bioRxiv Channel: Queensland University of Technology https://biorxiv.org This feed contains articles for bioRxiv Channel "Queensland University of Technology" bioRxiv bioRxiv https://biorxiv.org <![CDATA[ Hip and knee kinematics display complex and time-varying sagittal kinematics during repetitive stepping: Implications for design of a functional fatigue model of the knee extensors and flexors ]]> https://biorxiv.org/content/10.1101/005538v1?rss=1 Corey Scholes Michael McDonald Anthony Parker 2014-05-26 doi:10.1101/005538 Cold Spring Harbor Laboratory Press 2014-05-26 <![CDATA[ Choosing an appropriate modelling framework for analysing multispecies co-culture cell biology experiments ]]> https://biorxiv.org/content/10.1101/008318v1?rss=1 Deborah C Markham Matthew J Simpson Ruth E Baker 2014-08-21 doi:10.1101/008318 Cold Spring Harbor Laboratory Press 2014-08-21 <![CDATA[ Exact solutions of linear reaction-diffusion processes on a uniformly growing domain: Criteria for successful colonization ]]> https://biorxiv.org/content/10.1101/011122v1?rss=1 Matthew J Simpson 2014-11-06 doi:10.1101/011122 Cold Spring Harbor Laboratory Press 2014-11-06 <![CDATA[ Exact solutions of coupled multispecies linear reaction-diffusion equations on a uniformly growing domain ]]> https://biorxiv.org/content/10.1101/026229v1?rss=1 Matthew Simpson Jesse Sharp Liam Morrow Ruth Baker 2015-09-07 doi:10.1101/026229 Cold Spring Harbor Laboratory Press 2015-09-07 <![CDATA[ Standard melanoma-associated markers do not identify the MM127 metastatic melanoma cell line ]]> https://biorxiv.org/content/10.1101/026633v1?rss=1 Parvathi Haridas Jacqui McGovern Ahishek Kashyap Sean McElwain Matthew Simpson 2015-09-11 doi:10.1101/026633 Cold Spring Harbor Laboratory Press 2015-09-11 <![CDATA[ Meta-analysis of 375,000 individuals identifies 38 susceptibility loci for migraine ]]> https://biorxiv.org/content/10.1101/030288v1?rss=1 Padhraig Gormley Verneri Anttila Bendik S Winsvold Priit Palta Tonu Esko Tune H Pers Kai-How Farh Ester Cuenca-Leon Mikko Muona Nicholas A Furlotte Tobias Kurth Andres Ingason George McMahon Lannie Ligthart Gisela M Terwindt Mikko Kallela Tobias M Freilinger Caroline Ran Scott G Gordon Anine H Stam Stacy Steinberg Guntram Borck Markku Koiranen Lydia Quaye Hieab HH Adams Terho Lehtimaki Antti-Pekka Sarin Juho Wedenoja David A Hinds Julie E Buring Markus Schurks Paul M Ridker Maria Gudlaug Hrafnsdottir Hreinn Stefansson Susan M Ring Jouke-Jan Hottenga Brenda WJH Penninx Markus Farkkila Ville Art 2015-11-03 doi:10.1101/030288 Cold Spring Harbor Laboratory Press 2015-11-03 <![CDATA[ mixMC: a multivariate statistical framework to gain insight into Microbial Communities ]]> https://biorxiv.org/content/10.1101/044206v1?rss=1 Kim-Anh Le Cao Mary-Ellen Costello Vanessa Anne Lakis Francois Bartolo Xin-Yi Chua Remi Brazeilles Pascale Rondeau 2016-03-16 doi:10.1101/044206 Cold Spring Harbor Laboratory Press 2016-03-16 <![CDATA[ Emergence of increased frequency and severity of multiple infections by viruses due to spatial clustering of hosts ]]> https://biorxiv.org/content/10.1101/048876v1?rss=1 Bradford P Taylor Catherine J Penington Joshua S Weitz 2016-04-15 doi:10.1101/048876 Cold Spring Harbor Laboratory Press 2016-04-15 <![CDATA[ Stochastic simulation tools and continuum models for describing two-dimensional collective cell spreading with universal growth functions ]]> https://biorxiv.org/content/10.1101/052969v1?rss=1 Wang Jin Catherine Penington Scott McCue Matthew Simpson 2016-05-16 doi:10.1101/052969 Cold Spring Harbor Laboratory Press 2016-05-16 <![CDATA[ Genomic analyses for age at menarche identify 389 independent signals and indicate BMI-independent effects of puberty timing on cancer susceptibility ]]> https://biorxiv.org/content/10.1101/076794v1?rss=1 Felix Day Deborah Thompson Hannes Helgason Daniel Chasman Hilary Finucane Patrick Sulem Katherine Ruth Sean Whalen Abhishek Sarkar Eva Albrecht Elisabeth Altmaier Marzyeh Amini Caterina Barbieri Thibaud Boutin Archie Campbell Ellen Demerath Ayush Giri Chunyan He Jouke Hottenga Robert Karlsson Ivana Kolcic Po-Ru Loh Kathryn Lunetta Massimo Mangino Brumat Marco Gerorge McMahon Sarah Medland Ilja Nolte Raymond Noordam Teresa Nutile Lavinia Paternoster Natalia Perjakova Eleonora Porcu Lynda Rose Katharina Schraut Ayellet Segre Albert Smith Lisette Stolk Alexander Teumer Irene Andrulis Stefania Ban 2016-09-23 doi:10.1101/076794 Cold Spring Harbor Laboratory Press 2016-09-23 <![CDATA[ Logistic proliferation of cells in scratch assays is delayed ]]> https://biorxiv.org/content/10.1101/077388v1?rss=1 Wang Jin Esha T Shah Catherine J Penington Scott W McCue Philip K Maini Matthew J Simpson 2016-09-26 doi:10.1101/077388 Cold Spring Harbor Laboratory Press 2016-09-26 <![CDATA[ A genetic risk score to guide age-specific, personalized prostate cancer screening ]]> https://biorxiv.org/content/10.1101/089383v1?rss=1 Seibert, T. M. Fan, C. C. Wang, Y. Zuber, V. Karunamuni, R. Parsons, J. K. Eeles, R. A. Easton, D. F. Kote-Jarai, Z. Amin Al Olama, A. Benlloch Garcia, S. Muir, K. Gronberg, H. Wiklund, F. Aly, M. Schleutker, J. Sipeky, C. Tammela, T. L. Nordestgaard, B. G. Nielsen, S. F. Weischer, M. Bisbjerg, R. Roder, M. A. Iversen, P. Key, T. J. Travis, R. C. Neal, D. E. Donovan, J. L. Hamdy, F. C. Pharoah, P. Pashayan, N. Khaw, K.-T. Maier, C. Vogel, W. Luedeke, M. Herkommer, K. Kibel, A. S. Cybulski, C. Wokolorczyk, D. Kluzniak, W. Cannon-Albright, L. Brenner, H. 2016-11-25 doi:10.1101/089383 Cold Spring Harbor Laboratory Press 2016-11-25 <![CDATA[ Ghrelin-Reactive Autoantibodies are elevated in Children with Prader-Willi Syndrome ]]> https://biorxiv.org/content/10.1101/093930v1?rss=1 Crisp, G. Nyunt, O. Chopin, L. Seim, I. Harris, M. Jeffery, P. 2016-12-16 doi:10.1101/093930 Cold Spring Harbor Laboratory Press 2016-12-16 <![CDATA[ A combined meta-barcoding and shotgun metagenomic analysis of spontaneous wine fermentation ]]> https://biorxiv.org/content/10.1101/098061v1?rss=1 Sternes, P. R. Lee, D. Kutyna, D. R. Borneman, A. R. 2017-01-10 doi:10.1101/098061 Cold Spring Harbor Laboratory Press 2017-01-10 <![CDATA[ A new and accurate continuum description of moving fronts ]]> https://biorxiv.org/content/10.1101/101824v1?rss=1 Johnston, S. T. Baker, R. E. Simpson, M. J. 2017-01-20 doi:10.1101/101824 Cold Spring Harbor Laboratory Press 2017-01-20 <![CDATA[ Bootstrap Distillation: Non-parametric Internal Validation of GWAS Results by Subgroup Resampling ]]> https://biorxiv.org/content/10.1101/104497v1?rss=1 Eccles, D. A. Lea, R. A. Chambers, G. K. 2017-01-31 doi:10.1101/104497 Cold Spring Harbor Laboratory Press 2017-01-31 <![CDATA[ propr: An R-package for Identifying Proportionally Abundant Features Using Compositional Data Analysis ]]> https://biorxiv.org/content/10.1101/104935v1?rss=1 Quinn, T. Richardson, M. F. Lovell, D. Crowley, T. 2017-02-01 doi:10.1101/104935 Cold Spring Harbor Laboratory Press 2017-02-01 <![CDATA[ Do Candidate Genes Affect the Brain’s White Matter Microstructure? Large-Scale Evaluation of 6,165 Diffusion MRI Scans ]]> https://biorxiv.org/content/10.1101/107987v1?rss=1 Jahanshad, N. Ganjgahi, H. Bralten, J. den Braber, A. Faskowitz, J. Knodt, A. Lemaitre, H. Nir, T. Patel, B. Richie, S. Sprooten, E. van Hulzen, K. Zavaliangos-Petropulu, A. Zwiers, M. Almasy, L. Bastin, M. Bernstein, M. Blangero, J. Curran, J. Deary, I. J. de Zubicary, G. Duggirala, R. Fisher, S. Franke, B. Fox, P. Goldman, D. Haberg, A. Hariri, A. Hong, L. E. Hoogman, M. Huentelman, M. Martin, N. Martinot, J.-L. McIntosh, A. McMahon, K. Medland, S. Mitchell, B. Munoz-Maniega, S. Olvera, R. Oosterlaan, J. Peterson, C. Royle, N. Saykin, A. Schumann, G 2017-02-20 doi:10.1101/107987 Cold Spring Harbor Laboratory Press 2017-02-20 <![CDATA[ Amending Published Articles: Time To Rethink Retractions And Corrections? ]]> https://biorxiv.org/content/10.1101/118356v1?rss=1 Barbour, V. Bloom, T. Lin, J. Moylan, E. 2017-03-20 doi:10.1101/118356 Cold Spring Harbor Laboratory Press 2017-03-20 <![CDATA[ Continuum approximations for lattice-free multi-species models of collective cell migration ]]> https://biorxiv.org/content/10.1101/119586v1?rss=1 Matsiaka, O. Penington, C. Baker, R. E. Simpson, M. J. 2017-03-22 doi:10.1101/119586 Cold Spring Harbor Laboratory Press 2017-03-22 <![CDATA[ PTSD Blood Transcriptome Mega-Analysis: Shared Inflammatory Pathways Across Genders And Modes Of Traumas ]]> https://biorxiv.org/content/10.1101/123182v1?rss=1 Breen, M. S. Tylee, D. S. Maihofer, A. X. Neylan, T. C. Mehta, D. Binder, E. Chandler, S. D. Kremen, W. S. Risbrough, V. B. Woelk, C. H. Baker, D. G. Nievergelt, C. M. Tsuang, M. T. Buxbaum, J. D. Glatt, S. J. 2017-04-01 doi:10.1101/123182 Cold Spring Harbor Laboratory Press 2017-04-01 <![CDATA[ Accounting For Cell Lineage And Sex Effects In The Identification Of Cell-Specific DNA Methylation Using A Bayesian Model Selection Algorithm ]]> https://biorxiv.org/content/10.1101/124826v1?rss=1 White, N. M. Benton, M. C. Kennedy, D. W. Fox, A. Griffiths, L. R. Lea, R. A. Mengersen, K. L. 2017-04-06 doi:10.1101/124826 Cold Spring Harbor Laboratory Press 2017-04-06 <![CDATA[ Quantifying Rates Of Cell Migration And Cell Proliferation In Co-Culture Barrier Assays Reveals How Skin And Melanoma Cells Interact During Melanoma Spreading And Invasion ]]> https://biorxiv.org/content/10.1101/124842v1?rss=1 Haridas, P. Penington, C. McGovern, J. McElwain, S. Simpson, M. J. 2017-04-06 doi:10.1101/124842 Cold Spring Harbor Laboratory Press 2017-04-06 <![CDATA[ Quantifying the efficacy of first aid treatments for burn injuries using mathematical modelling and in vivo porcine experiments ]]> https://biorxiv.org/content/10.1101/131391v1?rss=1 Simpson, M. J. McInerney, S. Carr, E. Cuttle, L. 2017-04-27 doi:10.1101/131391 Cold Spring Harbor Laboratory Press 2017-04-27 <![CDATA[ Differential Proportionality - A Normalization-Free Approach To Differential Gene Expression ]]> https://biorxiv.org/content/10.1101/134536v1?rss=1 Erb, I. Quinn, T. Lovell, D. Notredame, C. 2017-05-05 doi:10.1101/134536 Cold Spring Harbor Laboratory Press 2017-05-05 <![CDATA[ A Bayesian computational approach to explore the optimal duration of a cell proliferation assay ]]> https://biorxiv.org/content/10.1101/147678v1?rss=1 Browning, A. P. McCue, S. Simpson, M. J. 2017-06-08 doi:10.1101/147678 Cold Spring Harbor Laboratory Press 2017-06-08 <![CDATA[ Bat Detective - Deep Learning Tools for Bat Acoustic Signal Detection ]]> https://biorxiv.org/content/10.1101/156869v1?rss=1 0.7), but this was at the expense of recall rates. In particular, our deep learning approaches were better at detecting calls in road-transect data, which contained more noisy recordings. Our comparison of CNNFULL and CNNFAST algorithms was favourable, although CNNFAST had a slightly poorer performance, displaying a trade-off between speed and accuracy. Our example monitoring application demonstrated that our open-source, fully automatic, BatDetect CNNFAST pipeline does as well or better compared to a commercial system with manual verification previously used to analyse monitoring data.nC_LIO_LIWe show that it is possible to both accurately and automatically detect bat search-phase echolocation calls, particularly from noisy audio recordings. Our detection pipeline enables the automatic detection and monitoring of bat populations, and further facilitates their use as indicator species on a large scale, particularly when combined with automatic species identification. We release our system and datasets to encourage future progress and transparency.nC_LI ]]> Mac Aodha, O. Gibb, R. Barlow, K. Browning, E. Firman, M. Freeman, R. Harder, B. Kinsey, L. Mead, G. Newson, S. Pandourski, I. Parsons, S. Russ, J. Szodoray-Paradi, A. Szodoray-Paradi, F. Tilova, E. Girolami, M. Brostow, G. Jones, K. E. 2017-06-29 doi:10.1101/156869 Cold Spring Harbor Laboratory Press 2017-06-29 <![CDATA[ A computational modelling framework to quantify the effects of passaging cell lines ]]> https://biorxiv.org/content/10.1101/161265v1?rss=1 Jin, W. Penington, C. J. McCue, S. W. Simpson, M. J. 2017-07-09 doi:10.1101/161265 Cold Spring Harbor Laboratory Press 2017-07-09 <![CDATA[ Intrinsically photosensitive retinal ganglion cell mediated pupil function is impaired in Parkinson’s disease ]]> https://biorxiv.org/content/10.1101/169946v1?rss=1 Joyce, D. S. Feigl, B. Kerr, G. Roeder, L. Zele, A. J. 2017-07-28 doi:10.1101/169946 Cold Spring Harbor Laboratory Press 2017-07-28 <![CDATA[ Enhanced Pipeline ‘MetaGaAP-Py’ for the Analysis of Quasispecies and Non-Model Microbial Populations using Ultra-Deep ‘Meta-barcode’ Sequencing ]]> https://biorxiv.org/content/10.1101/171520v1?rss=1 Noune, C. Hauxwell, C. 2017-08-02 doi:10.1101/171520 Cold Spring Harbor Laboratory Press 2017-08-02 <![CDATA[ The impact of experimental design choices on parameter inference for models of growing cell colonies ]]> https://biorxiv.org/content/10.1101/171710v1?rss=1 Parker, A. Simpson, M. J. Baker, R. E. 2017-08-02 doi:10.1101/171710 Cold Spring Harbor Laboratory Press 2017-08-02 <![CDATA[ Novel pleiotropic risk loci for melanoma and nevus density implicate multiple biological pathways ]]> https://biorxiv.org/content/10.1101/173112v1?rss=1 Duffy, D. Zhu, G. Li, X. Sanna, M. Iles, M. Jacobs, L. C. Evans, D. M. Yazar, S. Beesley, J. Law, M. Kraft, P. Visconti, A. Taylor, J. C. Liu, F. Wright, M. J. Henders, A. K. Bowdler, L. Glass, D. Ikram, A. M. Uitterlinden, A. G. Madden, P. A. Heath, A. C. Nelson, E. C. Green, A. C. Chanock, S. Barrett, J. H. Brown, M. A. Hayward, N. K. MacGregor, S. Sturm, R. A. Hewitt, A. W. Melanoma GWAS Consortium, Kayser, M. Hunter, D. J. Newton Bishop, J. A. Spector, T. D. Montgomery, G. W. Mackey, D. A. Smith, G. D. Nijsten, T. E. Bishop, D. T. Bataille, V. Fa 2017-08-07 doi:10.1101/173112 Cold Spring Harbor Laboratory Press 2017-08-07 <![CDATA[ Genetic Architecture of Subcortical Brain Structures in Over 40,000 Individuals Worldwide ]]> https://biorxiv.org/content/10.1101/173831v1?rss=1 Satizabal, C. L. Adams, H. H. H. Hibar, D. P. White, C. C. Stein, J. L. Scholz, M. Sargurupremraj, M. Jahanshad, N. Smith, A. V. Bis, J. C. Jian, X. Luciano, M. Hofer, E. Teumer, A. van der Lee, S. J. Yang, J. Yanek, L. R. Lee, T. V. Li, S. Hu, Y. Koh, J. Y. Eicher, J. D. Desrivieres, S. Arias-Vasquez, A. Chauhan, G. Athanasiu, L. Renteria, M. E. Kim, S. Hohn, D. Armstrong, N. J. Chen, Q. Holmes, A. J. den Braber, A. Kloszewska, I. Andersson, M. Espeseth, T. Grimm, O. Abramovic, L. Alhusaini, S. Milaneschi, Y. Papmeyer, M. Axelsson, T. Ehrlich, S. Roi 2017-08-28 doi:10.1101/173831 Cold Spring Harbor Laboratory Press 2017-08-28 <![CDATA[ Dynamics of corticospinal motor control during overground and treadmill walking in humans ]]> https://biorxiv.org/content/10.1101/177915v1?rss=1 Roeder, L. Boonstra, T. W. Kerr, G. K. 2017-08-18 doi:10.1101/177915 Cold Spring Harbor Laboratory Press 2017-08-18 <![CDATA[ Inferring parameters for a lattice-free model of cell migration and proliferation using experimental data ]]> https://biorxiv.org/content/10.1101/186197v1?rss=1 Browning, A. McCue, S. W. Binny, R. N. Plank, M. J. Shah, E. T. Simpson, M. J. 2017-09-08 doi:10.1101/186197 Cold Spring Harbor Laboratory Press 2017-09-08 <![CDATA[ Comprehensive, Integrated, and Phased Whole-Genome Analysis of the Primary ENCODE Cell Line K562 ]]> https://biorxiv.org/content/10.1101/192344v1?rss=1 Zhou, B. Ho, S. S. Zhu, X. Zhang, X. Spies, N. Byeon, S. Arthur, J. G. Pattni, R. Ben-Efraim, N. Haney, M. S. Haraksingh, R. R. Song, G. Perrin, D. Wong, W. H. Abyzov, A. Urban, A. E. 2017-12-02 doi:10.1101/192344 Cold Spring Harbor Laboratory Press 2017-12-02 <![CDATA[ Mapping Cortical Brain Asymmetry in 17,141 Healthy Individuals Worldwide via the ENIGMA Consortium ]]> https://biorxiv.org/content/10.1101/196634v1?rss=1 Kong, X.-Z. Mathias, S. Guadalupe, T. Abe, C. Agartz, I. Akudjedu, T. N. Aleman, A. Alhusaini, S. Allen, N. B. Ames, D. Andreassen, O. A. Armstrong, N. J. Bergo, F. Bastin, M. E. Batalla, A. Bauer, J. Baune, B. Baur, R. Biederman, J. Blaine, S. K. Boedhoe, P. Boen, E. Bose, A. Bralten, J. Brandeis, D. Brem, S. Brodaty, H. Bröhl, H. Buitelaar, J. Bürger, C. Bülow, R. Calhoun, V. Calvo, A. Canales-Rodriguez, E. J. Canive, J. M. Cannon, D. M. Caparelli, E. C. Castellanos, F. X. Cavalleri, G. L. Cendes, F. Chaim-Avancini, T. M. Chant 2017-10-01 doi:10.1101/196634 Cold Spring Harbor Laboratory Press 2017-10-01 <![CDATA[ Small-scale spatial structure affects predator-prey dynamics and coexistence ]]> https://biorxiv.org/content/10.1101/2019.12.17.880104v1?rss=1 Surendran, A. Plank, M. J. Simpson, M. J. 2019-12-18 doi:10.1101/2019.12.17.880104 Cold Spring Harbor Laboratory Press 2019-12-18 <![CDATA[ Persistence is an optimal hedging strategy for bacteria in volatile environments ]]> https://biorxiv.org/content/10.1101/2019.12.19.883645v1?rss=1 Browning, A. P. Sharp, J. A. Mapder, T. Baker, C. M. Burrage, K. Simpson, M. J. 2019-12-20 doi:10.1101/2019.12.19.883645 Cold Spring Harbor Laboratory Press 2019-12-20 <![CDATA[ Transfer of antigen-encoding bone marrow under immune-preserving conditions deletes mature antigen-specific B cells in recipients and inhibits antigen-specific antibody production ]]> https://biorxiv.org/content/10.1101/2019.12.20.885343v1?rss=1 Brooks, J. F. Davies, J. M. Wells, J. W. Steptoe, R. J. 2019-12-21 doi:10.1101/2019.12.20.885343 Cold Spring Harbor Laboratory Press 2019-12-21 <![CDATA[ Sequence representations and their utility for predicting protein-protein interactions ]]> https://biorxiv.org/content/10.1101/2019.12.31.890699v1?rss=1 Kimothi, D. Biyani, P. Hogan, J. M. 2019-12-31 doi:10.1101/2019.12.31.890699 Cold Spring Harbor Laboratory Press 2019-12-31 <![CDATA[ Therapy-induced lipid uptake and remodeling underpin ferroptosis hypersensitivity in prostate cancer ]]> https://biorxiv.org/content/10.1101/2020.01.08.899609v1?rss=1 Tousignant, K. D. Rockstroh, A. Poad, B. L. J. Talebi, A. Young, R. R. S. Fard, A. T. Gupta, R. Zang, T. Wang, C. Lehman, M. L. Swinnen, J. V. Blanksby, S. J. Nelson, C. C. Sadowski, M. C. 2020-01-09 doi:10.1101/2020.01.08.899609 Cold Spring Harbor Laboratory Press 2020-01-09 <![CDATA[ Crowdsourcing digital health measures to predict Parkinson's disease severity: the Parkinson's Disease Digital Biomarker DREAM Challenge ]]> https://biorxiv.org/content/10.1101/2020.01.13.904722v1?rss=1 Sieberts, S. K. Schaff, J. Duda, M. Pataki, B. A. Sun, M. Snyder, P. Daneault, J.-F. Parisi, F. Costante, G. Rubin, U. Banda, P. Chae, Y. Neto, E. C. Dorsey, R. Aydın, Z. Chen, A. Elo, L. L. Espino, C. Glaab, E. Goan, E. Golabchi, F. N. Görmez, Y. Jaakkola, M. K. Jonnagaddala, J. KLEn, R. Li, D. McDaniel, C. Perrin, D. Rad, N. M. Rainaldi, E. Sapienza, S. Schwab, P. Shokhirev, N. Venäläinen, M. S. Vergara-Diaz, G. Zhang, Y. Parkinson's Disease Digital Biomarker Challenge Consortium, Wang, Y. Guan, Y. Brunner, D. Bonato, P. Mangravite, L. M. Omberg 2020-01-16 doi:10.1101/2020.01.13.904722 Cold Spring Harbor Laboratory Press 2020-01-16 <![CDATA[ New mathematical modelling tools for co-culture experiments: when do we need to explicitly account for signalling molecules? ]]> https://biorxiv.org/content/10.1101/2020.01.13.905414v1?rss=1 Jin, W. Wang, H. Liang, X. Roberts, M. S. Simpson, M. J. 2020-01-14 doi:10.1101/2020.01.13.905414 Cold Spring Harbor Laboratory Press 2020-01-14 <![CDATA[ Limiting Self-Renewal of the Basal Compartment Induces Differentiation and Alters Evolution of Mammary Tumors ]]> https://biorxiv.org/content/10.1101/2020.01.18.907741v1?rss=1 Ognjenovic, N. B. Bagheri, M. Mohamed, G. A. Xu, K. Brown, M. S. Chen, Y. Mohamed Saleem, M. A. Nagaraj, S. H. Muller, K. E. Christensen, B. Pattabiraman, D. R. 2020-01-18 doi:10.1101/2020.01.18.907741 Cold Spring Harbor Laboratory Press 2020-01-18 <![CDATA[ A novel mutation in KCNK16 causing a gain-of-function in the TALK-1 potassium channel: a new cause of maturity onset diabetes of the young. ]]> https://biorxiv.org/content/10.1101/2020.02.04.929430v1?rss=1 C, p.Leu114Pro) segregating with MODY. KCNK16 is the most abundant and {beta}-cell-restricted K+ channel transcript and encodes the two-pore-domain K+ channel TALK-1. Whole-cell K+ currents in transfected HEK293 cells demonstrated drastic (312-fold increase) gain-of-function with TALK-1 Leu144Pro vs. WT, due to greater single channel activity. Glucose-stimulated cytosolic Ca2+ influx was inhibited in mouse islets expressing TALK-1 Leu114Pro (area under the curve [AUC] at 20mM glucose: Leu114Pro 60.1 vs. WT 89.1; P=0.030) and less endoplasmic reticulum calcium storage (cyclopiazonic acid-induced release AUC: Leu114Pro 17.5 vs. WT 46.8; P=0.008). TALK-1 Leu114Pro significantly blunted GSIS compared to TALK-1 WT in both mouse (52% decrease, P=0.039) and human (38% decrease, P=0.019) islets. ConclusionsOur data identify a novel MODY-associated gene, KCNK16; with a gain-of-function mutation limiting Ca2+ influx and GSIS. A gain-of-function common polymorphism in KCNK16 is associated with type 2 diabetes (T2DM); thus, our findings have therapeutic implications not only for KCNK16-associated MODY but also for T2DM. ]]> Graff, S. Johnson, S. Leo, P. Dadi, P. Nakhe, A. McInerney-Leo, A. Marshall, M. Brown, M. Jacobson, D. Duncan, E. 2020-02-04 doi:10.1101/2020.02.04.929430 Cold Spring Harbor Laboratory Press 2020-02-04 <![CDATA[ Faster and better CRISPR guide RNA design with the Crackling method ]]> https://biorxiv.org/content/10.1101/2020.02.14.950261v1?rss=1 Bradford, J. Chappell, T. Perrin, D. 2020-02-15 doi:10.1101/2020.02.14.950261 Cold Spring Harbor Laboratory Press 2020-02-15 <![CDATA[ Greater male than female variability in regional brain structure across the lifespan ]]> https://biorxiv.org/content/10.1101/2020.02.17.952010v1?rss=1 Wierenga, L. M. Doucet, G. Dima, D. Agartz, I. Aghajani, M. Akudjedu, T. Albajes-Eizagirre, A. Alnaes, D. Alpert, K. Andreassen, O. A. Anticevic, A. Asherson, P. Banaschewski, T. Bargallo, N. Baumeister, S. Baur-Streubel, R. Bertolino, A. Bonvino, A. Boomsma, D. Borgwardt, S. Bourque, J. den Braber, A. Brandeis, D. Breier, A. Brodaty, H. Brouwer, R. Busatto, G. Calhoun, V. Canales-Rodriguez, E. Cannon, D. Caseras, X. Chaim-Avancini, T. Ching, C. Conrod, P. Conzelmann, A. Crivello, F. Davey, C. Dickie, E. Ehrlich, S. van 't Ent, D. Fouche, J.-P. Fuentes- 2020-02-17 doi:10.1101/2020.02.17.952010 Cold Spring Harbor Laboratory Press 2020-02-17 <![CDATA[ Survey of Australian STEMM Early Career Researchers: job insecurity and questionable research practices are major structural concerns ]]> https://biorxiv.org/content/10.1101/2020.02.19.955328v1?rss=1 Christian, K. Johnstone, C. Larkins, J.-a. Wright, W. Doran, M. R. 2020-02-20 doi:10.1101/2020.02.19.955328 Cold Spring Harbor Laboratory Press 2020-02-20 <![CDATA[ Identification of novel mitochondrial and mitochondrial related genetic loci associated with exercise response in the Gene SMART study ]]> https://biorxiv.org/content/10.1101/2020.02.20.957340v1?rss=1 Harvey, N. R. Voisin, S. Lea, R. A. Yan, X. Benton, M. C. Papadimitriou, I. D. Jacques, M. Haupt, L. M. Ashton, K. J. Eynon, N. Griffiths, L. R. 2020-02-20 doi:10.1101/2020.02.20.957340 Cold Spring Harbor Laboratory Press 2020-02-20 <![CDATA[ High-throughput cell-based assays for the preclinical development of DsbA inhibitors as antivirulence therapeutics. ]]> https://biorxiv.org/content/10.1101/2020.03.03.975938v1?rss=1 Verderosa, A. D. Dhouib, R. Hong, Y. Heras, B. Totsika, M. 2020-03-06 doi:10.1101/2020.03.03.975938 Cold Spring Harbor Laboratory Press 2020-03-06 <![CDATA[ Cell proliferation and migration explain pore bridging dynamics in 3D printed scaffolds of different pore size ]]> https://biorxiv.org/content/10.1101/2020.03.12.989053v1?rss=1 Buenzli, P. R. Lanaro, M. Wong, C. S. McLaughlin, M. P. Allenby, M. C. Woodruff, M. A. Simpson, M. J. 2020-03-13 doi:10.1101/2020.03.12.989053 Cold Spring Harbor Laboratory Press 2020-03-13 <![CDATA[ Synchronised oscillations in growing cell populations are explained by demographic noise ]]> https://biorxiv.org/content/10.1101/2020.03.13.987032v1?rss=1 Gavagnin, E. Vittadello, S. T. Guanasingh, G. Haass, N. K. Simpson, M. J. Rogers, T. Yates, C. A. 2020-03-13 doi:10.1101/2020.03.13.987032 Cold Spring Harbor Laboratory Press 2020-03-13 <![CDATA[ Targeting CXCR1 and CXCR2 to overcome radiotherapy resistance in PTEN-deficient prostate carcinoma ]]> https://biorxiv.org/content/10.1101/2020.03.16.993394v1?rss=1 Armstrong, C. W. D. Coulter, J. A. Ong, C. W. Maxwell, P. J. Walker, S. Butterworth, K. T. Lyubomska, O. Berlingeri, S. Gallagher, R. O'Sullivan, J. M. Jain, S. Mills, I. G. Prise, K. M. Bristow, R. G. LaBonte, M. J. Waugh, D. J. J. 2020-03-16 doi:10.1101/2020.03.16.993394 Cold Spring Harbor Laboratory Press 2020-03-16 <![CDATA[ Hormonal regulation of the BRC1-dependent strigolactone transcriptome involved in shoot branching responses ]]> https://biorxiv.org/content/10.1101/2020.03.19.999581v1?rss=1 Kerr, S. C. de Saint Germain, A. Dissanayake, I. M. Mason, M. G. Dun, E. A. Tanurdzic, M. Beveridge, C. A. 2020-03-20 doi:10.1101/2020.03.19.999581 Cold Spring Harbor Laboratory Press 2020-03-20 <![CDATA[ Minimising severity of dengue serotype 1 infection bytransmissible interfering particles ]]> https://biorxiv.org/content/10.1101/2020.04.21.052936v1?rss=1 Shausan, A. Aaskov, J. Drovandi, C. Mengersen, K. 2020-04-21 doi:10.1101/2020.04.21.052936 Cold Spring Harbor Laboratory Press 2020-04-21 <![CDATA[ A draft genome of grass pea (Lathyrus sativus), a resilient diploid legume ]]> https://biorxiv.org/content/10.1101/2020.04.24.058164v1?rss=1 Emmrich, P. M. F. Sarkar, A. Njaci, I. Kaithakottil, G. G. Ellis, N. Moore, C. Edwards, A. Heavens, D. Waite, D. Cheema, J. Trick, M. Moore, J. Webb, A. Calazzo, R. Thomas, J. Higgins, J. Swarbreck, D. Kumar, S. Mundree, S. Loose, M. W. Yant, L. Martin, C. Wang, T. L. 2020-04-27 doi:10.1101/2020.04.24.058164 Cold Spring Harbor Laboratory Press 2020-04-27 <![CDATA[ Australian rodents reveal conserved Cranial Evolutionary Allometry across 10 million years of murid evolution ]]> https://biorxiv.org/content/10.1101/2020.04.30.071308v1?rss=1 Marcy, A. E. Guillerme, T. Sherratt, E. Rowe, K. C. Phillips, M. J. Weisbecker, V. 2020-05-01 doi:10.1101/2020.04.30.071308 Cold Spring Harbor Laboratory Press 2020-05-01 <![CDATA[ Baseline pulmonary levels of CD8+ T cells and NK cells inversely correlate with expression of the SARS-CoV-2 entry receptor ACE2 ]]> https://biorxiv.org/content/10.1101/2020.05.04.075291v1?rss=1 Duijf, P. H. G. 2020-05-05 doi:10.1101/2020.05.04.075291 Cold Spring Harbor Laboratory Press 2020-05-05 <![CDATA[ Cortical Thickness Trajectories across the Lifespan: Data from 17,075 healthy individuals aged 3-90 years ]]> https://biorxiv.org/content/10.1101/2020.05.05.077834v1?rss=1 Frangou, S. Modabbernia, A. Doucet, G. E. Papachristou, E. Williams, S. C. Agartz, I. Aghajani, M. Akudjedu, T. N. Albajes-Eizagirre, A. Alnaes, D. Alpert, K. I. Andersson, M. Andreasen, N. Andreassen, O. A. Asherson, P. Banaschewski, T. Bargallo, N. Baumeister, S. Baur-Streubel, R. Bertolino, A. Bonvino, A. Boomsma, D. I. Borgwardt, S. Bourque, J. Brandeis, D. Breier, A. Brodaty, H. Brouwer, R. M. Buitelaar, J. K. Busatto, G. F. Buckner, R. L. Calhoun, V. Canales-Rodriguez, E. J. Cannon, D. M. Caseras, X. Castellanos, F. X. Cervenka, S. Chaim-Avancini, T. 2020-05-07 doi:10.1101/2020.05.05.077834 Cold Spring Harbor Laboratory Press 2020-05-07 <![CDATA[ Subcortical Volume Trajectories across the Lifespan: Data from 18,605 healthy individuals aged 3-90 years ]]> https://biorxiv.org/content/10.1101/2020.05.05.079475v1?rss=1 Dima, D. Papachristou, E. Modabbernia, A. Doucet, G. E. Agartz, I. Aghajani, M. Akudjedu, T. N. Albajes-Eizagirre, A. Alnaes, D. Alpert, K. I. Andersson, M. Andreasen, N. Andreassen, O. A. Asherson, P. Banaschewski, T. Bargallo, N. Baumeister, S. Baur-Streubel, R. Bertolino, A. Bonvino, A. Boomsma, D. I. Borgwardt, S. Bourque, J. Brandeis, D. Breier, A. Brodaty, H. Brouwer, R. M. Buitelaar, J. K. Busatto, G. F. Buckner, R. L. Calhoun, V. Canales-Rodriguez, E. J. Cannon, D. M. Caseras, X. Castellanos, F. X. Cervenka, S. Chaim-Avancini, T. M. Ching, C. R. Cl 2020-05-07 doi:10.1101/2020.05.05.079475 Cold Spring Harbor Laboratory Press 2020-05-07 <![CDATA[ Characterisation of ovine bone marrow-derived stromal cells (oBMSC) and evaluation of chondrogenically induced micro-pellets for cartilage tissue repair in vivo ]]> https://biorxiv.org/content/10.1101/2020.05.15.094847v1?rss=1 Futrega, K. Music, E. Robey, P. G. Gronthos, S. Crawford, R. W. Saifzadeh, S. Klein, T. J. Doran, M. R. 2020-05-16 doi:10.1101/2020.05.15.094847 Cold Spring Harbor Laboratory Press 2020-05-16 <![CDATA[ Using a supervised principal components analysis for variable selection in high-dimensional datasets reduces false discovery rates ]]> https://biorxiv.org/content/10.1101/2020.05.15.097774v1?rss=1 ULLAH, I. Mengersen, K. Pettitt, A. Liquet, B. 2020-05-15 doi:10.1101/2020.05.15.097774 Cold Spring Harbor Laboratory Press 2020-05-15 <![CDATA[ Germline ERBB3 mutation in familial non-small cell lung carcinoma: expanding the role of the ErbB family in oncogenesis. ]]> https://biorxiv.org/content/10.1101/2020.05.29.122796v1?rss=1 G: p.Iso649Arg), coding for receptor tyrosineprotein kinase erbB-3 (ErbB3), was identified, with appropriate segregation. There was no loss-of-heterozygosity in tumour samples. Both wtErbB3 and mutErbB3 were stably expressed. MutErbB3-transfected cells demonstrated an increased ratio of the 80kD form (which enhances proliferation) compared to the full-length (180kD) form. MutErbB3 and wtErbB3 had similar punctate cytoplasmic localisation pre- and post-EGF stimulation; however, EGFR levels decreased faster post-stimulation in mutErbB3-transfected cells, suggesting more rapid processing of the mutErbB3/EGFR heterodimer. Cellular proliferation was increased in mutErbB3-transfected cells compared to wtErbB3 transfection. MutErbB3-transfected cells also showed decreased pAkt/tAkt ratios and increased pERK/tERK 30 minutes post-stimulation compared to wtErbB3 transfection, demonstrating altered signalling pathway activation by mutErbB3. Cumulatively, these results support this mutation as tumorogenic. ConclusionsThis is the first reported family with a germline ERBB3 mutation causing heritable NSCLC, furthering understanding of the ErbB family pathway in oncogenesis. ]]> McInerney-Leo, A. M. Chew, H. Y. Inglis, P.-L. Leo, P. J. Joseph, S. R. Cooper, C. L. Okano, S. Hassall, T. Anderson, L. Bowman, R. V. Gattas, M. Harris, J. E. Marshall, M. S. Shaw, J. G. Wheeler, L. Yang, I. A. Brown, M. A. Fong, K. M. Simpson, F. Duncan, E. L. 2020-05-30 doi:10.1101/2020.05.29.122796 Cold Spring Harbor Laboratory Press 2020-05-30 <![CDATA[ Heparanase promotes Syndecan-1 expression to mediate fibrillar collagen and mammographic density in human breast tissue cultured ex vivo. ]]> https://biorxiv.org/content/10.1101/2020.06.04.135202v1?rss=1 Huang, X. Reye, G. Momot, K. I. Blick, T. Lloyd, T. Tilley, W. D. Hickey, T. E. Snell, C. E. Okolicsanyi, R. K. Haupt, L. M. Ferro, V. Thompson, E. W. Hugo, H. J. 2020-06-05 doi:10.1101/2020.06.04.135202 Cold Spring Harbor Laboratory Press 2020-06-05 <![CDATA[ Metabolic plasticity in cancer activates apocryphal pathways for lipid desaturation ]]> https://biorxiv.org/content/10.1101/2020.06.07.139089v1?rss=1 Young, R. S. E. Bowman, A. P. Williams, E. D. Tousignant, K. D. Bidgood, C. L. Narreddula, V. R. Gupta, R. Marshall, D. L. Poad, B. L. Nelson, C. C. Ellis, S. R. Heeren, R. M. Sadowski, M. Blanksby, S. J. 2020-06-08 doi:10.1101/2020.06.07.139089 Cold Spring Harbor Laboratory Press 2020-06-08 <![CDATA[ Mineral density differences between femoral cortical bone and trabecular bone are not explained by turnover rate alone ]]> https://biorxiv.org/content/10.1101/2020.06.08.141036v1?rss=1 Lerebours, C. Weinkamer, R. Roschger, A. Buenzli, P. R. 2020-06-09 doi:10.1101/2020.06.08.141036 Cold Spring Harbor Laboratory Press 2020-06-09 <![CDATA[ Functional melanoma cell heterogeneity is regulated by MITF-dependent cell-matrix interactions ]]> https://biorxiv.org/content/10.1101/2020.06.09.141747v1?rss=1 Spoerri, L. Tonnessen-Murray, C. A. Gunasingh, G. Hill, D. S. Beaumont, K. A. Jurek, R. J. Vanwalleghem, G. C. Fane, M. E. Daignault, S. M. Matigian, N. Scott, E. K. Smith, A. G. Stehbens, S. J. Schaider, H. Weninger, W. Gabrielli, B. Haass, N. K. 2020-06-11 doi:10.1101/2020.06.09.141747 Cold Spring Harbor Laboratory Press 2020-06-11 <![CDATA[ Population dynamics with spatial structure and an Allee effect ]]> https://biorxiv.org/content/10.1101/2020.06.26.173153v1?rss=1 Plank, M. J. Surendran, A. Simpson, M. J. 2020-06-28 doi:10.1101/2020.06.26.173153 Cold Spring Harbor Laboratory Press 2020-06-28 <![CDATA[ Conserved Role of the Large Conductance Calcium-Activated Potassium Channel, KCa1.1, in Sinus Node Function and Arrhythmia Risk ]]> https://biorxiv.org/content/10.1101/2020.06.28.176495v1?rss=1 Pined, S. Nikolova-Krstevski, V. Leimena, C. Atkinson, A. J. Altekoester, A.-K. Cox, C. D. Jacoby, A. Huttner, I. G. Ju, Y.-K. Soka, M. Ohanian, M. Trived, G. Johnson, R. Molenaar, P. Kuchar, D. Allen, D. G. Hill, A. P. Bodmer, R. Vogler, G. Dobrzyn, H. Ocorr, K. Fatkin, D. 2020-06-28 doi:10.1101/2020.06.28.176495 Cold Spring Harbor Laboratory Press 2020-06-28 <![CDATA[ A free boundary mechanobiological model of epithelial tissues ]]> https://biorxiv.org/content/10.1101/2020.07.02.185686v1?rss=1 Tambyah, T. Murphy, R. J. Buenzli, P. R. Simpson, M. J. 2020-07-04 doi:10.1101/2020.07.02.185686 Cold Spring Harbor Laboratory Press 2020-07-04 <![CDATA[ Genes associated with liver damage signalling pathways may impact the severity of COVID-19 symptoms in Spanish and Italian populations ]]> https://biorxiv.org/content/10.1101/2020.07.03.179028v1?rss=1 Leire Moya Samaneh Farashi Prashanth N Suravajhala Panchadsaram Janaththani Jyotsna Batra 2020-07-08 doi:10.1101/2020.07.03.179028 Cold Spring Harbor Laboratory Press 2020-07-08 <![CDATA[ Modelling cell guidance and curvature control in evolving biological tissues ]]> https://biorxiv.org/content/10.1101/2020.07.10.197020v1?rss=1 Solene G.D. Hegarty-Cremer Matthew J Simpson Thomas L. Andersen Pascal R Buenzli 2020-07-12 doi:10.1101/2020.07.10.197020 Cold Spring Harbor Laboratory Press 2020-07-12 <![CDATA[ Detection of clustered anomalies in single-voxel morphometry as a rapid automated method for identifying intracranial aneurysms. ]]> https://biorxiv.org/content/10.1101/2020.07.22.216812v1?rss=1 View larger version (24K): org.highwire.dtl.DTLVardef@166f3aborg.highwire.dtl.DTLVardef@76ea1org.highwire.dtl.DTLVardef@1f03619org.highwire.dtl.DTLVardef@16fd797_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG Highlights O_LIRapid and automated detection of unruptured intracranial aneurysms (UIAs) in MRAs C_LIO_LIHighly specific, sensitive UIA detection to reduce radiologist input for screening C_LIO_LIDetection is versatile to image resolution, modality and has tuneable mm sensitivity C_LI ]]> Allenby, M. C. Liang, E. S. Harvey, J. Woodruff, M. A. Prior, M. Winter, C. D. Alonso-Caneiro, D. 2020-07-24 doi:10.1101/2020.07.22.216812 Cold Spring Harbor Laboratory Press 2020-07-24 <![CDATA[ Passive muscle stretching reduces estimates of persistent inward current strength in soleus motor units ]]> https://biorxiv.org/content/10.1101/2020.07.31.230029v1?rss=1 Trajano, G. S. Taylor, J. L. Orssatto, L. B. R. McNulty, C. Blazevich, A. J. 2020-08-02 doi:10.1101/2020.07.31.230029 Cold Spring Harbor Laboratory Press 2020-08-02 <![CDATA[ Temperature alters gene expression in mosquitoes during arbovirus infection ]]> https://biorxiv.org/content/10.1101/2020.07.31.230425v1?rss=1 Wimalasiri-Yapa, B. R. Barrero, R. A. Stassen, L. Hafner, L. M. McGraw, E. A. Pyke, A. T. Jansen, C. C. Suhrbier, A. Yakob, L. Hu, W. Devine, G. J. Frentiu, F. D. 2020-07-31 doi:10.1101/2020.07.31.230425 Cold Spring Harbor Laboratory Press 2020-07-31 <![CDATA[ Listen to the noise: identifiability analysis for stochastic differential equation models in systems biology ]]> https://biorxiv.org/content/10.1101/2020.08.10.245233v1?rss=1 Browning, A. P. Warne, D. J. Burrage, K. Baker, R. E. Simpson, M. J. 2020-08-11 doi:10.1101/2020.08.10.245233 Cold Spring Harbor Laboratory Press 2020-08-11 <![CDATA[ Sex-Dependent Shared and Non-Shared Genetic Architecture Across Mood and Psychotic Disorders ]]> https://biorxiv.org/content/10.1101/2020.08.13.249813v1?rss=1 Blokland, G. A. Grove, J. Chen, C.-Y. Cotsapas, C. Tobet, S. Handa, R. Schizophrenia Working Group of the Psychiatric Genomics Consortium, St Clair, D. Lencz, T. Mowry, B. J. Periyasamy, S. Cairns, M. J. Tooney, P. A. Wu, J. Q. Kelly, B. Kirov, G. Sullivan, P. F. Corvin, A. Riley, B. P. Esko, T. Milani, L. Jönsson, E. G. Palotie, A. Ehrenreich, H. Begemann, M. Steixner-Kumar, A. Sham, P. C. Iwata, N. Weinberger, D. R. Gejman, P. V. Sanders, A. R. Buxbaum, J. D. Rujescu, D. Giegling, I. Konte, B. Hartmann, A. M. Bramon, E. Murray, R. M. Pato, M. T. Lee, 2020-08-17 doi:10.1101/2020.08.13.249813 Cold Spring Harbor Laboratory Press 2020-08-17 <![CDATA[ Responses to Loud Acoustic Stimuli: Short and Long Timescale Effects on Cortical and Sub-Cortical Preparation Reflect Conditional Probability. ]]> https://biorxiv.org/content/10.1101/2020.08.19.258327v1?rss=1 Nguyen, A. T. Tresilian, J. R. Lipp, O. V. Tavora-Vieira, D. Marinovic, W. 2020-08-20 doi:10.1101/2020.08.19.258327 Cold Spring Harbor Laboratory Press 2020-08-20 <![CDATA[ A biophysical and structural analysis of DNA binding by oligomeric hSSB1 (NABP2/OBFC2B) ]]> https://biorxiv.org/content/10.1101/2020.08.26.269084v1?rss=1 El-Kamand, S. Jergic, S. Lawson, T. Kariawasam, R. Richard, D. J. Cubeddu, L. Gamsjaeger, R. 2020-08-27 doi:10.1101/2020.08.26.269084 Cold Spring Harbor Laboratory Press 2020-08-27 <![CDATA[ Spatial analysis of ligand-receptor interactions in skin cancer at genome-wide and single-cell resolution ]]> https://biorxiv.org/content/10.1101/2020.09.10.290833v1?rss=1 20,000 genes), RNA In Situ Hybridization (multiplex 4-12 genes), digital droplet PCR, and Opal multiplex protein staining (4-9 proteins). To spatially integrate multimodal data, we developed a computational method called STRISH that can automatically scan across the whole tissue section for local expression of gene and/or protein markers to recapitulate an interaction landscape across the whole tissue. We evaluated the unique ability of this toolbox to discover and validate cell-cell interaction in situ through in-depth analysis of two types of cancer, basal cell carcinoma and squamous cell carcinoma, which account for over 70% of cancer cases. We expect that the approach described here will be widely applied to discover and validate ligand receptor interaction in different types of solid cancer tumors. ]]> Tran, M. Yoon, S. Andersen, S. Devitt, K. Lam, P. Raghubar, A. Purdue, B. Hanson, S. J. Jones, K. Walters, S. Tuong, Z. K. Soyer, P. H. Frazer, I. H. Nguyen, Q. 2020-09-10 doi:10.1101/2020.09.10.290833 Cold Spring Harbor Laboratory Press 2020-09-10 <![CDATA[ Design Principles Underlying Robust Perfect Adaptation of Complex Biochemical Networks ]]> https://biorxiv.org/content/10.1101/2020.09.21.307140v1?rss=1 Araujo, R. P. Liotta, L. A. 2020-09-22 doi:10.1101/2020.09.21.307140 Cold Spring Harbor Laboratory Press 2020-09-22 <![CDATA[ Meta-analysis of genome-wide DNA methylation and integrative OMICs in human skeletal muscle. ]]> https://biorxiv.org/content/10.1101/2020.09.28.315838v1?rss=1 Voisin, S. Jacques, M. Landen, S. Harvey, N. R. Haupt, L. M. Griffiths, L. R. Gancheva, S. Ouni, M. Jahnert, M. Ashton, K. J. Coffey, V. G. Thompson, J.-L. M. Doering, T. M. Gabory, A. Junien, C. Caiazzo, R. Verkindt, H. Pattou, F. Raverdi, V. Froguel, P. Craig, J. M. Blocquiaux, S. Thomis, M. Sharples, A. P. Schurmann, A. Roden, M. Horvath, S. Eynon, N. 2020-09-28 doi:10.1101/2020.09.28.315838 Cold Spring Harbor Laboratory Press 2020-09-28 <![CDATA[ APEX-Gold: A genetically-encoded particulate marker for robust 3D electron microscopy ]]> https://biorxiv.org/content/10.1101/2020.10.06.328831v1?rss=1 Rae, J. Ferguson, C. Ariotti, N. Webb, R. Cheng, H.-H. Mead, J. Riches, J. Hunter, D. Martel, N. Baltos, J. Christopoulos, A. Bryce, N. Cagigas, M. Fonseka, S. Hardeman, E. Gunning, P. Gambin, Y. Hall, T. E. Parton, R. G. 2020-10-06 doi:10.1101/2020.10.06.328831 Cold Spring Harbor Laboratory Press 2020-10-06 <![CDATA[ Automated AI labelling of optic nerve head enables new insights into cross-ancestry glaucoma risk and genetic discovery in over 280,000 images from the UK Biobank and Canadian Longitudinal Study on Aging ]]> https://biorxiv.org/content/10.1101/2020.11.03.367623v1?rss=1 Han, X. Steven, K. Qassim, A. Marshall, H. N. Bean, C. Tremeer, M. An, J. Siggs, O. Gharahkhani, P. Craig, J. E. Hewitt, A. W. Trzaskowski, M. MacGregor, S. 2020-11-05 doi:10.1101/2020.11.03.367623 Cold Spring Harbor Laboratory Press 2020-11-05 <![CDATA[ Evidence of genetic overlap between circadian preference and brain white matter microstructure ]]> https://biorxiv.org/content/10.1101/2020.11.09.374199v1?rss=1 Garcia-Marin, L. M. Alcauter, S. Campos, A. I. Mulcahy, A. Kho, P.-F. Cuellar-Partida, G. Renteria, M. E. 2020-11-09 doi:10.1101/2020.11.09.374199 Cold Spring Harbor Laboratory Press 2020-11-09 <![CDATA[ Attention and prediction modulations in expected and unexpected visuospatial trajectories. ]]> https://biorxiv.org/content/10.1101/2020.11.10.376368v1?rss=1 Baker, K. S. Pegna, A. J. Yamamoto, N. Johnston, P. 2020-11-10 doi:10.1101/2020.11.10.376368 Cold Spring Harbor Laboratory Press 2020-11-10 <![CDATA[ ChIP-R: Assembling reproducible sets of ChIP-seq and ATAC-seq peaks from multiple replicates ]]> https://biorxiv.org/content/10.1101/2020.11.24.396960v1?rss=1 Newell, R. J. P. Pienaar, R. Balderson, B. Piper, M. Essebier, A. Boden, M. 2020-11-25 doi:10.1101/2020.11.24.396960 Cold Spring Harbor Laboratory Press 2020-11-25 <![CDATA[ Mathematical model of tumour spheroid experiments with real-time cell cycle imaging ]]> https://biorxiv.org/content/10.1101/2020.12.06.413856v1?rss=1 Jin, W. Spoerri, L. Haass, N. K. Simpson, M. J. 2020-12-07 doi:10.1101/2020.12.06.413856 Cold Spring Harbor Laboratory Press 2020-12-07 <![CDATA[ The role of mechanical interactions in EMT ]]> https://biorxiv.org/content/10.1101/2020.12.09.418434v1?rss=1 Murphy, R. J. Buenzli, P. R. Tambyah, T. A. Thompson, E. W. Hugo, H. J. Baker, R. E. Simpson, M. J. 2020-12-10 doi:10.1101/2020.12.09.418434 Cold Spring Harbor Laboratory Press 2020-12-10 <![CDATA[ Persistent Inward Currents Increase With The Level Of Voluntary Drive In Plantar Flexor Low-Threshold Motor Units ]]> https://biorxiv.org/content/10.1101/2020.12.11.420570v1?rss=1 Orssatto, L. B. R. Mackay, K. Shield, A. J. Sakugawa, R. L. Blazevich, A. J. Trajano, G. S. 2020-12-11 doi:10.1101/2020.12.11.420570 Cold Spring Harbor Laboratory Press 2020-12-11 <![CDATA[ Do Motoneurons Slow With Aging? A Systematic Review And Meta-Analysis With Meta-Regression ]]> https://biorxiv.org/content/10.1101/2020.12.15.422812v1?rss=1 Orssatto, L. B. R. Borg, D. Pendrith, L. Shield, A. J. Blazevich, A. J. Trajano, G. S. 2020-12-16 doi:10.1101/2020.12.15.422812 Cold Spring Harbor Laboratory Press 2020-12-16 <![CDATA[ Ultrasensitivity and bistability in covalent modification cycles with positive autoregulation ]]> https://biorxiv.org/content/10.1101/2020.12.24.424291v1?rss=1 Jeynes-Smith, C. Araujo, R. 2020-12-24 doi:10.1101/2020.12.24.424291 Cold Spring Harbor Laboratory Press 2020-12-24 <![CDATA[ AusTraits: a curated plant trait database for the Australian flora ]]> https://biorxiv.org/content/10.1101/2021.01.04.425314v1?rss=1 Falster, D. S. Gallagher, R. Wenk, E. Wright, I. Indiarto, D. Baxter, C. Andrew, S. C. Lawson, J. Allen, S. Fuchs, A. Adams, M. A. Ahrens, C. W. Alfonzetti, M. Angevin, T. Atkin, O. K. Auld, T. Baker, A. Bean, A. Blackman, C. J. Bloomfield, K. Bowman, D. Bragg, J. Brodribb, T. J. Buckton, G. Burrows, G. Caldwell, E. Camac, J. Carpenter, R. Catford, J. A. Cawthray, G. R. Cernusak, L. A. Chandler, G. Chapman, A. R. Cheal, D. Cheesman, A. W. Chen, S.-C. Choat, B. Clinton, B. Clode, P. Coleman, H. Cornwell, W. K. Cosgrove, M. Crisp, M. Cross, E. Crous, K 2021-01-07 doi:10.1101/2021.01.04.425314 Cold Spring Harbor Laboratory Press 2021-01-07 <![CDATA[ Choosing optimal trigger points for ex situ, in toto conservation of single population threatened species ]]> https://biorxiv.org/content/10.1101/2021.01.08.425867v1?rss=1 Brown, K. Tambyah, T. Fenwick, J. Burke, A. Grant, P. Hegarty-Cremer, S. Muller, J. Bode, M. 2021-01-08 doi:10.1101/2021.01.08.425867 Cold Spring Harbor Laboratory Press 2021-01-08 <![CDATA[ Muscle-specific Cavin4 interacts with Bin1 to promote T-tubule formation and stability in developing skeletal muscle ]]> https://biorxiv.org/content/10.1101/2021.01.13.426456v1?rss=1 Lo, H. Lim, Y.-W. Xiong, Z. Martel, N. Ferguson, C. Ariotti, N. Giacomotto, J. Rae, J. Floetenmeyer, M. Moradi, S. V. Gao, Y. Tillu, V. Xia, D. Wang, H. Rahnama, S. Nixon, S. Bastiani, M. Day, R. Smith, K. Palpant, N. Johnston, W. Alexandrov, K. Collins, B. Hall, T. Parton, R. 2021-01-15 doi:10.1101/2021.01.13.426456 Cold Spring Harbor Laboratory Press 2021-01-15 <![CDATA[ RBCeq: An Integrated Bioinformatics Algorithm Designed to Improve Blood Type Compatibility Testing ]]> https://biorxiv.org/content/10.1101/2021.01.13.426510v1?rss=1 Jadhao, S. S. Davison, C. Roulis, E. V. Schoeman, E. M. Divate, M. D. Shankar, A. J. Lee, S. Pecheniuk, N. M. Irving, D. O. Hyland, C. A. Flower, R. L. Nagaraj, S. H. 2021-01-15 doi:10.1101/2021.01.13.426510 Cold Spring Harbor Laboratory Press 2021-01-15 <![CDATA[ BGvar - a comprehensive resource for blood group immunogenetics ]]> https://biorxiv.org/content/10.1101/2021.02.04.429861v1?rss=1 Rophina, M. Pandhare, K. Jadhao, S. Nagaraj, S. H. Scaria, V. 2021-02-05 doi:10.1101/2021.02.04.429861 Cold Spring Harbor Laboratory Press 2021-02-05 <![CDATA[ Osteomacs support osteoclast-mediated resorption and contribute to bone pathology in a postmenopausal osteoporosis mouse model ]]> https://biorxiv.org/content/10.1101/2021.02.05.429872v1?rss=1 Batoon, L. Millard, S. M. Raggatt, L. J. Wu, A. C. Kaur, S. Sun, L. W. H. Williams, K. Sandrock, C. Ng, P. Y. Bartnikowski, M. Glatt, V. Pavlos, N. Pettit, A. 2021-02-06 doi:10.1101/2021.02.05.429872 Cold Spring Harbor Laboratory Press 2021-02-06 <![CDATA[ Human primed endothelial colony forming cells exert neuroprotective effects in the growth restricted newborn piglet ]]> https://biorxiv.org/content/10.1101/2021.02.15.431307v1?rss=1 Chand, K. K. Patel, J. Bjorkman, S. T. Sim, S. L. Miller, S. M. Teo, E. Jones, L. Sun, J. Colditz, P. B. Khosrotehrani, K. Wixey, J. A. 2021-02-17 doi:10.1101/2021.02.15.431307 Cold Spring Harbor Laboratory Press 2021-02-17 <![CDATA[ Recoding enhances the metabolic capabilities of two novel methylotrophic Asgardarchaeota lineages ]]> https://biorxiv.org/content/10.1101/2021.02.19.431964v1?rss=1 Sun, J. Evans, P. N. Gagen, E. J. Woodcroft, B. J. Hedlund, B. P. Woyke, T. Hugenholtz, P. Rinke, C. 2021-02-19 doi:10.1101/2021.02.19.431964 Cold Spring Harbor Laboratory Press 2021-02-19 <![CDATA[ Biological networks with singular Jacobians: their origins and adaptation criteria ]]> https://biorxiv.org/content/10.1101/2021.03.01.433197v1?rss=1 Oellerich, T. G. Emelianenko, M. Liotta, L. Araujo, R. P. 2021-03-01 doi:10.1101/2021.03.01.433197 Cold Spring Harbor Laboratory Press 2021-03-01 <![CDATA[ Pediatric nasal epithelial cells are less permissive to SARS-CoV-2 replication compared to adult cells ]]> https://biorxiv.org/content/10.1101/2021.03.08.434300v1?rss=1 Zhu, Y. Chew, K. Y. Karawita, A. C. Yamamoto, A. Labzin, L. L. Yarlagadda, T. Khromykh, A. A. Stocks, C. J. Xia, Y. Kollmann, T. R. Martino, D. Kicic, A. Bielefeldt-Ohmann, H. Bowen, A. C. Sly, P. D. Spann, K. M. Short, K. R. 2021-03-08 doi:10.1101/2021.03.08.434300 Cold Spring Harbor Laboratory Press 2021-03-08 <![CDATA[ Characterization of the utility of three nebulizers in investigating infectivity of airborne viruses ]]> https://biorxiv.org/content/10.1101/2021.03.11.435057v1?rss=1 Niazi, S. Philp, L. K. Spann, K. Johnson, G. R. 2021-03-12 doi:10.1101/2021.03.11.435057 Cold Spring Harbor Laboratory Press 2021-03-12 <![CDATA[ Deep learning-based pan-cancer classification model reveals cancer-specific gene expression signatures ]]> https://biorxiv.org/content/10.1101/2021.03.15.435283v1?rss=1 97% prediction accuracy across cancer types. This strongly suggests that there are distinct gene expression signatures associated with various cancer types. We interpreted the model using SHapley Additive exPlanations (SHAP) to identify specific gene signatures that significantly contributed to the classification of cancer types. In addition to known biomarkers, we identified several novel biomarkers in different cancer types. These cancer-specific gene signatures are valuable candidates for future studies of their potential utility as cancer biomarkers and putative therapeutic targets. ]]> Divate, M. Tyagi, A. Richard, D. J. Prasad, P. A. Gowda, H. H Nagaraj, S. 2021-03-18 doi:10.1101/2021.03.15.435283 Cold Spring Harbor Laboratory Press 2021-03-18 <![CDATA[ Genome-wide DNA methylation and transcriptome integration reveal distinct sex differences in skeletal muscle. ]]> https://biorxiv.org/content/10.1101/2021.03.16.435733v1?rss=1 Landen, S. Jacques, M. Hiam, D. Romero, J. A. Harvey, N. R. Haupt, L. M. Griffiths, L. R. Ashton, K. J. Lamon, S. Voisin, S. Eynon, N. 2021-03-17 doi:10.1101/2021.03.16.435733 Cold Spring Harbor Laboratory Press 2021-03-17 <![CDATA[ Implementation and acceleration of optimal control for systems biology ]]> https://biorxiv.org/content/10.1101/2021.03.17.435721v1?rss=1 Sharp, J. A. Burrage, K. Simpson, M. J. 2021-03-17 doi:10.1101/2021.03.17.435721 Cold Spring Harbor Laboratory Press 2021-03-17 <![CDATA[ A short ERK5 isoform modulates nucleocytoplasmic shuttling of active ERK5 and associates with poor survival in breast cancer ]]> https://biorxiv.org/content/10.1101/2021.03.23.436061v1?rss=1 View larger version (58K): org.highwire.dtl.DTLVardef@1491ed5org.highwire.dtl.DTLVardef@1875fbeorg.highwire.dtl.DTLVardef@9edbbcorg.highwire.dtl.DTLVardef@16c34c8_HPS_FORMAT_FIGEXP M_FIG C_FIG ERK5 isoform-3 expression deploys active ERK5 (pERK5) outside the nucleus to facilitate EMT and cell migration. In cells dominantly expressing isoform-1, pERK5 shuttles to the nucleus to drive cell expansion. ]]> Miranda, M. S. Saunus, J. M. Akgül, S. Moradi Marjaneh, M. Kutasovic, J. R. Shi, W. Chatterjee, O. Casciello, F. Rozali, E. Handoko, H. Y. Wiegmans, A. P. Liu, T. Lee, J. S. Day, B. W. Edwards, S. French, J. D. McCart Reed, A. E. Chenevix-Trench, G. Khanna, K. K. D. Simpson, P. T. Lakhani, S. R. Al-Ejeh, F. 2021-03-23 doi:10.1101/2021.03.23.436061 Cold Spring Harbor Laboratory Press 2021-03-23 <![CDATA[ Model-based data analysis of tissue growth in thin 3D printed scaffolds ]]> https://biorxiv.org/content/10.1101/2021.03.25.436898v1?rss=1 Browning, A. P. Maclaren, O. J. Buenzli, P. R. Lanaro, M. Allenby, M. C. Woodruff, M. A. Simpson, M. J. 2021-03-25 doi:10.1101/2021.03.25.436898 Cold Spring Harbor Laboratory Press 2021-03-25 <![CDATA[ Genomic analysis of patient-derived xenograft models reveals intra-tumor heterogeneity in endometrial cancer and can predict tumor growth inhibition with talazoparib ]]> https://biorxiv.org/content/10.1101/2021.03.30.436914v1?rss=1 Bonazzi, V. F. Kondrashova, O. Smith, D. Nones, K. Sengal, A. T. Ju, R. Packer, L. M. Koufariotis, L. T. Kazakoff, S. H. Davidson, A. L. Ramarao-Milne, P. Lakis, V. Newell, F. Rogers, R. Davies, C. Nicklin, J. Garrett, A. Chetty, N. Perrin, L. Pearson, J. V. Patch, A.-M. Waddell, N. Pollock, P. 2021-03-31 doi:10.1101/2021.03.30.436914 Cold Spring Harbor Laboratory Press 2021-03-31 <![CDATA[ Epigenome erosion drives neural crest-like phenotypic mimicry in triple-negative breast cancer and other SOX10+ malignancies ]]> https://biorxiv.org/content/10.1101/2021.03.30.437624v1?rss=1 Saunus, J. M. De Luca, X. M. Northwood, K. Raghavendra, A. Hasson, A. McCart Reed, A. E. Lim, M. Lal, S. Vargas, A. C. Kutasovic, J. R. Dalley, A. J. Miranda, M. Kalaw, E. Kalita-de Croft, P. Gresshoff, I. Al-Ejeh, F. Gee, J. M. Ormandy, C. J. Khanna, K. K. Beesley, J. Chenevix-Trench, G. Green, A. R. Rakha, E. A. Ellis, I. O. Nicolau, D. V. Simpson, P. T. Lakhani, S. R. 2021-03-30 doi:10.1101/2021.03.30.437624 Cold Spring Harbor Laboratory Press 2021-03-30 <![CDATA[ The global ocean size-spectrum from bacteria to whales ]]> https://biorxiv.org/content/10.1101/2021.04.03.438320v1?rss=1 Hatton, I. A. Heneghan, R. F. Bar-On, Y. M. Galbraith, E. D. 2021-04-04 doi:10.1101/2021.04.03.438320 Cold Spring Harbor Laboratory Press 2021-04-04 <![CDATA[ A suite of activity-based probes to dissect the KLK activome in drug-resistant prostate cancer ]]> https://biorxiv.org/content/10.1101/2021.04.15.439906v1?rss=1 Lovell, S. Zhang, L. Kryza, T. Neodo, A. Bock, N. Williams, E. D. Engelsberger, E. Xu, C. Bakker, A. T. De Vita, E. Maneiro, M. Tanaka, R. J. Bevan, C. L. Clements, J. A. Tate, E. W. 2021-04-15 doi:10.1101/2021.04.15.439906 Cold Spring Harbor Laboratory Press 2021-04-15 <![CDATA[ Fine tuning the mechanism of Antigen 43 self-association to modulate aggregation levels of Escherichia coli pathogens ]]> https://biorxiv.org/content/10.1101/2021.04.19.440493v1?rss=1 Vo, J. Martinez Ortiz, G. C. Totsika, M. Lo, A. Whitten, A. E. Hor, L. Peters, K. M. Ageorges, V. Caccia, N. Desvaux, M. Schembri, M. A. Paxman, J. J. Heras, B. 2021-04-20 doi:10.1101/2021.04.19.440493 Cold Spring Harbor Laboratory Press 2021-04-20 <![CDATA[ Estimating parameters of a stochastic cell invasion model with fluorescent cell cycle labelling using Approximate Bayesian Computation ]]> https://biorxiv.org/content/10.1101/2021.04.20.440712v1?rss=1 Carr, M. J. Simpson, M. J. Drovandi, C. 2021-04-21 doi:10.1101/2021.04.20.440712 Cold Spring Harbor Laboratory Press 2021-04-21 <![CDATA[ Premovement inhibition protects motor actions from interference ]]> https://biorxiv.org/content/10.1101/2021.04.26.441384v1?rss=1 McInnes, A. N. Lipp, O. V. Tresilian, J. R. Vallence, A.-M. Marinovic, W. 2021-04-27 doi:10.1101/2021.04.26.441384 Cold Spring Harbor Laboratory Press 2021-04-27 <![CDATA[ Engagement of the contralateral limb can enhance the facilitation of motor output by loud acoustic stimuli ]]> https://biorxiv.org/content/10.1101/2021.04.26.441558v1?rss=1 McInnes, A. N. Nguyen, A. T. Carroll, T. J. Lipp, O. V. Marinovic, W. 2021-04-27 doi:10.1101/2021.04.26.441558 Cold Spring Harbor Laboratory Press 2021-04-27 <![CDATA[ Using 3D geometric morphometrics to aid taxonomic and ecological understanding of a recent speciation event within a small Australian marsupial (genus Antechinus) ]]> https://biorxiv.org/content/10.1101/2021.04.28.441717v1?rss=1 Viacava, P. Baker, A. M. Blomberg, S. P. Phillips, M. J. Weisbecker, V. 2021-04-28 doi:10.1101/2021.04.28.441717 Cold Spring Harbor Laboratory Press 2021-04-28 <![CDATA[ Axons-on-a-Chip for Mimicking Non-Disruptive Diffuse Axonal Injury underlying Traumatic Brain Injury ]]> https://biorxiv.org/content/10.1101/2021.05.06.442958v1?rss=1 Li, W. Wang, H. Pan, X. Gagoski, D. Durisic, N. Li, Z. Zhao, C. Wang, T. 2021-05-06 doi:10.1101/2021.05.06.442958 Cold Spring Harbor Laboratory Press 2021-05-06 <![CDATA[ High Dimensionality Reduction by Matrix Factorization for Systems Pharmacology ]]> https://biorxiv.org/content/10.1101/2021.05.30.446301v1?rss=1 Mehrpooya, A. Saberi-Movahed, F. Azizizadeh, N. Rezaei-Ravari, M. Eftekhari, M. Tavassoly, I. 2021-05-30 doi:10.1101/2021.05.30.446301 Cold Spring Harbor Laboratory Press 2021-05-30 <![CDATA[ Desiccation-driven senescence and its repression in Xerophyta schlechteri are regulated at extremely low water contents ]]> https://biorxiv.org/content/10.1101/2021.06.04.447054v1?rss=1 Radermacher, A. L. Williams, B. Iranzadeh, A. Dace, H. Mundree, S. Hilhorst, H. W. Farrant, J. M. 2021-06-05 doi:10.1101/2021.06.04.447054 Cold Spring Harbor Laboratory Press 2021-06-05 <![CDATA[ Parameter identifiability and model selection for sigmoid population growth models ]]> https://biorxiv.org/content/10.1101/2021.06.22.449499v1?rss=1 Simpson, M. J. Browning, A. Warne, D. J. Maclaren, O. J. Baker, R. E. 2021-06-23 doi:10.1101/2021.06.22.449499 Cold Spring Harbor Laboratory Press 2021-06-23 <![CDATA[ INTRINSIC MOTOR NEURONE EXCITABILITY IS REDUCED IN SOLEUS AND TIBIALIS ANTERIOR OF OLDER ADULTS ]]> https://biorxiv.org/content/10.1101/2021.06.23.449552v1?rss=1 Orssatto, L. B. R. Borg, D. N. Blazevich, A. J. Sakugawa, R. L. Shield, A. J. Trajano, G. S. 2021-06-23 doi:10.1101/2021.06.23.449552 Cold Spring Harbor Laboratory Press 2021-06-23 <![CDATA[ Modified defence peptides from horseshoe crab target and kill bacteria inside host cells ]]> https://biorxiv.org/content/10.1101/2021.06.27.450110v1?rss=1 Amiss, A. S. von Pein, J. B. Webb, J. R. Condon, N. D. Harvey, P. J. Phan, M.-D. Schembri, M. A. Currie, B. J. Sweet, M. J. Craik, D. J. Kapetanovic, R. Henriques, S. T. Lawrence, N. 2021-06-28 doi:10.1101/2021.06.27.450110 Cold Spring Harbor Laboratory Press 2021-06-28 <![CDATA[ Quantitative analysis of tumour spheroid structure ]]> https://biorxiv.org/content/10.1101/2021.08.05.455334v1?rss=1 Browning, A. P. Sharp, J. A. Murphy, R. J. Gunasingh, G. Lawson, B. Burrage, K. Haass, N. K. Simpson, M. J. 2021-08-06 doi:10.1101/2021.08.05.455334 Cold Spring Harbor Laboratory Press 2021-08-06 <![CDATA[ Systemic host inflammation induces stage-specific transcriptomic modification and slower maturation in malaria parasites ]]> https://biorxiv.org/content/10.1101/2021.08.18.456784v1?rss=1 Lansink, L. I. M. Engel, J. A. Lee, H. J. Soon, M. S. F. Williams, C. G. SheelaNair, A. Pernold, C. P. S. Laohamonthonkul, P. Akter, J. Stoll, T. Hill, M. M. Talman, A. M. Russell, A. J. C. Lawniczak, M. Davenport, M. P. Khoury, D. S. Haque, A. 2021-08-19 doi:10.1101/2021.08.18.456784 Cold Spring Harbor Laboratory Press 2021-08-19 <![CDATA[ Designing and interpreting 4D tumour spheroid experiments ]]> https://biorxiv.org/content/10.1101/2021.08.18.456910v1?rss=1 Murphy, R. J. Browning, A. P. Gunasingh, G. Haass, N. K. Simpson, M. J. 2021-08-19 doi:10.1101/2021.08.18.456910 Cold Spring Harbor Laboratory Press 2021-08-19 <![CDATA[ Bio-hybrid Soft Robotic Bioreactors for Mimicking Multi-Axial Femoropopliteal Artery Mechanobiology ]]> https://biorxiv.org/content/10.1101/2021.09.24.461639v1?rss=1 Fell, C. Brooks-Richards, T. L. Woodruff, M. A. Allenby, M. C. 2021-09-24 doi:10.1101/2021.09.24.461639 Cold Spring Harbor Laboratory Press 2021-09-24 <![CDATA[ Different plasticity of bud outgrowth at cauline and rosette nodes in Arabidopsis thaliana ]]> https://biorxiv.org/content/10.1101/2021.09.26.461886v1?rss=1 Fichtner, F. Barbier, F. F. Kerr, S. C. Dudley, C. Cubas, P. Turnbull, C. Brewer, P. B. Beveridge, C. A. 2021-09-27 doi:10.1101/2021.09.26.461886 Cold Spring Harbor Laboratory Press 2021-09-27 <![CDATA[ Biomimetic Vasculatures by 3D-Printed Porous Molds ]]> https://biorxiv.org/content/10.1101/2021.09.27.461981v1?rss=1 Ching, T. vasudevan, j. Chang, S.-Y. Tan, H. Y. Lim, C. T. Fernandez, J. G. Ng, J. J. Toh, Y.-C. Hashimoto, M. 2021-09-28 doi:10.1101/2021.09.27.461981 Cold Spring Harbor Laboratory Press 2021-09-28 <![CDATA[ An extremes of phenotype approach confirms significant genetic heterogeneity in patients with ulcerative colitis. ]]> https://biorxiv.org/content/10.1101/2021.10.04.462982v1?rss=1 Radford-Smith, G. Mortlock, S. Lord, A. Montgomery, G. Zakrzewski, M. Simms, L. A. Krishnaprasad, K. Hanigan, K. Doecke, J. D. Walsh, A. Lawrance, I. Bampton, P. A. Andrews, J. M. Mahy, G. Connor, S. Sparrow, M. Bell, S. Florin, T. Begun, J. Gearry, R. 2021-10-12 doi:10.1101/2021.10.04.462982 Cold Spring Harbor Laboratory Press 2021-10-12 <![CDATA[ EEG-based clusters differentiate psychological distress, sleep quality and cognitive function in adolescents ]]> https://biorxiv.org/content/10.1101/2021.10.14.464347v1?rss=1 Forbes, O. Schwenn, P. E. Wu, P. P.-Y. Santos-Fernandez, E. Xie, H.-B. Lagopoulos, J. McLoughlin, L. T. Sacks, D. D. Mengersen, K. Hermens, D. F. 2021-10-15 doi:10.1101/2021.10.14.464347 Cold Spring Harbor Laboratory Press 2021-10-15 <![CDATA[ Isomeric lipid signatures reveal compartmentalised fatty acid metabolism in cancer ]]> https://biorxiv.org/content/10.1101/2021.11.01.466716v1?rss=1 Young, R. S. E. Bowman, A. P. Tousignant, K. D. Poad, B. L. J. Gunter, J. H. Philp, L. K. Nelson, C. C. Ellis, S. Heeren, R. M. A. Sadowski, M. C. Blanksby, S. J. 2021-11-03 doi:10.1101/2021.11.01.466716 Cold Spring Harbor Laboratory Press 2021-11-03 <![CDATA[ Prioritising the eradication of invasive species from island archipelagos with high reinvasion risk ]]> https://biorxiv.org/content/10.1101/2021.11.04.467372v1?rss=1 Kumar, V. Nunez, A. Brown, K. Agarwal, K. Hall, S. Bode, M. 2021-11-05 doi:10.1101/2021.11.04.467372 Cold Spring Harbor Laboratory Press 2021-11-05 <![CDATA[ A Thin-Film Lubrication Model for Biofilm Expansion Under Strong Adhesion ]]> https://biorxiv.org/content/10.1101/2021.11.16.468738v1?rss=1 Tam, A. K. Y. Harding, B. Green, J. E. F. Balasuriya, S. Binder, B. J. 2021-11-19 doi:10.1101/2021.11.16.468738 Cold Spring Harbor Laboratory Press 2021-11-19 <![CDATA[ Marker-free characterization of single live circulating tumor cell full-length transcriptomes ]]> https://biorxiv.org/content/10.1101/2021.11.16.468747v1?rss=1 Poonia, S. Goel, A. Chawla, S. Bhattacharya, N. Rai, P. Lee, Y. F. Yap, Y. S. West, J. Bhagat, A. A. Juhi Tayal, J. Mehta, A. Ahuja, G. Majumdar, A. Ramalingam, N. Sengupta, D. 2021-11-19 doi:10.1101/2021.11.16.468747 Cold Spring Harbor Laboratory Press 2021-11-19 <![CDATA[ Gene expression based inference of drug resistance in cancer ]]> https://biorxiv.org/content/10.1101/2021.11.17.468905v1?rss=1 Chawla, S. Rockstroh, A. Lehman, M. Rather, E. Jain, A. Anand, A. Gupta, A. Bhattacharya, N. Poonia, S. Rai, P. Das, N. Majumdar, A. Jayadeva, J. Ahuja, G. Hollier, B. G. Nelson, C. C. Sengupta, D. 2021-11-19 doi:10.1101/2021.11.17.468905 Cold Spring Harbor Laboratory Press 2021-11-19 <![CDATA[ Intact double stranded RNA is mobile and triggers RNAi against viral and fungal plant pathogens ]]> https://biorxiv.org/content/10.1101/2021.11.24.469772v1?rss=1 Brosnan, C. A. Sawyer, A. Felippes, F. F. Carroll, B. J. Waterhouse, P. M. Mitter, N. 2021-11-25 doi:10.1101/2021.11.24.469772 Cold Spring Harbor Laboratory Press 2021-11-25 <![CDATA[ Identifying cell-to-cell variability in internalisation using flow cytometry ]]> https://biorxiv.org/content/10.1101/2021.11.24.469957v1?rss=1 Browning, A. P. Ansari, N. Drovandi, C. Johnston, A. Simpson, M. J. Jenner, A. L. 2021-11-25 doi:10.1101/2021.11.24.469957 Cold Spring Harbor Laboratory Press 2021-11-25 <![CDATA[ A stochastic mathematical model of 4D tumour spheroids with real-time fluorescent cell cycle labelling ]]> https://biorxiv.org/content/10.1101/2021.11.28.470300v1?rss=1 Klowss, J. J. Browning, A. P. Murphy, R. J. Carr, E. J. Plank, M. J. Gunasingh, G. Haass, N. K. Simpson, M. J. 2021-11-29 doi:10.1101/2021.11.28.470300 Cold Spring Harbor Laboratory Press 2021-11-29 <![CDATA[ ImaGene: A web-based software platform for tumor radiogenomic evaluation and reporting ]]> https://biorxiv.org/content/10.1101/2021.12.02.470994v1?rss=1 Sukhadia, S. S. Tyagi, A. K. Venkatraman, V. Mukherjee, P. P, P. A. Divate, M. D. Gevaert, O. Nagaraj, S. H. 2021-12-03 doi:10.1101/2021.12.02.470994 Cold Spring Harbor Laboratory Press 2021-12-03 <![CDATA[ Bridging functional annotation gaps in non-model plant genes with AlphaFold, DeepFRI and small molecule docking ]]> https://biorxiv.org/content/10.1101/2021.12.22.473925v1?rss=1 Stephan, G. Dugdale, B. Deo, P. Harding, R. Dale, J. Visendi, P. 2021-12-23 doi:10.1101/2021.12.22.473925 Cold Spring Harbor Laboratory Press 2021-12-23 <![CDATA[ Physiological responses of plants to in vivo XRF radiation damage: insights from elemental, histochemical, anatomical and ultrastructural analyses ]]> https://biorxiv.org/content/10.1101/2022.01.18.476760v1?rss=1 Montanha, G. S. Marques, J. P. R. Rodrigues, E. S. Jones, M. W. M. de Carvalho, H. W. P. 2022-01-20 doi:10.1101/2022.01.18.476760 Cold Spring Harbor Laboratory Press 2022-01-20 <![CDATA[ Population dynamics of epithelial-mesenchymal heterogeneity in cancer cells ]]> https://biorxiv.org/content/10.1101/2022.01.21.475826v1?rss=1 Jain, P. Bhatia, S. Thompson, E. W. Jolly, M. K. 2022-01-23 doi:10.1101/2022.01.21.475826 Cold Spring Harbor Laboratory Press 2022-01-23 <![CDATA[ Reliable and efficient parameter estimation using approximate continuum limit descriptions of stochastic models ]]> https://biorxiv.org/content/10.1101/2022.02.02.478913v1?rss=1 Simpson, M. J. Baker, R. E. Buenzli, P. R. Nicholson, R. Maclaren, O. J. 2022-02-04 doi:10.1101/2022.02.02.478913 Cold Spring Harbor Laboratory Press 2022-02-04 <![CDATA[ Novel AlphasynucleinPAN in human Mesenchymal Stem Cells-derived neurons masks SNCA140 and creates dissociation of deleterious SNCA98 in astrocytoma stem cells ]]> https://biorxiv.org/content/10.1101/2022.02.08.479501v1?rss=1 owoola, A. G. Okolicsanyi, R. K. Griffiths, L. R. Haupt, L. M. 2022-02-11 doi:10.1101/2022.02.08.479501 Cold Spring Harbor Laboratory Press 2022-02-11 <![CDATA[ Targeting OLIG2 increases therapeutic responses in SHH medulloblastoma mouse models and patient-derived medulloblastoma organoids ]]> https://biorxiv.org/content/10.1101/2022.02.14.480293v1?rss=1 Li, Y. Dismuke, T. Lim, C. Bruce, Z. C. Offenhauser, C. Baumgartner, U. Maybury, M. DSouza, R. C. J. Hassall, T. Wainwright, B. Stein, G. Piper, M. Johns, T. G. Sokolsky-Papkov, M. Gershon, T. R. Day, B. W. 2022-02-16 doi:10.1101/2022.02.14.480293 Cold Spring Harbor Laboratory Press 2022-02-16 <![CDATA[ Loss of β-ketoacyl acyl carrier protein synthase III activity restores multidrug-resistant Escherichia coli sensitivity to previously ineffective antibiotics ]]> https://biorxiv.org/content/10.1101/2022.02.18.481121v1?rss=1 Hong, Y. Qin, J. Verderosa, A. Hawas, S. Zhang, B. Blaskovich, M. A. T. Cronan, J. Totsika, M. 2022-02-20 doi:10.1101/2022.02.18.481121 Cold Spring Harbor Laboratory Press 2022-02-20 <![CDATA[ What are the reference strains of Acinetobacter baumannii referring to? ]]> https://biorxiv.org/content/10.1101/2022.02.27.482139v1?rss=1 Philippe, C. Valcek, A. Whiteway, C. Robino, E. Nesporova, K. Bove, M. Coenye, T. De Pooter, T. De Coster, W. Strazisar, M. Kenyon, J. J. Van der Henst, C. 2022-02-27 doi:10.1101/2022.02.27.482139 Cold Spring Harbor Laboratory Press 2022-02-27 <![CDATA[ Dissociable Cellular and Genetic Mechanisms of Cortical Thinning at Different Life Stages ]]> https://biorxiv.org/content/10.1101/2022.03.21.484899v1?rss=1 60 years) in the patterns of association between inter-regional profiles of cortical thickness and expression profiles of marker genes for CA1 and S1 pyramidal cells, astrocytes, and microglia. Gene ontology and enrichment analyses indicated that each of the three life-stages was associated with different biological processes and cellular components: synaptic modeling in early life, neurotransmission in mid-life, and neurodegeneration in late-life. These findings provide mechanistic insights into age-related cortical thinning during typical development and aging. ]]> Modabbernia, A. Vidal-Pineiro, D. Agartz, I. Andreassen, O. A. Ayesa-Arriola, R. Bertolino, A. Boomsma, D. I. Bourque, J. Breier, A. Brouwer, R. M. Buitelaar, J. K. Canales-Rodriguez, E. J. Caseras, X. Conrod, P. J. Crespo-Facorro, B. Crivello, F. Crone, E. A. de Zubicaray, G. I. Dickie, E. W. Dima, D. Frenzel, S. Fisher, S. E. Franke, B. Glahn, D. C. Grabe, H.-J. Grotegerd, D. Gruber, O. Guerrero-Pedraza, A. Gur, R. E. Gur, R. C. Hartman, C. A. Hoekstra, P. J. Hulshoff Pol, H. E. Jahanshad, N. Jernigan, T. L. Jiang, J. Kalnin, A. J. Kochan, N. A. Mazoyer, 2022-03-22 doi:10.1101/2022.03.21.484899 Cold Spring Harbor Laboratory Press 2022-03-22 <![CDATA[ Establishing combination PAC-1 and TRAIL regimens for treating ovarian cancer based on patient-specific pharmacokinetic profiles using in silico clinical trails ]]> https://biorxiv.org/content/10.1101/2022.03.29.486309v1?rss=1 Cardinal, O. Burlot, C. Fu, Y. Crosley, P. Hitt, M. Craig, M. Jenner, A. L. 2022-03-30 doi:10.1101/2022.03.29.486309 Cold Spring Harbor Laboratory Press 2022-03-30 <![CDATA[ Examining the efficacy of localised gemcitabine therapy for the treatment of pancreatic cancer using a hybrid agent-based model ]]> https://biorxiv.org/content/10.1101/2022.04.18.488716v1?rss=1 Jenner, A. Kelly, W. Dallaston, M. Araujo, R. Parfitt, I. Steinitz, D. Pooladvand, P. Kim, P. S. Wade, S. J. Vine, K. L. 2022-04-19 doi:10.1101/2022.04.18.488716 Cold Spring Harbor Laboratory Press 2022-04-19 <![CDATA[ Growth and adaptation mechanisms of tumour spheroids with time-dependent oxygen availability ]]> https://biorxiv.org/content/10.1101/2022.04.24.489294v1?rss=1 Murphy, R. J. Gunasingh, G. Haass, N. K. Simpson, M. J. 2022-04-24 doi:10.1101/2022.04.24.489294 Cold Spring Harbor Laboratory Press 2022-04-24 <![CDATA[ The climatic constrains of the historical global spread of mungbean ]]> https://biorxiv.org/content/10.1101/2022.04.27.489711v1?rss=1 Ong, P.-W. Lin, Y.-P. Chen, H.-W. Lo, C.-Y. Burlyaeva, M. Noble, T. Nair, R. M. Schafleitner, R. Vishnyakova, M. von Wettberg, E. Samsonova, M. G. Nuzhdin, S. Ting, C.-T. Lee, C.-R. 2022-04-28 doi:10.1101/2022.04.27.489711 Cold Spring Harbor Laboratory Press 2022-04-28 <![CDATA[ Rewiring of liver diurnal transcriptome rhythms by triiodothyronine (T3) supplementation ]]> https://biorxiv.org/content/10.1101/2022.04.28.489909v1?rss=1 de Assis, L. V. Harder, L. Lacerda, J. T. Parsons, R. Kaehler, M. Cascorbi, I. Nagel, I. Rawashdeh, O. Mittag, J. Oster, H. 2022-04-30 doi:10.1101/2022.04.28.489909 Cold Spring Harbor Laboratory Press 2022-04-30 <![CDATA[ Computationally efficient mechanism discovery for cell invasion with uncertainty quantification ]]> https://biorxiv.org/content/10.1101/2022.05.12.491596v1?rss=1 VandenHeuvel, D. J. Drovandi, C. Simpson, M. J. 2022-05-13 doi:10.1101/2022.05.12.491596 Cold Spring Harbor Laboratory Press 2022-05-13 <![CDATA[ An update to the database for Acinetobacter baumannii capsular polysaccharide locus typing extends the extensive and diverse repertoire of genes found at and outside the K locus ]]> https://biorxiv.org/content/10.1101/2022.05.19.492579v1?rss=1 400 genes for forming linkages between sugars or adding non-sugar substituents. A repertoire of 681 gene types were found across the 237 KL, with 88.4% found in <5% of KL. 3. Significance as a BioResource to the communityNew therapies that target the bacterial polysaccharide capsule (CPS) show promise as effective tools to curb the high mortality rates associated with extensively resistant A. baumannii; one of the worlds most troublesome Gram-negative pathogens. As important information about the CPS structure produced by an isolate can be extracted from Whole Genome Sequences (WGS), simple bioinformatic tools and definitive sequence databases are needed to facilitate robust prediction of CPS type from WGS data. Here, we provide a comprehensive update to the international CPS sequence typing database for A. baumannii, increasing the utility of this resource for prediction of CPS type from WGS to assist with clinical surveillance, and/or the design and application of CPS-targeted therapies. This study is expected to further inform epidemiological tracking efforts, as well as the design of therapeutics targeting the CPS, enhancing global efforts to identify, trace and treat infections caused by this pathogen. 4. Data summaryO_LIThe updated A. baumannii KL reference sequence database including 241 fully annotated gene clusters is available for download under Kaptive v. 2.0.1 at https://github.com/katholt/Kaptive. C_LIO_LIGenome assemblies, short read data, or GenBank records used as representative reference sequence for each K locus are listed in Supplementary Table S1, and are referenced within each entry in the A. baumannii KL reference sequence database. C_LI The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files. ]]> Cahill, S. M. Hall, R. M. Kenyon, J. J. 2022-05-20 doi:10.1101/2022.05.19.492579 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ The Queensland Twin Adolescent Brain Project, a longitudinal study of adolescent brain development ]]> https://biorxiv.org/content/10.1101/2022.05.19.492753v1?rss=1 Strike, L. T. Hansell, N. K. Chuang, K.-H. Miller, J. L. de Zubicaray, G. I. Thompson, P. M. McMahon, K. L. Wright, M. J. 2022-05-20 doi:10.1101/2022.05.19.492753 Cold Spring Harbor Laboratory Press 2022-05-20 <![CDATA[ Approaches to generating virtual patient cohorts with applications in oncology ]]> https://biorxiv.org/content/10.1101/2022.05.24.493265v1?rss=1 Surendran, A. Sauteur-Robitaille, J. L. Kleimeier, D. Gevertz, J. L. Wilkie, K. P. Jenner, A. L. Craig, M. 2022-05-25 doi:10.1101/2022.05.24.493265 Cold Spring Harbor Laboratory Press 2022-05-25 <![CDATA[ Design, development, and preliminary assessment of a novel peripheral intravenous catheter aimed at reducing early failure rates ]]> https://biorxiv.org/content/10.1101/2022.06.20.496233v1?rss=1 Doyle, B. Kelsey, L. Shelverton, C. Abbate, G. Ainola, C. Carr, P. Livingstone, S. Bouquet, M. Passmore, M. Wilson, E. Colombo, S. M. Sato, K. Liu, K. Heinsar, S. Sato, N. Wildi, K. Suen, J. Fraser, J. Li Bassi, G. Keogh, S. 2022-06-21 doi:10.1101/2022.06.20.496233 Cold Spring Harbor Laboratory Press 2022-06-21 <![CDATA[ CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning ]]> https://biorxiv.org/content/10.1101/2022.07.11.499243v1?rss=1 Chklovski, A. Parks, D. H. Woodcroft, B. J. Tyson, G. W. 2022-07-11 doi:10.1101/2022.07.11.499243 Cold Spring Harbor Laboratory Press 2022-07-11 <![CDATA[ Cysteine dependent conformation heterogeneity of Shigella flexneri autotransporter IcsA and implications in its function ]]> https://biorxiv.org/content/10.1101/2022.07.21.501072v1?rss=1 Qin, J. Hong, Y. Morona, R. Totsika, M. 2022-07-22 doi:10.1101/2022.07.21.501072 Cold Spring Harbor Laboratory Press 2022-07-22 <![CDATA[ Computationally efficient framework for diagnosing, understanding, and predicting biphasic population growth ]]> https://biorxiv.org/content/10.1101/2022.07.27.501797v1?rss=1 Murphy, R. J. Maclaren, O. J. Calabrese, A. R. Thomas, P. B. Warne, D. J. Williams, E. D. Simpson, M. J. 2022-07-29 doi:10.1101/2022.07.27.501797 Cold Spring Harbor Laboratory Press 2022-07-29 <![CDATA[ Deficiencies of Runx3 and tissue-resident CD4+ intestinal epithelial lymphocytes link intestinal dysbiosis and inflammation in mouse and human spondyloarthropathy ]]> https://biorxiv.org/content/10.1101/2022.07.28.501834v1?rss=1 Bhuyan, Z. Maradana, M. Rahman, M. A. Mehdi, A. Bergot, A.-S. Simone, D. Hanson, A. Nel, H. Mesa, J. G. El Kurdi, M. Kenna, T. Leo, P. Rehaume, L. Brown, M. Ciccia, F. Thomas, R. 2022-07-30 doi:10.1101/2022.07.28.501834 Cold Spring Harbor Laboratory Press 2022-07-30 <![CDATA[ Protein-protein complexes can undermine ultrasensitivity-dependent biological adaptation ]]> https://biorxiv.org/content/10.1101/2022.08.07.503111v1?rss=1 Jeynes-Smith, C. Araujo, R. 2022-08-08 doi:10.1101/2022.08.07.503111 Cold Spring Harbor Laboratory Press 2022-08-08 <![CDATA[ Facilitation-inhibition control of motor neuronal persistent inward currents in young and older adults ]]> https://biorxiv.org/content/10.1101/2022.08.08.503135v1?rss=1 Orssatto, L. B. R. Fernandes, G. L. Blazevich, A. Trajano, G. S. 2022-08-11 doi:10.1101/2022.08.08.503135 Cold Spring Harbor Laboratory Press 2022-08-11 <![CDATA[ Circadian ribosome profiling reveals a role for the Period2 upstream opening reading frame in sleep ]]> https://biorxiv.org/content/10.1101/2022.08.09.503391v1?rss=1 Millius, A. Yamada, R. Fujishima, H. Maeda, K. Standley, D. M. Sumiyama, K. Perrin, D. Ueda, H. R. 2022-08-11 doi:10.1101/2022.08.09.503391 Cold Spring Harbor Laboratory Press 2022-08-11 <![CDATA[ Insight on Selective Breeding the Robustness Based on Field Survival Records: New Genetic Evaluation of Survival Traits in White-leg Shrimp (Penaeus vannamei) Breeding Line ]]> https://biorxiv.org/content/10.1101/2022.08.14.503924v1?rss=1 0.8). Heritability estimates of body weight (BW) for BL2019 and BL2020 were 0.486 and 0.373, respectively. Trajectories of survival heritability across time showed a gradual increase across the grow-out test period but slowed or reached a plateau during the later grow-out test period. Genetic correlations among survival traits in the grow-out tests were moderate to high, and the closer the times were between estimates, the higher were their genetic correlations. In contrast, genetic correlations between both survival traits and body weight were low but positive. Here we provide the first report of the trajectory of heritability estimates for survival traits across time in aquaculture. Results will be useful for developing robust improved white-leg shrimp culture strains in selective breeding programs based on field survival data. ]]> Ren, S. Mather, P. Tang, B. Hurwood, D. 2022-08-15 doi:10.1101/2022.08.14.503924 Cold Spring Harbor Laboratory Press 2022-08-15 <![CDATA[ An Alzheimer's disease patient-derived olfactory cell model identifies gene expression changes associated with cognition ]]> https://biorxiv.org/content/10.1101/2022.08.22.504884v1?rss=1 Rantanen, L. M. Bitar, M. Lampinen, R. Stewart, R. Quek, H. Oikari, L. E. Cuni-Lopez, C. Sutharsan, R. Thillaiyampalam, G. Iqbal, J. Russell, D. Penttilä, E. Löppönen, H. Lehtola, J.-M. Saari, T. Hannonen, S. Koivisto, A. M. Haupt, L. M. Mackay-Sim, A. Cristino, A. S. Kanninen, K. M. White, A. R. 2022-08-23 doi:10.1101/2022.08.22.504884 Cold Spring Harbor Laboratory Press 2022-08-23 <![CDATA[ Profile likelihood-based parameter and predictive interval analysis guides model choice for ecological population dynamics ]]> https://biorxiv.org/content/10.1101/2022.09.05.506701v1?rss=1 Simpson, M. J. Walker, S. Studerus, E. N. Murphy, R. J. McCue, S. Maclaren, O. 2022-09-06 doi:10.1101/2022.09.05.506701 Cold Spring Harbor Laboratory Press 2022-09-06 <![CDATA[ Calibration of a Voronoi cell-based model for tumour growth using approximate Bayesian computation ]]> https://biorxiv.org/content/10.1101/2022.09.13.507714v1?rss=1 Wang, X. Drovandi, C. Jenner, A. L. Salomone, R. 2022-09-15 doi:10.1101/2022.09.13.507714 Cold Spring Harbor Laboratory Press 2022-09-15 <![CDATA[ IRF7 impacts on prostate cancer cell survival in response to radiation ]]> https://biorxiv.org/content/10.1101/2022.09.23.509205v1?rss=1 Pickard, A. Amoroso, F. McCulloch, K. Erickson, A. Sachdeva, A. Steele, R. Mukherjee, D. Dellett, M. McComb, J. McCaffrey, L. Hart, C. Brown, M. McDade, S. S. Waugh, D. Clarke, N. Butterworth, K. Illidge, T. Mirtti, T. Overton, I. M. Mills, I. 2022-09-23 doi:10.1101/2022.09.23.509205 Cold Spring Harbor Laboratory Press 2022-09-23 <![CDATA[ Divergent east-west lineages in an Australian fruit fly associated with the Carpentaria basin divide ]]> https://biorxiv.org/content/10.1101/2022.10.04.510875v1?rss=1 2000km, remains unknown. ]]> Manawaduge, C. G. Clarke, A. R. Hurwood, D. A. 2022-10-07 doi:10.1101/2022.10.04.510875 Cold Spring Harbor Laboratory Press 2022-10-07 <![CDATA[ Differences in gene expression in field populations of Wolbachia-infected Aedes aegypti mosquitoes with varying release histories in northern Australia ]]> https://biorxiv.org/content/10.1101/2022.10.10.511644v1?rss=1 8 years post-introgression into field populations, Wolbachia continues to profoundly impact host gene expression, particularly genes involved in insect immune response. We suggest that if gene expression changes underlie blocking of virus replication in Wolbachia-infected Ae. aegypti, then refractoriness of these mosquitoes to arboviruses may remain stable over the long-term. Author summaryThe Aedes aegypti mosquito is the main species responsible for urban transmission of dengue, Zika and chikungunya viruses. Control measures, including source reduction and insecticide treatment, have historically struggled to provide sustained control of this species to limit disease. An alternative approach involves releasing mosquitoes harbouring Wolbachia bacteria. Wolbachia inhibits virus transmission by Ae. aegypti and preliminary evidence indicates that dengue incidence is reduced in locations where it has been deployed. In this study, we found that Wolbachia significantly upregulates gene expression in Ae. aegypti at least 8 years after field deployment compared with uninfected controls, although some gene downregulation was also observed. We observed a more muted response in mosquitoes from populations with older release histories, with far fewer genes being differentially regulated versus those from the most recent release. Irrespective of release history, immune response and metabolism genes were significantly upregulated, and to a lesser extent genes related to behaviour. Our results, combined with previous studies that have revealed few changes in the Wolbachia genome post release, provide further evidence of the long-term stability of the Wolbachia-mosquito relationship in the field. ]]> Wimalasiri-Yapa, R. Huang, B. Ross, P. Hoffmann, A. Ritchie, S. Frentiu, F. Warrilow, D. van den Hurk, A. F. 2022-10-11 doi:10.1101/2022.10.10.511644 Cold Spring Harbor Laboratory Press 2022-10-11 <![CDATA[ OzFAD: Ozone-enabled fatty acid discovery reveals unexpected diversity in the human lipidome ]]> https://biorxiv.org/content/10.1101/2022.10.24.513604v1?rss=1 Menzel, J. P. Young, R. S. E. Benfield, A. H. Scott, J. S. Butler, L. M. Henriques, S. T. Poad, B. L. J. Blanksby, S. J. 2022-10-25 doi:10.1101/2022.10.24.513604 Cold Spring Harbor Laboratory Press 2022-10-25 <![CDATA[ Membrane-active peptides escape drug-resistance in cancer ]]> https://biorxiv.org/content/10.1101/2022.10.27.513961v1?rss=1 Benfield, A. H. Vernen, F. Young, R. S. E. Bufi, F. N. Hammerlindl, H. Craik, D. J. Schaider, H. Lawrence, N. Blanksby, S. J. Henriques, S. T. 2022-10-28 doi:10.1101/2022.10.27.513961 Cold Spring Harbor Laboratory Press 2022-10-28 <![CDATA[ Out of thin air: surveying tropical bat roosts through air sampling of eDNA ]]> https://biorxiv.org/content/10.1101/2022.11.07.515479v1?rss=1 Garrett, N. R. Watkins, J. Francis, C. Simmons, N. B. Ivanova, N. V. Naaum, A. Briscoe, A. Drinkwater, R. Clare, E. L. 2022-11-08 doi:10.1101/2022.11.07.515479 Cold Spring Harbor Laboratory Press 2022-11-08 <![CDATA[ IL-33-induced neutrophilic inflammation and NETosis underlie rhinovirus-triggered exacerbations of asthma ]]> https://biorxiv.org/content/10.1101/2022.11.07.515526v1?rss=1 Curren, B. Ahmed, T. Howard, D. R. Ullah, A. Sebina, I. Rashid, R. Sikder, A. A. Bissell, A. Ngo, S. Jackson, D. Toussaint, M. Edwards, M. Johnston, S. McSorley, H. J. Phipps, S. 2022-11-08 doi:10.1101/2022.11.07.515526 Cold Spring Harbor Laboratory Press 2022-11-08 <![CDATA[ Translational fusion of terpene synthases enhances metabolic flux by increasing protein stability ]]> https://biorxiv.org/content/10.1101/2022.11.08.515726v1?rss=1 110-fold improvement in nerolidol production upon translational fusion of nerolidol synthase (a sesquiterpene synthase) to farnesyl diphosphate synthase. This delivered a titre increase from 29.6 mg/L up to 4.2 g/L nerolidol in a single engineering step. Whole-cell proteomic analysis revealed that nerolidol synthase levels in the fusion strains were greatly elevated compared to the non-fusion control. Similarly, the fusion of nerolidol synthase to non-catalytic domains also produced comparable increases in titre, which coincided with improved enzyme expression. When farnesyl diphosphate synthase was fused to other terpene synthases, we observed more modest improvements in terpene titre (1.9- and 3.8-fold), which corresponds to increases of a similar magnitude in terpene synthase expression. Therefore, increased in vivo enzyme levels - resulting from improved expression and/or stability - is likely to be a major driver of catalytic enhancement from enzyme fusion. ]]> Cheah, L. C. Liu, L. Stark, T. Plan, M. Peng, B. Lu, Z. Schenk, G. Sainsbury, F. Vickers, C. E. 2022-11-09 doi:10.1101/2022.11.08.515726 Cold Spring Harbor Laboratory Press 2022-11-09 <![CDATA[ Bladder-draining lymph nodes support germinal centre B cell responses during urinary tract infection in mice ]]> https://biorxiv.org/content/10.1101/2022.11.10.516078v1?rss=1 Hawas, S. Vagenas, D. Haque, A. Totsika, M. 2022-11-12 doi:10.1101/2022.11.10.516078 Cold Spring Harbor Laboratory Press 2022-11-12 <![CDATA[ Fish Aggregating Devices could enhance the effectiveness of blue water MPAs ]]> https://biorxiv.org/content/10.1101/2022.11.16.516764v1?rss=1 Bode, M. Game, E. Wegmann, A. Pollack, K. 2022-11-17 doi:10.1101/2022.11.16.516764 Cold Spring Harbor Laboratory Press 2022-11-17 <![CDATA[ Costs and economic impacts of expanding marine protected area systems to 30% coverage ]]> https://biorxiv.org/content/10.1101/2022.11.20.517276v1?rss=1 Waldron, A. Heneghan, R. Steenbeek, J. Coll, M. Scherrer, K. J. 2022-11-22 doi:10.1101/2022.11.20.517276 Cold Spring Harbor Laboratory Press 2022-11-22 <![CDATA[ Synthetic in vivo compartmentalisation improves metabolic flux and modulates the product profile of promiscuous enzymes ]]> https://biorxiv.org/content/10.1101/2022.11.24.517869v1?rss=1 Cheah, L. C. Liu, L. Plan, M. Peng, B. Lu, Z. Schenk, G. Vickers, C. E. Sainsbury, F. 2022-11-25 doi:10.1101/2022.11.24.517869 Cold Spring Harbor Laboratory Press 2022-11-25 <![CDATA[ Investigation on key aspects of mating biology in the mosquito Aedes koreicus ]]> https://biorxiv.org/content/10.1101/2022.12.01.518615v1?rss=1 Ciocchetta, S. Frentiu, F. D. Montarsi, F. Capelli, G. Devine, G. J. 2022-12-03 doi:10.1101/2022.12.01.518615 Cold Spring Harbor Laboratory Press 2022-12-03 <![CDATA[ The landscape of alternative polyadenylation during EMT and its regulation by the RNA-binding protein Quaking ]]> https://biorxiv.org/content/10.1101/2022.12.01.518773v1?rss=1 Neumann, D. P. Pillman, K. A. Dredge, B. K. Bert, A. G. Bracken, C. P. Hollier, B. G. Selth, L. A. Beilharz, T. H. Goodall, G. J. Gregory, P. A. 2022-12-02 doi:10.1101/2022.12.01.518773 Cold Spring Harbor Laboratory Press 2022-12-02 <![CDATA[ The Australian academic STEMM workplace post-COVID: a picture of disarray ]]> https://biorxiv.org/content/10.1101/2022.12.06.519378v1?rss=1 Christian, K. Larkins, J.-a. Doran, M. R. 2022-12-07 doi:10.1101/2022.12.06.519378 Cold Spring Harbor Laboratory Press 2022-12-07 <![CDATA[ Genomic, Functional and Structural Analyses Reveal Mechanisms of Evolutionary Innovation within the Sea Anemone 8 Toxin Family ]]> https://biorxiv.org/content/10.1101/2022.12.08.518931v1?rss=1 Ashwood, L. M. Elnahriry, K. A. Stewart, Z. K. Shafee, T. M. Naseem, M. U. Szanto, T. G. van der Burg, C. A. Smith, H. L. Surm, J. M. Undheim, E. A. B. Madio, B. Hamilton, B. R. Guo, S. Wai, D. C. C. Coyne, V. L. Philips, M. J. Dudley, K. J. Hurwood, D. A. Panyi, G. King, G. F. Pavasovic, A. Norton, R. S. Prentis, P. J. 2022-12-10 doi:10.1101/2022.12.08.518931 Cold Spring Harbor Laboratory Press 2022-12-10 <![CDATA[ Transgenic mice overexpressing mutant TDP-43 show aberrant splicing of autism associated gene Zmynd11 prior to onset of motor symptoms ]]> https://biorxiv.org/content/10.1101/2022.12.11.519991v1?rss=1 Narayanan, R. Panwar, A. Butler, T. J. Cutrupi, A. N. Kennerson, M. Vucic, S. Balasubramaniem, A. Mangelsdorf, M. Wallace, R. H. 2022-12-13 doi:10.1101/2022.12.11.519991 Cold Spring Harbor Laboratory Press 2022-12-13 <![CDATA[ Probing the Biology of Zinc Alpha2-Glycoprotein and the role it plays in cachexia ]]> https://biorxiv.org/content/10.1101/2022.12.14.520465v1?rss=1 Pandit, P. G. Panigrahi, S. 2022-12-16 doi:10.1101/2022.12.14.520465 Cold Spring Harbor Laboratory Press 2022-12-16 <![CDATA[ Towards a General Approach for Bat Echolocation Detection and Classification ]]> https://biorxiv.org/content/10.1101/2022.12.14.520490v1?rss=1 Mac Aodha, O. Martinez Balvanera, S. Damstra, E. Cooke, M. Eichinski, P. Browning, E. Barataud, M. Boughey, K. Coles, R. Giacomini, G. Mac Swiney G., M. C. Obrist, M. K. Parsons, S. Sattler, T. Jones, K. 2022-12-16 doi:10.1101/2022.12.14.520490 Cold Spring Harbor Laboratory Press 2022-12-16 <![CDATA[ Formation and growth characteristics of co-culture tumour spheroids ]]> https://biorxiv.org/content/10.1101/2022.12.21.521515v1?rss=1 Murphy, R. J. Gunasingh, G. Haass, N. K. Simpson, M. J. 2022-12-22 doi:10.1101/2022.12.21.521515 Cold Spring Harbor Laboratory Press 2022-12-22 <![CDATA[ Exercise rejuvenates the skeletal muscle methylome and transcriptome in humans ]]> https://biorxiv.org/content/10.1101/2022.12.27.522062v1?rss=1 Voisin, S. Seale, K. Jacques, M. Landen, S. Harvey, N. R. Haupt, L. M. Griffiths, L. R. Ashton, K. J. Coffey, V. G. Thompson, J.-L. M. Doering, T. M. Lindholm, M. E. Walsh, C. Davison, G. Irwin, R. McBride, C. Hansson, O. Asplund, O. Heikkinen, A. E. Piirila, P. Pietilainen, K. Ollikainen, M. Blocquiaux, S. Thomis, M. Sharples, A. P. Eynon, N. 2022-12-29 doi:10.1101/2022.12.27.522062 Cold Spring Harbor Laboratory Press 2022-12-29 <![CDATA[ Latent representation of single-cell transcriptomes enables algebraic operations on cellular phenotypes ]]> https://biorxiv.org/content/10.1101/2022.12.28.522060v1?rss=1 Sengupta, D. Nelson, C. C. Bhattacharya, N. Rockstroh, A. Roquilly, A. Hollier, B. Ahuja, G. Kumar, H. Poschmann, J. Lehman, M. Thomas, S. K. Deshpande, S. S. Chawla, S. Solomon, P. Fourgeux, C. 2022-12-30 doi:10.1101/2022.12.28.522060 Cold Spring Harbor Laboratory Press 2022-12-30 <![CDATA[ A multi-omic Nicotiana benthamiana resource for fundamental research and biotechnology ]]> https://biorxiv.org/content/10.1101/2022.12.30.521993v1?rss=1 Ranawaka, B. An, J. Lorenc, M. Jung, H. Sulli, M. Aprea, G. Roden, S. Hayashi, S. Cooper, T. LeBlanc, Z. Llaca, V. Orzaez, D. Bombarely, A. Bally, J. Winefield, C. Giuliano, G. Waterhouse, P. M. 2022-12-30 doi:10.1101/2022.12.30.521993 Cold Spring Harbor Laboratory Press 2022-12-30 <![CDATA[ The maternal microbiome regulates infant respiratory disease susceptibility via intestinal Flt3L expression and plasmacytoid dendritic cell hematopoiesis ]]> https://biorxiv.org/content/10.1101/2023.01.05.522516v1?rss=1 View larger version (15K): org.highwire.dtl.DTLVardef@1a39990org.highwire.dtl.DTLVardef@1b6fe67org.highwire.dtl.DTLVardef@f8440dorg.highwire.dtl.DTLVardef@13bc67e_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Sikder, M. A. A. Rashid, R. B. Ahmed, T. Sebina, I. Howard, D. R. Ullah, M. A. Rahman, M. M. Lynch, J. P. Curren, B. Werder, R. B. Simpson, J. Bissell, A. Morrison, M. Walpole, C. Radford, K. J. Kumar, V. Woodruff, T. M. Tan, H. Ali, A. Kaiko, G. E. Upham, J. W. Hoelzle, R. D. O Cuiv, P. Holt, P. G. Dennis, P. G. Phipps, S. 2023-01-06 doi:10.1101/2023.01.05.522516 Cold Spring Harbor Laboratory Press 2023-01-06 <![CDATA[ Whole transcriptome profiling of placental pathobiology in SARS-CoV-2 pregnancies identifies a preeclampsia-like gene signature ]]> https://biorxiv.org/content/10.1101/2023.01.20.524893v1?rss=1 Stylianou, N. Sebina, I. Matigian, N. Deohler, H. Monkman, J. Rohl, J. Allenby, M. Nam, A. Pan, L. Rockstroh, A. Sadeghirad, H. Chung, K. Sobanski, T. O'Byrne, K. Rebutini, P. Z. Machado-Souza, C. Stonoga, E. T. S. Warkiani, M. E. Salomon, C. Short, K. R. McClements, L. de Noronha, L. Huang, R. Y.-J. Belz, G. Guimaraes, F. Clifton, V. Kulasinghe, A. 2023-01-21 doi:10.1101/2023.01.20.524893 Cold Spring Harbor Laboratory Press 2023-01-21 <![CDATA[ Normative Modeling of Brain Morphometry Across the Lifespan using CentileBrain: Algorithm Benchmarking and Model Optimization ]]> https://biorxiv.org/content/10.1101/2023.01.30.523509v1?rss=1 Ge, R. Yu, Y. Qi, Y. X. Fan, Y. V. Chen, S. Gao, C. Haas, S. S. Modabbernia, A. New, F. Agartz, I. Asherson, P. Ayesa-Arriola, R. Banaj, N. Banaschewski, T. Baumeister, S. Bertolino, A. Boomsma, D. I. Borgwardt, S. Bourque, J. Brandeis, D. Breier, A. Brodaty, H. Brouwer, R. M. Buckner, R. Buitelaar, J. K. Cannon, D. M. Caseras, X. Cervenka, S. Conrod, P. J. Crespo-Facorro, B. Crivello, F. Crone, E. A. de Haan, L. de Zubicaray, G. I. Di Giorgio, A. Erk, S. Fisher, S. E. Franke, B. Frodl, T. Glahn, D. C. Grotegerd, D. Gruber, O. Gruner, P. Gur, R. E. G 2023-01-31 doi:10.1101/2023.01.30.523509 Cold Spring Harbor Laboratory Press 2023-01-31 <![CDATA[ Low-dimensional dynamics of brain-muscle networks during gait ]]> https://biorxiv.org/content/10.1101/2023.02.02.526912v1?rss=1 Roeder, L. Breakspear, M. Kerr, G. K. Boonstra, T. W. 2023-02-03 doi:10.1101/2023.02.02.526912 Cold Spring Harbor Laboratory Press 2023-02-03 <![CDATA[ Bacterial suppressor-of-copper-sensitivity (Scs) proteins exhibit diverse thiol-disulfide oxidoreductase cellular functions ]]> https://biorxiv.org/content/10.1101/2023.02.07.527441v1?rss=1 Hong, Y. Qin, J. Mitchell, L. Paxman, J. J. Heras, B. Totsika, M. 2023-02-07 doi:10.1101/2023.02.07.527441 Cold Spring Harbor Laboratory Press 2023-02-07 <![CDATA[ Linguistic and attentional factors -not statistical regularities- contribute to word-selective neural responses with FPVS-oddball paradigms ]]> https://biorxiv.org/content/10.1101/2023.02.20.528973v1?rss=1 Lochy, A. Rossion, B. Lambon Ralph, M. Volfart, A. Hauk, O. Schiltz, C. 2023-02-20 doi:10.1101/2023.02.20.528973 Cold Spring Harbor Laboratory Press 2023-02-20 <![CDATA[ Active site mutations of F420-dependent alkene reductases reverse stereoselectivity ]]> https://biorxiv.org/content/10.1101/2023.02.21.529347v1?rss=1 Kang, S. W. Antoney, J. P. Lupton, D. W. Speight, R. Scott, C. Jackson, C. J. 2023-02-21 doi:10.1101/2023.02.21.529347 Cold Spring Harbor Laboratory Press 2023-02-21 <![CDATA[ Identification of further variation at the lipooligosaccharide outer core locus in Acinetobacter baumannii genomes and extension of the OCL reference sequence database for Kaptive ]]> https://biorxiv.org/content/10.1101/2023.02.23.529771v1?rss=1 Sorbello, B. Cahill, S. M. Kenyon, J. J. 2023-02-24 doi:10.1101/2023.02.23.529771 Cold Spring Harbor Laboratory Press 2023-02-24 <![CDATA[ Cross-species proteomic and microRNA comparison of extracellular vesicles in human milk, cows milk, and infant formula products: moving towards next generation infant formula products. ]]> https://biorxiv.org/content/10.1101/2023.02.23.529810v1?rss=1 Turner, N. P. Abeysinghe, P. Sadowski, P. Mitchell, M. D. 2023-02-24 doi:10.1101/2023.02.23.529810 Cold Spring Harbor Laboratory Press 2023-02-24 <![CDATA[ Identification of a Micropeptide Linked to Cancer Stem Cell Regulation and Chemoresistance ]]> https://biorxiv.org/content/10.1101/2023.03.14.532696v1?rss=1 Batra, J. Fernando, A. Liyanage, C. Janaththani, P. Srinivasan, S. 2023-03-15 doi:10.1101/2023.03.14.532696 Cold Spring Harbor Laboratory Press 2023-03-15 <![CDATA[ Extensive diversity in Escherichia coli Group 3 capsules is driven by recombination and plasmid transfer from multiple species ]]> https://biorxiv.org/content/10.1101/2023.04.05.535558v1?rss=1 Hong, Y. Qin, J. Forga, X. B. Totsika, M. 2023-04-05 doi:10.1101/2023.04.05.535558 Cold Spring Harbor Laboratory Press 2023-04-05 <![CDATA[ Second-order Citations in Altmetrics: A Case Study Analyzing the Audiences of COVID-19 Research in the News and on Social Media ]]> https://biorxiv.org/content/10.1101/2023.04.05.535734v1?rss=1 Alperin, J. P. Fleerackers, A. Riedlinger, M. Haustein, S. 2023-04-06 doi:10.1101/2023.04.05.535734 Cold Spring Harbor Laboratory Press 2023-04-06 <![CDATA[ Predicting Distant Recurrences in Invasive Breast Carcinoma Patients Using Clinicopathological Data: A cross-institutional and AI-based study ]]> https://biorxiv.org/content/10.1101/2023.04.16.537076v1?rss=1 Nagaraj, S. H. Sukhadia, S. S. Muller, K. E. Workman, A. A. 2023-04-19 doi:10.1101/2023.04.16.537076 Cold Spring Harbor Laboratory Press 2023-04-19 <![CDATA[ Fluid-Structure Interactions of Peripheral Arteries Using a Coupled in silico and in vitro Approach ]]> https://biorxiv.org/content/10.1101/2023.04.17.537257v1?rss=1 Schoenborn, S. Lorenz, T. Kuo, K.-C. Fletcher, D. F. Woodruff, M. A. Pirola, S. Allenby, M. C. 2023-04-17 doi:10.1101/2023.04.17.537257 Cold Spring Harbor Laboratory Press 2023-04-17 <![CDATA[ Pharmacological Induction of mesenchymal-epithelial transition chemosensitizes breast cancer cells and prevents metastatic progression ]]> https://biorxiv.org/content/10.1101/2023.04.19.537586v1?rss=1 Bagheri, M. Mohamed, G. A. Mohamed Saleem, M. A. Ognjenovic, N. B. Lu, H. Kolling, F. W. Wilkins, O. M. Das, S. LaCroix, I. S. Nagaraj, S. H. Muller, K. E. Gerber, S. A. Miller, T. W. Pattabiraman, D. R. 2023-04-21 doi:10.1101/2023.04.19.537586 Cold Spring Harbor Laboratory Press 2023-04-21 <![CDATA[ Imetelstat-Mediated Alterations in Fatty Acid Metabolism To Induce Ferroptosis As Therapeutic Strategy for Acute Myeloid Leukemia ]]> https://biorxiv.org/content/10.1101/2023.04.25.538357v1?rss=1 Bruedigam, C. Porter, A. H. Song, A. Vroeg in de Wei, G. Stoll, T. Straube, J. Cooper, L. Cheng, G. Kahl, V. F. S. Sobinoff, A. P. Ling, V. Y. Jebaraj, B. M. C. Janardhanan, Y. Haldar, R. Bray, L. J. Bullinger, L. Heidel, F. H. Kennedy, G. A. Hill, M. M. Pickett, H. A. Abdel-Wahab, O. Hartel, G. Lane, S. W. 2023-04-28 doi:10.1101/2023.04.25.538357 Cold Spring Harbor Laboratory Press 2023-04-28 <![CDATA[ O antigen biogenesis sensitises Escherichia coli K-12 to bile salts, a likely cause for how it lost its O antigen ]]> https://biorxiv.org/content/10.1101/2023.05.08.539823v1?rss=1 Qin, J. Hong, Y. Morona, R. Totsika, M. 2023-05-08 doi:10.1101/2023.05.08.539823 Cold Spring Harbor Laboratory Press 2023-05-08 <![CDATA[ Accelerated DNA methylation aging and increased resilience in veterans: the biological cost for soldiering on ]]> https://biorxiv.org/content/10.1101/207688v1?rss=1 Mehta, D. Bruenig, D. Lawford, B. Harvey, W. Carrillo-Roa, T. Morris, C. P. Jovanovic, T. Young, R. M. Binder, E. B. Voisey, J. 2017-10-23 doi:10.1101/207688 Cold Spring Harbor Laboratory Press 2017-10-23 <![CDATA[ Discrete and continuum approximations for collective cell migration in a scratch assay with cell size dynamics ]]> https://biorxiv.org/content/10.1101/219204v1?rss=1 Matsiaka, O. M. Penington, C. Baker, R. E. Simpson, M. 2017-11-14 doi:10.1101/219204 Cold Spring Harbor Laboratory Press 2017-11-14 <![CDATA[ Instructive starPEG-Heparin biohybrid 3D cultures for modeling human neural stem cell plasticity, neurogenesis, and neurodegeneration ]]> https://biorxiv.org/content/10.1101/225243v1?rss=1 Papadimitriou, C. Cosacak, M. I. Mashkaryan, V. Celikkaya, H. Bray, L. Bhattarai, P. Hollak, H. Chen, X. He, S. Antos, C. L. Thomas, A. Friedrichs, J. Dahl, A. Zhang, Y. Freudenberg, U. Werner, C. Kizil, C. 2017-11-27 doi:10.1101/225243 Cold Spring Harbor Laboratory Press 2017-11-27 <![CDATA[ Extended logistic growth model for heterogeneous populations ]]> https://biorxiv.org/content/10.1101/231100v1?rss=1 Jin, W. McCue, S. Simpson, M. 2017-12-08 doi:10.1101/231100 Cold Spring Harbor Laboratory Press 2017-12-08 <![CDATA[ Mathematical models for cell migration with real-time cell cycle dynamics ]]> https://biorxiv.org/content/10.1101/238303v1?rss=1 Vittadello, S. T. McCue, S. Gunasingh, G. Haass, N. Simpson, M. 2017-12-21 doi:10.1101/238303 Cold Spring Harbor Laboratory Press 2017-12-21 <![CDATA[ Longitudinal expression profiling of CD4+ and CD8+ cells in patients with active to quiescent Giant Cell Arteritis ]]> https://biorxiv.org/content/10.1101/243493v1?rss=1 De Smit, E. Lukowski, S. W. Anderson, L. Senabouth, A. Dauyey, K. Song, S. Wyse, B. Wheeler, L. Chen, C. Y. Cao, K. Yuen, A. W. T. Shuey, N. Clarke, L. Sanchez, I. L. Hung, S. S. Pebay, A. Mackey, D. A. Brown, M. A. Hewitt, A. Powell, J. E. 2018-01-05 doi:10.1101/243493 Cold Spring Harbor Laboratory Press 2018-01-05 <![CDATA[ Three-dimensional experiments and individual based simulations show that cell proliferation drives melanoma nest formation in human skin tissue ]]> https://biorxiv.org/content/10.1101/244582v1?rss=1 Haridas, P. Browning, A. McGovern, J. McElwain, S. Simpson, M. 2018-01-08 doi:10.1101/244582 Cold Spring Harbor Laboratory Press 2018-01-08 <![CDATA[ Using paired serology and surveillance data to quantify dengue transmission and control during a large outbreak in Fiji ]]> https://biorxiv.org/content/10.1101/246116v1?rss=1 Kucharski, A. J. Kama, M. Watson, C. H. Aubry, M. Funk, S. Henderson, A. D. Brady, O. Vanhomwegen, J. Manuguerra, J.-C. Lau, C. L. Edmunds, J. Aaskov, J. Nilles, E. J. Cao-Lormeau, V.-M. Hue, S. Hibberd, M. 2018-01-10 doi:10.1101/246116 Cold Spring Harbor Laboratory Press 2018-01-10 <![CDATA[ The soft explosive model of placental mammal evolution ]]> https://biorxiv.org/content/10.1101/251520v1?rss=1 Phillips, M. J. Fruciano, C. 2018-01-22 doi:10.1101/251520 Cold Spring Harbor Laboratory Press 2018-01-22 <![CDATA[ A survey on information sources used by academic researchers to evaluate scientific instruments ]]> https://biorxiv.org/content/10.1101/253799v1?rss=1 Bergenholtz, C. MacAulay, S. C. Kolympiris, C. Seim, I. 2018-01-31 doi:10.1101/253799 Cold Spring Harbor Laboratory Press 2018-01-31 <![CDATA[ Effects of Parathyroid Hormone, Alendronate and Odanacatib on the mineralisation process in intracortical and endocortical Haversian boneof ovariectomized rabbits ]]> https://biorxiv.org/content/10.1101/255703v1?rss=1 Vrahnas, C. Buenzli, P. Pearson, T. A. Pennypacker, B. L. Tobin, M. J. Bambery, K. R. Duong, L. T. Sims, N. A. 2018-01-29 doi:10.1101/255703 Cold Spring Harbor Laboratory Press 2018-01-29 <![CDATA[ Spatial moment description of birth-death-movementprocesses incorporating the effects of crowding andobstacles ]]> https://biorxiv.org/content/10.1101/267708v1?rss=1 Surendran, A. Plank, M. Simpson, M. J. 2018-02-18 doi:10.1101/267708 Cold Spring Harbor Laboratory Press 2018-02-18 <![CDATA[ Stochastic models of cell invasion with fluorescent cell cycle indicators ]]> https://biorxiv.org/content/10.1101/273995v1?rss=1 Simpson, M. J. Jin, W. Vittadello, S. T. Tambyah, T. Ryan, J. Gunasingh, G. Haass, N. McCue, S. 2018-03-01 doi:10.1101/273995 Cold Spring Harbor Laboratory Press 2018-03-01 <![CDATA[ A Bayesian sequential learning framework to parameterise continuum models of melanoma invasion into human skin ]]> https://biorxiv.org/content/10.1101/284612v1?rss=1 Browning, A. Haridas, P. Simpson, M. 2018-03-19 doi:10.1101/284612 Cold Spring Harbor Laboratory Press 2018-03-19 <![CDATA[ No effect of administration of unacylated ghrelin on subcutaneous PC3 xenograft growth in a Rag1-/- mouse model of metabolic dysfunction ]]> https://biorxiv.org/content/10.1101/328351v1?rss=1 Maugham, M. L. Chopin, L. K. Seim, I. Thomas, P. B. Crisp, G. J. Shah, E. T. Herington, A. C. Brown, K. A. Gregory, L. S. Nelson, C. C. Jeffery, P. L. 2018-05-22 doi:10.1101/328351 Cold Spring Harbor Laboratory Press 2018-05-22 <![CDATA[ Parameterising continuum models of heat transfer in heterogeneous living skin using experimental data ]]> https://biorxiv.org/content/10.1101/354563v1?rss=1 McInerney, S. Carr, E. Simpson, M. J. 2018-06-23 doi:10.1101/354563 Cold Spring Harbor Laboratory Press 2018-06-23 <![CDATA[ Haplotype-resolved and integrated genome analysis of ENCODE cell line HepG2 ]]> https://biorxiv.org/content/10.1101/378497v1?rss=1 Zhou, B. Ho, S. S. Greer, S. U. Spies, N. Bell, J. M. Zhang, X. Zhu, X. Arthur, J. G. Byeon, S. Pattni, R. Saha, I. Song, G. Ji, H. P. Perrin, D. Wong, W. H. Abyzov, A. Urban, A. E. 2018-07-27 doi:10.1101/378497 Cold Spring Harbor Laboratory Press 2018-07-27 <![CDATA[ Gene expression profiling of The Cancer Genome Atlas supports an inverse association between body mass index (BMI) and major oesophageal tumour subtypes ]]> https://biorxiv.org/content/10.1101/378778v1?rss=1 Seim, I. Jeffery, P. L. Chopin, L. K. 2018-07-28 doi:10.1101/378778 Cold Spring Harbor Laboratory Press 2018-07-28 <![CDATA[ Hippo Pathway Deregulation Drives Tissue Stiffness and Cancer Stem-like Cells in Lung Adenocarcinoma ]]> https://biorxiv.org/content/10.1101/390849v1?rss=1 Pankova, D. Jiang, Y. Vendrell, I. Buzzelli, J. Ryan, A. J. Brown, C. O'Neill, E. 2018-08-13 doi:10.1101/390849 Cold Spring Harbor Laboratory Press 2018-08-13 <![CDATA[ Mechanistic and experimental models of cell migration reveal the importance of intercellular interactions in cell invasion ]]> https://biorxiv.org/content/10.1101/391557v1?rss=1 Matisaka, O. Baker, R. Shah, E. Simpson, M. 2018-08-14 doi:10.1101/391557 Cold Spring Harbor Laboratory Press 2018-08-14 <![CDATA[ Assessment of abduction movement in older people with painful shoulder: an analysis based on inertial sensors ]]> https://biorxiv.org/content/10.1101/398123v1?rss=1 Roldan-Jimenez, C. Martin-Martin, J. Bennett, P. McPhail, S. Vargas, A. C. Kerr, G. 2018-08-22 doi:10.1101/398123 Cold Spring Harbor Laboratory Press 2018-08-22 <![CDATA[ The genetic architecture of the human cerebral cortex ]]> https://biorxiv.org/content/10.1101/399402v1?rss=1 Grasby, K. L. Jahanshad, N. Painter, J. N. Colodro-Conde, L. Bralten, J. Hibar, D. P. Lind, P. A. Pizzagalli, F. Ching, C. R. McMahon, M. A. Shatokhina, N. Zsembik, L. C. P. Agartz, I. Alhusaini, S. Almeida, M. A. Alnaes, D. Amlien, I. K. Andersson, M. Ard, T. Armstrong, N. J. Ashley-Koch, A. Bernard, M. Brouwer, R. M. Buimer, E. E. Bülow, R. Bürger, C. Cannon, D. M. Chakravarty, M. Chen, Q. Cheung, J. W. Couvy-Duchesne, B. Dale, A. M. Dalvie, S. de Araujo, T. K. de Zubicaray, G. I. de Zwarte, S. M. den Braber, A. Doan, N. T. Dohm, K. Ehrlich, S. Engel 2018-09-03 doi:10.1101/399402 Cold Spring Harbor Laboratory Press 2018-09-03 <![CDATA[ Comprehensive analysis of human hookworm secreted proteins using a proteogenomic approach ]]> https://biorxiv.org/content/10.1101/406843v1?rss=1 Logan, J. Manda, S. S. Choi, Y.-J. Field, M. Eichenberger, R. Mulvenna, J. Nagaraj, S. Fujiwara, R. Gazzinelli-Guimaraes, P. Bueno, L. Mati, V. Mitreva, M. Sotillo, J. Loukas, A. 2018-09-03 doi:10.1101/406843 Cold Spring Harbor Laboratory Press 2018-09-03 <![CDATA[ Large-scale genome-wide association meta-analysis of endometriosis reveals 13 novel loci and genetically-associated comorbidity with other pain conditions ]]> https://biorxiv.org/content/10.1101/406967v1?rss=1 Rahmioglu, N. Banasik, K. Christofidou, P. Danning, R. Galarneau, G. Giri, A. MacGregor, S. Mortlock, S. Sapkota, Y. Schork, A. J. Sobalska-Kwapis, M. Stefansdottir, L. Turman, C. Oimari, O. Adachi, S. Andrews, S. Arnadottir, R. Burgdorf, K. S. Campbell, A. Cheuk, C. S. Clementi, C. Cook, J. De Vivio, I. DiVasta, A. Dorien, O. Edwards, T. Fontanillas, P. Fung, J. N. Geirsson, R. T. Girling, J. Harris, H. R. Holdsworth-Carson, S. Houshdaran, S. Hu-Seliger, T. Jarvelin, M.-R. Kepka, E. Kulig, B. Laufer, M. R. Law, M. Low, S.-K. Mangino, M. Marciniak, B. 2018-09-07 doi:10.1101/406967 Cold Spring Harbor Laboratory Press 2018-09-07 <![CDATA[ Effects of Orientation Change during Environmental Learning on Age-Related Difference in Spatial Memory ]]> https://biorxiv.org/content/10.1101/412965v1?rss=1 Yamamoto, N. Fox, M. J. Boys, E. Ord, J. 2018-09-11 doi:10.1101/412965 Cold Spring Harbor Laboratory Press 2018-09-11 <![CDATA[ Genome-wide association study of suicide attempt in psychiatric disorders identifies association with major depression polygenic risk scores ]]> https://biorxiv.org/content/10.1101/416008v1?rss=1 Mullins, N. Bigdeli, T. B. Borglum, A. Coleman, J. R. Demontis, D. Fanous, A. Mehta, D. Power, R. A. Ripke, S. Stahl, E. Starnawska, A. Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium, Bipolar Disorder Working Group of the Psychiatric Genomics Consortium, Schizophrenia Working Group of the Psychiatric Genomics Consortium, Kendler, K. S. McQuillin, A. Lewis, C. M. 2018-09-14 doi:10.1101/416008 Cold Spring Harbor Laboratory Press 2018-09-14 <![CDATA[ Optimal control of acute myeloid leukaemia ]]> https://biorxiv.org/content/10.1101/429811v1?rss=1 Sharp, J. Browning, A. Mapder, T. Burrage, K. Simpson, M. 2018-09-28 doi:10.1101/429811 Cold Spring Harbor Laboratory Press 2018-09-28 <![CDATA[ A free boundary model of epithelial dynamics ]]> https://biorxiv.org/content/10.1101/433813v1?rss=1 Baker, R. E. Parker, A. Simpson, M. J. 2018-10-13 doi:10.1101/433813 Cold Spring Harbor Laboratory Press 2018-10-13 <![CDATA[ Using experimental data and information criteria to guide model selection for reaction--diffusion problems in mathematical biology ]]> https://biorxiv.org/content/10.1101/444679v1?rss=1 Warne, D. Baker, R. Simpson, M. 2018-10-16 doi:10.1101/444679 Cold Spring Harbor Laboratory Press 2018-10-16 <![CDATA[ Largest genome-wide association study for PTSD identifies genetic risk loci in European and African ancestries and implicates novel biological pathways ]]> https://biorxiv.org/content/10.1101/458562v1?rss=1 Nievergelt, C. M. Maihofer, A. X. Klengel, T. Atkinson, E. G. Chen, C.-Y. Choi, K. W. Coleman, J. R. I. Dalvie, S. Duncan, L. E. Logue, M. W. Provost, A. Ratanatharathorn, A. Stein, M. B. Torres, K. Aiello, A. E. Almli, L. M. Amstadter, A. B. Andersen, S. B. Andreassen, O. A. Arbisi, P. A. Ashley-Koch, A. E. Austin, S. B. Avdibegovic, E. Babic, D. Baekvad-Hansen, M. Baker, D. G. Beckham, J. C. Bierut, L. J. Bisson, J. I. Boks, M. P. Bolger, E. A. Borglum, A. D. Bradley, B. Brashear, M. Breen, G. Bryant, R. A. Bustamante, A. C. Bybjerg-Grauholm, J. Calabres 2018-11-01 doi:10.1101/458562 Cold Spring Harbor Laboratory Press 2018-11-01 <![CDATA[ Epigenome-wide meta-analysis of blood DNA methylation and its association with subcortical volumes: findings from the ENIGMA Epigenetics Working Group ]]> https://biorxiv.org/content/10.1101/460444v1?rss=1 Jia, T. Chu, C. Liu, Y. van Dongen, J. Armstrong, N. J. Bastin, M. E. Carrillo-Roa, T. den Braber, A. Harris, M. Jansen, R. Liu, J. Luciano, M. Ori, A. P. S. Roiz Santianez, R. Ruggeri, B. Sarkisyan, D. Shin, J. Sungeun, K. Tordesillas Gutierrez, D. van't Ent, D. Ames, D. Artiges, E. Bakalkin, G. Banaschewski, T. Bokde, A. L. W. Brodaty, H. Bromberg, U. Brouwer, R. Buchel, C. Burke Quinlan, E. Cahn, W. de Zubicaray, G. I. Ekstrom, T. J. Flor, H. Frohner, J. H. Frouin, V. Garavan, H. Gowland, P. Heinz, A. Ittermann, B. Jahanshad, N. Jiang, J. Kwok, J. 2018-11-05 doi:10.1101/460444 Cold Spring Harbor Laboratory Press 2018-11-05 <![CDATA[ Spatial structure arising from chase-escape interactions with crowding ]]> https://biorxiv.org/content/10.1101/470799v1?rss=1 Surendran, A. Plank, M. Simpson, M. 2018-11-14 doi:10.1101/470799 Cold Spring Harbor Laboratory Press 2018-11-14 <![CDATA[ Prediction-error signals to violated expectations about person identity and head orientation are doubly-dissociated across the dorsal and ventral visual streams ]]> https://biorxiv.org/content/10.1101/471276v1?rss=1 Robinson, J. E. Woods, W. Leung, S. Kaufman, J. Breakspear, M. Young, A. W. Johnston, P. J. 2018-11-19 doi:10.1101/471276 Cold Spring Harbor Laboratory Press 2018-11-19 <![CDATA[ The Biology of Risk-On. Decreasing Inflammatory and Stress Responses on a London Trading Floor ]]> https://biorxiv.org/content/10.1101/473157v1?rss=1 Xie, N. Page, L. Granger, D. Coates, J. M. 2018-11-24 doi:10.1101/473157 Cold Spring Harbor Laboratory Press 2018-11-24 <![CDATA[ A population of bang-bang switches of defective interfering particles makes within-host dynamics of dengue virus controllable ]]> https://biorxiv.org/content/10.1101/479527v1?rss=1 Mapder, T. Clifford, S. Aaskov, J. Burrage, K. 2018-11-26 doi:10.1101/479527 Cold Spring Harbor Laboratory Press 2018-11-26 <![CDATA[ An individual-based mechanical model of cell movement in heterogeneous tissues and its coarse-grained approximation ]]> https://biorxiv.org/content/10.1101/485276v1?rss=1 Murphy, R. Buenzli, P. Baker, r. E. Simpson, M. J. 2018-12-03 doi:10.1101/485276 Cold Spring Harbor Laboratory Press 2018-12-03 <![CDATA[ A benchmark of computational CRISPR-Cas9 guide design methods ]]> https://biorxiv.org/content/10.1101/498782v1?rss=1 Bradford, J. Perrin, D. 2018-12-20 doi:10.1101/498782 Cold Spring Harbor Laboratory Press 2018-12-20 <![CDATA[ HLA alleles associated with risk of ankylosing spondylitis and rheumatoid arthritis influence the gut microbiome ]]> https://biorxiv.org/content/10.1101/517813v1?rss=1 Asquith, M. Sternes, P. R. Costello, M.-E. Karstens, L. Diamond, S. Martin, T. M. Spector, T. D. le Cao, K.-A. Rosenbaum, J. T. Brown, M. A. 2019-01-11 doi:10.1101/517813 Cold Spring Harbor Laboratory Press 2019-01-11 <![CDATA[ Superadditive and subadditive dynamics are not inherent to the types of interacting threat ]]> https://biorxiv.org/content/10.1101/522755v1?rss=1 Haller-Bull, V. Bode, M. 2019-01-16 doi:10.1101/522755 Cold Spring Harbor Laboratory Press 2019-01-16 <![CDATA[ The effectiveness and cost effectiveness of a hospital avoidance program in a residential aged care facility ]]> https://biorxiv.org/content/10.1101/523969v1?rss=1 Carter, H. Lee, X. Dwyer, T. Jeffrey, D. O'Neill, B. Doran, C. Parkinson, L. Osborne, S. Reid-Searl, K. Graves, N. 2019-01-18 doi:10.1101/523969 Cold Spring Harbor Laboratory Press 2019-01-18 <![CDATA[ Validity and internal consistency of EQ-5D-3L quality of life tool among pre-dialysis patients with chronic kidney disease in Sri Lanka, a lower middle-income country ]]> https://biorxiv.org/content/10.1101/524603v1?rss=1 Senanayake, S. Mahesh, P. Gunawardena, N. Graves, N. Kularatna, S. 2019-01-20 doi:10.1101/524603 Cold Spring Harbor Laboratory Press 2019-01-20 <![CDATA[ A chromosome-level genome of black rockfish, Sebastes schlegelii, provides insights into the evolution of live birth ]]> https://biorxiv.org/content/10.1101/527036v1?rss=1 He, Y. Chang, Y. Bao, L. Yu, M. Li, R. Niu, J. Fan, G. Song, W. Seim, I. Qin, Y. Li, X. Liu, J. Kong, X. Peng, M. Sun, M. Wang, M. Qu, J. Wang, X. Liu, X. Wu, X. Zhao, X. Wang, X. Zhao, Y. Guo, J. Liu, Y. Liu, K. Wang, Y. Zhang, H. Liu, L. Wang, M. Yu, H. Wang, X. Cheng, J. Wang, Z. Xu, X. Wang, J. Yang, H. Lee, S. M.-Y. Liu, X. Zhang, Q. Qi, J. 2019-01-22 doi:10.1101/527036 Cold Spring Harbor Laboratory Press 2019-01-22 <![CDATA[ Process noise distinguishes between indistinguishable population dynamics ]]> https://biorxiv.org/content/10.1101/533182v1?rss=1 Simpson, M. Ryan, J. McGree, J. Baker, R. E. 2019-01-29 doi:10.1101/533182 Cold Spring Harbor Laboratory Press 2019-01-29 <![CDATA[ An Event-Related Potential Study of Onset Primacy in Visual Change Detection ]]> https://biorxiv.org/content/10.1101/539932v1?rss=1 Van Pelt, J. Donaldson, M. J. Johnston, P. Yamamoto, N. 2019-02-04 doi:10.1101/539932 Cold Spring Harbor Laboratory Press 2019-02-04 <![CDATA[ Mathematical models incorporating a multi-stage cell cycle explain synchronisation in proliferation experiments ]]> https://biorxiv.org/content/10.1101/557702v1?rss=1 Vittadello, S. McCue, S. Gunasingh, G. Haass, N. Simpson, M. 2019-02-22 doi:10.1101/557702 Cold Spring Harbor Laboratory Press 2019-02-22 <![CDATA[ A rare SMAD9 mutation identifies the BMP signalling pathway as a potential osteoanabolic target ]]> https://biorxiv.org/content/10.1101/560565v1?rss=1 C, p.Leu22Pro) segregating with HBM in an autosomal dominant family. The same mutation was identified in another two unrelated individuals with HBM. In-silico protein modelling predicts the mutation severely disrupts the MH1 DNA-binding domain of SMAD9. Affected individuals have bone mineral density [BMD] Z-Scores +3 to +5, with increased volumetric cortical and trabecular BMD, increased cortical thickness, and low/normal bone turnover. Fractures and nerve compressions are not seen. Both genome-wide, and gene-based association testing of heel estimated-BMD in >362,924 UK-Biobank British subjects showed strong associations with SMAD9 (PGWAS=6x10-16; PGENE =8x10-17). Smad9 is highly expressed in murine osteocytes and zebrafish bone tissue. Our findings support SMAD9 as a novel HBM gene, and a potential novel osteoanabolic target. ]]> Gregson, C. L. Bergen, D. Leo, P. Sessions, R. B. Wheeler, L. Hartley, A. Youlten, S. Croucher, P. I. McInerney-Leo, A. M. Fraser, W. Tang, J. C. Anderson, L. Marshall, M. Sergot, L. Paternoster, L. Davey Smith, G. The AOGC Consortium, Brown, M. A. Hammond, C. Kemp, J. P. Tobias, J. H. Duncan, E. L. 2019-02-25 doi:10.1101/560565 Cold Spring Harbor Laboratory Press 2019-02-25 <![CDATA[ Brain Aging in Major Depressive Disorder: Results from the ENIGMA Major Depressive Disorder working group ]]> https://biorxiv.org/content/10.1101/560623v1?rss=1 Han, L. K. Dinga, R. Hahn, T. Ching, C. Eyler, L. Aftanas, L. Aghajani, M. Aleman, A. Baune, B. Berger, K. Brak, I. Busatto Filho, G. Carballedo, A. Connolly, C. Couvy-Duchesne, B. Cullen, K. Dannlowski, U. Davey, C. Dima, D. Duran, F. Enneking, V. Filimonova, E. Frenzel, S. Frodl, T. Fu, C. Godlewska, B. Gotlib, I. Grabe, H. Groenewold, N. Grotegerd, D. Gruber, O. Hall, G. Harrison, B. Hatton, S. Hermesdorf, M. Hickie, I. Ho, T. Hosten, N. Jansen, A. Kahler, C. Kircher, T. Klimes-Dougan, B. Kramer, B. Krug, A. Lagopoulos, J. Leenings, R. MacMaster 2019-02-26 doi:10.1101/560623 Cold Spring Harbor Laboratory Press 2019-02-26 <![CDATA[ KLK4 inhibition by cyclic and acyclic peptides: structural and dynamical insights into standard-mechanism protease inhibitors ]]> https://biorxiv.org/content/10.1101/570390v1?rss=1 Riley, B. T. Ilyichova, O. de Veer, S. swedberg, J. Wilson, E. Hoke, D. E. Harris, J. Buckle, A. 2019-03-08 doi:10.1101/570390 Cold Spring Harbor Laboratory Press 2019-03-08 <![CDATA[ Shotgun metagenomics reveals an enrichment of potentially cross-reactive bacterial epitopes in ankylosing spondylitis patients, as well as the effects of TNFi therapy and the host’s genotype upon microbiome composition ]]> https://biorxiv.org/content/10.1101/571430v1?rss=1 Yin, J. Sternes, P. R. Wang, M. Morrison, M. Song, J. Li, T. Zhou, L. Wu, X. He, F. Zhu, J. Brown, M. A. Xu, H. 2019-03-08 doi:10.1101/571430 Cold Spring Harbor Laboratory Press 2019-03-08 <![CDATA[ The genetic architecture of sporadic and recurrent miscarriage ]]> https://biorxiv.org/content/10.1101/575167v1?rss=1 Laisk, T. Soares, A. L. G. Ferreira, T. Painter, J. N. Laber, S. Bacelis, J. Chen, C.-Y. Lepamets, M. Lin, K. Liu, S. Millwood, I. Y. Ramu, A. Southcombe, J. Andersen, M. S. Yang, L. Becker, C. M. Gordon, S. D. Byberg-Grauholm, J. Helgeland, O. Hougaard, D. M. Jin, X. Johansson, S. Juodakis, J. Kartsonaki, C. Kukushkina, V. Lind, P. A. Metspalu, A. Montgomery, G. W. Morris, A. P. Mortensen, P. B. Njolstad, P. R. Nyholt, D. R. Lippincott, M. Seminara, S. Salumets, A. Snieder, H. Zondervan, K. Chen, Z. Conrad, D. F. Jacobsson, B. Li, L. Martin, N. G. Nea 2019-03-12 doi:10.1101/575167 Cold Spring Harbor Laboratory Press 2019-03-12 <![CDATA[ Nitroxide functionalized antibiotics are promising eradication agents against Staphylococcus aureus biofilms. ]]> https://biorxiv.org/content/10.1101/579896v1?rss=1 Verderosa, A. D. Dhouib, R. Fairfull-Smith, K. E. Totsika, M. 2019-03-16 doi:10.1101/579896 Cold Spring Harbor Laboratory Press 2019-03-16 <![CDATA[ Predicting sediment and nutrient concentrations from high-frequency water-quality data ]]> https://biorxiv.org/content/10.1101/599712v1?rss=1 Leigh, C. Kandanaarachchi, S. McGree, J. M. Hyndman, R. J. Alsibai, O. Mengersen, K. Peterson, E. E. 2019-04-04 doi:10.1101/599712 Cold Spring Harbor Laboratory Press 2019-04-04 <![CDATA[ Chemical biofilm dislodgement with chelating and reducing agents in comparison to sonication: implications for the diagnosis of implant associated infection ]]> https://biorxiv.org/content/10.1101/604637v1?rss=1 Karbysheva, S. Butini, M. E. Di Luca, M. Winkler, T. Schuetz, M. Trampuz, A. 2019-04-11 doi:10.1101/604637 Cold Spring Harbor Laboratory Press 2019-04-11 <![CDATA[ A genetic hazard score to personalize prostate cancer screening, applied to population data ]]> https://biorxiv.org/content/10.1101/619718v1?rss=1 Huynh-Le, M.-P. Fan, C. C. Karunamuni, R. Walsh, E. I. Turner, E. L. Lane, J. A. Martin, R. M. Neal, D. E. Donovan, J. L. Hamdy, F. C. Parsons, J. K. Eeles, R. A. Easton, D. F. Kote-Jarai, Z. Amin Al Olama, A. Benlloch Garcia, S. Muir, K. Gronberg, H. Wiklund, F. Aly, M. Schleutker, J. Sipeky, C. Tammela, T. L. Nordestgaard, B. G. Key, T. J. Travis, R. C. Pharoah, P. Pashayan, N. Khaw, K.-T. Thibodeau, S. N. McDonnell, S. K. Schaid, D. J. Maier, C. Vogel, W. Luedeke, M. Herkommer, K. Kibel, A. S. Cybulski, C. Wokolorczyk, D. Kluzniak, W. Cannon-Albright, 2019-04-26 doi:10.1101/619718 Cold Spring Harbor Laboratory Press 2019-04-26 <![CDATA[ Learning supervised embeddings for large scale sequence comparisons ]]> https://biorxiv.org/content/10.1101/620153v1?rss=1 Kimothi, D. Biyani, P. Hogan, J. M. Soni, A. Kelly, W. 2019-04-26 doi:10.1101/620153 Cold Spring Harbor Laboratory Press 2019-04-26 <![CDATA[ Corticomuscular control of walking in older people and people with Parkinson’s disease ]]> https://biorxiv.org/content/10.1101/628016v1?rss=1 Roeder, L. Boonstra, T. W. Kerr, G. K. 2019-05-05 doi:10.1101/628016 Cold Spring Harbor Laboratory Press 2019-05-05 <![CDATA[ Homoploid hybridization signals due to ancestral subdivision: a case study on the D lineage in wheat ]]> https://biorxiv.org/content/10.1101/628685v1?rss=1 Jiang, Y. Yuan, Z. Hu, H. Ye, X. Zheng, Z. Wei, Y. Zheng, Y.-L. Wang, Y.-G. Liu, C. 2019-05-05 doi:10.1101/628685 Cold Spring Harbor Laboratory Press 2019-05-05 <![CDATA[ Amplification of the V5 - V8 region of the 16S rRNA gene effectively speciates medically important genital tract Lactobacillus species in the upper female genital tract ]]> https://biorxiv.org/content/10.1101/630004v1?rss=1 O'Callaghan, J. L. Willner, D. Buttini, M. Huygens, F. Pelzer, E. S. 2019-05-07 doi:10.1101/630004 Cold Spring Harbor Laboratory Press 2019-05-07 <![CDATA[ The rapid regenerative response of a model sea anemone species Exaiptasia pallida is characterised by tissue plasticity and highly coordinated cell communication ]]> https://biorxiv.org/content/10.1101/644732v1?rss=1 van der Burg, C. A. Pavasovic, A. Gilding, E. K. Pelzer, E. S. Surm, J. M. Walsh, T. P. Prentis, P. J. 2019-05-24 doi:10.1101/644732 Cold Spring Harbor Laboratory Press 2019-05-24 <![CDATA[ Using virtual reality and thermal imagery to improve statistical modelling of vulnerable and protected species ]]> https://biorxiv.org/content/10.1101/645291v1?rss=1 Leigh, C. Heron, G. Wilson, E. Gregory, T. Clifford, S. Holloway, J. McBain, M. Gonzalez, F. McGree, J. Brown, R. Mengersen, K. Peterson, E. E. 2019-05-21 doi:10.1101/645291 Cold Spring Harbor Laboratory Press 2019-05-21 <![CDATA[ Numerical Investigation of Drug Transport from Blood Vessels to Tumor Tissue Using a Tumor-Vasculature-on-a-Chip ]]> https://biorxiv.org/content/10.1101/652099v1?rss=1 Li, W. Wang, H.-F. Li, Z.-Y. Wang, T. Zhao, C.-X. 2019-05-28 doi:10.1101/652099 Cold Spring Harbor Laboratory Press 2019-05-28 <![CDATA[ Optimizing functional groups in ecosystem models: Case study of the Great Barrier Reef ]]> https://biorxiv.org/content/10.1101/655076v1?rss=1 Haller-Bull, V. Rovenskaya, E. 2019-05-31 doi:10.1101/655076 Cold Spring Harbor Laboratory Press 2019-05-31 <![CDATA[ Spatial and epidemiologic features of dengue in Sabah, Malaysia ]]> https://biorxiv.org/content/10.1101/657031v1?rss=1 Murphy, A. Rajahram, G. S. Jilip, J. Maluda, M. William, T. Hu, W. Reid, S. Devine, G. J. Frentiu, F. D. 2019-05-31 doi:10.1101/657031 Cold Spring Harbor Laboratory Press 2019-05-31 <![CDATA[ Perlin Noise Generation of Physiologically Realistic Patterns of Fibrosis ]]> https://biorxiv.org/content/10.1101/668848v1?rss=1 Jakes, D. Burrage, K. Drovandi, C. C. Burrage, P. Bueno-Orovio, A. dos Santos, R. W. Rodriguez, B. Lawson, B. A. J. 2019-06-19 doi:10.1101/668848 Cold Spring Harbor Laboratory Press 2019-06-19 <![CDATA[ Revisiting the Fisher-KPP equation to interpret the spreading-extinction dichotomy ]]> https://biorxiv.org/content/10.1101/673202v1?rss=1 El-Hachem, M. McCue, S. Jin, W. Du, Y. Simpson, M. J. 2019-06-16 doi:10.1101/673202 Cold Spring Harbor Laboratory Press 2019-06-16 <![CDATA[ Inorganic salts and compatible solutes help mesophilic bacteria inhabit the high temperature waters of a Trans-Himalayan sulfur-borax spring ]]> https://biorxiv.org/content/10.1101/678680v1?rss=1 45{degrees}C. We, therefore, hypothesized that native geomicrobial factors could be potent determinants of the microbial habitability of hot spring environments. To test this hypothesis, aquatic microbial communities were revealed metataxonomically, and considered in the context of spring-water chemistry, along the 85-14{degrees}C hydrothermal gradient of a sulfur-boron spring named Lotus Pond located at 4,436 m, within the Puga geothermal area of the Indian Trans-Himalayan region of Ladakh. Water samples were studied from four distinct sites along Lotus Ponds spring-water transit from the vent to an adjacent river called Rulang. Insinuations obtained from geomicrobiological data were tested via pure-culture growth experiments in habitat-inspired media. Microbial diversities were found to be high at all the sample-sites; majority of the genera identified at the 70-85{degrees}C sites were found to have no report of laboratory growth at >45{degrees}C; concurrently, these sample-sites had high concentrations of the kosmotropic solutes boron, lithium, sodium, sulfide, thiosulfate and sulfate, which are known to biophysically stabilize macromolecules. Based on the universal thermodynamic status of these solutes, we conjectured that they may be instrumental in helping mesophiles withstand high in situ temperatures. Corroboratively, growth experiments with a mesophilic, 80{degrees}C-isolate, Paracoccus SMMA_5 showed that at 50{degrees}C and 70{degrees}C, depending on the incubation-time, lithium/boron/sulfate/sodium/glycine-betaine either increases the number of colony-forming units present in the culture or arrests decline of the same. Incubations at 70{degrees}C, followed by fluorescein diacetate staining and flow cytometry, showed that these solutes keep more cells under viable condition than in ready-to-divide state. We concluded that kosmotropes and compatible solutes help mesophiles overcome the chaotropic effects of heat by augmenting such indigenous, entropy-minimizing biophysical mechanisms that apparently trade-off cell division for cell viability. ]]> Mondal, N. Roy, C. Peketi, A. Alam, M. Mapder, T. Mandal, S. Fernandes, S. Bhattacharya, S. Rameez, M. J. Haldar, P. K. Volvoikar, S. P. Nandi, N. Bhattacharya, T. Mazumdar, A. Chakraborty, R. Ghosh, W. 2019-06-21 doi:10.1101/678680 Cold Spring Harbor Laboratory Press 2019-06-21 <![CDATA[ The effect of sample size on polygenic hazard models for prostate cancer ]]> https://biorxiv.org/content/10.1101/679092v1?rss=1 Karunamuni, R. Huynh-Le, M.-P. Fan, C. Eeles, R. Easton, D. Kote-Jarai, Z. Al Olama, A. A. Garcia, S. Muir, K. Gronberg, H. Wiklund, F. Aly, M. Schleutker, J. Sipeky, C. Tammela, T. Nordestgaard, B. Key, T. Travis, R. Neal, D. Donovan, J. Hamdy, F. Pharoah, P. Pashayan, N. Khaw, K.-T. Thibodeau, S. McDonnell, S. Schaid, D. Maier, C. Vogel, W. Luedeke, M. Herkommer, K. Kibel, A. Cybulski, C. Wokolorczyk, D. Kluzniak, W. Cannon-Albright, L. Brenner, H. Schöttker, B. Holleczek, B. Park, J. Sellers, T. Lin, H.-Y. Slavov, C. Kaneva, R. Mitev, V. Batra, 2019-06-21 doi:10.1101/679092 Cold Spring Harbor Laboratory Press 2019-06-21 <![CDATA[ Cell-type specific analysis of heterogeneous methylation signal using a Bayesian model-based approach ]]> https://biorxiv.org/content/10.1101/682070v1?rss=1 Kennedy, D. W. White, N. M. Benton, M. C. Lea, R. A. Mengersen, K. 2019-06-26 doi:10.1101/682070 Cold Spring Harbor Laboratory Press 2019-06-26 <![CDATA[ The long non-coding RNA GHSROS reprograms prostate cancer cell lines toward a more aggressive phenotype ]]> https://biorxiv.org/content/10.1101/682203v1?rss=1 Thomas, P. B. Jeffery, P. L. Gahete, M. D. Whiteside, E. J. Walpole, C. Maugham, M. L. Jovanovic, L. Gunter, J. H. Williams, E. D. Nelson, C. C. Herington, A. C. Luque, R. M. Veedu, R. N. Chopin, L. K. Seim, I. 2019-06-26 doi:10.1101/682203 Cold Spring Harbor Laboratory Press 2019-06-26 <![CDATA[ The chromatin remodeler SMARCD3 regulates cell cycle progression and its expression predicts survival outcome in ER+ breast cancer ]]> https://biorxiv.org/content/10.1101/684217v1?rss=1 Tropee, R. de la Pena Avalos, B. L. Gough, M. Snell, C. Duijf, P. H. G. Dray, E. 2019-07-02 doi:10.1101/684217 Cold Spring Harbor Laboratory Press 2019-07-02 <![CDATA[ Extraction of common task features in EEG-fMRI data using coupled tensor-tensor decomposition ]]> https://biorxiv.org/content/10.1101/685941v1?rss=1 Jonmohamadi, Y. Muthukumaraswamy, S. Chen, J. Roberts, J. Crowford, R. Pandey, A. 2019-07-02 doi:10.1101/685941 Cold Spring Harbor Laboratory Press 2019-07-02 <![CDATA[ Accurate and efficient discretisations for stochastic models of cell migration and cell proliferation with crowding ]]> https://biorxiv.org/content/10.1101/686030v1?rss=1 Fadai, N. T. Baker, R. E. Simpson, M. J. 2019-06-28 doi:10.1101/686030 Cold Spring Harbor Laboratory Press 2019-06-28 <![CDATA[ Continuum descriptions of spatial spreading for heterogeneous cell populations: theory and experiment ]]> https://biorxiv.org/content/10.1101/705434v1?rss=1 Matsiaka, O. Baker, R. Simpson, M. J. 2019-07-17 doi:10.1101/705434 Cold Spring Harbor Laboratory Press 2019-07-17 <![CDATA[ Modulating the unfolded protein response: Impacts of radiation on the response of prostate cancer cells to ONC201 ]]> https://biorxiv.org/content/10.1101/710400v1?rss=1 Amoroso, F. Glass, K. Liberal, F. Steele, R. Maguire, S. Tarapore, R. Allen, J. Van Schaeybroeck, S. Butterworth, K. Prise, K. O'Sullivan, J. Jain, S. Waugh, D. Mills, I. 2019-07-31 doi:10.1101/710400 Cold Spring Harbor Laboratory Press 2019-07-31 <![CDATA[ Modelling Osteocyte Network Formation: Healthy and Cancerous Environments ]]> https://biorxiv.org/content/10.1101/729046v1?rss=1 Taylor-King, J. Buenzli, P. Chapman, S. J. Lynch, C. C. Basanta, D. 2019-08-08 doi:10.1101/729046 Cold Spring Harbor Laboratory Press 2019-08-08 <![CDATA[ Modelling the effects of leaky predator-exclusion fences and their surrounding halo ]]> https://biorxiv.org/content/10.1101/737924v1?rss=1 Agarwal, K. Bode, M. 2019-08-16 doi:10.1101/737924 Cold Spring Harbor Laboratory Press 2019-08-16 <![CDATA[ Hedgehog signaling regulates neurogenesis in the larval and adult zebrafish hypothalamus ]]> https://biorxiv.org/content/10.1101/740613v1?rss=1 Male, I. Ozacar, A. T. Fagan, R. R. Loring, M. D. Shen, M.-C. Pace, V. Devine, C. A. Lutservitz, A. Karlstrom, R. O. 2019-08-26 doi:10.1101/740613 Cold Spring Harbor Laboratory Press 2019-08-26 <![CDATA[ Estimating a novel stochastic model for within-field disease dynamics of banana bunchy top virus via approximate Bayesian computation ]]> https://biorxiv.org/content/10.1101/762765v1?rss=1 Varghese, A. Drovandi, C. Mira, A. Mengersen, K. 2019-09-09 doi:10.1101/762765 Cold Spring Harbor Laboratory Press 2019-09-09 <![CDATA[ Unpacking the Allee effect: determining individual-level mechanisms that drive global population dynamics ]]> https://biorxiv.org/content/10.1101/774000v1?rss=1 Fadai, N. T. Johnston, S. T. Simpson, M. J. 2019-09-18 doi:10.1101/774000 Cold Spring Harbor Laboratory Press 2019-09-18 <![CDATA[ The reliability and heritability of cortical folds and their genetic correlations across hemispheres. ]]> https://biorxiv.org/content/10.1101/795591v1?rss=1 3,000), and one cohort of largely unrelated individuals (N~9,000) to examine the robustness of our findings. Reliability was high (interquartile range for ICC: 0.65-0.85) for sulcal metrics. Most sulcal measures were moderately to highly heritable (heritability estimates = 0.3-0.7). These genetic influences vary regionally, with the earlier forming sulci having higher heritability estimates. The central sulcus, the subcallosal and the collateral fissure were the most highly heritable regions. For some frontal and temporal sulci, left and right genetic influences did not completely overlap, suggesting some lateralization of genetic effects on the cortex. ]]> Pizzagalli, F. Auzias, G. Yang, Q. Mathias, S. R. Faskowitz, J. Boyd, J. Amini, A. Riviere, D. McMahon, K. L. de Zubicaray, G. I. Martin, N. G. Mangin, J.-F. Glahn, D. C. Blangero, J. Wright, M. J. Thompson, P. M. Kochunov, P. Jahanshad, N. 2019-10-07 doi:10.1101/795591 Cold Spring Harbor Laboratory Press 2019-10-07 <![CDATA[ Examining go-or-grow using fluorescent cell-cycle indicators and cell cycle-inhibiting drugs ]]> https://biorxiv.org/content/10.1101/797142v1?rss=1 Vittadello, S. T. McCue, S. W. Gunasingh, G. Haass, N. K. Simpson, M. J. 2019-10-08 doi:10.1101/797142 Cold Spring Harbor Laboratory Press 2019-10-08 <![CDATA[ Identifying density-dependent interactions in collective cell behaviour ]]> https://biorxiv.org/content/10.1101/811257v1?rss=1 Browning, A. P. Jin, W. Plank, M. J. Simpson, M. J. 2019-10-20 doi:10.1101/811257 Cold Spring Harbor Laboratory Press 2019-10-20 <![CDATA[ Small-scale spatial structure influences large-scale invasion rates ]]> https://biorxiv.org/content/10.1101/814582v1?rss=1 Plank, M. J. Simpson, M. J. Binny, R. N. 2019-10-22 doi:10.1101/814582 Cold Spring Harbor Laboratory Press 2019-10-22 <![CDATA[ An epigenetic clock for skeletal muscle ]]> https://biorxiv.org/content/10.1101/821009v1?rss=1 Voisin, S. Harvey, N. R. Haupt, L. M. Griffiths, L. R. Ashton, K. J. Coffey, V. G. Doering, T. M. Benedict, C. Cedernaes, J. Lindholm, M. E. Craig, J. M. Rowlands, D. S. Sharples, A. P. Horvath, S. Eynon, N. 2019-11-11 doi:10.1101/821009 Cold Spring Harbor Laboratory Press 2019-11-11 <![CDATA[ Software for detecting heterogeneous evolutionary processes across aligned sequence data ]]> https://biorxiv.org/content/10.1101/828996v1?rss=1 Jermiin, L. S. Lovell, D. R. Misof, B. Foster, P. G. Robinson, J. 2019-11-04 doi:10.1101/828996 Cold Spring Harbor Laboratory Press 2019-11-04 <![CDATA[ Genome-wide association study identifies 49 common genetic variants associated with handedness. ]]> https://biorxiv.org/content/10.1101/831321v1?rss=1 Cuellar Partida, G. Tung, J. Y. Eriksson, N. Albrecht, E. Aliev, F. Andreassen, O. A. Barroso, I. Beckmann, J. S. Boks, M. P. Boomsma, D. I. Boyd, H. A. Breteler, M. M. Campbell, H. Chasman, D. I. Cherkas, L. F. Davies, G. de Geus, E. J. Deary, I. J. Deloukas, P. Dick, D. M. Duffy, D. L. Eriksson, J. G. Esko, T. Feenstra, B. Geller, F. Gieger, C. Giegling, I. Gordon, S. D. Han, J. Hansen, T. F. Hartmann, A. M. Heikkila, K. Hicks, A. A. Hayward, C. Hirschhorn, J. N. Hottenga, J.-J. Huffman, J. E. Hwang, L.-D. Ikram, M. A. Kaprio, J. Kemp, J. P. Khaw, K.- 2019-11-07 doi:10.1101/831321 Cold Spring Harbor Laboratory Press 2019-11-07 <![CDATA[ Administration of defective virus via bang-bang optimal control inhibits dengue transmission ]]> https://biorxiv.org/content/10.1101/837849v1?rss=1 Mapder, t. Aaskov, J. Burrage, K. 2019-11-11 doi:10.1101/837849 Cold Spring Harbor Laboratory Press 2019-11-11 <![CDATA[ Parameter identifiability analysis for spatiotemporal models of cell invasion ]]> https://biorxiv.org/content/10.1101/839282v1?rss=1 Simpson, M. J. Baker, r. E. Vittadello, S. T. Maclaren, O. 2019-11-12 doi:10.1101/839282 Cold Spring Harbor Laboratory Press 2019-11-12 <![CDATA[ Designing combination therapies using multiple optimal controls ]]> https://biorxiv.org/content/10.1101/850693v1?rss=1 Sharp, J. A. Browning, A. P. Mapder, T. Baker, C. M. Burrage, K. Simpson, M. J. 2019-11-21 doi:10.1101/850693 Cold Spring Harbor Laboratory Press 2019-11-21 <![CDATA[ Micro-pellet culture reveals that bone marrow mesenchymal stromal cell (BMSC) chondrogenic induction is triggered by a single day of TGF-β1 exposure ]]> https://biorxiv.org/content/10.1101/853556v1?rss=1 Futrega, K. Robey, P. G. Klein, T. J. Crawford, R. Doran, M. R. 2019-11-26 doi:10.1101/853556 Cold Spring Harbor Laboratory Press 2019-11-26 <![CDATA[ Identification of Acinetobacter baumannii loci for capsular polysaccharide (KL) and lipooligosaccharide outer core (OCL) synthesis in genome assemblies using curated reference databases compatible with Kaptive ]]> https://biorxiv.org/content/10.1101/869370v1?rss=1 630 assembled A. baumannii draft genomes for which the KL and OCL regions had been previously typed manually, and b) 3386 A. baumannii genome assemblies downloaded from NCBI. Among the previously typed genomes, Kaptive was able to confidently assign KL and OCL types with 100% accuracy. Among the genomes retrieved from NCBI, Kaptive detected known KL and OCL in 87% and 90% of genomes, respectively indicating that the majority of common KL and OCL types are captured within the databases; 13 KL were not detected in any public genome assembly. The failure to assign a KL or OCL type may indicate incomplete or poor-quality genomes. However, further novel variants may remain to be documented. Combining outputs with multi-locus sequence typing (Institut Pasteur scheme) revealed multiple KL and OCL types in collections of a single sequence type (ST) representing each of the two predominant globally-distributed clones, ST1 of GC1 and ST2 of GC2, and in collections of other clones comprising >20 isolates each (ST10, ST25, and ST140), indicating extensive within-clone replacement of these loci. The databases are available at https://github.com/katholt/Kaptive and will be updated as further locus types become available. Data Summary1. Databases including fully annotated gene cluster sequences for A. baumannii K loci and OC loci are available for download at https://github.com/katholt/Kaptive 2. The Kaptive software, which can be used to screen new genomes against the K and O locus database is available at https://github.com/katholt/Kaptive (command-line code) and http://kaptive.holtlab.net/ (interactive web service). 3. Details of the Kaptive search results validating in silico serotyping of K and O loci using our approach are provided as supplementary files, Dataset 1 (92 KL reference sequences and 12 OCL reference sequences), Dataset 2 (642 genomes assembled from reads available in NCBI SRA) and Dataset 3 (3415 genome assemblies downloaded from NCBI GenBank). Impact statementThe ability to identify and track closely related isolates is key to understanding, and ultimately controlling, the spread of multiply antibiotic resistant A. baumannii causing difficult to treat infections, which are an urgent public health threat. Extensive variation in the KL and OCL gene clusters responsible for biosynthesis of capsule and the outer core of lipooligosaccharide, respectively, are potentially highly informative epidemiological markers. However, clear, well-documented identification of each variant and simple-to-use tools and procedures are needed to reliably identify them in genome sequence data. Here, we present curated databases compatible with the available web-based and command-line Kaptive tool to make KL and OCL typing readily accessible to assist epidemiological surveillance of this species. As many bacteriophage recognise specific properties of the capsule and attach to it, capsule typing is also important in assessing the potential of specific phage for therapy on a case by case basis. ]]> Wyres, K. L. Cahill, S. M. Holt, K. E. Hall, R. M. Kenyon, J. J. 2019-12-10 doi:10.1101/869370 Cold Spring Harbor Laboratory Press 2019-12-10 <![CDATA[ Mechanical cell competition in heterogeneous epithelial tissues ]]> https://biorxiv.org/content/10.1101/869495v1?rss=1 Murphy, R. J. Buenzli, P. R. Baker, R. E. Simpson, M. J. 2019-12-09 doi:10.1101/869495 Cold Spring Harbor Laboratory Press 2019-12-09 <![CDATA[ Mono-phosphorylation at Ser4 of Barrier-to-autointegration Factor (Banf1) significantly reduces its DNA binding capability by inducing critical changes in its local conformation and DNA binding surface ]]> https://biorxiv.org/content/10.1101/2023.05.21.541616v1?rss=1 Tang, M. Suraweera, A. Nie, X. Li, Z. Wells, J. O'Byrne, K. Woods, R. Bolderson, E. Richard, D. J. 2023-05-21 doi:10.1101/2023.05.21.541616 Cold Spring Harbor Laboratory Press 2023-05-21 <![CDATA[ Deconstructing the contributions of heterogeneity to combination treatment of hormone sensitive breast cancer ]]> https://biorxiv.org/content/10.1101/2023.05.19.541369v1?rss=1 Linn, S. Moore-Ott, J. Shuttleworth, R. Zhang, W. Craig, M. Jenner, A. L. 2023-05-22 doi:10.1101/2023.05.19.541369 Cold Spring Harbor Laboratory Press 2023-05-22 <![CDATA[ Advancing scaffold biomimicry: engineering mechanics in microfiber scaffolds with independently controlled architecture using melt electrowriting ]]> https://biorxiv.org/content/10.1101/2023.05.28.542676v1?rss=1 Devlin, B. L. Pickering, E. Allenby, M. C. Paxton, N. C. Woodruff, M. 2023-05-30 doi:10.1101/2023.05.28.542676 Cold Spring Harbor Laboratory Press 2023-05-30 <![CDATA[ Single-cell Spatial Metabolic and Immune Phenotyping of Head and Neck Cancer Tissues Identifies Tissue Signatures of Response and Resistance to Immunotherapy ]]> https://biorxiv.org/content/10.1101/2023.05.30.540859v1?rss=1 Jhaveri, N. Ben Cheikh, B. Nikulina, N. Ma, N. Klymyshyn, D. DeRosa, J. Mihani, R. Pratapa, A. Kassim, Y. Bommakanti, S. Shang, O. He, Y. Zheng, Y. Monkman, J. Cooper, C. O'Byrne, K. Anand, B. Prater, M. Basu, S. Hughes, B. G. M. Kulasinghe, A. Braubach, O. 2023-06-01 doi:10.1101/2023.05.30.540859 Cold Spring Harbor Laboratory Press 2023-06-01 <![CDATA[ Epidermal Growth Factor potentiates EGFR(Y992/1173)-mediated therapeutic response of triple negative breast cancer cells to cold atmospheric plasma-activated medium ]]> https://biorxiv.org/content/10.1101/2023.05.30.542966v1?rss=1 Wang, P. Zhou, R. Zhou, R. Yu, L. Zhao, L. Li, W. Lin, J. Rajapakse, A. Lee, C.-H. Furnari, F. B. Burgess, A. W. Gunter, J. H. Liu, G. Ostrikov, K. Richard, D. J. Simpson, F. Dai, X. Thompson, E. 2023-06-02 doi:10.1101/2023.05.30.542966 Cold Spring Harbor Laboratory Press 2023-06-02 <![CDATA[ Population ecology and potential biogeochemical impacts of ssDNA and dsDNA soil viruses along a permafrost thaw gradient ]]> https://biorxiv.org/content/10.1101/2023.06.13.544858v1?rss=1 Trubl, G. Roux, S. Borton, M. A. Varsani, A. Li, Y.-F. Sun, C. Jang, H. B. Woodcroft, B. J. Tyson, G. W. Wrighton, K. C. Saleska, S. R. Eloe-Fadrosh, E. A. Sullivan, M. B. Rich, V. I. 2023-06-18 doi:10.1101/2023.06.13.544858 Cold Spring Harbor Laboratory Press 2023-06-18 <![CDATA[ Robust Homeostasis of Cellular Cholesterol via Antithetic Integral Control ]]> https://biorxiv.org/content/10.1101/2023.06.24.546224v1?rss=1 Scheepers, R. Araujo, R. 2023-06-24 doi:10.1101/2023.06.24.546224 Cold Spring Harbor Laboratory Press 2023-06-24 <![CDATA[ Methylotrophy in the Mire: direct and indirect routes for methane production in thawing permafrost ]]> https://biorxiv.org/content/10.1101/2023.07.09.548291v1?rss=1 1700 bacterial MAGs across 19 phyla encoded anaerobic methylotrophic potential, with expression across 12 phyla. Metabolomic analyses revealed the presence of diverse methylated compounds in the Mire, including some known methylotrophic substrates. Active methylotrophy was observed across all stages of a permafrost thaw gradient in Stordalen, with the most frozen non-methanogenic palsa found to host bacterial methylotrophy, and the partially thawed bog and fully thawed fen seen to house both methanogenic and bacterial methylotrophic activity. Methanogenesis across increasing permafrost thaw is thus revised from sole dominance of hydrogenotrophic production, and the appearance of acetoclastic at full thaw, to consider co-occurrence of methylotrophy throughout. Collectively, these findings indicate that methanogenic and bacterial methylotrophy may be an important and previously underappreciated component of carbon cycling and emissions in these rapidly changing wetland habitats. ]]> Ellenbogen, J. B. Borton, M. A. McGivern, B. B. Cronin, D. R. Hoyt, D. W. Freire-Zapata, V. McCalley, C. K. Varner, R. K. Crill, P. M. Wehr, R. A. Chanton, J. P. Woodcroft, B. J. Tfaily, M. M. Tyson, G. W. Rich, V. I. Wrighton, K. C. 2023-07-10 doi:10.1101/2023.07.09.548291 Cold Spring Harbor Laboratory Press 2023-07-10 <![CDATA[ A functional microbiome catalog crowdsourced from North American rivers ]]> https://biorxiv.org/content/10.1101/2023.07.22.550117v1?rss=1 Borton, M. A. McGivern, B. B. Willi, K. R. Woodcroft, B. J. Mosier, A. C. Bambakidis, T. Singleton, D. M. Liu, F. Edirisinghe, J. N. Faria, J. P. Leleiwi, I. Daly, R. A. Goldman, A. E. Wilkins, M. J. Hall, E. Pennacchio, C. Roux, S. Eloe-Fadrosh, E. A. Sullivan, M. B. Henry, C. S. Wood-Charlson, E. M. Ross, M. R. Miller, C. S. Crump, B. C. Stegen, J. Wrighton, K. C. 2023-07-22 doi:10.1101/2023.07.22.550117 Cold Spring Harbor Laboratory Press 2023-07-22 <![CDATA[ Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires ]]> https://biorxiv.org/content/10.1101/2023.08.01.549754v1?rss=1 Schoelmerich, M. C. Ly, L. West-Roberts, J. Shi, L.-D. Shen, C. Malvankar, N. Taib, N. Gribaldo, S. Woodcroft, B. J. Al-Shayeb, B. Dai, X. Mozsary, C. Hickey, S. He, C. Beaulaurier, J. A. Juul, S. Sachdeva, R. Banfield, J. 2023-08-01 doi:10.1101/2023.08.01.549754 Cold Spring Harbor Laboratory Press 2023-08-01 <![CDATA[ An evolutionary timescale for Bacteria calibrated using the Great Oxidation Event ]]> https://biorxiv.org/content/10.1101/2023.08.08.552427v1?rss=1 Davin, A. A. Woodcroft, B. J. Soo, R. M. Murali, R. Schrempf, D. Clark, J. Boussau, B. Moody, E. R. R. Szantho, L. L. Richy, E. Pisani, D. Hemp, J. Fischer, W. W. Donoghue, P. Spang, A. Hugenholtz, P. Williams, T. A. Szöllosi, G. J. 2023-08-11 doi:10.1101/2023.08.08.552427 Cold Spring Harbor Laboratory Press 2023-08-11 <![CDATA[ Foot position during plantarflexion changes gastrocnemii motor unit discharge rate in runners with Achilles tendinopathy but not in the way you might think ]]> https://biorxiv.org/content/10.1101/2023.08.14.553177v1?rss=1 Fernandes, G. L. Orssatto, L. B. Shield, A. J. Trajano, G. S. 2023-08-15 doi:10.1101/2023.08.14.553177 Cold Spring Harbor Laboratory Press 2023-08-15 <![CDATA[ Nitrate-driven anaerobic oxidation of ethane and butane by bacteria ]]> https://biorxiv.org/content/10.1101/2023.08.24.554723v1?rss=1 Wu, M. Li, J. Lai, C. Leu, A. O. Sun, S. Gu, R. Erler, D. V. Liu, L. Li, L. Tyson, G. W. Yuan, Z. McIlroy, S. J. Guo, J. 2023-08-25 doi:10.1101/2023.08.24.554723 Cold Spring Harbor Laboratory Press 2023-08-25 <![CDATA[ Impact of resistance on therapeutic design: a Moran model of cancer growth ]]> https://biorxiv.org/content/10.1101/2023.08.28.555214v1?rss=1 Lacy, M. S. Jenner, A. L. 2023-08-28 doi:10.1101/2023.08.28.555214 Cold Spring Harbor Laboratory Press 2023-08-28 <![CDATA[ Lineage maintenance due to assortative mating but not ecological divergence in a sympatric sibling species pair ]]> https://biorxiv.org/content/10.1101/2023.08.30.555036v1?rss=1 Irvine, M. Stewart, Z. Kumaran, N. Manawaduge, C. G. Balagawi, S. Missenden, B. Starkie, M. Clarke, A. R. Hurwood, D. A. Prentis, P. 2023-08-31 doi:10.1101/2023.08.30.555036 Cold Spring Harbor Laboratory Press 2023-08-31 <![CDATA[ Structural and mechanistic characterization of bifunctional heparan sulfate N-deacetylase-N-sulfotransferase 1 ]]> https://biorxiv.org/content/10.1101/2023.08.30.555497v1?rss=1 Mycroft-West, C. J. Abdelkarim, S. Duyvesteyn, H. M. E. Gandhi, N. S. Skidmore, M. A. Owens, R. J. Wu, L. 2023-08-31 doi:10.1101/2023.08.30.555497 Cold Spring Harbor Laboratory Press 2023-08-31 <![CDATA[ Modelling count data with partial differential equation models in biology ]]> https://biorxiv.org/content/10.1101/2023.09.09.556963v1?rss=1 Simpson, M. J. Murphy, R. J. Maclaren, O. J. 2023-09-12 doi:10.1101/2023.09.09.556963 Cold Spring Harbor Laboratory Press 2023-09-12 <![CDATA[ ACE2-Coated Virus-Like Particles Effectively Block SARS-CoV-2 Infection ]]> https://biorxiv.org/content/10.1101/2023.09.19.558424v1?rss=1 View larger version (16K): org.highwire.dtl.DTLVardef@30ac94org.highwire.dtl.DTLVardef@1926217org.highwire.dtl.DTLVardef@165d9f0org.highwire.dtl.DTLVardef@1c737f9_HPS_FORMAT_FIGEXP M_FIG In our study, we demonstrate the prevention of SARS-CoV-2 infection through the use of Ace2-coated VLPs. C_FIG ]]> Bayraktar, C. Kayabolen, A. Odabas, A. Durgun, A. Kok, I. Sevinc, K. Supramaniam, A. Idris, A. Bagci-Onder, T. 2023-09-20 doi:10.1101/2023.09.19.558424 Cold Spring Harbor Laboratory Press 2023-09-20 <![CDATA[ Tuning of liver circadian transcriptome rhythms by thyroid hormone state in male mice ]]> https://biorxiv.org/content/10.1101/2023.09.23.559037v1?rss=1 de Assis, L. V. Harder, L. Lacerda, J. T. Parsons, R. Kaehler, M. Cascorbi, I. Nagel, I. Rawashdeh, O. Mittag, J. Oster, H. 2023-09-24 doi:10.1101/2023.09.23.559037 Cold Spring Harbor Laboratory Press 2023-09-24 <![CDATA[ Genomic Analysis of Diverse Environmental Acinetobacter Isolates Identifies Plasmids, Antibiotic Resistance Genes, and Capsular Polysaccharides Shared with Clinical Strains ]]> https://biorxiv.org/content/10.1101/2023.10.18.562937v1?rss=1 Tobin, L. A. Jarocki, V. M. Kenyon, J. J. Drigo, B. Donner, E. Djordjevic, S. P. Hamidian, M. 2023-10-19 doi:10.1101/2023.10.18.562937 Cold Spring Harbor Laboratory Press 2023-10-19 <![CDATA[ Preventing extinction in an age of species migration and planetary change ]]> https://biorxiv.org/content/10.1101/2023.10.17.562809v1?rss=1 Lundgren, E. J. Wallach, A. D. Svenning, J.-C. Schlaepfer, M. Andersson, A. L. A. Ramp, D. 2023-10-20 doi:10.1101/2023.10.17.562809 Cold Spring Harbor Laboratory Press 2023-10-20 <![CDATA[ How osteons form: A quantitative hypothesis-testing analysis of cortical pore filling and wall asymmetry ]]> https://biorxiv.org/content/10.1101/2023.10.26.564273v1?rss=1 Hegarty-Cremer, S. G. Borggaard, X. G. Andreasen, C. M. van der Eerden, B. C. Simpson, M. J. Andersen, T. L. Buenzli, P. R. 2023-10-27 doi:10.1101/2023.10.26.564273 Cold Spring Harbor Laboratory Press 2023-10-27 <![CDATA[ SecDATA: Secure Data Access and de novo TranscriptAssembly protocol - To meet the challenge of reliableNGS data analysis ]]> https://biorxiv.org/content/10.1101/2023.10.26.564229v1?rss=1 Mondal, S. Bhattacharya, N. Das, T. Ghosh, Z. Khatua, S. 2023-10-31 doi:10.1101/2023.10.26.564229 Cold Spring Harbor Laboratory Press 2023-10-31 <![CDATA[ Increased force and elastic energy storage are not the mechanisms that improve jump performance with accentuated eccentric loading during a constrained vertical jump ]]> https://biorxiv.org/content/10.1101/2023.10.30.564851v1?rss=1 Su, E. Y.-S. Carroll, T. J. Farris, D. Lichtwark, G. A. 2023-11-02 doi:10.1101/2023.10.30.564851 Cold Spring Harbor Laboratory Press 2023-11-02 <![CDATA[ A High-Throughput Data-Independent Acquisition Workflow for Deep Characterisation of the sn-Isomer Lipidome ]]> https://biorxiv.org/content/10.1101/2023.11.04.565044v1?rss=1 Michael, J. A. Young, R. S. E. Balez, R. Jekimovs, L. J. Marshall, D. L. Poad, B. L. J. Mitchell, T. W. Blanksby, S. J. Ejsing, C. S. Ellis, S. R. 2023-11-05 doi:10.1101/2023.11.04.565044 Cold Spring Harbor Laboratory Press 2023-11-05 <![CDATA[ Decoding Remapped Spatial Information in the Peri-Saccadic Period ]]> https://biorxiv.org/content/10.1101/2023.11.07.565952v1?rss=1 Moran, C. Johnson, P. Landau, A. N. Hogendoorn, H. 2023-11-09 doi:10.1101/2023.11.07.565952 Cold Spring Harbor Laboratory Press 2023-11-09 <![CDATA[ Organ-on-a-Chip Fabrication using Dynamic Photomask ]]> https://biorxiv.org/content/10.1101/2023.11.22.568385v1?rss=1 Ching, T. Chang, S.-Y. Toh, Y.-C. Hashimoto, M. 2023-11-23 doi:10.1101/2023.11.22.568385 Cold Spring Harbor Laboratory Press 2023-11-23 <![CDATA[ Trade-off between light deprivation and desiccation in intertidal seagrasses due to periodic tidal inundation and exposure: insights from a data-calibrated model ]]> https://biorxiv.org/content/10.1101/2023.12.06.570383v1?rss=1 Wang, X. Adams, M. P. Shao, D. 2023-12-08 doi:10.1101/2023.12.06.570383 Cold Spring Harbor Laboratory Press 2023-12-08 <![CDATA[ Cell-state transitions and frequency-dependent interactions among subpopulations together explain the dynamics of spontaneous epithelial-mesenchymal heterogeneity in breast cancer ]]> https://biorxiv.org/content/10.1101/2023.12.07.567986v1?rss=1 Jain, P. Kizhuttil, R. Nair, M. B. Bhatia, S. Thompson, E. W. George, J. T. Jolly, M. K. 2023-12-08 doi:10.1101/2023.12.07.567986 Cold Spring Harbor Laboratory Press 2023-12-08 <![CDATA[ From Inhibition to Excitation and Why: The Role of Temporal Urgency in Modulating Corticospinal Activity ]]> https://biorxiv.org/content/10.1101/2023.12.27.573452v1?rss=1 McInnes, A. N. Smithers, B. Lipp, O. V. Tresilian, J. R. Vallence, A.-M. Rothwell, J. C. Marinovic, W. 2023-12-28 doi:10.1101/2023.12.27.573452 Cold Spring Harbor Laboratory Press 2023-12-28 <![CDATA[ A catalogue of small proteins from the global microbiome ]]> https://biorxiv.org/content/10.1101/2023.12.27.573469v1?rss=1 Duan, Y. Santos Junior, C. D. Schmidt, T. S. B. Fullam, A. de Almeida, B. L. S. Zhu, C. Michael, K. Zhao, X.-M. Bork, P. Coelho, L. P. 2023-12-28 doi:10.1101/2023.12.27.573469 Cold Spring Harbor Laboratory Press 2023-12-28 <![CDATA[ Complexity And Ergodicity In Chaos Game Representation Of Genomic Sequences ]]> https://biorxiv.org/content/10.1101/2023.12.30.573653v1?rss=1 Mehrpooya, A. Tavassoly, I. 2023-12-30 doi:10.1101/2023.12.30.573653 Cold Spring Harbor Laboratory Press 2023-12-30 <![CDATA[ A maternal high-fat diet predisposes to infant lung disease via increased neutrophil-mediated IL-6 trans-signaling ]]> https://biorxiv.org/content/10.1101/2024.03.13.584927v1?rss=1 Curren, B. Ahmed, T. Rashid, R. B. Sebina, I. Sikder, M. A. A. Howard, D. R. Alorro, M. Ullah, M. A. Bissell, A. Rahman, M. M. Pearen, M. A. Ramm, G. A. Varelias, A. Rose-John, S. Cuiv, P. O. Spann, K. M. Dennis, P. G. Phipps, S. 2024-03-15 doi:10.1101/2024.03.13.584927 Cold Spring Harbor Laboratory Press 2024-03-15 <![CDATA[ A distributed integral control mechanism for the regulation of cholesterol concentration in the human retina. ]]> https://biorxiv.org/content/10.1101/2024.03.14.584346v1?rss=1 Scheepers, R. Levi, N. L. Araujo, R. P. 2024-03-16 doi:10.1101/2024.03.14.584346 Cold Spring Harbor Laboratory Press 2024-03-16 <![CDATA[ When visual attention is divided in the flash-lag effect ]]> https://biorxiv.org/content/10.1101/2024.03.14.585092v1?rss=1 Yook, J. Hogendoorn, H. Fink, G. R. Vossel, S. Weidner, R. 2024-03-14 doi:10.1101/2024.03.14.585092 Cold Spring Harbor Laboratory Press 2024-03-14 <![CDATA[ Simulating animal movement trajectories from temporally dynamic step selection functions ]]> https://biorxiv.org/content/10.1101/2024.03.19.585696v1?rss=1 Forrest, S. W. Pagendam, D. Bode, M. Drovandi, C. Potts, J. R. Perry, J. Vanderduys, E. Hoskins, A. J. 2024-03-21 doi:10.1101/2024.03.19.585696 Cold Spring Harbor Laboratory Press 2024-03-21 <![CDATA[ Cyanamide-inducible expression of homing nuclease I-SceI for iterative genome engineering and parallel promoter characterisation in Saccharomyces cerevisiae ]]> https://biorxiv.org/content/10.1101/2024.03.26.586389v1?rss=1 McDonnell, L. Evans, S. Lu, Z. Suchoronczak, M. Leighton, J. Ordeniza, E. Ritchie, B. Valado, N. Walsh, N. Antoney, J. P. Wang, C. Scott, C. Speight, R. Vickers, C. Peng, B. 2024-03-27 doi:10.1101/2024.03.26.586389 Cold Spring Harbor Laboratory Press 2024-03-27 <![CDATA[ Cis-vaccenic acid is a key product of stearoyl-CoA desaturase 1 and a critical oncogenic factor in prostate cancer ]]> https://biorxiv.org/content/10.1101/2024.03.28.587238v1?rss=1 Scott, J. S. Young, R. S. Quek, L.-E. Miller, D. C. Evergren, E. S. Dehairs, J. Johnson, I. R. Brooks, D. A. Loda, M. Hoy, A. J. Blanksby, S. J. Swinnen, J. V. Nassar, Z. D. Butler, L. M. 2024-03-30 doi:10.1101/2024.03.28.587238 Cold Spring Harbor Laboratory Press 2024-03-30 <![CDATA[ Long term co-circulation of multiple arboviruses in southeast Australia revealed by xeno-monitoring of mosquitoes and metatranscriptomics ]]> https://biorxiv.org/content/10.1101/2024.03.29.587110v1?rss=1 Vieira, C. J. S. P. Onn, M. B. Shivas, M. A. Shearman, D. Darbro, J. M. Graham, M. Freitas, L. van den Hurk, A. F. Frentiu, F. F. Wallau, G. L. Devine, G. J. 2024-03-30 doi:10.1101/2024.03.29.587110 Cold Spring Harbor Laboratory Press 2024-03-30 <![CDATA[ GLMMcosinor: Flexible cosinor modeling with a generalized linear mixed modeling framework to characterize rhythmic time series. ]]> https://biorxiv.org/content/10.1101/2024.04.10.588934v1?rss=1 Parsons, R. Jayasinghe, O. White, N. M. Chunduri, P. Rawashdeh, O. 2024-04-14 doi:10.1101/2024.04.10.588934 Cold Spring Harbor Laboratory Press 2024-04-14 <![CDATA[ Optimising crown-of-thorns starfish control effort on the Great Barrier Reef ]]> https://biorxiv.org/content/10.1101/2024.04.10.588969v1?rss=1 Agarwal, K. Bode, M. Helmstedt, K. 2024-04-14 doi:10.1101/2024.04.10.588969 Cold Spring Harbor Laboratory Press 2024-04-14 <![CDATA[ Progressive multi-stage extrapolation of predictable motion in human visual cortex ]]> https://biorxiv.org/content/10.1101/2024.04.22.590502v1?rss=1 Turner, W. Sexton, C. Johnson, P. A. Wilson, E. Hogendoorn, H. 2024-04-25 doi:10.1101/2024.04.22.590502 Cold Spring Harbor Laboratory Press 2024-04-25 <![CDATA[ Large-scale estimation of bacterial and archaeal DNA prevalence in metagenomes reveals biome-specific patterns ]]> https://biorxiv.org/content/10.1101/2024.05.16.594470v1?rss=1 Eisenhofer, R. Alberdi, A. Woodcroft, B. J. 2024-05-17 doi:10.1101/2024.05.16.594470 Cold Spring Harbor Laboratory Press 2024-05-17 <![CDATA[ Using physiologically-based models to predict in vivo skeletal muscle energetics ]]> https://biorxiv.org/content/10.1101/2024.05.21.595083v1?rss=1 Konno, R. N. Lichtwark, G. A. Dick, T. J. 2024-05-23 doi:10.1101/2024.05.21.595083 Cold Spring Harbor Laboratory Press 2024-05-23 <![CDATA[ Cycling Cadence Selections at Different Saddle Heights Minimize Muscle Activation Rather Than Energy Cost ]]> https://biorxiv.org/content/10.1101/2024.05.30.596596v1?rss=1 Riveros-Matthey, C. D. Connick, M. J. Lichtwark, G. A. Carroll, T. J. 2024-06-02 doi:10.1101/2024.05.30.596596 Cold Spring Harbor Laboratory Press 2024-06-02 <![CDATA[ Optimal control of Multiple Myeloma assuming drug evasion and off-target effects ]]> https://biorxiv.org/content/10.1101/2024.06.06.597698v1?rss=1 Lefevre, J. Lawson, B. A. J. Burrage, P. M. Donovan, D. M. Burrage, K. 2024-06-09 doi:10.1101/2024.06.06.597698 Cold Spring Harbor Laboratory Press 2024-06-09 <![CDATA[ Applying rearrangement distances to enable plasmid epidemiology with pling ]]> https://biorxiv.org/content/10.1101/2024.06.12.598623v1?rss=1 Frolova, D. Lima, L. Roberts, L. Bohnenkamper, L. Wittler, R. Stoye, J. Iqbal, Z. 2024-06-12 doi:10.1101/2024.06.12.598623 Cold Spring Harbor Laboratory Press 2024-06-12 <![CDATA[ Microflora Danica: the atlas of Danish environmental microbiomes ]]> https://biorxiv.org/content/10.1101/2024.06.27.600767v1?rss=1 Singleton, C. M. Jensen, T. B. Delogu, F. Sorensen, E. A. Jorgensen, V. R. Karst, S. M. Yang, Y. Knudsen, K. S. Sereika, M. Petriglieri, F. Knuttson, S. Dall, S. M. Kirkegaard, R. H. Kristensen, J. M. Woodcroft, B. J. Speth, D. R. Aroney, S. The Microflora Danica Consortium, Wagner, M. Dueholm, M. M. Nielsen, P. H. Albertsen, M. 2024-06-27 doi:10.1101/2024.06.27.600767 Cold Spring Harbor Laboratory Press 2024-06-27 <![CDATA[ Tissue-specific immune transcriptional signatures in the bordering tissues of the mouse brain and retina ]]> https://biorxiv.org/content/10.1101/2024.06.30.601438v1?rss=1 Etebar, F. Whatmore, P. Harkin, D. G. Dando, S. J. 2024-07-02 doi:10.1101/2024.06.30.601438 Cold Spring Harbor Laboratory Press 2024-07-02 <![CDATA[ CompareM2 is a genomes-to-report pipeline for comparing microbial genomes ]]> https://biorxiv.org/content/10.1101/2024.07.12.603264v1?rss=1 Kobel, C. M. Aho, V. T. E. Oeyaas, O. Noerskov-Lauritsen, N. Woodcroft, B. J. Pope, P. B. 2024-07-16 doi:10.1101/2024.07.12.603264 Cold Spring Harbor Laboratory Press 2024-07-16 <![CDATA[ Probing the eukaryotic microbes of ruminants with a deep-learning classifier and comprehensive protein databases ]]> https://biorxiv.org/content/10.1101/2024.07.17.603995v1?rss=1 Yan, M. Andersen, T. O. Pope, P. B. Yu, Z. 2024-07-18 doi:10.1101/2024.07.17.603995 Cold Spring Harbor Laboratory Press 2024-07-18 <![CDATA[ No evidence that individual alpha frequency (IAF) represents a mechanism underlying motion-position illusions ]]> https://biorxiv.org/content/10.1101/2024.07.17.603862v1?rss=1 Cottier, T. V. Turner, W. Chae, V. J. Holcombe, A. O. Hogendoorn, H. 2024-07-22 doi:10.1101/2024.07.17.603862 Cold Spring Harbor Laboratory Press 2024-07-22 <![CDATA[ Using virtual patient cohorts to uncover immune response differences in cancer and immunosuppressed COVID-19 patients ]]> https://biorxiv.org/content/10.1101/2024.08.01.605860v1?rss=1 Gazeau, S. Deng, X. Brunet-Ratnasingham, E. Kaufmann, D. E. Larochelle, C. Morel, P. A. Heffernan, J. M. Davis, C. L. Smith, A. M. Jenner, A. L. Craig, M. 2024-08-02 doi:10.1101/2024.08.01.605860 Cold Spring Harbor Laboratory Press 2024-08-02 <![CDATA[ Methanogenesis inhibition remodels microbial fermentation and stimulates acetogenesis in ruminants ]]> https://biorxiv.org/content/10.1101/2024.08.15.608071v1?rss=1 Ni, G. Walker, N. Fischer, A. Stemmler, R. T. Schmidt, O. Jain, S. Jespersen, M. Grinter, R. Wang, M. Pope, P. B. Muller, V. Watson, M. Ver Loren van Themaat, E. Kindermann, M. Greening, C. 2024-08-15 doi:10.1101/2024.08.15.608071 Cold Spring Harbor Laboratory Press 2024-08-15 <![CDATA[ Growth rate-driven modelling reveals how phenotypic adaptation drives drug resistance in BRAFV600E-mutant melanoma ]]> https://biorxiv.org/content/10.1101/2024.08.14.607616v1?rss=1 HAMIS, S. Browning, A. P. Jenner, A. L. Villa, C. Maini, P. Cassidy, T. 2024-08-18 doi:10.1101/2024.08.14.607616 Cold Spring Harbor Laboratory Press 2024-08-18 <![CDATA[ Identifiability of heterogeneous phenotype adaptation from low-cell-count experiments and a stochastic model ]]> https://biorxiv.org/content/10.1101/2024.08.19.608540v1?rss=1 Browning, A. P. Crossley, R. M. Villa, C. Maini, P. K. Jenner, A. L. Cassidy, T. Hamis, S. 2024-08-19 doi:10.1101/2024.08.19.608540 Cold Spring Harbor Laboratory Press 2024-08-19 <![CDATA[ From impact metrics and open science to communicating research: Journalists' awareness of academic controversies ]]> https://biorxiv.org/content/10.1101/2024.09.03.609638v1?rss=1 Fleerackers, A. Moorhead, L. L. Alperin, J. P. Riedlinger, M. Maggio, L. A. 2024-09-04 doi:10.1101/2024.09.03.609638 Cold Spring Harbor Laboratory Press 2024-09-04 <![CDATA[ Functional Roles of Sensorimotor Alpha and Beta Oscillations in Overt Speech Production ]]> https://biorxiv.org/content/10.1101/2024.09.04.611312v1?rss=1 Huang, L. Z. Cao, Y. Janse, E. Piai, V. 2024-09-06 doi:10.1101/2024.09.04.611312 Cold Spring Harbor Laboratory Press 2024-09-06 <![CDATA[ PGR5 promotes energy-dependent non-photochemical quenching to enable efficient C4 photosynthesis under fluctuating light ]]> https://biorxiv.org/content/10.1101/2024.09.15.613160v1?rss=1 Woodford, R. Watkins, J. Moore, M. Nix, S. J. Yee, S. Chan, K. X. Pogson, B. J. von Caemmerer, S. Furbank, R. T. Ermakova, M. 2024-09-19 doi:10.1101/2024.09.15.613160 Cold Spring Harbor Laboratory Press 2024-09-19 <![CDATA[ Heterogeneous distribution of inhibitory inputs among motor units as a key mechanism for motor adaptations to pain ]]> https://biorxiv.org/content/10.1101/2024.10.05.616762v1?rss=1 Hug, F. Dernoncourt, F. Avrillon, S. Thorstensen, J. Besomi, M. van den Hoorn, W. Tucker, K. 2024-10-05 doi:10.1101/2024.10.05.616762 Cold Spring Harbor Laboratory Press 2024-10-05 <![CDATA[ A simple model of population dynamics with beneficial and harmful interaction networks for empirical applications. ]]> https://biorxiv.org/content/10.1101/2024.10.15.618620v1?rss=1 Bimler, M. D. Pascal, L. V. Adams, M. P. Baker, C. M. 2024-10-18 doi:10.1101/2024.10.15.618620 Cold Spring Harbor Laboratory Press 2024-10-18 <![CDATA[ A rational approach for the targeted discovery and characterisation of microbiome-derived therapeutics ]]> https://biorxiv.org/content/10.1101/2024.10.22.619608v1?rss=1 Krause, L. Boyd, J. Vivian, C. Krueger, A. Jimenez Loayza, J. Ljungberg, J. Zhou, J. Rabellino, A. Nyeverecz, B. Nissen, M. Tousignant, K. Bongers, M. Cooper, M. M. Parks, D. H. Alsheikh, A. Vera-Wolf, P. Sullivan, M. Newell, R. Masterman, K.-A. Evans, P. Fang, L. MacDonald, S. Chuvochina, M. Bessette, D. Zimmermann, K. Pribyl, A. Chipperfield, H. Caban, S. McCarthy, H. Soh, J. Reid, L. Frazer, I. H. Angel, N. Kenna, T. Wood, D. L. A. Wills, B. Begun, J. Keely, S. Munro, T. Tyson, G. Hugenholtz, P. O Cuiv, P. 2024-10-22 doi:10.1101/2024.10.22.619608 Cold Spring Harbor Laboratory Press 2024-10-22 <![CDATA[ Developing new technologies to protect ecosystems: planning with adaptive management ]]> https://biorxiv.org/content/10.1101/2024.10.24.619976v1?rss=1 Pascal, L. V. Chades, I. Adams, M. P. Helmstedt, K. 2024-10-28 doi:10.1101/2024.10.24.619976 Cold Spring Harbor Laboratory Press 2024-10-28 <![CDATA[ Functional split-tRNA: a new perspective on codon decoding mechanism ]]> https://biorxiv.org/content/10.1101/2024.11.24.624523v1?rss=1 Mureev, S. Wu, Y. Cui, Z. Alexandrov, K. 2024-11-24 doi:10.1101/2024.11.24.624523 Cold Spring Harbor Laboratory Press 2024-11-24 <![CDATA[ Bin Chicken: targeted metagenomic coassembly for the efficient recovery of novel genomes ]]> https://biorxiv.org/content/10.1101/2024.11.24.625082v1?rss=1 Aroney, S. T. N. Newell, R. J. P. Tyson, G. W. Woodcroft, B. J. 2024-11-25 doi:10.1101/2024.11.24.625082 Cold Spring Harbor Laboratory Press 2024-11-25 <![CDATA[ Remission spectroscopy resolves the mode of action of bedaquiline within living mycobacteria ]]> https://biorxiv.org/content/10.1101/2024.12.03.626386v1?rss=1 Harrison, S. H. Walters, R. C. Cheung, C.-Y. Springett, R. J. Cook, G. M. Osman, M. M. Blaza, J. N. 2024-12-05 doi:10.1101/2024.12.03.626386 Cold Spring Harbor Laboratory Press 2024-12-05 <![CDATA[ Crackling Cloud: an event-driven, cloud-based CRISPR-Cas9 guide RNA design tool ]]> https://biorxiv.org/content/10.1101/2024.12.04.626718v1?rss=1 Bradford, J. Joy, D. Winsen, M. Meurant, N. Wilkins, M. Wilson, L. Bauer, D. Perrin, D. 2024-12-05 doi:10.1101/2024.12.04.626718 Cold Spring Harbor Laboratory Press 2024-12-05 <![CDATA[ Metagenomic analysis of marsupial gut microbiomes provides a genetic basis for the low methane economy ]]> https://biorxiv.org/content/10.1101/2024.12.04.626884v1?rss=1 Bowerman, K. L. Lu, Y. McRae, H. Volmer, J. G. Zaugg, J. Pope, P. B. Hugenholtz, P. Greening, C. Morrison, M. Soo, R. M. Evans, P. N. 2024-12-05 doi:10.1101/2024.12.04.626884 Cold Spring Harbor Laboratory Press 2024-12-05 <![CDATA[ Protozoal populations drive system-wide variation in the rumen microbiome ]]> https://biorxiv.org/content/10.1101/2024.12.05.626740v1?rss=1 Kobel, C. M. Leu, A. Vera-Ponce de Leon, A. Oyas, O. Lai, W. Altshuler, I. Hagen, L. H. Wollenberg, R. D. Bakshani, C. R. Willats, W. G. T. Nicoll, L. McIlroy, S. J. Hvidsten, T. R. Schmidt, O. Greening, C. Tyson, G. W. Roehe, R. Aho, V. T. E. Pope, P. B. 2024-12-06 doi:10.1101/2024.12.05.626740 Cold Spring Harbor Laboratory Press 2024-12-06 <![CDATA[ Emergence of Sparse Coding, Balance and Decorrelation from a Biologically-Grounded Spiking Neural Network Model of Learning in the Primary Visual Cortex ]]> https://biorxiv.org/content/10.1101/2024.12.05.627100v1?rss=1 Ruslim, M. A. Spencer, M. J. Hogendoorn, H. Meffin, H. Lian, Y. Burkitt, A. N. 2024-12-10 doi:10.1101/2024.12.05.627100 Cold Spring Harbor Laboratory Press 2024-12-10 <![CDATA[ Simulating big mechanically-active culture systems (BigMACS) using paired biomechanics-histology FEA modelling to derive mechanobiology design relationships. ]]> https://biorxiv.org/content/10.1101/2024.12.08.627430v1?rss=1 Schoenborn, S. Yuan, M. Fell, C. A. Liu, C. Fletcher, D. F. Pirola, S. Chan, H. F. Woodruff, M. A. Li, Z. Toh, Y.-C. Allenby, M. C. 2024-12-12 doi:10.1101/2024.12.08.627430 Cold Spring Harbor Laboratory Press 2024-12-12 <![CDATA[ Microbial alginate foraging is conserved in geographically and taxonomically distinct ruminant microbiomes ]]> https://biorxiv.org/content/10.1101/2024.12.17.628917v1?rss=1 View larger version (43K): org.highwire.dtl.DTLVardef@eebe40org.highwire.dtl.DTLVardef@c6fb8org.highwire.dtl.DTLVardef@7a9b1borg.highwire.dtl.DTLVardef@15d30d7_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Ferrillo, A. Tingley, J. P. King, M. L. Sagaye, A. Bajwa, B. Xing, X. Johannessen, T. Lysberg, A. Mydland, L. T. Overland, M. Reintjes, G. Shearer, A. Y. Klassen, L. Low, K. E. Patel, T. R. Terry, S. Pope, P. B. Abbott, D. W. Hagen, L. H. 2024-12-18 doi:10.1101/2024.12.17.628917 Cold Spring Harbor Laboratory Press 2024-12-18 <![CDATA[ A comparative analysis of toxin gene families across diverse sea anemone species ]]> https://biorxiv.org/content/10.1101/2024.12.13.628455v1?rss=1 Smith, H. L. Broszczak, D. A. van der Burg, C. A. Surm, J. M. Liggins, L. Norton, R. S. Prentis, P. J. 2024-12-20 doi:10.1101/2024.12.13.628455 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ Targeting de novo lipogenesis improves gemcitabine efficacy in pancreatic ductal adenocarcinoma ]]> https://biorxiv.org/content/10.1101/2024.12.18.628624v1?rss=1 Hancock, S. E. Garthwaite, L. Harellis, K. Susetio, M. Ding, E. Choong, L. Contreras, O. Nguyen, A. Lising, J. Hansen, F. K. Wongsomboon, P. Menzel, J. P. Poad, B. L. Mitchell, T. W. Blanksby, S. J. Turner, N. 2024-12-20 doi:10.1101/2024.12.18.628624 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ Impact of wildfire smoke and diesel exhaust on inflammatory response in aging human microglia ]]> https://biorxiv.org/content/10.1101/2024.12.20.629570v1?rss=1 60 years of age) healthy individuals, focusing on immune response, cytokine secretion, nitrosative stress, and phagocytic activity. ResultsOur study demonstrated that DEP and WFS extract (WFSE) significantly upregulated expression of the oxidative stress marker, heme-oxygenase-1 (HO-1) in MDMi after 24 hr, with levels normalising by 96 hr, indicating a transient oxidative stress response. Both DEP and WFSE elicited distinct inflammatory cytokine profiles. DEP induced a rapid response, increasing TNF-, IL-6, IL-23, and IL-33 within 2 hr in young MDMi and 24 hr in aged MDMi. In contrast, WFSE triggered a delayed but sustained inflammatory response, with TNF-, IFN-{gamma}, IL-23, and IL-33 levels persisting at 96 hr in aged MDMi, highlighting an age-related vulnerability to air pollutant-induced inflammation. Both pollutants activated p38, ERK, and NF-{kappa}B pathways, with p38 activity resolving by 96 hours and ERK activation persisting, reflecting their distinct roles in cellular stress and inflammation. NF-{kappa}B p65 nuclear translocation, observed at 24 hours, highlighted its critical role in cytokine release and inflammation following exposure to DEP and WFSE. This is the first report of NF-{kappa}B activation in human microglia exposed to air pollutants. ConclusionsThese results highlight the distinct and potentially harmful effects of DEP and WFSE on immune and inflammatory responses in MDMi, particularly in ageing populations, with significant implications for brain health. DEP triggers acute oxidative stress and inflammatory responses, while WFSE induces more prolonged effects, especially in aged microglia. Both pollutants activate the MAPK and NF-{kappa}B pathways and exhibit unique cytokine profiles, underscoring their overlapping yet distinct mechanisms of action. These findings advance our understanding of air pollutant-induced neuroinflammation and its contribution to neurodegeneration, providing a foundation for developing targeted interventions to mitigate the neurotoxic effects of air pollution. ]]> Cuni-Lopez, C. Ng, M. F. Stewart, R. Milton, L. A. Etebar, F. Sun, Y. Vivian, E. Nguyen, T. Asare, P. F. Lupton, M. K. Roberts, T. L. Ristovski, Z. Hodge, S. Reynolds, P. N. White, A. R. Quek, H. 2024-12-20 doi:10.1101/2024.12.20.629570 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ Acoustic Recognition of Individual Animals in thePresence of Unknown Individuals ]]> https://biorxiv.org/content/10.1101/2024.12.18.629284v1?rss=1 Huang, L. Clarke, R. Teixeira, D. Chiaradia, A. Meyer, B. 2024-12-21 doi:10.1101/2024.12.18.629284 Cold Spring Harbor Laboratory Press 2024-12-21 <![CDATA[ Haemodynamic impact of implant materials and anastomotic angle in peripheral vascular grafts ]]> https://biorxiv.org/content/10.1101/2024.12.18.629298v1?rss=1 Schoenborn, S. Lloyd, T. Sivakumaran, Y. Woodruff, M. A. Fletcher, D. F. Pirola, S. Allenby, M. C. 2024-12-30 doi:10.1101/2024.12.18.629298 Cold Spring Harbor Laboratory Press 2024-12-30 <![CDATA[ Shared molecular regulation of quiescence in neural and glioma stem cells reveals therapeutic vulnerabilities. ]]> https://biorxiv.org/content/10.1101/2025.01.22.634421v1?rss=1 Choudhury, C. Singleton, M. Brauer, S. Friess, D. Hart, J. Skarne, N. Pullela, K. Mao, L. Day, B. W. Harris, L. 2025-01-25 doi:10.1101/2025.01.22.634421 Cold Spring Harbor Laboratory Press 2025-01-25 <![CDATA[ Optimal membrane fluidity modulates biofilm formation in Escherichia coli ]]> https://biorxiv.org/content/10.1101/2025.02.02.635587v1?rss=1 Hong, Y. Qin, J. Totsika, M. 2025-02-02 doi:10.1101/2025.02.02.635587 Cold Spring Harbor Laboratory Press 2025-02-02 <![CDATA[ Genetic and environmental contributions to ReHo and fALFF in early adolescence vary across brain regions ]]> https://biorxiv.org/content/10.1101/2025.01.31.635399v1?rss=1 Strike, L. T. McMahon, K. L. Medland, S. E. de Zubicaray, G. I. 2025-02-05 doi:10.1101/2025.01.31.635399 Cold Spring Harbor Laboratory Press 2025-02-05 <![CDATA[ A typology of Australian terrestrial bird communities ]]> https://biorxiv.org/content/10.1101/2025.02.03.635991v1?rss=1 Maron, M. Kutt, A. Maisey, A. Burbidge, A. Freeman, A. Bennett, A. F. Haslem, A. Reside, A. E. Tulloch, A. Hansen, B. Palmer, B. Melton, C. B. Teixeira, D. Watson, D. Robinson, D. Vanderduys, E. Rainsford, F. Maurer, G. Fraser, H. Mayfield, H. J. Mihailou, H. Possingham, H. Humphrey, J. Radford, J. Watson, J. Simmonds, J. S. Mills-Anderson, J. Reid, J. Indraswari, K. Selwood, K. Clarke, M. Gibson, M. Leseberg, N. P. Jackett, N. McDonald, P. Spindler, R. Loyn, R. Noske, R. Davis, R. Clarke, R. H. Verdon, S. Eyre, T. 2025-02-07 doi:10.1101/2025.02.03.635991 Cold Spring Harbor Laboratory Press 2025-02-07 <![CDATA[ Disruptions in Outer Membrane-Peptidoglycan Interactions Enhance Bile Salt Resistance in O-antigen-Producing E. coli ]]> https://biorxiv.org/content/10.1101/2025.02.09.637341v1?rss=1 Qin, J. Hong, Y. Vollmer, W. Morona, R. Totsika, M. 2025-02-10 doi:10.1101/2025.02.09.637341 Cold Spring Harbor Laboratory Press 2025-02-10 <![CDATA[ Mobile genetic elements that shape microbial diversity and functions inthawing permafrost soils ]]> https://biorxiv.org/content/10.1101/2025.02.12.637893v1?rss=1 Guo, J. Aroney, S. Dominguez-Huerta, G. Smith, D. Vik, D. Ansah, C. O. Pratama, A. A. Solonenko, S. Tian, F. Howard-Varona, C. Zhong, Z. Fofana, A. Smith, G. Hodgkins, S. B. Cronin, D. EMERGE Field Teams 2010-2019, EMERGE Coordinators, Woodcroft, B. J. Tyson, G. W. Rich, V. I. Sullivan, M. B. Roux, S. Bagby, S. C. 2025-02-13 doi:10.1101/2025.02.12.637893 Cold Spring Harbor Laboratory Press 2025-02-13 <![CDATA[ From Archaea to the atmosphere: remotely sensing Arctic methane ]]> https://biorxiv.org/content/10.1101/2025.02.13.638097v1?rss=1 Varner, R. K. Cronin, D. R. Crill, P. Palace, M. McCalley, C. K. Deng, J. Herrick, C. Kuhn, M. Hodgkins, S. B. McArthur, K. Singer, J. D. Bolduc, B. Li, Y.-F. The Archaea to Atmosphere (A2A) Project Team, EMERGE Institute Coordinators, Li, C. Tyson, G. Frolking, S. Chanton, J. P. Persson, A. Saleska, S. R. Rich, V. I. 2025-02-13 doi:10.1101/2025.02.13.638097 Cold Spring Harbor Laboratory Press 2025-02-13 <![CDATA[ Global distribution of microbial carrageenan foraging pathways reveals widespread latent traits within the genetic dark matter of ruminant intestinal microbiomes ]]> https://biorxiv.org/content/10.1101/2025.03.04.641501v1?rss=1 Tingley, J. P. Anderson, T. O. mihalynuk, L. G. Xing, X. Low, K. E. Whiteside, D. P. Shearer, A. Y. Altshuler, I. Jujihara, N. Serin, S. Smith, E. Reintjes, G. Patel, T. R. Boraston, A. B. Hagen, L. H. Pope, P. B. Abbott, D. W. 2025-03-04 doi:10.1101/2025.03.04.641501 Cold Spring Harbor Laboratory Press 2025-03-04 <![CDATA[ Nitric oxide donor sodium nitroprusside serves as a source of iron supporting Pseudomonas aeruginosa growth and biofilm formation ]]> https://biorxiv.org/content/10.1101/2025.03.12.642859v1?rss=1 Bertran i Forga, X. Hong, Y. Fairfull-Smith, K. E. Qin, J. Totsika, M. 2025-03-12 doi:10.1101/2025.03.12.642859 Cold Spring Harbor Laboratory Press 2025-03-12 <![CDATA[ Hydrogenase-driven ATP synthesis from air ]]> https://biorxiv.org/content/10.1101/2025.03.14.643271v1?rss=1 Soom, S. Moning, S. U. Cook, G. M. Lingford, J. P. Kropp, A. Tran, S. Grinter, R. Greening, C. von Ballmoos, C. 2025-03-15 doi:10.1101/2025.03.14.643271 Cold Spring Harbor Laboratory Press 2025-03-15 <![CDATA[ Functional Metagenomic Analysis Reveals Early Gut Microbiota Alterations in Alpha-Synuclein Transgenic Mice: Insights into Parkinson's Disease Progression ]]> https://biorxiv.org/content/10.1101/2025.03.18.644066v1?rss=1 Mondhe, D. O. Jayabalan, N. ocampo, J. S. Gordon, R. 2025-03-19 doi:10.1101/2025.03.18.644066 Cold Spring Harbor Laboratory Press 2025-03-19 <![CDATA[ Explainable machine learning identifies features and thresholds predictive of immunotherapy response ]]> https://biorxiv.org/content/10.1101/2025.03.23.643560v1?rss=1 Tran, K. A. Addala, V. Koufariotis, L. T. Zhang, J. Wood, S. Leonard, C. Hoeijmakers, L. L. Blank, C. U. Crispin-Ortuzar, M. Williams, E. D. Kondrashova, O. Pearson, J. V. Waddell, N. 2025-03-25 doi:10.1101/2025.03.23.643560 Cold Spring Harbor Laboratory Press 2025-03-25 <![CDATA[ The gut microbiome in early age-related macular degeneration ]]> https://biorxiv.org/content/10.1101/2025.03.25.645132v1?rss=1 Feigl, B. Adhikari, P. Huygens, F. Jayasundara, N. K. Zele, A. K. 2025-03-26 doi:10.1101/2025.03.25.645132 Cold Spring Harbor Laboratory Press 2025-03-26 <![CDATA[ AT1R and Integrin β3 Synergize to Drive Aortic Dissection via Non-Canonical Wnt/β-Catenin Signaling ]]> https://biorxiv.org/content/10.1101/2025.03.26.645618v1?rss=1 Jang, H. Liu, Z. Li, Y. Zhong, X. Qu, Y. Li, S. Dai, L. Zhang, Y. Wang, M. Zhang, W. Liu, W. He, X. Dong, W. Madhusudhan, T. Li, Z. Wang, H. Zeng, H. 2025-04-01 doi:10.1101/2025.03.26.645618 Cold Spring Harbor Laboratory Press 2025-04-01 <![CDATA[ Archaeological Bolivian maize genomes suggest Inca cultural expansion augmented maize diversity in South America ]]> https://biorxiv.org/content/10.1101/2025.03.31.646424v1?rss=1 Chen, H. Baetsen-Young, A. Thompson, A. Day, B. Madzima, T. Wasef, S. Rivera Casanovas, C. Lovis, W. Wrobel, G. 2025-04-01 doi:10.1101/2025.03.31.646424 Cold Spring Harbor Laboratory Press 2025-04-01 <![CDATA[ A mathematical model of metacarpal subchondral bone adaptation, microdamage, and repair in racehorses ]]> https://biorxiv.org/content/10.1101/2025.04.06.646486v1?rss=1 Pan, M. Malekipour, F. Pivonka, P. Morrice-West, A. V. Flegg, J. A. Whitton, C. Hitchens, P. L. 2025-04-07 doi:10.1101/2025.04.06.646486 Cold Spring Harbor Laboratory Press 2025-04-07 <![CDATA[ Enhanced Resistance and Resilience of Anaerobic Digestion Microbiome after Single and Dual Short-Term Disturbances ]]> https://biorxiv.org/content/10.1101/2025.06.17.659861v1?rss=1 Mohidin, A. F. Ng, T. C. A. Santillan, E. Lu, Y. Cokro, A. Wuertz, S. 2025-06-17 doi:10.1101/2025.06.17.659861 Cold Spring Harbor Laboratory Press 2025-06-17 <![CDATA[ Therapeutic targeting of oligodendrocytes in an agent-based model of multiple sclerosis ]]> https://biorxiv.org/content/10.1101/2025.06.26.661705v1?rss=1 Weatherley, G. R. Araujo, R. P. Dando, S. J. Jenner, A. L. 2025-06-27 doi:10.1101/2025.06.26.661705 Cold Spring Harbor Laboratory Press 2025-06-27 <![CDATA[ A Patient-Specific 3D Printed Carotid Artery Model Integrating Vascular Structure, Flow and Endothelium Responses ]]> https://biorxiv.org/content/10.1101/2025.06.29.661865v1?rss=1 Amaya Catano, J. A. Ong, L. J. Y. Yuan, M. Qu, Y. Benitez, J. Yarlagadda, P. K. Toh, Y.-C. Li, Z. 2025-07-03 doi:10.1101/2025.06.29.661865 Cold Spring Harbor Laboratory Press 2025-07-03 <![CDATA[ From Smartphone Images to Musculoskeletal Models: Personalized Inertial Parameter Estimation ]]> https://biorxiv.org/content/10.1101/2025.07.08.663673v1?rss=1 Gambietz, M. Azam, P. Q. Amon, P. Wechsler, I. Hille, E. M. Menzel, T. Ott, T. Botsch, M. Braun, M. Miehling, J. McMahon, K. L. Koelewijn, A. D. 2025-07-11 doi:10.1101/2025.07.08.663673 Cold Spring Harbor Laboratory Press 2025-07-11 <![CDATA[ Parameter-wise predictions and sensitivity analysis forrandom walk models in the life sciences ]]> https://biorxiv.org/content/10.1101/2025.07.12.664534v1?rss=1 Liu, Y. Warne, D. J. Simpson, M. J. 2025-07-14 doi:10.1101/2025.07.12.664534 Cold Spring Harbor Laboratory Press 2025-07-14 <![CDATA[ AEMB: a computationally efficient abundance estimation method for metagenomic binning ]]> https://biorxiv.org/content/10.1101/2025.07.30.667338v1?rss=1 Pan, S. Tolstoganov, I. Sahlin, K. Martin, M. Zhao, X.-M. Coelho, L. P. 2025-08-01 doi:10.1101/2025.07.30.667338 Cold Spring Harbor Laboratory Press 2025-08-01 <![CDATA[ Inhibition of BRN2 in Melanoma Reverses Anoikis Resistance and Sensitizes Cells to Killing by Vemurafenib ]]> https://biorxiv.org/content/10.1101/2025.07.31.667908v1?rss=1 View larger version (69K): org.highwire.dtl.DTLVardef@12ffd89org.highwire.dtl.DTLVardef@1ae6c8eorg.highwire.dtl.DTLVardef@58e49forg.highwire.dtl.DTLVardef@9b83e_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract.C_FLOATNO Role of BRN2 in driving anoikis resistance in melanoma. Upon detachment from the extra-cellular matrix (ECM) melanoma cells must evade cell death by anoikis to seed distant metastases. This study expanded the understanding of the role of the BRN2 transcription factor as a driver of resistance to anoikis in melanoma. The use of small molecule inhibitors targeting BRN2 revealed that the transcription factor drives anoikis resistance via the MAPK and NF-{kappa}B signaling pathways, resulting in PPAR{gamma} dysregulation and subsequently driving mitochondrial dysfunction. Green boxes = previously published drivers of anoikis resistance in melanoma. Blue box = changes to mitochondrial function following inhibition of BRN2 as determined by proteomics analysis. C_FIG ]]> Neuendorf, H. M. He, X. Adams, M. N. Tran, K. A. Smith, A. G. Bernhardt, P. V. Williams, C. M. Simmons, J. L. Boyle, G. M. 2025-08-02 doi:10.1101/2025.07.31.667908 Cold Spring Harbor Laboratory Press 2025-08-02 <![CDATA[ A mathematical model for inflammation and demyelination in multiple sclerosis ]]> https://biorxiv.org/content/10.1101/2025.07.31.667831v1?rss=1 Jenner, A. L. Weatherley, G. R. Frascoli, F. 2025-08-04 doi:10.1101/2025.07.31.667831 Cold Spring Harbor Laboratory Press 2025-08-04 <![CDATA[ The Latency of a Domain-General Visual Surprise Signal is Attribute Dependent ]]> https://biorxiv.org/content/10.1101/2025.08.18.670829v1?rss=1 Lowe, B. G. Yamamoto, N. Robinson, J. E. Johnston, P. 2025-08-18 doi:10.1101/2025.08.18.670829 Cold Spring Harbor Laboratory Press 2025-08-18 <![CDATA[ Distinct brain mechanisms support trust violations, belief integration, and bias in human-AI teams ]]> https://biorxiv.org/content/10.1101/2025.08.16.670645v1?rss=1 Roeder, L. Hoyte, P. Kerr, G. K. Bruza, P. van der Meer, J. N. 2025-08-19 doi:10.1101/2025.08.16.670645 Cold Spring Harbor Laboratory Press 2025-08-19 <![CDATA[ Revealing the Paper Mill Iceberg: AI-Based Screening of Cancer Research Publications. ]]> https://biorxiv.org/content/10.1101/2025.08.29.673016v1?rss=1 Scancar, B. Byrne, J. A. Causeur, D. Barnett, A. G. 2025-09-03 doi:10.1101/2025.08.29.673016 Cold Spring Harbor Laboratory Press 2025-09-03 <![CDATA[ Modelling the emergence of spiral colony morphology in the yeast Magnusiomyces magnusii ]]> https://biorxiv.org/content/10.1101/2025.09.07.674689v1?rss=1 Li, K. Black, A. J. Knezevic, T. Gardner, J. M. Zhang, J. Jiranek, V. Green, J. E. F. Binder, B. J. Tam, A. K. Y. 2025-09-07 doi:10.1101/2025.09.07.674689 Cold Spring Harbor Laboratory Press 2025-09-07 <![CDATA[ From Home to Transcriptome: Comparing the transcriptomic profile of induced immune response via lipopolysaccharide stimulation in homeRNA and venous blood ]]> https://biorxiv.org/content/10.1101/2025.09.27.678977v1?rss=1 Brown, L. G. Wei, X. Milton, L. A. Alizai, M. Y. MacDonald, J. W. Bammler, T. K. Zeng, Y. Robertson, I. H. Adams, K. N. Toh, Y.-C. Chaussabel, D. Berthier, E. Haack, A. J. Theberge, A. B. 2025-09-29 doi:10.1101/2025.09.27.678977 Cold Spring Harbor Laboratory Press 2025-09-29 <![CDATA[ Suspended Tissue Engineering with Assemblable Microfluidics (STEAM) ]]> https://biorxiv.org/content/10.1101/2025.10.28.684690v1?rss=1 Haack, A. J. Whitten, J. M. Knudsen, L. A. Bouker, E. E. Viswanathan, A. R. Brown, L. G. Kim, D. A. Milton, L. A. Lin, A. Georgiou, A. Schumacher, E. A. Alizai, M. Y. Toh, Y.-C. Berthier, J. DeForest, C. A. Sniadecki, N. J. Theberge, A. B. Berthier, E. 2025-10-29 doi:10.1101/2025.10.28.684690 Cold Spring Harbor Laboratory Press 2025-10-29 <![CDATA[ The emerging role of receptor trafficking insignalosome formation and sustained long-termWnt/β-catenin signaling ]]> https://biorxiv.org/content/10.1101/2025.11.20.689481v1?rss=1 Haack, F. Burrage, K. Uhrmacher, A. M. 2025-11-20 doi:10.1101/2025.11.20.689481 Cold Spring Harbor Laboratory Press 2025-11-20 <![CDATA[ The impact of mechanical requirements on the neural control of skeletal muscle and subsequent energetic rates ]]> https://biorxiv.org/content/10.64898/2025.12.04.692254v1?rss=1 Konno, R. N. Hug, F. Lichtwark, G. A. Dick, T. J. 2025-12-09 doi:10.64898/2025.12.04.692254 Cold Spring Harbor Laboratory Press 2025-12-09 <![CDATA[ CRISPR-DA: Adapting CRISPR gRNA design for detection assays ]]> https://biorxiv.org/content/10.64898/2025.12.05.692701v1?rss=1 Schmitz, C. Bradford, J. Perrin, D. 2025-12-09 doi:10.64898/2025.12.05.692701 Cold Spring Harbor Laboratory Press 2025-12-09 <![CDATA[ Intricate microbiome differences observed in lactating cows across methane intensity phenotypes ]]> https://biorxiv.org/content/10.64898/2025.12.11.692445v1?rss=1 Maynez Perez, A. O. Cahyo, H. N. Niu, P. Aho, V. T. E. Pope, P. B. Schwarm, A. 2025-12-11 doi:10.64898/2025.12.11.692445 Cold Spring Harbor Laboratory Press 2025-12-11 <![CDATA[ Deacetylation of β-Mannans by Two Complementary Carbohydrate Esterases from the Human Gut Microbe Bacteroides cellulosilyticus ]]> https://biorxiv.org/content/10.64898/2025.12.12.693890v1?rss=1 Lindstad, L. J. Mrozek, P. M. Boehlich, J. Leivers, S. Pope, P. La Rosa, S. L. Westereng, B. 2025-12-12 doi:10.64898/2025.12.12.693890 Cold Spring Harbor Laboratory Press 2025-12-12 <![CDATA[ Transcriptional profiling of Pseudomonas aeruginosa biofilm life cycle stages reveals dispersal-specific biomarkers ]]> https://biorxiv.org/content/10.64898/2025.12.18.695191v1?rss=1 Bertran i Forga, X. Fairfull-Smith, K. E. Qin, J. Totsika, M. 2025-12-20 doi:10.64898/2025.12.18.695191 Cold Spring Harbor Laboratory Press 2025-12-20 <![CDATA[ Development of a displacement-controlled uniaxial-strain bioreactor for high-throughput, dynamic in vitro cell culture ]]> https://biorxiv.org/content/10.64898/2025.12.18.695040v1?rss=1 Eames, M. L. Pickering, E. Subedi, P. Woodruff, M. Klein, T. 2025-12-22 doi:10.64898/2025.12.18.695040 Cold Spring Harbor Laboratory Press 2025-12-22 <![CDATA[ A multilevel hierarchical framework for quantification of experimental heterogeneity ]]> https://biorxiv.org/content/10.64898/2025.12.21.695338v1?rss=1 Warne, D. J. Zhu, X. Steele, T. P. Johnston, S. T. Sisson, S. A. Faria, M. Murphy, R. J. Browning, A. P. 2025-12-23 doi:10.64898/2025.12.21.695338 Cold Spring Harbor Laboratory Press 2025-12-23 <![CDATA[ A New Paradigm for the Mathematical Modelling of Multiple Sclerosis ]]> https://biorxiv.org/content/10.64898/2026.01.04.697229v1?rss=1 Hillen, T. Jenner, A. L. 2026-01-06 doi:10.64898/2026.01.04.697229 Cold Spring Harbor Laboratory Press 2026-01-06 <![CDATA[ Regional and sub-regional microglial heterogeneity in the steady-state mouse brain and retina ]]> https://biorxiv.org/content/10.64898/2026.01.16.699866v1?rss=1 Etebar, F. Whatmore, P. Harkin, D. G. Quek, H. Eme-Scolan, E. McMenamin, P. G. Dando, S. J. 2026-01-16 doi:10.64898/2026.01.16.699866 Cold Spring Harbor Laboratory Press 2026-01-16 <![CDATA[ When should we use non-stationary adaptive management? A value of information analysis ]]> https://biorxiv.org/content/10.64898/2026.01.19.699800v1?rss=1 Pascal, L. V. Chades, I. Adams, M. P. Helmstedt, K. J. 2026-01-20 doi:10.64898/2026.01.19.699800 Cold Spring Harbor Laboratory Press 2026-01-20 <![CDATA[ Ruminosignatures associated with methane emissions and feed efficiency across geographies and cattle breeds ]]> https://biorxiv.org/content/10.64898/2026.02.19.706774v1?rss=1 Vourlaki, I.-T. Furman, O. Tapio, I. Guan, L. L. Waters, S. M. 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