bioRxiv Channel: Carnegie Mellon University https://biorxiv.org This feed contains articles for bioRxiv Channel "Carnegie Mellon University" bioRxiv bioRxiv https://biorxiv.org <![CDATA[ Motor cortex retains and reorients neural dynamics during motor imagery ]]> https://biorxiv.org/content/10.1101/2023.01.17.524394v1?rss=1 Dekleva, B. M. Chowdhury, R. H. Batista, A. P. Chase, S. M. Yu, B. M. Boninger, M. L. Collinger, J. L. 2023-01-19 doi:10.1101/2023.01.17.524394 Cold Spring Harbor Laboratory Press 2023-01-19 <![CDATA[ Post-Ischemic Reorganization of Sensory Responses in Cerebral Cortex ]]> https://biorxiv.org/content/10.1101/2023.01.18.524583v1?rss=1 Hayley, P. Tuchek, C. Dalla, S. Borrell, J. Murphy, M. D. Nudo, R. J. Guggenmos, D. J. 2023-01-20 doi:10.1101/2023.01.18.524583 Cold Spring Harbor Laboratory Press 2023-01-20 <![CDATA[ Sensory constraints on volitional modulation of the motor cortex ]]> https://biorxiv.org/content/10.1101/2023.01.22.525098v1?rss=1 Fisac, C. F. Chase, S. M. 2023-01-23 doi:10.1101/2023.01.22.525098 Cold Spring Harbor Laboratory Press 2023-01-23 <![CDATA[ Measuring and Modeling Macrophage Growth using a Lab-on-CMOS Capacitance Sensing Microsystem ]]> https://biorxiv.org/content/10.1101/2023.01.27.525955v1?rss=1 Smith, K. Lin, C.-Y. Gilpin, Y. Wayne, E. C. Dandin, M. 2023-01-28 doi:10.1101/2023.01.27.525955 Cold Spring Harbor Laboratory Press 2023-01-28 <![CDATA[ Cell-free multi-omics analysis reveals tumor status-informative signatures in gastrointestinal cancer patients' plasma ]]> https://biorxiv.org/content/10.1101/2023.01.31.526431v1?rss=1 Tao, Y. Xing, S. Zuo, S. Bao, P. Jin, Y. Li, Y. Wu, Y. Chen, S. Wang, X. Zhu, Y. Feng, Y. Zhang, X. Wang, X. Xi, Q. Lu, Q. Wang, P. Lu, Z. J. 2023-02-03 doi:10.1101/2023.01.31.526431 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Bird wings are shaped by thermoregulatory demand for heat dissipation ]]> https://biorxiv.org/content/10.1101/2023.02.06.527306v1?rss=1 Weeks, B. C. Harvey, C. Tobias, J. A. Sheard, C. Zhou, Z. Fouhey, D. F. 2023-02-06 doi:10.1101/2023.02.06.527306 Cold Spring Harbor Laboratory Press 2023-02-06 <![CDATA[ Inferring context-dependent computations through linear approximations of prefrontal cortex dynamics ]]> https://biorxiv.org/content/10.1101/2023.02.06.527389v1?rss=1 Soldado Magraner, J. Mante, V. Sahani, M. 2023-02-06 doi:10.1101/2023.02.06.527389 Cold Spring Harbor Laboratory Press 2023-02-06 <![CDATA[ Neutralization of SARS-CoV-2 BQ.1.1 and XBB.1.5 by Breakthrough Infection Sera from Previous and Current Waves in China ]]> https://biorxiv.org/content/10.1101/2023.02.07.527406v1?rss=1 Wang, X. Jiang, S. Jiang, S. Li, X. Ai, J. Lin, K. Lv, S. Zhang, S. Li, M. He, X. Li, D. Li, C. Zhao, C. Zhao, X. Qiao, R. Cui, Y. Chen, Y. Li, J. Cai, G. Li, J. Dai, L. Hu, Z. Zhang, W. Zhang, Y. Wang, P. 2023-02-07 doi:10.1101/2023.02.07.527406 Cold Spring Harbor Laboratory Press 2023-02-07 <![CDATA[ ADAM10 mediates macroglial cell fate decisions in the developing brain ]]> https://biorxiv.org/content/10.1101/2023.02.11.527059v1?rss=1 40 substrates reported for ADAM10, including Notch, Delta-like ligand-1 (Dll1), and N-cadherin. To date, however, its function in the brain has been largely unknown. We used genetic manipulation to delete Adam10 specifically from glial progenitors in developing brains and observed that conditional knockout mice showed locomotor abnormalities. They all died within 4 months with apparent defects in the cerebellum. By comprehensively analyzing data from bulk RNA sequencing, single-cell RNA sequencing, and staining of the cerebellum, we found that ADAM10 promoted astrocyte generation under physiological conditions. Upon the removal of Adam10 in glial progenitors, the production of oligodendrocytes vastly increased, whereas the generation of astrocytes was substantially inhibited. Our results showed that ADAM10 plays a critical role in macroglial cell fate decisions during brain development. ]]> Ge, W.-p. Wang, Y. Liang, Y. Ai, D. Li, J.-L. Feng, Z. Guo, Z. Chen, X.-j. Zhang, T. zou, X. Gao, J.-L. Gao, X. Hu, X.-L. Wu, L.-J. Sun, W. Zhu, S. Duan, S. Wang, W. 2023-02-12 doi:10.1101/2023.02.11.527059 Cold Spring Harbor Laboratory Press 2023-02-12 <![CDATA[ Electroacupuncture prevents astrocyte atrophy to alleviate depression ]]> https://biorxiv.org/content/10.1101/2023.02.15.528709v1?rss=1 Lin, S.-S. Zhou, B. Chen, B.-J. Jiang, R. Li, B. Illes, P. Semyanov, A. Tang, Y. Verkhratsky, A. 2023-02-15 doi:10.1101/2023.02.15.528709 Cold Spring Harbor Laboratory Press 2023-02-15 <![CDATA[ Lipid nanoparticle structure and delivery route during pregnancy dictates mRNA potency, immunogenicity, and health in the mother and offspring ]]> https://biorxiv.org/content/10.1101/2023.02.15.528720v1?rss=1 Chaudhary, N. Newby, A. N. Arral, M. L. Yerneni, S. S. LoPresti, S. T. Doerfler, R. Petersen, D. M. S. Fox, B. Coon, T. Malaney, A. Sadovsky, Y. Whitehead, K. A. 2023-02-15 doi:10.1101/2023.02.15.528720 Cold Spring Harbor Laboratory Press 2023-02-15 <![CDATA[ Identifying promising sequences for protein engineering using a deep Transformer Protein Language Model ]]> https://biorxiv.org/content/10.1101/2023.02.15.528697v1?rss=1 Frisby, T. S. Langmead, C. J. 2023-02-16 doi:10.1101/2023.02.15.528697 Cold Spring Harbor Laboratory Press 2023-02-16 <![CDATA[ A Unified Pipeline for FISH Spatial Transcriptomics ]]> https://biorxiv.org/content/10.1101/2023.02.17.529010v1?rss=1 Cisar, C. Keener, N. Ruffalo, M. Paten, B. 2023-02-18 doi:10.1101/2023.02.17.529010 Cold Spring Harbor Laboratory Press 2023-02-18 <![CDATA[ Protective effect of plasma neutralization from prior SARS-CoV-2 Omicron infection against BA.5 subvariant symptomatic reinfection ]]> https://biorxiv.org/content/10.1101/2023.02.14.527605v1?rss=1 Chen, X. Xu, Y. Xie, Y. Song, W. Hu, Y. Yisimayi, A. Shao, F. Geng, L. Wang, Y. Gao, H. Shi, Y. Zhang, S. Jin, R. Shen, Z. Cao, Y. R. 2023-02-19 doi:10.1101/2023.02.14.527605 Cold Spring Harbor Laboratory Press 2023-02-19 <![CDATA[ Multi-omics and Pharmacological Characterization of Patient-derived Glioma Cell Lines ]]> https://biorxiv.org/content/10.1101/2023.02.20.529198v1?rss=1 Wu, M. Yuan, R. Ji, N. Lu, T. Wang, T. Zhang, J. Li, M. Cao, P. Zhao, J. Li, G. Li, J. Li, Y. Tang, Y. Gao, Z. Wang, X. Wu, A. Cheng, W. Ge, M. Cui, G. You, Y. Zhang, W. Wang, Q. Chen, J. 2023-02-21 doi:10.1101/2023.02.20.529198 Cold Spring Harbor Laboratory Press 2023-02-21 <![CDATA[ Distinct neurochemical influences on fMRI response polarity in the striatum ]]> https://biorxiv.org/content/10.1101/2023.02.20.529283v1?rss=1 Cerri, D. H. Albaugh, D. L. Walton, L. R. Katz, B. Wang, T.-W. Chao, T.-H. H. Zhang, W. Nonneman, R. J. Jiang, J. Lee, S.-H. Etkin, A. Hall, C. N. Stuber, G. D. Shih, Y.-Y. I. 2023-02-21 doi:10.1101/2023.02.20.529283 Cold Spring Harbor Laboratory Press 2023-02-21 <![CDATA[ Synthetic cell armor made of DNA origami ]]> https://biorxiv.org/content/10.1101/2023.02.20.529284v1?rss=1 Wang, W. Hayes, P. R. Ren, X. Taylor, R. E. 2023-02-21 doi:10.1101/2023.02.20.529284 Cold Spring Harbor Laboratory Press 2023-02-21 <![CDATA[ Integrating simultaneous motor imagery and spatial attention for EEG-BCI control ]]> https://biorxiv.org/content/10.1101/2023.02.20.529307v1?rss=1 Forenzo, D. Liu, Y. Kim, J. Ding, Y. Yoon, T. He, B. 2023-02-21 doi:10.1101/2023.02.20.529307 Cold Spring Harbor Laboratory Press 2023-02-21 <![CDATA[ Anesthesia suppressed gastric myoelectric power in the ferret ]]> https://biorxiv.org/content/10.1101/2023.02.23.529745v1?rss=1 Tomaselli, L. Sciullo, M. Fulton, S. Yates, B. J. Fisher, L. E. Ventura, V. Horn, C. C. 2023-02-24 doi:10.1101/2023.02.23.529745 Cold Spring Harbor Laboratory Press 2023-02-24 <![CDATA[ Detection of Influenza virus and Streptococcus pneumoniae in air sampled from co-infected ferrets and analysis of their influence on pathogen stability ]]> https://biorxiv.org/content/10.1101/2023.02.24.529988v1?rss=1 French, A. J. Rockey, N. Le Sage, V. Mueller Brown, K. Shephard, M. Frizzell, S. Myerburg, M. M. Hiller, N. L. Lakdawala, S. 2023-02-25 doi:10.1101/2023.02.24.529988 Cold Spring Harbor Laboratory Press 2023-02-25 <![CDATA[ The Role of HERG channel in the Secretion of Glucagon-Like Peptide-1 (GLP-1) from Murine Intestinal L-Cells ]]> https://biorxiv.org/content/10.1101/2023.02.28.530535v1?rss=1 ang, J.-K. Liu, C. Yuan, Y.- Xie, R.-R. Wang, H. 2023-03-01 doi:10.1101/2023.02.28.530535 Cold Spring Harbor Laboratory Press 2023-03-01 <![CDATA[ Capacitance measurements for assessing DNA origami nanostructures ]]> https://biorxiv.org/content/10.1101/2023.03.02.530881v1?rss=1 Walawalkar, V. Sajal, M. S. R. Gilpin, Y. Dandin, M. P. Taylor, R. E. 2023-03-03 doi:10.1101/2023.03.02.530881 Cold Spring Harbor Laboratory Press 2023-03-03 <![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[ Evolutionary constraint and innovation across hundreds of placental mammals ]]> https://biorxiv.org/content/10.1101/2023.03.09.531574v1?rss=1 Christmas, M. J. Kaplow, I. M. Genereux, D. P. Dong, M. X. Hughes, G. M. Li, X. Sullivan, P. F. Hindle, A. G. Andrews, G. Armstrong, J. C. Bianchi, M. Breit, A. M. Diekhans, M. Fanter, C. Foley, N. M. Goodman, D. B. Goodman, L. Keough, K. C. Kirilenko, B. Kowalczyk, A. Lawless, C. Lind, A. L. Meadows, J. R. S. Moreira, L. R. Redlich, R. W. Ryan, L. Swofford, R. Valenzuela, A. Wagner, F. Wallerman, O. Brown, A. R. Damas, J. Fan, K. Gatesy, J. Grimshaw, J. Johnson, J. Kozyrev, S. V. Lawler, A. J. Marinescu, V. D. Morrill, K. M. Osmanski, A. Paulat, N. S. 2023-03-09 doi:10.1101/2023.03.09.531574 Cold Spring Harbor Laboratory Press 2023-03-09 <![CDATA[ Membrane and glycocalyx tethering of DNA nanostructures for enhanced uptake ]]> https://biorxiv.org/content/10.1101/2023.03.09.529286v1?rss=1 Wang, W. Chopra, B. Walawalkar, V. Liang, Z. Adams, R. Deserno, M. Ren, X. Taylor, R. 2023-03-10 doi:10.1101/2023.03.09.529286 Cold Spring Harbor Laboratory Press 2023-03-10 <![CDATA[ Title: Leveraging Base Pair Mammalian Constraint to Understand Genetic Variation and Human Disease ]]> https://biorxiv.org/content/10.1101/2023.03.10.531987v1?rss=1 Sullivan, P. F. Meadows, J. R. S. Gazal, S. Phan, B. N. Li, X. Genereux, D. P. Dong, M. X. Bianchi, M. Andrews, G. Sakthikumar, S. Nordin, J. Roy, A. Christmas, M. J. Marinescu, V. D. Wang, C. Wallerman, O. Xue, J. R. Li, Y. Yao, S. Sun, Q. Szatkiewicz, J. Wen, J. Huckins, L. M. Lawler, A. J. Keough, K. C. Zheng, Z. Zeng, J. Wray, N. R. Johnson, J. Chen, J. Zoonomia Consortium, Paten, B. Reilly, S. K. Hughes, G. M. Weng, Z. Pollard, K. S. Pfenning, A. R. Forsberg-Nilsson, K. Karlsson, E. K. Lindblad-Toh, K. 2023-03-10 doi:10.1101/2023.03.10.531987 Cold Spring Harbor Laboratory Press 2023-03-10 <![CDATA[ Neural Selectivity for Real-World Object Size In Natural Images ]]> https://biorxiv.org/content/10.1101/2023.03.17.533179v1?rss=1 Luo, A. Wehbe, L. Tarr, M. Henderson, M. M. 2023-03-18 doi:10.1101/2023.03.17.533179 Cold Spring Harbor Laboratory Press 2023-03-18 <![CDATA[ Neural Mechanism Underlying NEergic Neurons-Modulated The Arousal Associated With Midazolam Anesthesia ]]> https://biorxiv.org/content/10.1101/2023.03.20.533578v1?rss=1 Gu, L. Liu, L. Shao, W. Gu, J. Xu, Q. Wang, Y. Yu, Q. Lian, X. Zhang, H. 2023-03-21 doi:10.1101/2023.03.20.533578 Cold Spring Harbor Laboratory Press 2023-03-21 <![CDATA[ Molecular compartmentalization in a syncytium: restricted mobility of proteins within the sea urchin skeletogenic mesenchyme ]]> https://biorxiv.org/content/10.1101/2023.03.22.533866v1?rss=1 Khor, J. M. Guerrero-Santoro, J. Ettensohn, C. A. 2023-03-24 doi:10.1101/2023.03.22.533866 Cold Spring Harbor Laboratory Press 2023-03-24 <![CDATA[ A neural basis of choking under pressure ]]> https://biorxiv.org/content/10.1101/2023.04.16.537007v1?rss=1 Smoulder, A. L. Marino, P. J. Oby, E. R. Snyder, S. E. Miyata, H. Pavlovsky, N. P. Bishop, W. E. Yu, B. M. Chase, S. M. Batista, A. P. 2023-04-16 doi:10.1101/2023.04.16.537007 Cold Spring Harbor Laboratory Press 2023-04-16 <![CDATA[ A Machine Learning Method to Characterize Conformational Changes of Amino Acids in Proteins ]]> https://biorxiv.org/content/10.1101/2023.04.16.536913v1?rss=1 Mollaei, P. farimani, A. B. 2023-04-18 doi:10.1101/2023.04.16.536913 Cold Spring Harbor Laboratory Press 2023-04-18 <![CDATA[ Proline provides a nitrogen source in the retinal pigment epithelium to synthesize and export amino acids for the neural retina ]]> https://biorxiv.org/content/10.1101/2023.04.18.537355v1?rss=1 Zhu, S. Xu, R. Engel, A. Wang, Y. McNeel, R. Hurley, J. B. Chao, J. R. Du, J. 2023-04-18 doi:10.1101/2023.04.18.537355 Cold Spring Harbor Laboratory Press 2023-04-18 <![CDATA[ CNC Knitting Micro-Resolution Mosquito Bite Blocking Textiles ]]> https://biorxiv.org/content/10.1101/2023.04.21.537869v1?rss=1 Beckmann, J. F. Holt, B. Oswalt, K. England, A. Murphy, R. Owens, I. Finney, M. Wong, N. Adhikari, S. McCann, J. 2023-04-23 doi:10.1101/2023.04.21.537869 Cold Spring Harbor Laboratory Press 2023-04-23 <![CDATA[ Stacked regressions and structured variance partitioning for interpretable brain maps ]]> https://biorxiv.org/content/10.1101/2023.04.23.537988v1?rss=1 Lin, R. Naselaris, T. Kay, K. Wehbe, L. 2023-04-24 doi:10.1101/2023.04.23.537988 Cold Spring Harbor Laboratory Press 2023-04-24 <![CDATA[ Three-dimensional characterization of medium spiny neuron heterogeneity in the adult mouse striatum ]]> https://biorxiv.org/content/10.1101/2023.05.04.539488v1?rss=1 Gayden, J. Puig, S. Srinivasan, C. Buck, S. A. Gamble, M. C. Glausier, J. R. Tejeda, H. A. Dong, Y. Pfenning, A. R. Logan, R. Freyberg, Z. 2023-05-05 doi:10.1101/2023.05.04.539488 Cold Spring Harbor Laboratory Press 2023-05-05 <![CDATA[ Evolutionary graph theory on rugged fitness landscapes ]]> https://biorxiv.org/content/10.1101/2023.05.04.539435v1?rss=1 Kuo, Y. P. Carja, O. 2023-05-07 doi:10.1101/2023.05.04.539435 Cold Spring Harbor Laboratory Press 2023-05-07 <![CDATA[ Parallels and contrasts between the cnidarian and bilaterian maternal-to-zygotic transition are revealed in Hydractinia embryos ]]> https://biorxiv.org/content/10.1101/2023.05.09.540083v1?rss=1 Ayers, T. N. Nicotra, M. Lee, M. T. 2023-05-10 doi:10.1101/2023.05.09.540083 Cold Spring Harbor Laboratory Press 2023-05-10 <![CDATA[ The organization and dynamics of corticostriatal pathways link the medial orbitofrontal cortex to future decisions ]]> https://biorxiv.org/content/10.1101/002311v1?rss=1 Timothy Verstynen 2014-02-03 doi:10.1101/002311 Cold Spring Harbor Laboratory Press 2014-02-03 <![CDATA[ Compression of short-read sequences using path encoding ]]> https://biorxiv.org/content/10.1101/006551v1?rss=1 Carl Kingsford Rob Patro 2014-06-24 doi:10.1101/006551 Cold Spring Harbor Laboratory Press 2014-06-24 <![CDATA[ Converging structural and functional connectivity of orbitofrontal, dorsolateral prefrontal, and posterior parietal cortex in the human striatum ]]> https://biorxiv.org/content/10.1101/006619v1?rss=1 Kevin Jarbo Timothy Verstynen 2014-06-25 doi:10.1101/006619 Cold Spring Harbor Laboratory Press 2014-06-25 <![CDATA[ A literature-based meta-analysis of brain-wide electrophysiological diversity ]]> https://biorxiv.org/content/10.1101/014720v1?rss=1 Shreejoy J Tripathy Shawn D Burton Matthew Geramita Richard C Gerkin Nathaniel N Urban 2015-02-04 doi:10.1101/014720 Cold Spring Harbor Laboratory Press 2015-02-04 <![CDATA[ Large-Scale Search of Transcriptomic Read Sets with Sequence Bloom Trees ]]> https://biorxiv.org/content/10.1101/017087v1?rss=1 Brad Solomon Carleton Kingsford 2015-03-26 doi:10.1101/017087 Cold Spring Harbor Laboratory Press 2015-03-26 <![CDATA[ Isoform-level Ribosome Occupancy Estimation Guided by Transcript Abundance with Ribomap ]]> https://biorxiv.org/content/10.1101/017509v1?rss=1 Hao Wang Joel McManus Carl Kingsford 2015-04-04 doi:10.1101/017509 Cold Spring Harbor Laboratory Press 2015-04-04 <![CDATA[ In vivo characterization of the connectivity and subcomponents of the human globus pallidus ]]> https://biorxiv.org/content/10.1101/017806v1?rss=1 Patrick Beukema Timothy Verstynen Fang-Cheng Yeh 2015-04-09 doi:10.1101/017806 Cold Spring Harbor Laboratory Press 2015-04-09 <![CDATA[ Salmon provides accurate, fast, and bias-aware transcript expression estimates using dual-phase inference ]]> https://biorxiv.org/content/10.1101/021592v1?rss=1 Rob Patro Geet Duggal Michael I Love Rafael A Irizarry Carl Kingsford 2015-06-27 doi:10.1101/021592 Cold Spring Harbor Laboratory Press 2015-06-27 <![CDATA[ Inference of multiple-wave population admixture by modeling decay of linkage disequilibrium with multiple exponential functions ]]> https://biorxiv.org/content/10.1101/026757v1?rss=1 Ying Zhou Kai Yuan Yaoliang Yu Xumin Ni Pengtao Xie Eric P Xing Shuhua Xu 2015-09-14 doi:10.1101/026757 Cold Spring Harbor Laboratory Press 2015-09-14 <![CDATA[ A pathway-centric view of spatial proximity in the 3D nucleome across cell lines ]]> https://biorxiv.org/content/10.1101/027045v1?rss=1 Hiren Karathia Carl Kingsford Michelle Girvan Sridhar Hannenhalli 2015-09-17 doi:10.1101/027045 Cold Spring Harbor Laboratory Press 2015-09-17 <![CDATA[ Learning structure in gene expression data using deep architectures, with an application to gene clustering ]]> https://biorxiv.org/content/10.1101/031906v1?rss=1 Aman Gupta Haohan Wang Madhavi Ganapathiraju 2015-11-16 doi:10.1101/031906 Cold Spring Harbor Laboratory Press 2015-11-16 <![CDATA[ A gene regulatory network for apical organ neurogenesis and its spatial control in sea star embryos. ]]> https://biorxiv.org/content/10.1101/036624v1?rss=1 Alys Jarvela Kristen Yankura Veronica Hinman 2016-01-13 doi:10.1101/036624 Cold Spring Harbor Laboratory Press 2016-01-13 <![CDATA[ Believer-Skeptic meets Actor-Critic: Rethinking the role basal ganglia pathways in decision-making and reinforcement learning ]]> https://biorxiv.org/content/10.1101/037085v1?rss=1 Kyle Dunovan Timothy Verstynen 2016-01-18 doi:10.1101/037085 Cold Spring Harbor Laboratory Press 2016-01-18 <![CDATA[ Estimation of Voxelwise Effective Connectivities: Applications to High Connectivity Sub-Regions within Hippocampal and within Corticostriatal Networks ]]> https://biorxiv.org/content/10.1101/039057v1?rss=1 Ruben Sanchez-Romero Joseph D. Ramsey Jackson C. Liang Kevin Jarbo Clark Glymour 2016-02-08 doi:10.1101/039057 Cold Spring Harbor Laboratory Press 2016-02-08 <![CDATA[ A method to exploit the structure of genetic ancestry space to enhance case-control studies ]]> https://biorxiv.org/content/10.1101/043166v1?rss=1 Corneliu A Bodea Benjamin M Neale Stephan Ripke The International IBD Genetics Consortium Mark J Daly Bernie Devlin Kathryn Roeder 2016-03-10 doi:10.1101/043166 Cold Spring Harbor Laboratory Press 2016-03-10 <![CDATA[ Multi-Connection Pattern Analysis: Decoding the Representational Content of Neural Communication ]]> https://biorxiv.org/content/10.1101/046441v1?rss=1 Yuanning Li Avniel Singh Ghuman 2016-03-31 doi:10.1101/046441 Cold Spring Harbor Laboratory Press 2016-03-31 <![CDATA[ Allele-Specific Quantification of Structural Variations in Cancer Genomes ]]> https://biorxiv.org/content/10.1101/048207v1?rss=1 Yang Li Shiguo Zhou David C. Schwartz Jian Ma 2016-04-13 doi:10.1101/048207 Cold Spring Harbor Laboratory Press 2016-04-13 <![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[ Chromosomal dynamics predicted by an elastic network model explains genome-wide accessibility and long-range couplings ]]> https://biorxiv.org/content/10.1101/081182v1?rss=1 50 megabases) have yet to be characterized. We adapted a well-established protein-modeling framework, the Gaussian Network Model (GNM), to the task of modeling chromatin dynamics using Hi-C contact data. We show that the GNM can identify structural dynamics at multiple scales: it can quantify the fluctuations in the positions of gene loci, find large genomic compartments and smaller TADs that undergo en-bloc movements, and identify dynamically coupled distal regions along the chromosomes. We show that the predictions of the GNM correlate well with DNase-seq and ATAC-seq measurements on accessibility, the previously identified A and B compartments of chromatin structure, and pairs of interacting loci identified by ChIA-PET. We describe a method to use the GNM to identify novel cross-correlated distal domains (CCDDs) representing regions of long-range dynamic coupling and show that CCDDs are often associated with increased gene coexpression using a large-scale analysis of 212 expression experiments. Together, these results show that GNM provides a mathematically well-founded unified framework for assessing chromatin dynamics and the structural basis of genome-wide observations. ]]> Sauerwald, N. Zhang, S. Kingsford, C. Bahar, I. 2016-10-16 doi:10.1101/081182 Cold Spring Harbor Laboratory Press 2016-10-16 <![CDATA[ Inference of multiple-wave population admixture by modeling decay of linkage disequilibrium with polynomial functions ]]> https://biorxiv.org/content/10.1101/082644v1?rss=1 zhou, Y. Yuan, K. Yu, Y. Ni, X. Xie, P. Xing, E. P. Xu, S. 2016-10-22 doi:10.1101/082644 Cold Spring Harbor Laboratory Press 2016-10-22 <![CDATA[ Predicting Enhancer-Promoter Interaction from Genomic Sequence with Deep Neural Networks ]]> https://biorxiv.org/content/10.1101/085241v1?rss=1 Singh, S. Yang, Y. Poczos, B. Ma, J. 2016-11-02 doi:10.1101/085241 Cold Spring Harbor Laboratory Press 2016-11-02 <![CDATA[ Improved Search of Large Transcriptomic Sequencing Databases Using Split Sequence Bloom Trees ]]> https://biorxiv.org/content/10.1101/086561v1?rss=1 Solomon, B. Kingsford, C. 2016-12-02 doi:10.1101/086561 Cold Spring Harbor Laboratory Press 2016-12-02 <![CDATA[ Efficient Heuristic for Decomposing a Flow with Minimum Number of Paths ]]> https://biorxiv.org/content/10.1101/087759v1?rss=1 Shao, M. Kingsford, C. 2016-11-16 doi:10.1101/087759 Cold Spring Harbor Laboratory Press 2016-11-16 <![CDATA[ Multiple Confounders Correction with Regularized Linear Mixed Effect Models, with Application in Biological Processes ]]> https://biorxiv.org/content/10.1101/089052v1?rss=1 Wang, H. Yang, J. 2016-11-22 doi:10.1101/089052 Cold Spring Harbor Laboratory Press 2016-11-22 <![CDATA[ Identification of Mechanisms of Functional Signaling Between Human Hippocampus Regions ]]> https://biorxiv.org/content/10.1101/099820v1?rss=1 Sanchez-Romero, R. Ramsey, J. D. Liang, J. C. Glymour, C. 2017-01-12 doi:10.1101/099820 Cold Spring Harbor Laboratory Press 2017-01-12 <![CDATA[ Altered topology of neural circuits in congenital prosopagnosia ]]> https://biorxiv.org/content/10.1101/100479v1?rss=1 Rosenthal, G. Tanzer, M. Simony, E. Hasson, U. Behrmann, M. Avidan, G. 2017-01-15 doi:10.1101/100479 Cold Spring Harbor Laboratory Press 2017-01-15 <![CDATA[ Improving the performance of minimizers andwinnowing schemes ]]> https://biorxiv.org/content/10.1101/104075v1?rss=1 Marcais, G. Pellow, D. Bork, D. Orenstein, Y. Shamir, R. Kingsford, C. 2017-01-29 doi:10.1101/104075 Cold Spring Harbor Laboratory Press 2017-01-29 <![CDATA[ New mutations, old statistical challenges ]]> https://biorxiv.org/content/10.1101/115964v1?rss=1 Barrett, J. C. Buxbaum, J. Cutler, D. Daly, M. Devlin, B. Gratten, J. Hurles, M. E. Kosmicki, J. A. Lander, E. S. MacArthur, D. G. Neale, B. M. Roeder, K. Visscher, P. M. Wray, N. R. 2017-03-12 doi:10.1101/115964 Cold Spring Harbor Laboratory Press 2017-03-12 <![CDATA[ Conserved processes of metazoan whole-body regeneration identified in sea star larvae ]]> https://biorxiv.org/content/10.1101/118232v1?rss=1 Hinman, V. Cary, G. 2017-03-18 doi:10.1101/118232 Cold Spring Harbor Laboratory Press 2017-03-18 <![CDATA[ Size uniformity of animal cells is actively maintained by a p38 MAPK-dependent regulation of G1-length ]]> https://biorxiv.org/content/10.1101/119867v1?rss=1 Liu, S. Ginzberg, M. B. Patel, N. Hild, M. Leung, B. Chen, Y.-C. Li, Z. Chang, N. Diena, S. Wang, Y. Trimble, W. Wasserman, L. Jenkins, J. Kirschner, M. W. Kafri, R. 2017-03-23 doi:10.1101/119867 Cold Spring Harbor Laboratory Press 2017-03-23 <![CDATA[ Local Connectome Phenotypes Predict Social, Health, and Cognitive Factors ]]> https://biorxiv.org/content/10.1101/122945v1?rss=1 Powell, M. Garcia, J. Yeh, F.-C. Vettel, J. Verstynen, T. 2017-03-31 doi:10.1101/122945 Cold Spring Harbor Laboratory Press 2017-03-31 <![CDATA[ Scallop Enables Accurate Assembly Of Transcripts Through Phasing-Preserving Graph Decomposition ]]> https://biorxiv.org/content/10.1101/123612v1?rss=1 Shao, M. Kingsford, C. 2017-04-03 doi:10.1101/123612 Cold Spring Harbor Laboratory Press 2017-04-03 <![CDATA[ Using Neural Networks To Improve Single-Cell RNA-Seq Data Analysis ]]> https://biorxiv.org/content/10.1101/129759v1?rss=1 Lin, C. Jain, S. Kim, H. Bar-Joseph, Z. 2017-04-23 doi:10.1101/129759 Cold Spring Harbor Laboratory Press 2017-04-23 <![CDATA[ Graph-Guided Assembly For Novel HLA Allele Discovery ]]> https://biorxiv.org/content/10.1101/138826v1?rss=1 30-fold) whole genome sequencing data. Our method delivers highly accurate HLA typing, comparable to the current state-of-the-art database-matching methods. We also demonstrate that our method can type novel alleles by experimenting on various data including simulated, Illumina Platinum Genomes, and 1000 Genomes data. ]]> Lee, H. Kingsford, C. 2017-05-17 doi:10.1101/138826 Cold Spring Harbor Laboratory Press 2017-05-17 <![CDATA[ Inferential Pitfalls In Decoding Neural Representations ]]> https://biorxiv.org/content/10.1101/141283v1?rss=1 Popov, V. Ostarek, M. Tenison, C. 2017-05-24 doi:10.1101/141283 Cold Spring Harbor Laboratory Press 2017-05-24 <![CDATA[ Opportunities And Obstacles For Deep Learning In Biology And Medicine ]]> https://biorxiv.org/content/10.1101/142760v1?rss=1 Ching, T. Himmelstein, D. S. Beaulieu-Jones, B. K. Kalinin, A. A. Do, B. T. Way, G. P. Ferrero, E. Agapow, P.-M. Xie, W. Rosen, G. L. Lengerich, B. J. Israeli, J. Lanchantin, J. Woloszynek, S. Carpenter, A. E. Shrikumar, A. Xu, J. Cofer, E. M. Harris, D. J. DeCaprio, D. Qi, Y. Kundaje, A. Peng, Y. Wiley, L. K. Segler, M. H. S. Gitter, A. Greene, C. S. 2017-05-28 doi:10.1101/142760 Cold Spring Harbor Laboratory Press 2017-05-28 <![CDATA[ Dual learning mechanisms drive adaptive inhibitory control ]]> https://biorxiv.org/content/10.1101/153676v1?rss=1 Dunovan, K. Verstynen, T. 2017-06-22 doi:10.1101/153676 Cold Spring Harbor Laboratory Press 2017-06-22 <![CDATA[ SQUID: Transcriptomic Structural Variation Detection from RNA-seq ]]> https://biorxiv.org/content/10.1101/162776v1?rss=1 Ma, C. Shao, M. Kingsford, C. 2017-07-12 doi:10.1101/162776 Cold Spring Harbor Laboratory Press 2017-07-12 <![CDATA[ Genetically Targeted Ratiometric and Activated pH Indicator Complexes (TRApHIC) for Receptor Trafficking ]]> https://biorxiv.org/content/10.1101/180141v1?rss=1 Perkins, L. A. Yan, Q. Schmidt, B. F. Kolodiezyni, D. Saurabh, S. Larsen, M. B. Watkins, S. C. Kremer, L. Bruchez, M. P. 2017-08-24 doi:10.1101/180141 Cold Spring Harbor Laboratory Press 2017-08-24 <![CDATA[ Project Dhaka: Variational Autoencoder for Unmasking Tumor Heterogeneity from Single Cell Genomic Data ]]> https://biorxiv.org/content/10.1101/183863v1?rss=1 Rashid, S. Shah, S. Pandya, R. 2017-09-04 doi:10.1101/183863 Cold Spring Harbor Laboratory Press 2017-09-04 <![CDATA[ Abdominal adiposity negatively associates with the rate of long term sequential skill learning ]]> https://biorxiv.org/content/10.1101/186742v1?rss=1 Millette, A. Lynch, B. Verstynen, T. 2017-09-10 doi:10.1101/186742 Cold Spring Harbor Laboratory Press 2017-09-10 <![CDATA[ Population-level distribution and putative immunogenicity of cancer neoepitopes ]]> https://biorxiv.org/content/10.1101/192716v1?rss=1 Wood, M. A. Paralkar, M. Paralkar, M. P. Nguyen, A. Struck, A. J. Ellrott, K. Margolin, A. Nellore, A. Thompson, R. F. 2017-09-22 doi:10.1101/192716 Cold Spring Harbor Laboratory Press 2017-09-22 <![CDATA[ Extracting Evidence Fragments for Distant Supervision of Molecular Interactions ]]> https://biorxiv.org/content/10.1101/192856v1?rss=1 Burns, G. A. Dasigi, P. Hovy, E. H. 2017-09-23 doi:10.1101/192856 Cold Spring Harbor Laboratory Press 2017-09-23 <![CDATA[ High Capacity poly(2-oxazoline) formulation of TLR 7/8 agonist extends survival in a chemo-insensitive, metastatic model of Lung Adenocarcinoma ]]> https://biorxiv.org/content/10.1101/2019.12.12.874198v1?rss=1 Vinod, N. Hwang, D. Azam, S. H. Van Swearingen, A. E. D. Wayne, E. Fussell, S. C. Sokolsky-Papkov, M. Pecot, C. V. Kabanov, A. V. 2019-12-12 doi:10.1101/2019.12.12.874198 Cold Spring Harbor Laboratory Press 2019-12-12 <![CDATA[ Finding ranges of optimal transcript expression quantification in cases of non-identifiability ]]> https://biorxiv.org/content/10.1101/2019.12.13.875625v1?rss=1 Ma, C. Zheng, H. Kingsford, C. 2019-12-13 doi:10.1101/2019.12.13.875625 Cold Spring Harbor Laboratory Press 2019-12-13 <![CDATA[ GCNG: Graph convolutional networks for inferring cell-cell interactions ]]> https://biorxiv.org/content/10.1101/2019.12.23.887133v1?rss=1 Yuan, Y. Bar-Joseph, Z. 2019-12-23 doi:10.1101/2019.12.23.887133 Cold Spring Harbor Laboratory Press 2019-12-23 <![CDATA[ VariantStore: A Large-Scale Genomic Variant Search Index ]]> https://biorxiv.org/content/10.1101/2019.12.24.888297v1?rss=1 Pandey, P. Gao, Y. Kingsford, C. 2019-12-26 doi:10.1101/2019.12.24.888297 Cold Spring Harbor Laboratory Press 2019-12-26 <![CDATA[ Supervised Adversarial Alignment of scRNA-seq Data ]]> https://biorxiv.org/content/10.1101/2020.01.06.896621v1?rss=1 Ge, S. Wang, H. Alavi, A. Xing, E. Bar-Joseph, Z. 2020-01-07 doi:10.1101/2020.01.06.896621 Cold Spring Harbor Laboratory Press 2020-01-07 <![CDATA[ RNA-binding protein Syncrip regulates Starvation-Induced Hyperactivity in adult Drosophila ]]> https://biorxiv.org/content/10.1101/2020.01.07.897652v1?rss=1 Chi, W. Liu, W. Fu, W. Heckscher, E. Zhuang, X. 2020-01-08 doi:10.1101/2020.01.07.897652 Cold Spring Harbor Laboratory Press 2020-01-08 <![CDATA[ Dissociable roles of central striatum and anterior lateral motor area in initiating and sustaining naturalistic behavior ]]> https://biorxiv.org/content/10.1101/2020.01.08.899070v1?rss=1 Corbit, V. Piantadosi, S. C. Wood, J. T. Liu, G. Choi, C. J. Y. Witten, I. Gittis, A. H. Ahmari, S. E. 2020-01-09 doi:10.1101/2020.01.08.899070 Cold Spring Harbor Laboratory Press 2020-01-09 <![CDATA[ Circadian Rhythm Is Disrupted by ZNF704 in Breast Carcinogenesis ]]> https://biorxiv.org/content/10.1101/2020.01.09.900548v1?rss=1 Yang, C. Wu, J. Liu, X. Wang, Y. Liu, B. Chen, X. Wu, X. Yan, D. Han, L. Liu, S. Shan, L. Shang, Y. 2020-01-09 doi:10.1101/2020.01.09.900548 Cold Spring Harbor Laboratory Press 2020-01-09 <![CDATA[ Slow drift of neural activity as a signature of impulsivity in macaque visual and prefrontal cortex ]]> https://biorxiv.org/content/10.1101/2020.01.10.902403v1?rss=1 Cowley, B. R. Snyder, A. C. Acar, K. Williamson, R. C. Yu, B. M. Smith, M. A. 2020-01-11 doi:10.1101/2020.01.10.902403 Cold Spring Harbor Laboratory Press 2020-01-11 <![CDATA[ Size regulation of multiple organelles competing for a shared subunit pool ]]> https://biorxiv.org/content/10.1101/2020.01.11.902783v1?rss=1 Banerjee, D. S. Banerjee, S. 2020-01-11 doi:10.1101/2020.01.11.902783 Cold Spring Harbor Laboratory Press 2020-01-11 <![CDATA[ Scalable generation of mesenchymal stem cells and adipocytes from human pluripotent stem cells ]]> https://biorxiv.org/content/10.1101/2020.01.11.902833v1?rss=1 Karam, M. Younis, I. Abdelalim, E. M. 2020-01-11 doi:10.1101/2020.01.11.902833 Cold Spring Harbor Laboratory Press 2020-01-11 <![CDATA[ A Paradigm for Measuring Resting State Functional Connectivity in Young Children Using fNIRS and Freeplay ]]> https://biorxiv.org/content/10.1101/2020.01.13.904029v1?rss=1 Kim, J. Ruesch, A. Kang, N. R. Huppert, T. J. Kainerstorfer, J. Thiessen, E. D. Fisher, A. V. 2020-01-13 doi:10.1101/2020.01.13.904029 Cold Spring Harbor Laboratory Press 2020-01-13 <![CDATA[ Chinese Glioma Genome Atlas (CGGA): A Comprehensive Resource with Functional Genomic Data for Chinese Glioma Patients ]]> https://biorxiv.org/content/10.1101/2020.01.20.911982v1?rss=1 Zhao, Z. Zhang, K. Wang, Q. Li, G. Zeng, F. Zhang, Y. Wu, F. Chai, R. Wang, Z. Zhang, C. Zhang, W. Bao, Z. Jiang, T. 2020-01-21 doi:10.1101/2020.01.20.911982 Cold Spring Harbor Laboratory Press 2020-01-21 <![CDATA[ Probing multi-way chromatin interaction with hypergraph representation learning ]]> https://biorxiv.org/content/10.1101/2020.01.22.916171v1?rss=1 Zhang, R. Ma, J. 2020-01-23 doi:10.1101/2020.01.22.916171 Cold Spring Harbor Laboratory Press 2020-01-23 <![CDATA[ Reciprocal transplant experiment in lakes with disparate trophic states show resolution dependent partial functional redundancy ]]> https://biorxiv.org/content/10.1101/2020.02.01.930198v1?rss=1 Tandon, K. Wan, M.-T. Yang, C.-C. Yang, S.-H. Baatar, B. Chiu, C.-Y. Tsai, J.-W. Liu, W.-C. Ng, C. S. Tang, S.-L. 2020-02-02 doi:10.1101/2020.02.01.930198 Cold Spring Harbor Laboratory Press 2020-02-02 <![CDATA[ Improved design and analysis of practical minimizers ]]> https://biorxiv.org/content/10.1101/2020.02.07.939025v1?rss=1 Zheng, H. Kingsford, C. Marcais, G. 2020-02-07 doi:10.1101/2020.02.07.939025 Cold Spring Harbor Laboratory Press 2020-02-07 <![CDATA[ Plasmin improves oedematous blood-gas barrier by cleaving epithelial sodium channels ]]> https://biorxiv.org/content/10.1101/2020.02.09.940619v1?rss=1 Zhao, R. Ali, G. Nie, H.-G. Chang, Y. Bhattarai, D. Su, X. Zhao, X. Matthay, M. A. Ji, H.-L. 2020-02-10 doi:10.1101/2020.02.09.940619 Cold Spring Harbor Laboratory Press 2020-02-10 <![CDATA[ Delta oscillations are a robust biomarker of dopamine depletion severity and motor dysfunction in awake mice ]]> https://biorxiv.org/content/10.1101/2020.02.09.941161v1?rss=1 Whalen, T. C. Willard, A. M. Rubin, J. E. Gittis, A. H. 2020-02-10 doi:10.1101/2020.02.09.941161 Cold Spring Harbor Laboratory Press 2020-02-10 <![CDATA[ Fibronectin-Based Nanomechanical Biosensors to Map 3D Strains in Live Cells and Tissues ]]> https://biorxiv.org/content/10.1101/2020.02.11.943696v1?rss=1 Shiwarski, D. J. Tashman, J. W. Tsamis, A. Bliley, J. M. Blundon, M. A. Aranda-Michel, E. Jallerat, Q. Szymanski, J. M. McCartney, B. M. Feinberg, A. W. 2020-02-12 doi:10.1101/2020.02.11.943696 Cold Spring Harbor Laboratory Press 2020-02-12 <![CDATA[ Induced copy-back RNA synthesis as a novel therapeutic mechanism against RNA viruses ]]> https://biorxiv.org/content/10.1101/2020.02.12.946558v1?rss=1 Janissen, R. Woodman, A. Lee, K.-M. Moustafa, I. Fitzgerald, F. Huang, P.-N. Kuijpers, L. Perkins, A. L. Harki, D. A. Arnold, J. J. Solano, B. Shih, S.-R. Cameron, C. E. Dekker, N. H. 2020-02-13 doi:10.1101/2020.02.12.946558 Cold Spring Harbor Laboratory Press 2020-02-13 <![CDATA[ Cross-Protection Against Zika Virus Infection Conferred by a Live Attenuated Japanese Encephalitis SA14-14-2 Vaccine ]]> https://biorxiv.org/content/10.1101/2020.02.14.950352v1?rss=1 Wang, R. Zhen, Z. Turtle, L. Hou, B. Li, Y. Gao, N. Fan, D. Chen, H. An, J. 2020-02-16 doi:10.1101/2020.02.14.950352 Cold Spring Harbor Laboratory Press 2020-02-16 <![CDATA[ A computational model explains and predicts substantia nigra pars reticulata responses to pallidal and striatal inputs ]]> https://biorxiv.org/content/10.1101/2020.02.17.952820v1?rss=1 Phillips, R. S. Rosner, I. Gittis, A. H. Rubin, J. E. 2020-02-17 doi:10.1101/2020.02.17.952820 Cold Spring Harbor Laboratory Press 2020-02-17 <![CDATA[ Novel Electrodes for Reliable EEG Recordings on Coarse and Curly Hair ]]> https://biorxiv.org/content/10.1101/2020.02.26.965202v1?rss=1 Etienne, A. Laroia, T. Weigle, H. Afelin, A. Kelly, S. K. Krishnan, A. Grover, P. 2020-02-27 doi:10.1101/2020.02.26.965202 Cold Spring Harbor Laboratory Press 2020-02-27 <![CDATA[ Tumor heterogeneity assessed by sequencing and fluorescence in situ hybridization (FISH) data ]]> https://biorxiv.org/content/10.1101/2020.02.29.970392v1?rss=1 Lei, H. Gertz, E. M. Schäffer, A. A. Fu, X. Tao, Y. Heselmeyer-Haddad, K. Torres, I. Shi, X. Wu, K. LI, G. Xu, L. Hou, Y. Dean, M. Ried, T. Schwartz, R. 2020-03-01 doi:10.1101/2020.02.29.970392 Cold Spring Harbor Laboratory Press 2020-03-01 <![CDATA[ Effects of arousal and movement on secondary somatosensory and visual thalamus ]]> https://biorxiv.org/content/10.1101/2020.03.04.977348v1?rss=1 Petty, G. H. Kinnischtzke, A. Hong, Y. K. Bruno, R. M. 2020-03-05 doi:10.1101/2020.03.04.977348 Cold Spring Harbor Laboratory Press 2020-03-05 <![CDATA[ Nutrient-dependent trade-offs between ribosomes and division protein synthesis control bacterial growth and cell shape ]]> https://biorxiv.org/content/10.1101/2020.03.08.982728v1?rss=1 Serbanescu, D. Ojkic, N. Banerjee, S. 2020-03-09 doi:10.1101/2020.03.08.982728 Cold Spring Harbor Laboratory Press 2020-03-09 <![CDATA[ Chromatin-Bound PARP1 Correlates with Upregulation of Inflammatory Genes in Response to Long-Term Treatment with Veliparib ]]> https://biorxiv.org/content/10.1101/2020.03.08.982785v1?rss=1 Alvarado-Cruz, I. Mahmoud, M. Khan, M. Zhao, S. Oeck, S. Meas, R. Clairmont, K. Quintana, V. Zhu, Y. Porciuncula, A. Wyatt, H. Ma, S. Shyr, Y. Kong, Y. LoRusso, P. M. Laverty, D. Nagel, Z. D. Schalper, K. A. Krauthammer, M. Sweasy, J. B. 2020-03-09 doi:10.1101/2020.03.08.982785 Cold Spring Harbor Laboratory Press 2020-03-09 <![CDATA[ SPIN reveals genome-wide landscape of nuclear compartmentalization ]]> https://biorxiv.org/content/10.1101/2020.03.09.982967v1?rss=1 Wang, Y. Zhang, Y. Zhang, R. van Schaik, T. Zhang, L. Sasaki, T. Peric-Hupkes, D. Chen, Y. Gilbert, D. M. van Steensel, B. Belmont, A. S. Ma, J. 2020-03-10 doi:10.1101/2020.03.09.982967 Cold Spring Harbor Laboratory Press 2020-03-10 <![CDATA[ Novel Interaction between Prefrontal and Parietal Cortex during Memory Guided Saccades ]]> https://biorxiv.org/content/10.1101/2020.03.11.985259v1?rss=1 Hall, N. J. Colby, C. L. Olson, C. R. 2020-03-11 doi:10.1101/2020.03.11.985259 Cold Spring Harbor Laboratory Press 2020-03-11 <![CDATA[ From Farm to Pharmacy: Strawberry-Enabled Oral Delivery of Protein Drugs ]]> https://biorxiv.org/content/10.1101/2020.03.11.987461v1?rss=1 Lamson, N. G. Fein, K. C. Gleeson, J. P. Xian, S. Newby, A. Chaudhary, N. Melamed, J. R. Cochran, K. Ball, R. L. Suri, K. Ahuja, V. Zhang, A. Berger, A. Kolodieznyi, D. Schmidt, B. F. Silva, G. L. Whitehead, K. A. 2020-03-12 doi:10.1101/2020.03.11.987461 Cold Spring Harbor Laboratory Press 2020-03-12 <![CDATA[ Potential Neutralizing Antibodies Discovered for Novel Corona Virus Using Machine Learning ]]> https://biorxiv.org/content/10.1101/2020.03.14.992156v1?rss=1 Magar, R. Yadav, P. Barati Farimani, A. 2020-03-20 doi:10.1101/2020.03.14.992156 Cold Spring Harbor Laboratory Press 2020-03-20 <![CDATA[ Iatrogenic Iron Promotes Neurodegeneration and Activates Self-protection of Neural Cells against Exogenous Iron Attacks ]]> https://biorxiv.org/content/10.1101/2020.03.21.001925v1?rss=1 Xia, M. Liang, S. Li, S. Li, Z. Zhang, M. Chen, B. Dong, C. Chen, B. Ji, M. Gong, W. Guan, D. Verkhratsky, A. Li, B. 2020-03-24 doi:10.1101/2020.03.21.001925 Cold Spring Harbor Laboratory Press 2020-03-24 <![CDATA[ Senescent stromal cells promote cancer resistance through SIRT1 loss-potentiated overproduction of small extracellular vesicles ]]> https://biorxiv.org/content/10.1101/2020.03.22.002667v1?rss=1 Han, L. Long, Q. Li, S. Xu, Q. Zhang, B. Dou, X. Qian, M. Jiramongkol, Y. Guo, J. Cao, L. Chin, E. Lam, E. Jiang, J. Sun, Y. 2020-03-23 doi:10.1101/2020.03.22.002667 Cold Spring Harbor Laboratory Press 2020-03-23 <![CDATA[ HARVESTMAN: A framework for hierarchical featurelearning and selection from whole genome sequencingdata ]]> https://biorxiv.org/content/10.1101/2020.03.24.005603v1?rss=1 Frisby, T. S. Baker, S. J. Marcais, G. Hoang, Q. M. Kingsford, C. Langmead, C. J. 2020-03-25 doi:10.1101/2020.03.24.005603 Cold Spring Harbor Laboratory Press 2020-03-25 <![CDATA[ Ion transport mechanisms for smoke inhalation injured airway epithelial barrier ]]> https://biorxiv.org/content/10.1101/2020.03.25.007807v1?rss=1 Chang, J. Chen, Z. Zhao, R. Nie, H.-G. Ji, H.-L. 2020-03-25 doi:10.1101/2020.03.25.007807 Cold Spring Harbor Laboratory Press 2020-03-25 <![CDATA[ Cell type-specific histone acetylation profiling of Alzheimer's Disease subjects and integration with genetics ]]> https://biorxiv.org/content/10.1101/2020.03.26.010330v1?rss=1 Ramamurthy, E. Welch, G. Cheng, J. Yuan, Y. Gunsalus, L. Bennett, D. A. Tsai, L.-H. Pfenning, A. 2020-03-26 doi:10.1101/2020.03.26.010330 Cold Spring Harbor Laboratory Press 2020-03-26 <![CDATA[ Revealing the functions of supra-temporal and insular auditory responsive areas in humans ]]> https://biorxiv.org/content/10.1101/2020.03.30.015289v1?rss=1 65%), while sparsely on InsP (9.49%). The results of cortico-cortical evoked potentials (CCEPs) showed strong bidirectional connectivity within supra-temporal areas, but weak connectivity between supra-temporal areas and InsP. These findings suggest that even the InsP has similar basic auditory response properties to the primary or non-primary cortex, it may not directly participate in the formation of auditory perception. ]]> Wang, Q. Luo, L. Xu, N. Wang, J. Gao, Y. Li, S. Wang, M. Teng, P. Guan, Y. Zhou, J. Tian, X. Luan, G. 2020-03-31 doi:10.1101/2020.03.30.015289 Cold Spring Harbor Laboratory Press 2020-03-31 <![CDATA[ LY6E Restricts the Entry of Human Coronaviruses, including the currently pandemic SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2020.04.02.021469v1?rss=1 Zhao, X. Zheng, S. Chen, D. Zheng, M. Li, X. Li, G. Lin, H. Chang, J. Zeng, H. Guo, J.-T. 2020-04-05 doi:10.1101/2020.04.02.021469 Cold Spring Harbor Laboratory Press 2020-04-05 <![CDATA[ Computational Recipe for Designing Antibodies against the Ebola Virus ]]> https://biorxiv.org/content/10.1101/2020.04.04.024430v1?rss=1 Barati Farimani, A. Aluru, N. Tajkhorshid, E. Jakobsson, E. 2020-04-05 doi:10.1101/2020.04.04.024430 Cold Spring Harbor Laboratory Press 2020-04-05 <![CDATA[ Systemic analysis of tissue cells potentially vulnerable to SARS-CoV-2 infection by the protein-proofed single-cell RNA profiling of ACE2, TMPRSS2 and Furin proteases ]]> https://biorxiv.org/content/10.1101/2020.04.06.028522v1?rss=1 Zhou, L. Niu, Z. Jiang, X. Zhang, Z. Zheng, Y. Wang, Z. Zhu, Y. Gao, L. Wang, X. Sun, Q. 2020-04-10 doi:10.1101/2020.04.06.028522 Cold Spring Harbor Laboratory Press 2020-04-10 <![CDATA[ The spatial and cell-type distribution of SARS-CoV-2 receptor ACE2 in human and mouse brain ]]> https://biorxiv.org/content/10.1101/2020.04.07.030650v1?rss=1 Chen, R. Yu, J. Wang, K. Chen, Z. Wen, C. Xu, Z. 2020-04-09 doi:10.1101/2020.04.07.030650 Cold Spring Harbor Laboratory Press 2020-04-09 <![CDATA[ Mindfulness Improves Brain Computer Interface Performance by Increasing Control over Neural Activity in the Alpha Band ]]> https://biorxiv.org/content/10.1101/2020.04.13.039081v1?rss=1 Stieger, J. Engel, S. A. Jiang, H. Cline, C. C. Kreitzer, M. J. He, B. 2020-04-13 doi:10.1101/2020.04.13.039081 Cold Spring Harbor Laboratory Press 2020-04-13 <![CDATA[ Carbon Stock of Human-Disturbed Forest Areas in Bukidnon, Philippines ]]> https://biorxiv.org/content/10.1101/2020.04.14.041798v1?rss=1 Medina, M. A. P. Cabahug, V. C. Zapico, G. E. G. 2020-04-16 doi:10.1101/2020.04.14.041798 Cold Spring Harbor Laboratory Press 2020-04-16 <![CDATA[ Carbon Sequestration Potential of Oil Palm Plantations in Southern Philippines ]]> https://biorxiv.org/content/10.1101/2020.04.14.041822v1?rss=1 Borbon, S. M. C. Medina, M. A. P. Patricio, J. H. P. Bruno, A. G. T. 2020-04-16 doi:10.1101/2020.04.14.041822 Cold Spring Harbor Laboratory Press 2020-04-16 <![CDATA[ Immunity-and-Matrix-Regulatory Cells Derived from Human Embryonic Stem Cells Safely and Effectively Treat Mouse Lung Injury and Fibrosis ]]> https://biorxiv.org/content/10.1101/2020.04.15.042119v1?rss=1 Wu, J. Song, D. Li, Z. Guo, B. Xiao, Y. Liu, W. Liang, L. Feng, C. Gao, T. Wang, Z. Wen, J. Yang, S. Liu, P. Wang, L. Wang, Y. Peng, L. Feng, G. Huang, S. Stacey, G. N. Li, W. Huo, Y. Jin, R. Zhou, Q. Wang, L. Hu, B. Dai, H. Hao, J. 2020-04-16 doi:10.1101/2020.04.15.042119 Cold Spring Harbor Laboratory Press 2020-04-16 <![CDATA[ Incremental language comprehension difficulty predicts activity in the language network but not the multiple demand network ]]> https://biorxiv.org/content/10.1101/2020.04.15.043844v1?rss=1 Wehbe, L. Blank, I. A. Shain, C. Futrell, R. Levy, R. von der Malsburg, T. Smith, N. Gibson, E. Fedorenko, E. 2020-04-17 doi:10.1101/2020.04.15.043844 Cold Spring Harbor Laboratory Press 2020-04-17 <![CDATA[ Broad and differential animal ACE2 receptor usage by SARS-CoV-2 ]]> https://biorxiv.org/content/10.1101/2020.04.19.048710v1?rss=1 Zhao, X. Chen, D. Szabla, R. Zheng, M. Li, G. Du, P. Zheng, S. Li, X. Song, C. Li, R. Guo, J.-T. Junop, M. Zeng, H. Lin, H. 2020-04-19 doi:10.1101/2020.04.19.048710 Cold Spring Harbor Laboratory Press 2020-04-19 <![CDATA[ The mechanics of Temporal Interference stimulation ]]> https://biorxiv.org/content/10.1101/2020.04.23.051870v1?rss=1 Cao, J. Doiron, B. D. Goswami, C. Grover, P. 2020-04-25 doi:10.1101/2020.04.23.051870 Cold Spring Harbor Laboratory Press 2020-04-25 <![CDATA[ Transient and layer-specific reduction in neocortical PV inhibition during sensory association learning ]]> https://biorxiv.org/content/10.1101/2020.04.24.059865v1?rss=1 Kuljis, D. Park, E. Myal, S. E. Clopath, C. Barth, A. L. 2020-04-25 doi:10.1101/2020.04.24.059865 Cold Spring Harbor Laboratory Press 2020-04-25 <![CDATA[ MINERVA: A facile strategy for SARS-CoV-2 whole genome deep sequencing of clinical samples ]]> https://biorxiv.org/content/10.1101/2020.04.25.060947v1?rss=1 Chen, C. Li, J. Di, L. Jing, Q. Du, P. Song, C. Li, J. Li, Q. Cao, Y. Xie, S. Wu, A. R. Zeng, H. Huang, Y. Wang, J. 2020-04-25 doi:10.1101/2020.04.25.060947 Cold Spring Harbor Laboratory Press 2020-04-25 <![CDATA[ An automated homecage system for multiwhisker detection and discrimination learning in mice ]]> https://biorxiv.org/content/10.1101/2020.04.27.063750v1?rss=1 9 psi), animals showed markedly less participation in the task. Conversely, very weak air current intensities (1-2 psi) were not sufficient to generate rapid learning behavior. At intermediate stimulus intensities (5-6 psi), a majority of mice learned that the multiwhisker stimulus predicted the water reward after 24-48 hrs of training. Both exposure to isoflurane and lack of whiskers decreased animals ability to learn the task. Perceptual learning was assessed and following training at an intermediate stimulus intensity, perception was likely heightened as mice were able to transfer learning behavior when exposed to the lower stimulus intensity. Mice learned to discriminate between two directions of stimulation rapidly and accurately, even when the angular distance between the stimuli was <15 degrees. Switching the reward to a more desirable reward, aspartame, had little effect on learning trajectory. Our results show that a tactile association task in an automated homecage environment can be monitored by anticipatory licking to reveal rapid and progressive behavioral change. These Arduino-based, automated mouse cages enable high-throughput training that facilitate analysis of large numbers of genetically modified mice with targeted manipulations of neural activity. ]]> Bernhard, S. M. Lee, J. Zhu, M. Hsu, A. Erskine, A. Hires, S. A. Barth, A. L. 2020-04-27 doi:10.1101/2020.04.27.063750 Cold Spring Harbor Laboratory Press 2020-04-27 <![CDATA[ SIFNet: Electromagnetic Source Imaging Framework Using Deep Neural Networks ]]> https://biorxiv.org/content/10.1101/2020.05.11.089185v1?rss=1 Sun, R. Sohrabpour, A. Ye, S. He, B. 2020-05-13 doi:10.1101/2020.05.11.089185 Cold Spring Harbor Laboratory Press 2020-05-13 <![CDATA[ Iterative point set registration for aligning scRNA-seq data ]]> https://biorxiv.org/content/10.1101/2020.05.13.093948v1?rss=1 Alavi, A. Bar-Joseph, Z. 2020-05-13 doi:10.1101/2020.05.13.093948 Cold Spring Harbor Laboratory Press 2020-05-13 <![CDATA[ Once delayed non-invasive remote ischemic preconditioning protects against early stroke by modulating neuroinflammatory responses in rats ]]> https://biorxiv.org/content/10.1101/2020.05.14.095810v1?rss=1 Wang, X. Du, X. Yang, J. Zhao, Y. Geng, X. 2020-05-14 doi:10.1101/2020.05.14.095810 Cold Spring Harbor Laboratory Press 2020-05-14 <![CDATA[ Transcranial Focused Ultrasound Neuromodulation of Voluntary Movement-related Cortical Activity in Humans ]]> https://biorxiv.org/content/10.1101/2020.05.18.103176v1?rss=1 Yu, K. Liu, C. Niu, X. He, B. 2020-05-21 doi:10.1101/2020.05.18.103176 Cold Spring Harbor Laboratory Press 2020-05-21 <![CDATA[ Dopamine responses reveal efficient coding of cognitive variables ]]> https://biorxiv.org/content/10.1101/2020.05.20.100065v1?rss=1 Motiwala, A. Soares, S. Atallah, B. V. Paton, J. J. Machens, C. K. 2020-05-23 doi:10.1101/2020.05.20.100065 Cold Spring Harbor Laboratory Press 2020-05-23 <![CDATA[ Traction Force Microscopy by Deep Learning ]]> https://biorxiv.org/content/10.1101/2020.05.20.107128v1?rss=1 Wang, Y.-L. Lin, Y.-C. 2020-05-22 doi:10.1101/2020.05.20.107128 Cold Spring Harbor Laboratory Press 2020-05-22 <![CDATA[ Learning is shaped by abrupt changes in neural engagement ]]> https://biorxiv.org/content/10.1101/2020.05.24.112714v1?rss=1 Hennig, J. A. Oby, E. R. Golub, M. D. Bahureksa, L. A. Sadtler, P. T. Quick, K. M. Ryu, S. I. Tyler-Kabara, E. C. Batista, A. P. Chase, S. M. Yu, B. M. 2020-05-25 doi:10.1101/2020.05.24.112714 Cold Spring Harbor Laboratory Press 2020-05-25 <![CDATA[ Dynamic Loading of Human Engineered Heart Tissue Enhances Contractile Function and Drives Desmosome-linked Disease Phenotype ]]> https://biorxiv.org/content/10.1101/2020.05.25.111690v1?rss=1 10%. To do this, 3D EHTs are integrated with an elastic polydimethylsiloxane (PDMS) strip that provides mechanical pre- and afterload to the tissue in addition to enabling contractile force measurements based on strip bending. Our results demonstrate in wild-type EHTs that dynamic loading is beneficial based on the magnitude of the forces, leading to improved alignment, conduction velocity, and contractility. For disease modeling, we use hiPSC-derived cardiomyocytes from a patient with arrhythmogenic cardiomyopathy (ACM) due to mutations in desmoplakin. We demonstrate that manifestation of this desmosome-linked disease state requires the dyn-EHT conditioning and that it cannot be induced using 2D or standard 3D EHT approaches. Thus, dynamic loading strategy is necessary to provoke a disease phenotype (diastolic lengthening, reduction of desmosome counts, and reduced contractility), which are akin to primary endpoints of clinical disease, such as chamber thinning and reduced cardiac output. Single Sentence SummaryDevelopment of a dynamic mechanical loading platform to improve contractile function of engineered heart tissues and study cardiac disease progression. ]]> Bliley, J. M. Vermeer, M. Duffy, R. M. Batalov, I. Kramer, D. Tashman, J. W. Shiwarski, D. J. Lee, A. Teplenin, A. S. Volkers, L. Coffin, B. Hoes, M. F. Kalmykov, A. Palchesko, R. N. Sun, Y. Jongbloed, J. D. H. Bomer, N. de Boer, R. A. Suurmeijer, A. J. H. Pijnappels, D. A. Bolling, M. C. Meer, P. v. d. Feinberg, A. W. 2020-05-27 doi:10.1101/2020.05.25.111690 Cold Spring Harbor Laboratory Press 2020-05-27 <![CDATA[ SCAN-ATAC Sim: a scalable and efficient method to simulate single-cell ATAC-seq from bulk-tissue experiments ]]> https://biorxiv.org/content/10.1101/2020.05.29.123638v1?rss=1 Chen, Z. Zhang, J. Liu, J. Zhang, Z. Zhu, J. Xu, M. Gerstein, M. 2020-05-30 doi:10.1101/2020.05.29.123638 Cold Spring Harbor Laboratory Press 2020-05-30 <![CDATA[ Reconstructing SARS-CoV-2 response signaling and regulatory networks ]]> https://biorxiv.org/content/10.1101/2020.06.01.127589v1?rss=1 Ding, J. Lugo-Martinez, J. Yuan, Y. Kotton, D. N. Bar-Joseph, Z. 2020-06-01 doi:10.1101/2020.06.01.127589 Cold Spring Harbor Laboratory Press 2020-06-01 <![CDATA[ Tension promotes kinetochore-microtubule release in response to Aurora B activity ]]> https://biorxiv.org/content/10.1101/2020.06.01.127795v1?rss=1 Chen, G.-Y. Renda, F. Zhang, H. Gokden, A. Wu, D. Z. Chenoweth, D. M. Khodjakov, A. Lampson, M. 2020-06-02 doi:10.1101/2020.06.01.127795 Cold Spring Harbor Laboratory Press 2020-06-02 <![CDATA[ Cytoplasmic CPSF6 regulates HIV-1 capsid trafficking and infection in a cyclophilin A-dependent manner ]]> https://biorxiv.org/content/10.1101/2020.06.05.136697v1?rss=1 View larger version (48K): org.highwire.dtl.DTLVardef@646829org.highwire.dtl.DTLVardef@1f25cf9org.highwire.dtl.DTLVardef@b5e696org.highwire.dtl.DTLVardef@3593a7_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Zhong, Z. Ning, J. Boggs, E. A. Jang, S. Wallace, C. Telmer, C. Bruchez, M. Ahn, J. Engelman, A. zhang, p. Watkins, S. C. Ambrose, Z. 2020-06-05 doi:10.1101/2020.06.05.136697 Cold Spring Harbor Laboratory Press 2020-06-05 <![CDATA[ Beige adipocytes independently improve impaired glucose metabolism in the absence of brown adipose tissues in vivo ]]> https://biorxiv.org/content/10.1101/2020.06.05.136994v1?rss=1 Jia, X.-w. Fang, D.-l. Shi, X.-y. Lu, T. Yang, C. Gao, Y. 2020-06-05 doi:10.1101/2020.06.05.136994 Cold Spring Harbor Laboratory Press 2020-06-05 <![CDATA[ Bio-informed Protein Sequence Generation for Multi-class Virus Mutation Prediction ]]> https://biorxiv.org/content/10.1101/2020.06.11.146167v1?rss=1 Wang, Y. Yadav, P. Magar, R. Barati farimani, A. 2020-06-12 doi:10.1101/2020.06.11.146167 Cold Spring Harbor Laboratory Press 2020-06-12 <![CDATA[ An atlas of neural crest lineages along the posterior developing zebrafish at single-cell resolution ]]> https://biorxiv.org/content/10.1101/2020.06.14.150938v1?rss=1 Howard, A. G. A. Baker, P. A. Ibarra-Garcia-Padilla, R. Moore, J. A. Rivas, L. J. Singleton, E. W. Westheimer, J. L. Corteguera, J. A. Tallman, J. J. Uribe, R. A. 2020-06-14 doi:10.1101/2020.06.14.150938 Cold Spring Harbor Laboratory Press 2020-06-14 <![CDATA[ Syntactic representations in the human brain: beyond effort-based metrics ]]> https://biorxiv.org/content/10.1101/2020.06.16.155499v1?rss=1 Reddy, A. J. Wehbe, L. 2020-06-17 doi:10.1101/2020.06.16.155499 Cold Spring Harbor Laboratory Press 2020-06-17 <![CDATA[ Brainprint: identifying individuals from Magnetoencephalography ]]> https://biorxiv.org/content/10.1101/2020.06.18.159913v1?rss=1 View larger version (23K): org.highwire.dtl.DTLVardef@50c58corg.highwire.dtl.DTLVardef@d99cc1org.highwire.dtl.DTLVardef@c255cdorg.highwire.dtl.DTLVardef@8f2c13_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1:C_FLOATNO Graphical abstract. Identifying which subject a segment of MEG data belongs to is strikingly easy when other data from the same session is available for every subject. We propose three types of interpretable features that can also be used to identify individuals across sessions with high accuracy. Identifiability of individuals is influenced by factors such as resting state vs. task state, components of each feature, the sample size and the level of preprocessing. Our results reveal aspects of individual variability in MEG signals and highlight privacy risks associated with MEG data sharing. C_FIG ]]> Wu, S. Ramdas, A. Wehbe, L. 2020-06-20 doi:10.1101/2020.06.18.159913 Cold Spring Harbor Laboratory Press 2020-06-20 <![CDATA[ Spatio-temporal Characteristics of Noun and Verb Processing during Sentence Comprehension in the Brain ]]> https://biorxiv.org/content/10.1101/2020.06.22.163808v1?rss=1 Jat, S. Laing, E. J. C. Talukdar, P. Mitchell, T. 2020-06-22 doi:10.1101/2020.06.22.163808 Cold Spring Harbor Laboratory Press 2020-06-22 <![CDATA[ The discovery of potential natural products for targeting SARS-CoV-2 spike protein by virtual screening ]]> https://biorxiv.org/content/10.1101/2020.06.25.170639v1?rss=1 Wu, Y.-C. Chen, G.-Y. Yao, T.-Y. Ahmed, A. Pan, Y.-C. Yang, J.-C. 2020-06-25 doi:10.1101/2020.06.25.170639 Cold Spring Harbor Laboratory Press 2020-06-25 <![CDATA[ The eyes reflect an internal cognitive state embedded in the population activity of cortical neurons ]]> https://biorxiv.org/content/10.1101/2020.06.29.178251v1?rss=1 Johnston, R. Snyder, A. C. Khanna, S. Issar, D. Smith, M. A. 2020-06-30 doi:10.1101/2020.06.29.178251 Cold Spring Harbor Laboratory Press 2020-06-30 <![CDATA[ All hands on deck: Large-scale (re)sculpting of cortical circuits in post-resection children ]]> https://biorxiv.org/content/10.1101/2020.07.01.183400v1?rss=1 Maallo, A. M. S. Granovetter, M. C. Freud, E. Kastner, S. Pinsk, M. A. Patterson, C. Behrmann, M. 2020-07-02 doi:10.1101/2020.07.01.183400 Cold Spring Harbor Laboratory Press 2020-07-02 <![CDATA[ The Roles of Space and Stochasticity in Computational Simulations of Cellular Biochemistry: Quantitative Analysis and Qualitative Insights ]]> https://biorxiv.org/content/10.1101/2020.07.02.185595v1?rss=1 Johnson, M. E. Chen, A. Faeder, J. Henning, P. Moraru, I. I. Meier-Schellersheim, M. Murphy, R. F. Prustel, T. Theriot, J. A. Uhrmacher, A. 2020-07-04 doi:10.1101/2020.07.02.185595 Cold Spring Harbor Laboratory Press 2020-07-04 <![CDATA[ Combination Treatment Optimization Using aPan-Cancer Pathway Model ]]> https://biorxiv.org/content/10.1101/2020.07.05.184960v1?rss=1 Schmucker, R. Farina, G. Faeder, J. Froehlich, F. Saglam, A. S. Sandholm, T. 2020-07-06 doi:10.1101/2020.07.05.184960 Cold Spring Harbor Laboratory Press 2020-07-06 <![CDATA[ Astrocytes express DMT1 and transferrin receptors, which transport iron thus activating Ca2+ signalling: possible role in neuroprotection against iron overload? ]]> https://biorxiv.org/content/10.1101/2020.07.06.190652v1?rss=1 Xia, M. Guan, W. Ji, M. Li, S. Li, Z. Chen, B. Zhang, M. Liang, S. Gong, W. Dong, C. Chen, B. Wen, G. Zhan, X. Zhang, D. Li, X. Verkhratsky, A. Li, B. 2020-07-06 doi:10.1101/2020.07.06.190652 Cold Spring Harbor Laboratory Press 2020-07-06 <![CDATA[ Uncovering modeling features of viral replication dynamics from high-throughput single-cell virology experiments ]]> https://biorxiv.org/content/10.1101/2020.07.09.195925v1?rss=1 Ashley I. Teufel Wu Liu Jeremy A. Draghi Craig E. Cameron Claus O. Wilke 2020-07-09 doi:10.1101/2020.07.09.195925 Cold Spring Harbor Laboratory Press 2020-07-09 <![CDATA[ Endothelial Cell Polarization and Orientation to Flow in a Novel Microfluidic Multimodal Shear Stress Generator ]]> https://biorxiv.org/content/10.1101/2020.07.10.197244v1?rss=1 Utku M Somnez Ya-Wen Cheng Simon C Watkins Beth L. Roman Lance Davidson 2020-07-10 doi:10.1101/2020.07.10.197244 Cold Spring Harbor Laboratory Press 2020-07-10 <![CDATA[ Distributed Sampling-based Bayesian Inference in Coupled Neural Circuits ]]> https://biorxiv.org/content/10.1101/2020.07.20.212126v1?rss=1 Zhang, W. Lee, T. S. Doiron, B. Wu, S. 2020-07-22 doi:10.1101/2020.07.20.212126 Cold Spring Harbor Laboratory Press 2020-07-22 <![CDATA[ Arc1 modulates microbiota-responsive developmental and metabolic traits in Drosophila ]]> https://biorxiv.org/content/10.1101/2020.07.21.213835v1?rss=1 Keith, S. A. Bishop, C. Fallacaro, S. McCartney, B. M. 2020-07-22 doi:10.1101/2020.07.21.213835 Cold Spring Harbor Laboratory Press 2020-07-22 <![CDATA[ Cyclin G2 inhibits oral squamous cell carcinoma growth and metastasis by binding to insulin-like growth factor binding protein 3 and regulating the FAK-SRC-STAT signaling pathway ]]> https://biorxiv.org/content/10.1101/2020.07.21.214361v1?rss=1 Wang, D. Gao, J. Zhao, C. Li, S. Zhang, D. Hou, X. Zhuang, X. Liu, Q. Luo, Y. 2020-07-22 doi:10.1101/2020.07.21.214361 Cold Spring Harbor Laboratory Press 2020-07-22 <![CDATA[ Independently Regulated Multi-compartment Neuropeptide Release from a Clock Neuron Controls Circadian Behavior ]]> https://biorxiv.org/content/10.1101/2020.07.24.219725v1?rss=1 Klose, M. K. Bruchez, M. P. Deitcher, D. L. Levitan, E. S. 2020-07-26 doi:10.1101/2020.07.24.219725 Cold Spring Harbor Laboratory Press 2020-07-26 <![CDATA[ Identifying signaling genes in spatial single cell expression data ]]> https://biorxiv.org/content/10.1101/2020.07.27.221465v1?rss=1 Li, D. Ding, J. Bar-Joseph, Z. 2020-07-28 doi:10.1101/2020.07.27.221465 Cold Spring Harbor Laboratory Press 2020-07-28 <![CDATA[ Establishing live-cell single-molecule localization microscopy imaging and single-particle tracking in the archaeon Haloferax volcanii ]]> https://biorxiv.org/content/10.1101/2020.07.27.222935v1?rss=1 Turkowyd, B. Schreiber, S. Wörtz, J. Shtifman Segal, E. Mevarech, M. Duggin, I. G. Marchfelder, A. Endesfelder, U. 2020-07-27 doi:10.1101/2020.07.27.222935 Cold Spring Harbor Laboratory Press 2020-07-27 <![CDATA[ Elucidating the mechanism of cyclodextrins in the treatment of Niemann-Pick Disease Type C using crosslinked 2-hydroxypropyl-β-cyclodextrin ]]> https://biorxiv.org/content/10.1101/2020.07.31.230136v1?rss=1 View larger version (32K): org.highwire.dtl.DTLVardef@3dbaf1org.highwire.dtl.DTLVardef@bc255dorg.highwire.dtl.DTLVardef@390e7borg.highwire.dtl.DTLVardef@1e5e5c5_HPS_FORMAT_FIGEXP M_FIG C_FIG The 2-hydroxypropyl-{beta}-cyclodextrin (HP{beta}CD) is a well-established pharmaceutical excipient that can complex cholesterol and is currently under clinical investigation to treat Niemann-Pick Disease Type C (NPC). However, high doses of the drug are needed to achieve a therapeutic effect. Using stable and long circulating crosslinked HP{beta}CDs, this study attempts to further understand the mechanisms behind CDs activity. ]]> Carradori, D. Chen, H. Werner, B. Shah, A. Leonardi, C. Usuelli, M. Mezzenga, R. Platt, F. M. Leroux, J.-C. 2020-07-31 doi:10.1101/2020.07.31.230136 Cold Spring Harbor Laboratory Press 2020-07-31 <![CDATA[ EEG signals index a global signature of arousal embedded in neuronal population recordings ]]> https://biorxiv.org/content/10.1101/2020.08.03.235283v1?rss=1 Johnston, R. Snyder, A. C. Schibler, R. S. Smith, M. A. 2020-08-04 doi:10.1101/2020.08.03.235283 Cold Spring Harbor Laboratory Press 2020-08-04 <![CDATA[ Bayesian estimation of cell-type-specific gene expression per bulk sample with prior derived from single-cell data ]]> https://biorxiv.org/content/10.1101/2020.08.05.238949v1?rss=1 Wang, J. Roeder, K. Devlin, B. 2020-08-06 doi:10.1101/2020.08.05.238949 Cold Spring Harbor Laboratory Press 2020-08-06 <![CDATA[ Classic articles in Apoptotic Research: A Bibliometric Analysis ]]> https://biorxiv.org/content/10.1101/2020.08.06.239327v1?rss=1 Jallow, A. W. Lee, S.-D. Ho, Y.-S. 2020-08-06 doi:10.1101/2020.08.06.239327 Cold Spring Harbor Laboratory Press 2020-08-06 <![CDATA[ Systematic comparison of developmental GRNs explains how novelty is incorporated in early development ]]> https://biorxiv.org/content/10.1101/2020.08.07.231464v1?rss=1 Cary, G. A. McCauley, B. S. Zueva, O. Pattinato, J. Longabaugh, W. Hinman, V. 2020-08-07 doi:10.1101/2020.08.07.231464 Cold Spring Harbor Laboratory Press 2020-08-07 <![CDATA[ CoRhythMo: A Computational Framework for Modeling Biobehavioral Rhythms from Mobile and Wearable Data Streams ]]> https://biorxiv.org/content/10.1101/2020.08.10.244020v1?rss=1 Yan, R. Liu, X. Dutcher, J. Tumminia, M. Villalba, D. Cohen, S. Creswell, D. Creswell, K. Mankoff, J. Dey, A. Doryab, A. 2020-08-10 doi:10.1101/2020.08.10.244020 Cold Spring Harbor Laboratory Press 2020-08-10 <![CDATA[ Deep reinforcement learning for modeling human locomotion control in neuromechanical simulation ]]> https://biorxiv.org/content/10.1101/2020.08.11.246801v1?rss=1 Song, S. Kidzinski, Łukasz Peng, X. B. Ong, C. Hicks, J. L. Levine, S. Atkeson, C. Delp, S. 2020-08-12 doi:10.1101/2020.08.11.246801 Cold Spring Harbor Laboratory Press 2020-08-12 <![CDATA[ Deep and superficial layers of the primary somatosensory cortex are critical for whisker-based texture discrimination in mice ]]> https://biorxiv.org/content/10.1101/2020.08.12.245381v1?rss=1 View larger version (22K): org.highwire.dtl.DTLVardef@16c4d20org.highwire.dtl.DTLVardef@13b8832org.highwire.dtl.DTLVardef@16ac3aborg.highwire.dtl.DTLVardef@5426d8_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Park, J. M. Hong, Y. K. Rodgers, C. C. Dahan, J. B. Schmidt, E. R. Bruno, R. M. 2020-08-12 doi:10.1101/2020.08.12.245381 Cold Spring Harbor Laboratory Press 2020-08-12 <![CDATA[ Conditional resampling improves sensitivity and specificity of single cell CRISPR regulatory screens ]]> https://biorxiv.org/content/10.1101/2020.08.13.250092v1?rss=1 Katsevich, E. Roeder, K. 2020-08-14 doi:10.1101/2020.08.13.250092 Cold Spring Harbor Laboratory Press 2020-08-14 <![CDATA[ Inhibition of Severe Acute Respiratory Syndrome Coronavirus 2 main protease by tafenoquine in vitro ]]> https://biorxiv.org/content/10.1101/2020.08.14.250258v1?rss=1 Chen, Y. Yang, W.-H. Huang, L.-M. Wang, Y.-C. Yang, C.-S. Liu, Y.-L. Hou, M.-H. Tsai, C.-L. Chou, Y.-Z. Huang, B.-Y. Hung, C.-F. Hung, Y.-L. Chen, J.-S. Chiang, Y.-P. Cho, D.-Y. Jeng, L.-B. Tsai, C.-H. Hung, M.-C. 2020-08-15 doi:10.1101/2020.08.14.250258 Cold Spring Harbor Laboratory Press 2020-08-15 <![CDATA[ H-MAGMA, inheriting a shaky statistical foundation, yields excess false positives ]]> https://biorxiv.org/content/10.1101/2020.08.20.260224v1?rss=1 Yurko, R. J. Roeder, K. Devlin, B. G'Sell, M. 2020-08-22 doi:10.1101/2020.08.20.260224 Cold Spring Harbor Laboratory Press 2020-08-22 <![CDATA[ Detecting cell-type-specific allelic expression imbalance by integrative analysis of bulk and single-cell RNA sequencing data ]]> https://biorxiv.org/content/10.1101/2020.08.26.267815v1?rss=1 Fan, J. Wang, X. Xiao, R. Li, M. 2020-08-26 doi:10.1101/2020.08.26.267815 Cold Spring Harbor Laboratory Press 2020-08-26 <![CDATA[ Tissue pressure and cell traction compensate to drive robust aggregate spreading ]]> https://biorxiv.org/content/10.1101/2020.08.29.273334v1?rss=1 Yousafzai, M. S. Yadav, V. Amiri, S. Staddon, M. Tabatabai, A. P. Errami, Y. Jaspard, G. Amiri, S. Banerjee, S. Murrell, M. P. 2020-08-31 doi:10.1101/2020.08.29.273334 Cold Spring Harbor Laboratory Press 2020-08-31 <![CDATA[ cFIT: Integration and transfer learning of single cell transcriptomes, illustrated by fetal brain cell development ]]> https://biorxiv.org/content/10.1101/2020.08.31.276345v1?rss=1 Peng, M. Li, Y. Wamsley, B. Wei, Y. Roeder, K. 2020-08-31 doi:10.1101/2020.08.31.276345 Cold Spring Harbor Laboratory Press 2020-08-31 <![CDATA[ Integrating across neuroimaging modalities boosts prediction accuracy of cognitive ability ]]> https://biorxiv.org/content/10.1101/2020.09.01.278747v1?rss=1 Rasero, J. Sentis, A. I. Yeh, F.-C. Verstynen, T. V. 2020-09-03 doi:10.1101/2020.09.01.278747 Cold Spring Harbor Laboratory Press 2020-09-03 <![CDATA[ Single-cell RNA-seq reveals early heterogeneity during ageing in yeast ]]> https://biorxiv.org/content/10.1101/2020.09.04.282525v1?rss=1 Zhang, Y. Wang, J. Sang, Y. Jin, S. Wang, X. Azad, G. K. McCormick, M. A. Kennedy, B. K. Li, Q. Wang, J. Zhang, X. Huang, Y. 2020-09-04 doi:10.1101/2020.09.04.282525 Cold Spring Harbor Laboratory Press 2020-09-04 <![CDATA[ Benefits of Deep Learning Classification of Continuous Noninvasive Brain Computer Interface Control ]]> https://biorxiv.org/content/10.1101/2020.09.09.289462v1?rss=1 Stieger, J. R. Engel, S. A. Suma, D. He, B. 2020-09-10 doi:10.1101/2020.09.09.289462 Cold Spring Harbor Laboratory Press 2020-09-10 <![CDATA[ Effects of Long-Term Meditation Practices on Sensorimotor Rhythm Based BCI Learning ]]> https://biorxiv.org/content/10.1101/2020.09.09.290080v1?rss=1 Jiang, X. Lopez, E. Stieger, J. Greco, C. He, B. 2020-09-10 doi:10.1101/2020.09.09.290080 Cold Spring Harbor Laboratory Press 2020-09-10 <![CDATA[ Transcriptional alterations in opioid use disorder reveal an interplay between neuroinflammation and synaptic remodeling ]]> https://biorxiv.org/content/10.1101/2020.09.14.296707v1?rss=1 Seney, M. Kim, S.-M. Wang, J. Hildebrand, M. Xue, X. Glausier, J. Zong, W. Shelton, M. Phan, B. Srinivasan, C. Pfenning, A. Tseng, G. Lewis, D. Freyberg, Z. Logan, R. 2020-09-15 doi:10.1101/2020.09.14.296707 Cold Spring Harbor Laboratory Press 2020-09-15 <![CDATA[ Constrained brain volume in an efficient coding model explains the fraction of excitatory and inhibitory neurons in sensory cortices ]]> https://biorxiv.org/content/10.1101/2020.09.17.299040v1?rss=1 Alreja, A. Nemenman, I. Rozell, C. J. 2020-09-19 doi:10.1101/2020.09.17.299040 Cold Spring Harbor Laboratory Press 2020-09-19 <![CDATA[ Deep learning of gene interactions from single cell time-course expression data ]]> https://biorxiv.org/content/10.1101/2020.09.21.306332v1?rss=1 Yuan, Y. Bar-Joseph, Z. 2020-09-22 doi:10.1101/2020.09.21.306332 Cold Spring Harbor Laboratory Press 2020-09-22 <![CDATA[ Exponential-family embedding with application to cell developmental trajectories for single-cell RNA-seq data ]]> https://biorxiv.org/content/10.1101/2020.09.25.313882v1?rss=1 Lin, K. Lei, J. Roeder, K. 2020-09-25 doi:10.1101/2020.09.25.313882 Cold Spring Harbor Laboratory Press 2020-09-25 <![CDATA[ The meaning that emerges from combining words is robustly localizable in space but not in time ]]> https://biorxiv.org/content/10.1101/2020.09.28.316935v1?rss=1 Toneva, M. Mitchell, T. M. Wehbe, L. 2020-09-29 doi:10.1101/2020.09.28.316935 Cold Spring Harbor Laboratory Press 2020-09-29 <![CDATA[ Discovery and engineering of small SlugCas9 with broad targeting range and high specificity and activity ]]> https://biorxiv.org/content/10.1101/2020.09.29.316661v1?rss=1 Hu, Z. Zhang, C. Wang, S. Wei, J. Li, M. Hou, L. Liu, H. Liu, D. Lan, F. Lu, D. Wang, H. Li, J. Wang, Y. 2020-09-29 doi:10.1101/2020.09.29.316661 Cold Spring Harbor Laboratory Press 2020-09-29 <![CDATA[ Addiction-associated genetic variants implicate brain cell type- and region-specific cis-regulatory elements in addiction neurobiology ]]> https://biorxiv.org/content/10.1101/2020.09.29.318329v1?rss=1 Srinivasan, C. Phan, B. N. Lawler, A. J. Ramamurthy, E. Kleyman, M. Brown, A. R. Kaplow, I. M. Wirthlin, M. E. Pfenning, A. R. 2020-09-30 doi:10.1101/2020.09.29.318329 Cold Spring Harbor Laboratory Press 2020-09-30 <![CDATA[ A Diaphanous and Enabled dependent asymmetric actin cable array repositions nuclei during Drosophila oogenesis ]]> https://biorxiv.org/content/10.1101/2020.09.29.319533v1?rss=1 McCartney, B. Logan, G. 2020-10-01 doi:10.1101/2020.09.29.319533 Cold Spring Harbor Laboratory Press 2020-10-01 <![CDATA[ Probabilistic method corrects previously uncharacterized Hi-C artifact ]]> https://biorxiv.org/content/10.1101/2020.10.07.325332v1?rss=1 Shen, Y. Kingsford, C. 2020-10-08 doi:10.1101/2020.10.07.325332 Cold Spring Harbor Laboratory Press 2020-10-08 <![CDATA[ Functional Context Affects Scene Processing ]]> https://biorxiv.org/content/10.1101/2020.10.09.334102v1?rss=1 Aminoff, E. M. Tarr, M. J. 2020-10-10 doi:10.1101/2020.10.09.334102 Cold Spring Harbor Laboratory Press 2020-10-10 <![CDATA[ Neural silences can be localized rapidly using noninvasive scalp EEG ]]> https://biorxiv.org/content/10.1101/2020.10.11.334987v1?rss=1 Chamanzar, A. Behrmann, M. Grover, P. 2020-10-11 doi:10.1101/2020.10.11.334987 Cold Spring Harbor Laboratory Press 2020-10-11 <![CDATA[ Development of natural scene representation in primary visual cortex requires early postnatal experience ]]> https://biorxiv.org/content/10.1101/2020.10.14.338897v1?rss=1 Kowalewski, N. Kauttonen, J. Stan, P. L. Jeon, B. B. Fuchs, T. Chase, S. M. Lee, T. S. Kuhlman, S. 2020-10-15 doi:10.1101/2020.10.14.338897 Cold Spring Harbor Laboratory Press 2020-10-15 <![CDATA[ You-Gui-Wan ameliorates house dust mite-induced allergic asthma via modulating amino acid metabolic disorder and gut dysbiosis ]]> https://biorxiv.org/content/10.1101/2020.10.15.340646v1?rss=1 Hsu, W.-H. Lin, L.-J. Chao, Y.-M. Lu, C.-K. Kao, S.-T. Lin, Y.-L. 2020-10-15 doi:10.1101/2020.10.15.340646 Cold Spring Harbor Laboratory Press 2020-10-15 <![CDATA[ ESCO: single cell expression simulation incorporating gene co-expression ]]> https://biorxiv.org/content/10.1101/2020.10.20.347211v1?rss=1 Tian, J. Wang, J. Roeder, K. 2020-10-21 doi:10.1101/2020.10.20.347211 Cold Spring Harbor Laboratory Press 2020-10-21 <![CDATA[ Transcriptional Diversity of Medium Spiny Neurons in the Primate Striatum ]]> https://biorxiv.org/content/10.1101/2020.10.25.354159v1?rss=1 He, J. Kleyman, M. Chen, J. Alikaya, A. Rothenhoefer, K. M. Ozturk, B. E. Wirthlin, M. Fish, K. Byrne, L. C. T. Pfenning, A. R. Stauffer, W. R. 2020-10-25 doi:10.1101/2020.10.25.354159 Cold Spring Harbor Laboratory Press 2020-10-25 <![CDATA[ The Regulatory Evolution of the Primate Fine-Motor System ]]> https://biorxiv.org/content/10.1101/2020.10.27.356733v1?rss=1 Wirthlin, M. E. Kaplow, I. M. Lawler, A. J. He, J. Phan, B. N. Brown, A. R. Stauffer, W. R. Pfenning, A. R. 2020-10-27 doi:10.1101/2020.10.27.356733 Cold Spring Harbor Laboratory Press 2020-10-27 <![CDATA[ Hindbrain neuropore tissue geometry determines asymmetric cell-mediated closure dynamics ]]> https://biorxiv.org/content/10.1101/2020.11.02.364513v1?rss=1 Maniou, E. Staddon, M. Marshall, A. Greene, N. Copp, A. Banerjee, S. Galea, G. 2020-11-02 doi:10.1101/2020.11.02.364513 Cold Spring Harbor Laboratory Press 2020-11-02 <![CDATA[ Extensive MET alterations confer clinical response to MET inhibitors in gliomas ]]> https://biorxiv.org/content/10.1101/2020.11.02.364711v1?rss=1 Zhao, Z. Chen, J. Bao, Z. Chai, R. Zhang, K.-n. Wu, L. Liu, H. Mu, Q. Hu, H. Zeng, F. Wang, Z. Li, G. Chang, Y. Wang, Q. Wu, F. Zhang, Y. Liu, Y. Zhang, W. Kang, C. Wang, J. Tao, R. Wang, Q. Jiang, T. 2020-11-02 doi:10.1101/2020.11.02.364711 Cold Spring Harbor Laboratory Press 2020-11-02 <![CDATA[ Role and Dynamics of Vacuolar pH during Cell-in-Cell mediated Death ]]> https://biorxiv.org/content/10.1101/2020.11.03.364877v1?rss=1 Su, Y. Ren, H. Tang, M. Zheng, Y. Zhang, B. Wang, C. Hou, X. Niu, Z. Gao, L. Chen, Z. Luo, T. Sun, Q. 2020-11-04 doi:10.1101/2020.11.03.364877 Cold Spring Harbor Laboratory Press 2020-11-04 <![CDATA[ With Childhood Hemispherectomy, One Hemisphere Can Support--But is Suboptimal for--Word and Face Recognition ]]> https://biorxiv.org/content/10.1101/2020.11.06.371823v1?rss=1 Granovetter, M. C. Ettensohn, L. Behrmann, M. 2020-11-08 doi:10.1101/2020.11.06.371823 Cold Spring Harbor Laboratory Press 2020-11-08 <![CDATA[ Identification of cell-type-specific marker genes from co-expression patterns in tissue samples ]]> https://biorxiv.org/content/10.1101/2020.11.07.373043v1?rss=1 Qiu, Y. Wang, J. Lei, J. Roeder, K. 2020-11-08 doi:10.1101/2020.11.07.373043 Cold Spring Harbor Laboratory Press 2020-11-08 <![CDATA[ Coinfection of Streptococcus pneumoniae reduces airborne transmission of influenza virus ]]> https://biorxiv.org/content/10.1101/2020.11.10.376442v1?rss=1 Mueller Brown, K. Le Sage, V. French, A. J. Jones, J. E. Padovani, G. H. Avery, A. J. Myerburg, M. M. Schultz-Cherry, S. Rosch, J. W. Hiller, N. L. Lakdawala, S. S. 2020-11-10 doi:10.1101/2020.11.10.376442 Cold Spring Harbor Laboratory Press 2020-11-10 <![CDATA[ Entropy, complexity, and maturity in children's neural responses during naturalistic mathematics learning ]]> https://biorxiv.org/content/10.1101/2020.11.18.387431v1?rss=1 Amalric, M. Cantlon, J. 2020-11-20 doi:10.1101/2020.11.18.387431 Cold Spring Harbor Laboratory Press 2020-11-20 <![CDATA[ Forensic features and genetic legacy of the Baloch population of Pakistan and the Hazara population across Durand-line revealed by Y chromosomal STRs ]]> https://biorxiv.org/content/10.1101/2020.11.21.392456v1?rss=1 Adnan, A. Wen, S.-Q. Rakha, A. Alghafri, R. Nazir, S. Rehman, M. Wang, C.-C. Lu, J. 2020-11-22 doi:10.1101/2020.11.21.392456 Cold Spring Harbor Laboratory Press 2020-11-22 <![CDATA[ GEMC1-MCIDAS transcriptional program regulates multiciliogenesis in the choroid plexus and acts as a barrier to tumorigenesis ]]> https://biorxiv.org/content/10.1101/2020.11.22.393298v1?rss=1 Li, Q. Han, Z. Singh, N. Terre, B. Fame, R. M. Arif, U. Page, T. D. Zahran, T. Abdeltawab, A. Huang, Y. Cao, P. Wang, J. Lu, H. Lidov, H. G. W. Surendran, K. Wu, L. Schuller, U. Wechsler-Reya, R. J. Lehtinen, M. K. Roy, S. Liu, Z. Stracker, T. H. Zhao, H. 2020-11-22 doi:10.1101/2020.11.22.393298 Cold Spring Harbor Laboratory Press 2020-11-22 <![CDATA[ DANGO: Predicting higher-order genetic interactions ]]> https://biorxiv.org/content/10.1101/2020.11.26.400739v1?rss=1 Zhang, R. Ma, J. Ma, J. 2020-11-27 doi:10.1101/2020.11.26.400739 Cold Spring Harbor Laboratory Press 2020-11-27 <![CDATA[ A spiking neural circuit model for learning multi-sensory integration ]]> https://biorxiv.org/content/10.1101/2020.11.27.401216v1?rss=1 Song, D. Niu, X. Zhang, W.-H. Lee, T. S. 2020-11-27 doi:10.1101/2020.11.27.401216 Cold Spring Harbor Laboratory Press 2020-11-27 <![CDATA[ Dynamic decision policy reconfiguration under outcome uncertainty ]]> https://biorxiv.org/content/10.1101/2020.11.27.401737v1?rss=1 Bond, K. M. Dunovan, K. Porter, A. Rubin, J. Verstynen, T. 2020-11-27 doi:10.1101/2020.11.27.401737 Cold Spring Harbor Laboratory Press 2020-11-27 <![CDATA[ MolDiscovery: Learning Mass Spectrometry Fragmentation of Small Molecules ]]> https://biorxiv.org/content/10.1101/2020.11.28.401943v1?rss=1 Cao, L. Guler, M. Tagirdzhanov, A. Lee, Y. Gurevich, A. Mohimani, H. 2020-11-28 doi:10.1101/2020.11.28.401943 Cold Spring Harbor Laboratory Press 2020-11-28 <![CDATA[ SPICEMIX: Integrative single-cell spatial modeling for inferring cell identity ]]> https://biorxiv.org/content/10.1101/2020.11.29.383067v1?rss=1 Chidester, B. Zhou, T. Ma, J. 2020-11-30 doi:10.1101/2020.11.29.383067 Cold Spring Harbor Laboratory Press 2020-11-30 <![CDATA[ Bioelectrical Interfaces with Cortical Spheroids in Three-Dimensions ]]> https://biorxiv.org/content/10.1101/2020.11.29.401638v1?rss=1 Kalmykov, A. Reddy, J. W. Bedoyan, E. Wang, Y. Garg, R. Rastogi, S. K. Cohen-Karni, D. Chamanzar, M. Cohen-Karni, T. 2020-11-29 doi:10.1101/2020.11.29.401638 Cold Spring Harbor Laboratory Press 2020-11-29 <![CDATA[ Empty sella syndrome as a window into the neuroprotective effects of prolactin ]]> https://biorxiv.org/content/10.1101/2020.11.30.403576v1?rss=1 Paul, D. A. Strawderman, E. Rodriguez, A. Hoang, R. Schneider, C. Haber, S. Chernoff, B. L. Shafiq, I. Williams, Z. R. Vates, G. E. Mahon, B. Z. 2020-11-30 doi:10.1101/2020.11.30.403576 Cold Spring Harbor Laboratory Press 2020-11-30 <![CDATA[ A data harmonization pipeline to leverage external controls and boost power in GWAS ]]> https://biorxiv.org/content/10.1101/2020.11.30.405415v1?rss=1 Chen, D. Tashman, K. Palmer, D. S. Neale, B. Roeder, K. Bloemendal, A. Churchhouse, C. Ke, Z. T. 2020-12-02 doi:10.1101/2020.11.30.405415 Cold Spring Harbor Laboratory Press 2020-12-02 <![CDATA[ Deep learning enables rapid and robust analysis of fluorescence lifetime imaging in photon-starved conditions ]]> https://biorxiv.org/content/10.1101/2020.12.02.408195v1?rss=1 Yeh, H.-C. Chen, Y.-I. Chang, Y.-J. Liao, S.-C. Nguyen, T. D. Yang, J. Kuo, Y.-A. Hong, S. Liu, Y.-L. Rylander, H. G. Santacruz, S. R. Yankeelov, T. E. 2020-12-02 doi:10.1101/2020.12.02.408195 Cold Spring Harbor Laboratory Press 2020-12-02 <![CDATA[ Bridging neuronal correlations and dimensionality reduction ]]> https://biorxiv.org/content/10.1101/2020.12.04.383604v1?rss=1 Umakantha, A. Morina, R. Cowley, B. R. Snyder, A. C. Smith, M. A. Yu, B. M. 2020-12-04 doi:10.1101/2020.12.04.383604 Cold Spring Harbor Laboratory Press 2020-12-04 <![CDATA[ Predicting lineage-specific differences in open chromatin across dozens of mammalian genomes ]]> https://biorxiv.org/content/10.1101/2020.12.04.410795v1?rss=1 Kaplow, I. M. Wirthlin, M. E. Lawler, A. J. Brown, A. R. Kleyman, M. Pfenning, A. R. 2020-12-04 doi:10.1101/2020.12.04.410795 Cold Spring Harbor Laboratory Press 2020-12-04 <![CDATA[ Association of CD44-/CD24- Breast Cancer Cells with Late Stage Tumor Recurrence ]]> https://biorxiv.org/content/10.1101/2020.12.07.414599v1?rss=1 Liu, C. Qiao, X. Zhang, Y. Sun, L. Ma, Q. Yang, J. Ai, L. Xue, J. Chen, G. Zhang, H. Ji, C. Gu, X. Lei, H. Yang, Y. 2020-12-07 doi:10.1101/2020.12.07.414599 Cold Spring Harbor Laboratory Press 2020-12-07 <![CDATA[ Tuning electrical stimulation of the cervical vagus nerve for abdominal signaling while reducing cardiovascular side effects ]]> https://biorxiv.org/content/10.1101/2020.12.10.420398v1?rss=1 Horn, C. Forssell, M. Sciullo, M. Harms, J. E. Fulton, S. Mou, C. Sun, F. Simpson, T. W. Xiao, G. Fisher, L. E. Bettinger, C. Fedder, G. K. 2020-12-11 doi:10.1101/2020.12.10.420398 Cold Spring Harbor Laboratory Press 2020-12-11 <![CDATA[ Multiscale and integrative single-cell Hi-C analysis with Higashi ]]> https://biorxiv.org/content/10.1101/2020.12.13.422537v1?rss=1 Zhang, R. Zhou, T. Ma, J. 2020-12-15 doi:10.1101/2020.12.13.422537 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ Interplay between intraocular and intracranial pressure effects on the optic nerve head in vivo ]]> https://biorxiv.org/content/10.1101/2020.12.14.422760v1?rss=1 Zhu, Z. Waxman, S. Wang, B. Wallace, J. Schmitt, S. E. Tyler-Kabara, E. Ishikawa, H. Schuman, J. S. Smith, M. A. Wollstein, G. Sigal, I. A. 2020-12-15 doi:10.1101/2020.12.14.422760 Cold Spring Harbor Laboratory Press 2020-12-15 <![CDATA[ Quantifying a Frequency Modulation Response Biomarker in Responsive Neurostimulation ]]> https://biorxiv.org/content/10.1101/2020.12.17.423339v1?rss=1 Venkatesh, P. Sneider, D. Danish, M. Sisterson, N. D. Zaher, N. Urban, A. Grover, P. Richardson, R. M. Kokkinos, V. 2020-12-20 doi:10.1101/2020.12.17.423339 Cold Spring Harbor Laboratory Press 2020-12-20 <![CDATA[ Estimation of Kinematics from Inertial Measurement Units Using a Combined Deep Learning and Optimization Framework ]]> https://biorxiv.org/content/10.1101/2020.12.29.424030v1?rss=1 Rapp, E. Shin, S. Thomsen, W. Ferber, R. Halilaj, E. 2020-12-30 doi:10.1101/2020.12.29.424030 Cold Spring Harbor Laboratory Press 2020-12-30 <![CDATA[ Variability of the Surface Area of the V1, V2, and V3 Maps in a Large Sample of Human Observers ]]> https://biorxiv.org/content/10.1101/2020.12.30.424856v1?rss=1 Benson, N. C. Yoon, J. M. D. Forenzo, D. Kay, K. N. Engel, S. A. Winawer, J. 2021-01-02 doi:10.1101/2020.12.30.424856 Cold Spring Harbor Laboratory Press 2021-01-02 <![CDATA[ A read count-based method to detect multiplets and their cellular origins from snATAC-seq data ]]> https://biorxiv.org/content/10.1101/2021.01.04.425250v1?rss=1 2 uniquely aligned reads are observed at multiple loci. Here, we implemented the first read count-based multiplet detection method, ATAC-DoubletDetector, that detects multiplets independently of cell-type. Using PBMC and pancreatic islet datasets, ATAC-DoubletDetector captured simulated heterotypic multiplets (different cell-types) with [~]0.60 recall, showing [~]24% improvement over state of the art. ATAC-DoubletDetector detected homotypic multiplets with [~]0.61 recall, representing the first method to detect multiplets originating from the same cell type. Using our novel clustering-based algorithm, multiplets were annotated to their cellular origins with [~]85% accuracy. Application of ATAC-DoubletDetector will improve downstream analysis of snATAC-seq. ]]> Thibodeau, A. Eroglu, A. Lawlor, N. Nehar-Belaid, D. Kursawe, R. Marches, R. Kuchel, G. A. Banchereau, J. Stitzel, M. L. Cicek, A. E. Ucar, D. 2021-01-05 doi:10.1101/2021.01.04.425250 Cold Spring Harbor Laboratory Press 2021-01-05 <![CDATA[ Capturing the complexity of topologically associating domains through multi-feature optimization ]]> https://biorxiv.org/content/10.1101/2021.01.04.425264v1?rss=1 Sauerwald, N. Kingsford, C. 2021-01-05 doi:10.1101/2021.01.04.425264 Cold Spring Harbor Laboratory Press 2021-01-05 <![CDATA[ A sequence-based method for predicting extant fold switchers that undergo α-helix <-> β-strand transitions ]]> https://biorxiv.org/content/10.1101/2021.01.14.426714v1?rss=1 {beta}-strand prediction discrepancies from JPred4 are a robust predictor of fold switching, and (2) the fold-switching regions (FSRs) of some extant fold switchers have different secondary structure propensities when expressed in isolation (isolated FSRs) than when expressed within the context of their parent protein (contextualized FSRs). Combining these two observations, we ran JPred4 on the sequences of isolated and contextualized FSRs from 14 known extant fold switchers and found -helix <->{beta}-strand prediction discrepancies in every case. To test the overall robustness of this finding, we randomly selected regions of proteins not expected to switch folds (single-fold proteins) and found significantly fewer -helix <-> {beta}-strand prediction discrepancies (p < 4.2*10-20, Kolmogorov-Smirnov test). Combining these discrepancies with the overall percentage of predicted secondary structure, we developed a classifier that often robustly identifies extant fold switchers (Matthews Correlation Coefficient of 0.70). Although this classifier had a high false negative rate (6/14), its false positive rate was very low (1/211), suggesting that it can be used to predict a subset of extant fold switchers from billions of available genomic sequences. ]]> Mishra, S. Looger, L. L. Porter, L. 2021-01-16 doi:10.1101/2021.01.14.426714 β-strand transitions]]> Cold Spring Harbor Laboratory Press 2021-01-16 <![CDATA[ Accounting for fragments of unexpectedorigin improves transcript quantification inRNA-seq simulations focused on increased realism ]]> https://biorxiv.org/content/10.1101/2021.01.17.426996v1?rss=1 Srivastava, A. Zakeri, M. Sarkar, H. Soneson, C. Kingsford, C. Patro, R. 2021-01-19 doi:10.1101/2021.01.17.426996 Cold Spring Harbor Laboratory Press 2021-01-19 <![CDATA[ Prosodic categories in speech are acoustically multidimensional: evidence from dimension-based statistical learning ]]> https://biorxiv.org/content/10.1101/2021.01.18.427088v1?rss=1 Jasmin, K. Tierney, A. T. Holt, L. 2021-01-18 doi:10.1101/2021.01.18.427088 Cold Spring Harbor Laboratory Press 2021-01-18 <![CDATA[ DECODE: A Deep-learning Framework for Condensing Enhancers and Refining Boundaries with Large-scale Functional Assays ]]> https://biorxiv.org/content/10.1101/2021.01.27.428477v1?rss=1 Chen, Z. Zhang, J. Liu, J. Dai, Y. Lee, D. Min, M. R. Xu, M. Gerstein, M. 2021-01-28 doi:10.1101/2021.01.27.428477 Cold Spring Harbor Laboratory Press 2021-01-28 <![CDATA[ Talker discontinuity disrupts attention to speech: Evidence from EEG and pupillometry ]]> https://biorxiv.org/content/10.1101/2021.01.28.428718v1?rss=1 Lim, S.-J. Carter, Y. D. Njoroge, J. M. Shinn-Cunningham, B. G. Perrachione, T. K. 2021-01-30 doi:10.1101/2021.01.28.428718 Cold Spring Harbor Laboratory Press 2021-01-30 <![CDATA[ Sequence-specific minimizers via polar sets ]]> https://biorxiv.org/content/10.1101/2021.02.01.429246v1?rss=1 Zheng, H. Kingsford, C. Marcais, G. 2021-02-02 doi:10.1101/2021.02.01.429246 Cold Spring Harbor Laboratory Press 2021-02-02 <![CDATA[ Coupling Comprehensive Transcriptome-Metabolome Association and Phylogenetic Analysis Speed Dissecion of Polyphyllins Biosynthetic Pathway ]]> https://biorxiv.org/content/10.1101/2021.02.01.429277v1?rss=1 hua, x. Song, W. Wang, K. Yin, X. Hao, c. Xu, Z. Su, T. Xue, z. 2021-02-02 doi:10.1101/2021.02.01.429277 Cold Spring Harbor Laboratory Press 2021-02-02 <![CDATA[ LIFE AND WORK OF RESEARCHERS TRAPPED IN THE COVID-19PANDEMIC VICIOUS CYCLE ]]> https://biorxiv.org/content/10.1101/2021.02.02.429476v1?rss=1 Ghaffarizadeh, S. A. Ghaffarizadeh, S. A. Behbahani, A. H. Mehdizadeh, M. Olechowski, A. 2021-02-03 doi:10.1101/2021.02.02.429476 Cold Spring Harbor Laboratory Press 2021-02-03 <![CDATA[ Practical selection of representative sets of RNA-seq samples using a hierarchical approach ]]> https://biorxiv.org/content/10.1101/2021.02.04.429817v1?rss=1 Tung, L. H. Kingsford, C. 2021-02-05 doi:10.1101/2021.02.04.429817 Cold Spring Harbor Laboratory Press 2021-02-05 <![CDATA[ Cell Type Hierarchy Reconstruction via Reconciliation of Multi-resolution Cluster Tree ]]> https://biorxiv.org/content/10.1101/2021.02.06.430067v1?rss=1 Peng, M. Wamsley, B. Elkins, A. G. Geschwind, D. M. Wei, Y. Roeder, K. 2021-02-08 doi:10.1101/2021.02.06.430067 Cold Spring Harbor Laboratory Press 2021-02-08 <![CDATA[ A theory of evolutionary dynamics on any complex spatial structure ]]> https://biorxiv.org/content/10.1101/2021.02.07.430151v1?rss=1 Kuo, Y. P. Nombela-Arrieta, C. Carja, O. 2021-02-08 doi:10.1101/2021.02.07.430151 Cold Spring Harbor Laboratory Press 2021-02-08 <![CDATA[ Constructing smaller genome graphs via string compression ]]> https://biorxiv.org/content/10.1101/2021.02.08.430279v1?rss=1 Qiu, Y. Kingsford, C. 2021-02-09 doi:10.1101/2021.02.08.430279 Cold Spring Harbor Laboratory Press 2021-02-09 <![CDATA[ New skill acquisition does not perturb existing function in sensory cortex ]]> https://biorxiv.org/content/10.1101/2021.02.08.430302v1?rss=1 Jeon, B. B. Chase, S. M. Kuhlman, S. 2021-02-08 doi:10.1101/2021.02.08.430302 Cold Spring Harbor Laboratory Press 2021-02-08 <![CDATA[ Feedforward and feedback interactions between visual cortical areas use different population activity patterns ]]> https://biorxiv.org/content/10.1101/2021.02.08.430346v1?rss=1 Semedo, J. Jasper, A. I. Zandvakili, A. Aschner, A. Machens, C. Kohn, A. Yu, B. M. 2021-02-10 doi:10.1101/2021.02.08.430346 Cold Spring Harbor Laboratory Press 2021-02-10 <![CDATA[ Top-down attention modulates auditory-evoked neural responses in neurotypical, but not ADHD, young adults ]]> https://biorxiv.org/content/10.1101/2021.02.11.430824v1?rss=1 Kwasa, J. A. C. Noyce, A. L. Torres, L. M. Shinn-Cunningham, B. G. 2021-02-12 doi:10.1101/2021.02.11.430824 Cold Spring Harbor Laboratory Press 2021-02-12 <![CDATA[ Constructing Local Cell Sepcific Networks from Single Cell Data ]]> https://biorxiv.org/content/10.1101/2021.02.13.431104v1?rss=1 Wang, X. Choi, D. Roeder, K. 2021-02-14 doi:10.1101/2021.02.13.431104 Cold Spring Harbor Laboratory Press 2021-02-14 <![CDATA[ Competence-associated peptide BriC alters fatty acid biosynthesis in Streptococcus pneumoniae ]]> https://biorxiv.org/content/10.1101/2021.02.17.431746v1?rss=1 Aggarwal, S. D. Gullett, J. M. Fedder, T. Safi, J. P. F. Rock, C. O. Hiller, N. L. 2021-02-18 doi:10.1101/2021.02.17.431746 Cold Spring Harbor Laboratory Press 2021-02-18 <![CDATA[ CINS: Cell Interaction Network inference from Single cell expression data ]]> https://biorxiv.org/content/10.1101/2021.02.22.432206v1?rss=1 Yuan, Y. Cosme, C. Adams, T. S. Schupp, J. Sakamoto, K. Xylourgidis, N. Ruffalo, M. Kaminski, N. Bar-Joseph, Z. 2021-02-25 doi:10.1101/2021.02.22.432206 Cold Spring Harbor Laboratory Press 2021-02-25 <![CDATA[ Pulsatile contractions and pattern formation in excitable active gels ]]> https://biorxiv.org/content/10.1101/2021.02.22.432369v1?rss=1 Staddon, M. F. Munro, E. Banerjee, S. 2021-02-23 doi:10.1101/2021.02.22.432369 Cold Spring Harbor Laboratory Press 2021-02-23 <![CDATA[ Deep Brain Stimulation for Parkinson's Disease Induces Spontaneous Cortical Hypersynchrony In Extended Motor and Cognitive Networks ]]> https://biorxiv.org/content/10.1101/2021.02.23.432542v1?rss=1 Wang, M. B. Boring, M. J. Ward, M. J. Richardson, M. Ghuman, A. S. 2021-02-24 doi:10.1101/2021.02.23.432542 Cold Spring Harbor Laboratory Press 2021-02-24 <![CDATA[ Cell Type Assignments for Spatial Transcriptomics Data ]]> https://biorxiv.org/content/10.1101/2021.02.25.432887v1?rss=1 Teng, H. Yuan, Y. Bar-Joseph, Z. 2021-02-26 doi:10.1101/2021.02.25.432887 Cold Spring Harbor Laboratory Press 2021-02-26 <![CDATA[ AIM-CICs: automatic identification method for Cell-in-cell structures based on convolutional neural network ]]> https://biorxiv.org/content/10.1101/2021.02.26.432996v1?rss=1 0.99), but also accurately categorize CICs into five subclasses based on CICs stages and cell number involved (AUC > 0.97 for all subclasses). The application of AIM-CICs would systemically fuel researches on CICs-mediated cell death such as high-throughput screening. ]]> Tang, M. Su, Y. Zhao, W. Niu, Z. Ruan, B. Li, Q. Zheng, Y. Wang, C. Zhou, Y. Zhang, B. Zhou, F. Huang, H. Shi, H. Sun, Q. 2021-02-26 doi:10.1101/2021.02.26.432996 Cold Spring Harbor Laboratory Press 2021-02-26 <![CDATA[ Asymmetric Contraction of Adherens Junctions arises through RhoA and E-cadherin feedback ]]> https://biorxiv.org/content/10.1101/2021.02.26.433093v1?rss=1 Cavanaugh, K. Staddon, M. Chmiel, T. A. Harmon, R. M. Budnar, S. Yap, A. S. Banerjee, S. Gardel, M. 2021-02-26 doi:10.1101/2021.02.26.433093 Cold Spring Harbor Laboratory Press 2021-02-26 <![CDATA[ miRNA-dependent poly(A) length control in uncoupling transcription and translation of haploid male germ cells ]]> https://biorxiv.org/content/10.1101/2021.03.01.433315v1?rss=1 Tang, C. Guo, M. Shi, Z. Wang, Z. Luo, C. Chen, S. Ruan, F. Chen, Z. Yang, L. Wei, X. Wu, C. Luo, B. Huang, J. Zhang, D. Yu, C. Gao, Q. Zhang, Y. Yan, W. Sun, F. 2021-03-01 doi:10.1101/2021.03.01.433315 Cold Spring Harbor Laboratory Press 2021-03-01 <![CDATA[ Injury-Free In Vivo Delivery and Engraftment into the Cornea Endothelium Using Extracellular Matrix Shrink-Wrapped Cells ]]> https://biorxiv.org/content/10.1101/2021.03.01.433476v1?rss=1 Palchesko, R. N. Du, Y. Geary, M. Carrasquilla, S. Shiwarski, D. J. Khandaker, I. Feunderburgh, J. L. Feinberg, A. 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Kostka, D. 2021-03-07 doi:10.1101/2021.03.05.434138 Cold Spring Harbor Laboratory Press 2021-03-07 <![CDATA[ Spike mutations in SARS-CoV-2 variants confer resistance to antibody neutralization ]]> https://biorxiv.org/content/10.1101/2021.03.09.434497v1?rss=1 Wang, R. Zhang, Q. Ge, J. Ren, W. Zhang, R. Lan, J. Ju, B. Su, B. Yu, F. Chen, P. Liao, H. Feng, Y. Li, X. Shi, X. Zhang, Z. Zhang, F. Ding, Q. Zhang, T. Wang, X. Zhang, L. 2021-03-09 doi:10.1101/2021.03.09.434497 Cold Spring Harbor Laboratory Press 2021-03-09 <![CDATA[ BEdeepoff: an in silico tool for off-target prediction of ABE and CBE base editors ]]> https://biorxiv.org/content/10.1101/2021.03.14.435296v1?rss=1 Zhang, C. Wang, D. Qi, T. Zhang, Y. Hou, L. Lan, F. Yang, J. Ong, S.-G. Wang, H. Shi, L. Wang, Y. 2021-03-15 doi:10.1101/2021.03.14.435296 Cold Spring Harbor Laboratory Press 2021-03-15 <![CDATA[ BEdeepon: an in silico tool for prediction of base editor efficiencies and outcomes ]]> https://biorxiv.org/content/10.1101/2021.03.14.435303v1?rss=1 Zhang, C. Wang, D. Qi, T. Zhang, Y. Hou, L. Lan, F. Yang, J. Shi, L. Ong, S.-G. Wang, H. Wang, Y. 2021-03-15 doi:10.1101/2021.03.14.435303 Cold Spring Harbor Laboratory Press 2021-03-15 <![CDATA[ Cellar: Interactive single cell data annotation tool ]]> https://biorxiv.org/content/10.1101/2021.03.19.436162v1?rss=1 Hasanaj, E. Wang, J. Sarathi, A. Ding, J. Bar-Joseph, Z. 2021-03-20 doi:10.1101/2021.03.19.436162 Cold Spring Harbor Laboratory Press 2021-03-20 <![CDATA[ Bacterial cell shape control by nutrient-dependent synthesis of cell division inhibitors ]]> https://biorxiv.org/content/10.1101/2021.03.25.436990v1?rss=1 Ojkic, N. Banerjee, S. 2021-03-25 doi:10.1101/2021.03.25.436990 Cold Spring Harbor Laboratory Press 2021-03-25 <![CDATA[ Modulation masking and fine structure shape neural envelope coding to predict speech intelligibility across diverse listening conditions ]]> https://biorxiv.org/content/10.1101/2021.03.26.437273v1?rss=1 Viswanathan, V. Bharadwaj, H. M. Shinn-Cunningham, B. G. Heinz, M. G. 2021-03-27 doi:10.1101/2021.03.26.437273 Cold Spring Harbor Laboratory Press 2021-03-27 <![CDATA[ Discovery of target genes and pathways of blood trait loci using pooled CRISPR screens and single cell RNA sequencing ]]> https://biorxiv.org/content/10.1101/2021.04.07.438882v1?rss=1 Morris, J. A. Daniloski, Z. Domingo, J. Barry, T. Ziosi, M. Glinos, D. A. Hao, S. Mimitou, E. Smibert, P. Roeder, K. Katsevich, E. Lappalainen, T. Sanjana, N. E. 2021-04-08 doi:10.1101/2021.04.07.438882 Cold Spring Harbor Laboratory Press 2021-04-08 <![CDATA[ Barcoded Competitive Clone-Initiating Cell (BC-CIC) Analysis Reveals Differences in Ovarian Cancer Cell Genotype and Niche Specific Clonal Fitness During Growth and Metastasis In Vivo ]]> https://biorxiv.org/content/10.1101/2021.04.08.439098v1?rss=1 Aalam, S. M. M. Tang, X. Song, J. Bakkum-Gamez, J. N. Sherman, M. E. Ray, U. Shridhar, V. Kalari, K. R. Knapp, D. J. H. F. Kannan, N. 2021-04-11 doi:10.1101/2021.04.08.439098 Cold Spring Harbor Laboratory Press 2021-04-11 <![CDATA[ Machine learning sequence prioritization for cell type-specific enhancer design ]]> https://biorxiv.org/content/10.1101/2021.04.15.439984v1?rss=1 Lawler, A. J. Ramamurthy, E. Brown, A. R. Shin, N. Kim, Y. Toong, N. Kaplow, I. M. Wirthlin, M. Zhang, X. Fox, G. Pfenning, A. 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G. 2021-04-19 doi:10.1101/2021.04.19.440487 Cold Spring Harbor Laboratory Press 2021-04-19 <![CDATA[ Similarity in sensory modality and information domain impair processing in a dual-task context: Evidence from behavior, pupillometry, and EEG ]]> https://biorxiv.org/content/10.1101/2021.04.20.440675v1?rss=1 Fleming, J. T. Njoroge, J. M. Noyce, A. L. Perrachione, T. K. Shinn-Cunningham, B. G. 2021-04-21 doi:10.1101/2021.04.20.440675 Cold Spring Harbor Laboratory Press 2021-04-21 <![CDATA[ Sentinel cells enable genetic detection of SARS-CoV-2 Spike protein ]]> https://biorxiv.org/content/10.1101/2021.04.20.440678v1?rss=1 Weinberg, Z. Y. Hilburger, C. E. Kim, M. Cao, L. Khalid, M. M. Elmes, S. Diwanji, D. Hernandez, E. Lopez, J. Schaefer, K. Smith, A. M. Zhou, F. QCRG Structural Biology Consortium, Kumar, G. R. Ott, M. Baker, D. El-Samad, H. 2021-04-20 doi:10.1101/2021.04.20.440678 Cold Spring Harbor Laboratory Press 2021-04-20 <![CDATA[ Telomeric 8-oxoguanine drives rapid premature senescence in the absence of telomere shortening ]]> https://biorxiv.org/content/10.1101/2021.05.05.442662v1?rss=1 Barnes, R. P. de Rosa, M. Thosar, S. A. Detwiler, A. C. Roginskaya, V. Van Houten, B. Bruchez, M. P. Stewart-Ornstein, J. Opresko, P. L. 2021-05-05 doi:10.1101/2021.05.05.442662 Cold Spring Harbor Laboratory Press 2021-05-05 <![CDATA[ Thiolutin is a direct inhibitor of RNA Polymerase II ]]> https://biorxiv.org/content/10.1101/2021.05.05.442806v1?rss=1 Qiu, C. Malik, I. Arora, P. Laperuta, A. J. Pavlovic, E. M. Ugochuckwu, S. Naik, M. T. Kaplan, C. D. 2021-05-05 doi:10.1101/2021.05.05.442806 Cold Spring Harbor Laboratory Press 2021-05-05 <![CDATA[ Unilateral Resection of Both Cortical Visual Pathways Alters Action but not Perception ]]> https://biorxiv.org/content/10.1101/2021.05.06.442988v1?rss=1 Ahmad, Z. Behrmann, M. Patterson, C. M. Freud, E. 2021-05-07 doi:10.1101/2021.05.06.442988 Cold Spring Harbor Laboratory Press 2021-05-07 <![CDATA[ Frontostriatal Functional Connectivity Underlies Self-Enhancement During Social Evaluation ]]> https://biorxiv.org/content/10.1101/2021.05.07.443090v1?rss=1 Parrish, M. H. Dutcher, J. Muscatell, K. A. Inagaki, T. K. Moieni, M. Irwin, M. R. Eisenberger, N. I. 2021-05-07 doi:10.1101/2021.05.07.443090 Cold Spring Harbor Laboratory Press 2021-05-07 <![CDATA[ Temporal fine structure influences voicing confusions for consonant identification in multi-talker babble ]]> https://biorxiv.org/content/10.1101/2021.05.11.443678v1?rss=1 Viswanathan, V. Shinn-Cunningham, B. G. Heinz, M. G. 2021-05-12 doi:10.1101/2021.05.11.443678 Cold Spring Harbor Laboratory Press 2021-05-12 <![CDATA[ Inferring population structure in biobank-scale genomic data ]]> https://biorxiv.org/content/10.1101/2021.05.11.443705v1?rss=1 Chiu, A. M. Molloy, E. K. Tan, Z. Talwalkar, A. Sankararaman, S. 2021-05-13 doi:10.1101/2021.05.11.443705 Cold Spring Harbor Laboratory Press 2021-05-13 <![CDATA[ DISCA: high-throughput cryo-ET structural pattern mining by deep unsupervised clustering ]]> https://biorxiv.org/content/10.1101/2021.05.16.444381v1?rss=1 Zeng, X. Kahng, A. Xue, L. Mahamid, J. Chang, Y.-W. Xu, M. 2021-05-17 doi:10.1101/2021.05.16.444381 Cold Spring Harbor Laboratory Press 2021-05-17 <![CDATA[ An approach to gene-based testing accounting for dependence of tests among nearby genes ]]> https://biorxiv.org/content/10.1101/2021.05.24.445494v1?rss=1 Yurko, R. J. Roeder, K. Devlin, B. G'Sell, M. 2021-05-25 doi:10.1101/2021.05.24.445494 Cold Spring Harbor Laboratory Press 2021-05-25 <![CDATA[ Frontal language areas do not emerge in the absence of temporal language areas: A case study of an individual born without a left temporal lobe ]]> https://biorxiv.org/content/10.1101/2021.05.28.446230v1?rss=1 Tuckute, G. Paunov, A. Kean, H. Small, H. Mineroff, Z. Blank, I. Fedorenko, E. 2021-05-28 doi:10.1101/2021.05.28.446230 Cold Spring Harbor Laboratory Press 2021-05-28 <![CDATA[ A connectivity-constrained computational account of topographic organization in high-level visual cortex ]]> https://biorxiv.org/content/10.1101/2021.05.29.446297v1?rss=1 Blauch, N. M. Behrmann, M. Plaut, D. 2021-05-30 doi:10.1101/2021.05.29.446297 Cold Spring Harbor Laboratory Press 2021-05-30 <![CDATA[ Computational modeling of cell signaling and mutations in pancreatic cancer ]]> https://biorxiv.org/content/10.1101/2021.06.08.447557v1?rss=1 Telmer, C. A. Sayed, K. Butchy, A. A. Bocan, K. Kaltenmeier, C. Lotze, M. T. Miskov-Zivanov, N. 2021-06-09 doi:10.1101/2021.06.08.447557 Cold Spring Harbor Laboratory Press 2021-06-09 <![CDATA[ Three-dimensional organization of chromatin associated RNAs and their role in chromatin architecture in human cells ]]> https://biorxiv.org/content/10.1101/2021.06.10.447969v1?rss=1 Calandrelli, R. Wen, X. Nguyen, T. C. Chen, C.-J. Qi, Z. Chen, W. Yan, Z. Wu, W. Zaleta-Rivera, K. Hu, R. Yu, M. Wang, Y. Ma, J. Ren, B. Zhong, S. 2021-06-11 doi:10.1101/2021.06.10.447969 Cold Spring Harbor Laboratory Press 2021-06-11 <![CDATA[ Engineering 3D Vascularized Adipose Tissue Construct using a Decellularized Lung Matrix ]]> https://biorxiv.org/content/10.1101/2021.06.22.449445v1?rss=1 DeBari, M. K. Ng, W. H. Griffin, M. D. Kokai, L. E. Marra, K. G. Rubin, J. P. Ren, X. Abbott, R. D. 2021-06-22 doi:10.1101/2021.06.22.449445 Cold Spring Harbor Laboratory Press 2021-06-22 <![CDATA[ Evolutionary graph theory beyond pairwise interactions: higher-order network motifs shape times to fixation in structured populations ]]> https://biorxiv.org/content/10.1101/2021.06.26.450017v1?rss=1 Carja, O. Kuo, Y. 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Sheen, L.-Y. 2021-07-06 doi:10.1101/2021.07.06.451284 Cold Spring Harbor Laboratory Press 2021-07-06 <![CDATA[ Flexible utilization of spatial- and motor-based codes for the storage of visuo-spatial information ]]> https://biorxiv.org/content/10.1101/2021.07.08.451663v1?rss=1 Henderson, M. M. Rademaker, R. L. Serences, J. T. 2021-07-09 doi:10.1101/2021.07.08.451663 Cold Spring Harbor Laboratory Press 2021-07-09 <![CDATA[ Distribution-based comprehensive evaluation ofmethods for differential expression analysis inmetatranscriptomics ]]> https://biorxiv.org/content/10.1101/2021.07.14.452374v1?rss=1 Cho, H. Liu, C. Lin, B. M. Tang, B. Roach, J. de Ribeiro, A. Love, M. I. Divaris, K. Wu, D. 2021-07-14 doi:10.1101/2021.07.14.452374 Cold Spring Harbor Laboratory Press 2021-07-14 <![CDATA[ Online tests yield robust thresholds with the right auditory hygiene ]]> https://biorxiv.org/content/10.1101/2021.07.17.452796v1?rss=1 Zhao, S. Brown, C. A. Holt, L. L. Dick, F. 2021-07-19 doi:10.1101/2021.07.17.452796 Cold Spring Harbor Laboratory Press 2021-07-19 <![CDATA[ Diet modifies allele-specific phenotypes in Drosophila carrying epilepsy-associated PNPO variants ]]> https://biorxiv.org/content/10.1101/2021.07.19.452889v1?rss=1 Chi, W. Iyengar, A. Fu, W. Liu, W. Berg, A. E. Wu, C.-F. Zhuang, X. 2021-07-20 doi:10.1101/2021.07.19.452889 Cold Spring Harbor Laboratory Press 2021-07-20 <![CDATA[ Inferring cell-cell interactions from pseudotime ordering of scRNA-Seq data ]]> https://biorxiv.org/content/10.1101/2021.07.28.454054v1?rss=1 Li, D. Velazquez, J. J. Ding, J. Hislop, J. Ebrahimkhani, M. R. Bar-Joseph, Z. 2021-07-29 doi:10.1101/2021.07.28.454054 Cold Spring Harbor Laboratory Press 2021-07-29 <![CDATA[ Regeneration of the larval sea star nervous system by wounding induced respecification to the sox2 lineage ]]> https://biorxiv.org/content/10.1101/2021.08.07.455526v1?rss=1 Zheng, M. Zueva, O. Hinman, V. F. 2021-08-08 doi:10.1101/2021.08.07.455526 Cold Spring Harbor Laboratory Press 2021-08-08 <![CDATA[ Mathematical Modeling Reveals Quantitative Properties of KEAP1-NRF2 Signaling ]]> https://biorxiv.org/content/10.1101/2021.08.08.455554v1?rss=1 Liu, S. Pi, J. Zhang, Q. 2021-08-08 doi:10.1101/2021.08.08.455554 Cold Spring Harbor Laboratory Press 2021-08-08 <![CDATA[ ACE2 Pathway Regulates Thermogenesis and Energy Metabolism ]]> https://biorxiv.org/content/10.1101/2021.08.10.455823v1?rss=1 Cao, X. Shi, T. Zhang, C. Jin, W. Song, L. Zhang, Y. Liu, J. Yang, F. Rotimi, C. N. Xu, A. Yang, J. 2021-08-10 doi:10.1101/2021.08.10.455823 Cold Spring Harbor Laboratory Press 2021-08-10 <![CDATA[ Stimulation of the Dorsal Root Ganglion using an Injectrode ]]> https://biorxiv.org/content/10.1101/2021.08.16.456553v1?rss=1 Dalrymple, A. N. Ting, J. E. Bose, R. Trevathan, J. K. Nieuwoudt, S. Lempka, S. F. Franke, M. Ludwig, K. A. Shoffstall, A. Fisher, L. E. Weber, D. J. 2021-08-17 doi:10.1101/2021.08.16.456553 Cold Spring Harbor Laboratory Press 2021-08-17 <![CDATA[ Imaging-guided fine tuning of CAR synapse dynamics and T cell triggering ]]> https://biorxiv.org/content/10.1101/2021.08.18.456686v1?rss=1 Beppler, C. Eichorst, J. Marchuk, K. Cai, E. Castellanos, C. A. Sriram, V. Roybal, K. T. Krummel, M. F. 2021-08-19 doi:10.1101/2021.08.18.456686 Cold Spring Harbor Laboratory Press 2021-08-19 <![CDATA[ Progerin-Expressing Endothelial Cells are Unable to Adapt to Shear Stress ]]> https://biorxiv.org/content/10.1101/2021.08.20.456996v1?rss=1 Danielsson, B. E. Peters, H. C. Bathula, K. Spear, L. M. Noll, N. A. Dahl, K. N. Conway, D. E. 2021-08-20 doi:10.1101/2021.08.20.456996 Cold Spring Harbor Laboratory Press 2021-08-20 <![CDATA[ Reading Modality Modifies Reading Network: Insights from Neural basis of Braille in Proficient Blind Readers ]]> https://biorxiv.org/content/10.1101/2021.08.24.457544v1?rss=1 Tian, M. Saccone, E. J. Kim, J. S. Kanjlia, S. Bedny, M. 2021-08-25 doi:10.1101/2021.08.24.457544 Cold Spring Harbor Laboratory Press 2021-08-25 <![CDATA[ Structural dynamics determine voltage and pH gating in human voltage-gated proton channel ]]> https://biorxiv.org/content/10.1101/2021.08.25.457625v1?rss=1 Han, S. Peng, S. Vance, J. Tran, K. Do, N. Gates, D. Bui, N. Gui, Z. Wang, S. 2021-08-26 doi:10.1101/2021.08.25.457625 Cold Spring Harbor Laboratory Press 2021-08-26 <![CDATA[ Architecture and evolution of the cis-regulatory system of the echinoderm kirrelL gene ]]> https://biorxiv.org/content/10.1101/2021.08.27.457814v1?rss=1 Khor, J. M. Guerrero-Santoro, J. Ettensohn, C. A. 2021-08-28 doi:10.1101/2021.08.27.457814 Cold Spring Harbor Laboratory Press 2021-08-28 <![CDATA[ Disentangling the flow of signals between populations of neurons ]]> https://biorxiv.org/content/10.1101/2021.08.30.458230v1?rss=1 Gokcen, E. Jasper, A. I. Semedo, J. D. Zandvakili, A. Kohn, A. Machens, C. K. Yu, B. M. 2021-09-01 doi:10.1101/2021.08.30.458230 Cold Spring Harbor Laboratory Press 2021-09-01 <![CDATA[ ACKR3 induces the perturbation of rRNA biogenesis: a novel mechanism of colorectal tumorigenesis ]]> https://biorxiv.org/content/10.1101/2021.09.01.458501v1?rss=1 Qu, X. J. Yang, J. Li, Y.-N. Pan, T. Miao, R.-R. Zhang, Y.-Y. Wu, S.-H. Cui, S.-X. 2021-09-02 doi:10.1101/2021.09.01.458501 Cold Spring Harbor Laboratory Press 2021-09-02 <![CDATA[ Speech categorization reveals the role of early-stage temporal-coherence processing in auditory scene analysis ]]> https://biorxiv.org/content/10.1101/2021.09.06.459159v1?rss=1 Viswanathan, V. Shinn-Cunningham, B. G. Heinz, M. G. 2021-09-06 doi:10.1101/2021.09.06.459159 Cold Spring Harbor Laboratory Press 2021-09-06 <![CDATA[ Evaluation of cell segmentation methods without reference segmentations ]]> https://biorxiv.org/content/10.1101/2021.09.17.460800v1?rss=1 Chen, H. Murphy, R. F. 2021-09-19 doi:10.1101/2021.09.17.460800 Cold Spring Harbor Laboratory Press 2021-09-19 <![CDATA[ Topological insights into the neural basis of flexible behavior ]]> https://biorxiv.org/content/10.1101/2021.09.24.461717v1?rss=1 Rouse, T. C. Ni, A. M. Huang, C. Cohen, M. 2021-09-25 doi:10.1101/2021.09.24.461717 Cold Spring Harbor Laboratory Press 2021-09-25 <![CDATA[ A Neuromuscular Model of Human Locomotion Combines Spinal Reflex Circuits with Voluntary Movements ]]> https://biorxiv.org/content/10.1101/2021.09.26.461864v1?rss=1 Ramadan, R. Geyer, H. Jeka, J. J. Schoener, G. Reimann, H. 2021-09-26 doi:10.1101/2021.09.26.461864 Cold Spring Harbor Laboratory Press 2021-09-26 <![CDATA[ Predicting Knee Adduction Moment Response to Gait Retraining with Minimal Clinical Data ]]> https://biorxiv.org/content/10.1101/2021.09.29.462292v1?rss=1 Rokhmanova, N. Kuchenbecker, K. J. Shull, P. B. Ferber, R. Halilaj, E. 2021-09-30 doi:10.1101/2021.09.29.462292 Cold Spring Harbor Laboratory Press 2021-09-30 <![CDATA[ Profiling of mature stage human breastmilk cells identifies host-defense lactocyte sub-populations ]]> https://biorxiv.org/content/10.1101/2021.10.04.463125v1?rss=1 Gleeson, J. P. Chaudhary, N. Doerfler, R. Fein, K. C. Hredzak-Showalter, T. Whitehead, K. A. 2021-10-06 doi:10.1101/2021.10.04.463125 Cold Spring Harbor Laboratory Press 2021-10-06 <![CDATA[ Molecular rhythm alterations in prefrontal cortex and nucleus accumbens associated with opioid use disorder ]]> https://biorxiv.org/content/10.1101/2021.10.07.463568v1?rss=1 Xue, X. Zong, W. Glausier, J. Kim, S.-M. Shelton, M. Phan, B. N. Srinivasan, C. Pfenning, A. R. Tseng, G. Lewis, D. A. Seney, M. Logan, R. 2021-10-09 doi:10.1101/2021.10.07.463568 Cold Spring Harbor Laboratory Press 2021-10-09 <![CDATA[ De novo Prediction of Cell-Drug Sensitivities Using Deep Learning-based Graph Regularized Matrix Factorization ]]> https://biorxiv.org/content/10.1101/2021.10.11.462450v1?rss=1 Ren, S. Tao, Y. Yu, K. Xue, Y. Schwartz, R. Lu, X. 2021-10-13 doi:10.1101/2021.10.11.462450 Cold Spring Harbor Laboratory Press 2021-10-13 <![CDATA[ A multi-dataset evaluation of frame censoring for task-based fMRI ]]> https://biorxiv.org/content/10.1101/2021.10.12.464075v1?rss=1 Jones, M. S. Zhu, Z. Bajracharya, A. Luor, A. Peelle, J. E. 2021-10-14 doi:10.1101/2021.10.12.464075 Cold Spring Harbor Laboratory Press 2021-10-14 <![CDATA[ ConTreeDP: A consensus method of tumor trees based on maximum directed partition support problem ]]> https://biorxiv.org/content/10.1101/2021.10.13.463978v1?rss=1 Schwartz, R. Fu, X. 2021-10-14 doi:10.1101/2021.10.13.463978 Cold Spring Harbor Laboratory Press 2021-10-14 <![CDATA[ Antibiotic resistance via bacterial cell shape-shifting ]]> https://biorxiv.org/content/10.1101/2021.10.16.464635v1?rss=1 Ojkic, N. Serbanescu, D. Banerjee, S. 2021-10-16 doi:10.1101/2021.10.16.464635 Cold Spring Harbor Laboratory Press 2021-10-16 <![CDATA[ MiR-339-3p aggravates rat vascular inflammation induced by AT1R autoantibodies by down-regulating BKα protein expression ]]> https://biorxiv.org/content/10.1101/2021.10.17.464722v1?rss=1 Liu, H. Li, Y. Sun, Y. Yue, M. Gao, M. Wang, L. Wu, Y. Yin, X. Zhang, S. 2021-10-17 doi:10.1101/2021.10.17.464722 Cold Spring Harbor Laboratory Press 2021-10-17 <![CDATA[ Use-dependent biases primarily originate from a contaminated motor plan ]]> https://biorxiv.org/content/10.1101/2021.10.21.465112v1?rss=1 Tsay, J. S. Kim, H. E. Saxena, A. Parvin, D. E. Verstynen, T. V. Ivry, R. B. 2021-10-22 doi:10.1101/2021.10.21.465112 Cold Spring Harbor Laboratory Press 2021-10-22 <![CDATA[ Double-check the zebrafish 18s rRNA qPCR primers: they may be wrong ]]> https://biorxiv.org/content/10.1101/2021.10.23.464780v1?rss=1 Wang, J. Yang, Z. Xiao, A. 2021-10-25 doi:10.1101/2021.10.23.464780 Cold Spring Harbor Laboratory Press 2021-10-25 <![CDATA[ Extracellular Vesicles Deliver Mitochondria and HSP27 Protein to Protect the Blood-Brain Barrier ]]> https://biorxiv.org/content/10.1101/2021.10.29.466491v1?rss=1 View larger version (38K): org.highwire.dtl.DTLVardef@dc5493org.highwire.dtl.DTLVardef@134ad7forg.highwire.dtl.DTLVardef@16a8929org.highwire.dtl.DTLVardef@15315bc_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIMedium-to-large extracellular vesicles (m/lEVs), not small EVs contain mitochondria C_LIO_LIm/lEVs increased ATP and mitochondrial function in brain endothelial cells (BECs) C_LIO_LIm/lEVs from oligomycin-exposed BECs did not increase recipient BEC ATP levels C_LIO_LIIntravenously injected m/lEVs reduced brain infarct sizes in a mouse stroke model C_LIO_LIEV/HSP27 mixtures reduced small and large dextran molecule permeability across BECs C_LI ]]> Dave, K. Reynolds, M. J. Stolz, D. B. Babidhan, R. Dobbins, D. X. Yankello, H. Reddy, R. Bae, Y. Shiva, S. Soundara Manickam, D. 2021-10-31 doi:10.1101/2021.10.29.466491 Cold Spring Harbor Laboratory Press 2021-10-31 <![CDATA[ Emergence of an adaptive epigenetic cell state in human bladder urothelial carcinoma evolution ]]> https://biorxiv.org/content/10.1101/2021.10.30.466556v1?rss=1 Xiao, Y. Jin, W. Qian, K. Wu, K. Wang, G. Jiang, W. Cao, R. Ju, L. Zhao, Y. Zheng, H. Liu, T. Chang, L. Xu, Z. Wang, T. Luo, J. Shan, L. Yu, F. Chen, X. Liu, D. Cao, H. Yang, Z. Li, S. Shi, H. Guo, Z. Gong, Y. Liu, N. Li, S. Wang, Y. Cao, X. Ding, W. Zhou, W. Cui, D. Tian, Y. Ji, C. Luo, Y. Hong, X. Ma, H. Chen, F. Peng, M. Zhang, Y. Wang, X. 2021-11-02 doi:10.1101/2021.10.30.466556 Cold Spring Harbor Laboratory Press 2021-11-02 <![CDATA[ Emergence and maintenance of different sized actin filaments in a common pool of building blocks ]]> https://biorxiv.org/content/10.1101/2021.11.07.467615v1?rss=1 Banerjee, D. S. Banerjee, S. 2021-11-07 doi:10.1101/2021.11.07.467615 Cold Spring Harbor Laboratory Press 2021-11-07 <![CDATA[ Imaging the Extent and Location of Spatiotemporally Distributed Epileptiform Sources from MEG Measurements ]]> https://biorxiv.org/content/10.1101/2021.11.09.467915v1?rss=1 Jiang, X. Ye, S. Sohrabpour, A. Bagic, A. He, B. 2021-11-11 doi:10.1101/2021.11.09.467915 Cold Spring Harbor Laboratory Press 2021-11-11 <![CDATA[ Selective clonal persistence of human retroviruses in vivo: radial chromatin organization, integration site and host transcription ]]> https://biorxiv.org/content/10.1101/2021.11.10.467892v1?rss=1 160,000 HTLV-1 integration sites from T-cells isolated ex vivo from naturally-infected subjects with >230,000 integration sites from in vitro infection, to identify the genomic features that determine selective clonal survival. Three factors explained >40% of the observed variance in clone survival of HTLV-1 in vivo: the radial intranuclear position of the provirus, its absolute genomic distance from the centromere, and the intensity of host genome transcription flanking the provirus. The radial intranuclear position of the provirus and its distance from the centromere also explained ~7% of clonal persistence of HIV-1 in vivo. Selection for transcriptionally repressive nuclear compartments favours clonal persistence of human retroviruses in vivo. ]]> Melamed, A. Fitzgerald, T. W. Wang, Y. Ma, J. Birney, E. Bangham, C. R. M. 2021-11-10 doi:10.1101/2021.11.10.467892 Cold Spring Harbor Laboratory Press 2021-11-10 <![CDATA[ Low frequency somatic copy number alterations in normal human lymphocytes revealed by large scale single-cell whole genome profiling ]]> https://biorxiv.org/content/10.1101/2021.11.10.468149v1?rss=1 Liu, L. Chen, H. Sun, C. Zhang, J. Wang, J. Du, M. Li, J. Di, L. Shen, J. Geng, S. Pang, Y. Luo, Y. Wu, C. Fu, Y. Zheng, Z. Wang, J. Huang, Y. 2021-11-13 doi:10.1101/2021.11.10.468149 Cold Spring Harbor Laboratory Press 2021-11-13 <![CDATA[ Genome Compartmentalization with Nuclear Landmarks: Random yet Precise ]]> https://biorxiv.org/content/10.1101/2021.11.12.468401v1?rss=1 Kamat, K. Qi, Y. Wang, Y. Ma, J. Zhang, B. 2021-11-13 doi:10.1101/2021.11.12.468401 Cold Spring Harbor Laboratory Press 2021-11-13 <![CDATA[ The dorsal visual pathway represents object-centered spatial relations for object recognition ]]> https://biorxiv.org/content/10.1101/2021.11.12.468414v1?rss=1 Ayzenberg, V. Behrmann, M. 2021-11-13 doi:10.1101/2021.11.12.468414 Cold Spring Harbor Laboratory Press 2021-11-13 <![CDATA[ Unsupervised cell functional annotation for single-cell RNA-Seq ]]> https://biorxiv.org/content/10.1101/2021.11.20.469410v1?rss=1 Li, D. Ding, J. Bar-Joseph, Z. 2021-11-21 doi:10.1101/2021.11.20.469410 Cold Spring Harbor Laboratory Press 2021-11-21 <![CDATA[ CAMO: A molecular congruence analysis framework for evaluating model organisms ]]> https://biorxiv.org/content/10.1101/2021.11.21.469371v1?rss=1 Zong, W. Rahman, M. T. Zhu, L. Zeng, X. Zhang, Y. Zou, J. Liu, S. Ren, Z. Li, J. J. Oesterreich, S. Ma, T. Tseng, G. 2021-11-22 doi:10.1101/2021.11.21.469371 Cold Spring Harbor Laboratory Press 2021-11-22 <![CDATA[ Categorical encoding of voice in human superior temporal cortex ]]> https://biorxiv.org/content/10.1101/2021.11.23.469682v1?rss=1 Rupp, K. Hect, J. L. Remick, M. Ghuman, A. Chandresekaran, B. Holt, L. Abel, T. J. 2021-11-23 doi:10.1101/2021.11.23.469682 Cold Spring Harbor Laboratory Press 2021-11-23 <![CDATA[ Similarity in evoked responses does not imply similarity in macroscopic network states across tasks ]]> https://biorxiv.org/content/10.1101/2021.11.27.470015v1?rss=1 Rasero, J. Betzel, R. Sentis, A. I. Kraynak, T. E. Gianaros, P. J. Verstynen, T. 2021-11-27 doi:10.1101/2021.11.27.470015 Cold Spring Harbor Laboratory Press 2021-11-27 <![CDATA[ Simultaneous Super-Resolution and Distortion Correction for Single-shot EPI DWI using Deep Learning ]]> https://biorxiv.org/content/10.1101/2021.12.03.470880v1?rss=1 Ye, X. Wang, P. Li, S. Zhang, J. Lian, Y. Zhang, Y. Lu, J. Guo, H. 2021-12-03 doi:10.1101/2021.12.03.470880 Cold Spring Harbor Laboratory Press 2021-12-03 <![CDATA[ CRISPR Cas13-based tools to track and manipulate endogenous telomeric repeat-containing RNAs in living cells ]]> https://biorxiv.org/content/10.1101/2021.12.03.471109v1?rss=1 Xu, M. Chigumira, T. Chen, Z. Tones, J. Zhao, R. Dahl, K. N. Chenoweth, D. M. Zhang, H. 2021-12-04 doi:10.1101/2021.12.03.471109 Cold Spring Harbor Laboratory Press 2021-12-04 <![CDATA[ Decrowding Expansion Pathology: Unmasking Previously Invisible Nanostructures and Cells in Intact Human Brain Pathology Specimens ]]> https://biorxiv.org/content/10.1101/2021.12.05.471271v1?rss=1 Valdes, P. A. Yu, C.-C. Aronson, J. L. Zhao, Y. Bernstock, J. D. Bhere, D. An, B. Viapiano, M. S. Shah, K. Chiocca, E. A. Boyden, E. S. 2021-12-07 doi:10.1101/2021.12.05.471271 Cold Spring Harbor Laboratory Press 2021-12-07 <![CDATA[ B.1.1.529 escapes the majority of SARS-CoV-2 neutralizing antibodies of diverse epitopes ]]> https://biorxiv.org/content/10.1101/2021.12.07.470392v1?rss=1 Cao, Y. R. Wang, J. Jian, F. Xiao, T. Song, W. Yisimayi, A. Huang, W. Li, Q. Wang, P. An, R. Wang, J. Wang, Y. Niu, X. Yang, S. Liang, H. Sun, H. Li, T. Yu, Y. Cui, Q. Liu, S. Yang, X. Du, S. Zhang, Z. Hao, X. Shao, F. Jin, R. Wang, X. Xiao, J. Wang, Y. Xie, X. S. 2021-12-09 doi:10.1101/2021.12.07.470392 Cold Spring Harbor Laboratory Press 2021-12-09 <![CDATA[ Semantic representations during language comprehension are affected by context ]]> https://biorxiv.org/content/10.1101/2021.12.15.472839v1?rss=1 Deniz, F. Tseng, C. Wehbe, L. Gallant, J. L. 2021-12-16 doi:10.1101/2021.12.15.472839 Cold Spring Harbor Laboratory Press 2021-12-16 <![CDATA[ Super-resolution vibrational imaging using expansion stimulated Raman scattering microscopy ]]> https://biorxiv.org/content/10.1101/2021.12.22.473713v1?rss=1 Shi, L. Klimas, A. Gallagher, B. Cheng, Z. Fu, F. Wijesekara, P. Miao, Y. Ren, X. Zhao, Y. Min, W. 2021-12-23 doi:10.1101/2021.12.22.473713 Cold Spring Harbor Laboratory Press 2021-12-23 <![CDATA[ Identifying control ensembles for decision-making within the cortico-basal ganglia-thalamic circuit ]]> https://biorxiv.org/content/10.1101/2021.12.22.473901v1?rss=1 Vich, C. Clapp, M. Verstynen, T. Rubin, J. 2021-12-23 doi:10.1101/2021.12.22.473901 Cold Spring Harbor Laboratory Press 2021-12-23 <![CDATA[ Neurons burdened by DNA double strand breaks incite microglia activation through antiviral-like signaling in neurodegeneration. ]]> https://biorxiv.org/content/10.1101/2021.12.23.474002v1?rss=1 Welch, G. M. Boix, C. A. Schmauch, E. Davila-Velderrain, J. Victor, M. B. Dileep, V. Bozzelli, L. Cheng, J. D. Lee, A. Lee, A. Su, Q. Pfenning, A. R. Kellis, M. Tsai, L.-H. 2021-12-23 doi:10.1101/2021.12.23.474002 Cold Spring Harbor Laboratory Press 2021-12-23 <![CDATA[ SHERRY2: A method for rapid and sensitive single cell RNA-seq ]]> https://biorxiv.org/content/10.1101/2021.12.25.474161v1?rss=1 Di, L. Liu, B. Lyu, Y. Zhao, S. Pang, Y. Zhang, C. Wang, J. Qi, H. Shen, J. Huang, Y. 2021-12-25 doi:10.1101/2021.12.25.474161 Cold Spring Harbor Laboratory Press 2021-12-25 <![CDATA[ A Multimodal Approach to Investigate the Neural Mechanisms of Real World Social Vision ]]> https://biorxiv.org/content/10.1101/2021.12.26.474173v1?rss=1 Alreja, A. Ward, M. J. Ma, Q. Richardson, M. Russ, B. Bickel, S. Van Wouwe, N. Gonzalez-Martinez, J. A. Parker, L. S. Neimat, J. Schroeder, C. Morency, L.-P. Ghuman, A. S. 2021-12-28 doi:10.1101/2021.12.26.474173 Cold Spring Harbor Laboratory Press 2021-12-28 <![CDATA[ Characterizing RNA-binding Ligands on Structures, Chemical Information, Binding Affinity and Drug-likeness ]]> https://biorxiv.org/content/10.1101/2022.01.03.474753v1?rss=1 Fan, C. Wang, X. Wang, T. Zhao, H. 2022-01-04 doi:10.1101/2022.01.03.474753 Cold Spring Harbor Laboratory Press 2022-01-04 <![CDATA[ Common neural functions during children's naturalistic and controlled laboratory mathematics learning ]]> https://biorxiv.org/content/10.1101/2022.01.07.475365v1?rss=1 Amalric, M. Cantlon, J. 2022-01-07 doi:10.1101/2022.01.07.475365 Cold Spring Harbor Laboratory Press 2022-01-07 <![CDATA[ WNK kinases sense molecular crowding and rescue cell volume via phase separation ]]> https://biorxiv.org/content/10.1101/2022.01.10.475707v1?rss=1 Boyd-Shiwarski, C. R. Shiwarski, D. J. Griffiths, S. E. Beacham, R. T. Norrell, L. Morrison, D. E. Wang, J. Mann, J. R. Tennant, W. Anderson, E. N. Franks, J. Calderon, M. Connolly, K. A. Weaver, C. J. Weckerly, C. C. Pandey, U. B. Donnelly, C. J. Sun, D. Rodan, A. R. Subramanya, A. R. 2022-01-11 doi:10.1101/2022.01.10.475707 Cold Spring Harbor Laboratory Press 2022-01-11 <![CDATA[ TGF-β-R2 is required for HBP induced acute lung injury and vascular leakage for TGF-/Smad/Rho signaling pathway activation ]]> https://biorxiv.org/content/10.1101/2022.01.14.476433v1?rss=1 Liu, Z. Chen, M. Sun, Y. Li, X. Cao, L. Ma, X. 2022-01-16 doi:10.1101/2022.01.14.476433 Cold Spring Harbor Laboratory Press 2022-01-16 <![CDATA[ Engineering Rotating Apical-Out Airway Organoid for Assessing Respiratory Cilia Motility ]]> https://biorxiv.org/content/10.1101/2022.01.15.476455v1?rss=1 Wijesekara, P. Yadav, P. Perkins, L. A. Stolz, D. Franks, J. M. Watkins, S. Jacome, E. R. Brody, S. L. Horani, A. Xu, J. Barati farimani, A. Ren, X. 2022-01-18 doi:10.1101/2022.01.15.476455 Cold Spring Harbor Laboratory Press 2022-01-18 <![CDATA[ Context-aware information selection and model recommendation with ACCORDION ]]> https://biorxiv.org/content/10.1101/2022.01.22.477231v1?rss=1 Ahmed, Y. Telmer, C. Miskov-Zivanov, N. 2022-01-23 doi:10.1101/2022.01.22.477231 Cold Spring Harbor Laboratory Press 2022-01-23 <![CDATA[ Impact of various vaccine boosters on neutralization against Omicron following prime vaccinations with inactivated or adenovirus-vectored vaccine ]]> https://biorxiv.org/content/10.1101/2022.01.25.476850v1?rss=1 Huang, Q. Zeng, J. Lang, Q. Gao, F. Liu, D. Tian, S. Shi, R. Luo, L. Wang, H. Hu, L. Jiang, L. Liu, Y. Li, K. Wu, Y. Xu, J. Jiang, W. Guo, N. Chen, Z. Hao, X. Jin, R. Yan, J. Sun, Y. 2022-01-27 doi:10.1101/2022.01.25.476850 Cold Spring Harbor Laboratory Press 2022-01-27 <![CDATA[ The endoplasmic reticulum membrane protein complex (EMC) negatively regulates intestinal homeostasis through the Hippo signaling pathway ]]> https://biorxiv.org/content/10.1101/2022.01.25.477727v1?rss=1 Shi, L. Ma, H. Zhao, H. Ma, M. Wang, J. Kong, R. Li, Z. Ma, R. Wang, J.-H. Wu, S. Dong, M.-Q. Li, Z. 2022-01-26 doi:10.1101/2022.01.25.477727 Cold Spring Harbor Laboratory Press 2022-01-26 <![CDATA[ GLMsingle: a toolbox for improving single-trial fMRI response estimates ]]> https://biorxiv.org/content/10.1101/2022.01.31.478431v1?rss=1 Prince, J. S. Charest, I. Kurzawski, J. W. Pyles, J. A. Tarr, M. J. Kay, K. N. 2022-02-02 doi:10.1101/2022.01.31.478431 Cold Spring Harbor Laboratory Press 2022-02-02 <![CDATA[ Comprehensive Epitope Mapping of Broad Sarbecovirus Neutralizing Antibodies ]]> https://biorxiv.org/content/10.1101/2022.02.07.479349v1?rss=1 Cao, Y. Yisimayi, A. Jian, F. Xiao, T. Song, W. Wang, J. Du, S. Zhang, Z. Liu, P. Hao, X. Li, Q. Wang, P. An, R. Wang, Y. Wang, J. Sun, H. Zhao, L. Zhang, W. Zhao, D. Zheng, J. Yu, L. Li, C. Zhang, N. Wang, R. Niu, X. Yang, S. Song, X. Zheng, L. Li, Z. Gu, Q. Shao, F. Huang, W. Wang, Y. Jin, R. Xiao, J. Xie, X. S. 2022-02-07 doi:10.1101/2022.02.07.479349 Cold Spring Harbor Laboratory Press 2022-02-07 <![CDATA[ False-Positive IRESes from Hoxa9 and other genes resulting from errors in mammalian 5' UTR annotations ]]> https://biorxiv.org/content/10.1101/2022.02.10.479744v1?rss=1 Akirtava, C. May, G. E. McManus, C. J. 2022-02-10 doi:10.1101/2022.02.10.479744 Cold Spring Harbor Laboratory Press 2022-02-10 <![CDATA[ Comparative miRNA Transcriptomics of Mouse and Macaque Reveals Cytoskeleton is An Inhibitor for C. neoformans Invasion into Brain ]]> https://biorxiv.org/content/10.1101/2022.02.14.480319v1?rss=1 Li, H. Han, X. Du, W. Meng, Y. Li, Y. Sun, T. Liang, Q. Li, C. Suo, C. Gao, X. Qiu, Y. Tian, W. An, M. Zhang, H. Fu, Y. Li, X. Lan, T. Yang, S. Zhang, Z. Geng, W. Ding, C. Shang, H. 2022-02-14 doi:10.1101/2022.02.14.480319 Cold Spring Harbor Laboratory Press 2022-02-14 <![CDATA[ DeepMinimizer: A Differentiable Framework for Optimizing Sequence-Specific Minimizer Schemes ]]> https://biorxiv.org/content/10.1101/2022.02.17.480870v1?rss=1 Hoang, M. Zheng, H. Kingsford, C. 2022-02-19 doi:10.1101/2022.02.17.480870 Cold Spring Harbor Laboratory Press 2022-02-19 <![CDATA[ D2 dopamine receptor expression, sensitivity to rewards, and reinforcement learning in a complex value-based decision-making task ]]> https://biorxiv.org/content/10.1101/2022.02.18.481052v1?rss=1 Banuelos, C. Creswell, K. Walsh, C. Manuck, S. B. Gianaros, P. J. Verstynen, T. 2022-02-19 doi:10.1101/2022.02.18.481052 Cold Spring Harbor Laboratory Press 2022-02-19 <![CDATA[ The Effect of Genome Graph Expressiveness on the Discrepancy Between Genome Graph Distance and String Set Distance ]]> https://biorxiv.org/content/10.1101/2022.02.18.481102v1?rss=1 Qiu, Y. Kingsford, C. 2022-02-22 doi:10.1101/2022.02.18.481102 Cold Spring Harbor Laboratory Press 2022-02-22 <![CDATA[ Nucleome Browser: An integrative and multimodal data navigation platform for 4D Nucleome ]]> https://biorxiv.org/content/10.1101/2022.02.21.481225v1?rss=1 Zhu, X. Zhang, Y. Wang, Y. Tian, D. Belmont, A. S. Swedlow, J. R. Ma, J. 2022-02-22 doi:10.1101/2022.02.21.481225 Cold Spring Harbor Laboratory Press 2022-02-22 <![CDATA[ 3D bioprinting of an implantable xeno-free vascularized human skin graft ]]> https://biorxiv.org/content/10.1101/2022.02.21.481363v1?rss=1 Baltazar, T. Jiang, B. Moncayo, A. Merola, J. Albanna, M. Z. Saltzman, W. M. Pober, J. S. 2022-02-22 doi:10.1101/2022.02.21.481363 Cold Spring Harbor Laboratory Press 2022-02-22 <![CDATA[ T cells use distinct topological and membrane receptor scanning strategies that individually coalesce during receptor recognition ]]> https://biorxiv.org/content/10.1101/2022.02.23.481517v1?rss=1 Cai, E. Beppler, C. Eichorst, J. Marchuk, K. Krummel, M. F. 2022-02-25 doi:10.1101/2022.02.23.481517 Cold Spring Harbor Laboratory Press 2022-02-25 <![CDATA[ Physiologically Based Multiphysics Pharmacokinetic Model for Determining the Temporal Biodistribution of Targeted Nanoparticles ]]> https://biorxiv.org/content/10.1101/2022.03.07.483218v1?rss=1 glass, e. Kulkarni, S. Eng, C. feng, s. malavia, a. Radhakrishnan, R. 2022-03-07 doi:10.1101/2022.03.07.483218 Cold Spring Harbor Laboratory Press 2022-03-07 <![CDATA[ Dimensionality reduction of calcium-imaged neuronal population activity ]]> https://biorxiv.org/content/10.1101/2022.03.11.480682v1?rss=1 Koh, T. H. Bishop, W. E. Kawashima, T. Jeon, B. B. Srinivasan, R. Kuhlman, S. J. Ahrens, M. B. Chase, S. M. Yu, B. M. 2022-03-14 doi:10.1101/2022.03.11.480682 Cold Spring Harbor Laboratory Press 2022-03-14 <![CDATA[ Novel Murine models of Mania and Depression ]]> https://biorxiv.org/content/10.1101/2022.03.16.484557v1?rss=1 Chen, B. Xia, M. Ji, M. Gong, W. Zhang, D. Li, X. Wang, S. Feng, Y. Wu, X. Cui, L. Verkhratsky, A. Li, B. 2022-03-18 doi:10.1101/2022.03.16.484557 Cold Spring Harbor Laboratory Press 2022-03-18 <![CDATA[ High-level visual areas act like domain-general filters with strong selectivity and functional specialization ]]> https://biorxiv.org/content/10.1101/2022.03.16.484578v1?rss=1 Khosla, M. Wehbe, L. 2022-03-18 doi:10.1101/2022.03.16.484578 Cold Spring Harbor Laboratory Press 2022-03-18 <![CDATA[ Ultrasound Neuromodulation and Correlation Change in the Rat Somatosensory Cortex ]]> https://biorxiv.org/content/10.1101/2022.03.18.484914v1?rss=1 Ramachandran, S. Niu, X. Yu, K. He, B. 2022-03-20 doi:10.1101/2022.03.18.484914 Cold Spring Harbor Laboratory Press 2022-03-20 <![CDATA[ Model-free Prediction Test with Application to Genomics Data ]]> https://biorxiv.org/content/10.1101/2022.03.28.486116v1?rss=1 Cai, Z. Lei, J. Roeder, K. 2022-03-29 doi:10.1101/2022.03.28.486116 Cold Spring Harbor Laboratory Press 2022-03-29 <![CDATA[ Cellular and Molecular Organization of the Rhesus Macaque Dorsal Horn with a Comparison to Mouse ]]> https://biorxiv.org/content/10.1101/2022.04.01.486135v1?rss=1 Arokiaraj, C. Kleyman, M. Chamessian, A. Shiers, S. Kang, B. Kennedy, M. Chen, Y. Dum, R. Patterson, R. Lewis, D. Qadri, Y. Levine, A. Price, T. Pfenning, A. Seal, R. 2022-04-05 doi:10.1101/2022.04.01.486135 Cold Spring Harbor Laboratory Press 2022-04-05 <![CDATA[ Ultrafast and interpretable single-cell 3D genome analysis with Fast-Higashi ]]> https://biorxiv.org/content/10.1101/2022.04.18.488683v1?rss=1 Zhang, R. Zhou, T. Ma, J. 2022-04-19 doi:10.1101/2022.04.18.488683 Cold Spring Harbor Laboratory Press 2022-04-19 <![CDATA[ CONCERT: Genome-wide prediction of sequence elements that modulate DNA replication timing ]]> https://biorxiv.org/content/10.1101/2022.04.21.488684v1?rss=1 Yang, Y. Wang, Y. Zhang, Y. Ma, J. 2022-04-22 doi:10.1101/2022.04.21.488684 Cold Spring Harbor Laboratory Press 2022-04-22 <![CDATA[ A Fast, Provably Accurate Approximation Algorithm for Sparse Principal Component Analysis Reveals Human Genetic Variation Across the World ]]> https://biorxiv.org/content/10.1101/2022.04.21.489052v1?rss=1 Chowdhury, A. Bose, A. Zhou, S. Woodruff, D. P. Drineas, P. 2022-04-22 doi:10.1101/2022.04.21.489052 Cold Spring Harbor Laboratory Press 2022-04-22 <![CDATA[ Mechanisms regulating the frequency of inhibition-based gamma oscillations in primate prefrontal and parietal cortices ]]> https://biorxiv.org/content/10.1101/2022.04.26.489470v1?rss=1 Gonzalez-Burgos, G. Miyamae, T. Reddy, N. Dawkins, S. Chen, C. Hill, A. Enwright, J. F. Ermentrout, G. B. Lewis, D. A. 2022-04-27 doi:10.1101/2022.04.26.489470 Cold Spring Harbor Laboratory Press 2022-04-27 <![CDATA[ BA.2.12.1, BA.4 and BA.5 escape antibodies elicited by Omicron infection ]]> https://biorxiv.org/content/10.1101/2022.04.30.489997v1?rss=1 Cao, Y. R. Yisimayi, A. Jian, F. Song, W. Xiao, T. Wang, L. Du, S. Wang, J. Li, Q. Chen, X. Wang, P. Zhang, Z. Liu, P. An, R. Hao, X. Wang, Y. Wang, J. Feng, R. Sun, H. Zhao, L. Zhang, W. Zhao, D. Zheng, J. Yu, L. Li, C. Zhang, N. Wang, R. Niu, X. Yang, S. Song, X. Zheng, L. Li, Z. Gu, Q. Shao, F. Huang, W. Jin, R. Shen, Z. Wang, Y. Wang, X. Xiao, J. Xie, X. S. 2022-05-02 doi:10.1101/2022.04.30.489997 Cold Spring Harbor Laboratory Press 2022-05-02 <![CDATA[ A Simulator for Somatic Evolution Study Design ]]> https://biorxiv.org/content/10.1101/2022.05.01.487551v1?rss=1 Srivatsa, A. Lei, H. Schwartz, R. 2022-05-02 doi:10.1101/2022.05.01.487551 Cold Spring Harbor Laboratory Press 2022-05-02 <![CDATA[ Disentangling object category representations driven by dynamic and static visual input ]]> https://biorxiv.org/content/10.1101/2022.05.03.490462v1?rss=1 Robert, S. Ungerleider, L. G. Vaziri-Pashkam, M. 2022-05-04 doi:10.1101/2022.05.03.490462 Cold Spring Harbor Laboratory Press 2022-05-04 <![CDATA[ New hypotheses of cell type diversity and novelty from comparative single cell and nuclei transcriptomics in echinoderms ]]> https://biorxiv.org/content/10.1101/2022.05.06.490935v1?rss=1 Meyer, A. Ku, C. Hatleberg, W. Telmer, C. A. Hinman, V. 2022-05-07 doi:10.1101/2022.05.06.490935 Cold Spring Harbor Laboratory Press 2022-05-07 <![CDATA[ High-throughput discovery of TRAF6-interacting peptides identifies determinants of positive and negative design and shows known and candidate human interaction partner motifs are not optimized for affinity ]]> https://biorxiv.org/content/10.1101/2022.05.08.491058v1?rss=1 Halpin, J. C. Whitney, D. Rigoldi, F. Sivaraman, V. Singer, A. Keating, A. E. 2022-05-08 doi:10.1101/2022.05.08.491058 Cold Spring Harbor Laboratory Press 2022-05-08 <![CDATA[ MuSiC2: cell type deconvolution for multi-condition bulk RNA-seq data ]]> https://biorxiv.org/content/10.1101/2022.05.08.491077v1?rss=1 Fan, J. Lyu, Y. Zhang, Q. Wang, X. Li, M. Xiao, R. 2022-05-08 doi:10.1101/2022.05.08.491077 Cold Spring Harbor Laboratory Press 2022-05-08 <![CDATA[ VPS9D1-AS1 overexpression amplifies intratumoral TGF-β signaling and promotes tumor cell escape from CD8+ T cell killing in colorectal cancer ]]> https://biorxiv.org/content/10.1101/2022.05.12.491618v1?rss=1 Yang, L. Dong, X. Liu, Z. Huang, X. Tan, J. Wen, T. Qu, H. Wang, Z. 2022-05-13 doi:10.1101/2022.05.12.491618 Cold Spring Harbor Laboratory Press 2022-05-13 <![CDATA[ Visual experience has opposing influences on the quality of stimulus representation in adult primary visual cortex ]]> https://biorxiv.org/content/10.1101/2022.05.17.492357v1?rss=1 Jeon, B. B. Fuchs, T. Chase, S. M. Kuhlman, S. J. 2022-05-18 doi:10.1101/2022.05.17.492357 Cold Spring Harbor Laboratory Press 2022-05-18 <![CDATA[ Simulations of Pathogenic E1α Variants: Allostery and Impact on Pyruvate Dehydrogenase Complex-E1 Structure and Function ]]> https://biorxiv.org/content/10.1101/2022.05.17.492373v1?rss=1 Gokcan, H. Bedoyan, J. K. Isayev, O. 2022-05-17 doi:10.1101/2022.05.17.492373 Cold Spring Harbor Laboratory Press 2022-05-17 <![CDATA[ Longitudinal white matter alterations in SIVmac239 infected rhesus monkeys with and without regular cART treatment ]]> https://biorxiv.org/content/10.1101/2022.05.17.492395v1?rss=1 Li, H. Liu, J. Nguchu, B. A. Liu, D. Qi, Y. Xire, A. Han, S. Gao, Y. Wang, X. Qiao, H. Cai, C. Huang, X. 2022-05-19 doi:10.1101/2022.05.17.492395 Cold Spring Harbor Laboratory Press 2022-05-19 <![CDATA[ The Indirect Pathway of the Basal Ganglia Promotes Negative Reinforcement, But Not Motor Suppression ]]> https://biorxiv.org/content/10.1101/2022.05.18.492478v1?rss=1 Isett, B. R. Nguyen, K. P. Schwenk, J. C. Snyder, C. N. Adegbesan, K. A. Ziausyte, U. Gittis, A. H. 2022-05-19 doi:10.1101/2022.05.18.492478 Cold Spring Harbor Laboratory Press 2022-05-19 <![CDATA[ Reduced Neutralization of SARS-CoV-2 Omicron Variant in Sera from SARS-CoV-1 Survivors after 3-dose of Vaccination ]]> https://biorxiv.org/content/10.1101/2022.05.21.492903v1?rss=1 Zhao, X. Chen, D. Hao, X. Qiu, Y. Du, J. Zhang, Y. Xiao, F. Li, X. Song, Y. Song, R. Wang, X. Jin, R. 2022-05-23 doi:10.1101/2022.05.21.492903 Cold Spring Harbor Laboratory Press 2022-05-23 <![CDATA[ Super-exponential growth and stochastic shape dynamics in rod-like bacteria ]]> https://biorxiv.org/content/10.1101/2022.05.21.492931v1?rss=1 Cylke, K. C. Banerjee, S. 2022-05-21 doi:10.1101/2022.05.21.492931 Cold Spring Harbor Laboratory Press 2022-05-21 <![CDATA[ Food for thought: selectivity for food in human ventral visual cortex ]]> https://biorxiv.org/content/10.1101/2022.05.22.492983v1?rss=1 Jain, N. Wang, A. Henderson, M. M. Lin, R. Prince, J. S. Tarr, M. J. Wehbe, L. 2022-05-24 doi:10.1101/2022.05.22.492983 Cold Spring Harbor Laboratory Press 2022-05-24 <![CDATA[ Improving and evaluating deep learning models of cellular organization ]]> https://biorxiv.org/content/10.1101/2022.05.24.493229v1?rss=1 Sun, H. Fu, X. Abraham, S. Jin, S. Murphy, R. F. 2022-05-25 doi:10.1101/2022.05.24.493229 Cold Spring Harbor Laboratory Press 2022-05-25 <![CDATA[ TGF-β signaling and Creb5 cooperatively regulate Fgf18 to control pharyngeal muscle development ]]> https://biorxiv.org/content/10.1101/2022.05.25.493396v1?rss=1 Feng, J. Han, X. Yuan, Y. Cho, C. K. Janeckova, E. Guo, T. Pareek, S. Bi, J. Jing, J. Zhang, M. Ho, T.-V. Chai, Y. 2022-05-26 doi:10.1101/2022.05.25.493396 Cold Spring Harbor Laboratory Press 2022-05-26 <![CDATA[ Representing linguistic communicative goals in the premotor cortex ]]> https://biorxiv.org/content/10.1101/2022.05.26.493580v1?rss=1 Chang, W. Wang, L. Yang, R. Wang, X. Gao, Z. Zhou, X. 2022-05-26 doi:10.1101/2022.05.26.493580 Cold Spring Harbor Laboratory Press 2022-05-26 <![CDATA[ A fibrin enhanced thrombosis model for medical devices operating at low shear regimes or large surface areas ]]> https://biorxiv.org/content/10.1101/2022.06.06.494958v1?rss=1 5000 s-1), they cannot be directly applied to low-shear devices, such as blood oxygenators and catheters, where emerging information suggest that fibrin formation is the predominant mechanism of clotting and platelet activity plays a secondary role. In the current work, we augment an existing platelet-based model of thrombosis with a partial model of the coagulation cascade that includes contact activation of factor XII and fibrin production. To calibrate the model, we simulate a backward-facing-step flow channel that has been extensively characterized in-vitro. Next, we perform blood perfusion experiments through a microfluidic chamber mimicking a hollow fiber membrane oxygenator and validate the model against these observations. The simulation results closely match the time evolution of the thrombus height and length in the backward-facing-step experiment. Application of the model to the microfluidic hollow fiber bundle chamber capture both gross features such as the increasing clotting trend towards the outlet of the chamber, as well as finer local features such as the structure of fibrin around individual hollow fibers. Our results are in line with recent findings that suggest fibrin production, through contact activation of factor XII, drives the thrombus formation in medical devices operating at low shear rates with large surface area to volume ratios. Author summaryPatients treated with blood-contacting medical devices suffer from clotting complications. Over the past decades, a great effort has been made to develop computational tools to predict and prevent clot formation in these devices. However, most models have focused on platelet activity and neglected other important parts of the problem such as the coagulation cascade reactions that lead to fibrin formation. In the current work, we incorporate this missing element into a well-established and validated model for platelet activity. We then use this novel approach to predict thrombus formation in two experimental configurations. Our results confirm that to accurately predict the clotting process in devices where surface area to volume ratios are large and flow velocity and shear stresses remain low, coagulation reactions and subsequent fibrin formation must be considered. This new model could have great implications for the design and optimization of medical devices such as blood oxygenators. In the long term, the model could evolve into a functional tool to inform anticoagulation therapies for these patients. ]]> Mendez Rojano, R. Lai, A. Zhussupbekov, M. Burgreen, G. W. Cook, K. Antaki, J. F. 2022-06-06 doi:10.1101/2022.06.06.494958 Cold Spring Harbor Laboratory Press 2022-06-06 <![CDATA[ EZH2/ hSULF1 axis mediates receptor tyrosine kinase signaling to shape cartilage tumor progression ]]> https://biorxiv.org/content/10.1101/2022.06.07.495151v1?rss=1 Lin, Z.-S. Chung, C.-C. Liu, Y.-C. Chang, C.-H. Liu, H.-C. Liang, Y.-Y. Huang, T.-L. Chen, T.-M. Lee, C.-H. Tang, C.-H. Chen, Y.-H. Hung, M.-C. 2022-06-09 doi:10.1101/2022.06.07.495151 Cold Spring Harbor Laboratory Press 2022-06-09 <![CDATA[ Disentanglement of Resting State Brain Networks for Localizing Epileptogenic Zone in Focal Epilepsy ]]> https://biorxiv.org/content/10.1101/2022.06.13.495945v1?rss=1 Ye, S. Bagic, A. He, B. 2022-06-17 doi:10.1101/2022.06.13.495945 Cold Spring Harbor Laboratory Press 2022-06-17 <![CDATA[ Why is human vision so poor in early development? The impact of initial sensitivity to low spatial frequencies on visual category learning ]]> https://biorxiv.org/content/10.1101/2022.06.22.497205v1?rss=1 Jinsi, O. Henderson, M. M. Tarr, M. J. 2022-06-23 doi:10.1101/2022.06.22.497205 Cold Spring Harbor Laboratory Press 2022-06-23 <![CDATA[ DNA packaging via hierarchical chromatin structures revealed by live-cell 3D imaging ]]> https://biorxiv.org/content/10.1101/2022.06.22.497271v1?rss=1 ZHENG, Y. Ye, S. Li, S. Liu, C. Luo, S. Chen, Y. Li, Y. Huang, L. Deng, S. Chen, P. Zhang, Y. Ji, W. Luo, R. Li, G. Yang, D. 2022-06-25 doi:10.1101/2022.06.22.497271 Cold Spring Harbor Laboratory Press 2022-06-25 <![CDATA[ Underlying beneficial effects of Rhubarb on constipation-induced inflammation, disorder of gut microbiome and metabolism ]]> https://biorxiv.org/content/10.1101/2022.06.24.497289v1?rss=1 Gao, H. He, C. Hua, R. Liang, C. Wang, B. Du, Y. Guo, Y. Gao, L. Zhang, L. Shang, H. Xu, J. 2022-06-28 doi:10.1101/2022.06.24.497289 Cold Spring Harbor Laboratory Press 2022-06-28 <![CDATA[ Characterizing the landscape of viral expression in cancer by deep learning ]]> https://biorxiv.org/content/10.1101/2022.06.26.497658v1?rss=1 Elbasir, A. Ye, Y. Schaffer, D. E. Hao, X. Wickramasinghe, J. Lieberman, P. M. Morris, Q. M. Zhang, R. Schaffer, A. A. Auslander, N. 2022-06-29 doi:10.1101/2022.06.26.497658 Cold Spring Harbor Laboratory Press 2022-06-29 <![CDATA[ ZO1 scaffold isoforms differentially contribute to electrical synapse formation ]]> https://biorxiv.org/content/10.1101/2022.06.27.497867v1?rss=1 Michel, J. C. Grivette, M. M. B. Harshfield, A. T. Huynh, L. Loomis, B. McKinnis, K. Miller, B. T. Huang, T. W. Lauf, S. Michel, M. E. Marsh, A. J. Kaye, L. E. Lukowicz-Bedford, R. M. Farnsworth, D. R. Martin, E. A. Miller, A. C. 2022-06-29 doi:10.1101/2022.06.27.497867 Cold Spring Harbor Laboratory Press 2022-06-29 <![CDATA[ Improving Memory via Automated Targeted Memory Reactivation during Sleep ]]> https://biorxiv.org/content/10.1101/2022.06.28.497977v1?rss=1 Whitmore, N. W. Harris, J. C. Kovach, T. Paller, K. A. 2022-07-03 doi:10.1101/2022.06.28.497977 Cold Spring Harbor Laboratory Press 2022-07-03 <![CDATA[ Meta-analysis of metagenomes via machine learning and assembly graphs reveals strain switches in Crohn's disease ]]> https://biorxiv.org/content/10.1101/2022.06.30.498290v1?rss=1 Reiter, T. E. Irber, L. C. Gingrich, A. A. Haynes, D. Pierce-Ward, N. T. Brooks, P. T. Mizutani, Y. Moritz, D. Reidl, F. Willis, A. D. Sullivan, B. D. Brown, C. T. 2022-07-05 doi:10.1101/2022.06.30.498290 Cold Spring Harbor Laboratory Press 2022-07-05 <![CDATA[ Convergent gene expression highlights shared vocal motor microcircuitry in songbirds and humans ]]> https://biorxiv.org/content/10.1101/2022.07.01.498177v1?rss=1 Gedman, G. L. Biegler, M. T. Haase, B. Wirthlin, M. Fedrigo, O. Pfenning, A. R. Jarvis, E. D. 2022-07-02 doi:10.1101/2022.07.01.498177 Cold Spring Harbor Laboratory Press 2022-07-02 <![CDATA[ Loss of growth differentiation factor 9 causes an arrest of early folliculogenesis in zebrafish - a novel insight into its action mechanism ]]> https://biorxiv.org/content/10.1101/2022.07.01.498398v1?rss=1 Chen, W. Zhai, Y. Zhu, B. Wu, K. Fan, Y. Zhou, X. Liu, L. Ge, W. 2022-07-02 doi:10.1101/2022.07.01.498398 Cold Spring Harbor Laboratory Press 2022-07-02 <![CDATA[ Learning alters neural activity to simultaneously support memory and action ]]> https://biorxiv.org/content/10.1101/2022.07.05.498856v1?rss=1 Losey, D. M. Hennig, J. A. Oby, E. R. Golub, M. D. Sadlter, P. T. Quick, K. M. Ryu, S. I. Tyler-Kabara, E. C. Batista, A. P. Yu, B. M. Chase, S. M. 2022-07-06 doi:10.1101/2022.07.05.498856 Cold Spring Harbor Laboratory Press 2022-07-06 <![CDATA[ α-synucleinopathy associated calcium overload and autophagy failure is regulated by gain-of-function of Tousled-like kinase ]]> https://biorxiv.org/content/10.1101/2022.07.17.500360v1?rss=1 Gong, F. Chen, H. Xiong, Y. Cai, R. Zhang, J. Wang, N. Liu, L. 2022-07-18 doi:10.1101/2022.07.17.500360 Cold Spring Harbor Laboratory Press 2022-07-18 <![CDATA[ Neutralizing antibody evasion and receptor binding features of SARS-CoV-2 Omicron BA.2.75 ]]> https://biorxiv.org/content/10.1101/2022.07.18.500332v1?rss=1 Cao, Y. Yu, Y. Song, W. Jian, F. Yisimayi, A. Yue, C. Feng, R. Wang, P. Yu, L. Zhang, N. Wang, J. Xiao, T. An, R. Wang, Y. Wang, J. Liu, L. Yang, S. Niu, X. Gu, Q. Shao, F. Hao, X. Jin, R. Wang, X. Wang, Y. Xie, X. S. 2022-07-19 doi:10.1101/2022.07.18.500332 Cold Spring Harbor Laboratory Press 2022-07-19 <![CDATA[ Pervasive Transcriptome Interactions of Protein-Targeted Drugs ]]> https://biorxiv.org/content/10.1101/2022.07.18.500496v1?rss=1 Fang, L. Velema, W. A. Lee, Y. Xiao, L. Mohsen, M. G. Kietrys, A. M. Kool, E. T. 2022-07-20 doi:10.1101/2022.07.18.500496 Cold Spring Harbor Laboratory Press 2022-07-20 <![CDATA[ Establishment of Transgenic Fluorescent Mice for Screening Synaptogenic Adhesion Molecules ]]> https://biorxiv.org/content/10.1101/2022.07.20.500799v1?rss=1 Yang, L. Zhang, J. Zhang, Y. Wang, L. Wang, X. Wang, S. Li, K. Wei, M. Zhang, C. 2022-07-21 doi:10.1101/2022.07.20.500799 Cold Spring Harbor Laboratory Press 2022-07-21 <![CDATA[ Automated prediction of site and sequence of protein modification with ATRP initiators ]]> https://biorxiv.org/content/10.1101/2022.07.23.501081v1?rss=1 Patel, A. Smith, P. Russell, A. Carmali, S. 2022-07-23 doi:10.1101/2022.07.23.501081 Cold Spring Harbor Laboratory Press 2022-07-23 <![CDATA[ Robust probabilistic modeling for single-cell multimodal mosaic integration and imputation ]]> https://biorxiv.org/content/10.1101/2022.07.25.501456v1?rss=1 Du, J.-H. Cai, Z. Roeder, K. 2022-07-25 doi:10.1101/2022.07.25.501456 Cold Spring Harbor Laboratory Press 2022-07-25 <![CDATA[ Nardilysin-Regulated Scission Mechanism Activates Polo-like Kinase 3 to Suppress the Development of Pancreatic Cancer ]]> https://biorxiv.org/content/10.1101/2022.07.28.501759v1?rss=1 Fu, J. Li, J. Li, C.-F. Tsai, C.-L. Yin, W. Hou, J. Chen, P. Cao, Y. Kang, Y. Sun, Y. Xia, X. Furukawa, K. Lu, Y. Wu, M. Huang, Q. Yao, J. Hawke, D. H. Pan, B.-F. Zhao, J. Huang, J. Wang, H. Bahassi, E. M. Stambrook, P. J. Huang, P. Fleming, J. B. Maitra, A. B. Tainer, J. Hung, M.-C. Chiao, P. 2022-07-30 doi:10.1101/2022.07.28.501759 Cold Spring Harbor Laboratory Press 2022-07-30 <![CDATA[ Rational identification of potent and broad sarbecovirus-neutralizing antibody cocktails from SARS convalescents ]]> https://biorxiv.org/content/10.1101/2022.08.03.499114v1?rss=1 Cao, Y. R. Jian, F. Zhang, Z. Yisimayi, A. Hao, X. Bao, L. Yuan, F. Yu, Y. Du, S. Wang, J. Xiao, T. Song, W. Zhang, Y. Liu, P. An, R. Wang, P. Wang, Y. Yang, S. Niu, X. Zhang, Y. Gu, Q. Shao, F. Hu, Y. Yin, W. Zheng, A. Wang, Y. Qin, C. Jin, R. Xiao, J. Xie, X. S. 2022-08-04 doi:10.1101/2022.08.03.499114 Cold Spring Harbor Laboratory Press 2022-08-04 <![CDATA[ Low-level tuning biases in higher visual cortex reflect the semantic informativeness of visual features ]]> https://biorxiv.org/content/10.1101/2022.08.04.502850v1?rss=1 Henderson, M. M. Tarr, M. J. Wehbe, L. 2022-08-06 doi:10.1101/2022.08.04.502850 Cold Spring Harbor Laboratory Press 2022-08-06 <![CDATA[ Selection on sperm size in response to promiscuity and variation in female sperm storage organs ]]> https://biorxiv.org/content/10.1101/2022.08.05.502910v1?rss=1 Cramer, E. R. A. Yilma, Z. B. Lifjeld, J. T. 2022-08-05 doi:10.1101/2022.08.05.502910 Cold Spring Harbor Laboratory Press 2022-08-05 <![CDATA[ A unified analysis of atlas single cell data ]]> https://biorxiv.org/content/10.1101/2022.08.06.503038v1?rss=1 Chen, H. Nguyen, N. D. Ruffalo, M. Bar-Joseph, Z. 2022-08-06 doi:10.1101/2022.08.06.503038 Cold Spring Harbor Laboratory Press 2022-08-06 <![CDATA[ Further humoral immunity evasion of emerging SARS-CoV-2 BA.4 and BA.5 subvariants ]]> https://biorxiv.org/content/10.1101/2022.08.09.503384v1?rss=1 Jian, F. Yu, Y. Song, W. Yisimayi, A. Yu, L. Gao, Y. Zhang, N. Wang, Y. Shao, F. Hao, X. Xu, Y. Jin, R. Wang, Y. Xie, X. S. Cao, Y. 2022-08-10 doi:10.1101/2022.08.09.503384 Cold Spring Harbor Laboratory Press 2022-08-10 <![CDATA[ Expression QTLs in single-cell sequencing data ]]> https://biorxiv.org/content/10.1101/2022.08.14.503915v1?rss=1 Gewirtz, A. D. Townes, F. W. Engelhardt, B. E. 2022-08-15 doi:10.1101/2022.08.14.503915 Cold Spring Harbor Laboratory Press 2022-08-15 <![CDATA[ Relating enhancer genetic variation across mammals to complex phenotypes using machine learning ]]> https://biorxiv.org/content/10.1101/2022.08.26.505436v1?rss=1 Kaplow, I. M. Lawler, A. J. Schaffer, D. E. Srinivasan, C. Wirthlin, M. E. Phan, B. N. Zhang, X. Foley, K. Prasad, K. Brown, A. R. Zoonomia Consortium, Meyer, W. K. Pfenning, A. R. 2022-08-26 doi:10.1101/2022.08.26.505436 Cold Spring Harbor Laboratory Press 2022-08-26 <![CDATA[ Local Field Potentials, Spiking Activity, and Receptive Fields in Human Visual Cortex ]]> https://biorxiv.org/content/10.1101/2022.08.28.505627v1?rss=1 Luo, L. Wang, X. Lu, J. Chen, G. Luan, G. Li, W. Wang, Q. Fang, F. 2022-08-29 doi:10.1101/2022.08.28.505627 Cold Spring Harbor Laboratory Press 2022-08-29 <![CDATA[ High-Frequency Stimulation Does Not Improve Comfort of Transcutaneous Spinal Cord Stimulation ]]> https://biorxiv.org/content/10.1101/2022.09.06.506783v1?rss=1 View larger version (33K): org.highwire.dtl.DTLVardef@f013f3org.highwire.dtl.DTLVardef@1aded5eorg.highwire.dtl.DTLVardef@1bad2e0org.highwire.dtl.DTLVardef@6aaf96_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Dalrymple, A. N. Hooper, C. A. Kuriakose, M. G. Capogrosso, M. Weber, D. J. 2022-09-08 doi:10.1101/2022.09.06.506783 Cold Spring Harbor Laboratory Press 2022-09-08 <![CDATA[ Does Functional Recovery Imply Stable Circuitry in the Spinal Animal? ]]> https://biorxiv.org/content/10.1101/2022.09.09.507338v1?rss=1 Refy, O. Geyer, H. 2022-09-10 doi:10.1101/2022.09.09.507338 Cold Spring Harbor Laboratory Press 2022-09-10 <![CDATA[ Development of a High-Performance Open-Source 3D Bioprinter ]]> https://biorxiv.org/content/10.1101/2022.09.11.507416v1?rss=1 Shiwarksi, D. J. Tashman, J. W. Feinberg, A. W. 2022-09-13 doi:10.1101/2022.09.11.507416 Cold Spring Harbor Laboratory Press 2022-09-13 <![CDATA[ Hybridization led to a rewired pluripotency network in the allotetraploid Xenopus laevis ]]> https://biorxiv.org/content/10.1101/2022.09.14.507817v1?rss=1 Phelps, W. A. Hurton, M. D. Ayers, T. N. Carlson, A. E. Rosenbaum, J. C. Lee, M. T. 2022-09-17 doi:10.1101/2022.09.14.507817 Cold Spring Harbor Laboratory Press 2022-09-17 <![CDATA[ Imprinted SARS-CoV-2 humoral immunity induces converging Omicron RBD evolution ]]> https://biorxiv.org/content/10.1101/2022.09.15.507787v1?rss=1 Cao, Y. Jian, F. Wang, J. Yu, Y. Song, W. Yisimayi, A. Wang, J. An, R. Zhang, N. Wang, Y. Wang, P. Zhao, L. Sun, H. Yu, L. Yang, S. Niu, X. Xiao, T. Gu, Q. Shao, F. Hao, X. Xu, Y. Jin, R. Wang, Y. Xie, X. S. 2022-09-16 doi:10.1101/2022.09.15.507787 Cold Spring Harbor Laboratory Press 2022-09-16 <![CDATA[ 3D electron diffraction reveals the chiral nature of the malaria pigment crystal hemozoin ]]> https://biorxiv.org/content/10.1101/2022.09.15.507960v1?rss=1 Klar, P. B. Waterman, D. Gruene, T. Mullick, D. Song, Y. Gilchrist, J. B. Wen, W. Biran, I. Houben, L. Regev-Rudzki, N. Dzikowski, R. Palatinus, L. Zhang, P. Leiserowitz, L. Elbaum, M. 2022-09-16 doi:10.1101/2022.09.15.507960 Cold Spring Harbor Laboratory Press 2022-09-16 <![CDATA[ Temporal asymmetries and interactions between dorsal and ventral visual pathways during object recognition ]]> https://biorxiv.org/content/10.1101/2022.09.17.508376v1?rss=1 Ayzenberg, V. Simmons, C. Behrmann, M. 2022-09-18 doi:10.1101/2022.09.17.508376 Cold Spring Harbor Laboratory Press 2022-09-18 <![CDATA[ Comparing acute IOP-induced lamina cribrosa deformations pre-mortem and post-mortem ]]> https://biorxiv.org/content/10.1101/2022.09.18.508448v1?rss=1 Wei, J. Hua, Y. Yang, B. Wang, B. Schmitt, S. E. Wang, B. Lucy, K. A. Ishikawa, H. Schuman, J. S. Smith, M. A. Wollstein, G. Sigal, I. A. 2022-09-19 doi:10.1101/2022.09.18.508448 Cold Spring Harbor Laboratory Press 2022-09-19 <![CDATA[ A texture statistics encoding model reveals hierarchical feature selectivity across human visual cortex ]]> https://biorxiv.org/content/10.1101/2022.09.23.509292v1?rss=1 Henderson, M. M. Tarr, M. J. Wehbe, L. 2022-09-26 doi:10.1101/2022.09.23.509292 Cold Spring Harbor Laboratory Press 2022-09-26 <![CDATA[ Depletion of collagen IX alpha2 interferes osteochondral homeostasis of the knee joint which ultimately causing osteoarthritis-like articular cartilage damage ]]> https://biorxiv.org/content/10.1101/2022.09.24.509343v1?rss=1 Dong, R. Xu, H. Wang, P. Fang, L. Xiao, L. Lv, S. Tong, P. Jin, H. 2022-09-26 doi:10.1101/2022.09.24.509343 Cold Spring Harbor Laboratory Press 2022-09-26 <![CDATA[ Incorporating natural language into vision models improves prediction and understanding of higher visual cortex ]]> https://biorxiv.org/content/10.1101/2022.09.27.508760v1?rss=1 Wang, A. Y. Kay, K. Naselaris, T. Tarr, M. J. Wehbe, L. 2022-09-29 doi:10.1101/2022.09.27.508760 Cold Spring Harbor Laboratory Press 2022-09-29 <![CDATA[ Competition between action plans tracks with evidence accumulation during flexible decision-making ]]> https://biorxiv.org/content/10.1101/2022.10.03.510668v1?rss=1 Bond, K. A. M. Rasero, J. Madan, R. Bahuguna, J. Rubin, J. Verstynen, T. 2022-10-06 doi:10.1101/2022.10.03.510668 Cold Spring Harbor Laboratory Press 2022-10-06 <![CDATA[ Dynamic trade-offs between biomass accumulation and division determine bacterial cell size and proteome in fluctuating nutrient environments ]]> https://biorxiv.org/content/10.1101/2022.10.03.510720v1?rss=1 Banerjee, S. Kratz, J. C. 2022-10-06 doi:10.1101/2022.10.03.510720 Cold Spring Harbor Laboratory Press 2022-10-06 <![CDATA[ CryoFIB milling large tissue samples for cryo-electron tomography ]]> https://biorxiv.org/content/10.1101/2022.10.03.510728v1?rss=1 Li, X. Wang, S. Zhou, H. Chen, W. Jiang, Y. Yan, X. You, H. 2022-10-05 doi:10.1101/2022.10.03.510728 Cold Spring Harbor Laboratory Press 2022-10-05 <![CDATA[ Nonuniform structural properties of wings confer sensing advantages ]]> https://biorxiv.org/content/10.1101/2022.10.04.510910v1?rss=1 Weber, A. I. Babaei, M. Mamo, A. Brunton, B. W. Daniel, T. L. Bergbreiter, S. 2022-10-07 doi:10.1101/2022.10.04.510910 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Noninvasive, automated and reliable detection of spreading depolarizations in severe traumatic brain injury using scalp EEG ]]> https://biorxiv.org/content/10.1101/2022.10.07.511376v1?rss=1 Chamanzar, A. Elmer, J. Shutter, L. Hartings, J. A. Grover, P. 2022-10-08 doi:10.1101/2022.10.07.511376 Cold Spring Harbor Laboratory Press 2022-10-08 <![CDATA[ Innate immune sensing of self-derived double-stranded RNA by RIG-I-MAVS-TNF-α regulates the survival and senescence fate of SARS-2-S syncytia ]]> https://biorxiv.org/content/10.1101/2022.10.10.511541v1?rss=1 Wan, L. Li, H. Huang, L. Liu, M. Li, J. Yang, Y. Zhao, R. Liu, J. Yang, X. Ma, E. Sun, L. Hou, X. Zhang, X. Zhang, Y. Yan, Q. Liu, J. Li, X. Cheng, G. Gao, Q. Xu, J. Hou, L. Wei, C. Zhong, H. 2022-10-11 doi:10.1101/2022.10.10.511541 Cold Spring Harbor Laboratory Press 2022-10-11 <![CDATA[ An optimized Tet-On system for conditional control of gene expression in sea urchins ]]> https://biorxiv.org/content/10.1101/2022.10.12.511941v1?rss=1 Khor, J. M. Ettensohn, C. A. 2022-10-12 doi:10.1101/2022.10.12.511941 Cold Spring Harbor Laboratory Press 2022-10-12 <![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[ Towards Hierarchical Causal Representation Learning for Nonstationary Multi-Omics Data ]]> https://biorxiv.org/content/10.1101/2022.10.17.512602v1?rss=1 Mao, H. Jia, M. Di, M. Zhang, K. Benos, P. V. 2022-10-21 doi:10.1101/2022.10.17.512602 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Masked Minimizers: Unifying sequence sketching methods ]]> https://biorxiv.org/content/10.1101/2022.10.18.512430v1?rss=1 Hoang, M. Marcais, G. Kingsford, C. 2022-10-21 doi:10.1101/2022.10.18.512430 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ Physiological Changes Associated with Copper Sulfate-Induced Emesis in Felines ]]> https://biorxiv.org/content/10.1101/2022.10.20.512908v1?rss=1 Murphey, C. P. Shulgach, J. A. Amin, P. R. Douglas, N. K. Bielanin, J. P. Sampson, J. P. Horn, C. C. Yates, B. J. 2022-10-21 doi:10.1101/2022.10.20.512908 Cold Spring Harbor Laboratory Press 2022-10-21 <![CDATA[ SNCA Deletion Induced Aberrant Projection of Olfactory Sensory Neurons via NCK2-EphA4 Pathway ]]> https://biorxiv.org/content/10.1101/2022.10.25.513708v1?rss=1 Lu, L.-L. 2022-10-25 doi:10.1101/2022.10.25.513708 Cold Spring Harbor Laboratory Press 2022-10-25 <![CDATA[ Best Practices for Interpretable Machine Learning in Computational Biology ]]> https://biorxiv.org/content/10.1101/2022.10.28.513978v1?rss=1 Chen, V. Yang, M. Cui, W. Kim, J. S. Talwalkar, A. Ma, J. 2022-11-01 doi:10.1101/2022.10.28.513978 Cold Spring Harbor Laboratory Press 2022-11-01 <![CDATA[ Whole Human-Brain Mapping of Single Cortical Neurons for Profiling Morphological Diversity and Stereotypy ]]> https://biorxiv.org/content/10.1101/2022.10.29.514375v1?rss=1 Han, X. Guo, S. Ji, N. Li, T. Liu, J. Ye, X. Wang, Y. Yun, Z. Xiong, F. Rong, J. Liu, D. Ma, H. Wang, Y. Huang, Y. Zhang, P. Wu, W. Ding, L. Hawrylycz, M. Lein, E. Ascoli, G. A. Xie, W. Liu, L. Zhang, L. Peng, H. 2022-10-30 doi:10.1101/2022.10.29.514375 Cold Spring Harbor Laboratory Press 2022-10-30 <![CDATA[ USP10 strikes down Wnt/β-catenin signaling by dual-wielding deubiquitinase activity and phase transition potential ]]> https://biorxiv.org/content/10.1101/2022.10.31.514466v1?rss=1 Wang, Y. Mao, A. Liu, J. Li, P. Zheng, S. Tong, T. Li, Z. Zhang, H. Ma, L. Lin, J. Pang, Z. Han, Q. Li, F. Zhang, X. Chen, M. He, X. Zhang, X. Fei, T. Liu, B. Gao, D. Cao, L. Wang, Q. Li, Y. Sheng, R. 2022-11-01 doi:10.1101/2022.10.31.514466 Cold Spring Harbor Laboratory Press 2022-11-01 <![CDATA[ A-SOiD, an active learning platform for expert-guided, data efficient discovery of behavior ]]> https://biorxiv.org/content/10.1101/2022.11.04.515138v1?rss=1 Schweihoff, J. F. Hsu, A. I. Schwarz, M. K. Yttri, E. A. 2022-11-04 doi:10.1101/2022.11.04.515138 Cold Spring Harbor Laboratory Press 2022-11-04 <![CDATA[ Integrated Network Pharmacology and Experimental Analysis Unveil Modulation of EGFR/MAPK Signaling Cascades in Acute Cerebral Ischemia-Reperfusion Injury by Qing-Tong-Hua-Yu Decoction ]]> https://biorxiv.org/content/10.1101/2022.11.04.515245v1?rss=1 Hu, J. Zuo, L. Qu, W. He, H. Bao, J. Zhang, W. Zhang, Y. Zhu, M. Li, T. 2022-11-05 doi:10.1101/2022.11.04.515245 Cold Spring Harbor Laboratory Press 2022-11-05 <![CDATA[ Demographic Reporting and Phenotypic Exclusion in fNIRS ]]> https://biorxiv.org/content/10.1101/2022.11.08.515730v1?rss=1 Kwasa, J. Peterson, H. M. Jones, L. Karrobi, K. Parker, T. Nickerson, N. Wood, S. 2022-11-09 doi:10.1101/2022.11.08.515730 Cold Spring Harbor Laboratory Press 2022-11-09 <![CDATA[ Profiling of chimeric RNAs in human retinal development with retinal organoids ]]> https://biorxiv.org/content/10.1101/2022.11.10.515982v1?rss=1 Wang, W. Zhang, X. Zhao, N. Xu, Z.-H. Jin, K. Jin, Z.-B. 2022-11-10 doi:10.1101/2022.11.10.515982 Cold Spring Harbor Laboratory Press 2022-11-10 <![CDATA[ Personalized Deep Learning based Source Imaging Framework Improves the Imaging of Epileptic Sources from MEG Interictal Spikes ]]> https://biorxiv.org/content/10.1101/2022.11.13.516312v1?rss=1 Sun, R. Zhang, W. Bagic, A. He, B. 2022-11-16 doi:10.1101/2022.11.13.516312 Cold Spring Harbor Laboratory Press 2022-11-16 <![CDATA[ De novo design of modular peptide binding proteins by superhelical matching ]]> https://biorxiv.org/content/10.1101/2022.11.14.514089v1?rss=1 Wu, K. Bai, H. Chang, Y.-T. Redler, R. McNally, K. E. Sheffler, W. Brunette, T. Hicks, D. R. Morgan, T. E. Stevens, T. J. Broerman, A. Goreshnik, I. DeWitt, M. Chow, C. M. Shen, Y. Stewart, L. Derivery, E. Silva, D. A. Bhabha, G. Ekiert, D. Baker, D. 2022-11-15 doi:10.1101/2022.11.14.514089 Cold Spring Harbor Laboratory Press 2022-11-15 <![CDATA[ Fusion of Video and Inertial Sensing Data via Dynamic Optimization of a Biomechanical Model ]]> https://biorxiv.org/content/10.1101/2022.11.15.516673v1?rss=1 Pearl, O. D. Shin, S. Godura, A. Bergbreiter, S. Halilaj, E. 2022-11-17 doi:10.1101/2022.11.15.516673 Cold Spring Harbor Laboratory Press 2022-11-17 <![CDATA[ Functional gradients reveal altered functional segregation in patients with amnestic mild cognitive impairment and Alzheimer' s disease ]]> https://biorxiv.org/content/10.1101/2022.11.16.516698v1?rss=1 He, Y. Li, Q. Fu, Z. Zeng, D. Han, Y. Li, S. 2022-11-16 doi:10.1101/2022.11.16.516698 Cold Spring Harbor Laboratory Press 2022-11-16 <![CDATA[ Rapid and Signal Crowdedness-Robust In-Situ Sequencing through Hybrid Block Coding ]]> https://biorxiv.org/content/10.1101/2022.11.16.516714v1?rss=1 Chang, T. Han, W. Jiang, M. Li, J. Shen, J. Chen, Z. Fei, P. Ren, X. Pang, Y. Wang, G. Wang, J. Huang, Y. 2022-11-17 doi:10.1101/2022.11.16.516714 Cold Spring Harbor Laboratory Press 2022-11-17 <![CDATA[ An in vivo massively parallel platform for deciphering tissue-specific regulatory function ]]> https://biorxiv.org/content/10.1101/2022.11.23.517755v1?rss=1 Brown, A. R. Fox, G. A. Kaplow, I. M. Lawler, A. J. Phan, B. N. Wirthlin, M. E. Ramamurthy, E. May, G. E. Chen, Z. Su, Q. McManus, C. J. Pfenning, A. R. 2022-11-25 doi:10.1101/2022.11.23.517755 Cold Spring Harbor Laboratory Press 2022-11-25 <![CDATA[ Structural and functional specializations of human fast spiking neurons support fast cortical signaling ]]> https://biorxiv.org/content/10.1101/2022.11.29.518193v1?rss=1 Wilbers, R. Galakhova, A. A. Heistek, T. S. Metodieva, V. D. Hagemann, J. Heyer, D. B. Mertens, E. J. Deng, S. Idema, S. de Witt Hamer, P. C. Noske, D. P. van Schie, P. Kommers, I. Luan, G. Li, T. Shu, Y. de Kock, C. P. J. Mansvelder, H. D. Goriounova, N. A. 2022-11-29 doi:10.1101/2022.11.29.518193 Cold Spring Harbor Laboratory Press 2022-11-29 <![CDATA[ Targeted photodynamic neutralization of SARS-CoV-2 mediated by singlet oxygen ]]> https://biorxiv.org/content/10.1101/2022.11.29.518438v1?rss=1 Yao, R. Hou, J. Zhang, X. Li, Y. Lai, J. Wu, Q. Liu, Q. Zhou, L. 2022-11-30 doi:10.1101/2022.11.29.518438 Cold Spring Harbor Laboratory Press 2022-11-30 <![CDATA[ Regression convolutional neural network models implicate peripheral immune regulatory variants in the predisposition to Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2022.12.02.518903v1?rss=1 Ramamurthy, E. Agarwal, S. Toong, N. Kaplow, I. Phan, B. Pfenning, A. R. 2022-12-03 doi:10.1101/2022.12.02.518903 Cold Spring Harbor Laboratory Press 2022-12-03 <![CDATA[ Low-intensity transcranial focused ultrasound changes pain-associated behaviors by modulating pain processing brain circuits ]]> https://biorxiv.org/content/10.1101/2022.12.07.519518v1?rss=1 Kim, M. G. Yu, K. Fouda, R. Argueta, D. Kiven, S. Ni, Y. Niu, X. Chen, Q. Kim, K. Gupta, K. He, B. 2022-12-12 doi:10.1101/2022.12.07.519518 Cold Spring Harbor Laboratory Press 2022-12-12 <![CDATA[ Alteration of pro-carcinogenic gut microbiota is associated with clear cell renal cell carcinoma tumorigenesis ]]> https://biorxiv.org/content/10.1101/2022.12.07.519551v1?rss=1 Yang, B. Zhao, F. Li, X. Zhao, M. Lv, J. Shi, M. Li, J. Zhou, Z. Wang, J. Song, J. 2022-12-08 doi:10.1101/2022.12.07.519551 Cold Spring Harbor Laboratory Press 2022-12-08 <![CDATA[ Emergence of counting in the brains of 3- to 5-year-old children ]]> https://biorxiv.org/content/10.1101/2022.12.13.520249v1?rss=1 Kersey, A. J. Aulet, L. S. Cantlon, J. F. 2022-12-13 doi:10.1101/2022.12.13.520249 Cold Spring Harbor Laboratory Press 2022-12-13 <![CDATA[ Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements ]]> https://biorxiv.org/content/10.1101/2022.12.17.520895v1?rss=1 Wirthlin, M. E. Schmid, T. A. Elie, J. E. Zhang, X. Shvareva, V. A. Rakuljic, A. Ji, M. B. Bhat, N. S. Kaplow, I. M. Schäffer, D. E. Lawler, A. J. Annaldasula, S. Lim, B. Azim, E. Zoonomia Consortium, Meyer, W. K. Yartsev, M. M. Pfenning, A. R. 2022-12-18 doi:10.1101/2022.12.17.520895 Cold Spring Harbor Laboratory Press 2022-12-18 <![CDATA[ Auditory cortical responses to speech are shaped by statistical learning of short-term speech input regularities ]]> https://biorxiv.org/content/10.1101/2022.12.19.520832v1?rss=1 Wu, Y. C. Viswanathan, V. Abel, T. J. Holt, L. L. 2022-12-19 doi:10.1101/2022.12.19.520832 Cold Spring Harbor Laboratory Press 2022-12-19 <![CDATA[ HBM-CITEseq: a uniform CITE-seq processing pipeline for the HuBMAP Consortium ]]> https://biorxiv.org/content/10.1101/2022.12.19.521058v1?rss=1 Lu, X. Ruffalo, M. 2022-12-20 doi:10.1101/2022.12.19.521058 Cold Spring Harbor Laboratory Press 2022-12-20 <![CDATA[ Activity Map and Transition Pathways of G Protein Coupled Receptor Revealed by Machine Learning ]]> https://biorxiv.org/content/10.1101/2022.12.20.521237v1?rss=1 Mollaei, P. Barati farimani, A. 2022-12-21 doi:10.1101/2022.12.20.521237 Cold Spring Harbor Laboratory Press 2022-12-21 <![CDATA[ MYSM1 co-activates ERα action via histone and non-histone deubiquitination to confer antiestrogen resistance in breast cancer ]]> https://biorxiv.org/content/10.1101/2022.12.23.521780v1?rss=1 Zhao, Y. Luan, R. Sun, G. Zhou, B. Wang, M. Bai, Y. Wang, C. Wang, S. Zeng, K. Feng, J. He, M. Lin, L. Wei, Y. Zhang, Q. 2022-12-24 doi:10.1101/2022.12.23.521780 Cold Spring Harbor Laboratory Press 2022-12-24 <![CDATA[ Release of large synaptic DCV proteins is triggered by Ca2+-independent Rugose-localized complexin phosphorylation ]]> https://biorxiv.org/content/10.1101/2022.12.24.521856v1?rss=1 Bulgari, D. Cavolo, S. L. Schmidt, B. F. Buchan, K. Bruchez, M. P. Deitcher, D. L. Levitan, E. 2022-12-24 doi:10.1101/2022.12.24.521856 Cold Spring Harbor Laboratory Press 2022-12-24 <![CDATA[ Cataloguing and profiling of the gut virome in Chinese populations uncover extensive viral signatures across common diseases ]]> https://biorxiv.org/content/10.1101/2022.12.27.522048v1?rss=1 Li, S. Yan, Q. Wang, G. Zhang, Y. Guo, R. Zhang, P. Lv, Q. Chen, F. Zhiming, L. Meng, J. Li, J. Chen, C. ULLAH, H. Cheng, L. Fan, S. Li, R. You, W. Zhang, Y. Ma, J. Sun, W. Ma, X. 2022-12-28 doi:10.1101/2022.12.27.522048 Cold Spring Harbor Laboratory Press 2022-12-28 <![CDATA[ Induced Alpha And Beta Electroencephalographic Rhythms Covary With Single-Trial Speech Intelligibility In Competition ]]> https://biorxiv.org/content/10.1101/2022.12.31.522365v1?rss=1 Viswanathan, V. Bharadwaj, H. M. Heinz, M. G. Shinn-Cunningham, B. G. 2023-01-02 doi:10.1101/2022.12.31.522365 Cold Spring Harbor Laboratory Press 2023-01-02 <![CDATA[ Inducible in vivo genome editing in the sea star Patiria miniata ]]> https://biorxiv.org/content/10.1101/2023.01.09.523328v1?rss=1 Zueva, O. Hinman, V. 2023-01-10 doi:10.1101/2023.01.09.523328 Cold Spring Harbor Laboratory Press 2023-01-10 <![CDATA[ Cell segmentation for high-resolution spatial transcriptomics ]]> https://biorxiv.org/content/10.1101/2023.01.11.523658v1?rss=1 Chen, H. Li, D. Bar-Joseph, Z. 2023-01-15 doi:10.1101/2023.01.11.523658 Cold Spring Harbor Laboratory Press 2023-01-15 <![CDATA[ Insulin determines the effects of TGF-beta on HNF4alpha transcription and epithelial-to-mesenchymal transition in hepatocytes ]]> https://biorxiv.org/content/10.1101/2023.01.12.523351v1?rss=1 Feng, R. Tong, C. Lin, T. Liu, H. Shao, C. Li, Y. Sticht, C. Kan, K. Li, X. Liu, R. Wang, S. Wang, S. Munker, S. Niess, H. Meyer, C. Liebe, R. Ebert, M. P. Dooley, S. Wang, H. Ding, H. Weng, H.-L. 2023-01-12 doi:10.1101/2023.01.12.523351 Cold Spring Harbor Laboratory Press 2023-01-12 <![CDATA[ The natural tannins oligomeric proanthocyanidins and punicalagin are potent inhibitors of infection by SARS-CoV-2 in vitro ]]> https://biorxiv.org/content/10.1101/2023.01.12.523465v1?rss=1 Chen, H.-F. Wang, W.-J. Chen, C.-Y. Chang, W.-C. Hsueh, P.-R. Peng, S.-L. Wu, C.-S. Chen, Y. Huang, H.-Y. Shen, W.-J. Wang, S.-C. Hung, M.-C. 2023-01-12 doi:10.1101/2023.01.12.523465 Cold Spring Harbor Laboratory Press 2023-01-12 <![CDATA[ SARS-CoV-2 Envelope protein triggers depression and dysosmia via TLR2 mediated neuroinflammation ]]> https://biorxiv.org/content/10.1101/2023.01.15.524078v1?rss=1 Su, W. Ju, J. Gu, M.-h. Wang, X. Liu, S. Yu, J. Mu, D. 2023-01-17 doi:10.1101/2023.01.15.524078 Cold Spring Harbor Laboratory Press 2023-01-17 <![CDATA[ In vivo Modulation of Intraocular and Intracranial Pressures Causes Nonlinear and Non-monotonic Deformations of the Lamina Cribrosa and Scleral Canal ]]> https://biorxiv.org/content/10.1101/2023.01.29.526113v1?rss=1 Zhu, Z. Waxman, S. Wang, B. Wallace, J. Schmitt, S. E. Tyler-Kabara, E. Ishikawa, H. Schuman, J. S. Smith, M. A. Wollstein, G. Sigal, I. A. 2023-01-31 doi:10.1101/2023.01.29.526113 Cold Spring Harbor Laboratory Press 2023-01-31 <![CDATA[ Data-driven optimization of biomarker panels in highly multiplexed imaging ]]> https://biorxiv.org/content/10.1101/2023.01.29.526114v1?rss=1 Sun, H. Li, J. Murphy, R. F. 2023-01-31 doi:10.1101/2023.01.29.526114 Cold Spring Harbor Laboratory Press 2023-01-31 <![CDATA[ EstroGene database reveals diverse temporal, context-dependent and directional estrogen receptor regulomes in breast cancer ]]> https://biorxiv.org/content/10.1101/2023.01.30.526388v1?rss=1 Li, Z. Li, T. Yates, M. E. Wu, Y. Ferber, A. Chen, L. Brown, D. D. Carroll, J. Sikora, M. J. Tseng, G. Oesterreich, S. LEE, A. V. 2023-02-02 doi:10.1101/2023.01.30.526388 Cold Spring Harbor Laboratory Press 2023-02-02 <![CDATA[ Single-cell transcriptome analysis reveals the cellular atlas of human intracranial aneurysm and highlights inflammation features associated with aneurysm rupture ]]> https://biorxiv.org/content/10.1101/2023.04.06.535955v1?rss=1 ji, h. Yue, L. Sun, H. Chen, R. Zhou, R. Xiao, A. Yang, Y. Wang, R. You, C. Liu, Y. 2023-04-07 doi:10.1101/2023.04.06.535955 Cold Spring Harbor Laboratory Press 2023-04-07 <![CDATA[ A Unified Statistical Framework for Single Cell and Bulk RNA Sequencing Data ]]> https://biorxiv.org/content/10.1101/206532v1?rss=1 Zhu, L. Lei, J. Devlin, B. Roeder, K. 2017-10-19 doi:10.1101/206532 Cold Spring Harbor Laboratory Press 2017-10-19 <![CDATA[ A theory of multineuronal dimensionality, dynamics and measurement ]]> https://biorxiv.org/content/10.1101/214262v1?rss=1 Gao, P. Trautmann, E. Yu, B. M. Santhanam, G. Ryu, S. Shenoy, K. Ganguli, S. 2017-11-05 doi:10.1101/214262 Cold Spring Harbor Laboratory Press 2017-11-05 <![CDATA[ Removing unwanted variation between samples in Hi-C experiments ]]> https://biorxiv.org/content/10.1101/214361v1?rss=1 Fletez-Brant, K. Qiu, Y. Gorkin, D. U. Hu, M. Hansen, K. D. 2017-11-06 doi:10.1101/214361 Cold Spring Harbor Laboratory Press 2017-11-06 <![CDATA[ STIMULUS: Noninvasive Dynamic Patterns of Neurostimulation using Spatio-Temporal Interference ]]> https://biorxiv.org/content/10.1101/216622v1?rss=1 2 electrode pairs) that yields significantly higher spatial precision. To further improve precision, we develop STIMULUS techniques for generating spatial interference patterns in conjunction with temporal interference, and demonstrate strict and significant improvements over multielectrode TI. Finally, we utilize the adaptivity that is inherent in STIMULUS to create multisite neurostimulation patterns that can be dynamically steered over time. ]]> Cao, J. Grover, P. 2017-11-09 doi:10.1101/216622 Cold Spring Harbor Laboratory Press 2017-11-09 <![CDATA[ Whole-cell scale dynamic organization of lysosomes revealed by spatial statistical analysis ]]> https://biorxiv.org/content/10.1101/219790v1?rss=1 Ba, Q. Raghavan, G. Kiselyov, K. Yang, G. 2017-11-14 doi:10.1101/219790 Cold Spring Harbor Laboratory Press 2017-11-14 <![CDATA[ MetaRiPPquest: A Peptidogenomics Approach for the Discovery of Ribosomally Synthesized and Post-translationally Modified Peptides ]]> https://biorxiv.org/content/10.1101/227504v1?rss=1 Mohimani, H. Gurevich, A. Alexander, K. L. Naman, C. B. Leao, T. Glukhov, E. Moss, N. A. Luzzatto Knaan, T. Vargas, F. Nothias, L.-F. Singh, N. K. Sanders, J. G. Benitez, R. A. S. Thompson, L. R. Hamid, M. N. Morton, J. T. Mikheenko, A. Shlemov, A. Korobeynikov, A. Friedberg, I. Knight, R. Venkateswaran, K. Gerwick, W. Gerwick, L. Dorrestein, P. C. Pevzner, P. A. 2017-12-03 doi:10.1101/227504 Cold Spring Harbor Laboratory Press 2017-12-03 <![CDATA[ Variable Selection in Heterogeneous Datasets: A Truncated-rank Sparse Linear Mixed Model with Applications to Genome-wide Association Studies ]]> https://biorxiv.org/content/10.1101/228106v1?rss=1 Wang, H. Aragam, B. Xing, E. P. 2017-12-03 doi:10.1101/228106 Cold Spring Harbor Laboratory Press 2017-12-03 <![CDATA[ Multiplex Confounding Factor Correction for Genomic Association Mapping with Squared Sparse Linear Mixed Model ]]> https://biorxiv.org/content/10.1101/228114v1?rss=1 Wang, H. Liu, X. Xiao, Y. Xu, M. Xing, E. P. 2017-12-03 doi:10.1101/228114 Cold Spring Harbor Laboratory Press 2017-12-03 <![CDATA[ Cardiac directed differentiation using small molecule Wnt modulation at single-cell resolution ]]> https://biorxiv.org/content/10.1101/229294v1?rss=1 Friedman, C. Nguyen, Q. Lukowski, S. Helfer, A. Chiu, H. Voges, H. Suo, S. Han, J.-D. Osteil, P. Peng, G. Jing, N. Ballie, G. Senabouth, A. Christ, A. Bruxner, T. Murry, C. Wong, E. Ding, J. Wang, Y. Hudson, J. Bar-Joseph, Z. Tam, P. Powell, J. Palpant, N. 2017-12-07 doi:10.1101/229294 Cold Spring Harbor Laboratory Press 2017-12-07 <![CDATA[ Hercules: a profile HMM-based hybrid error correction algorithm for long reads ]]> https://biorxiv.org/content/10.1101/233080v1?rss=1 Firtina, C. Bar-Joseph, Z. Alkan, C. Cicek, A. E. 2017-12-13 doi:10.1101/233080 Cold Spring Harbor Laboratory Press 2017-12-13 <![CDATA[ The Streptococcus pneumoniae Competence-Induced BriC Peptide Promotes Nasopharyngeal Colonization and Impacts Biofilm Development ]]> https://biorxiv.org/content/10.1101/245902v1?rss=1 Aggarwal, S. D. Eutsey, R. West-Roberts, J. Domenech, A. Xu, W. Abdullah, I. T. Mitchell, A. P. Veening, J.-W. Yesilkaya, H. Hiller, N. L. 2018-01-24 doi:10.1101/245902 Cold Spring Harbor Laboratory Press 2018-01-24 <![CDATA[ Causal Discovery of Feedback Networks with Functional Magnetic Resonance Imaging ]]> https://biorxiv.org/content/10.1101/245936v1?rss=1 Sanchez-Romero, R. Ramsey, J. D. Zhang, K. Glymour, M. R. K. Huang, B. Glymour, C. 2018-01-10 doi:10.1101/245936 Cold Spring Harbor Laboratory Press 2018-01-10 <![CDATA[ Large-scale two-photon imaging revealed super-sparse population codes in V1 superficial layer of awake monkeys ]]> https://biorxiv.org/content/10.1101/252940v1?rss=1 Tang, S. Zhang, Y. Li, Z. Li, M. Liu, F. Jiang, H. Lee, T. S. 2018-01-25 doi:10.1101/252940 Cold Spring Harbor Laboratory Press 2018-01-25 <![CDATA[ Proteome-scale detection of drug-target interactions using correlations in transcriptomic perturbations ]]> https://biorxiv.org/content/10.1101/254367v1?rss=1 Pabon, N. A. Xia, Y. Estabrooks, S. K. Ye, Z. Herbrand, A. K. Sub, E. Biondi, R. M. Assimon, V. A. Gestwicki, J. E. Brodsky, J. L. Camacho, C. J. Bar-Joseph, Z. 2018-01-25 doi:10.1101/254367 Cold Spring Harbor Laboratory Press 2018-01-25 <![CDATA[ Binding during sequence learning does not alter cortical representations of individual actions ]]> https://biorxiv.org/content/10.1101/255794v1?rss=1 Beukema, P. Diedrichsen, J. Verstynen, T. 2018-01-30 doi:10.1101/255794 Cold Spring Harbor Laboratory Press 2018-01-30 <![CDATA[ Asymptotically optimal minimizers schemes ]]> https://biorxiv.org/content/10.1101/256156v1?rss=1 Marcais, G. DeBlasio, D. Kingsford, C. 2018-01-30 doi:10.1101/256156 Cold Spring Harbor Laboratory Press 2018-01-30 <![CDATA[ Deconvolution and phylogeny inference of structural variations in tumor genomic samples ]]> https://biorxiv.org/content/10.1101/257014v1?rss=1 Eaton, J. Wang, J. Schwartz, R. 2018-01-30 doi:10.1101/257014 Cold Spring Harbor Laboratory Press 2018-01-30 <![CDATA[ Regulation by competition: a hidden layer of gene regulatory network ]]> https://biorxiv.org/content/10.1101/258129v1?rss=1 Yuan, Y. Wei, L. Hu, T. Li, S. Cheng, T. Lei, J. Xie, Z. Zhang, M. Q. Wang, X. 2018-02-01 doi:10.1101/258129 Cold Spring Harbor Laboratory Press 2018-02-01 <![CDATA[ Predicting CTCF-mediated chromatin loops using CTCF-MP ]]> https://biorxiv.org/content/10.1101/259416v1?rss=1 Zhang, R. Wang, Y. Yang, Y. Zhang, Y. Ma, J. 2018-02-02 doi:10.1101/259416 Cold Spring Harbor Laboratory Press 2018-02-02 <![CDATA[ Redundancy makes music and speech robust to individual differences in perception ]]> https://biorxiv.org/content/10.1101/263079v1?rss=1 Jasmin, K. Dick, F. Tierney, A. T. 2018-02-12 doi:10.1101/263079 Cold Spring Harbor Laboratory Press 2018-02-12 <![CDATA[ Targeting redox regulatory site of protein kinase B impedes neutrophilic inflammation ]]> https://biorxiv.org/content/10.1101/264184v1?rss=1 Hwang, T.-L. Chen, P.-J. Ko, I.-L. Lee, C.-L. Hu, H.-C. Chang, F.-R. Wu, Y.-C. Leu, Y.-L. Wu, C.-C. Tsai, Y.-F. Lin, C.-Y. Pan, C.-Y. 2018-02-13 doi:10.1101/264184 Cold Spring Harbor Laboratory Press 2018-02-13 <![CDATA[ Data management and sharing in neuroimaging: Practices and perceptions of MRI researchers ]]> https://biorxiv.org/content/10.1101/266627v1?rss=1 Borghi, J. A. Van Gulick, A. E. 2018-02-18 doi:10.1101/266627 Cold Spring Harbor Laboratory Press 2018-02-18 <![CDATA[ Posterior and Mid-Fusiform Contribute to Distinct Stages of Facial Expression Processing ]]> https://biorxiv.org/content/10.1101/279166v1?rss=1 Li, Y. Richardson, R. M. Ghuman, A. S. 2018-03-08 doi:10.1101/279166 Cold Spring Harbor Laboratory Press 2018-03-08 <![CDATA[ Continuous-trait probabilistic model for comparing multi-species functional genomic data ]]> https://biorxiv.org/content/10.1101/283093v1?rss=1 Yang, Y. Gu, Q. Zhang, Y. Sasaki, T. Crivello, J. O'Neill, R. J. Gilbert, D. M. Ma, J. 2018-03-16 doi:10.1101/283093 Cold Spring Harbor Laboratory Press 2018-03-16 <![CDATA[ Semi-soft Clustering of Single Cell Data ]]> https://biorxiv.org/content/10.1101/285056v1?rss=1 Zhu, L. Lei, J. Devlin, B. Roeder, K. 2018-03-19 doi:10.1101/285056 Cold Spring Harbor Laboratory Press 2018-03-19 <![CDATA[ Reductions in Retrieval Competition Predict the Benefit of Repeated Testing ]]> https://biorxiv.org/content/10.1101/292557v1?rss=1 Rafidi, N. S. Hulbert, J. C. Pacheco, P. Norman, K. A. 2018-03-30 doi:10.1101/292557 Cold Spring Harbor Laboratory Press 2018-03-30 <![CDATA[ Personalized Regression Enables Sample-Specific Pan-Cancer Analysis ]]> https://biorxiv.org/content/10.1101/294496v1?rss=1 Lengerich, B. Aragam, B. Xing, E. P. 2018-04-05 doi:10.1101/294496 Cold Spring Harbor Laboratory Press 2018-04-05 <![CDATA[ Convolutional neural network models of V1 responses to complex patterns ]]> https://biorxiv.org/content/10.1101/296301v1?rss=1 Zhang, Y. Lee, T. S. Li, M. Liu, F. Tang, S. 2018-04-06 doi:10.1101/296301 Cold Spring Harbor Laboratory Press 2018-04-06 <![CDATA[ Molecular mechanisms controlling the multistage post-translational processing of endogenous Nrf1α/TCF11 proteins to yield distinct proteoforms within the coupled positive and negative feedback circuits ]]> https://biorxiv.org/content/10.1101/300327v1?rss=1 Xiang, Y. Wang, M. Hu, S. Qiu, L. Yang, F. Zhang, Z. Yu, S. Pi, J. Zhang, Y. 2018-04-12 doi:10.1101/300327 Cold Spring Harbor Laboratory Press 2018-04-12 <![CDATA[ Computational Modeling of the Dynamic Biomarker Cascade in Alzheimer’s Disease ]]> https://biorxiv.org/content/10.1101/313353v1?rss=1 Petrella, J. Hao, W. Rao, A. Doraiswamy, M. Alzheimer's Disease Computational Modeling Initiative, 2018-05-02 doi:10.1101/313353 Cold Spring Harbor Laboratory Press 2018-05-02 <![CDATA[ Learning the sequence of influenza A genome assembly during viral replication using point process models and fluorescence in situ hybridization ]]> https://biorxiv.org/content/10.1101/322966v1?rss=1 Majarian, T. D. Murphy, R. F. Lakdawala, S. 2018-05-15 doi:10.1101/322966 Cold Spring Harbor Laboratory Press 2018-05-15 <![CDATA[ scQuery: a web server for comparative analysis of single-cell RNA-seq data ]]> https://biorxiv.org/content/10.1101/323238v1?rss=1 Alavi, A. Ruffalo, M. Parvangada, A. Huang, Z. Bar-Joseph, Z. 2018-05-16 doi:10.1101/323238 Cold Spring Harbor Laboratory Press 2018-05-16 <![CDATA[ Molecular Detection of H.pylori Antibiotic-Resistant Genes and Bioinformatics Predictive Analysis ]]> https://biorxiv.org/content/10.1101/325654v1?rss=1 Wang, D. Guo, Q. Lv, Z. Yuan, Y. Gong, Y. 2018-05-18 doi:10.1101/325654 Cold Spring Harbor Laboratory Press 2018-05-18 <![CDATA[ A rational account of human memory search ]]> https://biorxiv.org/content/10.1101/326397v1?rss=1 Zhang, Q. Anderson, J. R. 2018-05-21 doi:10.1101/326397 Cold Spring Harbor Laboratory Press 2018-05-21 <![CDATA[ Coupled Mixed Model for joint genetic analysis of complex disorders from independently collected data sets: application to Alzheimer’s disease and substance use disorder ]]> https://biorxiv.org/content/10.1101/336727v1?rss=1 Wang, H. Liu, M. Lee, S. Vanyukov, M. M. Wu, W. Xing, E. P. 2018-06-01 doi:10.1101/336727 Cold Spring Harbor Laboratory Press 2018-06-01 <![CDATA[ Memory for non-painful auditory items is influenced by whether they are experienced in a context involving painful electrical stimulation ]]> https://biorxiv.org/content/10.1101/341891v1?rss=1 Vogt, K. M. Norton, C. M. Speer, L. E. Tremel, J. J. Ibinson, J. W. Reder, L. M. Fiez, J. A. 2018-06-08 doi:10.1101/341891 Cold Spring Harbor Laboratory Press 2018-06-08 <![CDATA[ Automatically eliminating errors induced by suboptimal parameter choices in transcript assembly ]]> https://biorxiv.org/content/10.1101/342865v1?rss=1 DeBlasio, D. Kingsford, C. 2018-06-08 doi:10.1101/342865 Cold Spring Harbor Laboratory Press 2018-06-08 <![CDATA[ Determinants of base-pair substitution patterns revealed by whole-genome sequencing of DNA mismatch repair defective Escherichia coli ]]> https://biorxiv.org/content/10.1101/346874v1?rss=1 G:C transitions, which occurred predominantly at the center base of 5'NAC3'+5'GTN3' triplets. Surprisingly, growth on minimal medium or at low temperature attenuated these mutations. Mononucleotide runs were also hotspots for base-pair substitutions, and the rate at which these occurred increased with run length. Comparison with {approx}2000 base-pair substitutions accumulated in MMR-proficient strains revealed that both kinds of hotspots appeared in the wild-type spectrum and so are likely to be sites of frequent replication errors. In MMR-defective strains transitions were strand biased, occurring twice as often when A and C rather than T and G were on the lagging-strand template. Loss of nucleotide diphosphate kinase increases the cellular concentration of dCTP, which resulted in increased rates of mutations due to misinsertion of C opposite A and T. In an mmr ndk double mutant strain, these mutations were more frequent when the template A and T were on the leading strand, suggesting that lagging-strand synthesis was more error-prone or less well corrected by proofreading than was leading strand synthesis. ]]> Foster, P. L. Niccum, B. A. Popodi, E. Townes, J. P. Lee, H. MohammedIsmail, W. Tang, H. 2018-06-14 doi:10.1101/346874 Cold Spring Harbor Laboratory Press 2018-06-14 <![CDATA[ A computational strategy for finding novel targets and therapeutic compounds for opioid dependence ]]> https://biorxiv.org/content/10.1101/359075v1?rss=1 Wu, X. Xie, S. Wang, L. Fan, P. Ge, S. Xie, X. Wu, W. 2018-06-29 doi:10.1101/359075 Cold Spring Harbor Laboratory Press 2018-06-29 <![CDATA[ G-quadruplex dynamics contribute to epigenetic regulation of mitochondrial function ]]> https://biorxiv.org/content/10.1101/359703v1?rss=1 Falabella, M. Kolesar, J. E. Xiang, I. M. Wang, T. Horne, W. Wallace, C. Sun, L. Taguchi, Y. Wang, C. Turek-Herman, J. St Croix, C. Sondheimer, N. Yatsunyk, L. Johnson, F. B. Kaufman, B. 2018-07-13 doi:10.1101/359703 Cold Spring Harbor Laboratory Press 2018-07-13 <![CDATA[ CNNC: Convolutional Neural Networks for Co-Expression Analysis ]]> https://biorxiv.org/content/10.1101/365007v1?rss=1 Yuan, Y. Bar-Joseph, Z. 2018-07-08 doi:10.1101/365007 Cold Spring Harbor Laboratory Press 2018-07-08 <![CDATA[ Coordinative Metabolism of Glutamine Carbon and Nitrogen in proliferating Cancer Cells Under Hypoxia ]]> https://biorxiv.org/content/10.1101/373720v1?rss=1 Wang, Y. Bai, C. Ruan, Y. Liu, M. Chu, Q. Qiu, L. Yang, C. Li, B. 2018-07-20 doi:10.1101/373720 Cold Spring Harbor Laboratory Press 2018-07-20 <![CDATA[ Using multiple measurements of tissue to estimate individual- and cell-type-specific gene expression via deconvolution ]]> https://biorxiv.org/content/10.1101/379099v1?rss=1 Wang, J. Devlin, B. Roeder, K. 2018-07-27 doi:10.1101/379099 Cold Spring Harbor Laboratory Press 2018-07-27 <![CDATA[ Continuous State HMMs for Modeling Time Series Single Cell RNA-Seq Data ]]> https://biorxiv.org/content/10.1101/380568v1?rss=1 Lin, C. Bar-Joseph, Z. 2018-07-30 doi:10.1101/380568 Cold Spring Harbor Laboratory Press 2018-07-30 <![CDATA[ Fine-mapping cis-regulatory variants in diverse human populations ]]> https://biorxiv.org/content/10.1101/384396v1?rss=1 Tehranchi, A. Hie, B. Dacre, M. Kaplow, I. Pettie, K. Combs, P. Fraser, H. B. 2018-08-03 doi:10.1101/384396 Cold Spring Harbor Laboratory Press 2018-08-03 <![CDATA[ Quantitative synapse analysis for cell-type specific connectomics ]]> https://biorxiv.org/content/10.1101/386912v1?rss=1 Kuljis, D. A. Zemoura, K. Telmer, C. A. Lee, J. Park, E. Ackerman, D. S. Xu, W. Watkins, S. C. Arnold, D. B. Bruchez, M. P. Barth, A. L. 2018-08-07 doi:10.1101/386912 Cold Spring Harbor Laboratory Press 2018-08-07 <![CDATA[ S100A4 inhibits cell proliferation by interfering with the RAGE V domain-S100A1 ]]> https://biorxiv.org/content/10.1101/391136v1?rss=1 Yu, C. Khan, M. I. Yuan, T. Chou, R.-H. 2018-08-13 doi:10.1101/391136 Cold Spring Harbor Laboratory Press 2018-08-13 <![CDATA[ An algorithm for automated, noninvasive detection of cortical spreading depolarizations based on EEG simulations ]]> https://biorxiv.org/content/10.1101/393058v1?rss=1 Chamanzar, A. George, S. Venkatesh, P. Chamanzar, M. Shutter, L. Elmer, J. Grover, P. 2018-08-16 doi:10.1101/393058 Cold Spring Harbor Laboratory Press 2018-08-16 <![CDATA[ Epigallocatechin-3-gallate yield in different temperature gradients in green tea (Camellia sinensis) brewing ]]> https://biorxiv.org/content/10.1101/396234v1?rss=1 Hsieh, M.-h. Hsieh, M.-j. Wu, C.-R. Peng, W.-h. Hsieh, M.-t. Hsieh, C.-c. 2018-08-20 doi:10.1101/396234 Cold Spring Harbor Laboratory Press 2018-08-20 <![CDATA[ Ex vivo dynamics of human glioblastoma cells in a microvasculature-on-a-chip system correlates with tumor heterogeneity and subtypes ]]> https://biorxiv.org/content/10.1101/400739v1?rss=1 Xiao, Y. Kim, D. Dura, B. Zhang, K. Yan, R. Li, H. Han, E. Ip, J. Zou, P. Liu, J. Chen, A. T. Vortmeyer, A. O. Zhou, J. Fan, R. 2018-09-03 doi:10.1101/400739 Cold Spring Harbor Laboratory Press 2018-09-03 <![CDATA[ Cell lineage inference from SNP and scRNA-Seq data ]]> https://biorxiv.org/content/10.1101/401943v1?rss=1 Ding, J. Lin, C. Bar-Joseph, Z. 2018-08-30 doi:10.1101/401943 Cold Spring Harbor Laboratory Press 2018-08-30 <![CDATA[ Learning Gene Networks Underlying Clinical Phenotypes Using SNP Perturbations ]]> https://biorxiv.org/content/10.1101/412817v1?rss=1 McCarter, C. Howrylak, J. Kim, S. 2018-09-10 doi:10.1101/412817 Cold Spring Harbor Laboratory Press 2018-09-10 <![CDATA[ Identifying functional targets from transcription factor binding data using SNP perturbation ]]> https://biorxiv.org/content/10.1101/412841v1?rss=1 Xiang, J. Kim, S. 2018-09-10 doi:10.1101/412841 Cold Spring Harbor Laboratory Press 2018-09-10 <![CDATA[ The Synergistic Effect of Antioxidant Interaction between Luteolin and Chlorogenic Acid in Lonicera japonica ]]> https://biorxiv.org/content/10.1101/418319v1?rss=1 Hsieh, M.-H. Hsieh, M.-j. Wu, C.-R. Peng, W.-H. Hsieh, M.-T. Hsieh, C.-C. 2018-09-14 doi:10.1101/418319 Cold Spring Harbor Laboratory Press 2018-09-14 <![CDATA[ Reward-driven changes in striatal pathway competition shape evidence evaluation in decision-making ]]> https://biorxiv.org/content/10.1101/418756v1?rss=1 Dunovan, K. Vich, C. Clapp, M. Verstynen, T. Rubin, J. 2018-09-17 doi:10.1101/418756 Cold Spring Harbor Laboratory Press 2018-09-17 <![CDATA[ Exploring spatio-temporal neural dynamics of the human visual cortex ]]> https://biorxiv.org/content/10.1101/422576v1?rss=1 Yang, Y. Tarr, M. J. Kass, R. E. Aminoff, E. M. 2018-09-20 doi:10.1101/422576 Cold Spring Harbor Laboratory Press 2018-09-20 <![CDATA[ BrainNet: A Multi-Person Brain-to-Brain Interface for Direct Collaboration Between Brains ]]> https://biorxiv.org/content/10.1101/425066v1?rss=1 Jiang, L. Stocco, A. Losey, D. M. Abernethy, J. A. Prat, C. Rao, R. P. N. 2018-09-26 doi:10.1101/425066 Cold Spring Harbor Laboratory Press 2018-09-26 <![CDATA[ Dynamic interaction network inference from longitudinal microbiome data ]]> https://biorxiv.org/content/10.1101/430462v1?rss=1 Lugo-Martinez, J. Ruiz-Perez, D. Narasimhan, G. Bar-Joseph, Z. 2018-09-29 doi:10.1101/430462 Cold Spring Harbor Laboratory Press 2018-09-29 <![CDATA[ Automatic Human-like Mining and Constructing Reliable Genetic Association Database with Deep Reinforcement Learning ]]> https://biorxiv.org/content/10.1101/434803v1?rss=1 Wang, H. Liu, X. Tao, Y. Ye, W. Jin, Q. Cohen, W. W. Xing, E. P. 2018-10-05 doi:10.1101/434803 Cold Spring Harbor Laboratory Press 2018-10-05 <![CDATA[ High local mutual information drives the response in the human language network ]]> https://biorxiv.org/content/10.1101/436204v1?rss=1 Mollica, F. Siegelman, M. Diachek, E. Piantadosi, S. T. Mineroff, Z. Futrell, R. Fedorenko, E. 2018-10-08 doi:10.1101/436204 Cold Spring Harbor Laboratory Press 2018-10-08 <![CDATA[ Removing Confounding Factors Associated Weights in Deep Neural Networks Improves the Prediction Accuracy for Healthcare Applications ]]> https://biorxiv.org/content/10.1101/442442v1?rss=1 Wang, H. Wu, Z. Xing, E. 2018-10-13 doi:10.1101/442442 Cold Spring Harbor Laboratory Press 2018-10-13 <![CDATA[ Microbiota-dependent elevation of Alcohol Dehydrogenase in Drosophila is associated with changes in alcohol-induced hyperactivity and alcohol preference ]]> https://biorxiv.org/content/10.1101/444471v1?rss=1 Blundon, M. A. Park, A. Keith, S. Oliver, S. L. Eutsey, R. A. Pyzel, A. M. Lau, T. W. Huang, J. H. Kolev, H. M. Hiller, N. L. Atkinson, N. S. Minden, J. S. McCartney, B. M. 2018-10-16 doi:10.1101/444471 Cold Spring Harbor Laboratory Press 2018-10-16 <![CDATA[ Comparative Pathway Integrator: a framework of meta-analytic integration of multiple transcriptomic studies for consensual and differential pathway analysis ]]> https://biorxiv.org/content/10.1101/444604v1?rss=1 Zeng, X. Fang, Z. Ma, T. Lin, C.-W. Tseng, G. 2018-10-16 doi:10.1101/444604 Cold Spring Harbor Laboratory Press 2018-10-16 <![CDATA[ HiAlc Klebsiella pneumonia, one of potential chief culprits of non-alcoholic fatty liver disease: through generation of endogenous ethanol ]]> https://biorxiv.org/content/10.1101/446765v1?rss=1 Wei, X. Zhao, X. Chen, C. Lu, J. Cheng, W. Li, B. Li, H. Lin, W. Tian, C. An, D. Han, J. Ma, X. Li, W. Wang, X. Chen, X. Zhao, J. Zhang, Z. Zeng, H. Sun, Y. Liu, D. Yang, R. Yuan, J. 2018-10-19 doi:10.1101/446765 Cold Spring Harbor Laboratory Press 2018-10-19 <![CDATA[ Anterior insular cortex plays a critical role in interoceptive attention ]]> https://biorxiv.org/content/10.1101/464867v1?rss=1 Wang, X. Wu, Q. Egan, L. Gu, X. Liu, P. Yang, Y. Gu, H. Luo, J. Wu, Y. Gao, Z. Fan, J. 2018-11-07 doi:10.1101/464867 Cold Spring Harbor Laboratory Press 2018-11-07 <![CDATA[ Sketching Algorithms for Genomic Data Analysis and Querying in a Secure Enclave ]]> https://biorxiv.org/content/10.1101/468355v1?rss=1 Kockan, C. Zhu, K. Dokmai, N. Karpov, N. Kulekci, O. Woodruff, D. Sahinalp, C. 2018-11-12 doi:10.1101/468355 Cold Spring Harbor Laboratory Press 2018-11-12 <![CDATA[ Novel genes for autism implicate both excitatory and inhibitory cell lineages in risk ]]> https://biorxiv.org/content/10.1101/484113v1?rss=1 Satterstrom, F. K. Kosmicki, J. A. Wang, J. Breen, M. De Rubeis, S. An, J.-Y. Peng, M. Collins, R. L. Grove, J. Klei, L. Stevens, C. Reichert, J. Mulhern, M. Artomov, M. Gerges, S. Sheppard, B. Xu, X. Bhaduri, A. Norman, U. Brand, H. Schwartz, G. Nguyen, R. Guerrero, E. Dias, C. Aleksic, B. Anney, R. J. Barbosa, M. Bishop, S. Brusco, A. Bybjerg-Grauholm, J. Carracedo, A. Chan, M. C. Y. Chiocchetti, A. Chung, B. Coon, H. Cuccaro, M. Curro, A. Dalla Bernardina, B. Doan, R. Domenici, E. Dong, S. Fallerini, C. Fernandez-Prieto, M. Ferrero, G. B. Freitag, 2018-11-30 doi:10.1101/484113 Cold Spring Harbor Laboratory Press 2018-11-30 <![CDATA[ A Strategy Study on Risk Communication of Pandemic Influenza ----A Mental Model Study of College Students in Beijing ]]> https://biorxiv.org/content/10.1101/490532v1?rss=1 Yang, H. Wang, L. Wang, Y. Zheng, B. Du, S. Lu, X. 2018-12-07 doi:10.1101/490532 Cold Spring Harbor Laboratory Press 2018-12-07 <![CDATA[ Analysis of the structural variability of topologically associated domains as revealed by Hi-C ]]> https://biorxiv.org/content/10.1101/498972v1?rss=1 Sauerwald, N. Singhal, A. Kingsford, C. 2018-12-18 doi:10.1101/498972 Cold Spring Harbor Laboratory Press 2018-12-18 <![CDATA[ Low-Density Lipoprotein Receptor-Mediated Lipidome-Transcriptome Reprogramming Impulses to Cisplatin Insensitivity ]]> https://biorxiv.org/content/10.1101/502401v1?rss=1 Chang, W.-C. Wang, H.-C. Cheng, W.-C. Yang, J.-C. Chung, W.-M. Chen, L. Ho, Y.-P. Hung, Y.-C. Ma, W.-L. 2018-12-21 doi:10.1101/502401 Cold Spring Harbor Laboratory Press 2018-12-21 <![CDATA[ The self-organization model reveals systematic characteristics of aging ]]> https://biorxiv.org/content/10.1101/502815v1?rss=1 Wang, Y. Huang, T. Sha, X. Li, Y. Xing, C. 2018-12-20 doi:10.1101/502815 Cold Spring Harbor Laboratory Press 2018-12-20 <![CDATA[ Revealing Hi-C subcompartments by imputing high-resolution inter-chromosomal chromatin interactions ]]> https://biorxiv.org/content/10.1101/505503v1?rss=1 Xiong, K. Ma, J. 2018-12-23 doi:10.1101/505503 Cold Spring Harbor Laboratory Press 2018-12-23 <![CDATA[ Tumor Copy Number Deconvolution Integrating Bulk and Single-Cell Sequencing Data ]]> https://biorxiv.org/content/10.1101/519892v1?rss=1 Lei, H. Lyu, B. Gertz, E. M. Schaeffer, A. A. Shi, X. Wu, K. Li, G. Xu, L. Hu, Y. Dean, M. Schwartz, R. 2019-01-16 doi:10.1101/519892 Cold Spring Harbor Laboratory Press 2019-01-16 <![CDATA[ Identification and mitigation of pervasive off-target activity in CRISPR-Cas9 screens for essential non-coding elements ]]> https://biorxiv.org/content/10.1101/520569v1?rss=1 Tycko, J. Wainberg, M. Marinov, G. K. Ursu, O. Hess, G. T. Ego, B. K. Aradhana, Li, A. Truong, A. Trevino, A. E. Spees, K. Yao, D. Kaplow, I. M. Greenside, P. G. Morgens, D. W. Phanstiel, D. H. Snyder, M. P. Bintu, L. Greenleaf, W. J. Kundaje, A. Bassik, M. C. 2019-01-18 doi:10.1101/520569 Cold Spring Harbor Laboratory Press 2019-01-18 <![CDATA[ De Novo Peptide Sequencing Reveals a Vast Cyclopeptidome in Human Gut and Other Environments ]]> https://biorxiv.org/content/10.1101/521872v1?rss=1 Behsaz, B. Mohimani, H. Gurevich, A. Prjibelski, A. Fisher, M. F. Smarr, L. Dorrestein, P. C. Mylne, J. S. Pevzner, P. A. 2019-01-16 doi:10.1101/521872 Cold Spring Harbor Laboratory Press 2019-01-16 <![CDATA[ Image-derived Models of Cell Organization Changes During Differentiation of PC12 Cells ]]> https://biorxiv.org/content/10.1101/522763v1?rss=1 Ruan, X. Johnson, G. R. Bierschenk, I. Nitschke, R. Boerries, M. Busch, H. Murphy, R. F. 2019-01-16 doi:10.1101/522763 Cold Spring Harbor Laboratory Press 2019-01-16 <![CDATA[ The symmetrical pattern of base-pair substitutions rates across the chromosome in Escherichia coli has multiple causes ]]> https://biorxiv.org/content/10.1101/523696v1?rss=1 Niccum, B. A. Lee, H. MohammedIsmail, W. Tang, H. Foster, P. L. 2019-01-17 doi:10.1101/523696 Cold Spring Harbor Laboratory Press 2019-01-17 <![CDATA[ Impoverished auditory cues fail to engage brain networks controlling spatial selective attention ]]> https://biorxiv.org/content/10.1101/533117v1?rss=1 Deng, Y. Choi, I. Shinn-Cunningham, B. G. Baumgartner, R. 2019-01-29 doi:10.1101/533117 Cold Spring Harbor Laboratory Press 2019-01-29 <![CDATA[ Locality sensitive hashing for the edit distance ]]> https://biorxiv.org/content/10.1101/534446v1?rss=1 Marcais, G. DeBlasio, D. Pandey, P. Kingsford, C. 2019-01-29 doi:10.1101/534446 Cold Spring Harbor Laboratory Press 2019-01-29 <![CDATA[ Topological data analysis reveals principles of chromosome structure throughout cellular differentiation ]]> https://biorxiv.org/content/10.1101/540716v1?rss=1 Sauerwald, N. Shen, Y. Kingsford, C. 2019-02-05 doi:10.1101/540716 Cold Spring Harbor Laboratory Press 2019-02-05 <![CDATA[ Detecting anomalies in RNA-seq quantification ]]> https://biorxiv.org/content/10.1101/541714v1?rss=1 Ma, C. Kingsford, C. 2019-02-05 doi:10.1101/541714 Cold Spring Harbor Laboratory Press 2019-02-05 <![CDATA[ MOCHI enables discovery of heterogeneous interactome modules in 3D nucleome ]]> https://biorxiv.org/content/10.1101/542092v1?rss=1 Tian, D. Zhang, R. Zhang, Y. Zhu, X. Ma, J. 2019-02-07 doi:10.1101/542092 Cold Spring Harbor Laboratory Press 2019-02-07 <![CDATA[ Differential Principal Components Reveal Patterns of Differentiation in Case/Control Studies ]]> https://biorxiv.org/content/10.1101/545798v1?rss=1 Lengerich, B. Xing, E. P. 2019-02-10 doi:10.1101/545798 Cold Spring Harbor Laboratory Press 2019-02-10 <![CDATA[ Corticostriatal synaptic weight evolution in a two-alternative forced choice task ]]> https://biorxiv.org/content/10.1101/549253v1?rss=1 Vich, C. Dunovan, K. Verstynen, T. V. Rubin, J. 2019-02-13 doi:10.1101/549253 Cold Spring Harbor Laboratory Press 2019-02-13 <![CDATA[ Comparing 3D genome organization in multiple species using Phylo-HMRF ]]> https://biorxiv.org/content/10.1101/552505v1?rss=1 Yang, Y. Zhang, Y. Ren, B. Dixon, J. Ma, J. 2019-02-19 doi:10.1101/552505 Cold Spring Harbor Laboratory Press 2019-02-19 <![CDATA[ Build a better mouse task: can an open-source rodent joystick enhance reaching behavior outcomes through improved monitoring of real-time spatiotemporal kinematics? ]]> https://biorxiv.org/content/10.1101/560961v1?rss=1 Belsey, P. Nicholas, M. A. Yttri, E. A. 2019-02-25 doi:10.1101/560961 Cold Spring Harbor Laboratory Press 2019-02-25 <![CDATA[ Identification of Microbiota-Induced Gene Expression Changes in the Drosophila melanogaster Head ]]> https://biorxiv.org/content/10.1101/561043v1?rss=1 Keith, S. A. Eutsey, R. Lee, H. Solomon, B. Oliver, S. Kingsford, C. Hiller, N. L. McCartney, B. M. 2019-02-25 doi:10.1101/561043 Cold Spring Harbor Laboratory Press 2019-02-25 <![CDATA[ Non-Invasive Assays of Cochlear Synaptopathy -- Candidates and Considerations ]]> https://biorxiv.org/content/10.1101/565655v1?rss=1 Bharadwaj, H. M. Mai, A. R. Simpson, J. M. Choi, I. Heinz, M. G. Shinn-Cunningham, B. G. 2019-03-05 doi:10.1101/565655 Cold Spring Harbor Laboratory Press 2019-03-05 <![CDATA[ Stalk Lodging: A Portable Device for Phenotyping Stalk Bending Strength of Maize and Sorghum ]]> https://biorxiv.org/content/10.1101/567578v1?rss=1 Cook, D. D. de la Chapelle, W. Lin, T.-C. Lee, S. Y. Sun, W. Robertson, D. J. 2019-03-05 doi:10.1101/567578 Cold Spring Harbor Laboratory Press 2019-03-05 <![CDATA[ Microsecond Molecular Dynamics Simulations of Diphtheria Toxin Translocation T-Domain pH-Dependent Unfolding in Solution ]]> https://biorxiv.org/content/10.1101/572040v1?rss=1 Flores-Canales, J. C. Simakov, N. A. Kurnikova, M. G. 2019-03-08 doi:10.1101/572040 Cold Spring Harbor Laboratory Press 2019-03-08 <![CDATA[ Developmental transcriptomes of the sea star, Patiria miniata, illuminate the relationship between conservation of gene expression and morphological conservation ]]> https://biorxiv.org/content/10.1101/573741v1?rss=1 Gildor, T. Cary, G. Lalzar, M. Hinman, V. Ben-Tabou de-Leon, S. 2019-03-11 doi:10.1101/573741 Cold Spring Harbor Laboratory Press 2019-03-11 <![CDATA[ Maximum Likelihood Reconstruction of Ancestral Networks by Integer Linear Programming ]]> https://biorxiv.org/content/10.1101/574814v1?rss=1 Rajan, V. Kingsford, C. Zhang, X. 2019-03-13 doi:10.1101/574814 Cold Spring Harbor Laboratory Press 2019-03-13 <![CDATA[ Intrinsic Cell-type Selectivity and Inter-neuronal Connectivity Alteration by Transcranial Focused Ultrasound ]]> https://biorxiv.org/content/10.1101/576066v1?rss=1 Yu, K. Niu, X. Krook-Magnuson, E. He, B. 2019-03-12 doi:10.1101/576066 Cold Spring Harbor Laboratory Press 2019-03-12 <![CDATA[ Inhibition of Osteoblast Proliferation and Migration by Exogenous and Endogenous Formaldehyde ]]> https://biorxiv.org/content/10.1101/584052v1?rss=1 Teng, X. Huang, W. Yu, H. Wang, P. Li, W. Chen, Z. Fan, D. 2019-03-20 doi:10.1101/584052 Cold Spring Harbor Laboratory Press 2019-03-20 <![CDATA[ Whole-genome and RNA sequencing reveal variation and transcriptomic coordination in the developing human prefrontal cortex ]]> https://biorxiv.org/content/10.1101/585430v1?rss=1 Werling, D. Pochareddy, S. Choi, J. An, J. Y. Sheppard, B. Peng, M. Li, Z. Dastmalchi, C. Santperebaro, G. Sousa, A. Tebbenkamp, A. Kaur, N. Gulden, F. Breen, M. Liang, L. Gilson, M. Zhao, X. Dong, S. Klei, L. Cicek, A. E. Buxbaum, J. Adle-Biassette, H. Thomas, J.-L. Aldinger, K. A. O'Day, D. R. Glass, I. Zaitlen, N. Talkowski, M. Roeder, K. State, M. W. Devlin, B. Sanders, S. Sestan, N. 2019-03-22 doi:10.1101/585430 Cold Spring Harbor Laboratory Press 2019-03-22 <![CDATA[ A Molecular Link between Cell Wall Modification and Stringent Response in a Gram-positive Bacteria ]]> https://biorxiv.org/content/10.1101/622340v1?rss=1 Aggarwal, S. D. Yerneni, S. S. Narciso, A. R. Filipe, S. R. Hiller, N. L. 2019-04-29 doi:10.1101/622340 Cold Spring Harbor Laboratory Press 2019-04-29 <![CDATA[ A flexible simulation toolkit for designing and evaluating ChIP-sequencing experiments ]]> https://biorxiv.org/content/10.1101/624486v1?rss=1 Zheng, A. Lamkin, M. Qiu, Y. Ren, K. Goren, A. Gymrek, M. 2019-05-01 doi:10.1101/624486 Cold Spring Harbor Laboratory Press 2019-05-01 <![CDATA[ Single-cell Lineage Tracing by Integrating CRISPR-Cas9 Mutations with Transcriptomic Data ]]> https://biorxiv.org/content/10.1101/630814v1?rss=1 Zafar, H. Lin, C. Bar-Joseph, Z. 2019-05-07 doi:10.1101/630814 Cold Spring Harbor Laboratory Press 2019-05-07 <![CDATA[ Multi-resolution localization of causal variants across the genome ]]> https://biorxiv.org/content/10.1101/631390v1?rss=1 Sesia, M. Katsevich, E. Bates, S. Candes, E. Sabatti, C. 2019-05-08 doi:10.1101/631390 Cold Spring Harbor Laboratory Press 2019-05-08 <![CDATA[ Quantifying the Benefit Offered by Transcript Assembly on Single-Molecule Long Reads ]]> https://biorxiv.org/content/10.1101/632703v1?rss=1 Tung, L. H. Shao, M. Kingsford, C. 2019-05-10 doi:10.1101/632703 Cold Spring Harbor Laboratory Press 2019-05-10 <![CDATA[ Entecavir resistance mutations rtL180M/T184L/M204V combined with rtA200V lead to tenofovir resistance ]]> https://biorxiv.org/content/10.1101/632984v1?rss=1 Jiang, D. Wang, J. Zhao, X. Li, Y. Zhang, Q. Song, C. Zeng, H. Wang, X. 2019-05-13 doi:10.1101/632984 Cold Spring Harbor Laboratory Press 2019-05-13 <![CDATA[ Liquid condensation drives telomere clustering during ALT ]]> https://biorxiv.org/content/10.1101/633040v1?rss=1 Zhang, H. Liu, M. Dilley, R. Chenoweth, D. M. Greenberg, R. A. Lampson, M. A. 2019-05-09 doi:10.1101/633040 Cold Spring Harbor Laboratory Press 2019-05-09 <![CDATA[ Landscape of tumor-infiltrating immune cells in human immunogenic cancers: B cells are inversely associated with CD8T cells, but positively correlated with Treg cells ]]> https://biorxiv.org/content/10.1101/641712v1?rss=1 Chae, Y. K. Bae, W. Jung, M. Kim, Y. S. Anker, J. F. Tamragouri, K. Matsangou, M. Giles, F. J. 2019-05-17 doi:10.1101/641712 Cold Spring Harbor Laboratory Press 2019-05-17 <![CDATA[ Bimodal Regulation of the PRC2 Complex by USP7 Underlies Melanomagenesis ]]> https://biorxiv.org/content/10.1101/641977v1?rss=1 Su, D. Wang, W. Hou, Y. Wang, L. Wang, Y. Yang, C. Liu, B. Chen, X. Wu, X. Wu, J. Yan, D. Wei, S. Han, L. Liu, S. Shi, L. Shan, L. 2019-05-18 doi:10.1101/641977 Cold Spring Harbor Laboratory Press 2019-05-18 <![CDATA[ Dissociation of disease phenotype and allele silencing in hypertrophic cardiomyopathy ]]> https://biorxiv.org/content/10.1101/642421v1?rss=1 Dainis, A. Zaleta-Rivera, K. Ribeiro, A. Chang, A. C. H. Shang, C. Lan, F. Burridge, P. W. Wu, J. C. Chang, A. C. Y. Pruitt, B. L. Wheeler, M. Ashley, E. 2019-06-12 doi:10.1101/642421 Cold Spring Harbor Laboratory Press 2019-06-12 <![CDATA[ Context-Aware Seeds for Read Mapping ]]> https://biorxiv.org/content/10.1101/643072v1?rss=1 Xin, H. Shao, M. Kingsford, C. 2019-05-20 doi:10.1101/643072 Cold Spring Harbor Laboratory Press 2019-05-20 <![CDATA[ Age-Related Changes in Neural Networks Supporting Complex Visual and Social Processing in Adolescence ]]> https://biorxiv.org/content/10.1101/650887v1?rss=1 Lerner, Y. Scherf, S. Katkov, M. Hasson, U. Behrmann, M. 2019-05-27 doi:10.1101/650887 Cold Spring Harbor Laboratory Press 2019-05-27 <![CDATA[ Practical universal k-mer sets for minimizer schemes ]]> https://biorxiv.org/content/10.1101/652925v1?rss=1 DeBlasio, D. Gbosibo, F. Kingsford, C. Marcais, G. 2019-05-30 doi:10.1101/652925 Cold Spring Harbor Laboratory Press 2019-05-30 <![CDATA[ Alignment and mapping methodology influence transcript abundance estimation ]]> https://biorxiv.org/content/10.1101/657874v1?rss=1 Srivastava, A. Malik, L. Zakeri, M. Sarkar, H. Soneson, C. Love, M. I. Kingsford, C. Patro, R. 2019-06-03 doi:10.1101/657874 Cold Spring Harbor Laboratory Press 2019-06-03 <![CDATA[ Shared and Distinct Dysfunction of Dynamic Connectivity Networks across Schizophrenia, Bipolar Disorder and Major Depression Disorder ]]> https://biorxiv.org/content/10.1101/670562v1?rss=1 Li, C. Xu, K. Wei, Y. Duan, J. Han, S. Feng, R. Chen, Y. Zhang, L. Jiang, X. Wei, S. Chen, H. Tang, Y. Wang, F. 2019-06-13 doi:10.1101/670562 Cold Spring Harbor Laboratory Press 2019-06-13 <![CDATA[ NMDA receptor in vasopressin 1b neurons is not required for short-term social memory, object memory or aggression. ]]> https://biorxiv.org/content/10.1101/670893v1?rss=1 Williams Avram, S. Fastman, J. Cymerblit-Sabba, A. Smith, A. Vincent, M. Song, J. Lee, H.-J. Granovetter, M. Lee, S. H. Cilz, N. Stackmann, M. Chaturvedi, R. Young, W. S. 2019-06-13 doi:10.1101/670893 Cold Spring Harbor Laboratory Press 2019-06-13 <![CDATA[ A way around the exploration-exploitation dilemma ]]> https://biorxiv.org/content/10.1101/671362v1?rss=1 Peterson, E. J. Verstynen, T. V. 2019-06-14 doi:10.1101/671362 Cold Spring Harbor Laboratory Press 2019-06-14 <![CDATA[ Increased O-GlcNAcylation rapidly decreases GABAAR currents in hippocampus yet depresses neuronal output ]]> https://biorxiv.org/content/10.1101/672055v1?rss=1 Stewart, L. T. Abiraman, K. Chatham, J. C. McMahon, L. L. 2019-06-15 doi:10.1101/672055 Cold Spring Harbor Laboratory Press 2019-06-15 <![CDATA[ Weak neural signatures of spatial selective auditory attention in hearing-impaired listeners ]]> https://biorxiv.org/content/10.1101/675595v1?rss=1 Bonacci, L. M. Dai, L. Shinn-Cunningham, B. G. 2019-06-26 doi:10.1101/675595 Cold Spring Harbor Laboratory Press 2019-06-26 <![CDATA[ Topographic specificity of alpha power during auditory spatial attention ]]> https://biorxiv.org/content/10.1101/681361v1?rss=1 Deng, Y. Choi, I. Shinn-Cunningham, B. 2019-06-24 doi:10.1101/681361 Cold Spring Harbor Laboratory Press 2019-06-24 <![CDATA[ Non-spatial features reduce the reliance on sustained spatial auditory attention ]]> https://biorxiv.org/content/10.1101/682088v1?rss=1 Bonacci, L. M. Bressler, S. Shinn-Cunningham, B. G. 2019-06-26 doi:10.1101/682088 Cold Spring Harbor Laboratory Press 2019-06-26 <![CDATA[ MAP2 is Hyperphosphorylated in Schizophrenia and Alters its Function ]]> https://biorxiv.org/content/10.1101/683912v1?rss=1 Grubisha, M. J. Sun, X. MacDonald, M. L. Garver, M. Sun, Z. DeGiosio, R. A. Lewis, D. A. Nates, N. A. Camacho, C. Ding, Y. Sweet, R. A. 2019-06-27 doi:10.1101/683912 Cold Spring Harbor Laboratory Press 2019-06-27 <![CDATA[ Area compressibility moduli of the monolayer leaflets of asymmetric bilayers from simulations ]]> https://biorxiv.org/content/10.1101/689679v1?rss=1 Nagle, J. F. 2019-07-05 doi:10.1101/689679 Cold Spring Harbor Laboratory Press 2019-07-05 <![CDATA[ Effects of unilateral cortical resection of the visual cortex on bilateral human white matter ]]> https://biorxiv.org/content/10.1101/689778v1?rss=1 Maallo, A. M. S. Freud, E. Liu, T. T. Patterson, C. Behrmann, M. 2019-07-03 doi:10.1101/689778 Cold Spring Harbor Laboratory Press 2019-07-03 <![CDATA[ Detecting Transcriptomic Structural Variants in Heterogeneous Contexts via the Multiple Compatible Arrangements Problem ]]> https://biorxiv.org/content/10.1101/697367v1?rss=1 1 to satisfy all edges and show such structures are prevalent in cancer samples. We evaluate our algorithms on 381 TCGA samples and 2 cancer cell lines and show improved performance compared to the state-of-the-art TSV-calling tool, SQUID. ]]> Qiu, Y. Ma, C. Xie, H. Kingsford, C. 2019-07-09 doi:10.1101/697367 Cold Spring Harbor Laboratory Press 2019-07-09 <![CDATA[ A Common Architecture for Human and Artificial Cognition Explains Brain Activity Across Domains ]]> https://biorxiv.org/content/10.1101/703777v1?rss=1 Stocco, A. Steine-Hanson, Z. Koh, N. Laird, J. Lebiere, C. Rosenbloom, P. 2019-07-16 doi:10.1101/703777 Cold Spring Harbor Laboratory Press 2019-07-16 <![CDATA[ Neural Taskonomy: Inferring the Similarity of Task-Derived Representations from Brain Activity ]]> https://biorxiv.org/content/10.1101/708016v1?rss=1 Wang, A. Y. Wehbe, L. Tarr, M. J. 2019-07-19 doi:10.1101/708016 Cold Spring Harbor Laboratory Press 2019-07-19 <![CDATA[ Functional innovation in the evolution of the calcium-dependent system of the eukaryotic endoplasmic reticulum ]]> https://biorxiv.org/content/10.1101/716472v1?rss=1 Schäffer, D. E. Iyer, L. M. Burroughs, A. M. Aravind, L. 2019-07-26 doi:10.1101/716472 Cold Spring Harbor Laboratory Press 2019-07-26 <![CDATA[ Post-EMT: Cadherin-11 mediates cancer hijacking fibroblasts ]]> https://biorxiv.org/content/10.1101/729491v1?rss=1 View larger version (40K): org.highwire.dtl.DTLVardef@11317f1org.highwire.dtl.DTLVardef@88fffaorg.highwire.dtl.DTLVardef@5da692org.highwire.dtl.DTLVardef@62f6ed_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Kang, W. Fan, Y. Du, Y. Tonkova, E. A. Hsu, Y.-H. Tan, K. V. Alexander, S. Wong, B. S. Yang, H. Luo, J. Yao, K. Yang, J. Hu, X. Liu, T. Gan, Y. Zhang, J. Zhao, J. J. Konstantopoulos, K. Friedl, P. Khong, P. L. Lu, A. Hung, M.-C. Brenner, M. B. Segall, J. E. Gu, Z. 2019-08-09 doi:10.1101/729491 Cold Spring Harbor Laboratory Press 2019-08-09 <![CDATA[ Low rank mechanisms underlying flexible visual representations ]]> https://biorxiv.org/content/10.1101/730978v1?rss=1 Ruff, D. A. Xue, C. Kramer, L. E. Baqai, F. Cohen, M. R. 2019-08-09 doi:10.1101/730978 Cold Spring Harbor Laboratory Press 2019-08-09 <![CDATA[ Molecular signatures for inflammation vary across cancer types and correlate significantly with tumor stage, gender and vital status of patients ]]> https://biorxiv.org/content/10.1101/732867v1?rss=1 So, A. R. Si, A. Lopez, D. Pellegrini, M. 2019-08-12 doi:10.1101/732867 Cold Spring Harbor Laboratory Press 2019-08-12 <![CDATA[ Shrinkage Classification for Overlapping Time Series: An interpretable method for mapping stimulus-differentiated evoked response ]]> https://biorxiv.org/content/10.1101/733279v1?rss=1 Elliott, P. W. Boring, M. J. Li, Y. Richardson, R. M. Ghuman, A. S. G'Sell, M. G. 2019-08-13 doi:10.1101/733279 Cold Spring Harbor Laboratory Press 2019-08-13 <![CDATA[ Integrated Multi-omic Framework of the Plant Response to Jasmonic Acid ]]> https://biorxiv.org/content/10.1101/736363v1?rss=1 Zander, M. Lewsey, M. G. Clarke, N. M. Yin, L. Bartlett, A. Saldierna Guzman, J. P. Hann, E. Langford, A. Jow, B. Wise, A. Nery, J. R. Chen, H. Bar-Joseph, Z. Walley, J. Solano, R. Ecker, J. R. 2019-08-19 doi:10.1101/736363 Cold Spring Harbor Laboratory Press 2019-08-19 <![CDATA[ Effects of Shift-Work on the Carotid Artery and Cerebral Blood Flow of SHR Rats and WKY Rats ]]> https://biorxiv.org/content/10.1101/740068v1?rss=1 Wang, Y. Zhang, T. Zhang, Y. Yu, Y. Bai, F. Zhang, H. Chi, Y. Gao, S. 2019-08-20 doi:10.1101/740068 Cold Spring Harbor Laboratory Press 2019-08-20 <![CDATA[ The CMU Array. A 3D Nano-Printed, Fully Customizable Ultra-High-Density Microelectrode Array ]]> https://biorxiv.org/content/10.1101/742346v1?rss=1 6000 channels/cm2) with tip diameters as small as 10 m. Most importantly, the probes are entirely customizable owing to the adaptive manufacturing process. Any combination of individual shank lengths, impedances, and layouts are possible. This is achieved in part via our new multi-layer, multi material, custom 3D-printed circuit boards, a fabrication advancement in itself. This device design enables new experimental avenues of targeted, large-scale recording of electrical signals from a variety of biological tissues. ]]> Saleh, M. S. Ritchie, S. Nicholas, M. A. Bezbaruah, R. Panat, R. Yttri, E. A. 2019-08-21 doi:10.1101/742346 Cold Spring Harbor Laboratory Press 2019-08-21 <![CDATA[ How structural brain network topologies associate with cognitive abilities in a value-based decision-making task ]]> https://biorxiv.org/content/10.1101/743245v1?rss=1 Banuelos, C. Verstynen, T. 2019-08-22 doi:10.1101/743245 Cold Spring Harbor Laboratory Press 2019-08-22 <![CDATA[ Sleep deprivation selectively down-regulates astrocytic 5-HT2B receptors and triggers depressive-like behaviors via stimulating P2X7 receptors ]]> https://biorxiv.org/content/10.1101/745505v1?rss=1 Xia, M. Li, S. Liang, S. Li, X. Li, Z. Verkhratsky, A. Guan, D. Li, B. 2019-08-23 doi:10.1101/745505 Cold Spring Harbor Laboratory Press 2019-08-23 <![CDATA[ Genomic history and ecology of the geographic spread of rice ]]> https://biorxiv.org/content/10.1101/748178v1?rss=1 1,400 landraces, coupled with geographic, environmental, archaeobotanical and paleoclimate data. We also identify extrinsic factors that impact genome diversity, with temperature a leading abiotic factor. Originating [~]9,000 years ago in the Yangtze Valley, rice diversified into temperate and tropical japonica during a global cooling event [~]4,200 years ago. Soon after, tropical rice reached Southeast Asia, where it rapidly diversified starting [~]2,500 yBP. The history of indica rice dispersal appears more complicated, moving into China [~]2,000 yBP. Reconstructing the dispersal history of rice and its climatic correlates may help identify genetic adaptation associated with the spread of a key domesticated species.nnOne sentence summaryWe reconstructed the ancient dispersal of rice in Asia and identified extrinsic factors that impact its genomic diversity. ]]> Gutaker, R. M. Groen, S. C. Bellis, E. S. Choi, J. Y. Pires, I. S. Bocinsky, R. K. Slayton, E. R. Wilkins, O. Castillo, C. C. Negrao, S. Oliveira, M. M. Fuller, D. Q. Guedes, J. A. d. Lasky, J. R. Purugganan, M. D. 2019-08-31 doi:10.1101/748178 Cold Spring Harbor Laboratory Press 2019-08-31 <![CDATA[ Visual acuity performance level is independent of locomotion ]]> https://biorxiv.org/content/10.1101/750844v1?rss=1 Swain, A. D. Park, E. Cheng, Z. Y. Kowalewski, N. Sun, A. Allen, T. Kuhlman, S. J. 2019-09-02 doi:10.1101/750844 Cold Spring Harbor Laboratory Press 2019-09-02 <![CDATA[ Fluoxetine improves behavioural deficits induced by chronic alcohol addiction by alleviating RNA editing of 5-HT2C receptors in astrocytes ]]> https://biorxiv.org/content/10.1101/751065v1?rss=1 Li, Z. Liang, S. Li, S. Chen, B. Zhang, M. Xia, M. Guan, D. Verkhratsky, A. Li, B. 2019-09-03 doi:10.1101/751065 Cold Spring Harbor Laboratory Press 2019-09-03 <![CDATA[ Integrative model to coordinate the oligomerization and aggregation mechanisms of CCL5 ]]> https://biorxiv.org/content/10.1101/755322v1?rss=1 Chen, Y.-C. Chen, S.-P. Li, J.-Y. Chen, P.-C. Lee, Y.-Z. Li, K.-M. Zarivach, R. Sun, Y.-J. Sue, S.-C. 2019-09-03 doi:10.1101/755322 Cold Spring Harbor Laboratory Press 2019-09-03 <![CDATA[ Improving personalized prediction of cancer prognoses with clonal evolution models ]]> https://biorxiv.org/content/10.1101/761510v1?rss=1 Tao, Y. Rajaraman, A. Cui, X. Cui, Z. Eaton, J. Kim, H. Ma, J. Schwartz, R. 2019-09-18 doi:10.1101/761510 Cold Spring Harbor Laboratory Press 2019-09-18 <![CDATA[ Learning Representations for Gene Ontology Terms by Contextualized Text Encoders ]]> https://biorxiv.org/content/10.1101/765644v1?rss=1 Duong, D. Uppunda, A. Ju, C. J.-T. Zhang, J. Chen, M. Eskin, E. Li, J. J. Chang, K.-W. 2019-09-18 doi:10.1101/765644 Cold Spring Harbor Laboratory Press 2019-09-18 <![CDATA[ B-SOiD: An Open Source Unsupervised Algorithm for Discovery of Spontaneous Behaviors ]]> https://biorxiv.org/content/10.1101/770271v1?rss=1 Hsu, A. I. Yttri, E. A. 2019-09-16 doi:10.1101/770271 Cold Spring Harbor Laboratory Press 2019-09-16 <![CDATA[ Causal links between parietal alpha activity and spatial auditory attention ]]> https://biorxiv.org/content/10.1101/775718v1?rss=1 Deng, Y. Reinhart, R. M. G. Choi, I. Shinn-Cunningham, B. G. 2019-09-19 doi:10.1101/775718 Cold Spring Harbor Laboratory Press 2019-09-19 <![CDATA[ Single-cell time-series mapping of cell fate trajectories reveals an expanded developmental potential for human PSC-derived distal lung progenitors ]]> https://biorxiv.org/content/10.1101/782896v1?rss=1 Hurley, K. Ding, J. Villacorta-Martin, C. Herriges, M. J. Jacob, A. Vedaie, M. Alysandratos, K. D. Sun, Y. L. Lin, C. Werder, R. B. Wilson, A. A. Mithal, A. Mostoslavsky, G. Caballero, I. S. Guttentag, S. H. Ahangari, F. Kaminski, N. Rodriguez- Fraticelli, A. Camargo, F. Bar-Joseph, Z. Kotton, D. 2019-09-26 doi:10.1101/782896 Cold Spring Harbor Laboratory Press 2019-09-26 <![CDATA[ Control of cytokinesis by β-adrenergic receptors indicates an approach for regulating cardiomyocyte endowment ]]> https://biorxiv.org/content/10.1101/782920v1?rss=1 Liu, H. Zhang, C.-H. Ammanamanchi, N. Suresh, S. Lewarchik, C. Rao, K. Uys, G. M. Han, L. Abrial, M. Yimlamai, D. Ganapathy, B. Guillermier, C. Chen, N. Khaladkar, M. Spaethling, J. Eberwine, J. H. Kim, J. Walsh, S. Choudhury, S. Little, K. Francis, K. Sharma, M. Viegas, M. Bais, A. Kostka, D. Ding, J. Bar-Joseph, Z. Wu, Y. Steinhauser, M. L. Kuhn, B. 2019-10-04 doi:10.1101/782920 Cold Spring Harbor Laboratory Press 2019-10-04 <![CDATA[ Double asymmetric percolation drives a quadruple transition in sexual contact networks ]]> https://biorxiv.org/content/10.1101/784587v1?rss=1 Zheng, H. Zeng, X. 2019-09-26 doi:10.1101/784587 Cold Spring Harbor Laboratory Press 2019-09-26 <![CDATA[ Pneumococcal attachment to epithelial cells is enhanced by the secreted peptide VP1 via its control of hyaluronic acid processing ]]> https://biorxiv.org/content/10.1101/788430v1?rss=1 Cuevas, R. A. Elnaz Ebrahimi, E. Gazioglu, O. Yesilkaya, H. Hiller, N. L. 2019-10-01 doi:10.1101/788430 Cold Spring Harbor Laboratory Press 2019-10-01 <![CDATA[ Motorized shoes induce robust sensorimotor adaptation in walking ]]> https://biorxiv.org/content/10.1101/788943v1?rss=1 Torres-Oviedo, G. Aucie, Y. Sargent, R. Zhang, X. 2019-10-01 doi:10.1101/788943 Cold Spring Harbor Laboratory Press 2019-10-01 <![CDATA[ SCRIBE: a new approach to dropout imputation and batch effects correction for single-cell RNA-seq data ]]> https://biorxiv.org/content/10.1101/793463v1?rss=1 Zhang, Y. Liang, K. Liu, M. Li, Y. Ge, H. Zhao, H. 2019-10-04 doi:10.1101/793463 Cold Spring Harbor Laboratory Press 2019-10-04 <![CDATA[ Effect of Geometric Sharpness on Translucent Material Perception ]]> https://biorxiv.org/content/10.1101/795294v1?rss=1 Xiao, B. Zhao, S. Gkioulekas, I. Bi, W. Bala, K. 2019-10-07 doi:10.1101/795294 Cold Spring Harbor Laboratory Press 2019-10-07 <![CDATA[ A dual role for shape skeletons in human vision: perceptual organization and object recognition ]]> https://biorxiv.org/content/10.1101/799650v1?rss=1 Ayzenberg, V. Kamps, F. S. Dilks, D. D. Lourenco, S. F. 2019-10-10 doi:10.1101/799650 Cold Spring Harbor Laboratory Press 2019-10-10 <![CDATA[ Bootstrapping promotes the RSFC-behavior associations: an application of individual cognitive traits prediction ]]> https://biorxiv.org/content/10.1101/800243v1?rss=1 Wei, L. Jing, B. Li, H. 2019-10-10 doi:10.1101/800243 Cold Spring Harbor Laboratory Press 2019-10-10 <![CDATA[ Application of post-selection inference to multi-omics data yields insights into the etiologies of human diseases ]]> https://biorxiv.org/content/10.1101/806471v1?rss=1 Yurko, R. J. G'Sell, M. Roeder, K. Devlin, B. 2019-10-16 doi:10.1101/806471 Cold Spring Harbor Laboratory Press 2019-10-16 <![CDATA[ Feature-based Molecular Networking in the GNPS Analysis Environment ]]> https://biorxiv.org/content/10.1101/812404v1?rss=1 Nothias, L. F. Petras, D. Schmid, R. Duehrkop, K. Rainer, J. Sarvepalli, A. Protsyuk, I. Ernst, M. Tsugawa, H. Fleischauer, M. Aicheler, F. Aksenov, A. Alka, O. Allard, P.-M. Barsch, A. Cachet, X. Caraballo, M. Da Silva, R. Dang, T. Garg, N. Gauglitz, J. M. Gurevich, A. Isaac, G. Jarmusch, A. K. Kamenik, Z. Kang, K. B. Kessler, N. Koester, I. Korf, A. Le Gouellec, A. Ludwig, M. Martin H., C. McCall, L.-I. McSayles, J. Meyer, S. Mohimani, H. Morsy, M. Moyne, O. Neumann, S. Neuweger, H. Nguyen, N. H. Esposito-Nothias, M. Paolini, J. Phelan, V. Pluskal, 2019-10-20 doi:10.1101/812404 Cold Spring Harbor Laboratory Press 2019-10-20 <![CDATA[ Cognitive and default mode networks support developmental stability in functional connectome fingerprinting through adolescence ]]> https://biorxiv.org/content/10.1101/812719v1?rss=1 Jalbrzikowski, M. Lei, F. Foran, W. Calabro, F. Roeder, K. Devlin, B. Luna, B. 2019-11-01 doi:10.1101/812719 Cold Spring Harbor Laboratory Press 2019-11-01 <![CDATA[ Emergence of opposite neurons in a firing-rate model of multisensory integration ]]> https://biorxiv.org/content/10.1101/814483v1?rss=1 Chau, H. Y. Zhang, W.-H. Lee, T. S. 2019-10-22 doi:10.1101/814483 Cold Spring Harbor Laboratory Press 2019-10-22 <![CDATA[ Association of Model Neurotransmitters with Lipid Bilayer Membranes ]]> https://biorxiv.org/content/10.1101/822189v1?rss=1 Loesche, M. Heinrich, F. Josey, B. Silin, V. 2019-10-29 doi:10.1101/822189 Cold Spring Harbor Laboratory Press 2019-10-29 <![CDATA[ Steering Molecular Dynamics Simulations of Membrane-Associated Proteins with Neutron Reflection Results ]]> https://biorxiv.org/content/10.1101/823740v1?rss=1 Treece, B. W. Heinrich, F. Ramanathan, A. Loesche, M. 2019-10-30 doi:10.1101/823740 Cold Spring Harbor Laboratory Press 2019-10-30 <![CDATA[ TSA-Seq 2.0 reveals both conserved and variable chromosomal distances to nuclear speckles ]]> https://biorxiv.org/content/10.1101/824433v1?rss=1 Zhang, L. Zhang, Y. Chen, Y. Gholamalamdari, O. Ma, J. Belmont, A. S. 2019-10-30 doi:10.1101/824433 Cold Spring Harbor Laboratory Press 2019-10-30 <![CDATA[ Ghost QTL and hotspots in experimental crosses - novel solution by mixed model with nonzero mean ]]> https://biorxiv.org/content/10.1101/825562v1?rss=1 Szulc, P. M. Wallin, J. Bogdan, M. Doerge, R. W. Siegmund, D. O. 2019-10-31 doi:10.1101/825562 Cold Spring Harbor Laboratory Press 2019-10-31 <![CDATA[ A statistical method for identifying consistently important features across samples ]]> https://biorxiv.org/content/10.1101/833624v1?rss=1 Sauerwald, N. Kingsford, C. 2019-11-07 doi:10.1101/833624 Cold Spring Harbor Laboratory Press 2019-11-07 <![CDATA[ Dynamic Bayesian networks for integrating multi-omics time-series microbiome data ]]> https://biorxiv.org/content/10.1101/835124v1?rss=1 Ruiz-Perez, D. Lugo-Martinez, J. Bourguignon, N. Mathee, K. Lerner, B. Bar-Joseph, Z. Narasimhan, G. 2019-11-08 doi:10.1101/835124 Cold Spring Harbor Laboratory Press 2019-11-08 <![CDATA[ genuMet: distinguish genuine untargeted metabolic features without quality control samples ]]> https://biorxiv.org/content/10.1101/837260v1?rss=1 Cao, L. Clish, C. Hu, F. B. Martinez-Gonzalez,, M. A. Bullo-Bonet, M. Corella, D. Gomez-Gracia, E. Fiol, M. Estruch, R. Lapetra, J. Fito, M. Aros, F. Serra-Majem, L. Ros, E. Liang, L. 2019-11-10 doi:10.1101/837260 Cold Spring Harbor Laboratory Press 2019-11-10 <![CDATA[ Unpaired Data Empowers Association Tests ]]> https://biorxiv.org/content/10.1101/839159v1?rss=1 Gong, M. Liu, P. Sciurba, F. C. Stojanov, P. Tao, D. Tseng, G. Zhang, K. Batmanghelich, K. 2019-11-12 doi:10.1101/839159 Cold Spring Harbor Laboratory Press 2019-11-12 <![CDATA[ Abnormal nitration and S-sulfhydration of Sp1-CSE-H2S pathway contribute to the progress of HHcy ]]> https://biorxiv.org/content/10.1101/843854v1?rss=1 Wang, W. Luo, C. Ji, D. Li, Y. Cao, Y. Zhang, S. Yan, W. Xue, K. Chai, J. Wu, Y. Liu, H. 2019-11-19 doi:10.1101/843854 Cold Spring Harbor Laboratory Press 2019-11-19 <![CDATA[ Quantum and Quantum-inspired Methods for de novo Discovery of Altered Cancer Pathways ]]> https://biorxiv.org/content/10.1101/845719v1?rss=1 Alghassi, H. Dridi, R. Robertson, A. G. Tayur, S. 2019-11-17 doi:10.1101/845719 Cold Spring Harbor Laboratory Press 2019-11-17 <![CDATA[ Emergence of opposite neurons in a decentralized firing-rate model of multisensory integration ]]> https://biorxiv.org/content/10.1101/845743v1?rss=1 Niu, X. Chau, H. Y. Lee, T. S. Zhang, W.-H. 2019-11-17 doi:10.1101/845743 Cold Spring Harbor Laboratory Press 2019-11-17 <![CDATA[ Estimating mutual information under measurement error ]]> https://biorxiv.org/content/10.1101/852384v1?rss=1 Ma, C. Kingsford, C. 2019-11-23 doi:10.1101/852384 Cold Spring Harbor Laboratory Press 2019-11-23 <![CDATA[ The Topology of Mutated Driver Pathways ]]> https://biorxiv.org/content/10.1101/860676v1?rss=1 Dridi, R. Alghassi, H. Obeidat, M. Tayur, S. 2019-11-30 doi:10.1101/860676 Cold Spring Harbor Laboratory Press 2019-11-30 <![CDATA[ Uncharacteristic task-evoked pupillary responses implicate atypical locus coeruleus activity in autism ]]> https://biorxiv.org/content/10.1101/863928v1?rss=1 Granovetter, M. C. Burlingham, C. S. Blauch, N. M. Minshew, N. J. Heeger, D. J. Behrmann, M. 2019-12-03 doi:10.1101/863928 Cold Spring Harbor Laboratory Press 2019-12-03 <![CDATA[ N6-methyladenosine demethylase FTO serves as an indicator for predicting prognosis and immunotherapy response in individuals with gastric cancer ]]> https://biorxiv.org/content/10.1101/2023.05.15.540747v1?rss=1 Jia, S. Zhou, H. Li, K. Li, Y. 2023-05-15 doi:10.1101/2023.05.15.540747 Cold Spring Harbor Laboratory Press 2023-05-15 <![CDATA[ Robust differential expression testing for single-cell CRISPR screens at low multiplicity of infection ]]> https://biorxiv.org/content/10.1101/2023.05.15.540875v1?rss=1 Barry, T. Mason, K. Roeder, K. Katsevich, E. 2023-05-15 doi:10.1101/2023.05.15.540875 Cold Spring Harbor Laboratory Press 2023-05-15 <![CDATA[ Single nucleus transcriptomics of human and monkey striatum implicates DNA damage, neuroinflammation, and neurodegeneration signaling in opioid use disorder ]]> https://biorxiv.org/content/10.1101/2023.05.17.541145v1?rss=1 Phan, B. N. Ray, M. H. Xue, X. Fenster, R. J. Kohut, S. J. Bergman, J. Haber, S. N. Mccullough, K. M. Kuppe-Fish, M. K. Glausier, J. R. Su, Q. Tipton, A. E. Lewis, D. A. Freyberg, Z. Tseng, G. C. Ressler, K. J. Russek, S. J. Alekseyev, Y. Seney, M. L. Pfenning, A. R. Logan, R. W. 2023-05-17 doi:10.1101/2023.05.17.541145 Cold Spring Harbor Laboratory Press 2023-05-17 <![CDATA[ scGHOST: Identifying single-cell 3D genome subcompartments ]]> https://biorxiv.org/content/10.1101/2023.05.24.542032v1?rss=1 Xiong, K. Zhang, R. Ma, J. 2023-05-25 doi:10.1101/2023.05.24.542032 Cold Spring Harbor Laboratory Press 2023-05-25 <![CDATA[ Developmental Alterations in Brain Network Asymmetry in 3- to 9-Month Infants with Congenital Sensorineural Hearing Loss ]]> https://biorxiv.org/content/10.1101/2023.05.31.543147v1?rss=1 Liu, G. Zhou, X. Hu, Z. Liu, Y. Huo, E. Bortfeld, H. Dong, Q. Liu, H. Niu, H. 2023-06-01 doi:10.1101/2023.05.31.543147 Cold Spring Harbor Laboratory Press 2023-06-01 <![CDATA[ Human subcutaneous adipose tissue variability is driven by VEGFA, ACTA2, adipocyte density, and ancestral history of the patient ]]> https://biorxiv.org/content/10.1101/2023.05.31.543052v1?rss=1 25) and a correlation matrix was used to identify interactions between quantitative variables. Vascular endothelial growth factor A (VEGFA) and actin alpha 2, smooth muscle (ACTA2) gene expression were the highest loading in the first two dimensions of the FAMD. The number of adipocytes was also a key driver of patient-related differences, where a decrease in the density of adipocytes was associated with aging. Aging was also correlated with a decrease in overall lipid percentage of subcutaneous tissue (with lipid deposition being favored extracellularly), an increase in transforming growth factor-{beta}1 (TGF{beta}1), and an increase in M1 macrophage polarization. An important finding was that self-identified race contributed to variance between patients in this study, where Black patients had significantly lower gene expression levels of TGF{beta}1 and ACTA2. This finding supports the urgent need to account for patient ancestry in biomedical research to develop better therapeutic strategies for all patients. Another important finding was that TGF{beta} induced factor homeobox 1 (TGIF1), an understudied signaling molecule, is highly correlated with leptin signaling and was correlated with metabolic inflammation. Finally, this study revealed an interesting gene expression pattern where M1 and M2 macrophage markers were correlated with each other, and leptin, in patients with a BMI > 25. This finding supports growing evidence that macrophage polarization in obesity involves a complex, interconnecting network system rather than a full switch in activation patterns from M2 to M1 with increasing body mass. Overall, this study reinforces key findings in animal studies and identifies important areas for future research, where human and animal studies are divergent. Understanding key drivers of human patient variability is required to unravel the complex metabolic health of unique patients. ]]> DeBari, M. K. Johnston, E. K. Scott, J. V. Iizuka, E. Sun, W. Webster-Wood, V. A. Abbott, R. D. 2023-06-03 doi:10.1101/2023.05.31.543052 Cold Spring Harbor Laboratory Press 2023-06-03 <![CDATA[ Circulating Small Extracellular Vesicle RNA Profiling for the Detection of T1a stage Colorectal Cancer and Precancerous Advanced Adenoma ]]> https://biorxiv.org/content/10.1101/2023.06.04.543604v1?rss=1 Min, L. Bu, F. Meng, J. Liu, X. Guo, Q. Zhao, L. Li, Z. Li, X. Zhu, S. Zhang, S. 2023-06-06 doi:10.1101/2023.06.04.543604 Cold Spring Harbor Laboratory Press 2023-06-06 <![CDATA[ Electrocatalytic on-site oxygenation for transplanted cell-based-therapies ]]> https://biorxiv.org/content/10.1101/2023.06.05.543794v1?rss=1 60k cells/mm3) in hypoxic conditions in vitro and in vivo. Our results demonstrate that exogenous oxygen production devices can be readily integrated into bioelectronic platforms and enable high cell loadings in smaller device footprints with broad applicability. ]]> Lee, I. Surendran, A. Fleury, S. Gimino, I. Curtiss, A. Fell, C. Shiwarski, D. El-Refy, O. Rothrock, B. Jo, S. Schwartzkopff, T. Singh Mehta, A. John, S. Ji, X. Nikiforidis, G. Hester, J. Weber, D. J. Veiseh, O. Feinberg, A. Rivnay, J. Cohen-Karni, T. 2023-06-07 doi:10.1101/2023.06.05.543794 Cold Spring Harbor Laboratory Press 2023-06-07 <![CDATA[ Catalytic growth in a shared enzyme pool ensures robust control of centrosome size ]]> https://biorxiv.org/content/10.1101/2023.06.06.543875v1?rss=1 Banerjee, D. S. Banerjee, S. 2023-06-07 doi:10.1101/2023.06.06.543875 Cold Spring Harbor Laboratory Press 2023-06-07 <![CDATA[ Modelling Human Post-Implantation Development via Extra-Embryonic Niche Engineering ]]> https://biorxiv.org/content/10.1101/2023.06.15.545118v1?rss=1 Hislop, J. J. Alavi, A. Song, Q. Schoenberger, R. L. Keshavarz F., K. LeGraw, R. Velazquez, J. J. Mokhtari, T. Taheri, M. N. Rytel, M. de Sousa Lopes, S. M. C. Watkins, S. C. Stolz, D. B. Kiani, S. Sozen, B. Bar-Joseph, Z. Ebrahimkhani, M. 2023-06-15 doi:10.1101/2023.06.15.545118 Cold Spring Harbor Laboratory Press 2023-06-15 <![CDATA[ Inferring the direction of introgression using genomic sequence data ]]> https://biorxiv.org/content/10.1101/2023.06.16.545313v1?rss=1 Thawornwattana, Y. Huang, J. Flouri, T. Mallet, J. L. Yang, Z. 2023-06-16 doi:10.1101/2023.06.16.545313 Cold Spring Harbor Laboratory Press 2023-06-16 <![CDATA[ Inactivation of face selective neurons alters eye movements when free viewing faces ]]> https://biorxiv.org/content/10.1101/2023.06.20.544678v1?rss=1 Azadi, R. Lopez, E. Taubert, J. Patterson, A. Afraz, A. 2023-06-24 doi:10.1101/2023.06.20.544678 Cold Spring Harbor Laboratory Press 2023-06-24 <![CDATA[ Nanoparticle endocytosis is driven by monocyte phenotype rather than nanoparticle size under high shear flow conditions ]]> https://biorxiv.org/content/10.1101/2023.06.29.547038v1?rss=1 Aldarondo, D. Hunyh, C. Dickey, L. Bilynsky, C. S. M. Lee, Y. Wayne, E. C. 2023-06-29 doi:10.1101/2023.06.29.547038 Cold Spring Harbor Laboratory Press 2023-06-29 <![CDATA[ Meta-analysis of macrophage nanoparticle targeting across blood and solid tumors using an eLDA Topic modeling Machine Learning approach ]]> https://biorxiv.org/content/10.1101/2023.06.29.547096v1?rss=1 Brown, C. Bilynsky, C. S. M. Gainey, M. Young, S. Kitchin, J. Wayne, E. C. 2023-06-30 doi:10.1101/2023.06.29.547096 Cold Spring Harbor Laboratory Press 2023-06-30 <![CDATA[ Prolonged activity-deprivation causes pre- and postsynaptic compensatory plasticity at neocortical excitatory synapses ]]> https://biorxiv.org/content/10.1101/2023.07.05.547850v1?rss=1 Wise, D. Escobedo-Lozoya, Y. Valakh, V. Isaac, B. Gao, E. Greene, S. Bhonsle, A. Lei, L. Cheng, X. Van Hooser, S. Nelson, S. B. 2023-07-07 doi:10.1101/2023.07.05.547850 Cold Spring Harbor Laboratory Press 2023-07-07 <![CDATA[ RNAGEN: A generative adversarial network-based model to generate synthetic RNA sequences to target proteins ]]> https://biorxiv.org/content/10.1101/2023.07.11.548246v1?rss=1 Ozden, F. Barazandeh, S. Akboga, D. Seker, U. O. S. Cicek, A. E. 2023-07-12 doi:10.1101/2023.07.11.548246 Cold Spring Harbor Laboratory Press 2023-07-12 <![CDATA[ Beyond the Visual Word Form Area: Characterizing a hierarchical, distributed and bilateral network for visual word processing ]]> https://biorxiv.org/content/10.1101/2023.07.11.548613v1?rss=1 Vin, R. Blauch, N. M. Plaut, D. Behrmann, M. 2023-07-12 doi:10.1101/2023.07.11.548613 Cold Spring Harbor Laboratory Press 2023-07-12 <![CDATA[ Neural representation of spatial and non-spatial auditory attention in EEG signals ]]> https://biorxiv.org/content/10.1101/2023.07.13.548897v1?rss=1 An, W. W. Noyce, A. L. Pei, A. Shinn-Cunningham, B. G. 2023-07-15 doi:10.1101/2023.07.13.548897 Cold Spring Harbor Laboratory Press 2023-07-15 <![CDATA[ A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data ]]> https://biorxiv.org/content/10.1101/2023.07.20.549584v1?rss=1 60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. Identification of microbial-derived metabolites and relative producers, without a priori knowledge, will vastly enhance the understanding of microorganisms role in ecology and human health. ]]> Zuffa, S. Schmid, R. Bauermeister, A. P. Gomes, P. W. Caraballo-Rodriguez, A. M. El Abiead, Y. Aron, A. T. Gentry, E. C. Zemlin, J. Meehan, M. J. Avalon, N. E. Cichewicz, R. H. Buzun, E. Carrillo Terrazas, M. Hsu, C.-Y. Oles, R. Vasquez Ayala, A. Zhao, J. Chu, H. Kuijpers, M. C. M. Jackrel, S. L. Tugizimana, F. Nephali, L. P. Dubery, I. A. Madala, N. E. Moreira, E. A. Costa-Lotufo, L. V. Lopes, N. P. Rezende-Teixeira, P. Jimenez, P. C. Rimal, B. Patterson, A. D. Traxler, M. F. Pessotti, R. d. C. Alvarado-Villalobos, D. Tamayo-Castillo, G. Chaverri, P. Escud 2023-07-20 doi:10.1101/2023.07.20.549584 Cold Spring Harbor Laboratory Press 2023-07-20 <![CDATA[ Five inhibitory receptors display distinct vesicular distributions in T cells ]]> https://biorxiv.org/content/10.1101/2023.07.21.550019v1?rss=1 Lu, J. Veler, A. Simonetti, B. Raj, T. Chou, P. H. Cross, S. J. Phillips, A. M. Ruan, X. J. Huynh, L. Dowsey, A. W. Ye, D. Murphy, R. F. Verkade, P. Cullen, P. J. Wuelfing, C. 2023-07-22 doi:10.1101/2023.07.21.550019 Cold Spring Harbor Laboratory Press 2023-07-22 <![CDATA[ Concurrent profiling of multiscale 3D genome organization and gene expression in single mammalian cells ]]> https://biorxiv.org/content/10.1101/2023.07.20.549578v1?rss=1 Zhou, T. Zhang, R. Jia, D. Doty, R. T. Munday, A. D. Gao, D. Xin, L. Abkowitz, J. L. Duan, Z. Ma, J. 2023-07-25 doi:10.1101/2023.07.20.549578 Cold Spring Harbor Laboratory Press 2023-07-25 <![CDATA[ Matrix stiffness modulates 3D spheroid sorting and burst-like collective migration ]]> https://biorxiv.org/content/10.1101/2023.07.23.549940v1?rss=1 Cai, G. Li, X. Lin, S.-S. Chen, S. J. Koning, K. Bi, D. Liu, A. P. 2023-07-25 doi:10.1101/2023.07.23.549940 Cold Spring Harbor Laboratory Press 2023-07-25 <![CDATA[ Mechanical control of cell proliferation patterns in growing tissues ]]> https://biorxiv.org/content/10.1101/2023.07.25.550581v1?rss=1 Carpenter, L. C. Perez-Verdugo, F. Banerjee, S. 2023-07-27 doi:10.1101/2023.07.25.550581 Cold Spring Harbor Laboratory Press 2023-07-27 <![CDATA[ LipidSIM: inferring mechanistic lipid biosynthesis perturbations from lipidomics with a flexible, low-parameter, systematic Markov Modeling framework ]]> https://biorxiv.org/content/10.1101/2023.07.26.550768v1?rss=1 Liang, C. Murray, S. Li, Y. Lee, R. Low, A. Sasaki, S. Chiang, W.-T. Lin, W.-J. Mathews, J. Barnes, W. Lewis, N. E. 2023-07-28 doi:10.1101/2023.07.26.550768 Cold Spring Harbor Laboratory Press 2023-07-28 <![CDATA[ Immunities Specific to Both of the M Protein Ectodomain and RBD Synergize to Confer Cross-protection against SARS-CoV-2 Infections ]]> https://biorxiv.org/content/10.1101/2023.07.31.551223v1?rss=1 Tang, Y. Tang, K. Hu, Y. Ye, Z.-W. Luo, W. Luo, C. Cao, H. Wang, R. Liu, D. Liu, C. Ge, X. Chen, Y. Yuan, S. Deng, L. 2023-07-31 doi:10.1101/2023.07.31.551223 Cold Spring Harbor Laboratory Press 2023-07-31 <![CDATA[ Rapid and unbiased enrichment of extracellular vesicles via meticulously engineered peptide ]]> https://biorxiv.org/content/10.1101/2023.08.04.551951v1?rss=1 Wang, L. Gong, Z. Wang, M. Liang, Y.-Z. Zhao, J. Xie, Q. Wu, X.-W. Li, Q.-Y. Zhang, C. Ma, L.-Y. Zheng, S.-Y. Yu, X. Xu, L. 2023-08-04 doi:10.1101/2023.08.04.551951 Cold Spring Harbor Laboratory Press 2023-08-04 <![CDATA[ Differential functional reorganization of ventral and dorsal visual pathways following childhood hemispherectomy ]]> https://biorxiv.org/content/10.1101/2023.08.03.551494v1?rss=1 Ayzenberg, V. Granovetter, M. C. Robert, S. Patterson, C. Behrmann, M. 2023-08-06 doi:10.1101/2023.08.03.551494 Cold Spring Harbor Laboratory Press 2023-08-06 <![CDATA[ Optimal transport for mapping senescent cells in spatial transcriptomics ]]> https://biorxiv.org/content/10.1101/2023.08.16.553591v1?rss=1 Nguyen, N. D. Rosas, L. Khaliullin, T. Jiang, P. Hasanaj, E. Ovando, J. A. Bueno, M. Konigshoff, M. Eickelberg, O. Rojas, M. Mora, A. L. Lugo-Martinez, J. Bar-Joseph, Z. 2023-08-17 doi:10.1101/2023.08.16.553591 Cold Spring Harbor Laboratory Press 2023-08-17 <![CDATA[ Polybacterial intracellular coinfection of epithelial stem cells in periodontitis ]]> https://biorxiv.org/content/10.1101/2023.08.23.554343v1?rss=1 Easter, Q. T. Matuck, B. F. Stark, G. B. Worth, C. L. Predeus, A. V. Fremin, B. Huynh, K. T. Ranganathan, V. Pereira, D. Weaver, T. Miller, K. Perez, P. Hasuike, A. Chen, Z. Bush, M. Qu, X. Warner, B. M. Lee, J. Wallet, S. M. Sequeira, I. Tyc, K. M. Liu, J. Ko, K. I. Teichmann, S. A. Byrd, K. M. 2023-08-24 doi:10.1101/2023.08.23.554343 Cold Spring Harbor Laboratory Press 2023-08-24 <![CDATA[ Combined topological data analysis and geometric deep learning reveal niches by the quantification of protein binding pockets ]]> https://biorxiv.org/content/10.1101/2023.08.25.554762v1?rss=1 Jiang, P. Lugo-Martinez, J. 2023-08-27 doi:10.1101/2023.08.25.554762 Cold Spring Harbor Laboratory Press 2023-08-27 <![CDATA[ Expectation reshapes V4 neuronal activity and improves perceptual performance ]]> https://biorxiv.org/content/10.1101/2023.08.27.555026v1?rss=1 Stan, P. L. Smith, M. A. 2023-08-28 doi:10.1101/2023.08.27.555026 Cold Spring Harbor Laboratory Press 2023-08-28 <![CDATA[ Convergent evolution of SARS-CoV-2 XBB lineages on receptor-binding domain 455-456 enhances antibody evasion and ACE2 binding ]]> https://biorxiv.org/content/10.1101/2023.08.30.555211v1?rss=1 Jian, F. Yang, S. Yu, Y. Song, W. Yisimayi, A. Chen, X. Xu, Y. Wang, P. Yu, L. Wang, J. Liu, L. Niu, X. Wang, J. Xiao, T. Gu, Q. Shao, F. Jin, R. Shen, Z. Wang, Y. Cao, Y. R. 2023-08-31 doi:10.1101/2023.08.30.555211 Cold Spring Harbor Laboratory Press 2023-08-31 <![CDATA[ Hydrogen Sulfide Coordinates Glucose Metabolism Switch through Destabilizing Tetrameric Pyruvate Kinase M2 ]]> https://biorxiv.org/content/10.1101/2023.09.02.555034v1?rss=1 Wang, R.-H. Chen, P.-R. Chen, Y.-T. Chen, Y.-C. Chu, Y.-H. Chien, C.-C. Chien, P.-C. Lo, S.-Y. Wang, Z.-L. Tsou, M.-C. Chen, S.-Y. Chiu, G.-S. Chen, W.-L. Wu, Y.-H. Wang, L. Wang, W.-C. Lin, S.-Y. Kung, H.-J. Wang, L.-H. Cheng, H.-C. Lin, K.-T. 2023-09-03 doi:10.1101/2023.09.02.555034 Cold Spring Harbor Laboratory Press 2023-09-03 <![CDATA[ Antigenicity and infectivity characterization of SARS-CoV-2 BA.2.86 ]]> https://biorxiv.org/content/10.1101/2023.09.01.555815v1?rss=1 Yang, S. Yu, Y. Jian, F. Song, W. Yisimayi, A. Chen, X. Xu, Y. Wang, P. Yu, L. Wang, J. Niu, X. Wang, J. Xiao, T. An, R. Wang, Y. Gu, Q. Shao, F. Jin, R. Shen, Z. Wang, Y. Cao, Y. R. 2023-09-04 doi:10.1101/2023.09.01.555815 Cold Spring Harbor Laboratory Press 2023-09-04 <![CDATA[ Transcranial Focused Ultrasound to V5 Enhances Human Visual Motion Brain-Computer Interface by Modulating Feature-Based Attention ]]> https://biorxiv.org/content/10.1101/2023.09.04.556252v1?rss=1 Kosnoff, J. Yu, K. Liu, C. He, B. 2023-09-05 doi:10.1101/2023.09.04.556252 Cold Spring Harbor Laboratory Press 2023-09-05 <![CDATA[ CBGTPy: An extensible cortico-basal ganglia-thalamic framework for modeling biological decision making ]]> https://biorxiv.org/content/10.1101/2023.09.05.556301v1?rss=1 Clapp, M. Bahuguna, J. Giossi, C. Rubin, J. Verstynen, T. V. Vich, C. 2023-09-05 doi:10.1101/2023.09.05.556301 Cold Spring Harbor Laboratory Press 2023-09-05 <![CDATA[ Categorization dynamically alters representations in human visual cortex ]]> https://biorxiv.org/content/10.1101/2023.09.11.557257v1?rss=1 Henderson, M. M. Serences, J. T. Rungratsameetaweemana, N. 2023-09-13 doi:10.1101/2023.09.11.557257 Cold Spring Harbor Laboratory Press 2023-09-13 <![CDATA[ Functional connectome through the human life span ]]> https://biorxiv.org/content/10.1101/2023.09.12.557193v1?rss=1 Sun, L. Zhao, T. Liang, X. Xia, M. Li, Q. Liao, X. Gong, G. Wang, Q. Pang, C. Yu, Q. Bi, Y. Chen, P. Chen, R. Chen, Y. Chen, T. Cheng, J. Cheng, Y. Cui, Z. Dai, Z. Deng, Y. Ding, Y. Dong, Q. Duan, D. Gao, J.-H. Gong, Q. Han, Y. Han, Z. Huang, C.-C. Huang, R. Li, L. Lin, C.-P. Lin, Q. Liu, B. Liu, C. Liu, N. Liu, Y. Lu, J. Ma, L. Men, W. Qin, S. Qiu, J. Qiu, S. Si, T. Tan, S. Tang, Y. Tao, S. Wang, D. Wang, F. Wang, J. Wang, P. Wang, X. Wang, Y. Wei, D. Wu, Y. Xie, P. Xu, X. Xu, Y. Xu, Z. Yang, L. Zeng, Z. Zhang, H. Zhang, X. Zhao, G 2023-09-13 doi:10.1101/2023.09.12.557193 Cold Spring Harbor Laboratory Press 2023-09-13 <![CDATA[ Heteroscedastic Personalized Regression Unveils Genetic Basis of Alzheimer's Disease Stratified by Cognitive Level ]]> https://biorxiv.org/content/10.1101/2023.09.12.557499v1?rss=1 Chen, Z. Wang, H. 2023-09-15 doi:10.1101/2023.09.12.557499 Cold Spring Harbor Laboratory Press 2023-09-15 <![CDATA[ Neural Data Transformer 2: Multi-context Pretraining for Neural Spiking Activity ]]> https://biorxiv.org/content/10.1101/2023.09.18.558113v1?rss=1 Ye, J. Collinger, J. Wehbe, L. Gaunt, R. 2023-09-22 doi:10.1101/2023.09.18.558113 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ Automated customization of large-scale spiking network models to neuronal population activity ]]> https://biorxiv.org/content/10.1101/2023.09.21.558920v1?rss=1 Wu, S. Huang, C. Snyder, A. Smith, M. A. Doiron, B. Yu, B. 2023-09-22 doi:10.1101/2023.09.21.558920 Cold Spring Harbor Laboratory Press 2023-09-22 <![CDATA[ Bi-directional communication between monocytes and trophoblasts under hypoxia and hypoxia-reperfusion conditions ]]> https://biorxiv.org/content/10.1101/2023.09.23.558721v1?rss=1 View larger version (24K): org.highwire.dtl.DTLVardef@15dae34org.highwire.dtl.DTLVardef@157dec7org.highwire.dtl.DTLVardef@1e2db81org.highwire.dtl.DTLVardef@b90ab6_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Yankello, H. Lee, Y. Megli, C. Wayne, E. C. 2023-09-24 doi:10.1101/2023.09.23.558721 Cold Spring Harbor Laboratory Press 2023-09-24 <![CDATA[ Cortical and subcortical brain networks predict prevailing heart rate ]]> https://biorxiv.org/content/10.1101/2023.09.23.559114v1?rss=1 Sentis, A. I. Rasero, J. Gianaros, P. J. Verstynen, T. V. 2023-09-24 doi:10.1101/2023.09.23.559114 Cold Spring Harbor Laboratory Press 2023-09-24 <![CDATA[ GET: a foundation model of transcription across human cell types ]]> https://biorxiv.org/content/10.1101/2023.09.24.559168v1?rss=1 1Mbp) regulatory regions that were missed by previous models. In B cells, we identified a lymphocyte-specific transcription factor-transcription factor interaction that explains the functional significance of a leukemia-risk predisposing germline mutation. In sum, we provide a generalizable and accurate model for transcription together with catalogs of gene regulation and transcription factor interactions, all with cell type specificity. ]]> Fu, X. Mo, S. Shao, A. Laurent, A. Buendia, A. Ferrando, A. A. Ciccia, A. Lan, Y. Palomero, T. Owens, D. M. Xing, E. P. Rabadan, R. 2023-09-24 doi:10.1101/2023.09.24.559168 Cold Spring Harbor Laboratory Press 2023-09-24 <![CDATA[ Microdroplet-enabled high-throughput cultivation of vaginal bacteria using cervicovaginal fluids ]]> https://biorxiv.org/content/10.1101/2023.09.26.559375v1?rss=1 Jackman, C. M. Tan, J. Y. Lin, X. N. 2023-09-26 doi:10.1101/2023.09.26.559375 Cold Spring Harbor Laboratory Press 2023-09-26 <![CDATA[ Integrative analysis of multi-omics and machine learning highlighted an m6A-related mRNA signature as a robust AAA progression predictor ]]> https://biorxiv.org/content/10.1101/2023.09.25.559437v1?rss=1 He, Y. Xing, J. Wang, S. Jiang, H. Lun, Y. Han, Y. Erhart, P. Böckler, D. Xin, S. Zhang, J. 2023-09-29 doi:10.1101/2023.09.25.559437 Cold Spring Harbor Laboratory Press 2023-09-29 <![CDATA[ PhyGCN: Pre-trained Hypergraph Convolutional Neural Networks with Self-supervised Learning ]]> https://biorxiv.org/content/10.1101/2023.10.01.560404v1?rss=1 Deng, Y. Zhang, R. Xu, P. Ma, J. Gu, Q. 2023-10-02 doi:10.1101/2023.10.01.560404 Cold Spring Harbor Laboratory Press 2023-10-02 <![CDATA[ Beta-catenin inhibition disrupts the homeostasis of osteogenic/adipogenic differentiation leading to the development of glucocorticoid-induced osteonecrosis of femoral head ]]> https://biorxiv.org/content/10.1101/2023.10.04.560853v1?rss=1 Xia, C. Xu, H. Fang, L. Chen, J. Yuan, W. Fu, D. Wang, X. He, B. Xiao, L. Wu, C. Tong, P. Chen, D. Wang, P. Jin, H. 2023-10-06 doi:10.1101/2023.10.04.560853 Cold Spring Harbor Laboratory Press 2023-10-06 <![CDATA[ Decoding Internal Decision Making During Reverse Engineering Tasks ]]> https://biorxiv.org/content/10.1101/2023.10.10.561734v1?rss=1 Marsh, B. Rego, J. Levy, M. M. Sayer, M. P. Waagen, A. Barbieux, A. Cranford, E. A. Morrison, D. F. Maldonado, F. Johnson, J. P. DiVita, J. Buch, J. M. Kim, T. H.-J. Lebiere, C. Fugate, S. Bhattacharyya, R. 2023-10-10 doi:10.1101/2023.10.10.561734 Cold Spring Harbor Laboratory Press 2023-10-10 <![CDATA[ Analyzing Drumming Technique with Trajectory Optimization ]]> https://biorxiv.org/content/10.1101/2023.10.09.561270v1?rss=1 Pearl, O. D. 2023-10-11 doi:10.1101/2023.10.09.561270 Cold Spring Harbor Laboratory Press 2023-10-11 <![CDATA[ Ependymocytes control cerebrospinal fluid flow to the peripheral organs through periaxonal pathway ]]> https://biorxiv.org/content/10.1101/2023.10.09.560634v1?rss=1 Li, X. Wang, S. Zhang, D. Feng, Y. Liu, Y. Yu, W. Li, S. Cui, L. Harkany, T. Verkhratsky, A. Xia, M. Li, B. 2023-10-13 doi:10.1101/2023.10.09.560634 Cold Spring Harbor Laboratory Press 2023-10-13 <![CDATA[ Continuous Tracking using Deep Learning-based Decoding for Non-invasive Brain-Computer Interface ]]> https://biorxiv.org/content/10.1101/2023.10.12.562084v1?rss=1 Forenzo, D. Zhu, H. Shanahan, J. Lim, J. He, B. 2023-10-17 doi:10.1101/2023.10.12.562084 Cold Spring Harbor Laboratory Press 2023-10-17 <![CDATA[ Enhanced K Na 1.1 Channel Underlies Cortical Hyperexcitability and Seizure Susceptibility after Traumatic Brain Injury ]]> https://biorxiv.org/content/10.1101/2023.10.14.562359v1?rss=1 Liu, R. Sun, L. Du, L. Guo, X. Jia, M. Wang, Q. Wu, J. 2023-10-17 doi:10.1101/2023.10.14.562359 Cold Spring Harbor Laboratory Press 2023-10-17 <![CDATA[ Learning gene networks under SNP perturbation using SNP and allele-specific expression data ]]> https://biorxiv.org/content/10.1101/2023.10.23.563661v1?rss=1 Yoon, J. H. Kim, S. 2023-10-24 doi:10.1101/2023.10.23.563661 Cold Spring Harbor Laboratory Press 2023-10-24 <![CDATA[ Effect of homotypic vs. heterotypic interactions on the cellular uptake of extracellular vesicles ]]> https://biorxiv.org/content/10.1101/2023.10.23.563628v1?rss=1 View larger version (54K): org.highwire.dtl.DTLVardef@d5cb50org.highwire.dtl.DTLVardef@172d1dorg.highwire.dtl.DTLVardef@192caf6org.highwire.dtl.DTLVardef@4b16ba_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Jhaveri, J. R. Khare, P. Kamte, Y. S. Chandwani, M. N. Pinky, P. P. Milosevic, J. Abraham, N. Zheng, S.-y. O'Donnell, L. Manickam, D. S. 2023-10-25 doi:10.1101/2023.10.23.563628 Cold Spring Harbor Laboratory Press 2023-10-25 <![CDATA[ A Fuzzy sequencer for rapid DNA fragment counting and genotyping ]]> https://biorxiv.org/content/10.1101/2023.10.24.563729v1?rss=1 Zhou, W. Kang, L. Qiao, S. Duan, H. Yin, C. Liao, Z. Tang, M. Zhang, R. Li, L. Shi, L. Du, M. Wang, Y. Yue, W. Xiao, Y. Di, L. Zhang, X. Pang, Y. Li, M. Ren, L. Wang, J. Chen, Z. Huang, Y. 2023-10-27 doi:10.1101/2023.10.24.563729 Cold Spring Harbor Laboratory Press 2023-10-27 <![CDATA[ Ornaments for Accurate and Efficient Allele-Specific Expression Estimation with Bias Correction ]]> https://biorxiv.org/content/10.1101/2023.10.25.564046v1?rss=1 Adduri, A. Kim, S. 2023-10-29 doi:10.1101/2023.10.25.564046 Cold Spring Harbor Laboratory Press 2023-10-29 <![CDATA[ Nucleolus and centromere TSA-Seq reveals variable localization of heterochromatin in different cell types ]]> https://biorxiv.org/content/10.1101/2023.10.29.564613v1?rss=1 Kumar, P. Gholamalamdari, O. Zhang, Y. Zhang, L. Vertii, A. van Schaik, T. Peric-Hupkes, D. Sasaki, T. Gilbert, D. M. van Steensel, B. Ma, J. Kaufman, P. D. Belmont, A. S. 2023-11-01 doi:10.1101/2023.10.29.564613 Cold Spring Harbor Laboratory Press 2023-11-01 <![CDATA[ Energy in functional brain states correlates with cognition in adolescent schizophrenia and healthy persons ]]> https://biorxiv.org/content/10.1101/2023.11.06.565753v1?rss=1 Theis, N. Bahuguna, J. Rubin, J. Muldoon, B. Prasad, K. M. 2023-11-07 doi:10.1101/2023.11.06.565753 Cold Spring Harbor Laboratory Press 2023-11-07 <![CDATA[ In-silico analysis of Myocardial Infarction-related missense SNPs to identify novel biomarkers to predict susceptibility. ]]> https://biorxiv.org/content/10.1101/2023.11.07.565946v1?rss=1 Tarlochan, F. F. Rasool, S. 2023-11-09 doi:10.1101/2023.11.07.565946 Cold Spring Harbor Laboratory Press 2023-11-09 <![CDATA[ FFCM-MRF: An accurate and generalizable cerebrovascular segmentation pipeline for humans and rhesus monkeys based on TOF-MRA ]]> https://biorxiv.org/content/10.1101/2023.11.07.566142v1?rss=1 Cui, Y. Huang, H. Liu, J. Zhao, M. Li, C. Han, X. Luo, N. Gao, J. Yan, D. Zhang, C. Jiang, T. Yu, S. 2023-11-11 doi:10.1101/2023.11.07.566142 Cold Spring Harbor Laboratory Press 2023-11-11 <![CDATA[ Modeling the effect of spatial structure on solid tumor evolution and ctDNA composition ]]> https://biorxiv.org/content/10.1101/2023.11.10.566658v1?rss=1 Rachman, T. Bartlett, D. Laframboise, W. Wagner, P. Schwartz, R. Carja, O. 2023-11-11 doi:10.1101/2023.11.10.566658 Cold Spring Harbor Laboratory Press 2023-11-11 <![CDATA[ Improving Hi-C contact matrices using genome graphs ]]> https://biorxiv.org/content/10.1101/2023.11.08.566275v1?rss=1 Shen, Y. Yu, L. Qiu, Y. Zhang, T. Kingsford, C. 2023-11-12 doi:10.1101/2023.11.08.566275 Cold Spring Harbor Laboratory Press 2023-11-12 <![CDATA[ Urine proteomic analysis of patients with schizophrenia ]]> https://biorxiv.org/content/10.1101/2023.11.11.566683v1?rss=1 Zhao, C. Dong, F. Zhou, F. Huan, Y. Gao, Y. Yang, J. 2023-11-12 doi:10.1101/2023.11.11.566683 Cold Spring Harbor Laboratory Press 2023-11-12 <![CDATA[ Genome folding principles revealed in condensin-depleted mitotic chromosomes ]]> https://biorxiv.org/content/10.1101/2023.11.09.566494v1?rss=1 Zhao, H. Lin, Y. Lin, E. Liu, F. Shu, L. Jing, D. Wang, B. Wang, M. Shan, F. Zhang, L. Lam, J. Midla, S. Giardine, B. Keller, C. Hardison, R. Blobel, G. Zhang, H. 2023-11-13 doi:10.1101/2023.11.09.566494 Cold Spring Harbor Laboratory Press 2023-11-13 <![CDATA[ Dorsolateral striatum encodes a temporal basis for the organization of behavior ]]> https://biorxiv.org/content/10.1101/2023.11.13.566826v1?rss=1 Rodrigues, F. S. Monteiro, T. Motiwala, A. Paton, J. J. 2023-11-14 doi:10.1101/2023.11.13.566826 Cold Spring Harbor Laboratory Press 2023-11-14 <![CDATA[ Fast evolution of SARS-CoV-2 BA.2.86 to JN.1 under heavy immune pressure ]]> https://biorxiv.org/content/10.1101/2023.11.13.566860v1?rss=1 Cao, Y. Yang, S. Yu, Y. Xu, Y. Jian, F. Song, W. Yisimayi, A. Wang, P. Wang, J. Liu, J. Yu, L. Niu, X. Wang, J. Wang, Y. Shao, F. Jin, R. Wang, Y. 2023-11-16 doi:10.1101/2023.11.13.566860 Cold Spring Harbor Laboratory Press 2023-11-16 <![CDATA[ PPARγ controls ESCRT-dependent fibroblast-like synoviocyte exosome biogenesis and Alleviates Chondrocyte Osteoarthritis Mediated by Exosomal ANXA1 ]]> https://biorxiv.org/content/10.1101/2023.11.19.567728v1?rss=1 Jia, S. Yang, Y. Liu, J. Wei, Y. Wang, Z. Yue, L. Bai, L. 2023-11-19 doi:10.1101/2023.11.19.567728 Cold Spring Harbor Laboratory Press 2023-11-19 <![CDATA[ Metagenome profiling and containment estimation through abundance-corrected k-mer sketching with sylph ]]> https://biorxiv.org/content/10.1101/2023.11.20.567879v1?rss=1 Shaw, J. Yu, Y. W. 2023-11-20 doi:10.1101/2023.11.20.567879 Cold Spring Harbor Laboratory Press 2023-11-20 <![CDATA[ Compact deep neural network models of visual cortex ]]> https://biorxiv.org/content/10.1101/2023.11.22.568315v1?rss=1 Cowley, B. R. Stan, P. L. Pillow, J. W. Smith, M. A. 2023-11-23 doi:10.1101/2023.11.22.568315 Cold Spring Harbor Laboratory Press 2023-11-23 <![CDATA[ eSVD-DE: Cohort-wide differential expression in single-cell RNA-seq data using exponential-family embeddings ]]> https://biorxiv.org/content/10.1101/2023.11.22.568369v1?rss=1 Lin, K. Qiu, Y. Roeder, K. 2023-11-23 doi:10.1101/2023.11.22.568369 Cold Spring Harbor Laboratory Press 2023-11-23 <![CDATA[ VirusImmu: a novel ensemble machine learning approach for viral immunogenicity prediction ]]> https://biorxiv.org/content/10.1101/2023.11.23.568426v1?rss=1 Li, J. Zhao, Z. Tai, C. Sun, T. Tan, L. Li, X. He, W. Li, H. Zhang, J. 2023-11-23 doi:10.1101/2023.11.23.568426 Cold Spring Harbor Laboratory Press 2023-11-23 <![CDATA[ Familiarity training enhance straightening of neural trajectory for video prediction ]]> https://biorxiv.org/content/10.1101/2023.11.29.569215v1?rss=1 Qiu, W. Huang, S. Mukundan, M. Lee, T. S. 2023-12-01 doi:10.1101/2023.11.29.569215 Cold Spring Harbor Laboratory Press 2023-12-01 <![CDATA[ Mechanical positive feedback and biochemical negative feedback combine to generate complex contractile oscillations in cytokinesis ]]> https://biorxiv.org/content/10.1101/2023.12.01.569672v1?rss=1 Werner, M. E. Ray, D. D. Breen, C. Staddon, M. F. Jug, F. Banerjee, S. Maddox, A. S. 2023-12-03 doi:10.1101/2023.12.01.569672 Cold Spring Harbor Laboratory Press 2023-12-03 <![CDATA[ Contextualized Networks Reveal Heterogeneous Transcriptomic Regulation in Tumors at Sample-Specific Resolution ]]> https://biorxiv.org/content/10.1101/2023.12.01.569658v1?rss=1 Ellington, C. N. Lengerich, B. J. Watkins, T. B. Yang, J. Xiao, H. Kellis, M. Xing, E. P. 2023-12-04 doi:10.1101/2023.12.01.569658 Cold Spring Harbor Laboratory Press 2023-12-04 <![CDATA[ Sc-TUSV-ext: Single-cell clonal lineage inference from single nucleotide variants (SNV), copy number alterations (CNA) and structural variants (SV) ]]> https://biorxiv.org/content/10.1101/2023.12.07.570724v1?rss=1 Bristy, N. A. Fu, X. Schwartz, R. 2023-12-08 doi:10.1101/2023.12.07.570724 Cold Spring Harbor Laboratory Press 2023-12-08 <![CDATA[ Targeting F-actin stress fibers to suppress the dedifferentiated phenotype in chondrocytes ]]> https://biorxiv.org/content/10.1101/2023.12.08.570865v1?rss=1 Schofield, M. M. Rzepski, A. Hammerstedt, J. Shah, S. Mirack, C. Parreno, J. 2023-12-09 doi:10.1101/2023.12.08.570865 Cold Spring Harbor Laboratory Press 2023-12-09 <![CDATA[ Stimulus-reward contingencies drive long-lasting alterations in neocortical somatostatin inhibition during learning ]]> https://biorxiv.org/content/10.1101/2023.12.08.570881v1?rss=1 Park, E. Kuljis, D. A. Zhu, M. Christian, J. A. Barth, A. L. 2023-12-09 doi:10.1101/2023.12.08.570881 Cold Spring Harbor Laboratory Press 2023-12-09 <![CDATA[ Aberrant methylation and expression of TNXB promotes chondrocyte apoptosis and extracullar matrix degradation in hemophilic arthropathy via AKT signaling ]]> https://biorxiv.org/content/10.1101/2023.12.11.570472v1?rss=1 Chen, J. Zeng, Q. Wang, X. Xu, R. Wang, W. Huang, Y. Sun, Q. Yuan, W. Wang, P. Chen, D. Tong, P. Jin, H. 2023-12-11 doi:10.1101/2023.12.11.570472 Cold Spring Harbor Laboratory Press 2023-12-11 <![CDATA[ FOXA2 is essential for maintaining the urea cycle in acute liver failure ]]> https://biorxiv.org/content/10.1101/2023.12.11.570955v1?rss=1 Feng, R. Liu, R. Tong, C. Lin, T. Li, X. Liu, H. Shao, C. Kan, K. Sticht, C. Li, Y. Wang, S. Munker, S. Wirth, U. Niess, H. Liebe, R. Meyer, C. Wang, S. Ebert, M. P. Dooley, S. Ding, H. Wang, H. Weng, H. 2023-12-11 doi:10.1101/2023.12.11.570955 Cold Spring Harbor Laboratory Press 2023-12-11 <![CDATA[ Pneumococcal Extracellular Vesicles Mediate Horizontal Gene Transfer via the Transformation Machinery ]]> https://biorxiv.org/content/10.1101/2023.12.15.571797v1?rss=1 Werner Lass, S. Camphire, S. Smith, B. E. Smith, R. A. Prentice, J. A. Yerneni, S. S. Arun, A. Bridges, A. A. Rosch, J. W. Conway, J. F. Campbell, P. Hiller, N. L. 2023-12-15 doi:10.1101/2023.12.15.571797 Cold Spring Harbor Laboratory Press 2023-12-15 <![CDATA[ Effect of Artificial Lung Fiber Bundle Geometric Design on Micro- and Macro-scale Clot Formation ]]> https://biorxiv.org/content/10.1101/2024.01.05.574443v1?rss=1 Lai, A. Omori, N. Napolitano, J. E. Antaki, J. F. Cook, K. 2024-01-08 doi:10.1101/2024.01.05.574443 Cold Spring Harbor Laboratory Press 2024-01-08 <![CDATA[ Transcranial Focused Ultrasound Remotely Modulates Extrastriate Visual Cortex with Subregion Specificity ]]> https://biorxiv.org/content/10.1101/2024.01.20.576476v1?rss=1 Yu, K. Schmitt, S. Ni, Y. Crane, E. C. Smith, M. A. He, B. 2024-01-22 doi:10.1101/2024.01.20.576476 Cold Spring Harbor Laboratory Press 2024-01-22 <![CDATA[ Prognostic Significance of preoperative serum CA125, CA19-9, CA72-4, CEA, and AFP in Patients with Endometrial cancer ]]> https://biorxiv.org/content/10.1101/2024.01.23.576857v1?rss=1 Wang, Z.-h. Zhang, Y.-z. Ge, S.-w. Shan, L.-h. Wang, B. Zhang, Z.-y. Wu, Q.-j. Ma, X.-x. 2024-01-26 doi:10.1101/2024.01.23.576857 Cold Spring Harbor Laboratory Press 2024-01-26 <![CDATA[ k-nonical space: sketching with reverse complements ]]> https://biorxiv.org/content/10.1101/2024.01.25.577301v1?rss=1 Marcais, G. Elder, S. Kingsford, C. 2024-01-27 doi:10.1101/2024.01.25.577301 Cold Spring Harbor Laboratory Press 2024-01-27 <![CDATA[ High Shear Stress Reduces ERG Causing Endothelial-Mesenchymal Transition and Pulmonary Arterial Hypertension ]]> https://biorxiv.org/content/10.1101/2024.02.02.578526v1?rss=1 Shinohara, T. Moonen, J.-R. A. J. Chun, Y. H. Lee-Yow, Y. C. Okamura, K. Szafron, J. M. Kaplan, J. Cao, A. Wang, L. Taylor, S. Isobe, S. Dong, M. Yang, W. Guo, K. Franco, B. D. Pacharinsak, C. Pisani, L. J. Saitoh, S. Mitani, Y. Marsden, A. L. Engreitz, J. Korbelin, J. Rabinovitch, M. 2024-02-05 doi:10.1101/2024.02.02.578526 Cold Spring Harbor Laboratory Press 2024-02-05 <![CDATA[ AttentionPert: Accurately Modeling Multiplexed Genetic Perturbations with Multi-scale Effects ]]> https://biorxiv.org/content/10.1101/2024.02.02.578656v1?rss=1 Bai, D. Ellington, C. Mo, S. Song, L. Xing, E. 2024-02-07 doi:10.1101/2024.02.02.578656 Cold Spring Harbor Laboratory Press 2024-02-07 <![CDATA[ A Vascular Dissection and Rupture Linked Metabolite Acts Via BLT2 Receptor ]]> https://biorxiv.org/content/10.1101/2024.02.15.580482v1?rss=1 Wang, Y. Li, Y. Yu, J. Chen, W. Tan, X. Xu, X. Lin, R. Wang, X. Jiang, W. Du, J. 2024-02-16 doi:10.1101/2024.02.15.580482 Cold Spring Harbor Laboratory Press 2024-02-16 <![CDATA[ EGF/STAT1 signals to maintain ECM1 expression in hepatic homeostasis are disrupted by IFNγ/NRF2 in chronic liver disease ]]> https://biorxiv.org/content/10.1101/2024.02.17.580798v1?rss=1 Li, Y. Link, F. Fan, W. Nwosu, Z. C. Pioronska, W. Gould, K. Meyer, C. Yao, Y. Hammad, S. Feng, R. Liu, H. Shao, C. Sun, B. Ding, H. Liebe, R. Ebert, M. P. A. Weng, H.-L. ten Dijke, P. Dooley, S. Wang, S. 2024-02-19 doi:10.1101/2024.02.17.580798 Cold Spring Harbor Laboratory Press 2024-02-19 <![CDATA[ CNVeil enables accurate and robust tumor subclone identification and copy number estimation from single-cell DNA sequencing data ]]> https://biorxiv.org/content/10.1101/2024.02.21.581409v1?rss=1 Yuan, W. Luo, C. Hu, Y. Zhang, L. Wen, Z. Liu, Y. H. Mallory, X. Zhou, X. M. 2024-02-23 doi:10.1101/2024.02.21.581409 Cold Spring Harbor Laboratory Press 2024-02-23 <![CDATA[ Feature-independent Encoding of Visual Salience inthe Mouse Superior Colliculus ]]> https://biorxiv.org/content/10.1101/2024.03.04.583246v1?rss=1 Wu, R. Xu, J. Li, C. Zhang, Z. Li, L.-y. Li, Y. 2024-03-06 doi:10.1101/2024.03.04.583246 Cold Spring Harbor Laboratory Press 2024-03-06 <![CDATA[ Antigenicity assessment of SARS-CoV-2 saltation variant BA.2.87.1 ]]> https://biorxiv.org/content/10.1101/2024.03.07.583823v1?rss=1 Yang, S. Yu, Y. Jian, F. Yisimayi, A. Song, W. Liu, J. Wang, P. Xu, Y. Wang, J. Niu, X. Yu, L. Wang, Y. Shao, F. Jin, R. Wang, Y. Cao, Y. 2024-03-08 doi:10.1101/2024.03.07.583823 Cold Spring Harbor Laboratory Press 2024-03-08 <![CDATA[ 3DCellComposer - A Versatile Pipeline Utilizing 2D Cell Segmentation Methods for 3D Cell Segmentation ]]> https://biorxiv.org/content/10.1101/2024.03.08.584082v1?rss=1 Chen, H. Murphy, R. F. 2024-03-12 doi:10.1101/2024.03.08.584082 Cold Spring Harbor Laboratory Press 2024-03-12 <![CDATA[ Determining Optimal Placement of Copy Number Aberration Impacted Single Nucleotide Variants in a Tumor Progression History ]]> https://biorxiv.org/content/10.1101/2024.03.10.584318v1?rss=1 Wu, C. H. Joshi, S. Robinson, W. Robbins, P. F. Schwartz, R. Sahinalp, C. Malikic, S. 2024-03-13 doi:10.1101/2024.03.10.584318 Cold Spring Harbor Laboratory Press 2024-03-13 <![CDATA[ Impact of Reduced Spectral Resolution on Temporal-Coherence-Based Source Segregation ]]> https://biorxiv.org/content/10.1101/2024.03.11.584489v1?rss=1 Viswanathan, V. Heinz, M. G. Shinn-Cunningham, B. G. 2024-03-13 doi:10.1101/2024.03.11.584489 Cold Spring Harbor Laboratory Press 2024-03-13 <![CDATA[ Widespread variation in molecular interactions and regulatory properties among transcription factor isoforms ]]> https://biorxiv.org/content/10.1101/2024.03.12.584681v1?rss=1 Lambourne, L. Mattioli, K. Santoso, C. Sheynkman, G. Inukai, S. Kaundal, B. Berenson, A. Spirohn-Fitzgerald, K. Bhattacharjee, A. Rothman, E. Shrestha, S. Laval, F. Yang, Z. Bisht, D. Sewell, J. A. Li, G. Prasad, A. Phanor, S. Lane, R. Campbell, D. M. Hunt, T. Balcha, D. Gebbia, M. Twizere, J.-C. Hao, T. Frankish, A. Riback, J. Salomonis, N. Calderwood, M. A. Hill, D. E. Sahni, N. Vidal, M. Bulyk, M. L. Fuxman Bass, J. I. 2024-03-14 doi:10.1101/2024.03.12.584681 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ CAR T cell infiltration and cytotoxic killing within the core of 3D breast cancer spheroids under control of antigen sensing in microwell arrays ]]> https://biorxiv.org/content/10.1101/2024.03.14.585033v1?rss=1 Cho, Y. Laird, M. Bishop, T. Li, R. Ruffo, E. Lohmueller, J. Zervantonakis, I. K. 2024-03-15 doi:10.1101/2024.03.14.585033 Cold Spring Harbor Laboratory Press 2024-03-15 <![CDATA[ Optimizing Design of Genomics Studies for Clonal Evolution Analysis ]]> https://biorxiv.org/content/10.1101/2024.03.14.585055v1?rss=1 Srivatsa, A. Schwartz, R. 2024-03-15 doi:10.1101/2024.03.14.585055 Cold Spring Harbor Laboratory Press 2024-03-15 <![CDATA[ CHAI: Consensus Clustering Through Similarity Matrix Integration for Cell-Type Identification ]]> https://biorxiv.org/content/10.1101/2024.03.19.585758v1?rss=1 Lodi, M. Lodi, M. Osei, K. Ranganathan, V. Hwang, P. Ghosh, P. 2024-03-22 doi:10.1101/2024.03.19.585758 Cold Spring Harbor Laboratory Press 2024-03-22 <![CDATA[ Marker selection strategies for circulating tumor DNA guided by phylogenetic inference ]]> https://biorxiv.org/content/10.1101/2024.03.21.585352v1?rss=1 Fu, X. Luo, Z. Deng, Y. LaFramboise, W. A. Bartlett, D. Schwartz, R. 2024-03-27 doi:10.1101/2024.03.21.585352 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences ]]> https://biorxiv.org/content/10.1101/2024.03.22.586363v1?rss=1 Xu, C. Bao, S. Chen, H. Jiang, T. Zhang, C. 2024-03-25 doi:10.1101/2024.03.22.586363 Cold Spring Harbor Laboratory Press 2024-03-25 <![CDATA[ Augmented Doubly Robust Post-Imputation Inference for Proteomic data ]]> https://biorxiv.org/content/10.1101/2024.03.23.586387v1?rss=1 Moon, H. Du, J.-H. Lei, J. Roeder, K. 2024-03-27 doi:10.1101/2024.03.23.586387 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Completion of the DrugMatrix Toxicogenomics Database using ToxCompl ]]> https://biorxiv.org/content/10.1101/2024.03.26.586669v1?rss=1 Cong, G. Patton, R. M. Chao, F. Svoboda, D. L. Casey, W. M. Schmitt, C. P. Murphy, C. Erickson, J. N. Combs, P. A. Auerbach, S. S. 2024-03-29 doi:10.1101/2024.03.26.586669 Cold Spring Harbor Laboratory Press 2024-03-29 <![CDATA[ Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas Construction and Usage ]]> https://biorxiv.org/content/10.1101/2024.03.27.587041v1?rss=1 Boerner, K. Blood, P. D. Silverstein, J. C. Ruffalo, M. Teichmann, S. A. Pryhuber, G. Misra, R. S. Purkerson, J. M. Fan, J. Hickey, J. W. Molla, G. Xu, C. Zhang, Y. Weber, G. M. Jain, Y. Qaurooni, D. Kong, Y. Bueckle, A. Herr, B. W. 2024-04-02 doi:10.1101/2024.03.27.587041 Cold Spring Harbor Laboratory Press 2024-04-02 <![CDATA[ Intracranial Mapping of Response Latencies and Task Effects for Spoken Syllable Processing in the Human Brain ]]> https://biorxiv.org/content/10.1101/2024.04.05.588349v1?rss=1 Viswanathan, V. Rupp, K. M. Hect, J. L. Harford, E. E. Holt, L. L. Abel, T. J. 2024-04-05 doi:10.1101/2024.04.05.588349 Cold Spring Harbor Laboratory Press 2024-04-05 <![CDATA[ The ER Thioredoxin-Related Transmembrane Protein TMX2 Controls Redox-Mediated Tethering of ER-Mitochondria Contacts (ERMCS) ]]> https://biorxiv.org/content/10.1101/2024.04.12.589228v1?rss=1 View larger version (71K): org.highwire.dtl.DTLVardef@809587org.highwire.dtl.DTLVardef@1d8ef0corg.highwire.dtl.DTLVardef@135fdc6org.highwire.dtl.DTLVardef@1a7f7b6_HPS_FORMAT_FIGEXP M_FIG C_FIG The transmembrane thioredoxin-related TMX2 prevents TOM70 sulfenylation at ERMCS, thus maintaining normal mitochondria metabolism in wild-type cells. TMX2 knockout leads to TOM70 sulfenylation and tight ERMCS formation. This then increases ROS production, unbalances mitochondrial lipids, and relatively shifts OXPHOS electron supply to complex II. ]]> Chen, J. Yap, M. C. Bassot, A. Pascual, D. M. Makio, T. Zimmermann, J. Mast, H. Bhat, R. Fleury, S. G. Fan, Y. Zardini Buzatto, A. Moore, J. Ballanyi, K. Li, L. Overduin, M. Lemieux, M. J. Lemieux, H. Tan, W.-H. Mancini, G. M. S. Morgan, B. Marcogliese, P. C. Simmen, T. 2024-04-13 doi:10.1101/2024.04.12.589228 Cold Spring Harbor Laboratory Press 2024-04-13 <![CDATA[ UK BioCoin: Swift Trait-Specific Summary Statistics Regression for UK Biobank ]]> https://biorxiv.org/content/10.1101/2024.04.12.589273v1?rss=1 He, J.-C. Qi, G.-A. Ying, J. Qian, Y. Han, L. Mao, Y. Zheng, H.-F. Jiang, H. Chen, G.-B. 2024-04-15 doi:10.1101/2024.04.12.589273 Cold Spring Harbor Laboratory Press 2024-04-15 <![CDATA[ Competition for resources can reshape the evolutionary properties of spatial structure ]]> https://biorxiv.org/content/10.1101/2024.04.13.589370v1?rss=1 Devadhasan, A. Kolodny, O. Carja, O. 2024-04-16 doi:10.1101/2024.04.13.589370 Cold Spring Harbor Laboratory Press 2024-04-16 <![CDATA[ Lipid Nanoparticle-Associated Inflammation is Triggered by Sensing of Endosomal Damage: Engineering Endosomal Escape without Side Effects ]]> https://biorxiv.org/content/10.1101/2024.04.16.589801v1?rss=1 Omo-Lamai, S. Wang, Y. Patel, M. N. Essien, E.-o. Shen, M. Majumder, A. Espy, C. Wu, J. Channer, B. Tobin, M. P. Murali, S. Papp, T. E. Maheshwari, R. Wang, L. Chase, L. S. Zamora, M. E. Arral, M. L. Marcos-Contreras, O. A. Myerson, J. W. Hunter, C. A. Tsourkas, A. Muzykantov, V. Brodsky, I. E. Shin, S. Whitehead, K. A. Gaskill, P. Discher, D. Parhiz, H. Brenner, J. S. 2024-04-18 doi:10.1101/2024.04.16.589801 Cold Spring Harbor Laboratory Press 2024-04-18 <![CDATA[ A theory of brain-computer interface learning via low-dimensional control ]]> https://biorxiv.org/content/10.1101/2024.04.18.589952v1?rss=1 Menendez, J. A. Hennig, J. A. Golub, M. D. Oby, E. R. Sadtler, P. T. Batista, A. P. Chase, S. M. Yu, B. M. Latham, P. E. 2024-04-22 doi:10.1101/2024.04.18.589952 Cold Spring Harbor Laboratory Press 2024-04-22 <![CDATA[ Nuclear speckle rejuvenation alleviates proteinopathies at the expense of YAP1 ]]> https://biorxiv.org/content/10.1101/2024.04.18.590103v1?rss=1 Dion, W. Tao, Y. Chambers, M. Zhao, S. Arbuckle, R. K. Sun, M. Kubra, S. Nie, Y. Ye, M. Larsen, M. B. Camarco, D. Ickes, E. DuPont, C. Wang, H. Wang, B. Liu, S. Pi, S. Chen, B. B. Chen, Y. Chen, X. Zhu, B. 2024-04-21 doi:10.1101/2024.04.18.590103 Cold Spring Harbor Laboratory Press 2024-04-21 <![CDATA[ Humoral immunogenicity comparison of XBB and JN.1 in human infections ]]> https://biorxiv.org/content/10.1101/2024.04.19.590276v1?rss=1 Jian, F. Yisimayi, A. Song, W. Wang, J. Xu, Y. Chen, X. Yu, Y. Niu, X. Yang, S. Wang, P. Sun, H. Yu, L. Wang, J. Wang, Y. An, R. Wang, W. Xiao, T. Gu, Q. Shao, F. Wang, Y. Shen, Z. Jin, R. Cao, Y. 2024-04-22 doi:10.1101/2024.04.19.590276 Cold Spring Harbor Laboratory Press 2024-04-22 <![CDATA[ A new series of fluorogen-activating proteins for quantitative protein trafficking and co-localization studies in S. cerevisiae ]]> https://biorxiv.org/content/10.1101/2024.04.20.590399v1?rss=1 Oppenheimer, K. G. Hager, N. A. McAtee, C. K. Filiztekin, E. Shang, C. Warnick, J. A. Bruchez, M. P. Brodsky, J. L. Prosser, D. C. Kwiatkowski, A. V. O'Donnell, A. F. 2024-04-22 doi:10.1101/2024.04.20.590399 Cold Spring Harbor Laboratory Press 2024-04-22 <![CDATA[ Short-Term Disruption of TGFβ Signaling in Adult Mice Renders the Aorta Vulnerable to Hypertension-Induced Dissection ]]> https://biorxiv.org/content/10.1101/2024.04.22.590484v1?rss=1 Jiang, B. Ren, P. He, C. Wang, M. Murtada, S.-I. Chen, Y. Ramachandra, A. B. Li, G. Qin, L. Assi, R. Schwartz, M. A. Humphrey, J. D. Tellides, G. 2024-04-26 doi:10.1101/2024.04.22.590484 Cold Spring Harbor Laboratory Press 2024-04-26 <![CDATA[ Fairy: fast approximate coverage for multi-samplemetagenomic binning ]]> https://biorxiv.org/content/10.1101/2024.04.23.590803v1?rss=1 250x faster than read alignment and accurate enough for binning. Fairy is compatible with several existing binners on host and non-host-associated datasets. Using MetaBAT2, fairy recovers 98.5% of MAGs with > 50% completeness and < 5% incompleteness relative to alignment with BWA. Notably, multi-sample binning with fairy is always better than single-sample binning using BWA (> 1.5x more > 50% complete MAGs on average) while still being faster. For a public sediment metagenome project, we demonstrate that multisample binning recovers higher quality Asgard archaea MAGs than single-sample binning and that fairys results are indistinguishable from read alignment. ConclusionsFairy is a new tool for approximately and quickly calculating multi-sample coverage for binning, resolving a longstanding computational bottleneck for metagenomics. ]]> Shaw, J. Yu, Y. W. 2024-04-28 doi:10.1101/2024.04.23.590803 Cold Spring Harbor Laboratory Press 2024-04-28 <![CDATA[ Beyond A and B Compartments: how major nuclear locales define nuclear genome organization and function ]]> https://biorxiv.org/content/10.1101/2024.04.23.590809v1?rss=1 Gholamalamdari, O. van Schaik, T. Wang, Y. Kumar, P. Zhang, L. Zhang, Y. Gonzalez, G. A. H. Vouzas, A. E. Zhao, P. A. Gilbert, D. M. Ma, J. van Steensel, B. Belmont, A. S. 2024-04-23 doi:10.1101/2024.04.23.590809 Cold Spring Harbor Laboratory Press 2024-04-23 <![CDATA[ Exploring differences between depression and bipolar disorder through the urinary proteome ]]> https://biorxiv.org/content/10.1101/2024.04.24.590930v1?rss=1 Liu, Y. Li, Z. Dong, Y. Yang, J. Li, M. Zhou, J. Gao, Y. Li, J. Wang, G. Gao, Y. 2024-04-26 doi:10.1101/2024.04.24.590930 Cold Spring Harbor Laboratory Press 2024-04-26 <![CDATA[ Mimicking opioid analgesia in cortical pain circuits ]]> https://biorxiv.org/content/10.1101/2024.04.26.591113v1?rss=1 View larger version (28K): org.highwire.dtl.DTLVardef@d294c0org.highwire.dtl.DTLVardef@123d4f4org.highwire.dtl.DTLVardef@1720deborg.highwire.dtl.DTLVardef@efc632_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> James, J. G. McCall, N. M. Hsu, A. I. Oswell, C. S. Salimando, G. J. Mahmood, M. Wooldridge, L. M. Wachira, M. Jo, A. Sandoval Ortega, R. A. Wojick, J. A. Beattie, K. Farinas, S. A. Chehimi, S. N. Rodrigues, A. Ejoh, L. L. Kimmey, B. A. Lo, E. Azouz, G. Vasquez, J. J. Banghart, M. R. Creasy, K. T. Beier, K. T. Ramakrishnan, C. Crist, R. C. Reiner, B. C. Deisseroth, K. Yttri, E. A. Corder, G. 2024-04-29 doi:10.1101/2024.04.26.591113 Cold Spring Harbor Laboratory Press 2024-04-29 <![CDATA[ Brain-wide arousal signals are segregated from movement planning in the superior colliculus ]]> https://biorxiv.org/content/10.1101/2024.04.26.591284v1?rss=1 Johnson, R. Smith, M. A. 2024-04-29 doi:10.1101/2024.04.26.591284 Cold Spring Harbor Laboratory Press 2024-04-29 <![CDATA[ Heterogeneous Cardiac- and Neural Crest-Derived Aortic Smooth Muscle Cells have Similar Transcriptional Changes after TGFβ Signaling Disruption ]]> https://biorxiv.org/content/10.1101/2024.04.28.591539v1?rss=1 Ren, P. Jiang, B. Hassab, A. Li, G. Li, W. Assi, R. Tellides, G. 2024-04-30 doi:10.1101/2024.04.28.591539 Cold Spring Harbor Laboratory Press 2024-04-30 <![CDATA[ Spontaneous HFO Sequences Reveal Propagation Pathways for Precise Delineation of Epileptogenic Networks ]]> https://biorxiv.org/content/10.1101/2024.05.02.592202v1?rss=1 Cai, Z. Jiang, X. Bagic, A. Worrell, G. A. Richardson, M. He, B. 2024-05-05 doi:10.1101/2024.05.02.592202 Cold Spring Harbor Laboratory Press 2024-05-05 <![CDATA[ Arkypallidal neurons in the external globus pallidus can mediate inhibitory control by altering competition in the striatum ]]> https://biorxiv.org/content/10.1101/2024.05.03.592321v1?rss=1 Giossi, C. Bahuguna, J. Rubin, J. Verstynen, T. Vich, C. 2024-05-05 doi:10.1101/2024.05.03.592321 Cold Spring Harbor Laboratory Press 2024-05-05 <![CDATA[ FKBP11 targeted plasma cells promote abdominal aortic aneurysm progression through an m6A-dependent mechanism ]]> https://biorxiv.org/content/10.1101/2024.05.05.592616v1?rss=1 He, Y. Xing, J. Wang, S. Jiang, H. Lun, Y. Han, Y. Erhart, P. Boeckler, D. Zhang, J. 2024-05-06 doi:10.1101/2024.05.05.592616 Cold Spring Harbor Laboratory Press 2024-05-06 <![CDATA[ Interplay of condensate material properties and chromatin heterogeneity governs nuclear condensate ripening ]]> https://biorxiv.org/content/10.1101/2024.05.07.593010v1?rss=1 Banerjee, D. S. Chigumira, T. Lackner, R. M. Kratz, J. C. Chenoweth, D. M. Banerjee, S. Zhang, H. 2024-05-10 doi:10.1101/2024.05.07.593010 Cold Spring Harbor Laboratory Press 2024-05-10 <![CDATA[ Functional resilience of the neural visual recognition system post-pediatric occipitotemporal resection ]]> https://biorxiv.org/content/10.1101/2024.05.08.592792v1?rss=1 Granovetter, M. C. Maallo, A. M. S. Ling, S. Robert, S. Freud, E. Patterson, C. Behrmann, M. 2024-05-08 doi:10.1101/2024.05.08.592792 Cold Spring Harbor Laboratory Press 2024-05-08 <![CDATA[ Volumetric mesoscopic electrophysiology: a new imaging modality for the non-human primate ]]> https://biorxiv.org/content/10.1101/2024.05.13.593946v1?rss=1 Teichert, T. Papp, L. Vincze, F. Burns, N. Goodell, B. Ahmed, Z. Holmes, A. Gray, C. M. Chamanzar, M. Gurnsey, K. 2024-05-14 doi:10.1101/2024.05.13.593946 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ Omicron-specific naive B cell maturation alleviates immune imprinting induced by SARS-CoV-2 inactivated vaccine ]]> https://biorxiv.org/content/10.1101/2024.05.13.594034v1?rss=1 Yisimayi, A. Song, W. Wang, J. Jian, F. Yu, Y. Chen, X. Xu, Y. An, R. Wang, Y. Wang, J. Sun, H. Wang, P. Yu, L. Shao, F. Jin, R. Shen, Z. Wang, Y. Cao, Y. 2024-05-14 doi:10.1101/2024.05.13.594034 Cold Spring Harbor Laboratory Press 2024-05-14 <![CDATA[ iLipidome: enhancing statistical power and interpretability using hidden biosynthetic interdependencies in the lipidome ]]> https://biorxiv.org/content/10.1101/2024.05.16.594607v1?rss=1 Lin, W.-J. CHIANG, A. W. T. Zhou, E. H. Liang, C. Liu, C.-H. Ma, W.-L. Cheng, W.-C. Lewis, N. E. 2024-05-21 doi:10.1101/2024.05.16.594607 Cold Spring Harbor Laboratory Press 2024-05-21 <![CDATA[ Epidural Spinal Cord Recordings (ESRs): Sources of Artifact in Stimulation Evoked Compound Action Potentials ]]> https://biorxiv.org/content/10.1101/2024.05.17.594739v1?rss=1 Deshmukh, A. Settell, M. L. Cheng, K. L. Knudsen, B. Trevathan, J. K. LaLuzerne, M. Blanz, S. Skubal, A. Verma, N. Romanauski, B. Brucker-Hahn, M. Lam, D. Lavrov, I. Suminski, A. Weber, D. Fisher, L. Lempka, S. Shoffstall, A. Park, H. Ross Ellison, E. Zhang, M. Ludwig, K. 2024-05-17 doi:10.1101/2024.05.17.594739 Cold Spring Harbor Laboratory Press 2024-05-17 <![CDATA[ Human birth tissue products as a regenerative medicine to inhibit post-surgical pain through multi-modal action ]]> https://biorxiv.org/content/10.1101/2024.05.19.594874v1?rss=1 Zhang, C. Huang, Q. Ford, N. C. Limjunyawong, N. Lin, Q. Yang, F. Cui, X. Uniyal, A. Liu, J. Mahabole, M. He, H. Wang, X. Duff, I. Wang, Y. Wan, J. Zhu, G. Raja, S. N. Jia, H. Yang, D. Dong, X. Tseng, S. He, S. Guan, Y. 2024-05-20 doi:10.1101/2024.05.19.594874 Cold Spring Harbor Laboratory Press 2024-05-20 <![CDATA[ How cortico-basal ganglia-thalamic subnetworks can shift decision policies to maximize reward rate ]]> https://biorxiv.org/content/10.1101/2024.05.21.595174v1?rss=1 Bahuguna, J. Verstynen, T. V. Rubin, J. 2024-05-22 doi:10.1101/2024.05.21.595174 Cold Spring Harbor Laboratory Press 2024-05-22 <![CDATA[ Strain concentration drives the anatomical distribution of injury in acute and chronic traumatic brain injury ]]> https://biorxiv.org/content/10.1101/2024.05.22.595352v1?rss=1 Hirad, A. A. Mix, D. Venkataraman, A. Meyers, S. P. Mahon, B. Z. 2024-05-23 doi:10.1101/2024.05.22.595352 Cold Spring Harbor Laboratory Press 2024-05-23 <![CDATA[ Different state-dependence of population codes across cortex ]]> https://biorxiv.org/content/10.1101/2024.05.23.595581v1?rss=1 Bandi, A. Runyan, C. A. 2024-05-26 doi:10.1101/2024.05.23.595581 Cold Spring Harbor Laboratory Press 2024-05-26 <![CDATA[ Natural killer cell migration in HIV-infected individuals is inhibited by impairment of HIF-1alpha-mediated glycolysis ]]> https://biorxiv.org/content/10.1101/2024.05.31.596765v1?rss=1 Yu, X. Zhou, J. Lei, J. Ge, H. Zhang, Z. Fu, Y. Han, X. Hu, Q. Ding, H. Geng, W. Shang, H. Jiang, Y. 2024-06-03 doi:10.1101/2024.05.31.596765 Cold Spring Harbor Laboratory Press 2024-06-03 <![CDATA[ Magnified interaural level differences enhance spatial release from masking in bilateral cochlear implant users ]]> https://biorxiv.org/content/10.1101/2024.06.03.597254v1?rss=1 Richardson, B. N. Kainerstorfer, J. M. Shinn-Cunningham, B. G. Brown, C. A. 2024-06-04 doi:10.1101/2024.06.03.597254 Cold Spring Harbor Laboratory Press 2024-06-04 <![CDATA[ Insula uses overlapping codes for emotion in self and others ]]> https://biorxiv.org/content/10.1101/2024.06.04.596966v1?rss=1 Xiao, J. Adkinson, J. A. Allawala, A. B. Banks, G. Bartoli, E. Fan, X. Mocchi, M. Pascuzzi, B. Pulapaka, S. Franch, M. C. Mathew, S. J. Mathura, R. K. Myers, J. Pirtle, V. Provenza, N. R. Shofty, B. Watrous, A. J. Pitkow, X. Goodman, W. K. Pouratian, N. Sheth, S. A. Bijanki, K. R. Hayden, B. Y. 2024-06-08 doi:10.1101/2024.06.04.596966 Cold Spring Harbor Laboratory Press 2024-06-08 <![CDATA[ Hierarchical Bayesian inference to model continuous phenotypical progression in Alzheimer's Disease ]]> https://biorxiv.org/content/10.1101/2024.06.10.597236v1?rss=1 Agrawal, A. Rachleff, V. M. Travaglini, K. J. Mukherjee, S. Crane, P. Hawrylycz, M. Keene, C. D. Lein, E. Mena, G. E. Gabitto, M. I. 2024-06-10 doi:10.1101/2024.06.10.597236 Cold Spring Harbor Laboratory Press 2024-06-10 <![CDATA[ Evaluation of Machine Learning Models for Aqueous Solubility Prediction in Drug Discovery ]]> https://biorxiv.org/content/10.1101/2024.06.10.598383v1?rss=1 Liu, S. Zhang, Y. Xue, N. 2024-06-11 doi:10.1101/2024.06.10.598383 Cold Spring Harbor Laboratory Press 2024-06-11 <![CDATA[ Brain-derived exosomal hemoglobin transfer contributes to neuronal mitochondrial homeostasis under hypoxia ]]> https://biorxiv.org/content/10.1101/2024.06.11.598477v1?rss=1 Tian, Z. Jin, F. Xu, Z. Gu, Y. Guo, M. Li, Y. Shao, Q. Liu, Y. Luo, H. Wang, Y. Zhang, S. Yang, C. Liu, X. Ji, X. Liu, J. 2024-06-13 doi:10.1101/2024.06.11.598477 Cold Spring Harbor Laboratory Press 2024-06-13 <![CDATA[ A larval zebrafish model of TBI: Optimizing the dose of neurotrauma for discovery of treatments and aetiology ]]> https://biorxiv.org/content/10.1101/2024.06.14.599067v1?rss=1 Locskai, L. F. Gill, T. Tan, S. A. W. Burton, A. H. Alyenbaawi, H. Burton, E. A. Allison, W. T. 2024-06-14 doi:10.1101/2024.06.14.599067 Cold Spring Harbor Laboratory Press 2024-06-14 <![CDATA[ Central nucleus of the amygdala to medial prefrontal cortex 5-HTergic neural circuit modulates the recovery of consciousness during sevoflurane anesthesia ]]> https://biorxiv.org/content/10.1101/2024.06.19.599720v1?rss=1 Wang, Y. Yang, Y. Wu, Y. Xu, X. Xu, Q. Zhang, Z. Di, X. Zhang, H. 2024-06-23 doi:10.1101/2024.06.19.599720 Cold Spring Harbor Laboratory Press 2024-06-23 <![CDATA[ Transcranial focused ultrasound activates feedforward and feedback cortico-thalamo-cortical pathways by selectively activating excitatory neurons ]]> https://biorxiv.org/content/10.1101/2024.06.26.600794v1?rss=1 Gao, H. Ramachandran, S. Yu, K. He, B. 2024-06-30 doi:10.1101/2024.06.26.600794 Cold Spring Harbor Laboratory Press 2024-06-30 <![CDATA[ PRISM: Multiplexed Profiling of RNA In-Situ through Single-round of Imaging in Three-Dimensional Tissue ]]> https://biorxiv.org/content/10.1101/2024.06.29.601330v1?rss=1 Chang, T. Zhao, S. Deng, K. Liao, Z. Tang, M. Zhu, Y. Han, W. Yu, C. Fan, W. Jiang, M. Wang, G. Liu, D. Peng, J. Pang, Y. Fei, P. Wang, J. Zheng, C. Huang, Y. 2024-07-02 doi:10.1101/2024.06.29.601330 Cold Spring Harbor Laboratory Press 2024-07-02 <![CDATA[ Unsilenced inhibitory cortical ensemble gates remote memory retrieval ]]> https://biorxiv.org/content/10.1101/2024.07.01.601454v1?rss=1 Wang, S. Sheng, T. Su, F. Yang, H. Cao, R. Wang, Q. Zhang, C. Lu, W. 2024-07-03 doi:10.1101/2024.07.01.601454 Cold Spring Harbor Laboratory Press 2024-07-03 <![CDATA[ Differential Aging Effects on Implicit and Explicit Sensorimotor Learning ]]> https://biorxiv.org/content/10.1101/2024.07.02.601091v1?rss=1 Cisneros, E. Karny, S. Ivry, R. B. Tsay, J. S. 2024-07-04 doi:10.1101/2024.07.02.601091 Cold Spring Harbor Laboratory Press 2024-07-04 <![CDATA[ BiRNA-BERT Allows Efficient RNA Language Modeling with Adaptive Tokenization ]]> https://biorxiv.org/content/10.1101/2024.07.02.601703v1?rss=1 Tahmid, M. T. Shahgir, H. S. Mahbub, S. Dong, Y. Bayzid, M. S. 2024-07-04 doi:10.1101/2024.07.02.601703 Cold Spring Harbor Laboratory Press 2024-07-04 <![CDATA[ CACHE Challenge #1: targeting the WDR domain of LRRK2, a Parkinson's Disease associated protein. ]]> https://biorxiv.org/content/10.1101/2024.07.18.603797v1?rss=1 Ackloo, S. Arrowsmith, C. H. Ban, F. Barden, C. J. Beck, H. Beranek, J. Berenger, F. Bolotokova, A. Bret, G. Breznik, M. Carosati, E. Chau, I. Chen, Y. Cherkasov, A. Della Corte, D. Denzinger, K. Dong, A. Draga, S. Dunn, I. Edfeldt, K. Edwards, A. Eguida, M. Eisenhuth, P. Friedrich, L. Fuerll, A. Gardiner, S. Gentile, F. Ghiabi, P. Gibson, E. Glavatskikh, M. Gorgulla, C. Guenther, J. Gunnarsson, A. Guseve, F. Gutkin, E. Hillisch, A. Hoffer, L. Hogner, A. Irwin, J. J. Isayev, O. Ivanova, A. Jacquemard, C. Jarrett, A. J. Jensen, J. H. Kireev, D. Klebe 2024-07-18 doi:10.1101/2024.07.18.603797 Cold Spring Harbor Laboratory Press 2024-07-18 <![CDATA[ An Omni-Mesoscope for multiscale high-throughput quantitative phase imaging of cellular dynamics and high-content molecular characterization ]]> https://biorxiv.org/content/10.1101/2024.07.18.604137v1?rss=1 Ma, H. Chen, M. Xu, J. Zhao, Y. Liu, Y. 2024-07-19 doi:10.1101/2024.07.18.604137 Cold Spring Harbor Laboratory Press 2024-07-19 <![CDATA[ Modulation Of SUDEP By Central Serotonergic Cooperating with Noradrenergic Circuits: A Synergistic-Dependent Manner ]]> https://biorxiv.org/content/10.1101/2024.07.20.604434v1?rss=1 Xu, Q. Xu, X. Wu, Y. Yang, Y. Gu, L. Zhang, Z. Zhang, Z. Di, X. Wang, Y. Yu, Q. Lian, X. Ma, H. Zhang, H. 2024-07-23 doi:10.1101/2024.07.20.604434 Cold Spring Harbor Laboratory Press 2024-07-23 <![CDATA[ Context-driven interaction retrieval and classification for modeling, curation, and reuse ]]> https://biorxiv.org/content/10.1101/2024.07.21.604448v1?rss=1 Luo, H. Hansen, C. Telmer, C. A. Tang, D. Arazkhani, N. Zhou, G. Spirtes, P. Miskov-Zivanov, N. 2024-07-23 doi:10.1101/2024.07.21.604448 Cold Spring Harbor Laboratory Press 2024-07-23 <![CDATA[ Confidence-Enhanced Semi-supervised Learning for Mediastinal Neoplasm Segmentation ]]> https://biorxiv.org/content/10.1101/2024.07.22.604560v1?rss=1 Fu, X. Zhang, S. Zhou, J. Ji, Y. 2024-07-23 doi:10.1101/2024.07.22.604560 Cold Spring Harbor Laboratory Press 2024-07-23 <![CDATA[ Aging trajectories of memory CD8+ T cells differ by their antigen specificity ]]> https://biorxiv.org/content/10.1101/2024.07.26.605197v1?rss=1 65-years, different T cell specificities had undergone largely distinct aging trajectories, which had in common a loss in adaptive and a gain in innate immunity signatures. No evidence was seen for cellular senescence or exhaustion. While naive/stem-like EBV-specific T cells disappeared with age, T cell diversity of EBV-specific memory cells did not change or even increased. In summary, by controlling for antigen specificity we uncover age-associated shifts in gene expression and TCR diversity that have implications for optimizing vaccination strategies and adoptive T cell therapy. ]]> Sturmlechner, I. Jain, A. Hu, B. Jadhav, R. Cao, W. Okuyama, H. Tian, L. Weyand, C. Goronzy, J. 2024-07-29 doi:10.1101/2024.07.26.605197 Cold Spring Harbor Laboratory Press 2024-07-29 <![CDATA[ Complete sequencing of ape genomes ]]> https://biorxiv.org/content/10.1101/2024.07.31.605654v1?rss=1 Yoo, D. Rhie, A. Hebbar, P. Antonacci, F. Logsdon, G. A. Solar, S. J. Antipov, D. Pickett, B. D. Safonova, Y. Montinaro, F. Luo, Y. Malukiewicz, J. Storer, J. M. Lin, J. Sequeira, A. N. Mangan, R. J. Hickey, G. Anez, G. M. Balachandran, P. Bankevich, A. Beck, C. R. Biddanda, A. Borchers, M. Bouffard, G. G. Brannan, E. Brooks, S. Y. Carbone, L. Carrel, L. Chan, A. P. Crawford, J. Diekhans, M. Engelbrecht, E. Feschotte, C. Formenti, G. Garcia, G. H. Gennaro, L. d. Gilbert, D. Green, R. E. Guarracino, A. Gupta, I. Haddad, D. Han, J. Harris, R. S. Hartley 2024-07-31 doi:10.1101/2024.07.31.605654 Cold Spring Harbor Laboratory Press 2024-07-31 <![CDATA[ Extensive mutual influences of SMC complexes shape 3D genome folding ]]> https://biorxiv.org/content/10.1101/2024.07.31.606012v1?rss=1 Zhang, H. Zhao, H. Shu, L. Liu, F. Lin, E. Xia, S. Wang, B. Wang, M. Shan, F. Lin, Y. Zhang, L. Gu, Y. Blobel, G. 2024-08-01 doi:10.1101/2024.07.31.606012 Cold Spring Harbor Laboratory Press 2024-08-01 <![CDATA[ A posture subspace in primary motor cortex ]]> https://biorxiv.org/content/10.1101/2024.08.12.607361v1?rss=1 Marino, P. J. Bahureksa, L. Fernandez Fisac, C. Oby, E. R. Smoulder, A. L. Motiwala, A. Degenhart, A. D. Grigsby, E. M. Joiner, W. M. Chase, S. M. Yu, B. M. Batista, A. P. 2024-08-12 doi:10.1101/2024.08.12.607361 Cold Spring Harbor Laboratory Press 2024-08-12 <![CDATA[ Premature cleavage and polyadenylation in the minor intron of PTEN modulate its expression and generates a functional long non-coding RNA in breast cancer ]]> https://biorxiv.org/content/10.1101/2024.08.15.608023v1?rss=1 Elesnawy, M. Elghandour, R. Hasna, H. Fakhroo, A. Al-Sulaiti, B. Younis, I. 2024-08-16 doi:10.1101/2024.08.15.608023 Cold Spring Harbor Laboratory Press 2024-08-16 <![CDATA[ High-Performance Classification of Breast CancerHistopathological Images Using Fine-TunedVision Transformers on the BreakHis Dataset ]]> https://biorxiv.org/content/10.1101/2024.08.17.608410v1?rss=1 Gella, V. 2024-08-21 doi:10.1101/2024.08.17.608410 Cold Spring Harbor Laboratory Press 2024-08-21 <![CDATA[ Endoplasmic reticulum patterns insect cuticle nanostructure ]]> https://biorxiv.org/content/10.1101/2024.08.20.608717v1?rss=1 Inagaki, S. Wada, H. Itabashi, T. Itakura, Y. Nakagawa, R. Chen, L. Murata, K. Iwane, A. H. Hayashi, S. 2024-08-21 doi:10.1101/2024.08.20.608717 Cold Spring Harbor Laboratory Press 2024-08-21 <![CDATA[ Global Scientific Trends in Organoids from 2004 to 2023: A Data Bibliometric and Visualized Analysis ]]> https://biorxiv.org/content/10.1101/2024.08.28.610094v1?rss=1 Zhao, M. Kuang, L. Guo, H. Cao, X. Dai, J. Wang, Y. Wang, Z. Peng, C. 2024-08-28 doi:10.1101/2024.08.28.610094 Cold Spring Harbor Laboratory Press 2024-08-28 <![CDATA[ Cellular processing of beneficial de novo emerging proteins ]]> https://biorxiv.org/content/10.1101/2024.08.28.610198v1?rss=1 Houghton, C. J. Castilho Coelho, N. Chiang, A. Hedayati, S. Parikh, S. B. Ozbaki-Yagan, N. Wacholder, A. Iannotta, J. Berger, A. Carvunis, A.-R. O'Donnell, A. F. 2024-08-29 doi:10.1101/2024.08.28.610198 Cold Spring Harbor Laboratory Press 2024-08-29 <![CDATA[ Co-zorbs: Motile, multispecies biofilms aid transport of diverse bacterial species ]]> https://biorxiv.org/content/10.1101/2024.08.29.607786v1?rss=1 Magesh, S. Schrope, J. Mercado-Soto, N. Li, C. Hurley, A. Huttenlocher, A. Beebe, D. J. Handelsman, J. 2024-08-29 doi:10.1101/2024.08.29.607786 Cold Spring Harbor Laboratory Press 2024-08-29 <![CDATA[ RNA functional control by hydrolysis reversible acylation ]]> https://biorxiv.org/content/10.1101/2024.08.29.610419v1?rss=1 View larger version (14K): org.highwire.dtl.DTLVardef@1cbce3org.highwire.dtl.DTLVardef@b51bc4org.highwire.dtl.DTLVardef@31e96dorg.highwire.dtl.DTLVardef@d42578_HPS_FORMAT_FIGEXP M_FIG Liu et al. introduce EST1A, a hydrolysis-responsive 2'-OH acylating reagent whose RNA adducts are removed by endogenous esterases or histidine, enabling reversible control of RNA function. By exploiting differences in esterase activity between noncancerous and cancer-derived cell lines, EST1A-treated mRNA exhibits enzyme-guided and cell-selective translational reactivation. C_FIG ]]> Liu, K. Kietrys, A. M. 2024-08-30 doi:10.1101/2024.08.29.610419 Cold Spring Harbor Laboratory Press 2024-08-30 <![CDATA[ Organoid Modeling and Single-Cell Profiling Uncover the Migration Mechanism of Smooth Muscle Cells in Moyamoya Disease ]]> https://biorxiv.org/content/10.1101/2024.09.01.610617v1?rss=1 He, S. Zhang, J. Wang, X. Qi, Z. Zhou, Z. Wang, Y. Xu, S. Li, D. Ye, X. Liu, Z. Hao, X. Zhao, Y. Wang, R. 2024-09-03 doi:10.1101/2024.09.01.610617 Cold Spring Harbor Laboratory Press 2024-09-03 <![CDATA[ Musical training does not enhance neural sound encoding at early stages of the auditory system: A large-scale multisite investigation ]]> https://biorxiv.org/content/10.1101/2024.09.02.610856v1?rss=1 260) to replicate and extend the findings underpinning this important relationship. We failed to replicate any of the major findings published previously in smaller studies. Musical training was related neither to enhanced spectral encoding strength of a speech stimulus (/da/) in babble nor to a stronger neural-stimulus correlation. Similarly, the strength of neural tracking of a speech sound with a time-varying pitch was not related to either years of musical training or age of onset of musical training. Our findings provide no evidence for plasticity of early auditory responses based on musical training and exposure. ]]> Whiteford, K. L. Baltzell, L. S. Chiu, M. Cooper, J. K. Faucher, S. Goh, P. Y. Hagedorn, A. Irsik, V. C. Irvine, A. Lim, S.-J. Mesik, J. L. Mesquita, B. Oakes, B. Rajappa, N. Roverud, E. Schrlau, A. E. Van Hedger, S. C. Bharadwaj, H. M. Johnsrude, I. S. Kidd, G. Luebke, A. E. Maddox, R. K. Marvin, E. W. Perrachione, T. K. Shinn-Cunningham, B. G. Oxenham, A. J. 2024-09-04 doi:10.1101/2024.09.02.610856 Cold Spring Harbor Laboratory Press 2024-09-04 <![CDATA[ Proliferation symmetry breaking in growing tissues ]]> https://biorxiv.org/content/10.1101/2024.09.03.610990v1?rss=1 Li, X. Datta, A. Banerjee, S. 2024-09-06 doi:10.1101/2024.09.03.610990 Cold Spring Harbor Laboratory Press 2024-09-06 <![CDATA[ Porosome reconstitution therapy: A biologic rescue from cystic fibrosis ]]> https://biorxiv.org/content/10.1101/2024.09.11.612494v1?rss=1 70% decrease in MUC5B and MUC5AC secretion. Our studies using differentiated 3D cultures of human airway epithelial cell line, also demonstrate loss of both chloride and mucus secretion following exposure to CFTR inhibitors thiazolidinone 172 or the hydrazide GlyH101. Our studies show that human bronchial epithelial (HBE) cells with {Delta}F508 CFTR mutation, affects nearly a dozen porosome proteins including CFTR. Therefore, we hypothesized that the introduction of normal functional porosomes carrying wild type CFTR into the cell plasma membrane of CF cells would rescue from all forms of CF. Air liquid interface (ALI) 3D differentiated HBE WT-CFTR cells and {Delta}F508-CFTR CF HBE cell cultures mimicking normal lung physiology, responding to CFTR inhibitors and CF corrector and modulator drugs Tezacaftor, Ivacaftor and TRIKAFTA, was used in the study. Introduction of functional porosome complexes obtained from WT-CFTR HBE cells into the plasma membrane (PM) of {Delta}F508-CFTR CF cells, was demonstrated by an increase in PM-associated CFTR using Magnify expansion microscopy. Mucin secretion assays demonstrate porosome reconstitution to restore mucin secretion more than twice as effectively as TRIKAFTA. These results are further supported by preliminary nasal potential different studies in {Delta}F508 mice, where treatment of the nasal passage with porosome isolates from WT-CFTR HBE cells, restore chloride secretion in the nasal passage of mice, a further validation of the highly effective porosome reconstitution therapy for CF. ]]> Cho, W. J. Vo, H. Zhao, Y. Taatjes, D. J. Jena, B. P. 2024-09-12 doi:10.1101/2024.09.11.612494 Cold Spring Harbor Laboratory Press 2024-09-12 <![CDATA[ A benchmarking study of copy number variation inference methods using single-cell RNA-sequencing data ]]> https://biorxiv.org/content/10.1101/2024.09.09.612120v1?rss=1 Chen, X. Fang, L. T. Chen, Z. Chen, W. Zhu, B. Wu, H. Moos, M. Farmer, A. Zeng, F. Song, L. Zhang, X. Xiong, W. Gong, S. Jones, W. Mason, C. Wu, S. Xiao, C. Wang, C. 2024-09-14 doi:10.1101/2024.09.09.612120 Cold Spring Harbor Laboratory Press 2024-09-14 <![CDATA[ Identification of Growth Differentiation Factor-15 as An Early Predictive Biomarker for Metabolic Dysfunction-Associated Steatohepatitis: A Nested Case-control Study of UK Biobank Proteomic Data ]]> https://biorxiv.org/content/10.1101/2024.09.12.612665v1?rss=1 Wang, H. Xu, X. Sun, Y. You, H. Jia, J. He, Y.-W. Kong, Y. 2024-09-15 doi:10.1101/2024.09.12.612665 Cold Spring Harbor Laboratory Press 2024-09-15 <![CDATA[ Flexible and robust cell type annotation for highly multiplexed tissue images ]]> https://biorxiv.org/content/10.1101/2024.09.12.612510v1?rss=1 Sun, H. Yu, S. Casals, A. M. Bäckström, A. Lu, Y. Lindskog, C. Lundberg, E. Murphy, R. F. 2024-09-16 doi:10.1101/2024.09.12.612510 Cold Spring Harbor Laboratory Press 2024-09-16 <![CDATA[ Few-shot Algorithms for Consistent Neural Decoding (FALCON) Benchmark ]]> https://biorxiv.org/content/10.1101/2024.09.15.613126v1?rss=1 Karpowicz, B. M. Ye, J. Fan, C. Tostado-Marcos, P. Rizzoglio, F. Washington, C. Scodeler, T. de Lucena, D. Nason-Tomaszewski, S. R. Mender, M. J. Ma, X. Arneodo, E. M. Hochberg, L. R. Chestek, C. A. Henderson, J. M. Gentner, T. Q. Gilja, V. Miller, L. E. Rouse, A. G. Gaunt, R. A. Collinger, J. L. Pandarinath, C. 2024-09-16 doi:10.1101/2024.09.15.613126 Cold Spring Harbor Laboratory Press 2024-09-16 <![CDATA[ Striatal indirect pathway mediates hesitation ]]> https://biorxiv.org/content/10.1101/2024.09.16.613332v1?rss=1 Geramita, M. A. Ahmari, S. E. Yttri, E. A. 2024-09-16 doi:10.1101/2024.09.16.613332 Cold Spring Harbor Laboratory Press 2024-09-16 <![CDATA[ Interpretable high-resolution dimension reduction of spatial transcriptomics data by DeepFuseNMF ]]> https://biorxiv.org/content/10.1101/2024.09.12.612666v1?rss=1 Tang, J. Chen, Z. Qian, Q. Huang, S. Yin, S. He, Y. He, X. Ye, B. Zhuang, Y. Meng, H. Xi, J. Xi, R. 2024-09-17 doi:10.1101/2024.09.12.612666 Cold Spring Harbor Laboratory Press 2024-09-17 <![CDATA[ Deep Video Analysis for Bacteria Genotype Prediction ]]> https://biorxiv.org/content/10.1101/2024.09.16.613253v1?rss=1 Dabouei, A. Mishra, I. Kapur, K. Cao, C. A. Bridges, A. Xu, M. 2024-09-19 doi:10.1101/2024.09.16.613253 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ An integrated view of the structure and function of the human 4D nucleome ]]> https://biorxiv.org/content/10.1101/2024.09.17.613111v1?rss=1 The 4D Nucleome Consortium, Dekker, J. Oksuz, B. A. Zhang, Y. Wang, Y. Minsk, M. K. Kuang, S. Yang, L. Gibcus, J. H. Krietenstein, N. Rando, O. Xu, J. Janssens, D. H. Henikoff, S. Kukalev, A. Willemin, A. Winick-Ng, W. Kempfer, R. Pombo, A. Yu, M. Kumar, P. Zhang, L. Belmont, A. S. Sasaki, T. van Schaik, T. Brueckner, L. Peric-Hupkes, D. van Steensel, B. Wang, P. Chai, H. Kim, M. Ruan, Y. Zhang, R. Quinodoz, S. A. Bhat, P. Guttman, M. Zhao, W. Chien, S. Liu, Y. Venev, S. V. Plewczynski, D. Irastorza Azcarate, I. Szabo, D. Thieme, C. J. Szczepinska, 2024-09-19 doi:10.1101/2024.09.17.613111 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ Incorporating buccal mass planar mechanics and anatomical features improves neuromechanical modeling of Aplysia feeding behavior ]]> https://biorxiv.org/content/10.1101/2024.09.17.613591v1?rss=1 Bennington, M. J. Liao, A. S. Sukhnandan, R. Kundu, B. Rogers, S. M. Gill, J. P. McManus, J. M. Sutton, G. P. Chiel, H. J. Webster-Wood, V. A. 2024-09-19 doi:10.1101/2024.09.17.613591 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ Transient Notch Activation Converts Pluripotent Stem Cell-Derived Cardiomyocytes towards a Purkinje Fiber Fate ]]> https://biorxiv.org/content/10.1101/2024.09.22.614353v1?rss=1 Gonzalez, D. M. Dariolli, R. Moyett, J. Song, S. Shewale, B. Bliley, J. M. Ma'ayan, A. Rentschler, S. Feinberg, A. W. Sobie, E. Dubois, N. 2024-09-23 doi:10.1101/2024.09.22.614353 Cold Spring Harbor Laboratory Press 2024-09-23 <![CDATA[ Learning-Augmented Sketching Offers Improved Performance for Privacy Preserving and Secure GWAS ]]> https://biorxiv.org/content/10.1101/2024.09.19.613975v1?rss=1 Xu, J. Zhu, K. Cai, J. Kockan, C. Dokmai, N. Cho, H. Woodruff, D. Sahinalp, C. 2024-09-24 doi:10.1101/2024.09.19.613975 Cold Spring Harbor Laboratory Press 2024-09-24 <![CDATA[ ProteinAligner: A Multi-modal Pretraining Framework for Protein Foundation Models ]]> https://biorxiv.org/content/10.1101/2024.10.06.616870v1?rss=1 Zhang, L. Guo, H. Schaffer, L. V. Ko, Y. S. Singh, D. Rahmani, H. Grotjahn, D. Villa, E. Gilson, M. Wang, W. Ideker, T. Xing, E. Xie, P. 2024-10-06 doi:10.1101/2024.10.06.616870 Cold Spring Harbor Laboratory Press 2024-10-06 <![CDATA[ DeepFocus: A Transnasal Approach for Optimized Deep Brain Stimulation of Reward Circuit Nodes ]]> https://biorxiv.org/content/10.1101/2024.10.08.617133v1?rss=1 Guo, Y. Forssell, M. Kusyk, D. M. Jain, V. Swink, I. Corcoran, O. Lee, Y. Goswami, C. Whiting, A. C. Cheng, B. C. Grover, P. 2024-10-12 doi:10.1101/2024.10.08.617133 Cold Spring Harbor Laboratory Press 2024-10-12 <![CDATA[ Design of a biomolecular adaptive controller to restore sustained periodic behavior ]]> https://biorxiv.org/content/10.1101/2024.10.11.617962v1?rss=1 Britto Bisso, F. Dey, S. Stan, G.-B. V. Cuba Samaniego, C. 2024-10-12 doi:10.1101/2024.10.11.617962 Cold Spring Harbor Laboratory Press 2024-10-12 <![CDATA[ Active RNA synthesis patterns nuclear condensates ]]> https://biorxiv.org/content/10.1101/2024.10.12.614958v1?rss=1 Banani, S. F. Goychuk, A. Natarajan, P. Zheng, M. M. Dall'Agnese, G. Henninger, J. E. Kardar, M. Young, R. A. Chakraborty, A. K. 2024-10-13 doi:10.1101/2024.10.12.614958 Cold Spring Harbor Laboratory Press 2024-10-13 <![CDATA[ Physical traits of supercompetitors in cell competition ]]> https://biorxiv.org/content/10.1101/2024.10.14.618306v1?rss=1 Carpenter, L. C. Banerjee, S. 2024-10-15 doi:10.1101/2024.10.14.618306 Cold Spring Harbor Laboratory Press 2024-10-15 <![CDATA[ Individual variation in the functional lateralization of human ventral temporal cortex: Local competition and long-range coupling ]]> https://biorxiv.org/content/10.1101/2024.10.15.618268v1?rss=1 Blauch, N. M. Plaut, D. C. Vin, R. Behrmann, M. 2024-10-16 doi:10.1101/2024.10.15.618268 Cold Spring Harbor Laboratory Press 2024-10-16 <![CDATA[ The Taiwan Precision Medicine Initiative: A Cohort for Large-Scale Studies ]]> https://biorxiv.org/content/10.1101/2024.10.14.616932v1?rss=1 1.4 billion people around the world and serve as a model for developing population-based precision medicine. ]]> Yang, H.-C. Kwok, P.-Y. Li, L.-H. Liu, Y.-M. Jong, Y.-J. Lee, K.-Y. Wang, D.-W. Tsai, M.-F. Yang, J.-H. Chen, C.-H. Yeh, E.-C. Wei, C.-y. Fann, C. S.- J. Huang, Y.-T. Chen, C.-W. Lee, Y.-J. Chu, S.-K. Ho, C.-h. Yang, C.-S. Lee, Y. L. Chen, H.-H. Hou, M.-C. Chiou, J.-F. Yang, S.-F. Wang, C.-H. Huang, C.-Y. Chiu, K.-M. Chen, M. Chiang, F.-T. Lee, S.-L. Chen, S.-S. Yao, W.-J. Chien, C.-C. Lin, S.-Y. Chang, F.-P. Ho, H.-L. Yeh, Y.-C. Tseng, W.-C. Lin, M.-H. Chang, H.-T. Tseng, L.-M. Liang, W.-Y. Chen, P. C.-H. Hang, J.-F. Lin, S.-C. Chan, Y.-J. Kuo, Y. 2024-10-17 doi:10.1101/2024.10.14.616932 Cold Spring Harbor Laboratory Press 2024-10-17 <![CDATA[ All-trans retinoic acid-mediated ADAR1 degradation synergizes with PD-1 blockade to suppress pancreatic cancer ]]> https://biorxiv.org/content/10.1101/2024.10.20.619300v1?rss=1 Li, C.-F. Bai, L.-Y. Wei, Y. Lee, H.-H. Yang, R. Yao, J. Wang, H. Wang, Y.-N. Chang, W.-C. Shen, Y.-C. Wang, S.-C. Chou, C.-W. Fu, J. Ling, J. Chu, Y.-Y. Chiu, C.-F. Wang, M. Yu, D. Chiao, P. J. Liang, H. Maitra, A. Ying, H. Hung, M.-C. 2024-10-23 doi:10.1101/2024.10.20.619300 Cold Spring Harbor Laboratory Press 2024-10-23 <![CDATA[ Using synthetic RNA to benchmark poly(A) length inference from direct RNA sequencing. ]]> https://biorxiv.org/content/10.1101/2024.10.25.620206v1?rss=1 Chang, J. J.-Y. Yang, X. Teng, H. Reames, B. Corbin, V. Coin, L. J. M. 2024-10-25 doi:10.1101/2024.10.25.620206 Cold Spring Harbor Laboratory Press 2024-10-25 <![CDATA[ Single-cell atlas of developing mouse palates reveals cellular and molecular transitions in periderm cell fate ]]> https://biorxiv.org/content/10.1101/2024.10.28.620753v1?rss=1 Huang, W. Qian, Z. Zhang, J. Ding, Y. Wang, B. Lin, J. Zhang, X. Zhao, H. Chen, F. 2024-11-03 doi:10.1101/2024.10.28.620753 Cold Spring Harbor Laboratory Press 2024-11-03 <![CDATA[ Nitrate Promoting Hair Growth Through Enhancing Wnt/β-catenin and Downregulating TGF-β/Samd/BMP signaling pathway in C57BL/6 Mice ]]> https://biorxiv.org/content/10.1101/2024.11.02.621646v1?rss=1 Lan, Y. Li, S. Wang, J. Duan, L. Huang, M. Yang, X. Zhang, C. Wang, S. Li, W. 2024-11-03 doi:10.1101/2024.11.02.621646 Cold Spring Harbor Laboratory Press 2024-11-03 <![CDATA[ devider: long-read reconstruction of many diverse haplotypes ]]> https://biorxiv.org/content/10.1101/2024.11.05.621838v1?rss=1 8000x coverage. Benchmarking on synthetic mixtures of antimicrobial resistance (AMR) genes showed that devider recovered 83% of haplotypes, 23 percentage points higher than the next best method. On real PacBio and Nanopore datasets, devider recapitulates previously known results in seconds, disentan-gling a bacterial community with > 10 strains and an HIV-1 co-infection dataset. We used devider to investigate the within-host diversity of a long-read bovine gut metagenome enriched for AMR genes, discovering 13 distinct haplotypes for a tet(Q) tetracycline resistance gene with > 18, 000x coverage and 6 haplotypes for a CfxA2 beta-lactamase gene. We found clear recombination blocks for these AMR gene haplotypes, showcasing deviders ability to unveil ecological signals for heterogeneous mixtures. ]]> Shaw, J. Boucher, C. Yu, Y. W. Noyes, N. Li, H. 2024-11-08 doi:10.1101/2024.11.05.621838 Cold Spring Harbor Laboratory Press 2024-11-08 <![CDATA[ Single-Cell Analysis of Gene Regulatory Networks in the Mammary Glands of P4HA1-knockout mice ]]> https://biorxiv.org/content/10.1101/2024.11.05.622022v1?rss=1 Gupta, A. Huang, L. Liu, J. Xu, R. Wu, W. 2024-11-08 doi:10.1101/2024.11.05.622022 Cold Spring Harbor Laboratory Press 2024-11-08 <![CDATA[ scLong: A Billion-Parameter Foundation Model for Capturing Long-Range Gene Context in Single-Cell Transcriptomics ]]> https://biorxiv.org/content/10.1101/2024.11.09.622759v1?rss=1 Bai, D. Mo, S. Zhang, R. Luo, Y. Gao, J. Yang, J. P. Wu, Q. Singh, D. Rahmani, H. Amariuta, T. Grotjahn, D. Zhong, S. Lewis, N. Wang, W. Ideker, T. Xing, E. Xie, P. 2024-11-11 doi:10.1101/2024.11.09.622759 Cold Spring Harbor Laboratory Press 2024-11-11 <![CDATA[ Wound state monitoring by multiplexed, electrochemical, real-time, localized, inflammation-tracking nitric oxide sensor (MERLIN) ]]> https://biorxiv.org/content/10.1101/2024.11.12.623289v1?rss=1 Wang, L. Wang, Y. Bartlett, M. San Roman, D. Balakrishnan, G. Gershanok, S. Khan, R. Skillen, C. Butler, S. Kulkarni, M. Cohen-Karni, D. Brown, B. Cohen-Karni, T. 2024-11-15 doi:10.1101/2024.11.12.623289 Cold Spring Harbor Laboratory Press 2024-11-15 <![CDATA[ Long-lasting, subtype-specific regulation of somatostatin interneurons during sensory learning ]]> https://biorxiv.org/content/10.1101/2024.11.19.624383v1?rss=1 Zhu, M. Mosso, M. B. Ma, X. Park, E. Barth, A. L. 2024-11-21 doi:10.1101/2024.11.19.624383 Cold Spring Harbor Laboratory Press 2024-11-21 <![CDATA[ Self-organized cell patterning via mechanical feedback in hindbrain neuropore morphogenesis ]]> https://biorxiv.org/content/10.1101/2024.11.21.624679v1?rss=1 Perez-Verdugo, F. Maniou, E. Galea, G. L. Banerjee, S. 2024-11-21 doi:10.1101/2024.11.21.624679 Cold Spring Harbor Laboratory Press 2024-11-21 <![CDATA[ Stage-Specific Transcriptome Landscape of Hepatocellular Carcinoma: Insights from Super and Poor Survivors with Prognostic Signature Identification ]]> https://biorxiv.org/content/10.1101/2024.11.26.625545v1?rss=1 Xu, X. Wang, H. Shi, L. Huang, C. You, H. Jia, J. He, Y.-W. Kong, Y. 2024-11-28 doi:10.1101/2024.11.26.625545 Cold Spring Harbor Laboratory Press 2024-11-28 <![CDATA[ Dorsolateral prefrontal cortex drives strategic aborting by optimizing long-run policy extraction ]]> https://biorxiv.org/content/10.1101/2024.11.28.625897v1?rss=1 Noel, J.-P. G. Zhang, R. Pitkow, X. Angelaki, D. 2024-11-28 doi:10.1101/2024.11.28.625897 Cold Spring Harbor Laboratory Press 2024-11-28 <![CDATA[ A Large-Scale Foundation Model for RNA Function and Structure Prediction ]]> https://biorxiv.org/content/10.1101/2024.11.28.625345v1?rss=1 Zou, S. Tao, T. Mahbub, S. Ellington, C. N. Algayres, R. J. Li, D. Zhuang, Y. Wang, H. Song, L. Xing, E. P. 2024-11-29 doi:10.1101/2024.11.28.625345 Cold Spring Harbor Laboratory Press 2024-11-29 <![CDATA[ Engineering cell fate with adaptive feedback control ]]> https://biorxiv.org/content/10.1101/2024.11.29.625974v1?rss=1 Britto Bisso, F. Giordano, G. Cuba Samaniego, C. 2024-11-29 doi:10.1101/2024.11.29.625974 Cold Spring Harbor Laboratory Press 2024-11-29 <![CDATA[ Deep conservation of cis-regulatory elements and chromatin organization in echinoderms uncover ancestral regulatory features of animal genomes ]]> https://biorxiv.org/content/10.1101/2024.11.30.626178v1?rss=1 Magri, M. S. Voronov, D. Foley, S. Martinez-Garcia, P. M. Franke, M. Cary, G. A. Santos-Pereira, J. M. Cuomo, C. Fernandez-Moreno, M. Gil-Galvez, A. Acemel, R. D. Paganos, P. Ku, C. Ranđelovic, J. Rusciano, M. L. Firbas, P. N. Gomez-Skarmeta, J. L. Hinman, V. F. Arnone, M. I. Maeso, I. 2024-12-01 doi:10.1101/2024.11.30.626178 Cold Spring Harbor Laboratory Press 2024-12-01 <![CDATA[ Cell Type Specific Enhancers for Dorsolateral Prefrontal Cortex. ]]> https://biorxiv.org/content/10.1101/2024.12.01.626253v1?rss=1 He, J. Phan, B. N. Kerkhoff, W. G. Alikaya, A. Brull, O. R. Fredericks, J. M. Hong, T. Sedorovitz, M. Srinivasan, C. Leone, M. J. Wirfel, O. M. Dauby, S. Tittle, R. K. Lin, M. K. Bostan, A. C. Hooks, B. M. Gharbawie, O. A. Byrne, L. C. Pfenning, A. R. Stauffer, W. R. 2024-12-02 doi:10.1101/2024.12.01.626253 Cold Spring Harbor Laboratory Press 2024-12-02 <![CDATA[ Scaling Dense Representations for Single Cell with Transcriptome-Scale Context ]]> https://biorxiv.org/content/10.1101/2024.11.28.625303v1?rss=1 Ho, N. Ellington, C. N. Hou, J. Addagudi, S. Mo, S. Tao, T. Li, D. Zhuang, Y. Wang, H. Cheng, X. Song, L. Xing, E. P. 2024-12-03 doi:10.1101/2024.11.28.625303 Cold Spring Harbor Laboratory Press 2024-12-03 <![CDATA[ Mixture of Experts Enable Efficient and Effective Protein Understanding and Design ]]> https://biorxiv.org/content/10.1101/2024.11.29.625425v1?rss=1 Sun, N. Zou, S. Tao, T. Mahbub, S. Li, D. Zhuang, Y. Wang, H. Cheng, X. Song, L. Xing, E. P. 2024-12-03 doi:10.1101/2024.11.29.625425 Cold Spring Harbor Laboratory Press 2024-12-03 <![CDATA[ PqsE acts as an adaptor protein for the quorum-sensing transcription factor RhlR in Pseudomonas aeruginosa ]]> https://biorxiv.org/content/10.1101/2024.12.03.626663v1?rss=1 Tchadi, B. V. Derringer, J. J. Detweiler, A. K. Taylor, I. R. 2024-12-03 doi:10.1101/2024.12.03.626663 Cold Spring Harbor Laboratory Press 2024-12-03 <![CDATA[ Accurate and General DNA Representations Emerge from Genome Foundation Models at Scale ]]> https://biorxiv.org/content/10.1101/2024.12.01.625444v1?rss=1 Ellington, C. N. Sun, N. Ho, N. Tao, T. Mahbub, S. Li, D. Zhuang, Y. Wang, H. Song, L. Xing, E. P. 2024-12-05 doi:10.1101/2024.12.01.625444 Cold Spring Harbor Laboratory Press 2024-12-05 <![CDATA[ Centella asiatica Tissue Culture-Derived Extracellular Vesicles: A Multifaceted Approach to Skincare Applications ]]> https://biorxiv.org/content/10.1101/2024.12.03.624435v1?rss=1 Chang, T.-M. Wu, C.-C. Huang, H.-C. Wang, S.-S. Chuang, C.-H. Kao, P.-L. Tang, W.-H. Liu, L. T.-C. Qiu, W.-Y. Percec, I. Chen, C. Kuo, T.-Y. 2024-12-07 doi:10.1101/2024.12.03.624435 Cold Spring Harbor Laboratory Press 2024-12-07 <![CDATA[ Reduced expression of PER2 protein contrbutes to β1-AA induced cardiac autophagy rhythm disorder ]]> https://biorxiv.org/content/10.1101/2024.12.06.627296v1?rss=1 Li, P. feng, J. Guo, J. Xue, J. Li, Y. Wen, S. Wang, X. Liu, H. Wang, l. 2024-12-07 doi:10.1101/2024.12.06.627296 Cold Spring Harbor Laboratory Press 2024-12-07 <![CDATA[ Longitudinal cellular and humoral immune responses following Covid-19 BNT162b2-mRNA-based booster vaccination of craft and manual workers in Qatar. ]]> https://biorxiv.org/content/10.1101/2024.12.10.627725v1?rss=1 Thomas, R. Zaqout, A. Meqbel, B. Jafar, U. Vaikath, N. Aldushain, A. Naik, A. Shaath, H. Al-Akl, N. S. Adam, A. Ali Moussa, H. Y. Shin, K. C. Taha, R. Z. Abukhattab, M. Almaslamani, M. A. Alajez, N. M. Arredouani, A. Park, Y. Abdulla, S. A. El-Agnaf, O. M. Omrani, A. S. Decock, J. 2024-12-10 doi:10.1101/2024.12.10.627725 Cold Spring Harbor Laboratory Press 2024-12-10 <![CDATA[ L2G: Repurposing Language Models for Genomics Tasks ]]> https://biorxiv.org/content/10.1101/2024.12.09.627422v1?rss=1 Cheng, W. Shen, J. Khodak, M. Ma, J. Talwalkar, A. 2024-12-11 doi:10.1101/2024.12.09.627422 Cold Spring Harbor Laboratory Press 2024-12-11 <![CDATA[ Space- and object-based attention in patientswith a single hemisphere following childhood resection ]]> https://biorxiv.org/content/10.1101/2024.12.06.627251v1?rss=1 Robert, S. Granovetter, M. C. Ling, S. Behrmann, M. 2024-12-12 doi:10.1101/2024.12.06.627251 Cold Spring Harbor Laboratory Press 2024-12-12 <![CDATA[ Cross-sectional and longitudinal changes in category-selectivity in visual cortex following pediatric cortical resection ]]> https://biorxiv.org/content/10.1101/2024.12.08.627367v1?rss=1 Liu, T. T. Granovetter, M. C. Maallo, A. M. S. Robert, S. Fu, J. Z. Patterson, C. Plaut, D. Behrmann, M. 2024-12-12 doi:10.1101/2024.12.08.627367 Cold Spring Harbor Laboratory Press 2024-12-12 <![CDATA[ Developmentally regulated actin-microtubule crosstalk in Drosophila oogenesis ]]> https://biorxiv.org/content/10.1101/2024.12.12.628281v1?rss=1 Chou, W.-C. Lakonishok, M. Lu, W. Gelfand, V. I. McCartney, B. 2024-12-17 doi:10.1101/2024.12.12.628281 Cold Spring Harbor Laboratory Press 2024-12-17 <![CDATA[ Clathrins are involved in the endocytosis of host cytosol in the malaria parasite ]]> https://biorxiv.org/content/10.1101/2024.12.17.629030v1?rss=1 Miao, J. Ning, G. Xia, X. Liang, X. Lucky, A. B. Siddiqui, F. A. Min, H. Wang, C. Li, X. Zhou, H. Cui, L. 2024-12-18 doi:10.1101/2024.12.17.629030 Cold Spring Harbor Laboratory Press 2024-12-18 <![CDATA[ SenSet, a novel human lung senescence cell gene signature, identifies cell-specific senescence mechanisms ]]> https://biorxiv.org/content/10.1101/2024.12.21.629928v1?rss=1 Hasanaj, E. Beaulieu, D. Wang, C. Hu, Q. Bueno, M. Sembrat, J. C. Pineda, R. H. Melo-Narvaez, M. C. Cardenes, N. Yanwu, Z. Yingze, Z. Lafyatis, R. Morris, A. Mora, A. Rojas, M. Li, D. Rahman, I. Pryhuber, G. S. Lehmann, M. Alder, J. Gurkar, A. Finkel, T. Ma, Q. Poczos, B. Bar-Joseph, Z. Eickelberg, O. Koenigshoff, M. 2024-12-22 doi:10.1101/2024.12.21.629928 Cold Spring Harbor Laboratory Press 2024-12-22 <![CDATA[ Red-shifted GRAB acetylcholine sensors for multiplex imaging in vivo ]]> https://biorxiv.org/content/10.1101/2024.12.22.627112v1?rss=1 Xie, S. Miao, X. Li, G. Zheng, Y. Li, M. Ji, E. Wang, J. Li, S. Cai, R. Geng, L. Feng, J. Wei, C. Li, Y. 2024-12-23 doi:10.1101/2024.12.22.627112 Cold Spring Harbor Laboratory Press 2024-12-23 <![CDATA[ Computationally reconstructing the evolution of cancer progression risk ]]> https://biorxiv.org/content/10.1101/2024.12.23.629914v1?rss=1 Cao, K. Schwartz, R. 2024-12-23 doi:10.1101/2024.12.23.629914 Cold Spring Harbor Laboratory Press 2024-12-23 <![CDATA[ Engineering 3D Skeletal Muscle Tissue with Complex Multipennate Myofiber Architectures ]]> https://biorxiv.org/content/10.1101/2025.01.06.631119v1?rss=1 Stang, M. A. Lee, A. Bliley, J. M. Coffin, B. D. Yerneni, S. S. Campbell, P. G. Feinberg, A. W. 2025-01-08 doi:10.1101/2025.01.06.631119 Cold Spring Harbor Laboratory Press 2025-01-08 <![CDATA[ DNALONGBENCH: A Benchmark Suite for Long-Range DNA Prediction Tasks ]]> https://biorxiv.org/content/10.1101/2025.01.06.631595v1?rss=1 Cheng, W. Song, Z. Zhang, Y. Wang, S. Wang, D. Yang, M. Li, L. Ma, J. 2025-01-08 doi:10.1101/2025.01.06.631595 Cold Spring Harbor Laboratory Press 2025-01-08 <![CDATA[ EEG-Informed fMRI Analysis Reveals Neurovascular Coupling in Motor Execution and Imagery ]]> https://biorxiv.org/content/10.1101/2025.01.13.632624v1?rss=1 Bondi, E. Ding, Y. Zhang, Y. Maggioni, E. He, B. 2025-01-13 doi:10.1101/2025.01.13.632624 Cold Spring Harbor Laboratory Press 2025-01-13 <![CDATA[ HIF-1α/STOML2 mediated PINK1-dependent mitophagy activation against hypoxia-induced neuronal injury ]]> https://biorxiv.org/content/10.1101/2025.04.16.649120v1?rss=1 Li, Y. Guo, M. Tian, Z. Shao, Q. Liu, Y. Gu, Y. Xu, Z. Jin, F. Ji, X. Liu, J. 2025-04-21 doi:10.1101/2025.04.16.649120 Cold Spring Harbor Laboratory Press 2025-04-21 <![CDATA[ Midbrain organoids with an SNCA gene triplication display dopamine-dependent alterations in network activity ]]> https://biorxiv.org/content/10.1101/2025.04.23.650231v1?rss=1 Deyab, G. Thomas, R. A. Ding, X. E. Li, J. Sirois, J. Al Azzawi, Z. Niu, S. Durcan, T. Fon, E. A. 2025-04-24 doi:10.1101/2025.04.23.650231 Cold Spring Harbor Laboratory Press 2025-04-24 <![CDATA[ Power-law memory governs bacterial adaptation and learning in fluctuating environments ]]> https://biorxiv.org/content/10.1101/2025.04.26.650739v1?rss=1 Kratz, J. Wang, H. Si, F. Banerjee, S. 2025-04-30 doi:10.1101/2025.04.26.650739 Cold Spring Harbor Laboratory Press 2025-04-30 <![CDATA[ Development of an Open-source Low-cost Pressure Myography and Cardiac Flow Simulator, HemoLens, for Mechanical Characterization of Native and Engineered Blood Vessels ]]> https://biorxiv.org/content/10.1101/2025.04.29.651300v1?rss=1 View larger version (33K): org.highwire.dtl.DTLVardef@6b87d0org.highwire.dtl.DTLVardef@1a17b5eorg.highwire.dtl.DTLVardef@aa6056org.highwire.dtl.DTLVardef@19ac816_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> PereiraTavares, A. J. Aranda-Michel, L. Hahn, S. A. Coffin, B. D. Ashraf, S. F. Szafron, J. M. Straub, A. C. Shiwarski, D. J. 2025-05-04 doi:10.1101/2025.04.29.651300 Cold Spring Harbor Laboratory Press 2025-05-04 <![CDATA[ Sialin2 Senses Nitrate to Activate Endosomal PI3K-AKT-NOS Signaling ]]> https://biorxiv.org/content/10.1101/2025.05.04.652107v1?rss=1 Li, X. Jiang, O. Cao, Z. Zhou, B. Chen, X. Feng, Y. Zhang, C. Wang, J. Zhou, J. Yan, R. Chen, M. Wang, S. 2025-05-06 doi:10.1101/2025.05.04.652107 Cold Spring Harbor Laboratory Press 2025-05-06 <![CDATA[ Locus Coeruleus to Medial Prefrontal Cortex Noradrenergic Neural Circuit Modulates States of Consciousness during Sevoflurane Anesthesia in Mice ]]> https://biorxiv.org/content/10.1101/2025.05.01.651682v1?rss=1 Shao, W. Yang, Y. Wu, Y. Di, X. Zhang, Z. Liu, L. Gu, L. Xu, X. Zhang, Z. Gu, J. Zhang, H. 2025-05-07 doi:10.1101/2025.05.01.651682 Cold Spring Harbor Laboratory Press 2025-05-07 <![CDATA[ Large Reaching Datasets Quantify the Impact of Age, Sex/Gender, and Experience on Motor Control ]]> https://biorxiv.org/content/10.1101/2025.05.01.651757v1?rss=1 Zhang, A. Ruitenberg, M. Warburton, M. Scott, S. Tsay, J. S. 2025-05-07 doi:10.1101/2025.05.01.651757 Cold Spring Harbor Laboratory Press 2025-05-07 <![CDATA[ In vitro monitoring of Babesia microti infection dynamics in whole blood microenvironments ]]> https://biorxiv.org/content/10.1101/2025.05.07.652765v1?rss=1 Li, C. Bache, E. G. Apgar, A. L. Tufts, D. M. Niepa, T. H. R. 2025-05-13 doi:10.1101/2025.05.07.652765 Cold Spring Harbor Laboratory Press 2025-05-13 <![CDATA[ Economic and Social Modulations of Innate Decision-Making in Mice Exposed to Visual Threats ]]> https://biorxiv.org/content/10.1101/2025.05.12.653401v1?rss=1 Li, Z. Wang, J. Sun, Y. Li, J. Li, L.-y. Li, Y.-t. 2025-05-15 doi:10.1101/2025.05.12.653401 Cold Spring Harbor Laboratory Press 2025-05-15 <![CDATA[ Magnetically Responsive Nanocultures for Direct Microbial Assessment in Soil Environments ]]> https://biorxiv.org/content/10.1101/2025.05.17.654660v1?rss=1 Usman, H. Molaei, M. House, S. Haase, M. F. Dennis, C. L. Niepa, T. H. R. 2025-05-18 doi:10.1101/2025.05.17.654660 Cold Spring Harbor Laboratory Press 2025-05-18 <![CDATA[ DNA2 and FANCM function in two distinctive pathways in disrupting TERRA R-loops and suppressing replication stress at ALT telomeres ]]> https://biorxiv.org/content/10.1101/2025.05.22.655602v1?rss=1 Ragupathi, A. Abid, H. Z. Chen, Y. Zhao, R. Kosiyatrakul, S. T. Yetil, D. I. Neiswander, J. Feltman, R. Thomas, S. Yusupov, B. Singh, M. Zheng, L. Shen, B. Zhang, H. Chu, H.-P. C. Schildkraut, C. L. Xiao, M. Zhang, D. 2025-05-24 doi:10.1101/2025.05.22.655602 Cold Spring Harbor Laboratory Press 2025-05-24 <![CDATA[ Head-related transfer function predictions reveal dominant sound transmission mechanisms in a dolphin head ]]> https://biorxiv.org/content/10.1101/2025.05.22.655550v1?rss=1 Cheong, Y. Ruesch, A. Schalles, M. Kainerstorfer, J. Shinn-Cunningham, B. G. Lee, W.-J. 2025-05-27 doi:10.1101/2025.05.22.655550 Cold Spring Harbor Laboratory Press 2025-05-27 <![CDATA[ The genomic and transcriptional landscape of the spinal cord H3K27-altered diffuse midline glioma suggests the potential therapeutic strategy ]]> https://biorxiv.org/content/10.1101/2025.05.25.655886v1?rss=1 Xiao, Y. Li, M. Gao, Q. Qian, Z. Shang, Y. Jing, L. Zhen, Z. Ai, Y. Wang, G. Kee, K. Zhang, W. 2025-05-29 doi:10.1101/2025.05.25.655886 Cold Spring Harbor Laboratory Press 2025-05-29 <![CDATA[ A Transcriptomics-Based Computational Drug Repositioning Pipeline Identifies Simvastatin And Primaquine As Novel Therapeutics For Endometriosis Pain ]]> https://biorxiv.org/content/10.1101/2025.05.28.656743v1?rss=1 Oskotsky, T. T. Tang, X. Arthurs, E. Govil, A. Abbasi, F. Bhoja, A. Bunis, D. J. Lau, A. Einhaus, J. Diop, M. Irwin, J. C. Gaudilliere, B. Stevenson, D. K. Giudice, L. C. McAllister, S. L. Sirota, M. 2025-05-30 doi:10.1101/2025.05.28.656743 Cold Spring Harbor Laboratory Press 2025-05-30 <![CDATA[ Low-Rank Tensor Encoding Models Decompose Natural Speech Comprehension Processes ]]> https://biorxiv.org/content/10.1101/2025.06.02.657514v1?rss=1 Lewis, L. Pitkow, X. Wehbe, L. 2025-06-03 doi:10.1101/2025.06.02.657514 Cold Spring Harbor Laboratory Press 2025-06-03 <![CDATA[ Training-induced alterations in the modulation of human motoneuron discharge patterns with contraction force ]]> https://biorxiv.org/content/10.1101/2025.06.02.657380v1?rss=1 Skarabot, J. Thomason, H. Nazaroff, B. M. Connelly, C. D. Valencic, T. Ho, M. L. Tyagi, K. Beauchamp, J. A. Pearcey, G. E. 2025-06-05 doi:10.1101/2025.06.02.657380 Cold Spring Harbor Laboratory Press 2025-06-05 <![CDATA[ TGF-β serves as a critical signaling determinant of liver progenitor cell fate and function ]]> https://biorxiv.org/content/10.1101/2025.06.04.657336v1?rss=1 Tong, C. Lin, T. Wang, H. La Torre, C. D. Liu, H. Shao, C. Hammad, S. Liebe, R. Ebert, M. P. Ding, H. Dooley, S. Weng, H.-L. 2025-06-05 doi:10.1101/2025.06.04.657336 Cold Spring Harbor Laboratory Press 2025-06-05 <![CDATA[ Target configuration determines how and what we learn during sensorimotor adaptation ]]> https://biorxiv.org/content/10.1101/2025.06.10.658797v1?rss=1 Villavicencio, P. Tsay, J. S. de la Malla, C. 2025-06-11 doi:10.1101/2025.06.10.658797 Cold Spring Harbor Laboratory Press 2025-06-11 <![CDATA[ Composition of Carotid Plaques Differs Between Chinese and United States Patients: A Histology Study ]]> https://biorxiv.org/content/10.1101/2025.06.10.658993v1?rss=1 View larger version (83K): org.highwire.dtl.DTLVardef@14f16corg.highwire.dtl.DTLVardef@f60d66org.highwire.dtl.DTLVardef@1e9a822org.highwire.dtl.DTLVardef@11d7a31_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Cao, J.-L. Ferguson, M. Sun, J. shen, M. Small, R. C. Hippe, D. S. Zhao, X. Zhang, D. Watase, H. Yuan, C. Gao, P.-y. Demarco, J. K. Nicosia, R. F. Wang, Y.-J. Li, H.-W. Li, Z.-R. Wang, Y. Kohler, T. R. Hatsukami, T. Sui, B. 2025-06-13 doi:10.1101/2025.06.10.658993 Cold Spring Harbor Laboratory Press 2025-06-13 <![CDATA[ Interactions across hemispheres in prefrontal cortex reflect global cognitive processing ]]> https://biorxiv.org/content/10.1101/2025.06.12.659406v1?rss=1 McDonnell, M. E. Umakantha, A. Williamson, R. C. Smith, M. A. Yu, B. M. 2025-06-13 doi:10.1101/2025.06.12.659406 Cold Spring Harbor Laboratory Press 2025-06-13 <![CDATA[ Population-specific brain charts reveal Chinese-Western differences in neurodevelopmental trajectories ]]> https://biorxiv.org/content/10.1101/2025.06.17.659820v1?rss=1 Sun, L. Qin, W. Liang, X. Wang, C. Men, W. Duan, Y. Fan, X.-R. Cai, Q. Qiu, S. Wang, M. Gong, Q. Tian, Y. Liang, P. Liu, Z. Zhang, X. Song, H. Ye, Z. Zhang, P. Dong, Q. Tao, S. Zhu, W. Zhang, J. Xie, F. Feng, J. Zhang, J. Liu, C. Qian, Q. Zhang, B. Meng, M. Hu, L. Gao, J.-H. Jiang, T. Zhu, X. Zhang, Y. Liu, L. Liu, H. Liao, W. Wang, D. Wang, H. Guo, T. Dai, Z. Lui, S. Xu, K. Li, L. Xie, P. Feng, C. Cui, G. Wu, J. Yin, X. Ding, G. Xian, J. Zhao, L. Lu, J. Liu, Z. Han, Y. Yuan, Z. Zhang, X. Si, T. Zhou, F. Bi, Y. Wu, D. Gao, F. Wang, 2025-06-18 doi:10.1101/2025.06.17.659820 Cold Spring Harbor Laboratory Press 2025-06-18 <![CDATA[ Evaporation and Focus Degradation Mitigation in In-Incubator Live Cell Imaging for Capacitance Lab-on-CMOS Microsystem Calibration ]]> https://biorxiv.org/content/10.1101/2025.06.14.659688v1?rss=1 Gilpin, Y. Lin, C.-Y. Dandin, M. P. 2025-06-20 doi:10.1101/2025.06.14.659688 Cold Spring Harbor Laboratory Press 2025-06-20 <![CDATA[ Combining Machine Learning and Multiplexed, In Situ Profiling to Engineer Cell Type and Behavioral Specificity ]]> https://biorxiv.org/content/10.1101/2025.06.20.660790v1?rss=1 Leone, M. J. van de Weerd, R. Brown, A. R. Noh, M.-C. Phan, B. N. Wang, A. Corrigan, K. A. Yeramosu, D. Sestili, H. H. Arokiaraj, C. M. Lopes, B. C. Cherupally, V. K. Fields, D. Babu, S. Srinivasan, C. Podder, R. Gadey, L. headrick, D. Chen, Z. Franusich, M. E. Dum, R. Lewis, D. Mathys, H. Stauffer, W. R. Seal, R. P. Pfenning, A. R. 2025-06-21 doi:10.1101/2025.06.20.660790 Cold Spring Harbor Laboratory Press 2025-06-21 <![CDATA[ NAD+ boosting by oral nicotinamide mononucleotide administration regulates key metabolic and immune pathways through SIRT1 dependent and independent mechanisms to mitigate diet-induced obesity and dyslipidemia in mice. ]]> https://biorxiv.org/content/10.1101/2025.06.20.660826v1?rss=1 Majeed, Y. Halabi, N. M. Engelke, R. Sarwath, H. Al-Noubi, M. N. Choi, S. Madani, A. Y. Agha, M. V. Vakayil, M. Schmidt, F. Mazloum, N. A. 2025-06-26 doi:10.1101/2025.06.20.660826 Cold Spring Harbor Laboratory Press 2025-06-26 <![CDATA[ Unsupervised Multi-scale Segmentation of Cellular Cryo-electron Tomograms with Stable Diffusion Foundation Model ]]> https://biorxiv.org/content/10.1101/2025.06.25.661425v1?rss=1 Uddin, M. R. Nguyen, T.-H. Tabib, H. M. S. Gandhi, K. Xu, M. 2025-06-28 doi:10.1101/2025.06.25.661425 Cold Spring Harbor Laboratory Press 2025-06-28 <![CDATA[ Unlocking efficiency: Native circular RNA surpass linear isoforms in RNase P activity ]]> https://biorxiv.org/content/10.1101/2025.06.30.662392v1?rss=1 Chawla, A. K. Kietrys, A. M. 2025-07-02 doi:10.1101/2025.06.30.662392 Cold Spring Harbor Laboratory Press 2025-07-02 <![CDATA[ Punctuated mutagenesis promotes multi-stepevolutionary adaptation in human cancers ]]> https://biorxiv.org/content/10.1101/2025.06.30.662384v1?rss=1 Michor, F. Graser, C. J. Wu, W. Christini, C. Peljak, M. 2025-07-04 doi:10.1101/2025.06.30.662384 Cold Spring Harbor Laboratory Press 2025-07-04 <![CDATA[ An Intrinsic-hoc Framework for Heterogeneous Cellular Senescence Elucidation Using Deep Graph Representation Learning and Experimental Validation ]]> https://biorxiv.org/content/10.1101/2025.07.01.662364v1?rss=1 Ma, A. Cheng, H. Vanegas, N. D. P. Ghobashi, A. Chen, H. Rodriguez, J. Rosas, L. Wang, C. Shao, J. Jiang, Y. Wang, X. Rahman, I. Lugo-Martinez, J. Li, D. Pryhuber, G. S. Bar-Joseph, Z. Eickelberg, O. Konigshoff, M. Chung, D. Chen, R. Finkel, T. Mora, A. Rojas, M. Ma, Q. 2025-07-04 doi:10.1101/2025.07.01.662364 Cold Spring Harbor Laboratory Press 2025-07-04 <![CDATA[ Large Language Model Agent for Modular Task Execution in Drug Discovery ]]> https://biorxiv.org/content/10.1101/2025.07.02.662875v1?rss=1 0.6 increased from 34 to 55, and those passing at least four out of five empirical drug-likeness rules rose from 29 to 52, within a pool of 194 molecules. The framework also employed Boltz-2 to generate 3D protein-ligand complexes and provide rapid binding affinity estimates for candidate compounds. These results demonstrate that the approach effectively supports molecular screening, prioritization, and structure evaluation. Its modular design enables flexible integration of evolving tools and models, providing a scalable foundation for AI-assisted therapeutic discovery. ]]> Ock, J. Meda, R. S. Badrinarayanan, S. Aluru, N. S. Chandrasekhar, A. farimani, A. B. 2025-07-05 doi:10.1101/2025.07.02.662875 Cold Spring Harbor Laboratory Press 2025-07-05 <![CDATA[ Evolution of the Metazoan Protein Domain Toolkit Revealed by a Birth-Death-Gain Model ]]> https://biorxiv.org/content/10.1101/2025.07.03.659011v1?rss=1 Xiao, Y. Stolzer, M. Wasserman, L. Durand, D. 2025-07-07 doi:10.1101/2025.07.03.659011 Cold Spring Harbor Laboratory Press 2025-07-07 <![CDATA[ Deciphering the Nrf2/ARE Mechanism: GanCaoXieXin Decoction Combats Oxidative Stress in Ulcerative Colitis Pathogenesis ]]> https://biorxiv.org/content/10.1101/2025.07.02.662699v1?rss=1 Ling, P. Bing, Z. Zhang, X. Liu, Y. Shen, Y. 2025-07-08 doi:10.1101/2025.07.02.662699 Cold Spring Harbor Laboratory Press 2025-07-08 <![CDATA[ Modular Assembly of Biohybrid Machines Using Force-Enhanced Skeletal Muscle Actuators ]]> https://biorxiv.org/content/10.1101/2025.07.06.663299v1?rss=1 Yang, H. Williamson, A. S. Seok, J. M. Ranke, D. McGee, D. Trotto, E. Chin, K. Patel, D. K. Feinberg, A. W. Cohen-Karni, T. Webster-Wood, V. 2025-07-10 doi:10.1101/2025.07.06.663299 Cold Spring Harbor Laboratory Press 2025-07-10 <![CDATA[ Vector semantics of multidomain protein architectures ]]> https://biorxiv.org/content/10.1101/2025.07.07.663606v1?rss=1 Cui, X. Xiao, Y. Stolzer, M. Durand, D. 2025-07-10 doi:10.1101/2025.07.07.663606 Cold Spring Harbor Laboratory Press 2025-07-10 <![CDATA[ Context-dependent regulatory variants in Alzheimer's disease ]]> https://biorxiv.org/content/10.1101/2025.07.11.659973v1?rss=1 Chen, Z. Liu, Y. Brown, A. R. Sestili, H. Ramamurthy, E. Xiong, X. Prokopenko, D. Phan, B. N. Gadey, L. Hu, P. Tsai, L.-H. Bertram, L. Hide, W. Tanzi, R. E. Kellis, M. Pfenning, A. R. 2025-07-11 doi:10.1101/2025.07.11.659973 Cold Spring Harbor Laboratory Press 2025-07-11 <![CDATA[ DANCE 2.0: Transforming single-cell analysis from black box to transparent workflow ]]> https://biorxiv.org/content/10.1101/2025.07.17.665427v1?rss=1 Ding, J. Xing, Z. Wang, Y. Liu, R. Liu, S. Huang, Z. Tang, W. Xie, Y. Zou, J. Qiu, X. Ma, J. Yu, G. Tang, J. 2025-07-22 doi:10.1101/2025.07.17.665427 Cold Spring Harbor Laboratory Press 2025-07-22 <![CDATA[ Goal Uncertainty Attenuates Sensorimotor Adaptation ]]> https://biorxiv.org/content/10.1101/2025.07.18.665537v1?rss=1 Padmanabhan, S. Shadmehr, R. S. Klatzky, R. Tsay, J. S. 2025-07-23 doi:10.1101/2025.07.18.665537 Cold Spring Harbor Laboratory Press 2025-07-23 <![CDATA[ Big1 is a cell cycle regulator linking cell size to basal body number ]]> https://biorxiv.org/content/10.1101/2025.07.24.666660v1?rss=1 Stemm-Wolf, A. Soh, A. Mitchell, L. Sun, H. Collet, E. Dholakia, G. Raju, V. Hesselberth, J. Taliaferro, M. G. Murphy, R. F. Heasley, L. R. Pearson, C. G. 2025-07-25 doi:10.1101/2025.07.24.666660 Cold Spring Harbor Laboratory Press 2025-07-25 <![CDATA[ Innate Immune Remodeling Drives Therapy Resistance via Macrophage-NK Cell Crosstalk. ]]> https://biorxiv.org/content/10.1101/2025.07.22.666055v1?rss=1 Hsu, C.-H. Lee, K.-J. Chen, J. Donahue, L. R. Lin, J. Kacaj, D. Zhang, Z.-Y. White, A. 2025-07-26 doi:10.1101/2025.07.22.666055 Cold Spring Harbor Laboratory Press 2025-07-26 <![CDATA[ Activation-Free Upgrading of Carboxylic Acids to Aldehydes and Alcohols ]]> https://biorxiv.org/content/10.1101/2025.07.28.667276v1?rss=1 1 g/L, in some cases, after optimization of thermodynamic driving forces. Additionally, we applied this system to upgrade waste-derived carboxylic acid effluent streams from wastewater sludge, food waste, and waste gas (CO2). This activation-free process, termed "reverse aldehyde oxidation" (rAOX), establishes a broadly applicable, energy-efficient platform for carboxylic acid valorization at 100% carbon yield. Analogous to the reverse tricarboxylic acid cycle (rTCA) and reverse {beta}-oxidation (rBOX), rAOX exemplifies that metabolic reactions classically defined as unidirectional may have unexpected plasticity to operate in reverse and open new avenues in biomanufacturing. ]]> Black, W. B. Saleh, S. Perea, S. Luu, E. Cui, Y. Sun, J. Wang, Z. Lambrecht, S. Awachi, S. Hayworth, D. Wang, A. Chuayiuso, C. Hagerty, R. Gilcrease, P. C. Jiao, F. He, Z. Siegel, J. B. Li, H. 2025-07-28 doi:10.1101/2025.07.28.667276 Cold Spring Harbor Laboratory Press 2025-07-28 <![CDATA[ Minimal Impact of Low Vision on Explicit Sensorimotor Adaptation ]]> https://biorxiv.org/content/10.1101/2025.07.29.667489v1?rss=1 Cipleu, M. Padmanabhan, S. Cooper, E. Tsay, J. S. 2025-07-30 doi:10.1101/2025.07.29.667489 Cold Spring Harbor Laboratory Press 2025-07-30 <![CDATA[ Coiled-coil interactions drive ectopic condensation of overexpressed MAD1 to promote mitotic slippage in cancer cells ]]> https://biorxiv.org/content/10.1101/2025.07.29.667513v1?rss=1 Tones, J. Jeffrey, J. Lackner, R. M. Chenoweth, D. M. Zhang, H. 2025-07-31 doi:10.1101/2025.07.29.667513 Cold Spring Harbor Laboratory Press 2025-07-31 <![CDATA[ A molecular and spinal circuit basis for the functional segregation of itch and pain ]]> https://biorxiv.org/content/10.1101/2025.07.31.667966v1?rss=1 Noh, M.-c. Corrigan, K. A. Williams, S.-P. G. Peirs, C. Leone, M. J. Headrick, D. J. Guvercin, M. Lee, S. Phan, B. N. Yeramosu, D. Babu, S. Brown, A. R. van de Weerd, R. Zhao, X. Dum, R. P. Mathys, H. Pfenning, A. R. Seal, R. P. 2025-08-01 doi:10.1101/2025.07.31.667966 Cold Spring Harbor Laboratory Press 2025-08-01 <![CDATA[ DALE-Eval: A comprehensive cell type-specific expression deconvolution benchmark for transcriptomics data ]]> https://biorxiv.org/content/10.1101/2025.07.31.667984v1?rss=1 Hu, M. Chikina, M. Zhang, M. J. 2025-08-02 doi:10.1101/2025.07.31.667984 Cold Spring Harbor Laboratory Press 2025-08-02 <![CDATA[ Learning from B Cell Evolution: Adaptive Multi-Expert Diffusion for AntibodyDesign via Online Optimization ]]> https://biorxiv.org/content/10.1101/2025.08.02.668313v1?rss=1 Feng, H. Qiu, P. Poczos, B. 2025-08-03 doi:10.1101/2025.08.02.668313 Cold Spring Harbor Laboratory Press 2025-08-03 <![CDATA[ Dynamic, behavior-dependent interactions between dorsal striatal dopamine and glutamate release predict cognitive flexibility and punishment resistant cocaine use ]]> https://biorxiv.org/content/10.1101/2025.08.11.669720v1?rss=1 Bortz, D. M. Obaidi, K. Deldin, A. Weber, D. J. Torregrossa, M. M. 2025-08-12 doi:10.1101/2025.08.11.669720 Cold Spring Harbor Laboratory Press 2025-08-12 <![CDATA[ Cell Geometry Limits Bacterial Metabolic Efficiency ]]> https://biorxiv.org/content/10.1101/2025.08.11.669779v1?rss=1 Cylke, A. Banerjee, S. 2025-08-15 doi:10.1101/2025.08.11.669779 Cold Spring Harbor Laboratory Press 2025-08-15 <![CDATA[ Reduced TRPC3 conductance underlies altered SNr activity under dopamine depletion: predictions from data-driven network models ]]> https://biorxiv.org/content/10.1101/2025.08.15.670540v1?rss=1 Parker, J. E. Aristieta, A. Gao, Y. E. Gittis, A. H. Rubin, J. E. 2025-08-18 doi:10.1101/2025.08.15.670540 Cold Spring Harbor Laboratory Press 2025-08-18 <![CDATA[ SARS-CoV-2 S protein activates the HIV latent reservoir through the mTOR pathway ]]> https://biorxiv.org/content/10.1101/2025.08.18.670887v1?rss=1 View larger version (48K): org.highwire.dtl.DTLVardef@f6d87aorg.highwire.dtl.DTLVardef@1fe4cc0org.highwire.dtl.DTLVardef@60eefeorg.highwire.dtl.DTLVardef@1ea9a34_HPS_FORMAT_FIGEXP M_FIG S protein interacts with mTOR and activates the mTOR-p-p70S6K-pS6 pathway, which promotes HIV transcription C_FIG ]]> Xu, L. Shi, H. Chen, L. Wang, H. Shi, H. Miao, X. Li, S. Jiang, Y. 2025-08-19 doi:10.1101/2025.08.18.670887 Cold Spring Harbor Laboratory Press 2025-08-19 <![CDATA[ ARCADE: Controllable Codon Design from Foundation Models via Activation Engineering ]]> https://biorxiv.org/content/10.1101/2025.08.19.668819v1?rss=1 Li, J. Liang, L. Du, S. Tang, S. Lai, H.-s. Kingsford, C. 2025-08-23 doi:10.1101/2025.08.19.668819 Cold Spring Harbor Laboratory Press 2025-08-23 <![CDATA[ Recapitulating apicobasal tissue polarity in extracellular matrix incorporated airway organoids ]]> https://biorxiv.org/content/10.1101/2025.09.03.672699v1?rss=1 Gong, Z. Bhattaram, D. Porritt, L. Golestan, K. farimani, A. B. Ryan, A. L. Weiss, D. Ren, X. 2025-09-04 doi:10.1101/2025.09.03.672699 Cold Spring Harbor Laboratory Press 2025-09-04 <![CDATA[ Toward Precision Detection of Pyrazinamide Resistance: Critical Concentration Assessment and Rapid Molecular Method Validation ]]> https://biorxiv.org/content/10.1101/2025.09.03.673939v1?rss=1 Zhao, Y.-F. Tian, L. Wang, N.-H. Chen, H. Chen, S. Yu, L. Pang, M.-D. Ding, B. C. Li, J. Li, C.-Y. Dai, X. 2025-09-05 doi:10.1101/2025.09.03.673939 Cold Spring Harbor Laboratory Press 2025-09-05 <![CDATA[ The biosynthetic gene cluster landscape of the oral microbiome across health and dental caries ]]> https://biorxiv.org/content/10.1101/2025.09.04.674288v1?rss=1 5000 that could distinguish healthy and dental caries samples in the metatranscriptomic dataset, which demonstrated that BGCs could be predictive markers of disease. This analysis emphasizes the importance of high-quality metagenomic and metatranscriptomic datasets to resolve BGC expression patterns and to guide discovery of metabolites relevant to oral health and disease. ]]> Yao, M. L. Lin, P. Hua, K. Zhang, W. 2025-09-08 doi:10.1101/2025.09.04.674288 Cold Spring Harbor Laboratory Press 2025-09-08 <![CDATA[ A neuroendocrine principle: Pancreatic islets actively shape sympathetic innervation ]]> https://biorxiv.org/content/10.1101/2025.09.03.673215v1?rss=1 Li, D.-X. Luo, J.-M. Wang, J.-J. Qian, Y.-Z. Abudujilile, D. Mutailifu, M. Yang, T. Hong, Y.-X. Shi, W.-T. Ma, X.-Y. Ye, Q. Zhu, L. Li, H. Yang, X.-M. Zhang, Y.-L. Jiang, S.-H. Yu, Y.-Q. Wang, K. Li, J. Li, Q. Hu, L.-P. Zhang, X.-L. Zhang, Z.-G. 2025-09-09 doi:10.1101/2025.09.03.673215 Cold Spring Harbor Laboratory Press 2025-09-09 <![CDATA[ Capturing instantaneous neural signal-behavior relationships with concurrent functional mixed models ]]> https://biorxiv.org/content/10.1101/2025.09.08.671383v1?rss=1 Xin, A. W. Cui, E. Pereira, F. Loewinger, G. 2025-09-12 doi:10.1101/2025.09.08.671383 Cold Spring Harbor Laboratory Press 2025-09-12 <![CDATA[ Visible Light-Controllable Surgical Hemostatic Adhesives Enabled by Vitamin B12-Stabilized Poly(α-Lipoic Acid) ]]> https://biorxiv.org/content/10.1101/2025.09.09.675035v1?rss=1 Huang, Y. Yi, Q. Wang, S. Deng, C. He, L. Ma, J. Zhang, M. Tan, H. Li, P. Sun, F. 2025-09-14 doi:10.1101/2025.09.09.675035 Cold Spring Harbor Laboratory Press 2025-09-14 <![CDATA[ Beyond Ornithine Metabolism in Gyrate Atrophy: Tissue-Specific Proteomic Insights into Neonatal and Adult OAT Deficiency ]]> https://biorxiv.org/content/10.1101/2025.09.10.675383v1?rss=1 Puja, A. Du, J. Eminhizer, M. Ngo, T. Xu, R. Zhang, Y. Wang, Q. Saravanan, M. 2025-09-16 doi:10.1101/2025.09.10.675383 Cold Spring Harbor Laboratory Press 2025-09-16 <![CDATA[ Mitochondria-containing large extracellular vesicles target mouse motor neurons upon intramuscular injection ]]> https://biorxiv.org/content/10.1101/2025.09.15.675842v1?rss=1 View larger version (52K): org.highwire.dtl.DTLVardef@af590aorg.highwire.dtl.DTLVardef@1fed11dorg.highwire.dtl.DTLVardef@52d339org.highwire.dtl.DTLVardef@1a97182_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Pinky, P. P. Wang, Z.-M. Khare, P. Jhaveri, J. Basudkar, V. Rao, K. Lawrence, A. Pingali, A. Dave, K. Stolz, D. B. Sun, M. Zheng, S.-y. Shiva, S. Milligan, C. Delbono, O. Soundara Manickam, D. 2025-09-17 doi:10.1101/2025.09.15.675842 Cold Spring Harbor Laboratory Press 2025-09-17 <![CDATA[ A Rare Multipotent Peg-like Epithelial Cell is a Candidate Cell-of-Origin for High-Grade Serous Ovarian Cancer ]]> https://biorxiv.org/content/10.1101/2025.09.23.677404v1?rss=1 Ritting, M. L. Yang, W. Aalam, S. M. M. Zhao, H. Feng, L. Song, J. Dumbrava, M. Ismail, W. M. Mun, D.-G. Hu, C. Roy, O. Chaludiya, K. Shi, G. X. Crasta, D. N. Schaufelberger, K. Janus, J. R. Kalthur, G. Weroha, S. J. Kaufmann, S. Sadanandam, A. Knapp, D. J. Wang, C. Pandey, A. Gaspar-Maia, A. Couch, F. J. Sherman, M. E. Bakkum-Gamez, J. N. Kannan, N. 2025-09-25 doi:10.1101/2025.09.23.677404 Cold Spring Harbor Laboratory Press 2025-09-25 <![CDATA[ Pocket-based molecule generation with an SE(3)-equivariant language model leads to a potent and selective HPK1 inhibitor with in vivo efficacy ]]> https://biorxiv.org/content/10.1101/2025.09.23.678079v1?rss=1 Xi, B. Wang, H. Sun, G. Zhang, B. Mao, R. Ge, Y. Wang, Y. Zhang, J. Pan, Y. Zhou, F. Wang, Y. Liu, Z. Jiang, D. Wang, H. Zhou, W. Huang, B. 2025-09-25 doi:10.1101/2025.09.23.678079 Cold Spring Harbor Laboratory Press 2025-09-25 <![CDATA[ SOFT METROPOLIS-HASTINGS CORRECTION FOR GENERATIVE MODEL SAMPLING ]]> https://biorxiv.org/content/10.1101/2025.09.24.678433v1?rss=1 Feng, H. Qiu, P. Poczos, B. 2025-09-27 doi:10.1101/2025.09.24.678433 Cold Spring Harbor Laboratory Press 2025-09-27 <![CDATA[ Streptolancidin D mediates intra-species competition in Streptococcus pneumoniae through the Rgg144/SHP144 quorum-sensing system ]]> https://biorxiv.org/content/10.1101/2025.09.26.678837v1?rss=1 Valente, C. Dias, S. Gazioglu, O. Cruz, A. R. Henriques, A. O. Yesilkaya, H. Hiller, N. L. Sa-Leao, R. 2025-09-29 doi:10.1101/2025.09.26.678837 Cold Spring Harbor Laboratory Press 2025-09-29 <![CDATA[ Crosstalk between Immune Microenvironment and Hair Follicle Cells Underlies Sexual Dimorphism in Androgenetic Alopecia ]]> https://biorxiv.org/content/10.1101/2025.09.28.678997v1?rss=1 Zhang, J. Zhi, D. Deng, Z. Xiao, T. Du, F. Yang, Y. Ge, L. Wang, J. Sun, Z. Chen, J. Li, M. 2025-09-29 doi:10.1101/2025.09.28.678997 Cold Spring Harbor Laboratory Press 2025-09-29 <![CDATA[ GCP-VQVAE: A Geometry-Complete Language for Protein 3D Structure ]]> https://biorxiv.org/content/10.1101/2025.10.01.679833v1?rss=1 Pourmirzaei, M. Morehead, A. Esmaili, F. Ren, J. Pourmirzaei, M. Xu, D. 2025-10-03 doi:10.1101/2025.10.01.679833 Cold Spring Harbor Laboratory Press 2025-10-03 <![CDATA[ Low-intensity transcranial focused ultrasound engages parvalbumin-positive GABAergic interneurons in a humanized mouse model of chronic pain: from electrophysiology to cellular investigation ]]> https://biorxiv.org/content/10.1101/2025.10.08.680737v1?rss=1 Kim, M. G. Yeh, C.-Y. Gao, H. Lee, K. Gupta, K. He, B. 2025-10-08 doi:10.1101/2025.10.08.680737 Cold Spring Harbor Laboratory Press 2025-10-08 <![CDATA[ Causal Modeling Reveals Cell-Cell Communication Dynamics in the Tumor Microenvironment During Anti-PD-1 Therapy in Breast Cancer Patients ]]> https://biorxiv.org/content/10.1101/2025.10.08.681192v1?rss=1 Qiu, A. Zhang, H. Ramsey, J. D. Andrews, B. Sun, B. Ren, S. Lu, M. Zhang, K. Cooper, G. Lu, B. Chen, L. Lu, X. 2025-10-14 doi:10.1101/2025.10.08.681192 Cold Spring Harbor Laboratory Press 2025-10-14 <![CDATA[ Deep Disentangled Representation Learning Reveals Neuron Subtype-Specific Nuclear Morphologies Across Aging in Mice and Humans ]]> https://biorxiv.org/content/10.1101/2025.10.16.682849v1?rss=1 Uddin, M. R. Zheng, Z. Gandhi, K. Chang, H.-C. Kozel, J. Gali, Y. Buck, S. A. Glausier, J. R. Tseng, G. C. Freyberg, Z. Xu, M. 2025-10-17 doi:10.1101/2025.10.16.682849 Cold Spring Harbor Laboratory Press 2025-10-17 <![CDATA[ Azotobacter vinelandii glutaredoxin D delivers the core cluster to nitrogenase cofactor scaffold protein NifU ]]> https://biorxiv.org/content/10.1101/2025.10.21.683637v1?rss=1 Collantes, J. A. Rosa-Nunez, E. Armas, A. M. Raimunda, D. C. Perez-Gonzalez, A. Guo, Y. Echavarri-Erasun, C. Rubio, L. M. Gonzalez-Guerrero, M. 2025-10-21 doi:10.1101/2025.10.21.683637 Cold Spring Harbor Laboratory Press 2025-10-21 <![CDATA[ Distinct and compensatory roles of Stag1 and Stag2 in post-mitotic genome refolding ]]> https://biorxiv.org/content/10.1101/2025.10.24.684407v1?rss=1 Wang, M. Shan, F. Shu, L. Xia, S. Liu, F. Jing, D. Zhang, Y. Weng, Y. Li, B. Zhao, H. Lin, Y. Yu, Y. Wang, B. Zhang, H. 2025-10-24 doi:10.1101/2025.10.24.684407 Cold Spring Harbor Laboratory Press 2025-10-24 <![CDATA[ LRP8 is a Receptor for Yellow Fever Virus ]]> https://biorxiv.org/content/10.1101/2025.10.28.685229v1?rss=1 Mei, M. Yang, Y. Zhang, Z. Yin, Y. Tan, J. Jiang, C. Gao, Y. Wang, Z. Wang, D. Li, Y. Cong, Y. Zhang, Z. Peng, Y. Tan, W. Li, J. Li, L. Wang, H. Lang, R. He, Q. Deng, Z. huang, X. Luo, B. Shan, C. Zhang, Y. Mei, L. Cheng, G. Tan, X. 2025-10-29 doi:10.1101/2025.10.28.685229 Cold Spring Harbor Laboratory Press 2025-10-29 <![CDATA[ Interaural time and level differences contribute differently to source segregation and spatial selection ]]> https://biorxiv.org/content/10.1101/2025.10.30.685652v1?rss=1 Richardson, B. N. Luthra, S. Kainerstorfer, J. M. Shinn-Cunningham, B. G. Brown, C. A. 2025-10-31 doi:10.1101/2025.10.30.685652 Cold Spring Harbor Laboratory Press 2025-10-31 <![CDATA[ Rank- and Threat-Dependent Social Modulation of Innate Defensive Behaviors ]]> https://biorxiv.org/content/10.1101/2025.10.31.685719v1?rss=1 Li, L.-y. Gao, X. Li, Y.-t. 2025-11-01 doi:10.1101/2025.10.31.685719 Cold Spring Harbor Laboratory Press 2025-11-01 <![CDATA[ Population genomic structure of sorghum landraces across landscape, environment and culture ]]> https://biorxiv.org/content/10.1101/2025.11.02.686151v1?rss=1 Vasquez Cerda, E. E. Bellis, E. S. Das, A. Slayton, E. R. Morris, G. P. Lasky, J. R. 2025-11-04 doi:10.1101/2025.11.02.686151 Cold Spring Harbor Laboratory Press 2025-11-04 <![CDATA[ Two cortical mechanisms of audiovisual processing in the human brain ]]> https://biorxiv.org/content/10.1101/2025.11.05.686819v1?rss=1 Pushpita, S. N. Wehbe, L. 2025-11-06 doi:10.1101/2025.11.05.686819 Cold Spring Harbor Laboratory Press 2025-11-06 <![CDATA[ HEIMDALL: A Modular Framework for Tokenization in Single-Cell Foundation Models ]]> https://biorxiv.org/content/10.1101/2025.11.09.687403v1?rss=1 Haber, E. Alam, S. Ho, N. Liu, R. Trop, E. Liang, S. Yang, M. Krieger, S. Ma, J. 2025-11-10 doi:10.1101/2025.11.09.687403 Cold Spring Harbor Laboratory Press 2025-11-10 <![CDATA[ Challenges in predicting chromatin accessibility differences between species ]]> https://biorxiv.org/content/10.1101/2025.11.09.687449v1?rss=1 Stephen, A. Z. M. Raje, A. Sestili, H. H. Wirthlin, M. E. Lawler, A. J. Brown, A. R. Stauffer, W. R. Pfenning, A. R. Kaplow, I. M. 2025-11-10 doi:10.1101/2025.11.09.687449 Cold Spring Harbor Laboratory Press 2025-11-10 <![CDATA[ Design, synthesis, and pharmacological evaluation of novel PROTAC degraders targeting 11β-HSD1 for metabolic disease intervention ]]> https://biorxiv.org/content/10.1101/2025.11.09.687522v1?rss=1 View larger version (35K): org.highwire.dtl.DTLVardef@60aa3borg.highwire.dtl.DTLVardef@484120org.highwire.dtl.DTLVardef@1abca2eorg.highwire.dtl.DTLVardef@166b1a3_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Wang, L. Tao, X. He, M. Lu, Y. Wang, Y. Zhu, J. 2025-11-10 doi:10.1101/2025.11.09.687522 Cold Spring Harbor Laboratory Press 2025-11-10 <![CDATA[ Large Language Models for Accessible Reporting of Bioinformatics Analyses in Interdisciplinary Contexts ]]> https://biorxiv.org/content/10.1101/2025.11.09.687479v1?rss=1 Yu, L. Kim, D. Cao, Y. Shu, M. W. S. Shen, M. Liang, X. Gu, J. Jayakumar, R. Ding, W. Yang, F. Zhang, X. Kim, J. Yang, P. Yang, J. Y. H. 2025-11-11 doi:10.1101/2025.11.09.687479 Cold Spring Harbor Laboratory Press 2025-11-11 <![CDATA[ Developmental exposure to a PFAS mixture impairs the anamnestic response to influenza A virus infection in mice ]]> https://biorxiv.org/content/10.1101/2025.11.10.687657v1?rss=1 Post, C. M. Agyemang, J. J. McDonald, K. A. McDonough, C. A. Lawrence, B. P. 2025-11-12 doi:10.1101/2025.11.10.687657 Cold Spring Harbor Laboratory Press 2025-11-12 <![CDATA[ Extracting task-relevant preserved dynamics from contrastive aligned neural recordings ]]> https://biorxiv.org/content/10.1101/2025.11.11.686428v1?rss=1 Jiang, Y. Sheng, K. Gao, Y. Buchanan, E. K. Shikano, Y. Kim, T. H. Zhao, Y. Woo, S. J. Dinc, F. Linderman, S. W. Schnitzer, M. J. 2025-11-13 doi:10.1101/2025.11.11.686428 Cold Spring Harbor Laboratory Press 2025-11-13 <![CDATA[ A unified language model bridging de novo and fragment-based 3D molecule design delivers potent CBL-B inhibitors for cancer treatment ]]> https://biorxiv.org/content/10.1101/2025.11.13.688260v1?rss=1 Wang, H. Sun, G. Zhang, B. Wang, Y. Xi, B. Yang, M. Liu, C. Ge, Y. Fan, F. Feng, W. Zhu, Y. Xiao, Y. Wang, Y. Liu, Z. Jiang, D. Wang, H. Zhou, W. Huang, B. 2025-11-14 doi:10.1101/2025.11.13.688260 Cold Spring Harbor Laboratory Press 2025-11-14 <![CDATA[ Genetic Convergence Analysis of CRISPR Perturbations Deciphers Gene Functional Similarity ]]> https://biorxiv.org/content/10.1101/2025.11.13.688060v1?rss=1 Zhang, T. Shang, E. Roeder, K. 2025-11-15 doi:10.1101/2025.11.13.688060 Cold Spring Harbor Laboratory Press 2025-11-15 <![CDATA[ A Multimodal Atlas Reveals the Anatomical Distribution of Medium Spiny Neuron Subtypes and a Novel RGS6+ Population in the Primate Striatum ]]> https://biorxiv.org/content/10.1101/2025.11.16.688724v1?rss=1 Abdelhady, G. Brull, O. R. He, J. Lin, M. K. Galvan, A. Pfenning, A. R. Bostan, A. C. Stauffer, W. R. 2025-11-17 doi:10.1101/2025.11.16.688724 Cold Spring Harbor Laboratory Press 2025-11-17 <![CDATA[ Genetic and Functional Characterization of AMH Signaling in Zebrafish - Evidence for Roles of Amh-Bmpr2a-Bmpr1bb Pathway in Controlling Gonadal Homeostasis ]]> https://biorxiv.org/content/10.1101/2025.11.17.688792v1?rss=1 Ge, W. Yue, Y. Zeng, C. Zhang, X. Bian, C. Zhang, Z. Wu, K. Chen, W. Zhou, X. Lu, L. Ai, N. 2025-11-17 doi:10.1101/2025.11.17.688792 Cold Spring Harbor Laboratory Press 2025-11-17 <![CDATA[ SpaTRACE: Spatiotemporal recurrent auto-encoder for reconstructing signaling and regulatory networks from spatiotemporal transcriptomics data ]]> https://biorxiv.org/content/10.1101/2025.11.20.689569v1?rss=1 Zhou, H. Chen, H. Rudnick, Z. Baalbaki, S. I. Lee, Y. J. Lugo-Martinez, J. 2025-11-21 doi:10.1101/2025.11.20.689569 Cold Spring Harbor Laboratory Press 2025-11-21 <![CDATA[ Theoretical estimates on the expected number of mutations for reconstructing clonal lineage trees ]]> https://biorxiv.org/content/10.1101/2025.11.20.689642v1?rss=1 Bristy, N. A. Schwartz, R. 2025-11-21 doi:10.1101/2025.11.20.689642 Cold Spring Harbor Laboratory Press 2025-11-21 <![CDATA[ PertAdapt: Unlocking Single-Cell Foundation Models for Genetic Perturbation Prediction via Condition-Sensitive Adaptation ]]> https://biorxiv.org/content/10.1101/2025.11.21.689655v1?rss=1 Bai, D. Song, L. Xing, E. 2025-11-21 doi:10.1101/2025.11.21.689655 Cold Spring Harbor Laboratory Press 2025-11-21 <![CDATA[ Reinforcement learning for adaptive control of phenotypically heterogeneous bacterial populations ]]> https://biorxiv.org/content/10.1101/2025.11.21.689767v1?rss=1 Kratz, J. Wen, Z. Banerjee, S. Carja, O. 2025-11-24 doi:10.1101/2025.11.21.689767 Cold Spring Harbor Laboratory Press 2025-11-24 <![CDATA[ Single-cell disentangled representations for perturbation modeling and treatment effect estimation ]]> https://biorxiv.org/content/10.1101/2025.11.21.689783v1?rss=1 Sun, J. Stojanov, P. Zhang, K. 2025-11-24 doi:10.1101/2025.11.21.689783 Cold Spring Harbor Laboratory Press 2025-11-24 <![CDATA[ β-Nicotinamide mononucleotide: a novel broad-spectrum CRISPR inhibitor ]]> https://biorxiv.org/content/10.1101/2025.11.22.685598v1?rss=1 Wei, T. Shen, W. Li, W. Song, Y. Fa, Y. An, J. Sun, Y. Li, H. 2025-11-26 doi:10.1101/2025.11.22.685598 Cold Spring Harbor Laboratory Press 2025-11-26 <![CDATA[ MIMYR: Generative modeling of missing tissue in spatial transcriptomics ]]> https://biorxiv.org/content/10.1101/2025.11.24.690239v1?rss=1 Deshpande, A. Bei, Z. Ma, J. Krieger, S. 2025-11-27 doi:10.1101/2025.11.24.690239 Cold Spring Harbor Laboratory Press 2025-11-27 <![CDATA[ TissueNarrator: Generative Modeling of Spatial Transcriptomics with Large Language Models ]]> https://biorxiv.org/content/10.1101/2025.11.24.690325v1?rss=1 Liu, S. Tang, J. Ma, J. Liang, S. 2025-11-27 doi:10.1101/2025.11.24.690325 Cold Spring Harbor Laboratory Press 2025-11-27 <![CDATA[ Scalable integration and prediction of unpaired single-cell and spatial multi-omics via regularized disentanglement ]]> https://biorxiv.org/content/10.1101/2025.11.25.689803v1?rss=1 Sun, J. Liang, C. Wei, R. Zheng, P. Yan, H. Bai, L. Zhang, K. Ouyang, W. Ye, P. 2025-11-29 doi:10.1101/2025.11.25.689803 Cold Spring Harbor Laboratory Press 2025-11-29 <![CDATA[ Functional Landscape of Zebrafish Gonadotropins and Receptors: A Comprehensive Genetic Analysis ]]> https://biorxiv.org/content/10.1101/2025.11.26.690707v1?rss=1 ZENG, C. ZHANG, Z. ZHOU, L. ZHOU, X. AI, N. Ge, W. 2025-11-29 doi:10.1101/2025.11.26.690707 Cold Spring Harbor Laboratory Press 2025-11-29 <![CDATA[ Epitope and functional classification of human neutralizing antibodies against SFTSV Gn ]]> https://biorxiv.org/content/10.1101/2025.11.26.690690v1?rss=1 Wang, Q. Li, H. Jian, F. Han, A. Liu, Y. Liu, J. Yu, Y. Wang, J. Yu, L. Wang, Y. Sun, H. Ma, M. Shao, F. Zhu, L. Liu, W. Cao, Y. 2025-11-30 doi:10.1101/2025.11.26.690690 Cold Spring Harbor Laboratory Press 2025-11-30 <![CDATA[ Improved Estimation of Correlation Accuracy for Machine Learning Brain-Phenotype Associations ]]> https://biorxiv.org/content/10.1101/2025.11.26.690778v1?rss=1 Jones, M. T. Gadiyar, I. Zhang, X. Kang, K. Liu, J. Chen, A. Seidlitz, J. Alexander-Bloch, A. Kennedy, E. Vandekar, S. 2025-12-01 doi:10.1101/2025.11.26.690778 Cold Spring Harbor Laboratory Press 2025-12-01 <![CDATA[ Hypothesis Testing Governs an Efficiency-Flexibility Trade-off in Strategic Motor Learning ]]> https://biorxiv.org/content/10.64898/2025.11.29.691289v1?rss=1 Ding, W. Niyogi, A. Tsay, J. S. 2025-12-03 doi:10.64898/2025.11.29.691289 Cold Spring Harbor Laboratory Press 2025-12-03 <![CDATA[ Design principles of neuromorphic computing using genetic circuits ]]> https://biorxiv.org/content/10.64898/2025.12.01.691482v1?rss=1 Britto Bisso, F. Shree, D. Zhu, Y. Cuba Samaniego, C. 2025-12-03 doi:10.64898/2025.12.01.691482 Cold Spring Harbor Laboratory Press 2025-12-03 <![CDATA[ Sequestration-based Protein Neural Networks Tolerate the Effects of Shared Translational Resources ]]> https://biorxiv.org/content/10.64898/2025.12.01.691641v1?rss=1 He, E. Britto Bisso, F. Cuba Samaniego, C. 2025-12-04 doi:10.64898/2025.12.01.691641 Cold Spring Harbor Laboratory Press 2025-12-04 <![CDATA[ Transcranial focused ultrasound induces source localizable cortical activation in resting state humans when applied concurrently with transcranial electric stimulation ]]> https://biorxiv.org/content/10.64898/2025.12.03.692212v1?rss=1 Kosnoff, J. Gonsisko, C. Yu, K. Zhang, J. Ding, Y. Zhang, Y. He, B. 2025-12-08 doi:10.64898/2025.12.03.692212 Cold Spring Harbor Laboratory Press 2025-12-08 <![CDATA[ Elucidation and engineering of arabinofuranosyltransferase to enable total de novo biosynthesis of paris saponins in yeast ]]> https://biorxiv.org/content/10.64898/2025.12.07.692791v1?rss=1 Wang, H. Yang, Y. Wu, Z. Zhao, H. Ba, Y. Zhang, C. Sun, C. Yu, Z. Qiu, B. Liu, X. Hu, Y. Zhang, X. 2025-12-08 doi:10.64898/2025.12.07.692791 Cold Spring Harbor Laboratory Press 2025-12-08 <![CDATA[ KuPID: Kmer-based Upstream Preprocessing of Long Reads forIsoform Discovery ]]> https://biorxiv.org/content/10.64898/2025.12.05.692400v1?rss=1 Borowiak, M. Yu, Y. W. 2025-12-09 doi:10.64898/2025.12.05.692400 Cold Spring Harbor Laboratory Press 2025-12-09 <![CDATA[ RAmpSim: A Thermodynamic Simulator for Hybridization Capturein Metagenomic Sequencing ]]> https://biorxiv.org/content/10.64898/2025.12.05.692407v1?rss=1 Zhang, A. Boucher, C. Noyes, N. Yu, Y. W. 2025-12-09 doi:10.64898/2025.12.05.692407 Cold Spring Harbor Laboratory Press 2025-12-09 <![CDATA[ Normative modeling of brain morphology reveals neuroanatomical heterogeneity and biological subtypes in major depressive disorder ]]> https://biorxiv.org/content/10.64898/2025.12.07.692810v1?rss=1 Fan, Q. Gao, J. Wu, Y. Wang, Y. Zhang, L. Zhou, J. Feng, Y. Lu, Y. Wang, G. Zhou, Y. 2025-12-10 doi:10.64898/2025.12.07.692810 Cold Spring Harbor Laboratory Press 2025-12-10 <![CDATA[ Coexistence of two divergent TprA/PhrA cell-cell communication systems in Streptococcus mitis coordinate bacteriocin production, competence, oxidative stress responses, and interspecies competition with S. pneumoniae ]]> https://biorxiv.org/content/10.64898/2025.12.10.693483v1?rss=1 Ferreira, B. Valente, C. Gazioglu, O. Yesilkaya, H. Camphire, S. Hiller, N. L. Sa-Leao, R. 2025-12-10 doi:10.64898/2025.12.10.693483 Cold Spring Harbor Laboratory Press 2025-12-10 <![CDATA[ Network rewiring of a pneumococcal communication system promotes stress adaptation in a globally successful lineage ]]> https://biorxiv.org/content/10.64898/2025.12.10.693554v1?rss=1 Ferreira, B. Valente, C. Gazioglu, O. Yesilkaya, H. Hiller, N. L. Sa-Leao, R. 2025-12-10 doi:10.64898/2025.12.10.693554 Cold Spring Harbor Laboratory Press 2025-12-10 <![CDATA[ DAWN-SCAPE: Discovering Associations With Networks through Shared Contextual Analysis of Phenotype and Expression ]]> https://biorxiv.org/content/10.64898/2025.12.09.691744v1?rss=1 Shen, M. Tian, J. Devlin, B. Roeder, K. 2025-12-11 doi:10.64898/2025.12.09.691744 Cold Spring Harbor Laboratory Press 2025-12-11 <![CDATA[ Sparse, random sampling is sufficient for central tolerance ]]> https://biorxiv.org/content/10.64898/2025.12.09.693230v1?rss=1 Meyer, H. V. Dasgupta, S. Banerjee, A. Lin, Y. Prabakar, R. K. Chapin, S. R. Kiingsford, C. Navlakha, S. 2025-12-12 doi:10.64898/2025.12.09.693230 Cold Spring Harbor Laboratory Press 2025-12-12 <![CDATA[ A distinct set of brain areas process prosody--the melody of speech ]]> https://biorxiv.org/content/10.64898/2025.12.12.693781v1?rss=1 Regev, T. I. Kim, H. S. Jhingan, N. Swords, S. Kean, H. Casto, C. Cole, J. S. Fedorenko, E. 2025-12-14 doi:10.64898/2025.12.12.693781 Cold Spring Harbor Laboratory Press 2025-12-14 <![CDATA[ Attention to Psuedo-Tone Melodies Enhances Cortical but Not Brainstem Responses in Humans ]]> https://biorxiv.org/content/10.64898/2025.12.15.694407v1?rss=1 Figarola, V. Li, Y. Tierney, A. T. Dick, F. Noyce, A. Maddox, R. K. Shinn-Cunningham, B. G. 2025-12-16 doi:10.64898/2025.12.15.694407 Cold Spring Harbor Laboratory Press 2025-12-16 <![CDATA[ Reverberation exacerbates effects of interruption on auditory spatial selective attention ]]> https://biorxiv.org/content/10.64898/2025.12.15.694434v1?rss=1 Figarola, V. Liang, W. Luthra, S. Brown, C. Shinn-Cunningham, B. G. 2025-12-17 doi:10.64898/2025.12.15.694434 Cold Spring Harbor Laboratory Press 2025-12-17 <![CDATA[ Canonical cortical architecture supports the emergence of noise-invariant auditory representations ]]> https://biorxiv.org/content/10.64898/2025.12.19.695511v1?rss=1 Suarez Omedas, T. Williamson, R. S. 2025-12-22 doi:10.64898/2025.12.19.695511 Cold Spring Harbor Laboratory Press 2025-12-22 <![CDATA[ In situ cryo-ET reveals restricted docking of intraflagellar transport at the base of the trypanosome flagellum ]]> https://biorxiv.org/content/10.64898/2025.12.23.690766v1?rss=1 Staggers, S. R. Zhao, M. Harrigan, O. Absalon, S. Huang, Y. Cheng, Z. Zhao, Y. Chen, M. Sun, S. Y. 2025-12-25 doi:10.64898/2025.12.23.690766 Cold Spring Harbor Laboratory Press 2025-12-25 <![CDATA[ Investigating the mechanisms underlying saccade generation in the frontal eye fields using multi-site microstimulation ]]> https://biorxiv.org/content/10.64898/2025.12.29.696832v1?rss=1 Johnston, R. Konecky, R. Katnani, H. A. Gandhi, N. J. Smith, M. A. 2025-12-29 doi:10.64898/2025.12.29.696832 Cold Spring Harbor Laboratory Press 2025-12-29 <![CDATA[ The inactivation of DHHC7 in mouse liver promotes diet-induced obesity through a hepatic Prg4-GPR146 axis ]]> https://biorxiv.org/content/10.64898/2025.12.30.697005v1?rss=1 Sun, Y. Liu, Y. Wang, S. Wu, H. Hou, X. Duan, J. Pei, J. Xu, Y. Hu, X. Chen, B. 2025-12-31 doi:10.64898/2025.12.30.697005 Cold Spring Harbor Laboratory Press 2025-12-31 <![CDATA[ Murine Neutrophil Chemotaxis Following Burn Injury with Poloxamer 188 Treatment in a Microfluidic Platform ]]> https://biorxiv.org/content/10.64898/2026.01.07.698204v1?rss=1 Razmi Bagtash, H. Alatrash, N. Sree Datla, U. Vundurthy, B. Shao, S. Koduri, R. Islam, M. Mutore, K. Salari, E. Wu, R. Nomellini, V. Jones, C. N. 2026-01-08 doi:10.64898/2026.01.07.698204 Cold Spring Harbor Laboratory Press 2026-01-08 <![CDATA[ Enabling Skilled Human-Computer Interaction After Paralysis via a Wearable sEMG Interface ]]> https://biorxiv.org/content/10.64898/2026.01.09.698484v1?rss=1 Despradel Rumaldo, D. L. Murphy, M. Borda, L. Marshall, N. Formento, E. Bracklein, M. Lee, J. Ye, J. Walkington, P. Morrison, D. Naufel, S. Kacker, K. Verma, N. Shannahan, J. Saavedra, M. Siu, P. H. Alam, Z. Boos, A. Collinger, J. Gutnisky, D. Weber, D. 2026-01-12 doi:10.64898/2026.01.09.698484 Cold Spring Harbor Laboratory Press 2026-01-12 <![CDATA[ Sexually dimorphic plasticity of PV inhibition in sensory neocortex during learning ]]> https://biorxiv.org/content/10.64898/2026.01.10.698814v1?rss=1 Park, E. Kuljis, D. A. Myal, S. E. Christian, J. A. Barth, A. L. 2026-01-12 doi:10.64898/2026.01.10.698814 Cold Spring Harbor Laboratory Press 2026-01-12 <![CDATA[ Iron Deficiency Drives Sarcopenia in the Elderly: HIF-1α-Mediated Fibro-Adipogenic Progenitor Differentiation Induces Fat Infiltration and Impairs Muscle Function ]]> https://biorxiv.org/content/10.64898/2026.01.15.699636v1?rss=1 Ren, Q. Yang, G. Wang, D. Wu, W. Wang, Y. Feng, J. Ma, K. Guo, A. Fan, M. Sun, Y. Lang, Z. Jiang, X. Liu, Y. Wang, L. Wang, R. 2026-01-19 doi:10.64898/2026.01.15.699636 Cold Spring Harbor Laboratory Press 2026-01-19 <![CDATA[ UBA1 Mitigates Myocardial Ischemia/Reperfusion Injury by Attenuating Endoplasmic Reticulum-Mitochondria Contacts via Pdzd8 ubiquitination ]]> https://biorxiv.org/content/10.64898/2026.01.21.700963v1?rss=1 Xu, L.-L. Li, P.-B. Jiang, W. Du, J. Li, H.-H. 2026-01-23 doi:10.64898/2026.01.21.700963 Cold Spring Harbor Laboratory Press 2026-01-23 <![CDATA[ A brain dynamic model based on graph neural network reflect the inter-region interaction of cortical areas ]]> https://biorxiv.org/content/10.64898/2026.01.26.701662v1?rss=1 Li, S. Zeng, D. Dong, X. He, Y. Che, T. Zhang, J. Yang, Z. Jiang, J. Chu, L. Han, Y. Li, S. 2026-01-27 doi:10.64898/2026.01.26.701662 Cold Spring Harbor Laboratory Press 2026-01-27 <![CDATA[ Ybx1 Deficiency Causes ROS-Driven IBD-Like Intestinal Inflammation and Postnatal Lethality ]]> https://biorxiv.org/content/10.64898/2026.01.26.701719v1?rss=1 Zhu, B. PARDESHI, L. A. CHEN, Y. Zhou, X. Ge, W. 2026-01-28 doi:10.64898/2026.01.26.701719 Cold Spring Harbor Laboratory Press 2026-01-28 <![CDATA[ The Shape of Control: How Going in Circles Keeps RNA Catalytically Switched On ]]> https://biorxiv.org/content/10.64898/2026.01.28.702370v1?rss=1 Billings, M. J. Chawla, A. K. Mulla-Feroze, A. Kietrys, A. M. v. 2026-01-28 doi:10.64898/2026.01.28.702370 Cold Spring Harbor Laboratory Press 2026-01-28 <![CDATA[ Mapping Gene Drive Dynamics onto Mendelian Models ]]> https://biorxiv.org/content/10.64898/2026.01.28.702305v1?rss=1 Wen, Z. Wan, M. Greenbaum, G. Carja, O. 2026-01-30 doi:10.64898/2026.01.28.702305 Cold Spring Harbor Laboratory Press 2026-01-30 <![CDATA[ Efficient task generalization and humanlike face perception in models that learn to discriminate face geometry ]]> https://biorxiv.org/content/10.64898/2026.01.31.703048v1?rss=1 Lee, S. Ying, Z. Dey, A. Jeon, Y.-N. Issa, E. B. 2026-02-03 doi:10.64898/2026.01.31.703048 Cold Spring Harbor Laboratory Press 2026-02-03 <![CDATA[ Distinct neural modes carry information about grasp force and phase in the sensorimotor cortex ]]> https://biorxiv.org/content/10.64898/2026.02.01.702680v1?rss=1 Blumenthal, G. H. Dekleva, B. M. Gontier, C. Gonzalez, I. C. Gonzalez-Martinez, J. A. Yu, B. M. Batista, A. P. Sobinov, A. R. Miller, L. E. Gaunt, R. A. Boninger, M. L. Chase, S. M. Collinger, J. L. 2026-02-03 doi:10.64898/2026.02.01.702680 Cold Spring Harbor Laboratory Press 2026-02-03 <![CDATA[ Reversible RNA Acylating Reagents with Nitro Reduction Strategy ]]> https://biorxiv.org/content/10.64898/2026.02.04.703650v1?rss=1 Hong, Y. Liu, K. Chawla, A. K. Tsingi, C.-P. Yao, C. Kietrys, A. M. 2026-02-04 doi:10.64898/2026.02.04.703650 Cold Spring Harbor Laboratory Press 2026-02-04 <![CDATA[ TREM2 agonist antibody rebuilds the resident synovial macrophage lining barrier in rheumatoid arthritis ]]> https://biorxiv.org/content/10.64898/2026.02.02.703430v1?rss=1 Yuan, H. Wang, J. Wang, Q. Jiang, L. Liu, L. Shen, W. Li, P. Liu, W. Liu, Z. Hu, F. Cai, X. Liu, W. Wu, Q. Wang, X. Yan, H. Sun, X. 2026-02-05 doi:10.64898/2026.02.02.703430 Cold Spring Harbor Laboratory Press 2026-02-05 <![CDATA[ Neurons in the Human Substantia Nigra Respond to Cognitive Boundaries and Predict Memory ]]> https://biorxiv.org/content/10.64898/2026.02.04.703556v1?rss=1 Shi, L. Flores, A. Shimelis, L. Liu, Y. Jiang, C. Zhang, J. Meng, F. Zheng, J. 2026-02-06 doi:10.64898/2026.02.04.703556 Cold Spring Harbor Laboratory Press 2026-02-06 <![CDATA[ A Population Coupling Model Identifies Reduced Propagation from V1 to Higher Visual Areas During Locomotion ]]> https://biorxiv.org/content/10.64898/2026.02.04.703681v1?rss=1 Xin, Q. Urban, K. N. Siegle, J. H. Kass, R. E. 2026-02-06 doi:10.64898/2026.02.04.703681 Cold Spring Harbor Laboratory Press 2026-02-06 <![CDATA[ Extracting large-scale neural activity with Suite2p ]]> https://biorxiv.org/content/10.64898/2026.02.04.703741v1?rss=1 Stringer, C. Ki, C. Del Grosso, N. LaFosse, P. Zhang, Q. Pachitariu, M. 2026-02-06 doi:10.64898/2026.02.04.703741 Cold Spring Harbor Laboratory Press 2026-02-06 <![CDATA[ Capacitance Sensor Array for Lab-on-CMOS Applications using a Passive RFID Interface ]]> https://biorxiv.org/content/10.64898/2026.02.05.704137v1?rss=1 Lin, K.-C. Dandin, M. 2026-02-09 doi:10.64898/2026.02.05.704137 Cold Spring Harbor Laboratory Press 2026-02-09 <![CDATA[ seq2ribo: Structure-aware integration of machine learning and simulation to predict ribosome location profiles from RNA sequences ]]> https://biorxiv.org/content/10.64898/2026.02.08.700508v1?rss=1 Kaynar, G. Kingsford, C. 2026-02-09 doi:10.64898/2026.02.08.700508 Cold Spring Harbor Laboratory Press 2026-02-09 <![CDATA[ SenNet Portal: Build, Optimization and Usage ]]> https://biorxiv.org/content/10.64898/2026.02.06.704469v1?rss=1 Borner, K. Blood, P. D. Silverstein, J. C. Ruffalo, M. Satija, R. Gehlenborg, N. Honick, B. Bueckle, A. Jain, Y. Qaurooni, D. Shirey, B. Sibilla, M. Metis, K. Bisciotti, J. Morgan, R. S. Betancur, D. Sablosky, G. R. Turner, M. L. Kim, S.-J. Lee, P. J. Bartz, J. Domanskyi, S. Peters, S. T. Enninful, A. Farzad, N. Fan, R. SenNet Team, Herr, B. W. 2026-02-10 doi:10.64898/2026.02.06.704469 Cold Spring Harbor Laboratory Press 2026-02-10 <![CDATA[ CodonRL: Multi-Objective Codon Sequence Optimization Using Demonstration-Guided Reinforcement Learning ]]> https://biorxiv.org/content/10.64898/2026.02.12.705465v1?rss=1 Du, S. Kaynar, G. Li, J. You, Z. Tang, S. Kingsford, C. 2026-02-14 doi:10.64898/2026.02.12.705465 Cold Spring Harbor Laboratory Press 2026-02-14 <![CDATA[ A scalable approach to resolving variants of uncertain significance ]]> https://biorxiv.org/content/10.64898/2026.02.14.705848v1?rss=1 90,000 unobserved variants; 62% had enough evidence to be "preclassified" as pathogenic or benign. We validated our data, evidence and classifications using All of Us and created interactive resources to enable clinical use of the calibrated data. Thus, for 40 genes, representing 1% of the clinical genome, we resolve most existing VUS and future variants, illustrating how systematic use of scalable evidence can empower genomic medicine. ]]> Tejura, M. Chen, Y. McEwen, A. E. Stewart, R. Sverchkov, Y. Laval, F. Woo, I. Zeiberg, D. Shen, R. Fayer, S. Stone, J. Smith, N. Casadei, S. Wang, Z. R. Snyder, M. Capodanno, B. J. Gupta, P. Benazouz, M. Jain, S. Heidl, S. Muffley, L. Dong, S. Lin, K. Hitz, B. C. Gabdank, I. Da, E. Y. Best, S. Grindstaff, S. Reinhart, D. Rodriguez-Salas, L. Seid, O. Vandi, A. J. Wenman, C. Wheelock, M. K. Pendyala, S. Holmes, D. Xu, A. Hosokai, A. Tixhon, M. Reno, C. Ewald, J. D. Spirohn-Fitzgerald, K. Teelucksingh, T. Hao, T. Chen, Z. S. Haghighi, M. Hamid, A. K. 2026-02-15 doi:10.64898/2026.02.14.705848 Cold Spring Harbor Laboratory Press 2026-02-15 <![CDATA[ Learning reweights the decision dynamics of cortico-basal ganglia-thalamic pathways from deliberation to commitment ]]> https://biorxiv.org/content/10.64898/2026.02.17.706272v1?rss=1 Yu, Z. Rubin, J. E. Verstynen, T. 2026-02-18 doi:10.64898/2026.02.17.706272 Cold Spring Harbor Laboratory Press 2026-02-18 <![CDATA[ Phase response curve and RNA-sequencing demonstrate spiders' sensitivity to light and pinpoint candidate light-responsive genes ]]> https://biorxiv.org/content/10.64898/2026.02.17.706298v1?rss=1 6 hour) phase advance and delays when the light pulse was applied during circadian time (CT) 16-18, with a break point of advances to delays at CT 17. We then investigated the genetic mechanism of the phase response to light by splitting M. wittfeldae adult females entrained to 12 hours light:12 hours dark (LD 12:12) into two groups. One group received a 1-hour light pulse 5 hours after lights off (CT17), and one group did not. We then sacrificed spiders for RNA isolations 1 and 10 hours after the light pulse. We identified numerous genes that were downregulated by the light pulse 1 hour after the pulse relative to no pulse group. Intriguingly, many of these genes had a flipped pattern of expression 9 hours later - the pulse group had higher expression than the no pulse group. This pattern is consistent with the shifted phase of locomotor activity expected after the light pulse application. We also identified clock gene homologs in M. wittfeldae that had distinct expression patterns from other arthropods. ]]> Toporikova, N. Cheng, W. Cheng, L. Mah, A. Clarke, T. Jones, T. C. Moore, D. Ayoub, N. A. 2026-02-18 doi:10.64898/2026.02.17.706298 Cold Spring Harbor Laboratory Press 2026-02-18 <![CDATA[ Inference of cancer driver mutations from tumor microenvironmentcomposition: a pan-cancer study with cross-platform external validation ]]> https://biorxiv.org/content/10.64898/2026.02.20.707104v1?rss=1 Baker, E. A. Mehaffy, N. S. 2026-02-23 doi:10.64898/2026.02.20.707104 Cold Spring Harbor Laboratory Press 2026-02-23 <![CDATA[ Expert Motor Synergies Emerge Predominantly Offline During Early Skill Learning ]]> https://biorxiv.org/content/10.64898/2026.02.24.707000v1?rss=1 Kistler, W. Fakhreddine, R. Rodriguez, G. R. Hayward, M. Buch, E. R. Bestmann, S. Cohen, L. 2026-02-25 doi:10.64898/2026.02.24.707000 Cold Spring Harbor Laboratory Press 2026-02-25 <![CDATA[ Uncertainty-aware synthetic lethality prediction with pretrained foundation models ]]> https://biorxiv.org/content/10.64898/2026.02.25.708096v1?rss=1 Hua, K. Haber, E. Ma, J. 2026-02-27 doi:10.64898/2026.02.25.708096 Cold Spring Harbor Laboratory Press 2026-02-27 <![CDATA[ Early proteomic signatures of Alzheimer`s disease in the retina and brain of 3xTg-AD mice ]]> https://biorxiv.org/content/10.64898/2026.02.26.708380v1?rss=1 Puja, A. McNeel, R. Xu, R. Zhu, S. Hansman, D. Du, J. 2026-02-27 doi:10.64898/2026.02.26.708380 Cold Spring Harbor Laboratory Press 2026-02-27 <![CDATA[ Early electrical stimulation promotes functional recovery after volumetric muscle loss ]]> https://biorxiv.org/content/10.64898/2026.03.01.708642v1?rss=1 Gershanok, S. Behre, A. Jin, R. Vinokurova, S. Blount, J. Garg, R. Ersoz, A. Wang, L. Jo, S. Ranke, D. Kulkarni, M. Cohen-Karni, D. Feinberg, A. W. Weber, D. Brown, B. Cohen-Karni, T. 2026-03-03 doi:10.64898/2026.03.01.708642 Cold Spring Harbor Laboratory Press 2026-03-03 <![CDATA[ The role of the locus coeruleus in eye movements during perceptual decision making ]]> https://biorxiv.org/content/10.64898/2026.03.01.708911v1?rss=1 Acar, K. Smith, M. A. 2026-03-03 doi:10.64898/2026.03.01.708911 Cold Spring Harbor Laboratory Press 2026-03-03 <![CDATA[ Minimal biophysical rules are sufficient for the emergence of computational intelligence at the neuronal scale ]]> https://biorxiv.org/content/10.64898/2026.03.01.708921v1?rss=1 Wang, G. Qi, L. Li, K. Tang, C. Chen, X. Mao, Y. Occhipinti, L. G. Nathan, A. Wang, N. Pan, Y. Smielewski, P. Wang, Y. Han, H. Guo, X. Gao, S. 2026-03-03 doi:10.64898/2026.03.01.708921 Cold Spring Harbor Laboratory Press 2026-03-03 <![CDATA[ Introducing a fusogenicity metric for lipid nanoparticle formulation ]]> https://biorxiv.org/content/10.64898/2026.03.02.708638v1?rss=1 Zheng, L. Baliga, M. Gallagher, S. F. Gao, A. Z. Rueben, J. Go, Y. K. Deserno, M. Leal, C. 2026-03-04 doi:10.64898/2026.03.02.708638 Cold Spring Harbor Laboratory Press 2026-03-04 <![CDATA[ Fall risk-aware adaptation explains suboptimal locomotor performance ]]> https://biorxiv.org/content/10.64898/2026.03.02.709033v1?rss=1 Kang, I. Mitra, K. Seethapathi, N. 2026-03-04 doi:10.64898/2026.03.02.709033 Cold Spring Harbor Laboratory Press 2026-03-04 <![CDATA[ Ligand-guided Sequence-structure Co-design of De Novo Functional Enzymes ]]> https://biorxiv.org/content/10.64898/2026.03.02.709205v1?rss=1 Song, Z. Liu, H. Zhao, Y. Yang, Y. Li, L. 2026-03-04 doi:10.64898/2026.03.02.709205 Cold Spring Harbor Laboratory Press 2026-03-04 <![CDATA[ A minimally invasive floating-wire interface for transcranial deep brain stimulation ]]> https://biorxiv.org/content/10.64898/2026.03.04.709293v1?rss=1 Jain, V. Forssell, M. Grover, P. Chamanzar, M. 2026-03-06 doi:10.64898/2026.03.04.709293 Cold Spring Harbor Laboratory Press 2026-03-06 <![CDATA[ Saturating hepatic clearance drives elevated cfDNA and fragment shortening in cancer ]]> https://biorxiv.org/content/10.64898/2026.03.04.709433v1?rss=1 Rachman, T. Laframboise, W. Gallo, P. Petrosko, P. Liu, D. Kumar, R. Balic, M. Oesterreich, S. Foldi, J. Lee, A. Wagner, P. Bartlett, D. Schwartz, R. Carja, O. 2026-03-06 doi:10.64898/2026.03.04.709433 Cold Spring Harbor Laboratory Press 2026-03-06 <![CDATA[ Epigenetic Silencing of Carotid Body TRPM7 Attenuates Hypertension in Obese Mice ]]> https://biorxiv.org/content/10.64898/2026.03.05.709322v1?rss=1 Shin, M. K. Roy, A. Paudel, O. Gudapati, S. Sham, J. Tang, W.-Y. Polotsky, V. 2026-03-07 doi:10.64898/2026.03.05.709322 Cold Spring Harbor Laboratory Press 2026-03-07 <![CDATA[ Zhi-Shi-Huang-Wu slows Parkinson's disease progression in transgenic C. elegans models ]]> https://biorxiv.org/content/10.64898/2026.03.11.709540v1?rss=1 View larger version (47K): org.highwire.dtl.DTLVardef@1a6f1f7org.highwire.dtl.DTLVardef@157a270org.highwire.dtl.DTLVardef@69a238org.highwire.dtl.DTLVardef@1194b5e_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Fahim, M. Liu, Y. Hui, R. Zhou, Y. Yang, H. Hongyu, L. 2026-03-16 doi:10.64898/2026.03.11.709540 Cold Spring Harbor Laboratory Press 2026-03-16 <![CDATA[ CHPT1-LCAT rewires lipolysis towards ferroptosis ]]> https://biorxiv.org/content/10.64898/2026.03.15.711301v1?rss=1 Ma, L. Teng, P. Zhang, Q. Liu, Q. Lu, J. Wang, H. Zhang, Y. Guo, Z. Yang, R. Qiao, L. Li, L. Fu, Y. Li, B. 2026-03-16 doi:10.64898/2026.03.15.711301 Cold Spring Harbor Laboratory Press 2026-03-16 <![CDATA[ Exploration of Orally Disintegrating Tablet for Sublingual Vaccination against Mucosal Bacterial Infection ]]> https://biorxiv.org/content/10.64898/2026.03.14.711758v1?rss=1 Liu, Y. Cai, Q. Hu, X. Liu, X. Guo, P. Zhang, Y. Liu, H. Wang, W. Zheng, D. Pan, C. Guo, L. Yu, X. Zhang, Q. Wang, D. Qiu, Y. Wang, D. Li, W. Du, Y. Ma, G. Xu, J. Wang, S. Liu, Y. Wei, W. 2026-03-17 doi:10.64898/2026.03.14.711758 Cold Spring Harbor Laboratory Press 2026-03-17 <![CDATA[ From Breath to Behavior: Respiratory Features Predict Visual Detection Performance ]]> https://biorxiv.org/content/10.64898/2026.03.18.712638v1?rss=1 Skog, E. E. Issar, D. Grigg, M. Nelson, S. E. Kainerstorfer, J. M. Smith, M. A. 2026-03-19 doi:10.64898/2026.03.18.712638 Cold Spring Harbor Laboratory Press 2026-03-19 <![CDATA[ A feed-forward loop between niche adenosine and Gzmk⁺ CD8 T cells propagates systemic inflammaging ]]> https://biorxiv.org/content/10.64898/2026.03.18.712515v1?rss=1 Guo, L. Zheng, R. Zhan, Q. Yu, X. Zhang, Q. Yao, J. Tan, X. Li, X. Zhang, O. Liu, P. Wang, C. Yao, Y. Ma, R. Wu, X. Wang, C. Zhou, H. Sun, Y. Xiong, K. Li, L. Xu, H. Jin, J. Wu, Y. Liu, T. Wang, Z. Liu, Y. Wang, Z.-y. Cao, W. 2026-03-20 doi:10.64898/2026.03.18.712515 Cold Spring Harbor Laboratory Press 2026-03-20 <![CDATA[ Linking reaction time variability to physiological markers of arousal across timescales ]]> https://biorxiv.org/content/10.64898/2026.03.19.713034v1?rss=1 Issar, D. Skog, E. E. Grigg, M. Kainerstorfer, J. M. Smith, M. A. 2026-03-23 doi:10.64898/2026.03.19.713034 Cold Spring Harbor Laboratory Press 2026-03-23 <![CDATA[ A cerebellar cognitive rheostat bidirectionally controls attention ]]> https://biorxiv.org/content/10.64898/2026.03.22.713532v1?rss=1 Jiang, S. Dong, Z. Song, Z. Yang, G. Shen, Z. Yin, X. Li, H. Ma, X. Ding, T. Zhao, Z. Yang, J. Wang, H. Shen, W. Jiang, H. Chen, L. Wu, H. 2026-03-24 doi:10.64898/2026.03.22.713532 Cold Spring Harbor Laboratory Press 2026-03-24 <![CDATA[ Cell-Type-Specific Bidirectional Modulation of the Cortico-Thalamo-Cortical Sensory Pathway by Transcranial Focused Ultrasound (tFUS) ]]> https://biorxiv.org/content/10.64898/2026.03.23.713540v1?rss=1 Gao, H. Ramachandran, S. Torregrossa, M. M. He, B. 2026-03-25 doi:10.64898/2026.03.23.713540 Cold Spring Harbor Laboratory Press 2026-03-25 <![CDATA[ Scaling and Generalization of Discrete Diffusion Models for Tumor Phylogenies ]]> https://biorxiv.org/content/10.64898/2026.03.23.713822v1?rss=1 Sabata, S. Schwartz, R. 2026-03-26 doi:10.64898/2026.03.23.713822 Cold Spring Harbor Laboratory Press 2026-03-26 <![CDATA[ Time-Resolved Neuronal Network Dynamics Distinguish Pathological States in Organoid Models ]]> https://biorxiv.org/content/10.64898/2026.03.25.714227v1?rss=1 McCrimmon, C. M. Sinha, P. Cao, Q. Monsoor, T. Sharma, K. Turali, M. Y. Samarasinghe, R. Roychowdhury, V. 2026-03-26 doi:10.64898/2026.03.25.714227 Cold Spring Harbor Laboratory Press 2026-03-26 <![CDATA[ EEG Foundation Model Improves Online Directional Motor Imagery Brain-computer Interface Control ]]> https://biorxiv.org/content/10.64898/2026.03.24.714020v1?rss=1 Karrenbach, M. A. Wang, H. Johnson, Z. Ding, Y. He, B. 2026-03-27 doi:10.64898/2026.03.24.714020 Cold Spring Harbor Laboratory Press 2026-03-27 <![CDATA[ Evaluating the reliability of tools for mRNA annotation and IRES studies ]]> https://biorxiv.org/content/10.64898/2026.03.29.707813v1?rss=1 May, G. E. Akirtava, C. McManus, J. 2026-03-31 doi:10.64898/2026.03.29.707813 Cold Spring Harbor Laboratory Press 2026-03-31 <![CDATA[ Acoustic Salience Drives Pupillary Dynamics in an Interrupted, Reverberant Task ]]> https://biorxiv.org/content/10.64898/2026.03.31.715639v1?rss=1 Figarola, V. Liang, W. Luthra, S. Parker, E. Winn, M. Brown, C. Shinn-Cunningham, B. G. 2026-04-02 doi:10.64898/2026.03.31.715639 Cold Spring Harbor Laboratory Press 2026-04-02 <![CDATA[ Context-dependent mechanical reconfiguration is necessary for multifunctional behavior in a constrained hydrostat ]]> https://biorxiv.org/content/10.64898/2026.04.01.715937v1?rss=1 View larger version (87K): org.highwire.dtl.DTLVardef@130cdfcorg.highwire.dtl.DTLVardef@1237bcdorg.highwire.dtl.DTLVardef@94deadorg.highwire.dtl.DTLVardef@1a73234_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 1.C_FLOATNO Anatomy and kinematics of the Aplysia feeding system (a1) Adult Aplysia californica searching for food and (a2) feeding on Gracilaria macroalgae ((a1) photo credit: Dr. Jeffrey P. Gill, (a2) modified with permission from Bennington et al. 202514). Gray highlight shows the location of the feeding structure, the buccal mass (b). (b) An anatomical diagram of a midline sagittal view of a buccal mass. During feeding, the odontophore (the internal grasper of the buccal mass) protracts through the tubelike I3 muscle. In the midsagittal plane, the I3 is visible as two longitudinal elements, but is one continuous structure that runs circumferentially around the buccal mass. The inner wall of the distal I3 is shown in dark blue. The dashed white line shows the jaw line, which is used as the reference for both the translation and rotation measurements. (c) Configuration of the buccal mass (left: anatomical diagram; middle: MRI frames) showing (c1) peak retraction and (c2) peak protraction. (right) A diagram of the buccal mass was created to highlight key anatomical landmarks for each frame of the MRI video showing a complete biting sequence (d-e). The same diagrammatic representations of the landmarks are shown in (d) and (e) for the protraction and retraction portions of the biting sequence, respectively (See STAR Methods). The frames shown in (c1) and (c2) correspond to the 0 ms and 3410 ms frames, respectively, and are the same between the middle and right portions of the figure. Key frames referred to in the text: t0: start of the behavioral cycle, t1: peak rotation reached, t2: peak translation reached, t3: rotation plateau ended, t4: end of behavioral cycle. (f) Kinematic measurements were taken using the drawn diagrams for each frame in the sequence. See main text for definitions of variables. All scale bars correspond to 10 mm. C_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=84 SRC="FIGDIR/small/715937v1_fig2.gif" ALT="Figure 2"> View larger version (34K): org.highwire.dtl.DTLVardef@1d119b2org.highwire.dtl.DTLVardef@ee36acorg.highwire.dtl.DTLVardef@147943aorg.highwire.dtl.DTLVardef@549cb4_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 2.C_FLOATNO Kinetic/Kinematic biomechanical model of the buccal mass (a) Rest geometry of the biomechanical model. The grasper (odontophore) is modeled as a rigid ellipse (magenta with yellow radula). It is connected to the I1/I3 lumen (blue trapezoid) by the hinge muscle (green). The I2 protractor muscle (red) wraps conformally around the odontophore and attaches at the lateral groove. The net force and torque from the I2 on the odontophore are found by performing an instantaneous force balance on a small arc of the ellipse and integrating across the full region of contact between the I2 and the odontophore. The hinge muscle is modeled as a linearly elastic, geometrically exact beam. At each position along the beams midline, a quasistatic force balance is performed (see STAR Methods). (b1) The tension in the I2 is modeled using the length-tension relationship reported in Yu et al. 1999 scaled by a normalized activation level. (b2) The axial and bending stiffness of the beam hinge were calibrated to ex vivo animal data reported in Sutton et al. 2004. Gray region indicates odontophore displacements observed during biting behaviors (Sutton et al. 2004). (c1-c2) To investigate the effects of mechanical reconfiguration on odontophore position at peak protraction, (c1) the aspect ratio of the odontophore ellipse and (c2) the stretch of the lateral groove were added as additional kinematic constraints. (c1) and (c2) show results from the model but do not correspond to any particular behavior or configuration observed in the animal. These constraints impact the biomechanical model via contact forces from the I1/I3 (see STAR Methods). The lateral groove stretch is converted to a depression angle of the dorsal I1/I3 muscle as a proxy for the wrapping of the dorsal I3 around the odontophore observed during in vivo feeding behaviors (Fig 1). (d-e) MRI frames at peak protraction in (d1, with and without overlay) biting (t2) and (e1, with and without overlay) rejection ({tau}2) compared to corresponding frames from the biomechanical model (d2 and e2, respectively). C_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=184 SRC="FIGDIR/small/715937v1_fig3.gif" ALT="Figure 3"> View larger version (56K): org.highwire.dtl.DTLVardef@fc18acorg.highwire.dtl.DTLVardef@b80555org.highwire.dtl.DTLVardef@1663cf4org.highwire.dtl.DTLVardef@12bc433_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 3.C_FLOATNO Mechanical reconfiguration of the buccal mass (a) Midsagittal kinematics of the buccal mass during a (left) biting and (right) rejection behavior (see also Figs. S1 and S2). Colored circles (diamonds) show data for an individual frame, and the black line shows the two-point moving average of the signal. Vertical dashed lines show concurrent time points in the different kinematic signals (biting: t0: cycle starts, t1: peak rotation, t2: peak translation, t3: rotation plateau ended, t4: cycle ends. Rejection: {tau}0: cycle starts, {tau}1: rotation plateau ends, {tau}2: peak translation, {tau}3: peak rotation, {tau}4: cycle ends). (b) Model configurations for nine different pairs of aspect ratios ({Phi}) and lateral groove stretches ({lambda}LG ) (numbers correspond to the labeled points in (Fig. S6c)). Note that these simulated results from the model do not necessarily correspond to configurations observed in the animal but rather show changes in the systems configuration due to changes in the kinematic parameters. All configurations here were achieved with an I2 activation of AI2 = 65%. (c-d) Sensitivity of the model translation and rotation at peak protraction to lateral groove shortening ({lambda}LG, top row) and aspect ratio change ({Phi}, bottom row) for biting (c) and rejection (d). The y-axis for all panels reports the difference between the model prediction and observed animal value at peak protraction (for translation or rotation) normalized by the range of motion (ROM) for each behavior. For each panel, one kinematic parameter is held fixed (top:{Phi} fixed; bottom:{lambda} LG fixed) at the value observed in the animal at peak protraction, and the other is varied to determine the effect of changing this parameter on the translation and rotation of the odontophore. Vertical dashed lines show the observed value of the varied parameter in the animal at peak protraction. The horizontal dashed line shows 0 difference for reference. The steepness of the difference curve in the vicinity of the vertical dashed line indicates how sensitive the system is to changes in each kinematic parameter near peak protraction. Here, a steeper curve (with a positive or negative slope) indicates greater sensitivity. For biting simulations, AI2 = 15%, and for rejection, AI2 = 90% based on the results of the model validation. Each curve in (c) and (d) is a 1D cross-section of the 2D contour plots shown in Figs. S6-S7. For a complete view of the sensitivity of translation and rotation to lateral groove stretch and aspect ratio across the kinematic configuration space at different I2 activations, see Figs. S6-S7. Note that (c) and (d) use different vertical scales. The smaller scale for the rejection plots was chosen to better show the difference curves for rejection, and it reflects the overall decreased sensitivity to both lateral groove stretch and aspect ratio changes for the rejection behaviors. C_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/715937v1_fig4.gif" ALT="Figure 4"> View larger version (36K): org.highwire.dtl.DTLVardef@5df3f2org.highwire.dtl.DTLVardef@3abb02org.highwire.dtl.DTLVardef@1cbb0a2org.highwire.dtl.DTLVardef@1b98dd7_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 4.C_FLOATNO Mechanical reconfiguration facilitates behaviors in a variety of constrained hydrostat systems Combinations of the active shape change of internal structures (cyan), changes to the movement constraints and contact interaction (blue), and bending and conforming of structures (magenta) allow constrained hydrostats to mechanically reconfigure their neuromusculature (purple) to perform various behaviors. This can be seen in various systems across various species. As discussed here, the Aplysia buccal mass uses combinations of these mechanisms in (a) biting and (b) rejection behaviors to protract the buccal mass. (c) The pond snail, Lymnaea, has a morphologically similar buccal mass to Aplysia, but its I1/I3 homolog, the anterior jugalis, sits further posterior to the odontophore35, meaning it may more readily rely on the bending of the anterior jugalis and contact interactions during protraction. (d) The octopus and, more broadly, cephalopod buccal masses contain a beak that lacks a fixed articulation. Instead, by activating the lateral mandibular muscle (LMM), the buccal mass can create a stiff rotation point and may shift the function of the posterior mandibular muscle (PMM) from compressing the buccal mass to opening the beak36,37. (e) The human tongue (and other Type I tongues38) sits within the skull and makes use of contact with the hard palate to push food from the oral cavity into the pharynx27,48. (f) Additionally, by changing how the tongue interacts with the palate and teeth, while maintaining the same internal shape, humans can produce various vowel and consonant sounds39,49,50. This use of contact with the palate and teeth is known in the phonetics community as "bracing." Here, by creating a groove in the middle of the tongue, the phonemes /{varepsilon}/ and /ae/ can be produced. By raising the tongue and creating palatal contact while maintaining that groove, these vowels shift to the fricative consonants /s/ and /{theta}/49. Small insets show which of the mechanical configurations are used in each behavior. C_FIG ]]> Bennington, M. J. Rogers, S. M. Neustadter, D. M. Quinn, R. D. Sutton, G. P. Chiel, H. J. Webster-Wood, V. A. 2026-04-05 doi:10.64898/2026.04.01.715937 Cold Spring Harbor Laboratory Press 2026-04-05 <![CDATA[ Biohybrid Robots with Embedded Conductive Fibers for Actuation, Sensing, and Closed-loop Control ]]> https://biorxiv.org/content/10.64898/2026.04.01.715915v1?rss=1 Xie, X. Zhao, Y. Wu, R. Xu, W. Bennington, M. J. Daso, R. Liu, J. Surendran, A. Hester, J. Webster-Wood, V. Cheng, T. Rivnay, J. 2026-04-06 doi:10.64898/2026.04.01.715915 Cold Spring Harbor Laboratory Press 2026-04-06 <![CDATA[ Degradable porous PLGA/PCL membrane enable a lung alveoli-on-a-chip for modeling particulate-induced alveolar injury ]]> https://biorxiv.org/content/10.64898/2026.04.03.716399v1?rss=1 Choi, J. Azam, S. Hisaeda, M. Liu, S. Zheng, S. 2026-04-07 doi:10.64898/2026.04.03.716399 Cold Spring Harbor Laboratory Press 2026-04-07 <![CDATA[ A biodegradable porous membrane-based lung alveoli-on-a-chip for assessing particulate-matter-induced pulmonary toxicity ]]> https://biorxiv.org/content/10.64898/2026.04.03.716404v1?rss=1 50 % porosity, [~]2 {micro}m thickness, and mechanical compliance over 100-fold higher than conventional Transwell inserts, closely resembling the native interstitium. During co-culture, gradual PLGA degradation was compensated by cell-secreted extracellular-matrix (ECM) proteins such as collagen IV and laminin, forming a self-remodeling barrier that maintained integrity for at least 11 days. The platform supported stable epithelial-endothelial co-culture, high transepithelial electrical resistance, and physiologically relevant permeability. To demonstrate its utility, the chip was used to assess pulmonary toxicity of four types of waste-combustion-derived particulates, including rubber, plastic bags, plastic bottles, and textile fibers, delivered apically under ALI conditions. All combustion products reduced cell viability, increased hydrogen-peroxide release, and elevated {gamma}-H2AX expression, indicating oxidative and genotoxic stress, while disrupting barrier permeability. Rubber combustion particles elicited the most severe toxicity, causing the greatest loss of viability, accumulation of reactive oxygen species, and formation of DNA double-strand breaks. Together, these results establish a biodegradable, ECM-remodeling lung alveoli-on-a-chip as a physiologically relevant platform for investigating source-specific particulate toxicity and alveolar-barrier pathophysiology. By bridging environmental exposure models with human-relevant lung biology, this system provides a quantitative and translatable tool for evaluating respiratory risks and therapeutic interventions. ]]> Choi, J. Umalkar, V. Wang, X. Zheng, S. 2026-04-07 doi:10.64898/2026.04.03.716404 Cold Spring Harbor Laboratory Press 2026-04-07 <![CDATA[ Membrane-Free Alveolus-on-a-Chip via Biodegradable Scaffold Recapitulates Interstitial Mechanics, Immune Trafficking, and Aerosolized mRNA Delivery ]]> https://biorxiv.org/content/10.64898/2026.04.17.719302v1?rss=1 Choi, J.-W. Nguyen, H. H. Jalili, A. Andersen, M. Zheng, S.-Y. 2026-04-19 doi:10.64898/2026.04.17.719302 Cold Spring Harbor Laboratory Press 2026-04-19