxiv.org/content/10.1101/2024.05.02.592240v1?rss=1 Liu, S. Chou, M.-Y. Benucci, G. M. N. Eudes, A. Bonito, G. 2024-05-03 doi:10.1101/2024.05.02.592240 Cold Spring Harbor Laboratory Press 2024-05-03 <![CDATA[ Protective role of parenthood on age-related brain function in mid- to late-life ]]> https://biorxiv.org/content/10.1101/2024.05.03.592382v1?rss=1 Orchard, E. R. Chopra, S. Ooi, L. Q. R. Chen, P. An, L. Jamadar, S. D. Yeo, B. T. T. Rutherford, H. J. V. Holmes, A. J. 2024-05-04 doi:10.1101/2024.05.03.592382 Cold Spring Harbor Laboratory Press 2024-05-04 <![CDATA[ Age-specific dynamics of neutralizing antibodies, cytokines, and chemokines in response to La Crosse virus infection in mice ]]> https://biorxiv.org/content/10.1101/2024.05.07.592956v1?rss=1 Alatrash, R. Herrera, B. B. 2024-05-07 doi:10.1101/2024.05.07.592956 Cold Spring Harbor Laboratory Press 2024-05-07 <![CDATA[ De novo genome assembly for an endangered lemur using portable nanopore sequencing in rural Madagascar ]]> https://biorxiv.org/content/10.1101/2024.05.09.591673v1?rss=1 Hauff, L. R. Rasoanaivo, N. E. Razafindrakoto, A. Ravelonjanahary, H. Wright, P. C. Rakotoarivony, R. Bergey, C. M. 2024-05-10 doi:10.1101/2024.05.09.591673 Cold Spring Harbor Laboratory Press 2024-05-10 <![CDATA[ Proteasome regulation of petite-negativity in fission yeast ]]> https://biorxiv.org/content/10.1101/2024.05.09.593392v1?rss=1 Amberg, K. L. Hao, L. Cranz-Mileva, S. Zaratiegui, M. 2024-05-14 doi:10.1101/2024.05.09.593392 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Multiple Unfolded Protein Response pathways cooperate to link cytosolic dsDNA release to Stimulator of Interferon Gene (STING) activation ]]> https://biorxiv.org/content/10.1101/2024.05.10.593557v1?rss=1 Hu, T. Liu, Y. Fleck, J. King, C. Schalk, E. Zhang, Z. Mehle, A. Smith, J. A. 2024-05-14 doi:10.1101/2024.05.10.593557 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Alternative splicing of clock transcript mediates the response of circadian clocks to temperature changes ]]> https://biorxiv.org/content/10.1101/2024.05.10.593646v1?rss=1 Cai, Y. D. Chow, G. K. Hidalgo, S. Liu, X. Jackson, K. C. Vasquez, C. D. Gao, Y. Z. Lam, V. H. Tabuloc, C. A. Zheng, H. Zhao, C. Chiu, J. C. 2024-05-12 doi:10.1101/2024.05.10.593646 Cold Spring Harbor Laboratory Press 2024-05-12 <![CDATA[ Two retrotransposon-derived capsid genes PNMA1 and PNMA4 maintain reproductive capacity ]]> https://biorxiv.org/content/10.1101/2024.05.11.592987v1?rss=1 Wood, T. W. P. Henriques, W. S. Cullen, H. B. Romero, M. Blengini, C. S. Sarathy, S. Sorkin, J. Bekele, H. Jin, C. Kim, S. Chemiakine, A. Khondker, R. Isola, J. V. V. Stout, M. Gennarino, V. A. Mogessie, B. Jain, D. Schindler, K. Suh, Y. Wiedenheft, B. Berchowitz, L. E. 2024-05-14 doi:10.1101/2024.05.11.592987 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Microbiota and metabolic adaptation shape Staphylococcus aureus virulence and antimicrobial resistance during intestinal colonization ]]> https://biorxiv.org/content/10.1101/2024.05.11.593044v1?rss=1 Zhou, C. Pawline, M. B. Pironti, A. Morales, S. M. Perault, A. I. Ulrich, R. J. Podkowik, M. J. Lejeune, A. DuMont, A. Stubbe, F.-X. Korman, A. Jones, D. R. Schluter, J. Richardson, A. R. Fey, P. D. Drlica, K. Cadwell, K. Torres, V. J. Shopsin, B. 2024-05-11 doi:10.1101/2024.05.11.593044 Cold Spring Harbor Laboratory Press 2024-05-11 <![CDATA[ Sexually dimorphic regulatory T cell-derived enkephalin imparts pregnancy-induced analgesia ]]> https://biorxiv.org/content/10.1101/2024.05.11.593442v1?rss=1 Midavaine, E. Moraes, B. C. Benitez, J. Rodriguez, S. R. Braz, J. M. Kochhar, N. P. Eckalbar, W. L. Domingos, A. I. Pintar, J. E. Basbaum, A. I. Kashem, S. W. 2024-05-14 doi:10.1101/2024.05.11.593442 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ WUSCHEL-dependent chromatin regulation in maize inflorescence development at single-cell resolution ]]> https://biorxiv.org/content/10.1101/2024.05.13.593957v1?rss=1 Bang, S. Zhang, X. Gregory, J. Chen, Z. Galli, M. Gallavotti, A. Schmitz, R. J. 2024-05-14 doi:10.1101/2024.05.13.593957 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Development of RT-RPA-based point-of-care tests for epidemic arthritogenic alphaviruses ]]> https://biorxiv.org/content/10.1101/2024.05.14.594209v1?rss=1 Sridhar, S. Tonto, P. B. LUMKONG, L. Herrera, B. B. 2024-05-14 doi:10.1101/2024.05.14.594209 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Reducing neuronal nitric oxide synthase (nNOS) expression in the ventromedial hypothalamus (VMH) increases body weight and blood glucose levels while decreasing physical activity in female mice. ]]> https://biorxiv.org/content/10.1101/2024.05.15.594324v1?rss=1 Hirschberg, P. R. Siegel, D. M. Sarkar, P. Routh, V. H. 2024-05-15 doi:10.1101/2024.05.15.594324 Cold Spring Harbor Laboratory Press 2024-05-15 <![CDATA[ Analyzing RNA-Seq Data from Chlamydia with Super Broad Transcriptomic Activation: Challenges, Solutions, and Implications for Other Systems ]]> https://biorxiv.org/content/10.1101/2024.05.16.594566v1?rss=1 Wan, D. Cheng, A. Wang, Y. Zhong, G. Li, V. W. Fan, H. 2024-05-21 doi:10.1101/2024.05.16.594566 Cold Spring Harbor Laboratory Press 2024-05-21 <![CDATA[ Imaging of porphyrin-specific fluorescence in pathogenic bacteria in vitro using a wearable, hands-free system ]]> https://biorxiv.org/content/10.1101/2024.05.20.595019v1?rss=1 Sun, J. Vellappan, S. Akdemir, J. Steier, L. Feinbloom, R. Yadavalli, S. S. 2024-05-20 doi:10.1101/2024.05.20.595019 Cold Spring Harbor Laboratory Press 2024-05-20 <![CDATA[ Astrocytic RIPK3 exerts protective anti-inflammatory activity during viral encephalitis via induction of serpin protease inhibitors. ]]> https://biorxiv.org/content/10.1101/2024.05.21.595181v1?rss=1 Lindman, M. Estevez, I. Marmut, E. DaPrano, E. M. Chou, T.-W. Newman, K. Atkins, C. O'Brown, N. M. Daniels, B. P. 2024-05-22 doi:10.1101/2024.05.21.595181 Cold Spring Harbor Laboratory Press 2024-05-22 <![CDATA[ Parkinson's disease-associated shifts between DNA methylation and DNA hydroxymethylation in human brain ]]> https://biorxiv.org/content/10.1101/2024.05.21.595193v1?rss=1 Choza, J. I. Virani, M. Kuhn, N. C. Adams, M. Kochmanski, J. Bernstein, A. I. 2024-05-22 doi:10.1101/2024.05.21.595193 Cold Spring Harbor Laboratory Press 2024-05-22 <![CDATA[ Comprehensive network modeling approaches unravel dynamic enhancer-promoter interactions across neural differentiation ]]> https://biorxiv.org/content/10.1101/2024.05.22.595375v1?rss=1 DeGroat, W. Inoue, F. Ashuach, T. Yosef, N. Ahituv, N. Kreimer, A. 2024-05-23 doi:10.1101/2024.05.22.595375 Cold Spring Harbor Laboratory Press 2024-05-23 <![CDATA[ A cortical locus for modulation of arousal states ]]> https://biorxiv.org/content/10.1101/2024.05.24.595859v1?rss=1 Chintalacheruvu, N. Kalelkar, A. Boutin, J. Breton-Provencher, V. Huda, R. 2024-05-26 doi:10.1101/2024.05.24.595859 Cold Spring Harbor Laboratory Press 2024-05-26 <![CDATA[ Suppression of autophagy induces senescence in the heart ]]> https://biorxiv.org/content/10.1101/2024.05.26.595978v1?rss=1 View larger version (26K): org.highwire.dtl.DTLVardef@dd3551org.highwire.dtl.DTLVardef@d78a85org.highwire.dtl.DTLVardef@c7505aorg.highwire.dtl.DTLVardef@16c84b6_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Zhai, P. Sung, E.-A. Shiheido-Watanabe, Y. Takayama, K. Tian, Y. Sadoshima, J. 2024-05-30 doi:10.1101/2024.05.26.595978 Cold Spring Harbor Laboratory Press 2024-05-30 <![CDATA[ Structural and Biophysical Dynamics of Fungal Plasma Membrane Proteins and Implications for Echinocandin Action in Candida glabrata ]]> https://biorxiv.org/content/10.1101/2024.05.29.596243v1?rss=1 Jiang, J. Keniya, M. V. Puri, A. Zhan, X. Cheng, J. Wang, H. Lin, G. Lee, Y.-K. Jaber, N. Hassoun, Y. Shor, E. Shi, Z. Lee, S.-H. Xu, M. Perlin, D. S. Dai, W. 2024-05-30 doi:10.1101/2024.05.29.596243 Cold Spring Harbor Laboratory Press 2024-05-30 <![CDATA[ Benzylic Trifluoromethyl Accelerates 1,6-Elimination Toward Rapid Probe Activation ]]> https://biorxiv.org/content/10.1101/2024.05.30.596105v1?rss=1 Wang, L. Sivakumar, A. Zhang, R. Cho, S. Kim, Y. Aggarwal, T. Wang, L. Izgu, E. C. 2024-06-01 doi:10.1101/2024.05.30.596105 Cold Spring Harbor Laboratory Press 2024-06-01 <![CDATA[ RESPIRATION DEFECTS LIMIT SERINE SYNTHESIS REQUIRED FOR LUNG CANCER GROWTH AND SURVIVAL ]]> https://biorxiv.org/content/10.1101/2024.05.28.596339v1?rss=1 View larger version (60K): org.highwire.dtl.DTLVardef@3dac07org.highwire.dtl.DTLVardef@e93401org.highwire.dtl.DTLVardef@555c48org.highwire.dtl.DTLVardef@1d7d31_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Cararo Lopes, E. Shi, F. Sawant, A. Ibrahim, M. Gomez-Jenkins, M. Hu, Z. S. Manchiraju, P. Bhatt, V. Wang, W. S. Hinrichs, C. C. Wallace, D. Su, X. D. Rabinowitz, J. Chan, C. Guo, J. Y. Ganesan, S. C. Lattime, E. White, E. 2024-06-02 doi:10.1101/2024.05.28.596339 Cold Spring Harbor Laboratory Press 2024-06-02 <![CDATA[ Transcription factor binding site divergence across maize inbred lines drives transcriptional and phenotypic variation ]]> https://biorxiv.org/content/10.1101/2024.05.31.596834v1?rss=1 Galli, M. Chen, Z. Ghandour, T. Chaudhry, A. Gregory, J. Li, M. Zhang, X. Dong, Y. Song, G. Walley, J. Chuck, G. Whipple, C. J. Kaeppler, H. F. Huang, S.-s. C. Gallavotti, A. 2024-06-03 doi:10.1101/2024.05.31.596834 Cold Spring Harbor Laboratory Press 2024-06-03 <![CDATA[ LRRK2 mediates haloperidol-induced changes in indirect pathway striatal projection neurons ]]> https://biorxiv.org/content/10.1101/2024.06.06.597594v1?rss=1 Chen, C. Masotti, M. Shepard, N. Promes, V. Tombesi, G. Arango, D. Manzoni, C. Greggio, E. Hilfiker, S. Kozorovitskiy, Y. Parisiadou, L. 2024-06-08 doi:10.1101/2024.06.06.597594 Cold Spring Harbor Laboratory Press 2024-06-08 <![CDATA[ Disruption of Core Stress Granule Protein Aggregates Promotes CNS Axon Regeneration ]]> https://biorxiv.org/content/10.1101/2024.06.07.597743v1?rss=1 Sahoo, P. K. Hanovice, N. Ward, P. Agrawal, M. A. Smith, T. P. SiMa, H. Dulin, J. N. Vaughn, L. S. Tuszynski, M. Welshhans, K. Benowitz, L. English, A. Houle, J. D. Twiss, J. L. 2024-06-08 doi:10.1101/2024.06.07.597743 Cold Spring Harbor Laboratory Press 2024-06-08 <![CDATA[ The Leader of the Capsid protein from Feline calicivirus must be palmitoylated and form oligomers through disulfide bonds for efficient viral replication ]]> https://biorxiv.org/content/10.1101/2024.06.07.597891v1?rss=1 Penaflor Tellez, Y. Gomez de la Madrid, J. Monge Celestino, E. I. Perez-Ibanez, C. Miguel Rodriguez, C. E. Gutierrez-Escolano, A. L. 2024-06-08 doi:10.1101/2024.06.07.597891 Cold Spring Harbor Laboratory Press 2024-06-08 <![CDATA[ Association of GLOD4 with Alzheimers Disease in Humans and Mice ]]> https://biorxiv.org/content/10.1101/2024.06.07.597934v1?rss=1 Utyro, O. Wloczkowska-Lapinska, O. Jakubowski, H. 2024-06-08 doi:10.1101/2024.06.07.597934 Cold Spring Harbor Laboratory Press 2024-06-08 <![CDATA[ Coral larvae employ nitrogen sequestration mechanisms to stabilize carbon provisioning from algal symbionts under increased temperature ]]> https://biorxiv.org/content/10.1101/2024.06.07.598017v1?rss=1 Huffmyer, A. S. Ashey, J. Strand, E. Chiles, E. Su, X. Putnam, H. M. 2024-06-08 doi:10.1101/2024.06.07.598017 Cold Spring Harbor Laboratory Press 2024-06-08 <![CDATA[ Alignment of multiple protein sequences without using amino acid frequencies. ]]> https://biorxiv.org/content/10.1101/2024.06.05.597668v1?rss=1 Shirokov, R. Shelyekhova, V. 2024-06-09 doi:10.1101/2024.06.05.597668 Cold Spring Harbor Laboratory Press 2024-06-09 <![CDATA[ Immune Checkpoint Blockade Delays Cancer and Extends Survival in Murine DNA Polymerase Mutator Syndromes ]]> https://biorxiv.org/content/10.1101/2024.06.10.597960v1?rss=1 View larger version (25K): org.highwire.dtl.DTLVardef@6cd159org.highwire.dtl.DTLVardef@243fd1org.highwire.dtl.DTLVardef@1d9da6borg.highwire.dtl.DTLVardef@192be51_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Sawant, A. Shi, F. Lopes, E. C. Hu, Z. Abdelfattah, S. Baul, J. Powers, J. Hinrichs, C. Rabinowitz, J. Chan, C. Lattime, E. Ganesan, S. White, E. 2024-06-12 doi:10.1101/2024.06.10.597960 Cold Spring Harbor Laboratory Press 2024-06-12 <![CDATA[ Mealtime alters daily rhythm in nuclear O-GlcNAcome to regulate hepatic gene expression ]]> https://biorxiv.org/content/10.1101/2024.06.13.598946v1?rss=1 Liu, X. Cai, Y. D. Mendiola, A. J. P. Xu, X. Luo, Y. Zheng, H. Zhao, C. Chen, C.-H. Xiang, Y. Chiu, J. C. 2024-06-17 doi:10.1101/2024.06.13.598946 Cold Spring Harbor Laboratory Press 2024-06-17 <![CDATA[ Adaptive Wheel Exercise for Mouse Models of Parkinson's Disease ]]> https://biorxiv.org/content/10.1101/2024.06.19.598025v1?rss=1 Skelton, H. M. Grogan, D. Kotlure, A. Berglund, K. Gutekunst, C.-A. Gross, R. 2024-06-23 doi:10.1101/2024.06.19.598025 Cold Spring Harbor Laboratory Press 2024-06-23 <![CDATA[ The Mammalian KU70 C-terminus SAP Domain Is Required to Repair Exogenous DNA Damage ]]> https://biorxiv.org/content/10.1101/2024.06.30.601420v1?rss=1 Wang, Y. Czap, M. Kim, H. Lu, H. Liu, J. Chang, Y. Romanienko, P. Montagna, C. Shen, Z. 2024-07-02 doi:10.1101/2024.06.30.601420 Cold Spring Harbor Laboratory Press 2024-07-02 <![CDATA[ SID-2 localises to extracellular vesicles in parasitic nematodes and does not function in environmental RNAi ]]> https://biorxiv.org/content/10.1101/2024.07.03.599821v1?rss=1 Blow, F. Jeffrey, K. Wang-Ngai Chow, F. Nikonorova, I. A. Barr, M. M. Cook, A. G. Prevo, B. Cheerambathur, D. K. Buck, A. H. 2024-07-03 doi:10.1101/2024.07.03.599821 Cold Spring Harbor Laboratory Press 2024-07-03 <![CDATA[ Phylogenetic analysis reveals how selection and mutation shape the coevolution of mRNA and protein abundances ]]> https://biorxiv.org/content/10.1101/2024.07.08.602411v1?rss=1 Cope, A. L. Schraiber, J. G. Pennell, M. 2024-07-11 doi:10.1101/2024.07.08.602411 Cold Spring Harbor Laboratory Press 2024-07-11 <![CDATA[ Diet-induced obesity mediated through Estrogen-Related Receptor α is independent of intestinal function ]]> https://biorxiv.org/content/10.1101/2024.07.10.602978v1?rss=1 Vemuri, K. Iqbal, J. Kumar, S. Logerfo, A. Verzi, M. P. 2024-07-16 doi:10.1101/2024.07.10.602978 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ Controlled and orthogonal partitioning of large particles into biomolecular condensates ]]> https://biorxiv.org/content/10.1101/2024.07.11.603072v1?rss=1 5 nm excluded from condensates. Here, we asked whether larger particles, such as macromolecular complexes, can partition into condensates based on particle-condensate interactions. We sought to discover the biophysical principles that govern particle inclusion in or exclusion from condensates using polymer nanoparticles with tailored surface chemistries as models of macromolecular complexes. Particles coated with polyethylene glycol (PEG) did not partition into condensates. We next leveraged the PEGylated particles as an inert platform to which we conjugated specific adhesive moieties. Particles functionalized with biotin partitioned into condensates containing streptavidin, driven by high-affinity biotin-streptavidin binding. Oligonucleotide-decorated particles exhibited varying degrees of partitioning into condensates, depending on condensate composition. Partitioning of oligonucleotide-coated particles was tuned by altering salt concentration, oligonucleotide length, and oligonucleotide surface density. Remarkably, beads with distinct surface chemistries partitioned orthogonally into immiscible condensates. Based on our experiments, we conclude that arbitrarily large particles can controllably partition into biomolecular condensates given sufficiently strong condensate-particle interactions, a conclusion also supported by our coarse-grained molecular dynamics simulations and theory. These findings may provide insights into how various cellular processes are achieved based on partitioning of large clients into biomolecular condensates, as well as offer design principles for the development of drug delivery systems that selectively target disease-related biomolecular condensates. Significance StatementBiomolecular condensates are subcellular compartments that selectively recruit or exclude client molecules, even though condensates lack an enclosing membrane. Many biochemical reconstitution experiments have investigated mechanisms by which membraneless organelles control partitioning, modeling how cells spatiotemporally recruit components into condensates to regulate cellular functions. One outstanding question is whether partitioning is strictly limited by client size. In this work, we engineered nanoparticles with various sizes and surface functionalities and measured how these variables determine partitioning. We observed controlled and orthogonal partitioning of large particles into several condensate types, driven by strong particle-condensate interactions. Molecular simulations recapitulated key results. Our work advances understanding of how condensate composition is regulated, and our nanoparticle toolbox may also inspire a platform for drug delivery. ]]> Kelley, F. Ani, A. Pinlac, E. Linders, B. Favetta, B. Barai, M. Ma, Y. Singh, A. Dignon, G. L. Gu, Y. Schuster, B. S. 2024-07-16 doi:10.1101/2024.07.11.603072 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ Characterizing the Spatial Distribution of Dendritic RNA at Single Molecule Resolution ]]> https://biorxiv.org/content/10.1101/2024.07.18.602927v1?rss=1 Kim, J. Rosario, J. Mendoza, E. Kuang, D. Kim, J. 2024-07-19 doi:10.1101/2024.07.18.602927 Cold Spring Harbor Laboratory Press 2024-07-19 <![CDATA[ Structural basis of long-range transcription-translation coupling ]]> https://biorxiv.org/content/10.1101/2024.07.20.604413v1?rss=1 Wang, C. Molodtsov, V. Kaelber, J. Blaha, G. Ebright, R. H. 2024-07-20 doi:10.1101/2024.07.20.604413 Cold Spring Harbor Laboratory Press 2024-07-20 <![CDATA[ The Physical Basis of Osmosis in a Donnan Ionic System ]]> https://biorxiv.org/content/10.1101/2024.07.22.604593v1?rss=1 Manning, G. S. 2024-07-23 doi:10.1101/2024.07.22.604593 Cold Spring Harbor Laboratory Press 2024-07-23 <![CDATA[ SLC45A4 encodes a mitochondrial putrescine transporter that promotes GABA de novo synthesis ]]> https://biorxiv.org/content/10.1101/2024.07.23.604788v1?rss=1 Colson, C. Wang, Y. Atherton, J. W. Su, X. 2024-07-24 doi:10.1101/2024.07.23.604788 Cold Spring Harbor Laboratory Press 2024-07-24 <![CDATA[ Endothelial TRPV4/Cx43 Signaling Complex Regulates Vasomotor Tone in Resistance Arteries ]]> https://biorxiv.org/content/10.1101/2024.07.25.604930v1?rss=1 Burboa, P. C. Gaete, P. Shu, P. Araujo, P. A. Beuve, A. Contreras, J. E. Duran, W. Lillo Gallardo, M. A. 2024-07-25 doi:10.1101/2024.07.25.604930 Cold Spring Harbor Laboratory Press 2024-07-25 <![CDATA[ EFMouse: a Matlab toolbox to model electric fields in the mouse brain ]]> https://biorxiv.org/content/10.1101/2024.07.25.605227v1?rss=1 Sanchez-Romero, R. Akyuz, S. Krekelberg, B. 2024-07-26 doi:10.1101/2024.07.25.605227 Cold Spring Harbor Laboratory Press 2024-07-26 <![CDATA[ Using DeepLabCut-Live to probe state dependent neural circuits of behavior with closed-loop optogenetic stimulation ]]> https://biorxiv.org/content/10.1101/2024.07.28.605489v1?rss=1 Gonzalez, M. Gradwell, M. A. Thackray, J. K. Patel, K. R. Temkar, K. K. Abraira, V. E. G. 2024-07-29 doi:10.1101/2024.07.28.605489 Cold Spring Harbor Laboratory Press 2024-07-29 <![CDATA[ Direct quantification of condensate material properties in live cells reveals the regulation of synapsin condensates viscoelasticity by alpha-synuclein ]]> https://biorxiv.org/content/10.1101/2024.07.28.605529v1?rss=1 Wang, H. Hoffmann, C. Tromm, J. V. Su, X. Elliott, J. Wang, H. Baum, J. Pang, Z. P. Milovanovic, D. Shi, Z. 2024-07-29 doi:10.1101/2024.07.28.605529 Cold Spring Harbor Laboratory Press 2024-07-29 <![CDATA[ Time-resolved tracking of cellulose biosynthesis and microfibril network assembly during cell wall regeneration in live Arabidopsis protoplasts ]]> https://biorxiv.org/content/10.1101/2024.07.29.605709v1?rss=1 Huh, H. Jayachandran, D. Sun, J. Irfan, M. Lam, E. Chundawat, S. P. S. Lee, S.-H. 2024-07-30 doi:10.1101/2024.07.29.605709 Cold Spring Harbor Laboratory Press 2024-07-30 <![CDATA[ Unraveling cysteine deficiency-associated rapid weight loss ]]> https://biorxiv.org/content/10.1101/2024.07.30.605703v1?rss=1 Varghese, A. Gusarov, I. Gamallo-Lana, B. Dolgonos, D. Mankan, Y. Shamovsky, I. Phan, M. Jones, R. Gomez-Jenkins, M. White, E. Wang, R. Jones, D. Papagiannakopoulos, T. Pacold, M. E. Mar, A. C. Littman, D. R. Nudler, E. 2024-07-31 doi:10.1101/2024.07.30.605703 Cold Spring Harbor Laboratory Press 2024-07-31 <![CDATA[ Sphingosine-1-phosphate receptor 3 activation promotes sociability and regulates the expression of genes associated with anxiolytic-like behavior ]]> https://biorxiv.org/content/10.1101/2024.07.31.606030v1?rss=1 Castro-Vildosola, J. Bryan, C.-A. Tajamal, N. Jonnalagadda, S. A. Kasturi, A. Tilly, J. Garcia, I. Kumar, R. Fried, N. T. Hala, T. Corbett, B. F. 2024-08-01 doi:10.1101/2024.07.31.606030 Cold Spring Harbor Laboratory Press 2024-08-01 <![CDATA[ Quantifying microbial fitness in high-throughput experiments ]]> https://biorxiv.org/content/10.1101/2024.08.20.608874v1?rss=1 Fink, J. W. Manhart, M. 2024-08-20 doi:10.1101/2024.08.20.608874 Cold Spring Harbor Laboratory Press 2024-08-20 <![CDATA[ Distinct checkpoint and homolog biorientation pathways regulate meiosis I in Drosophila oocytes ]]> https://biorxiv.org/content/10.1101/2024.08.21.608908v1?rss=1 Shapiro, J. G. Changela, N. Jang, J. K. Joshi, J. N. McKim, K. S. 2024-08-21 doi:10.1101/2024.08.21.608908 Cold Spring Harbor Laboratory Press 2024-08-21 <![CDATA[ Development of an optimized machine learning approach to enhance brain metastatic burden assessment in preclinical models. ]]> https://biorxiv.org/content/10.1101/2024.08.21.608131v1?rss=1 Rappaport, J. Chen, Q. McGuire, T. Daugherty-Lopes, A. Goldszmid, R. S. 2024-08-23 doi:10.1101/2024.08.21.608131 Cold Spring Harbor Laboratory Press 2024-08-23 <![CDATA[ BRAIN-METASTATIC MELANOMA MODELS UNCOVER IMMUNE AND MOLECULAR CORRELATES OF RESPONSE TO IMMUNOTHERAPY ]]> https://biorxiv.org/content/10.1101/2024.08.26.609785v1?rss=1 Daugherty-Lopes, A. Perez-Guijarro, E. Gopalan, V. Rappaport, J. Chen, Q. Huang, A. Lam, K. C. Chin, S. Ebersole, J. Wu, E. Needle, G. A. Church, I. Kyriakopoulos, G. Xie, S. Zaho, Y. Gruen, C. Sassano, A. Araya, R. E. Thorkelsson, A. Smith, C. Lee, M. P. Hannenhalli, S. Day, C.-P. Merlino, G. Goldszmid, R. S. 2024-08-28 doi:10.1101/2024.08.26.609785 Cold Spring Harbor Laboratory Press 2024-08-28 <![CDATA[ Impaired S-nitrosylation of Cx43 prevents arrhythmogenicity and myocardial injury upon cardiac stress in Duchenne Muscular Dystrophy ]]> https://biorxiv.org/content/10.1101/2024.08.29.610357v1?rss=1 Munoz, M. F. Quan, J. J. Nguyen, T. T. Nuno, J. Sheehy, A. Burboa, P. C. Gaete, P. S. Lillo, M. A. Contreras, J. E. 2024-08-30 doi:10.1101/2024.08.29.610357 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ Refining Brain Stimulation Therapies: An Active Learning Approach to Personalization ]]> https://biorxiv.org/content/10.1101/2024.09.02.610880v1?rss=1 Sendi, M. S. Core, E. Piallat, B. Ellis, C. A. Eggers, T. E. Laxpati, N. G. Mahmoudi, B. Gutekunst, C.-A. Devergnas, A. D. Mayberg, H. S. Gross, R. E. Calhoun, V. 2024-09-03 doi:10.1101/2024.09.02.610880 Cold Spring Harbor Laboratory Press 2024-09-03 <![CDATA[ The partitioning of fatty acids between membrane and storage lipids controls ER membrane expansion. ]]> https://biorxiv.org/content/10.1101/2024.09.05.611378v1?rss=1 Lysyganicz, P. K. Barbosa, A. D. Khondker, S. Stewart, N. A. Carman, G. M. Stansfeld, P. J. Dymond, M. K. Siniossoglou, S. 2024-09-05 doi:10.1101/2024.09.05.611378 Cold Spring Harbor Laboratory Press 2024-09-05 <![CDATA[ Community-wide interactions sustain life in geothermal spring habitats ]]> https://biorxiv.org/content/10.1101/2024.09.03.611078v1?rss=1 Stephens, T. G. Van Etten, J. McDermott, T. Christian, W. Chaverra, M. Gurney, J. Lee, Y. Kim, H. Cho, C. H. Chovancek, E. Westhoff, P. Otte, A. Northen, T. R. Bowen, B. P. Louie, K. B. Barry, K. Grigoriev, I. V. Mock, T. Liu, S.-L. Miyagishima, S.-y. Yoshinaga, M. Weber, A. Yoon, H. S. Bhattacharya, D. 2024-09-07 doi:10.1101/2024.09.03.611078 Cold Spring Harbor Laboratory Press 2024-09-07 <![CDATA[ Interference with Systemic Negative Feedback Regulation as a Potential Mechanism for Nonmonotonic Dose-Responses of Endocrine-Disrupting Chemicals ]]> https://biorxiv.org/content/10.1101/2024.09.04.611257v1?rss=1 Shi, Z. Xiao, S. Zhang, Q. 2024-09-08 doi:10.1101/2024.09.04.611257 Cold Spring Harbor Laboratory Press 2024-09-08 <![CDATA[ A blended genome and exome sequencing method captures genetic variation in an unbiased, high-quality, and cost-effective manner ]]> https://biorxiv.org/content/10.1101/2024.09.06.611689v1?rss=1 53,000 samples from the Populations Underrepresented in Mental Illness Associations Studies (PUMAS) Project, which included participants across African, African American, and Latin American populations. We evaluated the accuracy of BGE imputed genotypes against raw genotype calls from the Illumina Global Screening Array. All PUMAS cohorts had R2 concordance [≥]95% among SNPs with MAF[≥]1%, and never fell below [≥]90% R2 for SNPs with MAF<1%. Furthermore, concordance rates among local ancestries within two recently admixed cohorts were consistent among SNPs with MAF[≥]1%, with only minor deviations in SNPs with MAF<1%. We also benchmarked the discovery capacity of BGE to access protein-coding copy number variants (CNVs) against deep whole genome data, finding that deletions and duplications spanning at least 3 exons had a positive predicted value of [~]90%. Our results demonstrate BGE scalability and efficacy in capturing SNPs, indels, and CNVs in the human genome at 28% of the cost of deep whole-genome sequencing. BGE is poised to enhance access to genomic testing and empower genomic discoveries, particularly in underrepresented populations. ]]> Boltz, T. A. Chu, B. B. Liao, C. Sealock, J. M. Ye, R. Majara, L. Fu, J. M. Service, S. Zhan, L. Medland, S. E. Chapman, S. B. Rubinacci, S. DeFelice, M. Grimsby, J. L. Abebe, T. Alemayehu, M. Ashaba, F. K. Atkinson, E. G. Bigdeli, T. Bradway, A. B. Brand, H. Chibnik, L. B. Fekadu, A. Gatzen, M. Gelaye, B. Gichuru, S. Gildea, M. L. Hill, T. C. Huang, H. Hubbard, K. M. Injera, W. E. James, R. Joloba, M. Kachulis, C. Kalmbach, P. R. Kamulegeya, R. Kigen, G. Kim, S. Koen, N. Kwobah, E. K. Kyebuzibwa, J. Lee, S. Lennon, N. J. Lind, P. A. Lopera-Maya, E. 2024-09-09 doi:10.1101/2024.09.06.611689 Cold Spring Harbor Laboratory Press 2024-09-09 <![CDATA[ Ablation of LRP6 in alpha-smooth muscle actin-expressing cells abrogates lung inflammation and fibrosis upon bleomycin-induced lung injury ]]> https://biorxiv.org/content/10.1101/2024.09.05.611327v1?rss=1 Sung, E.-A. Dozmorov, M. G. Song, S. Aung, T. Park, M. H. Sime, P. J. Chae, W.-J. 2024-09-10 doi:10.1101/2024.09.05.611327 Cold Spring Harbor Laboratory Press 2024-09-10 <![CDATA[ The Importance of Nonsense Errors: Estimating the Rate and Implications of Drop-Off Errors during Protein Synthesis ]]> https://biorxiv.org/content/10.1101/2024.09.05.611510v1?rss=1 Cope, A. L. Pak, D. Gilchrist, M. A. 2024-09-10 doi:10.1101/2024.09.05.611510 Cold Spring Harbor Laboratory Press 2024-09-10 <![CDATA[ A bioengineered model of human placental exposure to environmental metals during pregnancy ]]> https://biorxiv.org/content/10.1101/2024.09.06.611636v1?rss=1 Fattahi, P. Younesi, M. Lee, W. D. Whang, K. Kang, T. Rabinowitz, J. D. Aleksunes, L. M. Huh, D. D. 2024-09-11 doi:10.1101/2024.09.06.611636 Cold Spring Harbor Laboratory Press 2024-09-11 <![CDATA[ Stochasticity in dietary restriction-mediated lifespan outcomes in Drosophila ]]> https://biorxiv.org/content/10.1101/2024.09.06.611756v1?rss=1 Mosley, O. L. Villa, J. A. Kamalakkannan, A. James, E. Hoffman, J. M. Lyu, Y. 2024-09-12 doi:10.1101/2024.09.06.611756 Cold Spring Harbor Laboratory Press 2024-09-12 <![CDATA[ Diversification and conservation of DNA binding specificities of SPL family of transcription factors ]]> https://biorxiv.org/content/10.1101/2024.09.13.612952v1?rss=1 View larger version (24K): org.highwire.dtl.DTLVardef@1154c42org.highwire.dtl.DTLVardef@1419f5borg.highwire.dtl.DTLVardef@1454a7aorg.highwire.dtl.DTLVardef@1cbd5f_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGRAPHICAL ABSTRACTC_FLOATNO C_FIG SQUAMOSA Promoter-Binding Protein-Like (SPL) transcription factors are key regulators of plant development and stress responses. Here, we present a comprehensive DNA affinity purification sequencing (DAP-seq) analysis of 14 of the 16 SPL members in Arabidopsis thaliana, revealing two major classes based on distinct DNA-binding motifs. Gene Ontology enrichment of target genes indicated both shared and specialized functions among AtSPLs, including roles in hormone signaling, metal ion homeostasis, and developmental transitions. Comparative analysis of closely related paralogs, AtSPL9 and AtSPL15, uncovered divergence in their genomic binding locations and target gene regulation, particularly in auxin and abscisic acid pathways. These differences were supported by motif analysis and protoplast reporter assays. Extending our study across species, we analyzed DAP-seq data from maize (Zea mays) and wheat (Triticum aestivum) SPL homologs, identifying conserved target genes but species-specific DNA motifs. Notably, wheat SPLs preferentially bind to longer, palindromic motifs distinct from the GTAC core motif in Arabidopsis. Using AlphaFold3 structure modeling, we show that these motif differences may arise from enhanced protein-protein interactions that stabilize dimeric binding. Our results highlight how SPL family members diversify through DNA-binding evolution and suggest that transcription factor dimerization contributes to motif complexity and regulatory specialization across plant genomes. ]]> Li, M. Yao, T. Galli, M. Lin, W. Zhou, Y. Chen, J.-G. Gallavotti, A. Huang, S.-s. C. 2024-09-16 doi:10.1101/2024.09.13.612952 Cold Spring Harbor Laboratory Press 2024-09-16 <![CDATA[ YAP/TAZ signaling in allantois-derived cells is required for placental vascularization ]]> https://biorxiv.org/content/10.1101/2024.09.15.613151v1?rss=1 Gao, S. Thillaikumaran, T. Dominguez, M. H. Giang, W. Hayes, K. Chen, X. Pace, J. Bockman, J. Jathan, D. Sung, D. C. Narayan, S. Frankfurter, M. Chen, M. Mericko, P. Yang, J. Castro, M. Potente, M. Kahn, M. 2024-09-16 doi:10.1101/2024.09.15.613151 Cold Spring Harbor Laboratory Press 2024-09-16 <![CDATA[ Exercise Evokes Retained Motor Performance without Neuroprotection in a Mouse Model of Parkinson's Disease ]]> https://biorxiv.org/content/10.1101/2024.09.20.614034v1?rss=1 Skelton, H. M. Hyman, N. Fernandez, A. Acerbo, E. Scott, M. Berglund, K. Gutekunst, C.-A. Gross, R. E. 2024-09-20 doi:10.1101/2024.09.20.614034 Cold Spring Harbor Laboratory Press 2024-09-20 <![CDATA[ Differential representations for affective and informative components of reward in the striatum and hippocampus ]]> https://biorxiv.org/content/10.1101/2024.09.20.614186v1?rss=1 Shen, X. Wang, S. Murty, V. P. Delgado, M. Smith, D. V. 2024-09-21 doi:10.1101/2024.09.20.614186 Cold Spring Harbor Laboratory Press 2024-09-21 <![CDATA[ Cohesin-mediated chromatin remodeling controls the differentiation and function of conventional dendritic cells ]]> https://biorxiv.org/content/10.1101/2024.09.18.613709v1?rss=1 Adams, N. M. Galitsyna, A. Tiniakou, I. Esteva, E. Lau, C. M. Reyes, J. Abdennur, N. Shkolikov, A. Yap, G. S. Khodadadi-Jamayran, A. Mirny, L. Reizis, B. 2024-09-22 doi:10.1101/2024.09.18.613709 Cold Spring Harbor Laboratory Press 2024-09-22 <![CDATA[ Organellular imaging in vivo reveals a depletion of endoplasmic reticular calcium during post-ictal cortical spreading depolarization ]]> https://biorxiv.org/content/10.1101/2024.09.21.614252v1?rss=1 Stern, M. A. Cole, E. R. Gutekunst, C.-A. Yang, J. J. Berglund, K. Gross, R. E. 2024-09-24 doi:10.1101/2024.09.21.614252 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ Framework for Martini-based Coarse-grained Model of Enzymes: Model Development and Experimental Validation ]]> https://biorxiv.org/content/10.1101/2024.09.22.614383v1?rss=1 Hooten, M. Murthy, S. Pal, N. Khare, S. Gormley, A. Dutt, M. 2024-09-24 doi:10.1101/2024.09.22.614383 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ Auditory decision-making deficits after permanent noise-induced hearing loss ]]> https://biorxiv.org/content/10.1101/2024.09.23.614535v1?rss=1 Berns, M. P. Nunez, G. M. Zhang, X. Chavan, A. Zemlianova, K. Mowery, T. M. Yao, J. D. 2024-09-24 doi:10.1101/2024.09.23.614535 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ The fate of pyruvate dictates cell growth by modulating cellular redox potential ]]> https://biorxiv.org/content/10.1101/2024.09.23.614588v1?rss=1 Toshniwal, A. G. Lam, G. Bott, A. J. Cluntun, A. Nam, H.-J. Skabelund, R. Wisidagama, D. R. Thummel, C. S. Rutter, J. 2024-09-24 doi:10.1101/2024.09.23.614588 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ Predicting bacterial fitness in Mycobacterium tuberculosis with transcriptional regulatory network-informed interpretable machine learning ]]> https://biorxiv.org/content/10.1101/2024.09.23.614645v1?rss=1 Bustad, E. Petry, E. Gu, O. Griebel, B. T. Rustad, T. R. Sherman, D. R. Yang, J. H. Ma, S. 2024-09-25 doi:10.1101/2024.09.23.614645 Cold Spring Harbor Laboratory Press 2024-09-25 <![CDATA[ Regulation of alternative polyadenylation isoforms of Timp2 is an effector event of RAS signaling in cell transformation ]]> https://biorxiv.org/content/10.1101/2024.09.26.613909v1?rss=1 Ai, Y. Ding, Q. Wan, Z. Tyagi, S. Indeglia, A. Murphy, M. Tian, B. 2024-09-26 doi:10.1101/2024.09.26.613909 Cold Spring Harbor Laboratory Press 2024-09-26 <![CDATA[ Evolution of tRNA pool shapes variation in selection on codon usage across the Saccharomycotina subphylu ]]> https://biorxiv.org/content/10.1101/2024.09.27.615277v1?rss=1 Cope, A. L. Shah, P. 2024-09-28 doi:10.1101/2024.09.27.615277 Cold Spring Harbor Laboratory Press 2024-09-28 <![CDATA[ Zebrafish glial-vascular interactions progressively expand over the course of brain development ]]> https://biorxiv.org/content/10.1101/2024.09.27.615488v1?rss=1 Gall, L. G. Stains, C. M. Freitas-Andrade, M. Jia, B. Z. Patel, N. Megason, S. G. Lacoste, B. O'Brown, N. M. 2024-09-30 doi:10.1101/2024.09.27.615488 Cold Spring Harbor Laboratory Press 2024-09-30 <![CDATA[ A heteromeric nicotinic acetylcholine receptor promotes sleep by relaying GABAergic signals within a locus of motor and sensory integration ]]> https://biorxiv.org/content/10.1101/2024.10.02.616374v1?rss=1 Yumita, T. Ahamed, H. Hatch, H. A. Cossentino, I. Louka, C. Stavropoulos, N. 2024-10-03 doi:10.1101/2024.10.02.616374 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ Gut Microbial Impact on Colitis and Colitis-Associated Carcinogenesis in a Primary Sclerosing Cholangitis-IBD Model ]]> https://biorxiv.org/content/10.1101/2024.10.03.616279v1?rss=1 Awoniyi, M. Meadows, V. Ngo, B. Conskuner, D. Montgomery, S. A. Farmer, M. Liu, B. Zhou, H. Roach, J. Stappenbeck, T. Sartor, B. 2024-10-03 doi:10.1101/2024.10.03.616279 Cold Spring Harbor Laboratory Press 2024-10-03 <![CDATA[ Blunted anterior midcingulate response to reward in opioid users is normalized by prefrontal transcranial magnetic stimulation ]]> https://biorxiv.org/content/10.1101/2024.10.03.616476v1?rss=1 Biernacki, K. Goldstein, R. Z. Guth, M. R. Alia-Klein, N. Ray, S. Baker, T. E. 2024-10-07 doi:10.1101/2024.10.03.616476 Cold Spring Harbor Laboratory Press 2024-10-07 <![CDATA[ Structural and molecular basis of FAN1 defects in promoting Huntington's disease ]]> https://biorxiv.org/content/10.1101/2024.10.07.617005v1?rss=1 Pluciennik, A. Li, F. Phadte, A. A. Bhatia, M. Barndt, S. Monte Carlo, A. R. Hou, C.-f. D. Yang, R. Strock, S. 2024-10-07 doi:10.1101/2024.10.07.617005 Cold Spring Harbor Laboratory Press 2024-10-07 <![CDATA[ DNA Polymerase Locks Replication Fork Under Stress ]]> https://biorxiv.org/content/10.1101/2024.10.09.617451v1?rss=1 Jia, X. Inman, J. T. Singh, A. Patel, S. S. Wang, M. D. 2024-10-10 doi:10.1101/2024.10.09.617451 Cold Spring Harbor Laboratory Press 2024-10-10 <![CDATA[ Antibody-Fab and -Fc features promote Mycobacterium tuberculosis restriction. ]]> https://biorxiv.org/content/10.1101/2024.10.07.617070v1?rss=1 Grace, P. S. Peters, J. M. Sixsmith, J. Lu, R. Fenderson, B. A. Vickers, A. Slein, M. D. Irvine, E. B. McKitrick, T. Wei, M.-H. Cummings, R. D. Wallace, A. Cavacini, L. Choudhary, A. K. Proulx, M. K. Sundling, C. Källenius, G. Reljic, R. Ernst, J. D. Casadevall, A. Locht, C. Pinter, A. Sassetti, C. M. Bryson, B. D. Fortune, S. M. Alter, G. 2024-10-11 doi:10.1101/2024.10.07.617070 Cold Spring Harbor Laboratory Press 2024-10-11 <![CDATA[ Privacy-Preserving Visualization of Brain Functional Connectivity ]]> https://biorxiv.org/content/10.1101/2024.10.11.617267v1?rss=1 Tao, Y. Sarwate, A. D. Panta, S. Plis, S. Calhoun, V. 2024-10-15 doi:10.1101/2024.10.11.617267 Cold Spring Harbor Laboratory Press 2024-10-15 <![CDATA[ Treadmill step training promotes corticospinal tract plasticity after incomplete spinal cord injury ]]> https://biorxiv.org/content/10.1101/2024.10.14.618099v1?rss=1 Eisdorfer, J. T. Nacht, H. D. Kowalski, T. Thackray, J. T. Martinez, A. M. Zymoro, L. Phu, M. V. Hirpara, R. R. Danish, B. S. Wang, R. Khondker, A. Eisdorfer, A. B. Tischfield, M. Abraira, V. E. G. 2024-10-16 doi:10.1101/2024.10.14.618099 Cold Spring Harbor Laboratory Press 2024-10-16 <![CDATA[ Torsion is a Dynamic Regulator of DNA Replication Stalling and Reactivation ]]> https://biorxiv.org/content/10.1101/2024.10.14.618227v1?rss=1 Jia, X. Gao, X. Zhang, S. Inman, J. T. Hong, Y. T. Singh, A. Patel, S. S. Wang, M. D. 2024-10-17 doi:10.1101/2024.10.14.618227 Cold Spring Harbor Laboratory Press 2024-10-17 <![CDATA[ A percolation-type criticality threshold controls immune protein coating of surfaces ]]> https://biorxiv.org/content/10.1101/2024.10.15.618530v1?rss=1 Wang, Z. Kulkarni, S. Nong, J. Zamora, M. E. Ebrahimimojarad, A. Hood, E. Shuvaeva, T. Zaleski, M. Gullipalli, D. Wolfe, E. Espy, C. Arguiri, E. Wang, Y. Marcos-Contreras, O. A. Song, W. Muzykantov, V. R. Fu, J. Radhakrishnan, R. Myerson, J. W. Brenner, J. S. 2024-10-18 doi:10.1101/2024.10.15.618530 Cold Spring Harbor Laboratory Press 2024-10-18 <![CDATA[ Phosphorylation Toggles the SARS-CoV-2 Nucleocapsid Protein Between Two Membrane-Associated Condensate States ]]> https://biorxiv.org/content/10.1101/2024.10.17.618867v1?rss=1 Favetta, B. Wang, H. Cubuk, J. Barai, M. Ramirez, C. Gormley, A. J. Murthy, S. Soranno, A. Shi, Z. Schuster, B. S. 2024-10-18 doi:10.1101/2024.10.17.618867 Cold Spring Harbor Laboratory Press 2024-10-18 <![CDATA[ Shared and unique lifetime stressor characteristics and brain networks predict adolescent anxiety and depression ]]> https://biorxiv.org/content/10.1101/2024.10.25.620373v1?rss=1 Qu, Y. Chopra, S. Qu, S. Cocuzza, C. V. Labache, L. Bauer, C. C. C. Morfini, F. Whitfield-Gabrieli, S. Slavich, G. M. Joormann, J. Holmes, A. J. 2024-10-26 doi:10.1101/2024.10.25.620373 Cold Spring Harbor Laboratory Press 2024-10-26 <![CDATA[ Soluble guanylyl cyclase, the NO-receptor, regulates endothelium-dependent vascular relaxation via its transnitrosation activity. ]]> https://biorxiv.org/content/10.1101/2024.10.28.620487v1?rss=1 Younis, W. Cui, C. Sadeghian, T. Burboa, P. Shu, P. Qin, Y. Xie, L. Lillo, M. Beuve, A. 2024-10-28 doi:10.1101/2024.10.28.620487 Cold Spring Harbor Laboratory Press 2024-10-28 <![CDATA[ Altered renal vascular patterning reduces ischemic kidney injury and limits vascular loss associated with aging ]]> https://biorxiv.org/content/10.1101/2024.10.29.620969v1?rss=1 McLarnon, S. R. Honeycutt, S. E. N'Guetta, P.-E. Y. Xiong, Y. Li, X. Abe, K. Kitai, H. Souma, T. O'Brien, L. 2024-11-01 doi:10.1101/2024.10.29.620969 Cold Spring Harbor Laboratory Press 2024-11-01 <![CDATA[ The Interaction Of Diet-Induced Obesity And Chronic Stress In A Mouse Model Of Menopause ]]> https://biorxiv.org/content/10.1101/2024.11.11.622997v1?rss=1 Knox, N. Yasrebi, A. Caramico, D. Wiersielis, K. Samuels, B. A. Roepke, T. A. 2024-11-12 doi:10.1101/2024.11.11.622997 Cold Spring Harbor Laboratory Press 2024-11-12 <![CDATA[ Deconstructing evolutionary histories of complex genomic rearrangements in lung malignancies ]]> https://biorxiv.org/content/10.1101/2024.11.11.623122v1?rss=1 Hu, X. Venkat, V. Riedlinger, G. Shen, Z. Malhotra, J. De, S. 2024-11-12 doi:10.1101/2024.11.11.623122 Cold Spring Harbor Laboratory Press 2024-11-12 <![CDATA[ Chronic variable mild stress alters the transcriptome and signaling properties of the anterodorsal bed nuceleus of the stria terminalis in a sex-dependent manner ]]> https://biorxiv.org/content/10.1101/2024.11.11.623087v1?rss=1 Degroat, T. J. Paladino, S. Samuels, B. A. Roepke, T. A. 2024-11-13 doi:10.1101/2024.11.11.623087 Cold Spring Harbor Laboratory Press 2024-11-13 <![CDATA[ Caveolin-1 and Aquaporin-4 as Mediators of Fibrinogen-Driven Cerebrovascular Pathology in Hereditary Cerebral Amyloid Angiopathy ]]> https://biorxiv.org/content/10.1101/2024.11.11.623066v1?rss=1 Singh, V. Rochakim, N. Ferraresso, F. Choudhury, A. Kastrup, C. J. Ahn, H. J. 2024-11-14 doi:10.1101/2024.11.11.623066 Cold Spring Harbor Laboratory Press 2024-11-14 <![CDATA[ The circadian gene Dec2 promotes pancreatic cancer dormancy by regulating tumor cell antigen presentation to facilitate immune evasion ]]> https://biorxiv.org/content/10.1101/2024.11.12.623005v1?rss=1 Harris, C. R. Wang, L. Dudgeon, C. Prela, O. Cazarin de Menezes, J. Shih, C.-H. Davidson, C. Casabianca, A. De, S. Narrow, W. Becker, J. Balachandran, V. Grandgenett, P. Grem, J. Hollingsworth, M. A. Kim, M. Hong, Y. Gerber, S. A. Vertino, P. M. Gao, C. Repesh, A. Klamer, Z. Hao, Y. Altman, B. J. Haab, B. B. Carpizo, D. R. 2024-11-15 doi:10.1101/2024.11.12.623005 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ Disruptive changes in tissue microenvironment prime oncogenic processes at different stages of carcinogenesis in lung ]]> https://biorxiv.org/content/10.1101/2024.11.12.623197v1?rss=1 Venkat, V. Hu, X. Biswas, A. Saxena, A. Malhotra, J. Riedlinger, G. De, S. 2024-11-15 doi:10.1101/2024.11.12.623197 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ Analysis of Categorical Data with Logistic Regression and the Cochran-Mantel-Haenszel Tests in Biological Experiments ]]> https://biorxiv.org/content/10.1101/2024.11.14.623695v1?rss=1 Androwski, R. J. Popovitchenko, T. Smart, A. J. Ogino, S. Wang, G. Rongo, C. Driscoll, M. Roy, J. 2024-11-15 doi:10.1101/2024.11.14.623695 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ Chlamydia plasmid-encoded protein Pgp2 is a replication initiator with a unique beta-hairpin necessary for iteron-binding and plasmid replication ]]> https://biorxiv.org/content/10.1101/2024.11.14.623704v1?rss=1 Wan, D. Pan, M. Zhong, G. Fan, H. 2024-11-15 doi:10.1101/2024.11.14.623704 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ Filling-in of the Blindspot is Multisensory ]]> https://biorxiv.org/content/10.1101/2024.11.15.623713v1?rss=1 Chan, A. Stiles, N. R. B. Levitan, C. A. Tanguay, A. R. Shimojo, S. 2024-11-15 doi:10.1101/2024.11.15.623713 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ Right posterior theta reflects human parahippocampal phase resetting by salient cues during goal-directed navigation ]]> https://biorxiv.org/content/10.1101/2024.11.16.623803v1?rss=1 Güth, M. R. Reid, A. Zhang, Y. Huntgeburth, S. C. Mill, R. D. Dagher, A. Kerns, K. Holroyd, C. B. Petrides, M. Cole, M. W. Baker, T. E. 2024-11-17 doi:10.1101/2024.11.16.623803 Cold Spring Harbor Laboratory Press 2024-11-17 <![CDATA[ Critical assessment of nanopore sequencing for the detection of multiple forms of DNA modifications ]]> https://biorxiv.org/content/10.1101/2024.11.19.624260v1?rss=1 Kong, Y. Zhang, Y. Mead, E. A. Chen, H. Loo, C. E. Fan, Y. Ni, M. Zhang, X.-S. Kohli, R. Fang, G. 2024-11-19 doi:10.1101/2024.11.19.624260 Cold Spring Harbor Laboratory Press 2024-11-19 <![CDATA[ Transcriptional landscape of the archaeal cell cycle is broadly conserved in eukaryotes ]]> https://biorxiv.org/content/10.1101/2024.11.20.624502v1?rss=1 Gomez-Raya-Vilanova, M. V. Teuliere, J. Medvedeva, S. Dai, Y. Corel, E. Lopez, P. Lapointe, F.-J. Bhattacharya, D. Haraoui, L.-P. Turc, E. Monot, M. Cvirkaite-Krupovic, V. Bapteste, E. Krupovic, M. 2024-11-20 doi:10.1101/2024.11.20.624502 Cold Spring Harbor Laboratory Press 2024-11-20 <![CDATA[ Integrative Computational Framework, Dyscovr, Links Mutated Driver Genes to Expression Dysregulation Across 19 Cancer Types ]]> https://biorxiv.org/content/10.1101/2024.11.20.624509v1?rss=1 View larger version (78K): org.highwire.dtl.DTLVardef@18ad7d9org.highwire.dtl.DTLVardef@610b3aorg.highwire.dtl.DTLVardef@1281c6aorg.highwire.dtl.DTLVardef@61af3d_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Geraghty, S. E. Boyer, J. A. Fazel-Zarandi, M. Arzouni, N. Ryseck, R.-P. McBride, M. J. Parsons, L. R. Rabinowitz, J. D. Singh, M. 2024-11-21 doi:10.1101/2024.11.20.624509 Cold Spring Harbor Laboratory Press 2024-11-21 <![CDATA[ OrthologAL: A Shiny application for quality-aware humanization of non-human pre-clinical high-dimensional gene expression data ]]> https://biorxiv.org/content/10.1101/2024.11.25.625000v1?rss=1 CHOWDARY, R. Suter, R. D'Antuono, M. Gomes, C. Stein, J. Lee, K. Lee, J. K. Ayad, N. G. 2024-11-26 doi:10.1101/2024.11.25.625000 Cold Spring Harbor Laboratory Press 2024-11-26 <![CDATA[ Synergistic Multi-Pronged Interactions Mediate the Effective Inhibition of Alpha-Synuclein Aggregation by the Chaperone HtrA1 ]]> https://biorxiv.org/content/10.1101/2024.11.25.624572v1?rss=1 Chinchilla, P. Wang, B. Lubin, J. H. Yang, X. Roth, J. A. Khare, S. D. Baum, J. 2024-11-28 doi:10.1101/2024.11.25.624572 Cold Spring Harbor Laboratory Press 2024-11-28 <![CDATA[ Human mitochondrial RNA polymerase structures reveal transcription start-site and slippage mechanism ]]> https://biorxiv.org/content/10.1101/2024.12.02.626445v1?rss=1 Shen, J. Goovaerts, Q. Ajjugal, Y. De Wijngaert, B. Das, K. Patel, S. S. 2024-12-02 doi:10.1101/2024.12.02.626445 Cold Spring Harbor Laboratory Press 2024-12-02 <![CDATA[ Bulk Transcriptomic Analysis with InMoose, the Integrated Multi-Omic Open-Source Environment in Python ]]> https://biorxiv.org/content/10.1101/2024.11.29.625982v1?rss=1 Colange, M. Appe, G. Meunier, L. Weill, S. Johnson, W. E. Nordor, A. Behdenna, A. 2024-12-03 doi:10.1101/2024.11.29.625982 Cold Spring Harbor Laboratory Press 2024-12-03 <![CDATA[ Alpha-synuclein knockout impairs melanoma development and alters DNA damage repair in the TG3 mouse model in a sex-dependent manner ]]> https://biorxiv.org/content/10.1101/2024.12.01.626256v1?rss=1 Arnold, M. R. Chen, S. Unni, V. K. 2024-12-05 doi:10.1101/2024.12.01.626256 Cold Spring Harbor Laboratory Press 2024-12-05 <![CDATA[ Prediction of peptide structural conformations with AlphaFold2 ]]> https://biorxiv.org/content/10.1101/2024.12.03.626727v1?rss=1 Ille, A. M. Markosian, C. Burley, S. K. Pasqualini, R. Arap, W. 2024-12-07 doi:10.1101/2024.12.03.626727 Cold Spring Harbor Laboratory Press 2024-12-07 <![CDATA[ A Label-free Nanowell-based Impedance Sensor for Ten-minute SARS-CoV-2 Detection ]]> https://biorxiv.org/content/10.1101/2024.12.11.627986v1?rss=1 View larger version (58K): org.highwire.dtl.DTLVardef@1a9f2a7org.highwire.dtl.DTLVardef@79d5acorg.highwire.dtl.DTLVardef@bb1bc1org.highwire.dtl.DTLVardef@1b5098_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Meng, Z. White, L. Xie, P. Mahmoodi, S. R. Karapiperis, A. Lin, H. Drazer, G. Javanmard, M. DeMauro, E. P. 2024-12-12 doi:10.1101/2024.12.11.627986 Cold Spring Harbor Laboratory Press 2024-12-12 <![CDATA[ Dynamics of β-cardiac myosin between the super-relaxed and disordered-relaxed states ]]> https://biorxiv.org/content/10.1101/2024.12.14.628474v1?rss=1 Cail, R. C. Baez-Cruz, F. A. Winkelmann, D. A. Goldman, Y. E. Ostap, E. M. 2024-12-14 doi:10.1101/2024.12.14.628474 Cold Spring Harbor Laboratory Press 2024-12-14 <![CDATA[ Extracellular Exosomal RNAs are Glyco-Modified ]]> https://biorxiv.org/content/10.1101/2024.12.17.628987v1?rss=1 Sharma, S. Jiao, X. Yang, J. Kiledjian, M. 2024-12-18 doi:10.1101/2024.12.17.628987 Cold Spring Harbor Laboratory Press 2024-12-18 <![CDATA[ Binding items to contexts through conjunctive neural representations with the Method of Loci ]]> https://biorxiv.org/content/10.1101/2024.12.19.629352v1?rss=1 Huang, J. Manglik, A. Dutra, N. Tarder-Stoll, H. Chamberlain, T. A. Ajemian, R. Zhang, Q. Norman, K. A. Baldassano, C. 2024-12-20 doi:10.1101/2024.12.19.629352 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ Marine fishes exhibit exceptional variation in biofluorescent emission spectra ]]> https://biorxiv.org/content/10.1101/2024.12.18.629237v1?rss=1 Carr, E. Thurman, M. Martin, R. Sparks, T. Sparks, J. 2024-12-21 doi:10.1101/2024.12.18.629237 Cold Spring Harbor Laboratory Press 2024-12-21 <![CDATA[ Evolutionary conserved reciprocal senescence and tumor suppressor signals limit lifetime cancer ]]> https://biorxiv.org/content/10.1101/2024.12.28.630560v1?rss=1 Liu, L. Davis, S. Yusuff, S. Strange, A. Zhuang, Y. Vaddi, P. Flaherty, K. Jara, K. Kramer, J. Archer, C. Lee, S. Gao, B. van Bokhoven, A. Wang, W. Pine, S. R. Nakamura, T. Sabaawy, H. E. 2024-12-29 doi:10.1101/2024.12.28.630560 Cold Spring Harbor Laboratory Press 2024-12-29 <![CDATA[ Bipolar and schizophrenia risk gene AKAP11 encodes an autophagy receptor coupling the regulation of PKA kinase network homeostasis to synaptic transmission ]]> https://biorxiv.org/content/10.1101/2024.12.30.630813v1?rss=1 Lee, Y.-K. Xiao, C. Zhou, X. Wang, L. McReynolds, M. G. Wu, Z. Purisic, E. Kim, H. Li, X. Pang, Z. P. Dai, J. Peng, J. Yang, N. Yue, Z. 2024-12-31 doi:10.1101/2024.12.30.630813 Cold Spring Harbor Laboratory Press 2024-12-31 <![CDATA[ MAIT cell deficiency exacerbates neuroinflammation in P301S human tau transgenic mice ]]> https://biorxiv.org/content/10.1101/2025.01.03.631124v1?rss=1 Zhang, Y. Yang, Z. Tan, X. Jiang, N. Cao, G. Yang, Q. 2025-01-03 doi:10.1101/2025.01.03.631124 Cold Spring Harbor Laboratory Press 2025-01-03 <![CDATA[ Zero-phase-delay connectivity increases the reliability, concordance with structure, and prognostic ability of functional connectivity metrics ]]> https://biorxiv.org/content/10.1101/2025.01.04.631256v1?rss=1 Mehra, C. Beyh, A. Laiou, P. Garces, P. Murphy, D. Loth, E. Dell' Acqua, F. Ewen, J. Richardson, M. O'Muircheartaigh, J. 2025-01-04 doi:10.1101/2025.01.04.631256 Cold Spring Harbor Laboratory Press 2025-01-04 <![CDATA[ Polymerase Eta Recruits FANCD2 to Common Fragile Sites to Maintain Genome Stability ]]> https://biorxiv.org/content/10.1101/2025.01.06.631600v1?rss=1 Niljikar, M. Barreto-Galvez, A. Patel, S. Gagliardi, J. E. Kumar, V. Pradeep, A. Juwarwala, A. Gerhardt, J. Chang, Y. Montagna, C. Madireddy, A. 2025-01-08 doi:10.1101/2025.01.06.631600 Cold Spring Harbor Laboratory Press 2025-01-08 <![CDATA[ CpgD is a phosphoglycerate cytidylyltransferase required for ceramide diphosphoglycerate synthesis ]]> https://biorxiv.org/content/10.1101/2025.01.09.632243v1?rss=1 Dhakephalkar, T. Guan, Z. Klein, E. A. 2025-01-10 doi:10.1101/2025.01.09.632243 Cold Spring Harbor Laboratory Press 2025-01-10 <![CDATA[ Epigenetic phase variation in the gut microbiome enhances bacterial adaptation ]]> https://biorxiv.org/content/10.1101/2025.01.11.632565v1?rss=1 Ni, M. Fan, Y. Liu, Y. Li, Y. Qiao, W. Davey, L. E. Zhang, X.-S. Ksiezarek, M. Mead, E. Touracheau, A. Jiang, W. Blaser, M. J. Valdivia, R. Fang, G. 2025-01-12 doi:10.1101/2025.01.11.632565 Cold Spring Harbor Laboratory Press 2025-01-12 <![CDATA[ Loss of Effort in Chronic Low-Back Pain Patients: Motivational Anhedonia in Chronic Pain ]]> https://biorxiv.org/content/10.1101/2025.01.09.632293v1?rss=1 Alldritt, S. Jammoul, M. Makary, M. Becker, S. Maeng, D. Keane, B. Zald, D. Geha, P. 2025-01-13 doi:10.1101/2025.01.09.632293 Cold Spring Harbor Laboratory Press 2025-01-13 <![CDATA[ Q-score as a reliability measure for protein, nucleic acid, and small molecule atomic coordinate models derived from 3DEM density maps ]]> https://biorxiv.org/content/10.1101/2025.01.14.633006v1?rss=1 Pintilie, G. Shao, C. Wang, Z. Hudson, B. P. Flatt, J. W. Schmid, M. F. Morris, K. L. Burley, S. K. Chiu, W. 2025-01-15 doi:10.1101/2025.01.14.633006 Cold Spring Harbor Laboratory Press 2025-01-15 <![CDATA[ Chronic social instability stress differentially affects the behavior and the transcriptome of the anterodorsal bed nucleus of the stria terminalis between male and female mice ]]> https://biorxiv.org/content/10.1101/2025.01.21.634142v1?rss=1 Degroat, T. J. Paladino, S. E. Denney, K. Moran, K. M. Samuels, B. A. Roepke, T. A. 2025-01-21 doi:10.1101/2025.01.21.634142 Cold Spring Harbor Laboratory Press 2025-01-21 <![CDATA[ Valosin-containing Protein is Cargo in Amyloid Precursor Protein Extracellular Vesicles ]]> https://biorxiv.org/content/10.1101/2025.01.20.633888v1?rss=1 Lue, Y. Abdullah, M. Healy, L. R. Tambini, M. D. 2025-01-22 doi:10.1101/2025.01.20.633888 Cold Spring Harbor Laboratory Press 2025-01-22 <![CDATA[ Selection and transmission of the gut microbiome alone shifts mammalian behavior ]]> https://biorxiv.org/content/10.1101/2025.01.21.634013v1?rss=1 Suzuki, T. A. Akbuga-Schon, T. Waters, J. L. Jakob, D. Vu, D. L. Ballinger, M. A. Di Rienzi, S. C. Chang, H. de Araujo, I. E. Tyakht, A. V. Ley, R. E. 2025-01-23 doi:10.1101/2025.01.21.634013 Cold Spring Harbor Laboratory Press 2025-01-23 <![CDATA[ Revisiting the cancer microbiome using PRISM ]]> https://biorxiv.org/content/10.1101/2025.01.21.634087v1?rss=1 Ghaddar, B. C. Blaser, M. J. De, S. 2025-01-24 doi:10.1101/2025.01.21.634087 Cold Spring Harbor Laboratory Press 2025-01-24 <![CDATA[ CD8+ T cells mediate vaccination-induced lymphatic containment of latent Mycobacterium tuberculosis infection following immunosuppression, while B cells are dispensable ]]> https://biorxiv.org/content/10.1101/2025.01.23.634479v1?rss=1 View larger version (26K): org.highwire.dtl.DTLVardef@151fdd6org.highwire.dtl.DTLVardef@1efed47org.highwire.dtl.DTLVardef@c2e7e0org.highwire.dtl.DTLVardef@555c7_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Miranda-Hernandez, S. Kumar, M. Henderson, A. Graham, E. Tan, X. Taylor, J. Meehan, M. Ceja, Z. del Pozo-Ramos, L. Pan, Y. Tsui, E. Donovan, M. L. Renteria, M. E. Flores-Valdez, M. A. Blumenthal, A. Nguyen, Q. Subbian, S. Field, M. A. Kupz, A. 2025-01-24 doi:10.1101/2025.01.23.634479 Cold Spring Harbor Laboratory Press 2025-01-24 <![CDATA[ Complex Water Networks Visualized through 2.2-2.3 Angstrom Cryogenic Electron Microscopy of RNA ]]> https://biorxiv.org/content/10.1101/2025.01.23.634578v1?rss=1 Kretsch, R. C. Li, S. Pintilie, G. Palo, M. Z. Case, D. A. Das, R. Zhang, K. Chiu, W. 2025-01-24 doi:10.1101/2025.01.23.634578 Cold Spring Harbor Laboratory Press 2025-01-24 <![CDATA[ Dynamic Reprogramming of Stromal Pdgfra-expressing cells during WNT-Mediated Transformation of the Intestinal Epithelium ]]> https://biorxiv.org/content/10.1101/2025.01.22.634326v1?rss=1 Pellon-Cardenas, O. Hassan, S. Fokas, E. He, P. Patel, I. Patel, J. Plotsker, O. Wu, A. Kumar, R. Akther, M. Logerfo, A. Wu, S. Wagner, D. Boffelli, D. Walton, K. D. Manieri, E. Tong, K. Spence, J. R. Bessman, N. J. Shivdasani, R. A. Verzi, M. P. 2025-01-25 doi:10.1101/2025.01.22.634326 Cold Spring Harbor Laboratory Press 2025-01-25 <![CDATA[ Complete genome sequence assembly elucidates evolution and regulation of 5S rDNA loci in the greater duckweed Spirodela polyrhiza ]]> https://biorxiv.org/content/10.1101/2025.01.26.634961v1?rss=1 60 copies of 5S rDNA repeat units with intergenic spacer (IGS) of 400 bp. The ChrSp13 locus is represented by 5S rDNA clusters of rRNA genes spaced by IGSs of 1,056 or 1,069 bp arranged in two sub-clusters, suggesting a different rate of repeat homogenization between loci. The G/C-rich 5S rDNA arrays in both loci are embedded in A/T-enriched chromosome regions with possible regulatory functions. The TATA-like boxes of the 5S rDNA repeat on ChrSp6 and ChrSp13 exhibit different affinities for the TATA-binding protein in 3D modeling of protein/DNA interactions, suggesting a locus-specific regulation of rRNA transcription. Our findings shed light on the molecular architecture of the 5S rDNA loci, which could foster an innovative era for the principles of evolution and regulation of rRNA genes in plants. ]]> Stepanenko, A. Schubert, V. Chen, G. Kishchenko, O. Michael, T. P. Lam, E. Hrmova, M. Schubert, I. Borisjuk, N. 2025-01-27 doi:10.1101/2025.01.26.634961 Cold Spring Harbor Laboratory Press 2025-01-27 <![CDATA[ Ancient origin of an urban underground mosquito ]]> https://biorxiv.org/content/10.1101/2025.01.26.634793v1?rss=1 1000 years, likely in concert with the rise of agricultural civilizations. Our results highlight the role of early human society in priming taxa for contemporary urban evolution and have important implications for understanding arbovirus transmission. ]]> Haba, Y. Aardema, M. L. Afonso, M. O. Agramonte, N. M. Albright, J. Alho, A. M. Almeida, A. P. G. Alout, H. Alten, B. Altinli, M. Amara Korba, R. Andreadis, S. S. Anghel, V. Arich, S. Arsenault-Benoit, A. Atyame, C. Aubry, F. Avila, F. W. Ayala, D. Azrag, R. S. Babayan, L. Bear, A. Becker, N. Bega, A. G. Bejarano, S. Ben-Avi, I. Benoit, J. B. Boubidi, S. C. Bradshaw, W. E. Bravo-Barriga, D. Bueno-Mari, R. Busic, N. Cabanova, V. Cabeje, B. Caputo, B. Cardo, M. V. Carpenter, S. Carreton, E. Chouaibou, M. S. Christian, M. Coetzee, M. Conner, W. R. Cornel, 2025-01-28 doi:10.1101/2025.01.26.634793 Cold Spring Harbor Laboratory Press 2025-01-28 <![CDATA[ Gut microbiota phospholipids regulate intestinal gene expression and can counteract the effects of antibiotic treatment ]]> https://biorxiv.org/content/10.1101/2025.01.28.633906v1?rss=1 Zhang, X.-S. Wang, Y. Sun, H. Zerbe, C. Falcone, E. Bhattacharya, S. Zhang, M. Gao, Z. Diaz-Rubio, M. E. Bharj, D. Patel, D. Pan, S. Ro, G. Grenard, J. Armstrong, A. Yin, Y. S. Dominguez-Bello, M. G. Holland, S. Su, X. Blaser, M. J. 2025-01-28 doi:10.1101/2025.01.28.633906 Cold Spring Harbor Laboratory Press 2025-01-28 <![CDATA[ The number of immune defense and counter-defense systems sustained in the arms race between procaryotes and viruses ]]> https://biorxiv.org/content/10.1101/2025.02.02.636159v1?rss=1 Ispolatov, Y. Lekontseva, A. Severinov, K. 2025-02-03 doi:10.1101/2025.02.02.636159 Cold Spring Harbor Laboratory Press 2025-02-03 <![CDATA[ Post-Ictal Gamma Oscillations Predict Hippocampal Structural Integrity in Mesial Temporal Lobe Epilepsy ]]> https://biorxiv.org/content/10.1101/2025.02.02.636164v1?rss=1 Valdivia, D. Tescarollo, F. Ercan, K. Huang, I. Vasquez, B. Parsonnet, L. S. Chung, S. Boison, D. Gross, R. E. Gleichgerrcht, E. Chen, S. C.-Y. Sun, H. 2025-02-03 doi:10.1101/2025.02.02.636164 Cold Spring Harbor Laboratory Press 2025-02-03 <![CDATA[ Identification of Antituberculars with Favorable Potency and Pharmacokinetics through Structure-Based and Ligand-Based Modeling ]]> https://biorxiv.org/content/10.1101/2025.02.03.636334v1?rss=1 Waradpande, V. Meng, F. Bozan, A. Graff, D. E. Fromer, J. C. Mughal, K. Mohideen, F. K. Shivangi, F. Paruchuri, S. Johnston, M. L. Sharma, P. Crea, T. R. Rudraraju, R. George, A. Folvar, C. Nelson, A. M. Neiditch, M. B. Zimmerman, M. D. Coley, C. W. Freundlich, J. S. 2025-02-04 doi:10.1101/2025.02.03.636334 Cold Spring Harbor Laboratory Press 2025-02-04 <![CDATA[ Disruption of Mitochondrial Dynamics and Stasis Leads to Liver Injury and Tumorigenesis ]]> https://biorxiv.org/content/10.1101/2025.02.11.637688v1?rss=1 Ma, X. Wei, X. Niu, m. Zhang, C. Peng, Z. Liu, W. Yan, J. Su, X. Lu, S. Cui, W. Sesaki, H. Zong, W.-X. Ni, H.-M. Ding, W.-X. 2025-02-12 doi:10.1101/2025.02.11.637688 Cold Spring Harbor Laboratory Press 2025-02-12 <![CDATA[ Circuit-Based Understanding of Fine Spatial Scale Clustering of Orientation Tuning in Mouse Visual Cortex ]]> https://biorxiv.org/content/10.1101/2025.02.11.637768v1?rss=1 20 {micro}m) are irregularly and randomly organized, while neuron pairs that are extremely close (< 20 {micro}m) have strongly correlated orientation tuning, indicating a narrow yet strong spatially clustered organization of orientation preference, which we term micro-clustered organization. Exploring a circuit-based model of recurrently coupled mouse V1 we derived two key predictions for the micro-cluster: spatially localized recurrent connections over a comparable narrow spatial scale, and common relative spatial spreads of balanced excitation and inhibition in the network over broad spatial scales. These predictions are validated by both anatomical and optogenetic-based physiological circuit mapping experiments. Altogether, our work takes an important step in building a circuit-based theory of visual processing in mouse V1 over spatial scales that are often ignored, yet contain powerful synaptic interactions. ]]> Yu, P. Yang, Y. Gozel, O. Oldenburg, I. Dipoppa, M. Rossi, F. Miller, K. Adesnik, H. Ji, N. Doiron, B. 2025-02-13 doi:10.1101/2025.02.11.637768 Cold Spring Harbor Laboratory Press 2025-02-13 <![CDATA[ Towards machine learning fairness in classifying multicategory causes of deaths in colorectal or lung cancer patients ]]> https://biorxiv.org/content/10.1101/2025.02.14.638368v1?rss=1 Feng, C. H. Deng, F. Disis, M. L. Gao, N. Zhang, L. 2025-02-19 doi:10.1101/2025.02.14.638368 Cold Spring Harbor Laboratory Press 2025-02-19 <![CDATA[ Dehalobacter converts 2,3-dichloroaniline to aniline via 2-chloroaniline in a methanogenic enrichment culture ]]> https://biorxiv.org/content/10.1101/2025.02.21.639126v1?rss=1 View larger version (38K): org.highwire.dtl.DTLVardef@5d59c4org.highwire.dtl.DTLVardef@b05a3aorg.highwire.dtl.DTLVardef@1f39f6borg.highwire.dtl.DTLVardef@1676753_HPS_FORMAT_FIGEXP M_FIG C_FIG Created in BioRender. Wang, S. (2025) https://BioRender.com/f47t993 ]]> Wang, S. Araujo, S. P. Lomheim, L. Mack, E. E. Edwards, E. A. Passeport, E. 2025-02-23 doi:10.1101/2025.02.21.639126 Cold Spring Harbor Laboratory Press 2025-02-23 <![CDATA[ Autophagy Suppresses CCL2 to Preserve Appetite and Prevent Lethal Cachexia ]]> https://biorxiv.org/content/10.1101/2025.02.20.638910v1?rss=1 Ibrahim, M. Gomez-Jenkins, M. Scheinfeld, A. Zhao, Z. Lopes, E. C. Sawant, A. Hu, Z. S. Dharani, A. Sun, M. Siddiqui, S. Mirek, E. T. Saliba, J. A. Lattime, E. Su, X. Janowitz, T. Goncalves, M. Dunn, S. Pritykin, Y. Anthony, T. Rabinowitz, J. White, E. 2025-02-24 doi:10.1101/2025.02.20.638910 Cold Spring Harbor Laboratory Press 2025-02-24 <![CDATA[ Structural Plasticity of RRE Stem-Loop II Modulates Nuclear Export of HIV-1 RNA ]]> https://biorxiv.org/content/10.1101/2025.02.20.639096v1?rss=1 Ojha, M. Hudson, L. Photenhauer, A. Zang, T. Lerew, L. Ekesan, S. Daniels, J. Nguyen, M. Paudyal, H. York, D. M. Ohi, M. D. Marchant, J. Bieniasz, P. D. Koirala, D. 2025-02-26 doi:10.1101/2025.02.20.639096 Cold Spring Harbor Laboratory Press 2025-02-26 <![CDATA[ The first chromosomal-level genome assembly of an allotetraploid oyster ]]> https://biorxiv.org/content/10.1101/2025.02.25.639704v1?rss=1 Li, A. Zhao, J. Zhao, M. Zhang, M. Huo, M. Deng, J. Wang, L. Wang, W. Qi, H. Li, Y. Li, X. Fu, J. Guo, X. Xu, Z. Li, L. Guo, X. Zhang, G. 2025-02-28 doi:10.1101/2025.02.25.639704 Cold Spring Harbor Laboratory Press 2025-02-28 <![CDATA[ Multi-scale structural similarity embedding search across entire proteomes ]]> https://biorxiv.org/content/10.1101/2025.02.28.640875v1?rss=1 Segura, J. Sanchez Garcia, R. Bittrich, S. Rose, Y. Burley, S. Duarte, J. 2025-03-06 doi:10.1101/2025.02.28.640875 Cold Spring Harbor Laboratory Press 2025-03-06 <![CDATA[ Assigning Targetable Molecular Pathways to Transdiagnostic Subgroups Across Autism and Related Neurodevelopmental Disorders ]]> https://biorxiv.org/content/10.1101/2025.03.04.641443v1?rss=1 Ellegood, J. Beauchamp, A. Yee, Y. Devenyi, G. Ziolkowski, J. Qiu, L. Askalan, R. Ayub, M. Suetterlin, P. Donovan, A. Basson, M. A. Quesnel, K. M. Berube, N. G. Woo, T. Beversdorf, D. Bjornsson, H. Blakely, R. Crawley, J. Crosbie, J. Orr, B. O. Davis, G. W. Genestine, M. DiCicco-Bloom, E. Egan, S. Fink, K. D. Asbury, S. Lai, J. Rilett, K. Foster, J. A. Vincent, J. B. Frankland, P. Georgiades, S. Penagarikano, O. Geschwind, D. Giger, R. J. Markx, S. Gogos, J. Golzio, C. Pagani, M. Gozzi, A. Pacey, L. K. Hampson, D. Huang, T.-N. Yen, T.-L. Hsueh, Y.-P. 2025-03-10 doi:10.1101/2025.03.04.641443 Cold Spring Harbor Laboratory Press 2025-03-10 <![CDATA[ APC loss promotes intestinal transformation through induction of bistable stem cell states ]]> https://biorxiv.org/content/10.1101/2025.03.06.641686v1?rss=1 Lengner, C. J. Li, N. Myers, R. L. Zhu, Q. Tian, Y. Durning, K. D. Wang, X. Leu, N. A. Rhoades, J. H. Bankler-Jukes, D. M. Monaghan, K. E. Adams-Tzivelekidis, S. Pomp, O. Pellon-Cardenas, O. Blanco, A. Verzi, M. Klein, P. S. 2025-03-11 doi:10.1101/2025.03.06.641686 Cold Spring Harbor Laboratory Press 2025-03-11 <![CDATA[ A cascade of structural rearrangements positions peptide release factor II for polypeptide hydrolysis on the ribosome ]]> https://biorxiv.org/content/10.1101/2025.03.09.642146v1?rss=1 Michael, N. Huang, B. Ray, K. K. Kinz-Thompson, C. D. Gonzalez, R. L. 2025-03-13 doi:10.1101/2025.03.09.642146 Cold Spring Harbor Laboratory Press 2025-03-13 <![CDATA[ Pollen DNA reveals urban cavity-nesting bees feed primarily on weeds and frequently nest in urban farms ]]> https://biorxiv.org/content/10.1101/2025.03.09.642154v1?rss=1 Turo, K. J. Richardson, R. T. Frabotta, M. Johnson, R. M. Gardiner, M. M. 2025-03-13 doi:10.1101/2025.03.09.642154 Cold Spring Harbor Laboratory Press 2025-03-13 <![CDATA[ Network geometry shapes multi-task representational transformations across human cortex ]]> https://biorxiv.org/content/10.1101/2025.03.14.643366v1?rss=1 Nallan Chakravarthula, L. Ito, T. Tzalavras, A. Cole, M. W. 2025-03-15 doi:10.1101/2025.03.14.643366 Cold Spring Harbor Laboratory Press 2025-03-15 <![CDATA[ Targeting Monoallelic CREBBP/EP300 Mutations in Germinal Center-Derived B-Cell Lymphoma with a First-in-Class Histone Acetyltransferase Activator ]]> https://biorxiv.org/content/10.1101/2025.03.13.642871v1?rss=1 Liu, Y. Piorczynski, T. B. Estrella, B. Ricker, E. C. Pazos, M. Gonzalez, Y. Tolu, S. S. Ryu Tiger, Y. K. Karan, C. Cremers, S. Nandakumar, R. Honig, B. Hwang, H. Kelleher, N. L. Camarillo, J. M. Abshiru, N. A. Amengual, J. E. 2025-03-17 doi:10.1101/2025.03.13.642871 Cold Spring Harbor Laboratory Press 2025-03-17 <![CDATA[ Microbiota promote enhanced CD39 expression in γδ intraepithelial lymphocytes through the activation of TCR and IL-15 signaling ]]> https://biorxiv.org/content/10.1101/2025.03.22.644616v1?rss=1 Alonso, S. Kaur, H. Jia, L. Nguyen, M.-U. Fong, A. Skariah, N. Argüello, R. J. Verzi, M. P. Swamy, M. Lau, K. S. Edelblum, K. L. 2025-03-25 doi:10.1101/2025.03.22.644616 Cold Spring Harbor Laboratory Press 2025-03-25 <![CDATA[ A common network of residue-residue contacts underlies peptides' interactions with MHC class II complex ]]> https://biorxiv.org/content/10.1101/2025.03.22.644772v1?rss=1 Kister, A. E. Kister, I. 2025-03-25 doi:10.1101/2025.03.22.644772 Cold Spring Harbor Laboratory Press 2025-03-25 <![CDATA[ Metaproteome analysis of the coral holobiont demonstrates algal symbiont dampening under thermal stress ]]> https://biorxiv.org/content/10.1101/2025.03.25.645042v1?rss=1 Nandi, S. Stephens, T. G. Chille, E. E. Goyen, S. Bay, L. K. Bhattacharya, D. 2025-03-26 doi:10.1101/2025.03.25.645042 Cold Spring Harbor Laboratory Press 2025-03-26 <![CDATA[ Male and Female Mice Are Similarly Susceptible to Chronic Nondiscriminatory Social Defeat Stress Despite Differences in Attack Frequency from Aggressor ]]> https://biorxiv.org/content/10.1101/2025.03.25.645316v1?rss=1 Bazer, A. Denney, K. Chacona, M. Montgomery, C. Vinod, S. Datta, U. Samuels, B. A. 2025-03-26 doi:10.1101/2025.03.25.645316 Cold Spring Harbor Laboratory Press 2025-03-26 <![CDATA[ siRNA Features - Reproducible Structure-Based Chemical Features for Off-Target Prediction ]]> https://biorxiv.org/content/10.1101/2025.03.24.645065v1?rss=1 Richter, M. Admasu, A. 2025-03-28 doi:10.1101/2025.03.24.645065 Cold Spring Harbor Laboratory Press 2025-03-28 <![CDATA[ Deletion of the voltage-gated calcium channel gene, CaV1.3, reduces Purkinje cell dendritic complexity without altering cerebellar-mediated eyeblink conditioning ]]> https://biorxiv.org/content/10.1101/2025.03.27.645586v1?rss=1 Klomp, A. Pace, M. Mehr, J. Arrieta, M. F. H. Hayes, C. Fleck, A. Heiney, S. Williams, A. J. 2025-03-29 doi:10.1101/2025.03.27.645586 Cold Spring Harbor Laboratory Press 2025-03-29 <![CDATA[ CHD7 binds to insulators during neuronal differentiation ]]> https://biorxiv.org/content/10.1101/2025.03.28.646031v1?rss=1 Qiu, J. Jadali, A. Martinez, E. Song, Z. Ni, J. Z. Kwan, K. Y. 2025-03-29 doi:10.1101/2025.03.28.646031 Cold Spring Harbor Laboratory Press 2025-03-29 <![CDATA[ Dynamic Ontogeny of Auditory Lateralization in the Zebra Finch ]]> https://biorxiv.org/content/10.1101/2025.03.30.646178v1?rss=1 Cataldo, B. F. Dadika, P. Vicario, D. 2025-03-31 doi:10.1101/2025.03.30.646178 Cold Spring Harbor Laboratory Press 2025-03-31 <![CDATA[ Computational Modeling of the Biphasic Depletion of Ovarian Follicle Reserve and the Chemical Effects on Ovarian Aging ]]> https://biorxiv.org/content/10.1101/2025.03.27.645815v1?rss=1 Moyd, S. A. Xiao, S. Gaskins, A. J. Zhang, Q. 2025-04-01 doi:10.1101/2025.03.27.645815 Cold Spring Harbor Laboratory Press 2025-04-01 <![CDATA[ SIRT7 links H3K36ac epigenetic regulation with genome maintenance in the aging mouse testis ]]> https://biorxiv.org/content/10.1101/2025.03.31.645534v1?rss=1 Guitart-Solanes, A. Romero, M. Fernanadez-Duran, I. Niedenberger, B. A. Madrid-Sandin, C. Roig, I. Geyer, C. B. Vaquero, A. Schindler, K. Vazquez, B. N. 2025-04-01 doi:10.1101/2025.03.31.645534 Cold Spring Harbor Laboratory Press 2025-04-01 <![CDATA[ CHD7 binds distinct regions in the Sox11 locus to regulate neuronal differentiation ]]> https://biorxiv.org/content/10.1101/2025.04.02.646816v1?rss=1 Martinez, E. Jadali, A. Qiu, J. Hinman, A. M. Ni, J. Z. Kim, J. Kwan, K. Y. 2025-04-03 doi:10.1101/2025.04.02.646816 Cold Spring Harbor Laboratory Press 2025-04-03 <![CDATA[ Crystallographic fragment screening of the dengue virus polymerase reveals multiple binding sites for the development of non-nucleoside antiflavivirals ]]> https://biorxiv.org/content/10.1101/2025.03.31.646453v1?rss=1 Saini, M. Aschenbrenner, J. C. Ruiz, F. X. Chopra, A. Chandran, A. V. Marples, P. G. Balcomb, B. H. Fearon, D. von Delft, F. Arnold, E. 2025-04-05 doi:10.1101/2025.03.31.646453 Cold Spring Harbor Laboratory Press 2025-04-05 <![CDATA[ Functional synaptic connectivity of engrafted spinal cord neurons with locomotor circuitry in the injured spinal cord ]]> https://biorxiv.org/content/10.1101/2025.04.05.644402v1?rss=1 Tucker, A. Eisdorfer, J. T. Thackray, J. K. Vo, K. Thomas, H. Tandon, A. Moses, J. Singletary, B. Gillespie, T. Smith, A. Pauken, A. Nadella, S. Pitonak, M. Letchuman, S. Jang, J. Totty, M. Jalufka, F. L. Aceves, M. Adler, A. F. Maren, S. Blackmon, H. McCreedy, D. A. Abraira, V. E. G. Dulin, J. N. 2025-04-05 doi:10.1101/2025.04.05.644402 Cold Spring Harbor Laboratory Press 2025-04-05 <![CDATA[ Optimizing Biophysical Large-Scale Brain Circuit Models With Deep Neural Networks ]]> https://biorxiv.org/content/10.1101/2025.04.07.647497v1?rss=1 Zeng, T. Tian, F. Zhang, S. Li, X. Tan, A. P. Larsen, B. Gur, R. C. Gur, R. E. Moore, T. M. Satterthwaite, T. D. Deco, G. Holmes, A. J. Yeo, B. T. T. 2025-04-07 doi:10.1101/2025.04.07.647497 Cold Spring Harbor Laboratory Press 2025-04-07 <![CDATA[ Plant silicon defence disrupts cryptic colouration in an insect herbivore by restricting carotenoid sequestration into the haemolymph ]]> https://biorxiv.org/content/10.1101/2025.04.02.646851v1?rss=1 Islam, T. Anwar, S. Cazzonelli, C. I. Moore, B. D. Johnson, S. N. 2025-04-08 doi:10.1101/2025.04.02.646851 Cold Spring Harbor Laboratory Press 2025-04-08 <![CDATA[ Novel hyperplastic expansion of white adipose tissue underlies the metabolically healthy obese phenotype of male LFABP null mice ]]> https://biorxiv.org/content/10.1101/2025.04.07.647661v1?rss=1 4-fold smaller and adipocyte number was 5-fold higher in the LFABP-/-. Transcriptomic analysis of SAT revealed that Lfabp deletion alters the expression of multiple pathways that modulate adipose expansion and function including cholesterol biosynthesis, adipogenesis, and extracellular matrix remodeling. LFABP is expressed in liver and small intestine but not in adipose tissues, thus its ablation may promote interorgan crosstalk that drives hyperplastic expansion of metabolically beneficial SAT, contributing to the healthy obese phenotype of the LFABP-/- mouse. ]]> Diolintzi, A. Zhou, Y. Fomina, A. Husain, S. Sidossis, L. S. Fried, S. K. Storch, J. 2025-04-08 doi:10.1101/2025.04.07.647661 Cold Spring Harbor Laboratory Press 2025-04-08 <![CDATA[ Regulation of airway fumarate by host and pathogen promotes S. aureus pneumonia ]]> https://biorxiv.org/content/10.1101/2025.04.10.647998v1?rss=1 Chen, Y.-T. Liu, Z. Fucich, D. Giulieri, S. G. Liu, Z. Wadhwa, R. Rios, G. Henschel, H. Tyagi, N. Olivier, F. A. B. Monk, I. R. Shah, S. S. Sridhar, S. H. Drikic, M. Bianco, C. Lohia, G. K. Beg, A. Z. Planet, P. J. Lewis, I. A. Sebra, R. Traven, A. Hachani, A. Stinear, T. P. Howden, B. Boyd, J. Riquelme, S. A. Wang, C. Prince, A. S. Wong, T. 2025-04-10 doi:10.1101/2025.04.10.647998 Cold Spring Harbor Laboratory Press 2025-04-10 <![CDATA[ Insights on Chamelea gallina growth dynamics from the Holocene climate optimum in the Northern Adriatic Sea (Italy) ]]> https://biorxiv.org/content/10.1101/2025.04.09.647857v1?rss=1 Cheli, A. Mancuso, A. Prada, F. Rojas, A. Falini, G. Goffredo, S. Scarponi, D. 2025-04-15 doi:10.1101/2025.04.09.647857 Cold Spring Harbor Laboratory Press 2025-04-15 <![CDATA[ Phospholipid Scramblases TMEM16F and Xkr8 regulate distinct features of Phosphatidylserine (PS) externalization and immune regulation in the tumor microenvironment to regulate tumor growth ]]> https://biorxiv.org/content/10.1101/2025.04.17.649445v1?rss=1 Birge, R. B. Gadiyar, V. Pulica, R. Aquib, A. Tranos, J. A. Varsanyi, C. Almansa, L. F. Gaspers, L. De Lorenzo, M. Kotenko, S. V. Tripathi, S. Howell, R. W. Choudhary, A. Calianese, D. C. 2025-04-18 doi:10.1101/2025.04.17.649445 Cold Spring Harbor Laboratory Press 2025-04-18 <![CDATA[ Pathological Mechanisms of Motor Dysfunction in Familial Danish Dementia: Insights from a Knock-In Rat Model ]]> https://biorxiv.org/content/10.1101/2025.04.15.649002v1?rss=1 Choudhury, A. Yesiltepe, M. Lashley, T. Singh, V. Yin, T. Fernandez, A. D'Adamio, L. Ahn, H. J. 2025-04-20 doi:10.1101/2025.04.15.649002 Cold Spring Harbor Laboratory Press 2025-04-20 <![CDATA[ Pre-existing YFV-17D immunity mediates T cell cross-protection against DENV-2 infection ]]> https://biorxiv.org/content/10.1101/2025.04.16.649113v1?rss=1 Tonto, P. B. Gallon, S. Alatrash, R. Wang, W.-K. Herrera, B. B. 2025-04-20 doi:10.1101/2025.04.16.649113 Cold Spring Harbor Laboratory Press 2025-04-20 <![CDATA[ The Magnitude of Telomere Shortening per Cell Division In Vivo: Implications for Lifelong Hematopoiesis in Humans ]]> https://biorxiv.org/content/10.1101/2025.04.16.649166v1?rss=1 Harris, J. R. Steenstrup, T. Aviv, A. 2025-04-21 doi:10.1101/2025.04.16.649166 Cold Spring Harbor Laboratory Press 2025-04-21 <![CDATA[ Population analysis and immunologic landscape of melanoma in people living with HIV ]]> https://biorxiv.org/content/10.1101/2025.04.17.648995v1?rss=1 Barger, L. N. Wang, D. Saravia, A. Mezzano, V. Ward, G. Loomis, C. Feldman, C. Tuluc, M. Seedor, R. S. Gaskill, P. J. Coghill, A. E. Suneja, G. Dehzangi, I. Hope, J. L. Romano, G. 2025-04-22 doi:10.1101/2025.04.17.648995 Cold Spring Harbor Laboratory Press 2025-04-22 <![CDATA[ SARS-CoV E protein couples asymmetric leaflet thickness and curvature deformations ]]> https://biorxiv.org/content/10.1101/2025.04.18.649534v1?rss=1 View larger version (43K): org.highwire.dtl.DTLVardef@196eec7org.highwire.dtl.DTLVardef@168b3borg.highwire.dtl.DTLVardef@eef5corg.highwire.dtl.DTLVardef@848526_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Sandberg, J. W. Brannigan, G. 2025-04-22 doi:10.1101/2025.04.18.649534 Cold Spring Harbor Laboratory Press 2025-04-22 <![CDATA[ NewroBus for the brain: humanized TfR1-targeting nanobodies with high BBB permeability and cargo transport capacity ]]> https://biorxiv.org/content/10.1101/2025.04.20.649139v1?rss=1 Yin, T. Yesiltepe, M. Metkar, S. Ramon, A. E. Greening, M. Sormanni, P. D'Adamio, L. 2025-04-24 doi:10.1101/2025.04.20.649139 Cold Spring Harbor Laboratory Press 2025-04-24 <![CDATA[ Chromosomal Aneuploidy in Normal, Non-Neuronal Brain Nuclei of Glioblastoma Patients is Not a Cancer Driver ]]> https://biorxiv.org/content/10.1101/2025.04.22.649812v1?rss=1 Montagna, C. Albert, O. Sun, S. Lin, J.-R. Lee, M. Chan, C. Maslov, A. Y. Ellerby, L. Huttner, A. Zhang, Z. Vijg, J. V. 2025-04-24 doi:10.1101/2025.04.22.649812 Cold Spring Harbor Laboratory Press 2025-04-24 <![CDATA[ Characterization of betacoronavirus HKU-1 and OC43 internal proteins using a prototypic coronavirus ]]> https://biorxiv.org/content/10.1101/2025.04.23.650176v1?rss=1 Gunawardene, C. D. Pandey, I. Chatterjee, S. Penaflor-Tellez, Y. Odle, A. Messyasz, A. Rajsbaum, R. Sariol, A. Wong, L.-Y. R. 2025-04-24 doi:10.1101/2025.04.23.650176 Cold Spring Harbor Laboratory Press 2025-04-24 <![CDATA[ Characterizing semantic compositions in the brain: A model-driven fMRI re-analysis ]]> https://biorxiv.org/content/10.1101/2025.04.25.650708v1?rss=1 non-meaningful phrases) to identify brain regions sensitive to semantic composition. However, such an approach is less apt at addressing how composition is carried out, namely what functions best characterize the integration of constituent concepts. To address this limitation, we rely on simple computational models to explicitly characterize alternative compositional operations, and use representational similarity analysis to compare the representations of models to those of target regions of interest within the general semantic network. To better target composition beyond specific task demands, we re-analyze fMRI data aggregated from four published studies (N = 85), all employing two-word combinations but differing in task requirements. Converging evidence from confirmatory and exploratory analyses reveals compositional representations in the pars triangularis of the left inferior frontal gyrus (BA45), even when analyses are restricted to a subset where the task did not require participants to actively engage in semantic processing. These results suggest that BA45 represents combinatorial information automatically across task demands, and further characterize these combinatorial representations as resulting from the (symmetric) intersection of constituent features. Additionally, a cluster of compositional representations emerges in the left middle superior temporal sulcus, while semantic, but not compositional, representations are observed in the left angular gyrus. Overall, our work clarifies which brain regions represent semantic information compositionally across different contexts and task demands, and qualifies which operations best describe composition. ]]> Ciapparelli, M. Marelli, M. Graves, W. Reverberi, C. 2025-04-29 doi:10.1101/2025.04.25.650708 Cold Spring Harbor Laboratory Press 2025-04-29 <![CDATA[ Basement Membrane Structural Integrity Dictates Trans-Tissue Deposition of Laminin in Mammals ]]> https://biorxiv.org/content/10.1101/2025.04.28.650774v1?rss=1 Miner, J. H. Omachi, K. Yurchenco, P. McKee, K. K. Lin, M.-H. Fujiwara, H. Puapatanakul, P. 2025-04-29 doi:10.1101/2025.04.28.650774 Cold Spring Harbor Laboratory Press 2025-04-29 <![CDATA[ Early-life Helicobacter pylori infection worsens metabolic state in mice receiving a high-fat diet ]]> https://biorxiv.org/content/10.1101/2025.04.27.650497v1?rss=1 Klove, S. Graversen, K. B. Agerbo Rasmussen, J. Assis, J. Schluter, J. Blaser, M. J. Andersen, S. B. 2025-04-30 doi:10.1101/2025.04.27.650497 Cold Spring Harbor Laboratory Press 2025-04-30 <![CDATA[ Imbalance in gut microbial interactions as a marker of health and disease ]]> https://biorxiv.org/content/10.1101/2025.04.30.651474v1?rss=1 Lopez, R. C. Bonachela, J. Bello, M. G. D. Manhart, M. Levin, S. Blaser, M. Munoz, M. A. 2025-04-30 doi:10.1101/2025.04.30.651474 Cold Spring Harbor Laboratory Press 2025-04-30 <![CDATA[ S2Tag, a novel affinity tag for the capture and immobilization of coiled-coil proteins: application to the study of human β-cardiac myosin ]]> https://biorxiv.org/content/10.1101/2025.05.01.651501v1?rss=1 Barua, B. Cail, R. C. Goldman, Y. E. Ostap, E. M. Winkelmann, D. A. 2025-05-02 doi:10.1101/2025.05.01.651501 Cold Spring Harbor Laboratory Press 2025-05-02 <![CDATA[ Mechanistic Insights into Human Antimicrobial Peptide-Induced Activation of a Broadly Conserved Bacterial Signaling System ]]> https://biorxiv.org/content/10.1101/2025.05.06.652532v1?rss=1 Adeleye, S. A. Mechesso, A. F. Mukherjee, A. Wang, G. Yadavalli, S. S. 2025-05-06 doi:10.1101/2025.05.06.652532 Cold Spring Harbor Laboratory Press 2025-05-06 <![CDATA[ Fertility recovery after combined adriamycin, bleomycin, vinblastine and dacarbazine chemotherapy in mice ]]> https://biorxiv.org/content/10.1101/2025.05.01.651671v1?rss=1 Lu, X. Turathum, B. Chian, R.-C. Liu, Y. 2025-05-07 doi:10.1101/2025.05.01.651671 Cold Spring Harbor Laboratory Press 2025-05-07 <![CDATA[ Resolving Inflammation: The Impact of Antiretroviral Therapy on Macrophage Traffic In and Out of the CNS. ]]> https://biorxiv.org/content/10.1101/2025.05.02.651872v1?rss=1 Wallis, Z. Midkiff, C. Zhao, M. Kim, S. O. Amadeck, A. Wang, Y. Jakubowski, M. Burdo, T. Miller, A. Li, Q. Alvarez, X. Blair, R. Williams, K. 2025-05-08 doi:10.1101/2025.05.02.651872 Cold Spring Harbor Laboratory Press 2025-05-08 <![CDATA[ A Mechanism Based Pharmacokinetic/Pharmacodynamic Analysis of Polymyxin B-Based Combination Therapy Against Carbapenem-Resistant Klebsiella pneumoniae Isolates with Diverse Phenotypic and Genotypic Resistance Mechanisms ]]> https://biorxiv.org/content/10.1101/2025.05.06.652358v1?rss=1 73% reduction in area under the bacterial load-versus-time curve for four isolates. The triple combination showed 67.7% reduction in non-carbapenamase producing isolate. This study demonstrates that a low dosing regimen of PMB can produce synergistic effects in combination therapy and might be effective in managing infections caused by CRKP, including PMB resistant isolates. Author summaryAntimicrobial resistance is a major concern in treating infectious diseases. CRKP bacterial isolates are resistant to most of the novel antimicrobial agents. One of the primary resistant mechanisms is restricting the permeability of drugs to the site of action. Polymyxin B, an antimicrobial agent, disrupts the bacterial outer membrane, enhancing the permeability of other drugs. When using combination therapy with polymyxin B, selecting drugs with different mechanisms of action is crucial to enhance synergistic effects and improve treatment efficacy. In our study we chose to evaluate the efficacy of meropenem and fosfomycin in double and triple combination therapies. Mechanism based models (MBMs) are the strongest tool to analyse the time course bacterial load data. Our study provides insights into applying available phenotypic and genotypic information to refine and enhance the accuracy of MBMs. Final model simulations revealed that low exposure of polymyxin B below the nephrotoxic threshold was sufficient to produce synergistic effects when combined with fosfomycin and meropenem. Additionally, we found that polymyxin B combination with fosfomycin was more effective compared to meropenem in treating CRKP. ]]> Mahadevan, R. Garcia, E. Sharma, R. Qiu, H. Elsheikh, A. Parambi, R. Abboud, C. S. Pasteran, F. Ramirez, M. S. Kaye, K. S. Bonomo, R. A. Rao, G. G. 2025-05-10 doi:10.1101/2025.05.06.652358 Cold Spring Harbor Laboratory Press 2025-05-10 <![CDATA[ Guiding clustering and annotation in single-cell RNA sequencing using the average overlap metric ]]> https://biorxiv.org/content/10.1101/2025.05.06.652497v1?rss=1 Thai, C. Singh, A. Herranz, D. Khiabanian, H. 2025-05-10 doi:10.1101/2025.05.06.652497 Cold Spring Harbor Laboratory Press 2025-05-10 <![CDATA[ Impact of maternal compensation on developmental phenotypes in a zebrafish model of severe congenital muscular dystrophy ]]> https://biorxiv.org/content/10.1101/2025.05.13.653769v1?rss=1 Flannery, K. P. Mowla, S. Battula, N. Clark, L. R. Liu, D. Oliveira, C. D. Venkatesan, C. Simhon, L. M. Karas, B. F. Terez, K. R. Burbano Lombana, D. Manzini, M. C. 2025-05-13 doi:10.1101/2025.05.13.653769 Cold Spring Harbor Laboratory Press 2025-05-13 <![CDATA[ DNA-methylation markers associated with lung function at birth and childhood reveal early life programming of inflammatory pathways ]]> https://biorxiv.org/content/10.1101/2025.05.12.653131v1?rss=1 Kachroo, P. Shutta, K. H. Maiorino, E. Moll, M. Hecker, J. Carey, V. J. McGeachie, M. J. Litonjua, A. A. Celedon, J. C. National Heart, Lung, and Blood Institute Trans-Omics for Precision Medicine (TOPMed) Consortium, Weiss, S. T. DeMeo, D. L. 2025-05-14 doi:10.1101/2025.05.12.653131 Cold Spring Harbor Laboratory Press 2025-05-14 <![CDATA[ Extracellular Matrix Physical Properties Regulate Cancer Cell Morphological Transitions in 3D Hydrogel Microtissues ]]> https://biorxiv.org/content/10.1101/2025.05.10.653220v1?rss=1 Pourmostafa, A. Uskach, G. Jafari, M. Yogeshwaran, S. Wood, T. L. Alisafaei, F. Miri, A. K. 2025-05-15 doi:10.1101/2025.05.10.653220 Cold Spring Harbor Laboratory Press 2025-05-15 <![CDATA[ The broccoli derivative sulforaphane extends lifespan by slowing the transcriptional aging clock ]]> https://biorxiv.org/content/10.1101/2025.05.11.653363v1?rss=1 Sedore, C. A. Segerdell, E. Coleman-Hulbert, A. L. Johnson, E. Levi, J. N. Lithgow, G. J. Driscoll, M. Phillips, P. C. 2025-05-15 doi:10.1101/2025.05.11.653363 Cold Spring Harbor Laboratory Press 2025-05-15 <![CDATA[ Narrowed host ranges do not constrain future host range expansion in RNA phage phi6 ]]> https://biorxiv.org/content/10.1101/2025.05.12.653482v1?rss=1 Andrews, T. Isaac, A. Duffy, S. 2025-05-15 doi:10.1101/2025.05.12.653482 Cold Spring Harbor Laboratory Press 2025-05-15 <![CDATA[ Sustained Glucose Turnover Flux Distinguishes Cancer Cachexia from Nutrient Limitation ]]> https://biorxiv.org/content/10.1101/2025.05.15.654370v1?rss=1 Kwon, Y. Y. Liang, Y. Gomez-Jenkins, M. Ahmed, M. Jiang, G. Hsiang, J. Lewis, D. Janowitz, T. Goncalves, M. D. White, E. Hui, S. 2025-05-20 doi:10.1101/2025.05.15.654370 Cold Spring Harbor Laboratory Press 2025-05-20 <![CDATA[ Signaling and Mechanics influence the number and size of epithelial rosettes in the migrating zebrafish Posterior Lateral Line primordium ]]> https://biorxiv.org/content/10.1101/2025.05.17.650326v1?rss=1 Mukherjee, A. Hilzendeger, M. Rinvelt, A. Fatma, S. Schupp, M. Dalle Nogare, D. Chitnis, A. 2025-05-20 doi:10.1101/2025.05.17.650326 Cold Spring Harbor Laboratory Press 2025-05-20 <![CDATA[ Viral infection induces oxylipin chemical signaling at the end of a summer upwelling bloom: implications for carbon cycling. ]]> https://biorxiv.org/content/10.1101/2025.05.18.654734v1?rss=1 Edwards, B. R. Thamatrakoln, K. Kranzler, C. F. Ossolinski, J. Fredricks, H. Johnson, M. D. Krause, J. W. Bidle, K. D. Van Mooy, B. 2025-05-23 doi:10.1101/2025.05.18.654734 Cold Spring Harbor Laboratory Press 2025-05-23 <![CDATA[ Rescuing Ischemic Brain Injury by Rewiring Mitochondrial Electron Flow ]]> https://biorxiv.org/content/10.1101/2025.05.19.650489v1?rss=1 Yoval-Sanchez, B. Guerrero, I. Sosunov, S. Chen, Q. Ansari, F. Siragusa, M. Konrad, C. Niatsetskaya, Z. Stepanova, A. Starkov, A. Khruschev, S. Magrane, J. Nikitina, A. A. Bereshchenko, O. Witting, I. Zhou, P. Zhou, L. Szibor, M. Manfredi, G. Gross, S. Ten, V. Galkin, A. 2025-05-23 doi:10.1101/2025.05.19.650489 Cold Spring Harbor Laboratory Press 2025-05-23 <![CDATA[ Amazon biodiversity is at risk from metal contamination due to mining activity ]]> https://biorxiv.org/content/10.1101/2025.05.21.654597v1?rss=1 Moulatlet, G. M. Capparelli, M. Thomas, C. Boyle, B. Feng, X. Frazier, A. Hinojo-Hinojo, C. Herrera, J. Nahomi, L. Lechner, A. Maitner, B. Newman, E. Nikolopoulos, E. Roehrdanz, P. Song, L. Valencia-Rodriguez, D. Yang, W. Merow, C. Silman, M. VIllalobos, F. Macklin, M. Enquist, B. J. 2025-05-26 doi:10.1101/2025.05.21.654597 Cold Spring Harbor Laboratory Press 2025-05-26 <![CDATA[ MACHINE LEARNING FOR MISSING DATA IMPUTATION IN ALZHEIMER'S RESEARCH: PREDICTING MEDIAL TEMPORAL LOBE FLEXIBILITY ]]> https://biorxiv.org/content/10.1101/2025.05.22.655574v1?rss=1 Moallemian, S. Saghafi, A. Deshpande, R. Perez, J. M. Budak, M. Fausto, B. A. Elahi, F. Gluck, M. A. 2025-05-27 doi:10.1101/2025.05.22.655574 Cold Spring Harbor Laboratory Press 2025-05-27 <![CDATA[ Cellular and subcellular specialization enables biology-constrained deep learning ]]> https://biorxiv.org/content/10.1101/2025.05.22.655599v1?rss=1 Galloni, A. R. Peddada, A. Chennawar, Y. Milstein, A. D. 2025-05-27 doi:10.1101/2025.05.22.655599 Cold Spring Harbor Laboratory Press 2025-05-27 <![CDATA[ Brain network dynamics reflect psychiatric illness status and transdiagnostic symptom profiles across health and disease ]]> https://biorxiv.org/content/10.1101/2025.05.23.655864v1?rss=1 Cocuzza, C. V. Chopra, S. Segal, A. Labache, L. Chin, R. Joss, K. Holmes, A. J. 2025-05-28 doi:10.1101/2025.05.23.655864 Cold Spring Harbor Laboratory Press 2025-05-28 <![CDATA[ A lineage-specific heat-induced feedback loop controls HrcA to promote chlamydial fitness under stress ]]> https://biorxiv.org/content/10.1101/2025.05.30.657042v1?rss=1 Huang, Y. Wang, Y. Pan, M. Wan, D. Wang, L. Fondell, J. D. Wu, X. Zhong, G. Fan, H. 2025-05-30 doi:10.1101/2025.05.30.657042 Cold Spring Harbor Laboratory Press 2025-05-30 <![CDATA[ The mGluR5 Agonist, CHPG, Enhances Numbers of Differentiated Human Oligodendrocytes ]]> https://biorxiv.org/content/10.1101/2025.05.31.656838v1?rss=1 Huang, Y. Geywitz, C. Bandaru, A. Glass, I. Birth Defects Research Laboratory, Schirmer, L. Nobuta, H. Dreyfus, C. 2025-06-01 doi:10.1101/2025.05.31.656838 Cold Spring Harbor Laboratory Press 2025-06-01 <![CDATA[ Primary tumor microbiomes predict distant metastasis of colorectal cancer ]]> https://biorxiv.org/content/10.1101/2025.06.02.654060v1?rss=1 Parajuli, B. Midya, V. Kiddle, R. De Jager, N. Eggers, S. Spakowicz, D. Hoyd, R. Salhia, B. Chan, C. H. Churchman, M. Rounbehler, R. J. Yao, S. Rutkowski, M. R. Tarhini, A. A. Mudaranthakam, D. P. Masood, A. Bocklage, T. J. Lentz, R. W. Hatoum, H. Ilozumba, M. N. Hardikar, S. Ulrich, C. M. Round, J. L. Riedlinger, G. Shriver, C. D. Bosch, D. E. 2025-06-05 doi:10.1101/2025.06.02.654060 Cold Spring Harbor Laboratory Press 2025-06-05 <![CDATA[ A myosin hypertrophic cardiomyopathy mutation disrupts the super-relaxed state and boosts contractility by enhanced actin attachment ]]> https://biorxiv.org/content/10.1101/2025.06.02.657466v1?rss=1 Cail, R. C. Barua, B. Baez-Cruz, F. A. Winkelmann, D. A. Goldman, Y. E. Ostap, E. M. 2025-06-06 doi:10.1101/2025.06.02.657466 Cold Spring Harbor Laboratory Press 2025-06-06 <![CDATA[ Cardiac fibroblasts counterbalance cardiomyocytes in LMNA cardiomyopathy pathogenesis ]]> https://biorxiv.org/content/10.1101/2025.06.05.657412v1?rss=1 Sikder, K. Phillips, E. Bouhrira, N. Mothy, D. Wang, N. Bonne, G. Margulies, K. B. Choi, J. C. 2025-06-06 doi:10.1101/2025.06.05.657412 Cold Spring Harbor Laboratory Press 2025-06-06 <![CDATA[ Convergent and divergent brain-cognition relationships during development revealed by cross-sectional and longitudinal analyses in the ABCD Study ]]> https://biorxiv.org/content/10.1101/2025.06.06.658294v1?rss=1 Yeo, T. Xie, Y. Zhang, S. Orban, C. Ooi, L. Q. R. Kong, R. Floris, D. L. Zuo, X.-N. Dhamala, E. Holmes, A. J. Uddin, L. Q. Nichols, T. E. Di Martino, A. 2025-06-07 doi:10.1101/2025.06.06.658294 Cold Spring Harbor Laboratory Press 2025-06-07 <![CDATA[ Biological consequences of asymmetric hop diffusion in the cell membrane ]]> https://biorxiv.org/content/10.1101/2025.06.04.657947v1?rss=1 Hall, D. 2025-06-08 doi:10.1101/2025.06.04.657947 Cold Spring Harbor Laboratory Press 2025-06-08 <![CDATA[ Inflammasome activation differences underpin different Mycobacterium tuberculosis infection outcomes ]]> https://biorxiv.org/content/10.1101/2025.06.06.658135v1?rss=1 Kumar, R. Kolloli, A. Bhargavi, G. Husain, S. Ghanny, S. Soteropoulos, P. Subbian, S. 2025-06-09 doi:10.1101/2025.06.06.658135 Cold Spring Harbor Laboratory Press 2025-06-09 <![CDATA[ Dendritic cell-intrinsic TLR/MyD88 signaling promotes the clearance of a live-attenuated oral vaccine ]]> https://biorxiv.org/content/10.1101/2025.06.09.658568v1?rss=1 He, Y. Abdelsalam, A. M. Li, C. Liu, Z. Fan, H. Zhong, G. 2025-06-11 doi:10.1101/2025.06.09.658568 Cold Spring Harbor Laboratory Press 2025-06-11 <![CDATA[ Mycobacterium tuberculosis effector protein PE5 hijacks the host CRL2 ubiquitin ligase complex ]]> https://biorxiv.org/content/10.1101/2025.06.11.659056v1?rss=1 Madduri, B. T. S. A. Vehra, O. Han, A. Radeny, J. Resstel, C. Bell, S. L. 2025-06-11 doi:10.1101/2025.06.11.659056 Cold Spring Harbor Laboratory Press 2025-06-11 <![CDATA[ Convergence and conflict among telomere specialized transposons across 60 million years of Drosophilid evolution ]]> https://biorxiv.org/content/10.1101/2025.06.09.658640v1?rss=1 Son, J. H. Lawlor, M. A. Virani, M. Cao, W. Levine, M. T. Ellison, C. 2025-06-12 doi:10.1101/2025.06.09.658640 Cold Spring Harbor Laboratory Press 2025-06-12 <![CDATA[ Proteomic responses under differing pH and pCO2 levels in the diatom Thalassiosira pseudonana are consistent with a hybrid carbon concentrating mechanism ]]> https://biorxiv.org/content/10.1101/2025.06.11.659125v1?rss=1 Himes, A. R. Kustka, A. B. 2025-06-16 doi:10.1101/2025.06.11.659125 Cold Spring Harbor Laboratory Press 2025-06-16 <![CDATA[ Image-Based Meta- and Mega-Analysis (IBMMA): A Unified Framework for Large-Scale, Multi-Site, Neuroimaging Data Analysis ]]> https://biorxiv.org/content/10.1101/2025.06.16.657725v1?rss=1 Steele, N. Morey, R. Hussain, A. Russell, C. Suarez-Jimenez, B. Pozzi, E. Jameei, H. Schmaal, L. Veer, I. Waller, L. Jahanshad, N. Thomopoulos, S. Salminen, L. Olff, M. Frijling, J. Veltman, D. Koch, S. Nawijn, L. van Zuiden, M. Wang, L. Zhu, Y. Li, G. Stein, D. Ipser, J. Neria, Y. Zhu, X. Ravid, O. Zilcha-Mano, S. Lazarov, A. Huggins, A. Stevens, J. Ressler, K. Jovanovic, T. van Rooij, S. Fani, N. Mueller, S. Hudson, A. Daniels, J. Sierk, A. Manthey, A. Walter, H. van der Wee, N. van der Werff, S. Vermeiren, R. Schmahl, C. Herzog, J. Rektor, I. i 2025-06-17 doi:10.1101/2025.06.16.657725 Cold Spring Harbor Laboratory Press 2025-06-17 <![CDATA[ Testing the priming effect in the deep ocean: are microbes too starved to consume recalcitrant organic carbon? ]]> https://biorxiv.org/content/10.1101/2025.06.13.658936v1?rss=1 LaBrie, R. Selden, C. R. Mahmoudi, N. 2025-06-19 doi:10.1101/2025.06.13.658936 Cold Spring Harbor Laboratory Press 2025-06-19 <![CDATA[ Mannoprotein Cig1 Contributes to the Immunogenicity of a Heat-Killed F-box Protein Fbp1 Cryptococcus neoformans Vaccine Model ]]> https://biorxiv.org/content/10.1101/2025.06.17.660137v1?rss=1 Avina, S. Pawar, S. Rivera, A. Xue, C. 2025-06-19 doi:10.1101/2025.06.17.660137 Cold Spring Harbor Laboratory Press 2025-06-19 <![CDATA[ Stony coral tissue loss disease (SCTLD) destabilizes the coral microbiome ]]> https://biorxiv.org/content/10.1101/2025.06.19.660612v1?rss=1 Nandi, S. Stephens, T. G. Walsh, K. Garcia, R. Villalpando, M. F. Sellares-Blasco, R. I. Zubillaga, A. L. Croquer, A. Bhattacharya, D. 2025-06-20 doi:10.1101/2025.06.19.660612 Cold Spring Harbor Laboratory Press 2025-06-20 <![CDATA[ Amphiphilic protein surfactants reduce the interfacial tension of biomolecular condensates ]]> https://biorxiv.org/content/10.1101/2025.06.19.660548v1?rss=1 View larger version (33K): org.highwire.dtl.DTLVardef@b0d206org.highwire.dtl.DTLVardef@acb567org.highwire.dtl.DTLVardef@b99e5dorg.highwire.dtl.DTLVardef@4bf12b_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Favetta, B. Wang, H. Shi, Z. Schuster, B. S. 2025-06-21 doi:10.1101/2025.06.19.660548 Cold Spring Harbor Laboratory Press 2025-06-21 <![CDATA[ Antimicrobial Loaded Graft-Copolymer Nanoparticles for Treatment of Pseudomonas aeruginosa Infections ]]> https://biorxiv.org/content/10.1101/2025.07.03.663093v1?rss=1 Soler, Y. V. Xu, W. Lima, M. R. N. McDonald, J. Jagpal, S. K. Kirn, T. J. Hussain, S. Devore, D. I. Roth, C. M. 2025-07-04 doi:10.1101/2025.07.03.663093 Cold Spring Harbor Laboratory Press 2025-07-04 <![CDATA[ Hydration free energy is a significant predictor of globular protein incorporation into condensates ]]> https://biorxiv.org/content/10.1101/2025.07.03.663089v1?rss=1 Anderson, S. Harrison, M. Dignon, G. L. 2025-07-07 doi:10.1101/2025.07.03.663089 Cold Spring Harbor Laboratory Press 2025-07-07 <![CDATA[ Deep Learning Meets Sleep Medicine: A Proof-of-Concept Clustering of Minute-Resolution CPAP Telemetry ]]> https://biorxiv.org/content/10.1101/2025.07.03.663061v1?rss=1 Calbert, L. Scharf, M. T. Androulakis, I. P. 2025-07-08 doi:10.1101/2025.07.03.663061 Cold Spring Harbor Laboratory Press 2025-07-08 <![CDATA[ An orally available PfPKG inhibitor blocks sporozoite infection of the liver ]]> https://biorxiv.org/content/10.1101/2025.07.09.663303v1?rss=1 BHANOT, P. Dhiyebi, H. Mbaye, A. Thaniana, A. Gilleran, J. Eck, T. Ashraf, K. Fan, H. Seibold, S. Battaile, K. Siekierka, J. Johnson, E. Roth, A. De Rocher, A. Lovell, S. Miller, E. Roberge, J. Y. 2025-07-09 doi:10.1101/2025.07.09.663303 Cold Spring Harbor Laboratory Press 2025-07-09 <![CDATA[ c-di-GMP-Dependent Regulation of Motility by comFB and comFC ]]> https://biorxiv.org/content/10.1101/2025.07.11.664319v1?rss=1 Hahn, J. Celma, L. El-shereef, A. Samir, S. Dubnau, E. Selim, K. K. DUBNAU, D. 2025-07-11 doi:10.1101/2025.07.11.664319 Cold Spring Harbor Laboratory Press 2025-07-11 <![CDATA[ Evaluating long-term stool preservation methods for maximizing the recovery of viable human fecal microbiota ]]> https://biorxiv.org/content/10.1101/2025.07.11.664436v1?rss=1 Teo, Y. Lavrinienko, A. Albertos Torres, D. Asare, P. T. Ruder, A. Dominguez-Bello, M. G. Adrian, E. Bokulich, N. Vonaesch, P. 2025-07-14 doi:10.1101/2025.07.11.664436 Cold Spring Harbor Laboratory Press 2025-07-14 <![CDATA[ Frequency-dependent communication of information innetworks of non-oscillatory neurons in response to oscillatory inputs ]]> https://biorxiv.org/content/10.1101/2025.07.09.664007v1?rss=1 Bel, A. Rotstein, H. G. 2025-07-15 doi:10.1101/2025.07.09.664007 Cold Spring Harbor Laboratory Press 2025-07-15 <![CDATA[ One of these things is not like the others: Theta, beta, & ERP dynamics of mismatch detection ]]> https://biorxiv.org/content/10.1101/2025.07.11.664390v1?rss=1 Yarbrough, J. B. Shi, L. Chattopadhyay, K. Knight, R. T. Johnson, E. L. 2025-07-17 doi:10.1101/2025.07.11.664390 Cold Spring Harbor Laboratory Press 2025-07-17 <![CDATA[ Distinct Synaptic Mechanisms Drive NRXN1 Variant-Mediated Pathogenesis in iPSC-Derived Neuronal Models of Autism and Schizophrenia ]]> https://biorxiv.org/content/10.1101/2025.07.18.664735v1?rss=1 Pak, C. English, J. McSweeney, D. Geng, J. Howell, E. Ribbe, F. Hinderhofer, M. Proskauer, L. Sebastian, R. Wang, L. Sharf, T. Pang, Z. P. 2025-07-19 doi:10.1101/2025.07.18.664735 Cold Spring Harbor Laboratory Press 2025-07-19 <![CDATA[ Volumetric Differences of Thalamic Nuclei are Associated with Post-Trauma Psychopathology ]]> https://biorxiv.org/content/10.1101/2025.07.24.666644v1?rss=1 Steele, N. Hussain, A. Baird, C. L. Haswell, C. C. Sun, D. Rangel-Jimenez, L. Abdallah, C. G. Angstadt, M. August, G. Berg, H. Blackford, J. U. Cisler, J. Daniels, J. K. Davenport, N. D. Davidson, R. J. Densmore, M. Disner, S. G. El-Hage, W. Etkin, A. Fani, N. Frijling, J. L. Gordon, E. M. Grupe, D. W. Herringa, R. J. Hudson, A. R. Jahanshad, N. Jovanovic, T. King, A. Koch, S. B. J. Lanius, R. Lazarov, A. Li, G. Liberzon, I. Lissek, S. Lu, G. M. Manthey, A. Maron-Katz, A. Nawijn, L. Nelson, S. M. Neria, Y. Neufeld, R. W. J. Nitschke, J. B. Olatunji, B. 2025-07-25 doi:10.1101/2025.07.24.666644 Cold Spring Harbor Laboratory Press 2025-07-25 <![CDATA[ Humanized TfR1 and transferrin gene-replacement rats for in vivo evaluation of BBB transport ]]> https://biorxiv.org/content/10.1101/2025.07.25.666792v1?rss=1 Yesiltepe, M. Metkar, S. Yin, T. Chakraborty, I. D'Adamio, L. 2025-07-31 doi:10.1101/2025.07.25.666792 Cold Spring Harbor Laboratory Press 2025-07-31 <![CDATA[ Neural components underlying successful free recall are specific to episodic memory ]]> https://biorxiv.org/content/10.1101/2025.07.25.666835v1?rss=1 DeHaan, R. D. Ezzyat, Y. Randazzo, M. J. Rao, A. M. Papanastassiou, A. M. Geller, A. S. Lega, B. C. Aronson, J. P. Gross, R. E. Jobst, B. C. Zaghloul, K. A. Worrell, G. A. Sheth, S. A. Sperling, M. R. Kahana, M. J. 2025-07-31 doi:10.1101/2025.07.25.666835 Cold Spring Harbor Laboratory Press 2025-07-31 <![CDATA[ Exploring polycyclic scaffolds as adamantane replacements in M2 channel inhibitors of Influenza A virus ]]> https://biorxiv.org/content/10.1101/2025.07.26.666854v1?rss=1 Turcu, A. L. Leiva, R. Ma, C. Georgiou, K. Brea, J. M. Loza, M. I. Val, C. Naesens, L. Wang, J. Kolocouris, A. Vazquez, S. 2025-07-31 doi:10.1101/2025.07.26.666854 Cold Spring Harbor Laboratory Press 2025-07-31 <![CDATA[ Iron dysregulation in mice engineered with a mutation associated with stuttering ]]> https://biorxiv.org/content/10.1101/2025.07.30.667752v1?rss=1 Millwater, M. Bragg, C. Bishop, D. Adeck, A. Karutury, R. C. Weinhold, M. Rao, P. P. N. Zhang, R. SheikhBahaei, s. 2025-07-31 doi:10.1101/2025.07.30.667752 Cold Spring Harbor Laboratory Press 2025-07-31 <![CDATA[ Chromosome-Scale Assemblies of Flowering Dogwood Cultivars Enable Identification of Candidate Genes Regulating Anthocyanin Biosynthesis in Leaves and Bracts ]]> https://biorxiv.org/content/10.1101/2025.07.31.667920v1?rss=1 Hamm, T. P. Boggess, S. L. Nowicki, M. Hadziabdic, D. Shoemaker, D. Trigiano, R. N. Klingeman, W. E. Molnar, T. J. Leebens-Mack, J. Harkess, A. Simpson, S. A. Youngblood, R. C. Hulse-Kemp, A. M. Scheffler, B. E. Staton, M. E. 2025-07-31 doi:10.1101/2025.07.31.667920 Cold Spring Harbor Laboratory Press 2025-07-31 <![CDATA[ Validated ligand geometries for macromolecular refinement restraints and molecular mechanics force fields ]]> https://biorxiv.org/content/10.1101/2025.08.01.668229v1?rss=1 Moriarty, N. W. Case, D. A. Liebschner, D. Adams, P. D. 2025-08-02 doi:10.1101/2025.08.01.668229 Cold Spring Harbor Laboratory Press 2025-08-02 <![CDATA[ CX3CR1 Fate-Mapping In Vivo Distinguishes Cochlear Resident and Recruited Macrophages After Acoustic Trauma ]]> https://biorxiv.org/content/10.1101/2025.08.04.668473v1?rss=1 Murali, S. V. Stothert, A. R. Pereyra, E. Batalkina, L. Kaur, T. 2025-08-05 doi:10.1101/2025.08.04.668473 Cold Spring Harbor Laboratory Press 2025-08-05 <![CDATA[ Loss of Ag85A disrupts plasma membrane domains and promotes free mycolic acid accumulation in mycobacteria. ]]> https://biorxiv.org/content/10.1101/2025.08.05.668640v1?rss=1 Kado, T. Fnu, S. Jordan, J. D. Freundlic, J. Siegrist, M. S. Morita, Y. S. 2025-08-05 doi:10.1101/2025.08.05.668640 Cold Spring Harbor Laboratory Press 2025-08-05 <![CDATA[ Ethanol induces neuroimmune dysregulation and soluble TREM2 generation in a human iPSC neuron, astrocyte, microglia triculture model ]]> https://biorxiv.org/content/10.1101/2025.08.04.668469v1?rss=1 Boreland, A. J. Abbo, Y. Li, X. Stillitano, A. C. Zhang, S. Duan, J. Pang, Z. P. Hart, R. P. 2025-08-06 doi:10.1101/2025.08.04.668469 Cold Spring Harbor Laboratory Press 2025-08-06 <![CDATA[ Exoproteome of calorie-restricted humans identifies complement deactivation as an immunometabolic checkpoint reducing inflammaging ]]> https://biorxiv.org/content/10.1101/2025.08.04.668533v1?rss=1 Mishra, M. Kim, H.-H. Youm, Y.-H. Gonzalez-Hurtado, E. Zaitsev, K. Dlugos, T. Shchukina, I. Gliniak, C. Ravussin, E. Mohanty, S. Shaw, A. C. Scherer, P. E. Artyomov, M. N. Dixit, V. D. 2025-08-06 doi:10.1101/2025.08.04.668533 Cold Spring Harbor Laboratory Press 2025-08-06 <![CDATA[ Chromosomal Fusions and Evolutionary Forces: Exploring theNeo-Sex Chromosome System of Anolis distichus ]]> https://biorxiv.org/content/10.1101/2025.08.05.668756v1?rss=1 Falvey, C. de Mello, P. Taft, J. Vanerelli, A. Hime, P. Alexander, A. Glor, R. Geneva, A. J. 2025-08-07 doi:10.1101/2025.08.05.668756 Cold Spring Harbor Laboratory Press 2025-08-07 <![CDATA[ Predicting Spiking Activity from Scalp EEG ]]> https://biorxiv.org/content/10.1101/2025.08.06.668998v1?rss=1 Sharma, D. Krekelberg, B. 2025-08-09 doi:10.1101/2025.08.06.668998 Cold Spring Harbor Laboratory Press 2025-08-09 <![CDATA[ Non-vocal motor deficits in a transgenic mouse model linked to stuttering disorders ]]> https://biorxiv.org/content/10.1101/2025.08.08.669441v1?rss=1 Millwater, M. Weinhold, M. Bragg, C. Kaur, H. Zhang, R. SheikhBahaei, S. 2025-08-10 doi:10.1101/2025.08.08.669441 Cold Spring Harbor Laboratory Press 2025-08-10 <![CDATA[ Sound-evoked auditory neurophysiological signals are a window into prodromal functional differences in a preclinical model of Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2025.08.07.669134v1?rss=1 Aydin, A. G. Manoj, P. Ramadan, F. Youssef, E. Rajan, S. Torres, E. Bieszczad, K. M. 2025-08-11 doi:10.1101/2025.08.07.669134 Cold Spring Harbor Laboratory Press 2025-08-11 <![CDATA[ Dachsous-Fat Signaling Shapes the Drosophila Wing through Mechanical Forces ]]> https://biorxiv.org/content/10.1101/2025.08.08.669334v1?rss=1 Tripathi, B. Zhou, Z. Irvine, K. 2025-08-12 doi:10.1101/2025.08.08.669334 Cold Spring Harbor Laboratory Press 2025-08-12 <![CDATA[ CD300LG is a receptor for triglyceride-rich lipoproteins that facilitates postprandial lipid clearance ]]> https://biorxiv.org/content/10.1101/2025.08.08.669356v1?rss=1 Granade, M. E. Tveter, K. M. Kim, H. I. Yesian, A. R. Fowler, J. Ahn, Y. Culver, J. Tam Neale, K. Amar, N. Mazzocca, M. White, A. R. Archambault, D. Sonavane, R. Laforest, B. Piper, M. Roth Flach, R. J. Rong, X. 2025-08-12 doi:10.1101/2025.08.08.669356 Cold Spring Harbor Laboratory Press 2025-08-12 <![CDATA[ Distributed theta networks support the control of working memory: Evidence from scalp and intracranial EEG ]]> https://biorxiv.org/content/10.1101/2025.08.14.670214v1?rss=1 Shi, L. Chattopadhyay, K. Gray, S. M. Yarbrough, J. B. King-Stephens, D. Saez, I. Girgis, F. Shaikhouni, A. Schuele, S. U. Rosenow, J. M. Asano, E. Kim-McManus, O. Sattar, S. Knight, R. T. Johnson, E. L. 2025-08-15 doi:10.1101/2025.08.14.670214 Cold Spring Harbor Laboratory Press 2025-08-15 <![CDATA[ Effects of Cholesterol on Amyloid-induced Membrane Poration ]]> https://biorxiv.org/content/10.1101/2025.08.15.670631v1?rss=1 Yang, Y. Shah, B. Agapito, M. Nieuwkoop, A. 2025-08-17 doi:10.1101/2025.08.15.670631 Cold Spring Harbor Laboratory Press 2025-08-17 <![CDATA[ Intrinsic Reproductive Isolation among Ecologically Divergent Anolis Lizards ]]> https://biorxiv.org/content/10.1101/2025.08.14.670316v1?rss=1 Geneva, A. J. Glor, R. E. 2025-08-19 doi:10.1101/2025.08.14.670316 Cold Spring Harbor Laboratory Press 2025-08-19 <![CDATA[ Proteomic analysis of Mycobacterium tuberculosis lacking a putative short-chain dehydrogenase (Rv0148) ]]> https://biorxiv.org/content/10.1101/2025.08.20.671283v1?rss=1 Subbian, S. Bhargavi, G. Deenadayalan, A. Palaniyandi, K. 2025-08-20 doi:10.1101/2025.08.20.671283 Cold Spring Harbor Laboratory Press 2025-08-20 <![CDATA[ Distributed Cortical Network Dynamics of Binocular Convergent Eye Movements in Humans ]]> https://biorxiv.org/content/10.1101/2025.08.15.670412v1?rss=1 Hajebrahimi, F. Gohel, S. Cole, M. W. Alvarez, T. L. 2025-08-21 doi:10.1101/2025.08.15.670412 Cold Spring Harbor Laboratory Press 2025-08-21 <![CDATA[ DFFB suppresses interferon to enable cancer persister cell regrowth ]]> https://biorxiv.org/content/10.1101/2025.08.15.670603v1?rss=1 Williams, A. F. Gervasio, D. A. G. Turkal, C. E. Stuhlfire, A. E. Wang, M. X. Mauch, B. E. Plawat, R. Nguyen, A. H. Paw, M. H. Hairani, M. Lathrop, C. P. Harris, S. H. Page, J. L. Hangauer, M. J. 2025-08-21 doi:10.1101/2025.08.15.670603 Cold Spring Harbor Laboratory Press 2025-08-21 <![CDATA[ COX2-independent and COX2-dependent effects of naproxen on bone quality, osteocytes, and fatigue fracture healing in male and female mice ]]> https://biorxiv.org/content/10.1101/2025.08.20.669939v1?rss=1 Ciuciu, A. McLaughlin, E. Ciuciu, A. Barrientos, K. C. LaPoint, T. Tomlinson, R. E. 2025-08-25 doi:10.1101/2025.08.20.669939 Cold Spring Harbor Laboratory Press 2025-08-25 <![CDATA[ Evidence of Escherichia coli Regulating Drosophila melanogaster Behavior ]]> https://biorxiv.org/content/10.1101/2025.08.20.671414v1?rss=1 Darwish, H. A. Hart, T. Patel, D. Russo, S. Salama, S. Tariq, M. Sun, J. S. 2025-08-25 doi:10.1101/2025.08.20.671414 Cold Spring Harbor Laboratory Press 2025-08-25 <![CDATA[ HP1B and H3K9me3 Regulate Olfactory Receptor Choice and Transcriptional Identity ]]> https://biorxiv.org/content/10.1101/2025.08.21.671605v1?rss=1 Escamilla-del-Arenal, M. Duffie, R. Shayya, H. Loconte, V. Ekman, A. Street, L. A. Horta, A. Canzio, D. Monahan, K. Larabell, C. A. Jovanovic, M. Lomvardas, S. 2025-08-25 doi:10.1101/2025.08.21.671605 Cold Spring Harbor Laboratory Press 2025-08-25 <![CDATA[ Microbial source tracking of human and animal fecal contamination in Ecuadorian households ]]> https://biorxiv.org/content/10.1101/2025.08.22.671888v1?rss=1 Jesser, K. J. Alban, V. Lobos, A. E. Gallard-Gongora, J. Trueba, G. Lee, G. O. Eisenberg, J. N. S. Harwood, V. J. Levy, K. 2025-08-25 doi:10.1101/2025.08.22.671888 Cold Spring Harbor Laboratory Press 2025-08-25 <![CDATA[ An Efficient Lasso Framework for Admixture-Aware Polygenic Scores ]]> https://biorxiv.org/content/10.1101/2025.08.26.671106v1?rss=1 Ockerman, F. P. Chen, B. D. Sun, Q. Kharitonova, E. V. Chen, C. Zhou, L. Y. Loos, R. J. Kooperberg, C. Peters, U. Haessler, J. Reiner, A. P. Jung, S. Y. Manson, J. E. Nassir, R. North, K. E. Buyske, S. Haiman, C. A. Conti, D. V. Wilkens, L. R. Lange, E. M. Cox, N. J. Cao, H. Raffield, L. M. Li, Y. Tao, R. 2025-08-27 doi:10.1101/2025.08.26.671106 Cold Spring Harbor Laboratory Press 2025-08-27 <![CDATA[ A persistent intracellular bridge and cell cycle misregulation enable polar body cell divisions and tumor formation in Mos-deficient eggs ]]> https://biorxiv.org/content/10.1101/2025.08.26.672293v1?rss=1 Cairo, G. Haseeb, M. A. Schindler, K. Lacefield, S. 2025-08-27 doi:10.1101/2025.08.26.672293 Cold Spring Harbor Laboratory Press 2025-08-27 <![CDATA[ Subtyping psychotic disorders using a data-driven approach reveals divergent cortical and cellular signatures ]]> https://biorxiv.org/content/10.1101/2025.08.26.672411v1?rss=1 Hill, L. D. Zhang, X.-H. Rogers, B. P. Huang, A. S. Fox, V. Feola, B. Heckers, S. Holmes, A. J. Woodward, N. D. 2025-08-27 doi:10.1101/2025.08.26.672411 Cold Spring Harbor Laboratory Press 2025-08-27 <![CDATA[ Leucine-rich repeat kinase 2 impairs the release sites of Parkinson's disease vulnerable dopamine axons ]]> https://biorxiv.org/content/10.1101/2025.08.28.672006v1?rss=1 Chen, C. He, Q. Tombesi, G. Napier, E. Jaconelli, M. Moreno-Ramos, O. Serio, H. Naaldijk, Y. Promes, V. Schneeweis, A. Quinn, K. Nasios, C. Greggio, E. Kozorovitskiy, Y. Arango, D. Khan, A. R. Alessi, D. R. Dombeck, D. A. Hilfiker, S. Awatramani, R. Parisiadou, L. 2025-08-28 doi:10.1101/2025.08.28.672006 Cold Spring Harbor Laboratory Press 2025-08-28 <![CDATA[ Hypoxia-induced metastatic heterogeneity in pancreatic cancer ]]> https://biorxiv.org/content/10.1101/2025.08.26.672389v1?rss=1 Gunasekaran, P. M. Wang, Q. Chang, Y.-C. Guseva, P. Chauhan, R. Kley, A. Lee, G. Roy, S. G. Masoudpoor, Y. Roberts, A. Walton, K. W. Franciosa, L. Bhat, S. Zachariah, E. Patel, K. Zhou, Z. Chen, W. Ni, J. Z. Gu, S. G. Montagna, C. Chiou, S.-H. 2025-08-29 doi:10.1101/2025.08.26.672389 Cold Spring Harbor Laboratory Press 2025-08-29 <![CDATA[ Direction of motion decoding in mouse V1: Neuron predictive power relates to functional connectivity organization ]]> https://biorxiv.org/content/10.1101/2025.08.27.672292v1?rss=1 Savaglio, M. A. Brozi, C. Psilou, E. Koumpouzi, C. Papadostefanaki, M. Vasilakos, C. Nessis, S. Smyrnakis, E. Akoutas, V. Keliris, G. A. Palagina, G. Smirnakis, S. M. Papadopouli, M. 2025-09-01 doi:10.1101/2025.08.27.672292 Cold Spring Harbor Laboratory Press 2025-09-01 <![CDATA[ Evaluating Place Cell Detection Methods in Ratsand Humans: Implications for Cross-Species Spatial Coding ]]> https://biorxiv.org/content/10.1101/2025.08.29.672705v1?rss=1 Zhang, W. Donoghue, T. Qasim, S. E. Jacobs, J. 2025-09-03 doi:10.1101/2025.08.29.672705 Cold Spring Harbor Laboratory Press 2025-09-03 <![CDATA[ Genetically-based sperm discrimination in the vaginal tract of a primate species ]]> https://biorxiv.org/content/10.1101/2025.08.29.672970v1?rss=1 Petersen, R. M. Nonnamaker, L. M. Anderson, J. A. Bergey, C. M. Roos, C. Melin, A. D. Higham, J. P. 2025-09-04 doi:10.1101/2025.08.29.672970 Cold Spring Harbor Laboratory Press 2025-09-04 <![CDATA[ MetaScope: A High-Resolution Framework for Species-Level 16S Metataxonomic Classification ]]> https://biorxiv.org/content/10.1101/2025.08.29.673160v1?rss=1 Lu, S. Odom, A. R. Shah, A. Leng, Y. Quiles, K. R. Johnson, W. E. 2025-09-04 doi:10.1101/2025.08.29.673160 Cold Spring Harbor Laboratory Press 2025-09-04 <![CDATA[ Nanoscale Structural and Functional Impacts of Disease-Associated Collagen Mutations ]]> https://biorxiv.org/content/10.1101/2025.09.03.673992v1?rss=1 Tobita, C. A. Banerjee, S. Roth, J. Larson, E. K. Nikzad, A. Naiyer, A. Hoop, C. L. Baum, J. 2025-09-04 doi:10.1101/2025.09.03.673992 Cold Spring Harbor Laboratory Press 2025-09-04 <![CDATA[ Genome-wide overexpression screen reveals a novel transcription termination factor in Trypanosoma brucei ]]> https://biorxiv.org/content/10.1101/2025.09.02.673782v1?rss=1 Selvan, N. P. Mukherjee, A. Erben, E. Kim, H.-S. 2025-09-05 doi:10.1101/2025.09.02.673782 Cold Spring Harbor Laboratory Press 2025-09-05 <![CDATA[ Gene model for the ortholog of Ilp4 in Drosophila eugracilis ]]> https://biorxiv.org/content/10.1101/2025.09.05.674564v1?rss=1 Cowan, R. Uppal, A. Larsen, C. I. S. Ellison, C. E. Torosin, N. S. Thompson, J. S. Rele, C. P. Boies, L. 2025-09-08 doi:10.1101/2025.09.05.674564 Cold Spring Harbor Laboratory Press 2025-09-08 <![CDATA[ Mechanism-aware inference of response to targeted cancer therapies ]]> https://biorxiv.org/content/10.1101/2025.09.04.674143v1?rss=1 Bhattacharjee, N. Peela, S. C. M. Halder, A. Mathew, B. Samantha, S. Gujral, S. Kumari, S. Panda, S. Ganguly, R. Ahuja, G. De, S. Majumder, A. Sengupta, D. 2025-09-09 doi:10.1101/2025.09.04.674143 Cold Spring Harbor Laboratory Press 2025-09-09 <![CDATA[ Facial Micro-Movements as a Proxy of Increasingly Erratic Heart Rate Variability While Experiencing Pressure Pain ]]> https://biorxiv.org/content/10.1101/2025.09.09.674997v1?rss=1 Torres, E. B. Elsayed, M. 2025-09-10 doi:10.1101/2025.09.09.674997 Cold Spring Harbor Laboratory Press 2025-09-10 <![CDATA[ Cutaneous suction-mediated transfection in mice for delivery of DNA-encoded vaccines and proteins ]]> https://biorxiv.org/content/10.1101/2025.09.10.675275v1?rss=1 Lallow, E. O. Brandtjen, I. Mo, Y. Gulley, M. Osorio, L. Kudchodkar, S. Jhumur, N. C. Roberts, C. C. Denzin, L. K. Shreiber, D. I. Parekkadan, B. Lin, H. Maslow, J. N. 2025-09-11 doi:10.1101/2025.09.10.675275 Cold Spring Harbor Laboratory Press 2025-09-11 <![CDATA[ Neural responses to binocular in-phase and anti-phase stimuli ]]> https://biorxiv.org/content/10.1101/2025.09.08.674974v1?rss=1 Richard, B. Baker, D. H. 2025-09-13 doi:10.1101/2025.09.08.674974 Cold Spring Harbor Laboratory Press 2025-09-13 <![CDATA[ Frequency-dependent coupling in responses to oscillatory inputs in networks of electrically coupled nodes: Gap junction networks and spatially extended neurons ]]> https://biorxiv.org/content/10.1101/2025.09.12.675827v1?rss=1 Bel, A. Chialva, U. Rotstein, H. G. 2025-09-13 doi:10.1101/2025.09.12.675827 Cold Spring Harbor Laboratory Press 2025-09-13 <![CDATA[ Tectonic setting shapes microbial biosynthetic potential across global geothermal environments ]]> https://biorxiv.org/content/10.1101/2025.09.14.675129v1?rss=1 Pelliciari Silva, A. C. de Pins, B. d. P. Montemagno, F. Migliaccio, F. Cascone, M. Bastoni, D. Barosa, B. Selci, M. Vetriani, C. Chiodi, A. A. Vignale, F. Garcia-Alai, M. M. Vitale Brovarone, A. Jessen, G. L. M. Blamey, J. de Moor, J. M. Lloyd, K. G. Barry, P. H. Giovannelli, D. 2025-09-15 doi:10.1101/2025.09.14.675129 Cold Spring Harbor Laboratory Press 2025-09-15 <![CDATA[ Insulin-Like Growth Factor 1 Receptor Regulates Breast Cancer Cell Adhesion through Beta-1 Integrin ]]> https://biorxiv.org/content/10.1101/2025.09.11.674989v1?rss=1 Galifi, C. A. Dogan, E. Almansa, L. F. Maingrette, K. Shah, S. S. Bulatowicz, J. J. Ebenezer, K. Miri, A. K. Wood, T. L. 2025-09-16 doi:10.1101/2025.09.11.674989 Cold Spring Harbor Laboratory Press 2025-09-16 <![CDATA[ Evaluation of Antigen Expression and Early Immune Response following Cutaneous Suction-mediated DNA Delivery ]]> https://biorxiv.org/content/10.1101/2025.09.15.676388v1?rss=1 Jhumur, N. C. Um, Y. Park, S. H. Lallow, E. O. Roberts, C. C. Shan, J. W. Singer, J. P. Zahn, J. D. Park, Y. K. Denzin, L. K. Shreiber, D. I. Maslow, J. N. Lin, H. 2025-09-16 doi:10.1101/2025.09.15.676388 Cold Spring Harbor Laboratory Press 2025-09-16 <![CDATA[ Micro and nanoplastic inhalation during pregnancy elicits uterine endothelial dysfunction in Sprague Dawley rats by impeding NO signaling ]]> https://biorxiv.org/content/10.1101/2025.09.12.675811v1?rss=1 Cary, C. M. Moore, T. L. Gow, A. J. Stapleton, P. A. 2025-09-17 doi:10.1101/2025.09.12.675811 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ Ineffective behavioral rescue despite partial brain Dp427 restoration by AAV9-U7-mediated exon 51 skipping in mdx52 mice ]]> https://biorxiv.org/content/10.1101/2025.09.19.677185v1?rss=1 VACCA, O. SAOUDI, A. DOISY, M. PHONGSAVANH, X. M. Le Coz, O. NAGY, C. KUZNIAR, J. VAILLEND, C. GOYENVALLE, A. 2025-09-19 doi:10.1101/2025.09.19.677185 Cold Spring Harbor Laboratory Press 2025-09-19 <![CDATA[ Candida albicans infiltrates colon and rectal cancers causing therapeutic resistance and decreased survival ]]> https://biorxiv.org/content/10.1101/2025.09.19.677366v1?rss=1 Grencewicz, D. J. Loncar, A. Ferrandon, S. Chatterjee, D. Kreamer, M. Mehra, Y. Carson, A. Hoyd, R. Jahanbakhshi, S. Choueiry, F. Anderson, M. Z. Benej, M. Bosch, D. E. Zhu, J. Wu, J. Pallerla, A. Bocklage, T. McCarter, M. Tarhini, A. Salhia, B. Moskaluk, C. Riedlingeer, G. Yao, S. Masood, A. Hardikar, S. Ilozumba, M. Ulrich, C. M. Chan, C. H. F. Shiver, C. George, S. Mudaranthakam, D. P. Churchman, M. Rounbehler, R. Chambers, L. Carbone, D. Kalady, M. F. Denko, N. Spakowicz, D. 2025-09-21 doi:10.1101/2025.09.19.677366 Cold Spring Harbor Laboratory Press 2025-09-21 <![CDATA[ Optimized Ex Vivo Differentiation of CD103⁺ Dendritic Cells and High-Efficiency Retroviral Transduction of Mouse Bone Marrow HSCs ]]> https://biorxiv.org/content/10.1101/2025.09.21.677651v1?rss=1 Asnani, M. M. Yang, J. 2025-09-23 doi:10.1101/2025.09.21.677651 Cold Spring Harbor Laboratory Press 2025-09-23 <![CDATA[ Multiple Epigenetic Mechanisms Functionally Cooperate to Silence Expression of Somatostatin Receptor Type 2 in Pancreatic Neuroendocrine Tumors ]]> https://biorxiv.org/content/10.1101/2025.09.23.677935v1?rss=1 Madigan, J. P. Andrews, S. G. Farrell, R. B. Sharma, R. Ceribelli, M. Thomas, C. J. Shamsian, K. N. Lin, S. Cheng, K. C.-C. Sadowski, S. M. 2025-09-25 doi:10.1101/2025.09.23.677935 Cold Spring Harbor Laboratory Press 2025-09-25 <![CDATA[ A neural network model of free recall learns multiple memory strategies ]]> https://biorxiv.org/content/10.1101/2025.09.25.678592v1?rss=1 Li, M. Jensen, K. T. Zhang, Q. Lu, Q. Mattar, M. G. 2025-09-25 doi:10.1101/2025.09.25.678592 Cold Spring Harbor Laboratory Press 2025-09-25 <![CDATA[ Is synuclein aggregation a derived or ancestral trait? Ancestral sequence reconstruction uncovers stepwise evolution of synuclein aggregation ]]> https://biorxiv.org/content/10.1101/2025.09.27.678990v1?rss=1 Sam, A. Lee, S. Elliott, J. Larson, E. Naiyer, A. Williams, J. K. Baum, J. 2025-09-28 doi:10.1101/2025.09.27.678990 Cold Spring Harbor Laboratory Press 2025-09-28 <![CDATA[ Reference-guided Genome Assembly of Long Non-coding RNA Transcripts reveals Target Genes Associated With Crohn's Disease ]]> https://biorxiv.org/content/10.1101/2025.09.30.674088v1?rss=1 Kennedy Ng, M. M. Silverstein, S. Nishiyama, N. C. Beasley, C. Lian, G. Huan, B. Lau, G. Weaver, D. Awad, A. Schaner, M. R. Sheikh, S. Z. Furey, T. S. 2025-10-01 doi:10.1101/2025.09.30.674088 Cold Spring Harbor Laboratory Press 2025-10-01 <![CDATA[ Nephrobase Cell+: Multimodal Single-Cell Foundation Model for Decoding Kidney Biology ]]> https://biorxiv.org/content/10.1101/2025.09.30.679471v1?rss=1 90% zero-shot annotation accuracy for major kidney lineages in both human and mouse. Even its 1B-parameter and 500M variants consistently outperform all existing models. ConclusionsWith organ-scale multimodal pretraining and a specialized transformer architecture, Nephrobase Cell+ delivers a unified, high-fidelity representation of kidney biology that is robust, cross-species transferable, and unmatched by current single-cell foundation models, offering a powerful resource for kidney genomics and disease research. ]]> Li, C. Ziyadeh, E. Sharma, Y. Dumoulin, B. Levinsohn, J. Ha, E. Pan, S. Rao, V. Subramaniyam, M. Szegedy, M. Zhang, N. Susztak, K. 2025-10-01 doi:10.1101/2025.09.30.679471 Cold Spring Harbor Laboratory Press 2025-10-01 <![CDATA[ A single-cell transcriptomic atlas of inner ear morphogenesis in zebrafish ]]> https://biorxiv.org/content/10.1101/2025.09.30.679639v1?rss=1 Swinburne, I. A. Munjal, A. A. Kukreja, K. Williams, S. Kawanishi, T. O'Brown, N. Ishimatsu, K. Klein, A. M. Megason, S. 2025-10-01 doi:10.1101/2025.09.30.679639 Cold Spring Harbor Laboratory Press 2025-10-01 <![CDATA[ Vegetation clump size and number as indicators for alternative stable states in semi-arid ecosystems ]]> https://biorxiv.org/content/10.1101/2025.10.03.680294v1?rss=1 Chen, Z. Halder, K. Bonachela, J. A. 2025-10-04 doi:10.1101/2025.10.03.680294 Cold Spring Harbor Laboratory Press 2025-10-04 <![CDATA[ Complex HPV-human DNA structures revealed by large-scale DNA analyses in an HPV-cancer derived cell line ]]> https://biorxiv.org/content/10.1101/2025.10.06.680684v1?rss=1 View larger version (20K): org.highwire.dtl.DTLVardef@f3d584org.highwire.dtl.DTLVardef@470811org.highwire.dtl.DTLVardef@162c88corg.highwire.dtl.DTLVardef@5c80dd_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Montagna, C. Agosta, E. J. Chang, Y. C. Rao, V. Hollingsworth, J. Brown, M. Kabiraj, D. Einstein, M. Van Arsdale, A. Van Doorslaer, K. Chan, C. De, S. Madireddy, A. Haas, B. Miller, D. Lenz, J. 2025-10-06 doi:10.1101/2025.10.06.680684 Cold Spring Harbor Laboratory Press 2025-10-06 <![CDATA[ Widespread male-female expression imbalance of X-linked genes across phrynosomatid lizards ]]> https://biorxiv.org/content/10.1101/2025.10.06.680020v1?rss=1 Hale, M. de Mello, P. H. Nondorf, D. T. Robinson, C. D. John-Alder, H. B. Cox, C. L. Cox, R. M. 2025-10-07 doi:10.1101/2025.10.06.680020 Cold Spring Harbor Laboratory Press 2025-10-07 <![CDATA[ Controlled Delivery of a Neurotrophic Factor in the Adult Mouse Brain Using Engineered Microglia ]]> https://biorxiv.org/content/10.1101/2025.10.06.680702v1?rss=1 Hofland, R. J. Gronska-Peski, M. Nobuta, H. Buitrago, N. Malhotra, K. Hebert, J. M. Goncalves, J. T. 2025-10-07 doi:10.1101/2025.10.06.680702 Cold Spring Harbor Laboratory Press 2025-10-07 <![CDATA[ Evaluation and Aggregation of Active Module Identification Algorithms ]]> https://biorxiv.org/content/10.1101/2025.10.06.680790v1?rss=1 Liu, J. Xu, M. Xing, J. 2025-10-07 doi:10.1101/2025.10.06.680790 Cold Spring Harbor Laboratory Press 2025-10-07 <![CDATA[ Structural mechanism of lipid modulation of pentameric ligand-gated ion channel activity ]]> https://biorxiv.org/content/10.1101/2025.10.07.680764v1?rss=1 Tan, B. K. Xu, H. Sandberg, J. W. Brannigan, G. Cheng, W. W. 2025-10-07 doi:10.1101/2025.10.07.680764 Cold Spring Harbor Laboratory Press 2025-10-07 <![CDATA[ Neuropathic pain drives time-dependent reorganization of corticostriatal circuits ]]> https://biorxiv.org/content/10.1101/2025.10.07.680927v1?rss=1 3 months), suggesting a failed compensatory mechanism. These findings reveal that striatal circuits undergo dynamic, time-dependent reorganization after peripheral injury, with D1 and D2 pathways contributing distinct temporal signatures to pain-related behavior. The identification of critical windows of striatal plasticity provides new targets for therapeutic interventions that could prevent or reverse chronic pain states by modulating specific corticostriatal circuits during vulnerable transition periods. ]]> George, A. J. Linares-Garcia, I. Yonk, A. J. Zhang, X. C. Burdge, J. Abraira, V. E. G. Margolis, D. J. 2025-10-07 doi:10.1101/2025.10.07.680927 Cold Spring Harbor Laboratory Press 2025-10-07 <![CDATA[ Regulation of Hippo signaling by Atrophin in the developing Drosophila wing ]]> https://biorxiv.org/content/10.1101/2025.10.09.681328v1?rss=1 Mikalauskaite, D. Rauskolb, C. Lehan, T. Venkatramanan, S. Carnes, L. Irvine, K. D. 2025-10-10 doi:10.1101/2025.10.09.681328 Cold Spring Harbor Laboratory Press 2025-10-10 <![CDATA[ Type 2 Diabetes and Obesity Alter Exercise Training-Induced Transcriptional Adaptations to Subcutaneous White Adipose Tissue ]]> https://biorxiv.org/content/10.1101/2025.10.11.681273v1?rss=1 Middelbeek, R. J. W. Yang, J. Nigro, P. James, B. Papadopoulos, D. Simpson, L. K. Park, J. Vamvini, M. Ho, L.-L. Zhang, H. Carbone, N. P. Hirshman, M. F. Kellis, M. Goodyear, L. J. 2025-10-12 doi:10.1101/2025.10.11.681273 Cold Spring Harbor Laboratory Press 2025-10-12 <![CDATA[ PERINATAL ORGANOPHOSPHATE FLAME RETARDANT EXPOSURE ALTERS ADULT HPA AXIS FUNCTION AND AVOIDANCE BEHAVIOR IN A SEX-SPECIFIC MANNER IN MICE ]]> https://biorxiv.org/content/10.1101/2025.10.13.682090v1?rss=1 Rojas, C. M. DeLucca, J. Brown, C. A. Yasrebi, A. Chiou, S. Bello, N. T. Roepke, T. A. 2025-10-14 doi:10.1101/2025.10.13.682090 Cold Spring Harbor Laboratory Press 2025-10-14 <![CDATA[ Psychological stress and social support are associated with opposing single-cell pro-inflammatory gene regulatory mechanisms in adults ]]> https://biorxiv.org/content/10.1101/2025.10.14.682318v1?rss=1 Ranjbaran, A. Kalita, C. Wei, J. Davis, K. M. Bruinsma, J. Mair-Meijers, H. Garlicki, G. Alazizi, A. Petriello, M. Jiang, Y. Zilioli, S. Pique-Regi, R. Luca, F. 2025-10-15 doi:10.1101/2025.10.14.682318 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ Constrained Diffusion for Protein Design with Hard Structural Constraints ]]> https://biorxiv.org/content/10.1101/2025.10.15.682365v1?rss=1 Christopher, J. K. Seamann, A. Cui, J. Khare, S. Fioretto, F. 2025-10-15 doi:10.1101/2025.10.15.682365 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ Reaction kinetics of procainamide dye derivatization of N-linked glycans to enable robust process analytical workflows for glycoprotein-based biologics manufacturing ]]> https://biorxiv.org/content/10.1101/2025.10.15.682640v1?rss=1 Suaini, N. B. Narvekar, A. Chundawat, S. P. S. 2025-10-15 doi:10.1101/2025.10.15.682640 Cold Spring Harbor Laboratory Press 2025-10-15 <![CDATA[ There is an I in team: individual improvements in supercharged cellulase cocktail facilitates cooperative cellulose degradation ]]> https://biorxiv.org/content/10.1101/2025.10.16.682856v1?rss=1 DeChellis, A. Shimabukuro, S. Trivedi, S. Lubowski, R. Nemmaru, B. Chundawat, S. P. S. 2025-10-17 doi:10.1101/2025.10.16.682856 Cold Spring Harbor Laboratory Press 2025-10-17 <![CDATA[ Omega-3 Fatty Acid Derived Neuroactive Lipids - Docosahexaenoyl-Glycine and Its Epoxide Metabolites are Multifunctional Lipid Mediators ]]> https://biorxiv.org/content/10.1101/2025.10.17.681057v1?rss=1 Kim, J. Franchini, L. Yudin, Y. Denissiouk, A. Rohacs, T. Orlandi, C. Das, A. 2025-10-17 doi:10.1101/2025.10.17.681057 Cold Spring Harbor Laboratory Press 2025-10-17 <![CDATA[ Gene Delivery Mediated by Backbone-Degradable RAFT Copolymers ]]> https://biorxiv.org/content/10.1101/2025.10.17.682953v1?rss=1 Mulay, P. B. Radford, D. C. Rondon, B. Favetta, B. Schuster, B. S. Niu, J. Gormley, A. J. 2025-10-17 doi:10.1101/2025.10.17.682953 Cold Spring Harbor Laboratory Press 2025-10-17 <![CDATA[ Begomovirus species demarcation based on genome-sequence identity often yields non-monophyletic species: A case study of sweet potato-infecting begomoviruses ]]> https://biorxiv.org/content/10.1101/2025.10.17.683111v1?rss=1 Mauriello, M. A. Hoyer, J. S. Julian, A. D. Crespo Bellido, A. Seah, Y. M. Duffy, S. 2025-10-17 doi:10.1101/2025.10.17.683111 Cold Spring Harbor Laboratory Press 2025-10-17 <![CDATA[ Aberrant E-I Balance and Brain Criticality in Major Depressive Disorder ]]> https://biorxiv.org/content/10.1101/2025.10.19.683280v1?rss=1 Mitsuto, A. Bhardwaj, A. Parkes, L. Faruqi, F. Carpenter, L. Westbrook, A. 2025-10-20 doi:10.1101/2025.10.19.683280 Cold Spring Harbor Laboratory Press 2025-10-20 <![CDATA[ Emergence of population-level feedback control by transposon-plasmid coevolution ]]> https://biorxiv.org/content/10.1101/2025.10.20.683530v1?rss=1 Maddamsetti, R. Hamrick, G. S. Ha, Y. Baig, Y. Lu, J. Lee, C. T. You, L. 2025-10-20 doi:10.1101/2025.10.20.683530 Cold Spring Harbor Laboratory Press 2025-10-20 <![CDATA[ Reducing astrocyte calcium in the nucleus accumbens core increases reward valuation ]]> https://biorxiv.org/content/10.1101/2025.10.20.683571v1?rss=1 VanRyzin, J. W. Laraia, G. A. Gyawali, U. James, M. H. Reissner, K. J. 2025-10-21 doi:10.1101/2025.10.20.683571 Cold Spring Harbor Laboratory Press 2025-10-21 <![CDATA[ Regulatory T cells inhibit CD8+ TRM-like cells during the early stages of tumor immune escape ]]> https://biorxiv.org/content/10.1101/2025.10.21.683143v1?rss=1 Williams, J. B. Pant, S. M. Kley, A. L. Rajmalani, B. A. Yapp, C. Zhang, J. Rotrosen, E. Sales, A. Sorger, P. K. Kupper, T. S. 2025-10-22 doi:10.1101/2025.10.21.683143 Cold Spring Harbor Laboratory Press 2025-10-22 <![CDATA[ JAK1/2 Inhibition Delays Cachexia and Improves Survival through Increased Food Intake ]]> https://biorxiv.org/content/10.1101/2025.10.21.683287v1?rss=1 Dantas, E. C. Murthy, A. Kim, J. Ahmed, T. Ahmed, M. Perrier, T. Ramsamooj, S. Nathoo, I. Kniess Debarba, L. Lima Queiroz, A. Li, S. Ersoy, B. Ferrer, M. Goldstein, I. C. Gao, J. Lam, T. Nagler, M. Malbari, M. Altorki, N. Cararo Lopes, E. Gomez Jenkins, M. Das, T. Jamal-Hanjani, M. White, E. Janowitz, T. Goncalves, M. 2025-10-22 doi:10.1101/2025.10.21.683287 Cold Spring Harbor Laboratory Press 2025-10-22 <![CDATA[ Experimental community ecology in decline: A call to embrace technology ]]> https://biorxiv.org/content/10.1101/2025.10.22.683879v1?rss=1 Arancibia, P. A. Abrego, N. Morin, P. Roslin, T. Ovaskainen, O. T. 2025-10-23 doi:10.1101/2025.10.22.683879 Cold Spring Harbor Laboratory Press 2025-10-23 <![CDATA[ Dedifferentiation-Driven Oncogenic Stemness Promotes Tumor-Sustaining Adaptability in the Intestinal Epithelium ]]> https://biorxiv.org/content/10.1101/2025.10.22.683922v1?rss=1 Zgeib, K. Hui, T. Garcia, S. Hashemi, Z. Nejati, S. Lim, C. Matouba, D. Inamdar, A. Li, C. Khiabanian, H. Lu, B. Perekatt, A. O. 2025-10-23 doi:10.1101/2025.10.22.683922 Cold Spring Harbor Laboratory Press 2025-10-23 <![CDATA[ Is the whole more than the sum of its parts? Considering global and local features of the connectome improves prediction of individuals and phenotype ]]> https://biorxiv.org/content/10.1101/2025.10.22.683965v1?rss=1 Riley, S. Cheng, A. Wang, Y.-W. Shen, X. Zhao, Y. Holmes, A. Constable, R. T. Yip, S. W. 2025-10-23 doi:10.1101/2025.10.22.683965 Cold Spring Harbor Laboratory Press 2025-10-23 <![CDATA[ Corylus avellana disease management: using metagenomics to illuminate the rhizosphere microbiome of Corylus ]]> https://biorxiv.org/content/10.1101/2025.10.22.684018v1?rss=1 Robinson, J. K. Steele, J. Molnar, T. J. Regan, S. diCenzo, G. C. 2025-10-23 doi:10.1101/2025.10.22.684018 Cold Spring Harbor Laboratory Press 2025-10-23 <![CDATA[ Integrating theory and machine learning to reveal determinants of plasmid copy number ]]> https://biorxiv.org/content/10.1101/2025.10.23.684078v1?rss=1 10,000 plasmids, our machine learning model achieves significantly enhanced accuracy, with plasmid-encoded protein domains emerging as key predictors. Applying this framework, we conduct the first comprehensive analysis of PCN distributions across hundreds of thousands of metagenomic plasmids (IMG/PR database) and tens of thousands of clinical isolates, uncovering niche specific taxonomic PCN hotspots and ecological adaptations. These results provide critical insights into plasmid ecology, ARG surveillance and shed lights on the gut plasmidome, a "dark matter" in human microbiome. ]]> Shahzadi, I. Wang, T. Ullah, H. U. Maddamsetti, R. You, L. 2025-10-23 doi:10.1101/2025.10.23.684078 Cold Spring Harbor Laboratory Press 2025-10-23 <![CDATA[ Pharmacologic activation of HNF4α/γ restores epithelial barrier function in Crohn's disease. ]]> https://biorxiv.org/content/10.1101/2025.10.27.684895v1?rss=1 Halder, D. Ghazi, A. Wang, Y. Hou, J. K. Verzi, M. Khurana, S. 2025-10-27 doi:10.1101/2025.10.27.684895 Cold Spring Harbor Laboratory Press 2025-10-27 <![CDATA[ Acetylation of Axonal G3BP1 through ELP3 Accelerates Axon Regeneration ]]> https://biorxiv.org/content/10.1101/2025.10.28.685144v1?rss=1 Dalla Costa, I. Michenfelder, E. Siciliano, S. Tapita, A. Buchanan, C. N. Vaughn, L. S. Lee, J. Oses-Prieto, J. A. Ma, C. Thames, E. Samra, N. Ben-Dor, S. Haffner-Krausz, R. McElveen, M. Smith, T. P. Nawar, N. Manaswiyoungkul, P. Gunning, P. T. Fainzilber, M. Burlingame, A. Zhu, H. Perlson, E. Sahoo, P. K. Twiss, J. L. 2025-10-30 doi:10.1101/2025.10.28.685144 Cold Spring Harbor Laboratory Press 2025-10-30 <![CDATA[ Brain insulin signaling restores deficits in striatal dopamine release in overweight male mice with preexisting low D2-receptor expression ]]> https://biorxiv.org/content/10.1101/2025.10.28.685173v1?rss=1 Bocarsly, M. E. Mehr, J. B. Swanson, E. S. Sriramoji-Virdi, S. Authement, M. E. Shashikiran, S. Goldbach, H. Matsui, A. Rimondini, R. Bock, R. Alvarez, V. A. 2025-10-30 doi:10.1101/2025.10.28.685173 Cold Spring Harbor Laboratory Press 2025-10-30 <![CDATA[ Transcriptional Profiling of Commonly Used Liver Cancer Cell Lines Reveals Disease-Specific Modeling Potential and Authentication Concerns ]]> https://biorxiv.org/content/10.1101/2025.10.30.685599v1?rss=1 Sarfaraz, N. Rosen, G. Winkler, T. Patel, R. Somarowthu, S. Bouchard, M. 2025-10-31 doi:10.1101/2025.10.30.685599 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ Vibrio cholerae interaction with predatory bacteria on chitin suggests an alternative mode of biofilm formation in marine snow conditions ]]> https://biorxiv.org/content/10.1101/2025.10.31.685833v1?rss=1 Holt, J. D. Miller, K. A. Hunter, O. F. Zhang, E. Hinbest, A. J. Gerace, E. Olson, R. Kadouri, D. E. Nadell, C. D. 2025-10-31 doi:10.1101/2025.10.31.685833 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ RNA G-Quadruplexes Function as a Tunable Switch of FUS Phase Separation ]]> https://biorxiv.org/content/10.1101/2025.10.31.685846v1?rss=1 View larger version (21K): org.highwire.dtl.DTLVardef@1db3ea8org.highwire.dtl.DTLVardef@eec825org.highwire.dtl.DTLVardef@96187eorg.highwire.dtl.DTLVardef@2204ce_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Carey, J. L. Hayashi, M. Welebob, E. Ganser, L. R. Wang, H. Buckhaults, K. DePierro, J. A. Shi, Z. Shorter, J. Myong, S. Haeusler, A. Guo, L. 2025-11-01 doi:10.1101/2025.10.31.685846 Cold Spring Harbor Laboratory Press 2025-11-01 <![CDATA[ Genetic background and transient prenatal disruption of vitamin A signaling determine susceptibility to airway hyperresponsiveness in mice ]]> https://biorxiv.org/content/10.1101/2025.10.31.685835v1?rss=1 Otoshi, T. Kameshwar, A. K. S. Kotton, B. D. Seki, Y. Cardell, Z. Xiangyi, K. Matsuno, Y. Rajaram, P. Kim, Y.-K. Sharpton, S. M. Quadro, L. Cardoso, W. V. Suzuki, M. 2025-11-03 doi:10.1101/2025.10.31.685835 Cold Spring Harbor Laboratory Press 2025-11-03 <![CDATA[ Challenges and opportunities in detecting leaf water and carotenoid content across biomes from satellite multispectral indices ]]> https://biorxiv.org/content/10.1101/2025.11.01.686024v1?rss=1 Montes-Bojorquez, M. G. Robles-Zazueta, C. A. Tinoco-Ojanguren, C. Enquist, B. J. Frazier, A. E. Maitner, B. S. Massaine Moulatlet, G. Romo-Leon, J. R. Song, L. Hinojo-Hinojo, C. 2025-11-03 doi:10.1101/2025.11.01.686024 Cold Spring Harbor Laboratory Press 2025-11-03 <![CDATA[ Blind Prediction of Complex Water and Ion Ensembles Around RNA in CASP16 ]]> https://biorxiv.org/content/10.1101/2025.11.03.685595v1?rss=1 Kretsch, R. C. Posani, E. Baulin, E. F. Bujnicki, J. M. Bussi, G. Cheatham, T. E. Chen, S.-J. Elofsson, A. Farsani, M. A. Fisher, O. N. Gromiha, M. M. Gupta, A. Hamada, M. Harini, K. Hu, G. Huang, D. Iwakiri, J. Jain, A. Kagaya, Y. Kihara, D. Kmiecik, S. Krishnan, S. R. Kurisaki, I. Languin-Cattoen, O. Li, J. Li, S. Malekzadeh, K. Nakamura, T. Ni, W. Nithin, C. Palo, M. Z. Park, J. H. Pilla, S. P. Poblete, S. Pucci, F. Punuru, P. Saha, A. Sato, K. Srivastava, A. Terashi, G. Tugolukova, E. Verburgt, J. Wuyun, Q. Zerze, G. H. Zhang, K. Zhang, S. Zhen 2025-11-03 doi:10.1101/2025.11.03.685595 Cold Spring Harbor Laboratory Press 2025-11-03 <![CDATA[ Defining the Mycobacterium tuberculosis Pangenome and Suggestions for a New Composite Reference Sequence ]]> https://biorxiv.org/content/10.1101/2025.11.03.686283v1?rss=1 Chitale, P. Ocke, E. Odom, A. R. Fan, H. Henoch, A. Vasco, K. Fogarty, E. C. Grady, C. Lemenze, A. D. Kumar, P. Manning, S. Eren, A. M. Johnson, W. E. Alland, D. 2025-11-03 doi:10.1101/2025.11.03.686283 Cold Spring Harbor Laboratory Press 2025-11-03 <![CDATA[ Shell-bound archives: uncovering nematode encapsulations in the Galapagos' largest radiation ]]> https://biorxiv.org/content/10.1101/2025.11.03.686299v1?rss=1 Fuster-Calvo, A. Oiler, I. M. MacDonald, A. Parent, C. Massol, F. Burin, G. Phillips, J. G. Rae, R. Gravel, D. 2025-11-05 doi:10.1101/2025.11.03.686299 Cold Spring Harbor Laboratory Press 2025-11-05 <![CDATA[ Nitric oxide tunes secreted metabolite bioactivity ]]> https://biorxiv.org/content/10.1101/2025.11.05.686753v1?rss=1 Lonergan, Z. R. Weisflog, S. L. Scurria, M. Li, J. Thalhammer, K. Gutierrez, O. Conway, S. J. Newman, D. K. 2025-11-05 doi:10.1101/2025.11.05.686753 Cold Spring Harbor Laboratory Press 2025-11-05 <![CDATA[ Characterization of an Open-Channel Structure and Lateral Conduction Pathway in the Cation-Selective Pentameric Ligand-Gated Ion Channel, ELIC ]]> https://biorxiv.org/content/10.1101/2025.11.06.686614v1?rss=1 Arcario, M. J. Wu-Chen, E. J. Henin, J. Brannigan, G. Cheng, W. W.-L. 2025-11-08 doi:10.1101/2025.11.06.686614 Cold Spring Harbor Laboratory Press 2025-11-08 <![CDATA[ Graph attention with structural features improves the generalizability of identifying functional sequences at a protein interface ]]> https://biorxiv.org/content/10.1101/2025.11.04.686550v1?rss=1 Ash, J. E. Francino-Urdaniz, I. M. Kells, S. P. Davis, C. N. Whitehead, T. A. Khare, S. D. 2025-11-10 doi:10.1101/2025.11.04.686550 Cold Spring Harbor Laboratory Press 2025-11-10 <![CDATA[ Optical tweezers combined with FRET tension sensor reveal force-dependent vinculin dynamics ]]> https://biorxiv.org/content/10.1101/2025.11.10.687568v1?rss=1 Dubois, C. Cohen, R. I. Boustany, N. N. Westbrook, N. 2025-11-10 doi:10.1101/2025.11.10.687568 Cold Spring Harbor Laboratory Press 2025-11-10 <![CDATA[ CREG1 promotes autophagy and protects the heart against nutritional stress-induced injury and age-associated hypertrophy, fibrosis and diastolic dysfunction ]]> https://biorxiv.org/content/10.1101/2025.11.11.687936v1?rss=1 View larger version (60K): org.highwire.dtl.DTLVardef@1b9fc05org.highwire.dtl.DTLVardef@150e48aorg.highwire.dtl.DTLVardef@1cc47adorg.highwire.dtl.DTLVardef@75ed53_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Qi, Y. Pepe, R. J. Tejeda, G. Joo, Y. Yang, N. K. Hayes, K. B. rahimi, s. Zhou, Z. Li, S. Lee, L. 2025-11-13 doi:10.1101/2025.11.11.687936 Cold Spring Harbor Laboratory Press 2025-11-13 <![CDATA[ NUAK2 is a therapeutically tractable regulator of RNA splicing and tumor progression in neuroendocrine prostate cancer ]]> https://biorxiv.org/content/10.1101/2025.11.12.687734v1?rss=1 View larger version (91K): org.highwire.dtl.DTLVardef@1bb3e77org.highwire.dtl.DTLVardef@21857org.highwire.dtl.DTLVardef@18c2f26org.highwire.dtl.DTLVardef@6ba82e_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Mehraj, U. Maimekov, U. Manzoor, S. Cordova, E. Patel, M. Mancera-Ortiz, I. Y. Howell, S. Davis-Gilbert, Z. W. Wang, M.-E. Chen, M. Park, J. W. Wang, Y. Armstrong, A. J. Huang, J. Drewry, D. H. Mitrofanova, A. Macias, E. 2025-11-13 doi:10.1101/2025.11.12.687734 Cold Spring Harbor Laboratory Press 2025-11-13 <![CDATA[ Leveraging FracMinHash Containment for Genomic dN/dS ]]> https://biorxiv.org/content/10.1101/2025.11.12.688019v1?rss=1 Rodriguez, J. S. Hera, M. R. Koslicki, D. 2025-11-13 doi:10.1101/2025.11.12.688019 Cold Spring Harbor Laboratory Press 2025-11-13 <![CDATA[ Variable Schwann cell merlin inactivation is targetable with TEAD1 inhibition in schwannomas. ]]> https://biorxiv.org/content/10.1101/2025.11.15.688608v1?rss=1 Laws, M. T. Bhatt, D. Mandal, D. Ramavenkat, N. Asuzu, D. T. Stoica, S. Rampalli, I. Mullaney, D. Laraba, L. Odom, H. G. Ravindra, N. Varghese, S. Tang, T. Zhang, X. Shern, J. F. Elkahloun, A. Sisay, B. Maric, D. Johnson, K. Abdullaev, Z. Aldape, K. Hertzano, R. P. Kim, H. J. Parkinson, D. Chittiboina, P. 2025-11-16 doi:10.1101/2025.11.15.688608 Cold Spring Harbor Laboratory Press 2025-11-16 <![CDATA[ Nuclear α1A-Adrenergic Receptor Regulation of cAMP Production by an Inside-Out MAP Kinase Signaling Pathway in Cardiac Myocytes ]]> https://biorxiv.org/content/10.1101/2025.11.20.687712v1?rss=1 Fiore, C. M. Rudokas, M. Masuda, R. Khamsopha, B. Sherpa, R. T. Moshal, K. S. Agarwal, S. R. Harvey, R. D. 2025-11-21 doi:10.1101/2025.11.20.687712 Cold Spring Harbor Laboratory Press 2025-11-21 <![CDATA[ Lipid droplets promote the aberrant liquid-liquid phase separation of alpha-synuclein leading to impaired energy homeostasis ]]> https://biorxiv.org/content/10.1101/2025.11.20.689615v1?rss=1 Cevallos, J. Eubanks, E. Jung, S. Huang, Y. Guadagno, E. Suvvari, N. R. Doshi, A. Ravinutala, N. Mosera, A. Ramalingam, N. Tripathi, A. Bartels, T. Dettmer, U. Kara, E. 2025-11-21 doi:10.1101/2025.11.20.689615 Cold Spring Harbor Laboratory Press 2025-11-21 <![CDATA[ Independent Lateralization of Language, Attention, and Numerical Cognition Across Task and Rest ]]> https://biorxiv.org/content/10.1101/2025.11.23.690045v1?rss=1 Labache, L. Hesling, I. Zago, L. 2025-11-24 doi:10.1101/2025.11.23.690045 Cold Spring Harbor Laboratory Press 2025-11-24 <![CDATA[ Shift in pre-existing antibiotic heteroresistance explains AST change from susceptible to resistant during patient treatment ]]> https://biorxiv.org/content/10.1101/2025.11.27.690971v1?rss=1 Kittleson, B. Abbott, C. Kaye, K. Weiss, D. S. 2025-11-28 doi:10.1101/2025.11.27.690971 Cold Spring Harbor Laboratory Press 2025-11-28 <![CDATA[ Interplay of Spoonbill, Larp7 and survival motor neuron, in Drosophila model of Spinocerebellar Ataxia 8 non-coding RNA associated neurodegeneration ]]> https://biorxiv.org/content/10.64898/2025.11.30.691381v1?rss=1 Das, R. Pandey, P. Tripathi, B. K. Maurya, B. Mukherjee, A. Mutsuddi, M. 2025-12-02 doi:10.64898/2025.11.30.691381 Cold Spring Harbor Laboratory Press 2025-12-02 <![CDATA[ Cryptochrome 2 is necessary for promoting a blue light-independent chloroplast signal to control cellular degradation ]]> https://biorxiv.org/content/10.64898/2025.12.01.690775v1?rss=1 Tano, D. W. Palos, K. Fisher, K. E. Easter, R. A. Nelson, A. D. L. Woodson, J. D. 2025-12-03 doi:10.64898/2025.12.01.690775 Cold Spring Harbor Laboratory Press 2025-12-03 <![CDATA[ A developmentally regulated long-range enhancer-promoter contact mediates human neural development ]]> https://biorxiv.org/content/10.64898/2025.12.01.691702v1?rss=1 Bready, D. Wang, S. Ravn-Boess, N. Frenster, J. Sabio, J. Kushmakov, R. Clark, F. Guerrero, A. Lapierre, C. Galbraith, K. Do, C. Lhoumaud, P. Prado, J. Jiang, A. Haddock, S. Kim, C. D. Snuderl, M. Lionnet, T. Tsirigos, A. Skok, J. Placantonakis, D. G. 2025-12-03 doi:10.64898/2025.12.01.691702 Cold Spring Harbor Laboratory Press 2025-12-03 <![CDATA[ A foundation model for microbial growth dynamics ]]> https://biorxiv.org/content/10.64898/2025.12.01.691707v1?rss=1 Holmes, Z. A. Shyti, I. Hoffman, A. L. Duncker, K. E. Ma, H. R. Zhou, Z. Lee, D. Maddamsetti, R. Kim, K. Simsek, E. Hamrick, G. S. Son, H. Villalobos, C. A. Lu, J. Ha, Y. Shende, A. R. Yao, Z. Liu, S. Shapiro, D. M. Kholina, K. Davis, H. Baig, Y. Wu, F. Wang, S. Wang, X. Chatterjee, P. Lynch, M. D. Lopatkin, A. J. David, L. A. Chory, E. You, L. 2025-12-03 doi:10.64898/2025.12.01.691707 Cold Spring Harbor Laboratory Press 2025-12-03 <![CDATA[ Tex15 is required for vomeronasal sensory neuron diversity and male pheromone detection ]]> https://biorxiv.org/content/10.64898/2025.12.03.690614v1?rss=1 Boutros Ghali, N. Kramer, P. Edwards, R. Ruzina, I. Zaidi, Z. Monahan, K. 2025-12-05 doi:10.64898/2025.12.03.690614 Cold Spring Harbor Laboratory Press 2025-12-05 <![CDATA[ Decreased endothelial cell retinoic acid signaling accelerates progression of single ventricle pulmonary arteriovenous malformations ]]> https://biorxiv.org/content/10.64898/2025.12.08.693095v1?rss=1 Rousseau, H. Wan, T. Nguyen, N. Wendt Andrae, J. Tschannen, M. Mathison, A. J. Jin, V. Groh, O. Zhou, X. Meadows, S. M. Ramchandran, R. Shmarakov, I. Pan, A. Spearman, A. D. 2025-12-11 doi:10.64898/2025.12.08.693095 Cold Spring Harbor Laboratory Press 2025-12-11 <![CDATA[ Retrospective analysis of Pseudomonas aeruginosa clinical isolates for secreted PrpL protease: a key virulence factor associated with corneal tissue damage ]]> https://biorxiv.org/content/10.64898/2025.12.11.693724v1?rss=1 Parker, D. S. Azuama, O. C. Zafar, K. Goguen, J. D. Leong, J. M. Parveen, N. 2025-12-11 doi:10.64898/2025.12.11.693724 Cold Spring Harbor Laboratory Press 2025-12-11 <![CDATA[ Monoallelic expression characterizes a distinct molecular and clinical group of breast tumors ]]> https://biorxiv.org/content/10.64898/2025.12.09.692870v1?rss=1 Arabzadeh, M. Singh, A. Payne, K. K. Ganesan, S. Khiabanian, H. 2025-12-12 doi:10.64898/2025.12.09.692870 Cold Spring Harbor Laboratory Press 2025-12-12 <![CDATA[ Hierarchical Community Structure of the Adult Drosophila Connectome Reveals Conserved Circuit Archetypes ]]> https://biorxiv.org/content/10.64898/2025.12.10.689094v1?rss=1 Betzel, R. Del Rio, O. Labora, N. Dvali, S. Larsen, B. Lynn, C. W. Misic, B. Parkes, L. Sporns, O. Tervo-Clemmens, B. Puxeddu, M. G. Seguin, C. 2025-12-13 doi:10.64898/2025.12.10.689094 Cold Spring Harbor Laboratory Press 2025-12-13 <![CDATA[ HDAC3 inhibition harnesses learning-induced neurobiological mechanisms to enhance signal-in-noise responsivity in auditory cortex and behavior ]]> https://biorxiv.org/content/10.64898/2025.12.15.694497v1?rss=1 Atesyakar, N. Bieszczad, K. 2025-12-16 doi:10.64898/2025.12.15.694497 Cold Spring Harbor Laboratory Press 2025-12-16 <![CDATA[ Senescent CD8+ T Effector Memory Cells are Functionally Impaired, Enriched in Aging and Disease, and a Barrier to Immunotherapy ]]> https://biorxiv.org/content/10.64898/2025.12.16.694716v1?rss=1 Turano, P. S. Akbulut, E. Aquino, N. Garza-Martinez, L. Singh, S. Yap, G. S. Fitzgerald-Bocarsly, P. Martinez-Zamudio, R. I. Herbig, U. 2025-12-19 doi:10.64898/2025.12.16.694716 Cold Spring Harbor Laboratory Press 2025-12-19 <![CDATA[ Susceptibility of Glucose Regulation to Social Isolation ]]> https://biorxiv.org/content/10.64898/2025.12.18.695168v1?rss=1 Lamont, H. Oyama, R. Munoz, P. D. Siegel, D. Baringanire, P. Vargas, V. Bocarsly, M. E. Routh, V. Carcea, I. 2025-12-22 doi:10.64898/2025.12.18.695168 Cold Spring Harbor Laboratory Press 2025-12-22 <![CDATA[ 53BP1 condensates function as bioreactors for NHEJ directed DNA repair and insulators to determine pathway choice ]]> https://biorxiv.org/content/10.64898/2025.12.19.695596v1?rss=1 Garabedian, M. V. Zhang, T. Datta, A. Wang, W. Wadley, M. Greenberg, R. A. Good, M. C. 2025-12-23 doi:10.64898/2025.12.19.695596 Cold Spring Harbor Laboratory Press 2025-12-23 <![CDATA[ Combinatorial Protein Language Model-Guided Engineering of TEV Protease for Enhanced Stability and Production ]]> https://biorxiv.org/content/10.64898/2025.12.19.695604v1?rss=1 Lee, T. H. Liu, S. Li, Y. Nguyen, T. He, Z. Khare, S. Yi, L. 2025-12-23 doi:10.64898/2025.12.19.695604 Cold Spring Harbor Laboratory Press 2025-12-23 <![CDATA[ A dietary pan-amino acid dropout screen in vivo reveals a critical role for histidine in T-ALL ]]> https://biorxiv.org/content/10.64898/2025.12.21.694897v1?rss=1 Mandleywala, K. Ulrich, S. da Silva-Diz, V. Sharma, P. Thai, C. Kim, O. Aleksandrova, M. Chung, G. Eggers, C. Luetjohann, D. Kulkarni, T. Singh, A. Diaz-Rubio, M. E. Wierer, M. Leidel, S. A. Su, X. White, E. P. Rabinowitz, J. D. Morscher, R. J. Herranz, D. 2025-12-23 doi:10.64898/2025.12.21.694897 Cold Spring Harbor Laboratory Press 2025-12-23 <![CDATA[ The C. elegans WASH complex supports epithelial polarity by promoting endosomal sorting of Cadherin ]]> https://biorxiv.org/content/10.64898/2025.12.23.696084v1?rss=1 Irizarry-Barreto, P. Smolyn, J. Brown, V. Ramamurthy, B. Soto, M. C. 2025-12-25 doi:10.64898/2025.12.23.696084 Cold Spring Harbor Laboratory Press 2025-12-25 <![CDATA[ Combinational adjuvants delivered by ink-jet potentiate naked mRNA vaccines for robust protection against infectious diseases ]]> https://biorxiv.org/content/10.64898/2025.12.24.696305v1?rss=1 Qiao, N. Ishikawa, J. Yasui, F. Sano, K. Miyakawa, K. Hayashi, A. Amiry, A. F. Haonan, L. Xueyang, Z. Sato, T. Pasqualini, R. Arap, W. Kataoka, K. Hasegawa, H. Kohara, M. Uchida, S. 2025-12-26 doi:10.64898/2025.12.24.696305 Cold Spring Harbor Laboratory Press 2025-12-26 <![CDATA[ Did you see the sound? A Bayesian Perspective on Crossmodal Perception in Low Vision ]]> https://biorxiv.org/content/10.64898/2025.12.24.696433v1?rss=1 Chan, A. Y. C. Stiles, N. R. B. Levitan, C. A. Tanguay, A. R. Shimojo, S. 2025-12-26 doi:10.64898/2025.12.24.696433 Cold Spring Harbor Laboratory Press 2025-12-26 <![CDATA[ Combined antagonism of Oncostatin M (OSM) and Interleukin 6 (IL-6) provides both anti-fibrotic and anti-inflammatory benefit in pulmonary fibrosis ]]> https://biorxiv.org/content/10.64898/2025.12.25.695625v1?rss=1 Ratsimandresy, R. A. Doran, E. Dengler, H. S. Headland, S. E. Wedeles, C. J. Guidi, R. Xu, D. Liu, J. Shi, Y. Wang, J. Uttarwar, S. Abbas, A. R. Sun, T. DePianto, D. J. Morshead, K. B. Arron, J. Rock, J. R. Bevers, J. Yadav, R. Ramalingam, T. Gao, X. Brightbill, H. D. Emson, C. L. Jeet, S. Arlantico, A. Wong, A. Yu, S. Tran, T. H. Leong, L. Chen, W. Dohse, M. Austin, C. Caplazi, P. Panettieri, R. A. Koziol-White, C. Jester, W. F. Shaw, A. Avraham, S. Menon, H. Darmanis, S. Modrusan, Z. Kajihara, K. Kanamori, M. Shimada, H. West, N. R. Nakamura, G. 2025-12-26 doi:10.64898/2025.12.25.695625 Cold Spring Harbor Laboratory Press 2025-12-26 <![CDATA[ Comparative Transcriptomics Reveals Genes Commonly Induced by Distinct Stressors in Chlamydia ]]> https://biorxiv.org/content/10.64898/2025.12.30.696969v1?rss=1 Haines, R. Wan, D. Zhong, G. Fan, H. 2025-12-30 doi:10.64898/2025.12.30.696969 Cold Spring Harbor Laboratory Press 2025-12-30 <![CDATA[ Transcriptional Heterogeneity Reveals a Synaptic Gene Program in Developing and Adult Human Oligodendrocyte Precursor Cells ]]> https://biorxiv.org/content/10.64898/2026.01.01.697017v1?rss=1 2,300 highly pure OPCs from post-conceptional week (PCW) 17 human cortex using an optimized PDGFR-based immunopanning and performed single-cell RNA sequencing. Unsupervised clustering revealed four transcriptionally distinct embryonic OPC subsets, including a previously unrecognized population that expressed genes linked to synaptic development, synaptic signaling, and neuromodulation. This subset - designated embryonic synaptic OPCs (eSyn-OPCs) - comprised approximately 28.5% of all embryonic OPCs in the cortex and was characterized by robust expression of synapse-associated secreted factors (THBS2, WNT5A, WNT7A, PLAT, ACHE) and multiple neurotransmitter receptor subunits. Histological analyses across PCW 12-22 demonstrated that eSyn-OPCs first appear around PCW 15 and are enriched in proliferative germinal zones. Spatial transcriptomics confirmed their localization near neural stem and progenitor cells, suggesting proximal neuron-OPC communication during early cortical assembly. Purified eSyn-OPCs differentiated into mature oligodendrocytes in vitro, confirming their oligodendrocyte lineage identity. Reanalysis of adult human single-nucleus RNA-seq datasets uncovered a transcriptionally analogous OPC subset (adult synaptic OPCs, aSyn-OPCs), though with reduced representation of structural synaptic genes and neurotransmitter receptor diversity compared to eSyn-OPCs. Together, these results identify a synaptically specialized OPC population in both developing and adult human cortex and reveal that eSyn-OPCs possess unexpectedly rich synaptic signaling machinery. These findings suggest that human OPCs may participate directly in neuron-glia communication during early cortical development and raise the possibility of developmental stage-specific roles for eSyn-OPCs in shaping neural circuit formation. ]]> Grinberg, A. R. Liu, L. Patel, I. Guntur, B. Glass, I. A. Birth Defects Research Laboratory, Shinoda, K. Nobuta, H. 2026-01-02 doi:10.64898/2026.01.01.697017 Cold Spring Harbor Laboratory Press 2026-01-02 <![CDATA[ Treponema pallidum TprD and TprK Are Adhesins and Promote Spirochetes Opsonophagocytosis ]]> https://biorxiv.org/content/10.64898/2026.01.04.697605v1?rss=1 Parveen, N. Zafar, K. Azuama, O. C. Xu, L. H. Giacani, L. 2026-01-05 doi:10.64898/2026.01.04.697605 Cold Spring Harbor Laboratory Press 2026-01-05 <![CDATA[ The IKC-leptin axis functions as a molecular bridge between neurodevelopment and endocrine signaling ]]> https://biorxiv.org/content/10.64898/2026.01.05.697408v1?rss=1 Forzisi, E. Gaur, A. Gaur, A. Philip, R. Miranda, M. d. C. Anand, S. Impaloni, C. Leonard, K. Venkateswaran, S. Sesti, F. 2026-01-05 doi:10.64898/2026.01.05.697408 Cold Spring Harbor Laboratory Press 2026-01-05 <![CDATA[ Plasmid transfer and loss probabilities interactively determine antibiotic resistance spread in surface-associated bacterial biomass ]]> https://biorxiv.org/content/10.64898/2026.01.08.698332v1?rss=1 Ramoneda, J. Vinod, D. P. Ma, Y. Ruan, C. Schmidt, J. Angst, D. C. Manhart, M. Johnson, D. R. 2026-01-08 doi:10.64898/2026.01.08.698332 Cold Spring Harbor Laboratory Press 2026-01-08 <![CDATA[ Elucidating Odorant Masking Effects in Food Matrices Through Olfactory Receptor-Based Profiling ]]> https://biorxiv.org/content/10.64898/2026.01.13.699200v1?rss=1 View larger version (48K): org.highwire.dtl.DTLVardef@ea9d72org.highwire.dtl.DTLVardef@106ba4dorg.highwire.dtl.DTLVardef@b1293forg.highwire.dtl.DTLVardef@10afcfe_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Hu, B. Zheng, H. Liang, H. Lv, H. Xiao, Q. Jiang, Y. Lu, Q. Niu, Y. Wang, H. Xiao, Z. 2026-01-15 doi:10.64898/2026.01.13.699200 Cold Spring Harbor Laboratory Press 2026-01-15 <![CDATA[ Wasf1 deletion attenuates tau hyperphosphorylation, microglial state transition, and cognitive deficits in P301S tau mice ]]> https://biorxiv.org/content/10.64898/2026.01.14.699391v1?rss=1 Berdasco, C. Cho, W.-H. Lee, J. Annu, A. Ledo, J. H. Jeong, Y. Y. Kim, Y.-S. An, S. S. Tanaka, Y. Ahn, J.-H. Kim, Y. 2026-01-15 doi:10.64898/2026.01.14.699391 Cold Spring Harbor Laboratory Press 2026-01-15 <![CDATA[ Spindle biochemistry responds to compressive force from thenuclear envelope to tune spindle dynamics during closed mitosis ]]> https://biorxiv.org/content/10.64898/2026.01.15.699759v1?rss=1 Mahoney, T. Needham, C. Hakeem, R. Begley, M. Medina, C. P. Elting, M. W. 2026-01-15 doi:10.64898/2026.01.15.699759 Cold Spring Harbor Laboratory Press 2026-01-15 <![CDATA[ Structure and signaling mechanism of Helicobacter pylori transducer-like protein D ]]> https://biorxiv.org/content/10.64898/2026.01.16.699579v1?rss=1 Franco, K. DiIorio, M. Simpkin, A. J. Keegan, R. Kallio, K. Goers-Sweeney, E. Colbert, M. Remington, S. J. Cassidy, C. K. Kulczyk, A. Baylink, A. 2026-01-17 doi:10.64898/2026.01.16.699579 Cold Spring Harbor Laboratory Press 2026-01-17 <![CDATA[ SE3Bind: SE(3)-equivariant model for antibody-antigen binding affinity prediction ]]> https://biorxiv.org/content/10.64898/2026.01.17.700115v1?rss=1 Subedy, A. Bhadra-Lobo, S. Lamoureux, G. 2026-01-18 doi:10.64898/2026.01.17.700115 Cold Spring Harbor Laboratory Press 2026-01-18 <![CDATA[ Zero-shot ecological annotation of microbial genomes with myLLannotator accelerates scientific discovery ]]> https://biorxiv.org/content/10.64898/2026.01.18.700140v1?rss=1 Lee, A. L. Sharma, A. Maddamsetti, R. 2026-01-21 doi:10.64898/2026.01.18.700140 Cold Spring Harbor Laboratory Press 2026-01-21 <![CDATA[ Septins buffer actomyosin forces to protect the nucleus from genotoxic mechanical stress ]]> https://biorxiv.org/content/10.64898/2026.01.21.700789v1?rss=1 Mayca-Pozo, F. Butts, S. M. Schaefer, A. W. Montagna, C. Spiliotis, E. T. 2026-01-21 doi:10.64898/2026.01.21.700789 Cold Spring Harbor Laboratory Press 2026-01-21 <![CDATA[ Pol γ possesses separate metal binding sites for polymerase and strand displacement functions ]]> https://biorxiv.org/content/10.64898/2026.01.25.701366v1?rss=1 View larger version (39K): org.highwire.dtl.DTLVardef@1be1dborg.highwire.dtl.DTLVardef@8912c5org.highwire.dtl.DTLVardef@12f5e75org.highwire.dtl.DTLVardef@e25d2a_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Baruch-Torres, N. Park, J. Mora-Garduno, J. Roy, A. Singh, A. Cisneros, G. A. Brieba, L. G. Patel, S. S. Yin, Y. W. 2026-01-25 doi:10.64898/2026.01.25.701366 Cold Spring Harbor Laboratory Press 2026-01-25 <![CDATA[ OSTM1 is a ubiquitin E3 ligase that suppresses B-cell malignancy by activating the cAMP/PKA/CREB pathway ]]> https://biorxiv.org/content/10.64898/2026.01.23.701155v1?rss=1 Tariq, M. U. Sheshadri, N. Shen, J. Jung, J. Li, R. Lu, K. Yan, J. Koch, M. C. Caso, G. Sajjad, H. Vallat, B. Burley, S. K. Sun, Y. Liu, T. Li, H. Hinrichs, C. Bertoni, F. Lin, R. Z. Wang, J. Wang, L. Y. Vacher, J. Xie, P. Zong, W.-X. 2026-01-26 doi:10.64898/2026.01.23.701155 Cold Spring Harbor Laboratory Press 2026-01-26 <![CDATA[ Hepatic Ketogenesis Attenuates Cardiac Hypertrophy via Metabolic Reprogramming ]]> https://biorxiv.org/content/10.64898/2026.01.30.702687v1?rss=1 Yamada, T. Morikawa, K. Fujiyama, A. Nagakura, T. Xu, Y. Kataoka, M. Umemoto, T. Bundo, M. Iwamoto, K. Ahmed, Z. Linna-Kuosmanen, S. Hanatani, S. Usuku, H. Matsuzawa, Y. Izumiya, Y. Yamamoto, E. Tsujita, K. Arima, Y. 2026-02-02 doi:10.64898/2026.01.30.702687 Cold Spring Harbor Laboratory Press 2026-02-02 <![CDATA[ α-tACS Modulates Reward-Dependent Pupil Responses and Corticostriatal Connectivity ]]> https://biorxiv.org/content/10.64898/2026.01.30.702963v1?rss=1 Smith, D. V. Wyngaarden, J. B. Weinstein, S. M. Illenberger, N. Liu, Y. Siegel, J. Krekelberg, B. 2026-02-02 doi:10.64898/2026.01.30.702963 Cold Spring Harbor Laboratory Press 2026-02-02 <![CDATA[ Loss of PIK3CA allows in vitro growth but not in vivo progression of KRAS mutant lung adenocarcinoma in a syngeneic orthotopic implantation model ]]> https://biorxiv.org/content/10.64898/2026.02.02.701385v1?rss=1 Booth, A. L. Caso, G. Rosati, B. Jiang, Y.-P. Zong, W.-X. Lin, R. Z. Bien, H. 2026-02-04 doi:10.64898/2026.02.02.701385 Cold Spring Harbor Laboratory Press 2026-02-04 <![CDATA[ Spatial Trophic Dynamics Shape and are Shaped by Desertification Transitions ]]> https://biorxiv.org/content/10.64898/2026.02.04.703762v1?rss=1 Halder, K. Bonachela, J. A. 2026-02-06 doi:10.64898/2026.02.04.703762 Cold Spring Harbor Laboratory Press 2026-02-06 <![CDATA[ Identification of collaborative cross mouse strains susceptible to chlamydial induction of hydrosalpinx ]]> https://biorxiv.org/content/10.64898/2026.02.06.704472v1?rss=1 Wu, Y. Abdelsalam, A. M. Fan, H. Baxter, V. K. Sun, X. Zhong, G. 2026-02-07 doi:10.64898/2026.02.06.704472 Cold Spring Harbor Laboratory Press 2026-02-07 <![CDATA[ BAP1 Loss Induces Senescence and Enhances the Response to Radiation Therapy and Senolytics ]]> https://biorxiv.org/content/10.64898/2026.02.05.704104v1?rss=1 Elsayed, A. M. Mosbeh, A. Eltasawi, E. G. Hanpude, P. Uddin, M. N. Cebulla, C. M. Abdel-Rahman, M. H. 2026-02-09 doi:10.64898/2026.02.05.704104 Cold Spring Harbor Laboratory Press 2026-02-09 <![CDATA[ Dual AAV amelioration of Lama2-null muscular dystrophy and neuropathy ]]> https://biorxiv.org/content/10.64898/2026.02.09.704845v1?rss=1 McKee, K. K. Yurchenco, P. D. 2026-02-10 doi:10.64898/2026.02.09.704845 Cold Spring Harbor Laboratory Press 2026-02-10 <![CDATA[ Co-expression-based models improve eQTL predictions and highlightnovel transcriptome-wide genes associated with schizophrenia ]]> https://biorxiv.org/content/10.64898/2026.02.10.704353v1?rss=1 Rossi, F. Sportelli, L. Kikidis, G. C. Grassi, G. Di Camillo, F. Bertolino, A. Blasi, G. Borcuk, C. Fusco, D. Hyde, T. M. Kleinman, J. E. Marnetto, D. Pellegrini, S. Rampino, A. Vitiello, B. ripke, s. Braun, A. Kraft, J. Belangero, S. I. Menezes, P. R. Arango, C. Walters, J. O'Donovan, M. C. Owen, M. J. Braff, D. Corvin, A. Morris, D. W. Domenici, E. van Os, J. Atbasoglu, E. Saka, M. C. Di Forti, M. baune, B. T. Pato, C. N. McQuillin, A. Golimbet, V. Kondratyev, N. Escott-Price, V. Gareeva, A. Khusnutdinova, E. Cervilla, J. A. Rivera, M. Laurent-Levins 2026-02-11 doi:10.64898/2026.02.10.704353 Cold Spring Harbor Laboratory Press 2026-02-11 <![CDATA[ Enzyme Classification via Semi-Supervised Functional ResidueLearning ]]> https://biorxiv.org/content/10.64898/2026.02.11.705200v1?rss=1 Gong, C. Zhang, D. Ouyang-Zhang, J. Liu, Q. Klivans, A. Diaz, D. 2026-02-14 doi:10.64898/2026.02.11.705200 Cold Spring Harbor Laboratory Press 2026-02-14 <![CDATA[ Developmentally programmed nuclear pore complex replacement enables oocyte specification ]]> https://biorxiv.org/content/10.64898/2026.02.13.705775v1?rss=1 Venkat, S. Nguyen, T. Blangini, C. Pollak, M. Schindler, K. Capelson, M. Rangan, P. 2026-02-16 doi:10.64898/2026.02.13.705775 Cold Spring Harbor Laboratory Press 2026-02-16 <![CDATA[ Combination Drug Therapy Reduces Iron Accumulation and Microglia-Mediated Pathologies in Neonatal Intraventricular Hemorrhage: A Biochemical and Transcriptomic Analysis ]]> https://biorxiv.org/content/10.64898/2026.02.14.705043v1?rss=1 Diaz, V. C. Sunshine, M. Hu, F. Shah, S. Huang, W. Thompson, C. I. Wolin, M. s. Subbian, S. La Gamma, E. F. Vinukonda, G. 2026-02-17 doi:10.64898/2026.02.14.705043 Cold Spring Harbor Laboratory Press 2026-02-17 <![CDATA[ Disentangling Schwann Cell and Neuronal TRPA1 Function in Mouse Models of Familial Episodic Pain Syndrome ]]> https://biorxiv.org/content/10.64898/2026.02.14.705765v1?rss=1 Marini, M. Chieca, M. Coppi, E. Bonacchi, L. Landini, L. Scuffi, I. Kwan, K. Papini, A. De Siena, G. Bellantoni, E. Timotei, L. Albanese, V. Ferroni, G. do Nascimento Melo, E. D. Birling, M.-C. Lorentz, R. Nassini, R. De Logu, F. 2026-02-17 doi:10.64898/2026.02.14.705765 Cold Spring Harbor Laboratory Press 2026-02-17 <![CDATA[ Breaking β-sheets in FUS prion-like domain preserves phase separation and function but prevents aggregation and toxicity ]]> https://biorxiv.org/content/10.64898/2026.02.17.706410v1?rss=1 View larger version (53K): org.highwire.dtl.DTLVardef@d15f63org.highwire.dtl.DTLVardef@1cd6221org.highwire.dtl.DTLVardef@e58126org.highwire.dtl.DTLVardef@181ec67_HPS_FORMAT_FIGEXP M_FIG C_FIG SUMMARYThe RNA-binding protein Fused in Sarcoma (FUS) undergoes phase separation as part of its physiological function but can aberrantly aggregate into solid-like assemblies in amyotrophic lateral sclerosis and frontotemporal dementia. To dissect the role of {beta}-sheets in both function and pathological transition, we engineered {beta}-sheet-preventing FUS variants via targeted proline residue insertions in the prion-like disordered region. These variants retained native structure, motions, and phase behavior yet showed dramatically reduced aggregation, both as an isolated prion-like domain and in full-length FUS. Crucially, these variants maintained a panel of FUS cellular functions that depend on FUS condensation but prevented FUS toxicity in fly models of neurodegeneration. Our findings implicate {beta}-sheets as key drivers of FUS condensate maturation and neuronal toxicity, highlighting {beta}-sheet modulation as a therapeutic strategy against FUS-related neurodegeneration. HIGHLIGHTSO_LITargeted proline additions disrupt {beta}-sheet formation in FUS without altering native conformations, dynamics, or phase separation behavior C_LIO_LI{beta}-sheet-deficient FUS variants prevent aggregation and liquid-to-solid transitions while retaining key biological functions C_LIO_LIIn vivo models reveal attenuated toxicity of {beta}-sheet-deficient FUS in Drosophila C_LIO_LI{beta}-sheets are identified as central drivers of condensate maturation and neuronal death, offering a therapeutic entry point for modulating prion-like domain pathology C_LI ]]> Wake, N. Alcalde, J. Jutzi, D. Bajaj, A. Kour, S. Barai, M. Weng, S.-L. Cummings, S. Zheng, T. Anderson, E. N. Wang, S.-H. Puterbaugh, R. Z. Bosco, D. A. Schuster, B. S. Mittal, J. Pandey, U. B. Ruepp, M.-D. Fawzi, N. L. 2026-02-18 doi:10.64898/2026.02.17.706410 Cold Spring Harbor Laboratory Press 2026-02-18 <![CDATA[ Analysis and design of disordered polypeptides with optimized sequence patterning properties ]]> https://biorxiv.org/content/10.64898/2026.02.20.707115v1?rss=1 Singh, A. Ukperaj, A. I. Dignon, G. L. 2026-02-20 doi:10.64898/2026.02.20.707115 Cold Spring Harbor Laboratory Press 2026-02-20 <![CDATA[ Defective BRCA1-mediated DNA end resection drives tandem duplication formation and FANCM synthetic lethality ]]> https://biorxiv.org/content/10.64898/2026.02.20.706968v1?rss=1 Scully, R. Namrata, N. Marin Gonzalez, A. Menghi, F. Nguyen, D. Willis, N. Wientjens, E. Xia, B. Jonkers, J. Liu, E. 2026-02-22 doi:10.64898/2026.02.20.706968 Cold Spring Harbor Laboratory Press 2026-02-22 <![CDATA[ A method for assessing approach and avoidance behavior across multiple olfactory stimuli in mice including multivariate hypothesis comparisons ]]> https://biorxiv.org/content/10.64898/2026.02.21.707096v1?rss=1 Rosenthal, M. C. Bakir, A. K. Gaikwad, A. Clark, K. Garcia, A. T. McGann, J. P. 2026-02-23 doi:10.64898/2026.02.21.707096 Cold Spring Harbor Laboratory Press 2026-02-23 <![CDATA[ Generalization and extinction of learned fear alter primary sensory input to the brain ]]> https://biorxiv.org/content/10.64898/2026.02.25.708099v1?rss=1 Rosenthal, M. C. Bakir, A. K. McGann, J. P. 2026-02-27 doi:10.64898/2026.02.25.708099 Cold Spring Harbor Laboratory Press 2026-02-27 <![CDATA[ Female iPSC X-chromosome inactivation (XCI) erosion and its transcriptomic effects during CRISPR gene editing and neural differentiation ]]> https://biorxiv.org/content/10.64898/2026.02.27.708613v1?rss=1 Thapa, C. Oh, E. K. Sirkin, D. Lahey, J. Diaz de Leon Guerrerro, S. McCarroll, A. Gowda, P. Zhang, H. Barishman, A. Peyton, L. Zhang, S. Pollak, R. M. Hart, R. P. Pato, C. N. Kreimer, A. Mulle, J. G. Sanders, A. R. Pang, Z. Duan, J. 2026-03-01 doi:10.64898/2026.02.27.708613 Cold Spring Harbor Laboratory Press 2026-03-01 <![CDATA[ Pancreatic cancer-associated organ dysfunction promotes muscle autophagy and contributes to peripheral tissue wasting ]]> https://biorxiv.org/content/10.64898/2026.02.27.708635v1?rss=1 Gultekin, Y. Sivanand, S. Eghbalian, K. M. Barbeau, A. M. Abbott, K. L. Eng, G. Tavernier, V. L. Do, B. T. Shin, H. Ozcelik, E. Hu, S. Kunchok, T. Waite, M. Rideout, W. M. Kizlier, Y. K. Sharygin, D. A. Freed-Pastor, W. Jacks, T. White, E. Yilmaz, O. H. Nowak, J. A. Wolpin, B. M. Vander Heiden, M. G. 2026-03-01 doi:10.64898/2026.02.27.708635 Cold Spring Harbor Laboratory Press 2026-03-01 <![CDATA[ vToxiNet: a biologically constrained deep learning framework for interpretable prediction of drug-induced hepatotoxicity ]]> https://biorxiv.org/content/10.64898/2026.02.26.708259v1?rss=1 Jia, X. Wang, T. Russo, D. P. Aleksunes, L. M. Xiao, S. Zhu, H. 2026-03-02 doi:10.64898/2026.02.26.708259 Cold Spring Harbor Laboratory Press 2026-03-02 <![CDATA[ STCS: A Platform-Agnostic Framework for Cell-Level Reconstruction in Sequencing-Based Spatial Transcriptomics ]]> https://biorxiv.org/content/10.64898/2026.02.26.708370v1?rss=1 Chen Wu, L. Hu, X. Zhan, F. Sun, C. Gonzales, J. Ofer, R. Tran, T. Verzi, M. P. Liu, L. Yang, J. 2026-03-02 doi:10.64898/2026.02.26.708370 Cold Spring Harbor Laboratory Press 2026-03-02 <![CDATA[ An Inositol Receptor Orchestrates Carbon Utilization and Fungal Virulence ]]> https://biorxiv.org/content/10.64898/2026.03.02.708983v1?rss=1 Wang, Y. Tancer, R. Wear, M. Jackson, K. M. Zhang, Y. Gao, Y.-G. Nielsen, k. Casadevall, A. Xue, C. 2026-03-02 doi:10.64898/2026.03.02.708983 Cold Spring Harbor Laboratory Press 2026-03-02