bioRxiv Channel: European Molecular Biology Laboratory (EMBL) https://biorxiv.org This feed contains articles for bioRxiv Channel "European Molecular Biology Laboratory (EMBL)" bioRxiv bioRxiv https://biorxiv.org <![CDATA[ An RNA-binding tropomyosin recruits kinesin-1 dynamically to oskar mRNPs ]]> https://biorxiv.org/cgi/content/short/067876v1?rss=1" Imre Gaspar Vasily Sysoev Artem Komissarov Anne Ephrussi 2016-08-04 doi:10.1101/067876 Cold Spring Harbor Laboratory Press 2016-08-04 <![CDATA[ Enzymatic production of single molecule FISH and RNA capture probes ]]> https://biorxiv.org/cgi/content/short/107599v1?rss=1" 90 %, often >95 % labeled product with minimal carry-over of impurities and 3) the oligonucleotides can be labeled with different dyes or biotin, allowing single molecule FISH or RNA affinity purification to be performed.nnGraphical abstractnnO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=66 SRC="FIGDIR/small/107599_ufig1.gif" ALT="Figure 1">nView larger version (20K):norg.highwire.dtl.DTLVardef@a26162org.highwire.dtl.DTLVardef@a780d9org.highwire.dtl.DTLVardef@fc3a62org.highwire.dtl.DTLVardef@15d183c_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Gaspar, I. Wippich, F. Ephrussi, A. 2017-02-10 doi:10.1101/107599 Cold Spring Harbor Laboratory Press 2017-02-10 <![CDATA[ Transposon silencing in the Drosophila female germline ensures genome stability in progeny embryos ]]> https://biorxiv.org/cgi/content/short/363028v1?rss=1" Ephrussi, A. Durdevic, Z. Pillai, R. S. 2018-07-05 doi:10.1101/363028 Cold Spring Harbor Laboratory Press 2018-07-05 <![CDATA[ All four double-stranded RNA binding domains of Staufen2 contribute to efficient mRNA recognition and transcript localization ]]> https://biorxiv.org/cgi/content/short/396994v1?rss=1" Heber, S. Gaspar, I. Tants, J.-N. Günther, J. Fernandez Moya, S. M. Janowski, R. Ephrussi, A. Sattler, M. Niessing, D. 2018-08-21 doi:10.1101/396994 Cold Spring Harbor Laboratory Press 2018-08-21 <![CDATA[ Iterative model-based density improvement yields better atomic structures from cryo-EM maps ]]> https://biorxiv.org/cgi/content/short/121913v1?rss=1" Jakobi, A. J. Wilmanns, M. Sachse, C. 2017-03-29 doi:10.1101/121913 Cold Spring Harbor Laboratory Press 2017-03-29 <![CDATA[ NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language ]]> https://biorxiv.org/cgi/content/short/367755v1?rss=1" Coelho, L. P. Alves, R. Monteiro, P. Huerta-Cepas, J. Freitas, A. T. Bork, P. 2018-07-13 doi:10.1101/367755 Cold Spring Harbor Laboratory Press 2018-07-13 <![CDATA[ Software tools for automated transmission electron microscopy ]]> https://biorxiv.org/cgi/content/short/389502v1?rss=1" Schorb, M. Haberbosch, I. Hagen, W. Schwab, Y. Mastronarde, D. 2018-08-10 doi:10.1101/389502 Cold Spring Harbor Laboratory Press 2018-08-10 <![CDATA[ Curatr: a web application for creating, curating, and sharing a mass spectral library ]]> https://biorxiv.org/cgi/content/short/170571v1?rss=1" Palmer, A. Phapale, P. Fay, D. Alexandrov, T. 2017-08-15 doi:10.1101/170571 Cold Spring Harbor Laboratory Press 2017-08-15 <![CDATA[ Conserved SQ and QS motifs in bacterial effectors suggest pathogen interplay with the ATM kinase family during infection ]]> https://biorxiv.org/cgi/content/short/364117v1?rss=1" Sampietro, D. Samano-Sanchez, H. Davey, N. E. Sharan, M. Meszaros, B. Gibson, T. J. Kumar, M. 2018-07-09 doi:10.1101/364117 Cold Spring Harbor Laboratory Press 2018-07-09 <![CDATA[ An experimental and computational framework to build a dynamic protein atlas of human cell division ]]> https://biorxiv.org/cgi/content/short/227751v1?rss=1" Cai, Y. Hossain, M. J. Heriche, J.-K. Politi, A. Z. Walther, N. Koch, B. Wachsmuth, M. Nijmeijer, B. Kueblbeck, M. Martinic, M. Ladurner, R. Peters, J.-M. Ellenberg, J. 2017-12-01 doi:10.1101/227751 Cold Spring Harbor Laboratory Press 2017-12-01 <![CDATA[ Disruption of dual zygotic spindle assembly shows epigenetic asymmetry to be chromosome intrinsic ]]> https://biorxiv.org/cgi/content/short/198275v1?rss=1" Reichmann, J. Nijmeijer, B. Hossain, M. J. Eguren, M. Schneider, I. Politi, A. Z. Roberti, M. J. Hufnagel, L. Hiiragi, T. Ellenberg, J. 2017-10-04 doi:10.1101/198275 Cold Spring Harbor Laboratory Press 2017-10-04 <![CDATA[ Discovery of a new path for red blood cell generation in the mouse embryo ]]> https://biorxiv.org/cgi/content/short/309054v1?rss=1" Pinheiro, I. Vargel Bolukbasi, O. Ganter, K. Sabou, L. A. Tew, V. K. Bolasco, G. Shvartsman, M. Pavlovich, P. V. Buness, A. Nikolakopoulou, C. Bergiers, I. Kouskoff, V. Lacaud, G. Lancrin, C. 2018-04-28 doi:10.1101/309054 Cold Spring Harbor Laboratory Press 2018-04-28 <![CDATA[ Cytoskeleton mechanics determine resting size and activation dynamics of platelets. ]]> https://biorxiv.org/cgi/content/short/413377v1?rss=1" Mathur, A. Correia, S. R. Dmitrieff, S. Gibeaux, R. Kalinina, I. Quidwai, T. Ries, J. Nedelec, F. 2018-09-10 doi:10.1101/413377 Cold Spring Harbor Laboratory Press 2018-09-10 <![CDATA[ Non-Parametric Analysis of Thermal Proteome Profiles Reveals Novel Drug-Binding Proteins ]]> https://biorxiv.org/cgi/content/short/373845v1?rss=1" Childs, D. Bach, K. Franken, H. Anders, S. Kurzawa, N. Bantscheff, M. Mikhail, S. Huber, W. 2018-07-22 doi:10.1101/373845 Cold Spring Harbor Laboratory Press 2018-07-22 <![CDATA[ CausalTab: PSI-MITAB 2.8 updated format for signaling data representation and dissemination ]]> https://biorxiv.org/cgi/content/short/385773v1?rss=1" Perfetto, L. Acencio, M. L. Bradley, G. Cesareni, G. del Toro, N. Fazekas, D. Hermjakob, H. Korcsmaros, T. Kuiper, M. laegreid, A. Lo Surdo, P. Lovering, R. C. Orchard, S. Porras, P. Thomas, P. D. Toure, V. Zobolas, J. Licata, L. 2018-08-06 doi:10.1101/385773 Cold Spring Harbor Laboratory Press 2018-08-06 <![CDATA[ Hydraulic control of embryo size, tissue shape and cell fate ]]> https://biorxiv.org/cgi/content/short/389619v1?rss=1" Chan, C. J. Costanzo, M. Ruiz-Herrero, T. Monke, G. Petrie, R. Mahadevan, L. Hiiragi, T. 2018-08-10 doi:10.1101/389619 Cold Spring Harbor Laboratory Press 2018-08-10 <![CDATA[ Patient-specific logic models of signaling pathways from screenings on cancer biopsies to prioritize personalized combination therapies ]]> https://biorxiv.org/cgi/content/short/422998v1?rss=1" Eduati, F. Jaaks, P. Merten, C. A. Garnett, M. J. Saez-Rodriguez, J. 2018-09-21 doi:10.1101/422998 Cold Spring Harbor Laboratory Press 2018-09-21 <![CDATA[ Quantitative mapping of fluorescently tagged cellular proteins using FCS-calibrated four dimensional imaging ]]> https://biorxiv.org/cgi/content/short/188862v1?rss=1" Politi, A. Z. Cai, Y. Walther, N. Hossain, M. J. Koch, B. Wachsmuth, M. Ellenberg, J. 2017-09-14 doi:10.1101/188862 Cold Spring Harbor Laboratory Press 2017-09-14 <![CDATA[ Enabling rapid cloud-based analysis of thousands of human genomes via Butler ]]> https://biorxiv.org/cgi/content/short/185736v1?rss=1" Yakneen, S. Waszak, S. Gertz, M. Korbel, J. O. 2017-09-07 doi:10.1101/185736 Cold Spring Harbor Laboratory Press 2017-09-07 <![CDATA[ Xist lncRNA forms silencing granules that induce heterochromatin formation and repressive complexes recruitment by phase separation ]]> https://biorxiv.org/cgi/content/short/351015v1?rss=1" Cerase, A. Armaos, A. Cid-Samper, F. Avner, P. Tartaglia, G. G. 2018-06-20 doi:10.1101/351015 Cold Spring Harbor Laboratory Press 2018-06-20 <![CDATA[ Single-cell transcriptomics identifies CD44 as a new marker and regulator of haematopoietic stem cells development ]]> https://biorxiv.org/cgi/content/short/338178v1?rss=1" Oatley, M. Vargel Bolukbasi, O. Svensson, V. Shvartsman, M. Ganter, K. Zirngibl, K. Pavlovich, P. V. Milchevskaya, V. Foteva, V. Natarajan, K. N. Baying, B. Benes, V. Patil, K. R. Teichmann, S. A. Lancrin, C. 2018-06-06 doi:10.1101/338178 Cold Spring Harbor Laboratory Press 2018-06-06 <![CDATA[ A real-time compression library for microscopy images ]]> https://biorxiv.org/cgi/content/short/164624v1?rss=1" Balazs, B. Deschamps, J. Albert, M. Ries, J. Hufnagel, L. 2017-07-21 doi:10.1101/164624 Cold Spring Harbor Laboratory Press 2017-07-21 <![CDATA[ F-actin patches nucleated on chromosomes coordinate capture by microtubules in oocyte meiosis ]]> https://biorxiv.org/cgi/content/short/265009v1?rss=1" Burdyniuk, M. Callegari, A. Mori, M. Nedelec, F. Lenart, P. 2018-02-13 doi:10.1101/265009 Cold Spring Harbor Laboratory Press 2018-02-13 <![CDATA[ PDX Finder: A Portal for Patient-Derived tumor Xenograft Model Discovery ]]> https://biorxiv.org/cgi/content/short/291443v1?rss=1" Conte, N. Mason, J. Halmagyi, C. Neuhauser, S. Mosaku, A. Begley, D. A. Kupkre, D. M. Parkinson, H. Meehan, T. Bult, C. J. 2018-04-03 doi:10.1101/291443 Cold Spring Harbor Laboratory Press 2018-04-03 <![CDATA[ PathwayMatcher: multi-omics pathway mapping and proteoform network generation ]]> https://biorxiv.org/cgi/content/short/375097v1?rss=1" Hernandez Sanchez, L. F. Burger, B. Horro, C. Fabregat, A. Johansson, S. Njolstad, P. R. Barsnes, H. Hermjakob, H. Vaudel, M. 2018-07-23 doi:10.1101/375097 Cold Spring Harbor Laboratory Press 2018-07-23 <![CDATA[ Identifying alternative splicing isoforms in the human proteome with small proteotranscriptomic databases ]]> https://biorxiv.org/cgi/content/short/372995v1?rss=1" Lau, E. Lam, M. P. Y. 2018-07-27 doi:10.1101/372995 Cold Spring Harbor Laboratory Press 2018-07-27 <![CDATA[ Thresholding of cryo-EM density maps by false discovery rate control ]]> https://biorxiv.org/cgi/content/short/374546v1?rss=1" Beckers, M. Jakobi, A. Sachse, C. 2018-07-23 doi:10.1101/374546 Cold Spring Harbor Laboratory Press 2018-07-23 <![CDATA[ PlasmidTron: assembling the cause of phenotypes from NGS data ]]> https://biorxiv.org/cgi/content/short/188920v1?rss=1" Page, A. J. Wailan, A. Shao, Y. Judge, K. Dougan, G. Klemm, E. J. Thomson, N. R. Keane, J. A. 2017-09-15 doi:10.1101/188920 Cold Spring Harbor Laboratory Press 2017-09-15 <![CDATA[ Bicoid gradient formation mechanism and dynamics revealed by protein lifetime analysis ]]> https://biorxiv.org/cgi/content/short/280834v1?rss=1" Durrieu, L. Kirrmaier, D. Schneidt, T. Kats, I. Raghavan, S. Knop, M. Saunders, T. E. Hufnagel, L. 2018-03-13 doi:10.1101/280834 Cold Spring Harbor Laboratory Press 2018-03-13 <![CDATA[ Detection and removal of barcode swapping in single-cell RNA-seq data ]]> https://biorxiv.org/cgi/content/short/177048v1?rss=1" Griffiths, J. A. Lun, A. T. L. Richard, A. C. Bach, K. Marioni, J. C. 2017-08-16 doi:10.1101/177048 Cold Spring Harbor Laboratory Press 2017-08-16 <![CDATA[ PhenoMeNal: Processing and analysis of Metabolomics data in the Cloud ]]> https://biorxiv.org/cgi/content/short/409151v1?rss=1" Peters, K. Bradbury, J. Bergmann, S. Capuccini, M. Cascante, M. de Atauri, P. Ebbels, T. Foguet, C. Glen, R. Gonzalez-Beltran, A. Handakas, E. Hankemeier, T. Herman, S. Haug, K. Holub, P. Izzo, M. Jacob, D. Johnson, D. Jourdan, F. Kale, N. Karaman, I. Khalili, B. Emami Khoonsari, P. Kultima, K. Lampa, S. Larsson, A. Moreno, P. Neumann, S. Novella, J. A. O'Donovan, C. Pearce, J. T. Peluso, A. Pireddu, L. Piras, M. E. Reed, M. A. Rocca-Serra, P. Roger, P. Rosato, A. Rueedi, R. Ruttkies, C. Sadawi, N. Salek, R. Sansone, S.-A. Selivanov, V. Spjuth, O. 2018-09-06 doi:10.1101/409151 Cold Spring Harbor Laboratory Press 2018-09-06 <![CDATA[ Fast automated reconstruction of genome-scale metabolic models for microbial species and communities ]]> https://biorxiv.org/cgi/content/short/223198v1?rss=1" Machado, D. Andrejev, S. Tramontano, M. Patil, K. R. 2018-01-12 doi:10.1101/223198 Cold Spring Harbor Laboratory Press 2018-01-12 <![CDATA[ A congenital pain insensitivity mutation in the nerve growth factor gene uncouples nociception from affective pain in heterozygous humans and mice ]]> https://biorxiv.org/cgi/content/short/331587v1?rss=1" Testa, G. Perini, I. Mainardi, M. Morelli, C. Olimpico, F. Pancrazi, L. Petrella, C. Severini, C. Florio, R. Malerba, F. Heppenstall, P. Costa, M. Morrison, I. Capsoni, S. Cattaneo, A. 2018-05-25 doi:10.1101/331587 Cold Spring Harbor Laboratory Press 2018-05-25 <![CDATA[ Effect of Sec61 interaction with Mpd1 on Endoplasmic Reticulum-Associated Degradation ]]> https://biorxiv.org/cgi/content/short/411173v1?rss=1" Pereira, F. Rettel, M. Stein, F. Savitski, M. M. Collinson, I. Romisch, K. 2018-09-07 doi:10.1101/411173 Cold Spring Harbor Laboratory Press 2018-09-07 <![CDATA[ Generation and validation of homozygous fluorescent knock-in cells using genome editing ]]> https://biorxiv.org/cgi/content/short/188847v1?rss=1" Koch, B. Nijmeijer, B. Kueblbeck, M. Cai, Y. Walther, N. Ellenberg, J. 2017-09-14 doi:10.1101/188847 Cold Spring Harbor Laboratory Press 2017-09-14 <![CDATA[ A combinatorial extracellular code tunes the intracellular signaling network activity to distinct cellular responses ]]> https://biorxiv.org/cgi/content/short/346957v1?rss=1" Kuchenov, D. Ziebell, F. Salopiata, F. Citir, M. Klingmueller, U. Huber, W. Schultz, C. 2018-06-14 doi:10.1101/346957 Cold Spring Harbor Laboratory Press 2018-06-14 <![CDATA[ UniProt Genomic Mapping for Deciphering Functional Effects of Missense Variants ]]> https://biorxiv.org/cgi/content/short/192914v1?rss=1" McGarvey, P. Nightingale, A. Luo, J. Huang, H. Martin, M.-J. Wu, C. UniProt Consortium, 2017-09-22 doi:10.1101/192914 Cold Spring Harbor Laboratory Press 2017-09-22 <![CDATA[ Multi-Omics factor analysis disentangles heterogeneity in blood cancer ]]> https://biorxiv.org/cgi/content/short/217554v1?rss=1" Argelaguet, R. Velten, B. Arnol, D. Dietrich, S. Zenz, T. Marioni, J. C. Buettner, F. Huber, W. Stegle, O. 2017-11-10 doi:10.1101/217554 Cold Spring Harbor Laboratory Press 2017-11-10 <![CDATA[ Chromatin-dependent cryptic promoters encode alternative protein isoforms in yeast. ]]> https://biorxiv.org/cgi/content/short/403543v1?rss=1" Wei, W. Hennig, B. Wang, J. Zhang, Y. Chabbert, C. D. Adjalley, S. H. Steinmetz, L. M. Pelechano, V. 2018-08-29 doi:10.1101/403543 Cold Spring Harbor Laboratory Press 2018-08-29 <![CDATA[ Systematic analysis of the molecular architecture of endocytosis reveals a nanoscale actin nucleation template that drives efficient vesicle formation ]]> https://biorxiv.org/cgi/content/short/217836v1?rss=1" Mund, M. van der Beek, J. A. Deschamps, J. Dmitrieff, S. Monster, J. L. Picco, A. Nedelec, F. Kaksonen, M. Ries, J. 2017-11-15 doi:10.1101/217836 Cold Spring Harbor Laboratory Press 2017-11-15 <![CDATA[ Quantifying the impact of public omics data ]]> https://biorxiv.org/cgi/content/short/282517v1?rss=1" Perez-Riverol, Y. Zorin, A. Dass, G. Glont, M. Vizcaino, J. A. Jarnuczak, A. Petryszak, R. Ping, P. Hermjakob, H. 2018-03-14 doi:10.1101/282517 Cold Spring Harbor Laboratory Press 2018-03-14 <![CDATA[ Whole-body single-cell sequencing of the Platynereis larva reveals a subdivision into apical versus non-apical tissues ]]> https://biorxiv.org/cgi/content/short/167742v1?rss=1" Achim, K. Eling, N. Martinez Vergara, H. Bertucci, P. Y. Brunet, T. Collier, P. Benes, V. Marioni, J. C. Arendt, D. 2017-07-24 doi:10.1101/167742 Cold Spring Harbor Laboratory Press 2017-07-24 <![CDATA[ Genome-wide comparative analysis reveals human- mouse regulatory landscape and evolution ]]> https://biorxiv.org/cgi/content/short/010926v1?rss=1" Olgert Denas Richard Sandstrom Yong Cheng Kathryn Beal Javier Herrero Ross Hardison James Taylor 2014-10-30 doi:10.1101/010926 Cold Spring Harbor Laboratory Press 2014-10-30 <![CDATA[ Cooperative development of logical modelling standards and tools with CoLoMoTo ]]> https://biorxiv.org/cgi/content/short/010504v1?rss=1" Aurélien Naldi Pedro T Monteiro Christoph Müssel the Consortium for Logical Models and Tools Hans A Kestler Denis Thieffry Ioannis Xenarios Julio Saez-Rodriguez Tomas Helikar Claudine Chaouiya 2014-10-19 doi:10.1101/010504 Cold Spring Harbor Laboratory Press 2014-10-19 <![CDATA[ Conservation and structural analysis of the Xenopus laevis phospho-proteome ]]> https://biorxiv.org/cgi/content/short/009100v1?rss=1" Jeffrey R Johnson Silvia D Santos Tasha Johnson Ursula Pieper Andrej Sali Nevan J Krogan Pedro Beltrao 2014-09-14 doi:10.1101/009100 Cold Spring Harbor Laboratory Press 2014-09-14 <![CDATA[ DISEASES: Text mining and data integration of disease–gene associations ]]> https://biorxiv.org/cgi/content/short/008425v1?rss=1" Sune Pletscher-Frankild Albert Pallejà Kalliopi Tsafou Janos X Binder Lars Juhl Jensen 2014-08-25 doi:10.1101/008425 Cold Spring Harbor Laboratory Press 2014-08-25 <![CDATA[ HTSeq - A Python framework to work with high-throughput sequencing data ]]> https://biorxiv.org/cgi/content/short/002824v1?rss=1" Simon Anders Paul Theodor Pyl Wolfgang Huber 2014-02-20 doi:10.1101/002824 Cold Spring Harbor Laboratory Press 2014-02-20 <![CDATA[ RNA-Rocket: An RNA-Seq Analysis Resource for Infectious Disease Research ]]> https://biorxiv.org/cgi/content/short/007963v1?rss=1" Andrew S. Warren Cristina Aurrecoechea Brian Brunk Prerak Desai Scott Emrich Gloria I. Giraldo-Calderón Omar Harb Deborah Hix Daniel Lawson Dustin Machi Chunhong Mao Michael McClelland Eric Nordberg Maulik Shukla Leslie B. Vosshall Alice R. Wattam Rebecca Will Hyun Seung Yoo Bruno Sobral 2014-08-14 doi:10.1101/007963 Cold Spring Harbor Laboratory Press 2014-08-14 <![CDATA[ RNA-seq gene profiling - a systematic empirical comparison ]]> https://biorxiv.org/cgi/content/short/005207v1?rss=1" Nuno A Fonseca John A Marioni Alvis Brazma 2014-05-14 doi:10.1101/005207 Cold Spring Harbor Laboratory Press 2014-05-14 <![CDATA[ Mutated SF3B1 is associated with transcript isoform changes of the genes UQCC and RPL31 both in CLLs and uveal melanomas ]]> https://biorxiv.org/cgi/content/short/000992v1?rss=1" Alejandro Reyes Carolin Blume Vicent Pelechano Petra Jakob Lars M Steinmetz Thorsten Zenz Wolfgang Huber 2013-12-02 doi:10.1101/000992 Cold Spring Harbor Laboratory Press 2013-12-02 <![CDATA[ Identification, annotation and visualisation of extreme changes in splicing from RNA-seq experiments with SwitchSeq ]]> https://biorxiv.org/cgi/content/short/005967v1?rss=1" Mar Gonzàlez-Porta Alvis Brazma 2014-06-06 doi:10.1101/005967 Cold Spring Harbor Laboratory Press 2014-06-06 <![CDATA[ iRAP - an integrated RNA-seq Analysis Pipeline ]]> https://biorxiv.org/cgi/content/short/005991v1?rss=1" Nuno A. Fonseca Robert Petryszak John Marioni Alvis Brazma 2014-06-06 doi:10.1101/005991 Cold Spring Harbor Laboratory Press 2014-06-06 <![CDATA[ LIMIX: genetic analysis of multiple traits ]]> https://biorxiv.org/cgi/content/short/003905v1?rss=1" Christoph Lippert Francesco Paolo Casale Barbara Rakitsch Oliver Stegle 2014-05-21 doi:10.1101/003905 Cold Spring Harbor Laboratory Press 2014-05-21 <![CDATA[ Neural lineage induction reveals multi-scale dynamics of 3D chromatin organization ]]> https://biorxiv.org/cgi/content/short/004168v1?rss=1" Aleksandra Pekowska Bernd Klaus Felix Alexander Klein Simon Anders Malgorzata Oles Lars Michael Steinmetz Paul Bertone Wolfgang Huber 2014-04-11 doi:10.1101/004168 Cold Spring Harbor Laboratory Press 2014-04-11 <![CDATA[ Alignathon: A competitive assessment of whole genome alignment methods. ]]> https://biorxiv.org/cgi/content/short/003285v1?rss=1" Dent Earl Ngan K Nguyen Glenn Hickey Robert S. Harris Stephen Fitzgerald Kathryn Beal Igor Seledtsov Vladimir Molodtsov Brian Raney Hiram Clawson Jaebum Kim Carsten Kemena Jia-Ming Chang Ionas Erb Alexander Poliakov Minmei Hou Javier Herrero Victor Solovyev Aaron E. Darling Jian Ma Cedric Notredame Michael Brudno Inna Dubchak David Haussler Benedict Paten 2014-03-10 doi:10.1101/003285 Cold Spring Harbor Laboratory Press 2014-03-10 <![CDATA[ FourCSeq: Analysis of 4C sequencing data ]]> https://biorxiv.org/cgi/content/short/009548v1?rss=1" Felix A. Klein Tibor Pakozdi Simon Anders Yad Ghavi-Helm Eileen E. M. Furlong Wolfgang Huber 2014-09-23 doi:10.1101/009548 Cold Spring Harbor Laboratory Press 2014-09-23 <![CDATA[ Open science resources for the discovery and analysis of Tara Oceans Data ]]> https://biorxiv.org/cgi/content/short/019117v1?rss=1" Stéphane Pesant Fabrice Not Marc Picheral Stefanie Kandels-Lewis Noan Le Bescot Gabriel Gorsky Daniele Iudicone Eric Karsenti Sabrina Speich Romain Troublé Celine Dimier Sarah Searson Tara Oceans Consortium Coordinators 2015-05-08 doi:10.1101/019117 Cold Spring Harbor Laboratory Press 2015-05-08 <![CDATA[ SomaticSignatures: Inferring Mutational Signatures from Single Nucleotide Variants ]]> https://biorxiv.org/cgi/content/short/010686v1?rss=1" Julian S. Gehring Bernd Fischer Michael Lawrence Wolfgang Huber 2014-10-24 doi:10.1101/010686 Cold Spring Harbor Laboratory Press 2014-10-24 <![CDATA[ Mutational oncogenic signatures on structurally resolved protein interacting interfaces ]]> https://biorxiv.org/cgi/content/short/016204v1?rss=1" Luz Garcia-Alonso Joaquin Dopazo 2015-03-07 doi:10.1101/016204 Cold Spring Harbor Laboratory Press 2015-03-07 <![CDATA[ FORGE : A tool to discover cell specific enrichments of GWAS associated SNPs in regulatory regions. ]]> https://biorxiv.org/cgi/content/short/013045v1?rss=1" Ian Dunham Eugene Kulesha Valentina Iotchkova Sandro Morganella Ewan Birney 2014-12-20 doi:10.1101/013045 Cold Spring Harbor Laboratory Press 2014-12-20 <![CDATA[ Cell-Line Annotation on Europe PubMed Central ]]> https://biorxiv.org/cgi/content/short/011700v1?rss=1" Jee-Hyub Kim 2014-11-20 doi:10.1101/011700 Cold Spring Harbor Laboratory Press 2014-11-20 <![CDATA[ Triticeae resources in Ensembl Plants ]]> https://biorxiv.org/cgi/content/short/011585v1?rss=1" Dan M Bolser Arnaud Kerhornou Brandon Walts Paul Kersey 2014-11-18 doi:10.1101/011585 Cold Spring Harbor Laboratory Press 2014-11-18 <![CDATA[ Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 ]]> https://biorxiv.org/cgi/content/short/002832v1?rss=1" Michael I Love Wolfgang Huber Simon Anders 2014-02-19 doi:10.1101/002832 Cold Spring Harbor Laboratory Press 2014-02-19 <![CDATA[ The evolutionary fates of a large segmental duplication in mouse ]]> https://biorxiv.org/cgi/content/short/043687v1?rss=1" Andrew Parker Morgan James Matthew Holt Rachel Clara McMullan Timothy A Bell Amelia Mary-Frances Clayshulte John Paul Didion Liran Yadgary David Thybert Duncan T Odom Paul Flicek Leonard McMillan Fernando Pardo-Manuel de Villena 2016-03-15 doi:10.1101/043687 Cold Spring Harbor Laboratory Press 2016-03-15 <![CDATA[ Centrosome centering and decentering by microtubule network rearrangement ]]> https://biorxiv.org/cgi/content/short/057968v1?rss=1" Gaelle Letort Francois Nedelec Laurent Blanchoin Manuel Thery 2016-06-09 doi:10.1101/057968 Cold Spring Harbor Laboratory Press 2016-06-09 <![CDATA[ AtRTD2: A Reference Transcript Dataset for accurate quantification of alternative splicing and expression changes in Arabidopsis thaliana RNA-seq data ]]> https://biorxiv.org/cgi/content/short/051938v1?rss=1" Runxuan Zhang Cristiane P G Calixto Yamile Marquez Peter Venhuizen Nikoleta A Tzioutziou Wenbin Guo Mark Spensley Nicolas Frei dit Frey Heribert Hirt Allan B James Hugh G Nimmo Andrea Barta Maria Kalyna John W S Brown 2016-05-06 doi:10.1101/051938 Cold Spring Harbor Laboratory Press 2016-05-06 <![CDATA[ Molecular and functional variation in iPSC-derived sensory neurons ]]> https://biorxiv.org/cgi/content/short/095943v1?rss=1" Schwartzentruber, J. Foskolou, S. Kilpinen, H. Rodrigues, J. Alasoo, K. Knights, A. J. Patel, M. Goncalves, A. Ferreira, R. Benn, C. L. Wilbrey, A. Bictash, M. Impey, E. Cao, L. Lainez, S. Loucif, A. J. Whiting, P. J. HIPSCI Consortium, Gutteridge, A. Gaffney, D. J. 2017-01-06 doi:10.1101/095943 Cold Spring Harbor Laboratory Press 2017-01-06 <![CDATA[ Joint genetic analysis using variant sets reveals polygenic gene-context interactions ]]> https://biorxiv.org/cgi/content/short/097477v1?rss=1" Casale, F. P. Horta, D. Rakitsch, B. Stegle, O. 2016-12-31 doi:10.1101/097477 Cold Spring Harbor Laboratory Press 2016-12-31 <![CDATA[ Global changes in patterning, splicing and primate specific lncRNAs in autism brain ]]> https://biorxiv.org/cgi/content/short/077057v1?rss=1" Neelroop N Parikshak Vivek Swarup T Grant Belgard Michael J Gandal Manuel Irimia Virpi Leppa Jennifer K Lowe Robert Johnson Benjamin J. Blencowe Steve Horvath Daniel H. Geschwind 2016-09-23 doi:10.1101/077057 Cold Spring Harbor Laboratory Press 2016-09-23 <![CDATA[ Structure and evolutionary history of a large family of NLR proteins in the zebrafish ]]> https://biorxiv.org/cgi/content/short/022061v1?rss=1" Kerstin Howe Philipp H Schiffer Julia Zielinski Thomas Wiehe Gavin K Laird John Marioni Onuralp Soylemez Fyodor Kondrashov Maria Leptin 2015-07-07 doi:10.1101/022061 Cold Spring Harbor Laboratory Press 2015-07-07 <![CDATA[ Transcription factor activities enhance markers of drug response in cancer ]]> https://biorxiv.org/cgi/content/short/129478v1?rss=1" Garcia-Alonso, L. Iorio, F. Matchan, A. Fonseca, N. Jaaks, P. Falcone, F. Bignell, G. McDade, S. S. Garnett, M. J. Saez-Rodriguez, J. 2017-04-21 doi:10.1101/129478 Cold Spring Harbor Laboratory Press 2017-04-21 <![CDATA[ Meiotic interactors of a mitotic gene TAO3 revealed by functional analysis of its rare variant ]]> https://biorxiv.org/cgi/content/short/033167v1?rss=1" Saumya Gupta Aparna Radhakrishnan Rachana Nitin Pandu Raharja-Liu Gen Lin Lars M Steinmetz Julien Gagneur Himanshu Sinha 2015-11-27 doi:10.1101/033167 Cold Spring Harbor Laboratory Press 2015-11-27 <![CDATA[ Perturbation-response genes reveal signaling footprints in cancer gene expression ]]> https://biorxiv.org/cgi/content/short/065672v1?rss=1" Michael Schubert Bertram Klinger Martina Klünemann Mathew J Garnett Nils Blüthgen Julio Saez-Rodriguez 2016-07-25 doi:10.1101/065672 Cold Spring Harbor Laboratory Press 2016-07-25 <![CDATA[ An integrated genomic analysis of anaplastic meningioma identifies prognostic molecular signatures ]]> https://biorxiv.org/cgi/content/short/146811v1?rss=1" Collord, G. Tarpey, P. Kurbatova, N. Martincorena, I. Moran, S. Castro, M. Nagy, T. Bignell, G. Maura, F. Berna, J. Tubio, J. M. McMurran, C. E. Young, A. M. H. Young, M. D. Noorani, I. Price, S. J. Watts, C. Leipnitz, E. Kirsch, M. Schackert, G. Pearson, D. Devadass, A. Ram, Z. Collins, V. P. Allinson, K. Jenkinson, M. Zakaria, R. Syed, K. Hanemann, C. O. Dunn, J. McDermott, M. Kirollos, R. Vassiliou, G. S. Esteller, M. Behjati, S. Brazma, A. Santarius, T. McDermott, U. 2017-06-06 doi:10.1101/146811 Cold Spring Harbor Laboratory Press 2017-06-06 <![CDATA[ The wiring diagram of a glomerular olfactory system ]]> https://biorxiv.org/cgi/content/short/037721v1?rss=1" Matthew E. Berck Avinash Khandelwal Lindsey Claus Luis Hernandez-Nunez Guangwei Si Christopher J. Tabone Feng Li James W. Truman Richard D. Fetter Matthieu Louis Aravinthan D. T. Samuel Albert Cardona 2016-01-22 doi:10.1101/037721 Cold Spring Harbor Laboratory Press 2016-01-22 <![CDATA[ Bayesian analysis of normal mouse cell lineage trees allowing intra-individual, cell population specific mutation rates ]]> https://biorxiv.org/cgi/content/short/040733v1?rss=1" Attila Csordas Remco Bouckaert 2016-02-22 doi:10.1101/040733 Cold Spring Harbor Laboratory Press 2016-02-22 <![CDATA[ Genomic positional conservation identifies topological anchor point (tap)RNAs linked to developmental loci ]]> https://biorxiv.org/cgi/content/short/051052v1?rss=1" Paulo P Amaral Tommaso Leonardi Namshik Han Emmanuelle Vire Dennis K Gascoigne Raul Arias-Carrasco Magdalena Buscher Anda Zhang Stefano Pluchino Vinicius Maracaja-Coutinho Helder I Nakaya Martin Hemberg Ramin Shiekhattar Anton J Enright Tony Kouzarides 2016-04-29 doi:10.1101/051052 Cold Spring Harbor Laboratory Press 2016-04-29 <![CDATA[ Dynamic Maternal Gradients Control Timing and Shift-Rates for Gap Gene Expression ]]> https://biorxiv.org/cgi/content/short/068064v1?rss=1" Berta Verd Anton Crombach Johannes Jaeger 2016-08-05 doi:10.1101/068064 Cold Spring Harbor Laboratory Press 2016-08-05 <![CDATA[ A comprehensive map of genetic variation in the world’s largest ethnic group - Han Chinese ]]> https://biorxiv.org/cgi/content/short/162982v1?rss=1" Chiang, C. W. K. Mangul, S. Robles, C. R. Kretzschmar, W. W. Cai, N. Kendler, K. S. Sankararam, S. Flint, J. 2017-07-13 doi:10.1101/162982 Cold Spring Harbor Laboratory Press 2017-07-13 <![CDATA[ Characterising Complex Enzyme Reaction Data ]]> https://biorxiv.org/cgi/content/short/028142v1?rss=1" Handan Melike Dönertaş Sergio Martínez Cuesta Syed Asad Rahman Janet M. Thornton 2015-10-03 doi:10.1101/028142 Cold Spring Harbor Laboratory Press 2015-10-03 <![CDATA[ Principles for RNA metabolism and alternative transcription initiation within closely spaced promoters ]]> https://biorxiv.org/cgi/content/short/055731v1?rss=1" Yun Chen Athma A Pai Jan Herudek Michal Lubas Nicola Meola Aino I Jarvelin Robin Andersson Vicent Pelechano Lars M Steinmetz Torben Heick Jensen Albin Sandelin 2016-05-27 doi:10.1101/055731 Cold Spring Harbor Laboratory Press 2016-05-27 <![CDATA[ PARP mediated chromatin unfolding is coupled to long-range enhancer activation ]]> https://biorxiv.org/cgi/content/short/155325v1?rss=1" Benabdallah, N. S. Williamson, I. Illingworth, R. S. Boyle, S. Grimes, G. R. Therizols, P. Bickmore, W. 2017-06-25 doi:10.1101/155325 Cold Spring Harbor Laboratory Press 2017-06-25 <![CDATA[ Selective and mechanistic sources of recurrent rearrangements across the cancer genome ]]> https://biorxiv.org/cgi/content/short/187609v1?rss=1" Wala, J. A. Shapira, O. Li, Y. Craft, D. Schumacher, S. E. Imielinski, M. Haber, J. E. Roberts, N. Yao, X. Stewart, C. Zhang, C.-Z. Tubio, J. Ju, Y. S. Campbell, P. Weischenfeldt, J. Beroukhim, R. PCAWG-Structural Variation Working Group, the PCAWG Network, 2017-09-14 doi:10.1101/187609 Cold Spring Harbor Laboratory Press 2017-09-14 <![CDATA[ Pan-cancer study of heterogeneous RNA aberrations ]]> https://biorxiv.org/cgi/content/short/183889v1?rss=1" Fonseca, N. A. Kahles, A. Lehmann, K.-V. Calabrese, C. Chateigner, A. Davidson, N. R. Demircioglu, D. He, Y. Lamaze, F. C. Li, S. Liu, D. Liu, F. Perry, M. D. Su, H. Xiang, L. Zhang, J. Amin, S. B. Bailey, P. Craft, B. Frenkel-Morgenstern, M. Goldman, M. Greger, L. Hoadley, K. A. Hou, Y. Khurana, E. Korbel, J. O. Li, C. Li, X. Li, X. Liu, X. Lu, Y. Marin, M. G. Meyerson, M. Nandi, T. Nielsen, M. M. Ojesina, A. I. Ouellette, B. F. F. Pan-Hammarström, Q. Pedamallu, C. S. Pedersen, J. S. Shiraishi, Y. Siebert, R. Soulette, C. M. Stark, S. G. Tan 2017-09-03 doi:10.1101/183889 Cold Spring Harbor Laboratory Press 2017-09-03 <![CDATA[ Accurate prediction of single-cell DNA methylation states using deep learning ]]> https://biorxiv.org/cgi/content/short/055715v1?rss=1" Christof Angermueller Heather Lee Wolf Reik Oliver Stegle 2016-05-27 doi:10.1101/055715 Cold Spring Harbor Laboratory Press 2016-05-27 <![CDATA[ A compartmentalized, self-extinguishing signaling network mediates crossover control in meiosis ]]> https://biorxiv.org/cgi/content/short/168948v1?rss=1" Zhang, L. Koehler, S. Rillo-Bohn, R. Dernburg, A. F. 2017-07-26 doi:10.1101/168948 Cold Spring Harbor Laboratory Press 2017-07-26 <![CDATA[ Epigenomic co-localization and co-evolution reveal a key role for 5hmC as a communication hub in the chromatin network of ESCs ]]> https://biorxiv.org/cgi/content/short/008821v1?rss=1" David Juan Juliane Perner Enrique Carrillo de Santa Pau Simone Marsili David Ochoa Ho-Ryun Chung Martin Vingron Daniel Rico Alfonso Valencia 2014-09-06 doi:10.1101/008821 Cold Spring Harbor Laboratory Press 2014-09-06 <![CDATA[ Ten Simple Rules for Taking Advantage of git and GitHub ]]> https://biorxiv.org/cgi/content/short/048744v1?rss=1" Yasset Perez-Riverol Laurent Gatto Rui Wang Timo Sachsenberg Julian Uszkoreit Felipe Leprevost Christian Fufezan Tobias Ternent Stephen J Eglen Daniel S. S Katz Tom J Pollard Alexander Konovalov Robert M Flight Kai Blin Juan Antonio Vizcaino 2016-04-15 doi:10.1101/048744 Cold Spring Harbor Laboratory Press 2016-04-15 <![CDATA[ Complexity and conservation of regulatory landscapes underlie evolutionary resilience of mammalian gene expression ]]> https://biorxiv.org/cgi/content/short/125435v1?rss=1" Berthelot, C. Villar, D. Horvath, J. E. Odom, D. T. Flicek, P. 2017-04-07 doi:10.1101/125435 Cold Spring Harbor Laboratory Press 2017-04-07 <![CDATA[ Temporal mixture modelling of single-cell RNA-seq data resolves a CD4+ T cell fate bifurcation ]]> https://biorxiv.org/cgi/content/short/074971v1?rss=1" Tapio Lönnberg Valentine Svensson Kylie R James Daniel Fernandez-Ruiz Ismail Sebina Ruddy Montandon Megan S F Soon Lily G Fogg Michael J T Stubbington Frederik Otzen Bagger Max Zwiessele Neil Lawrence Fernando Souza-Fonseca- Guimaraes William R Heath Oliver Billker Oliver Stegle Ashraful Haque Sarah A Teichmann 2016-09-13 doi:10.1101/074971 Cold Spring Harbor Laboratory Press 2016-09-13 <![CDATA[ Flipping the odds of drug development success through human genomics ]]> https://biorxiv.org/cgi/content/short/170142v1?rss=1" Hingorani, A. D. Kuan, V. Finan, C. Kruger, F. A. Gaulton, A. Chopade, S. Sofat, R. MacAllister, R. J. Overington, J. Hemingway, H. Denaxas, S. Prieto-Merino, D. Casas, J. P. 2017-07-30 doi:10.1101/170142 Cold Spring Harbor Laboratory Press 2017-07-30 <![CDATA[ Inferring synteny between genome assemblies: a systematic evaluation ]]> https://biorxiv.org/cgi/content/short/149989v1?rss=1" Liu, D. Hunt, M. Tsai, I. J. 2017-06-14 doi:10.1101/149989 Cold Spring Harbor Laboratory Press 2017-06-14 <![CDATA[ Personally tailored cancer management based on knowledge banks of genomic and clinical data ]]> https://biorxiv.org/cgi/content/short/057497v1?rss=1" Moritz Gerstung Elli Papaemmanuil Inigo Martincorena Lars Bullinger Verena I Gaidzik Peter Paschka Michael Heuser Felicitas Thol Niccolo Bolli Peter Ganly Arnold Ganser Ultan McDermott Konstanze Dohner Richard F Schlenk Hartmut Dohner Peter J Campbell 2016-06-07 doi:10.1101/057497 Cold Spring Harbor Laboratory Press 2016-06-07 <![CDATA[ Ensembl Core Software Resources: storage and programmatic access for DNA sequence and genome annotation ]]> https://biorxiv.org/cgi/content/short/087239v1?rss=1" Ruffier, M. Kahari, A. Komorowska, M. Keenan, S. Laird, M. R. Longden, I. Proctor, G. Searle, S. Staines, D. Taylor, K. Vullo, A. Yates, A. Zerbino, D. Flicek, P. 2016-11-11 doi:10.1101/087239 Cold Spring Harbor Laboratory Press 2016-11-11 <![CDATA[ An unbiased reconstruction of the T helper cell type 2 differentiation network ]]> https://biorxiv.org/cgi/content/short/196022v1?rss=1" Henriksson, J. Chen, X. Gomes, T. Miragaia, R. Ullah, U. Pramanik, J. Meyer, K. Yusa, K. Lahesmaa, R. Teichmann, S. A. 2017-10-04 doi:10.1101/196022 Cold Spring Harbor Laboratory Press 2017-10-04 <![CDATA[ Immature HIV-1 Lattice Assembly Dynamics are Regulated by Scaffolding from Nucleic Acid and the Plasma Membrane ]]> https://biorxiv.org/cgi/content/short/163295v1?rss=1" Pak, A. J. Grime, J. M. A. Sengupta, P. Chen, A. K. Durumeric, A. E. P. Srivastava, A. Yeager, M. Briggs, J. A. G. Lippincott-Schwartz, J. Voth, G. A. 2017-07-13 doi:10.1101/163295 Cold Spring Harbor Laboratory Press 2017-07-13 <![CDATA[ Comparative analysis of neutrophil and monocyte epigenomes ]]> https://biorxiv.org/cgi/content/short/237784v1?rss=1" Rico, D. Martens, J. H. Downes, K. Carrillo-de-Santa-Pau, E. Pancaldi, V. Breschi, A. Richardson, D. Heath, S. Saeed, S. Frontini, M. Chen, L. Watt, S. Muller, F. Clarke, L. Kerstens, H. H. Wilder, S. P. Palumbo, E. Djebali, S. Rainieri, E. Merkel, A. Esteve-Codina, A. Sultan, M. van Bommel, A. Gut, M. Yaspo, M.-L. Rubio, M. Fernandez, J. M. Attwood, A. de la Torre, V. Royo, R. Fragkogianni, S. Gelpi, J. L. Torrents, D. Iotchkova, V. Logie, C. Aghajanirefah, A. Singh, A. A. Janssen-Megens, E. M. Berentsen, K. Erber, W. Rendon, A. Kostadima, M. Loos, R. 2017-12-22 doi:10.1101/237784 Cold Spring Harbor Laboratory Press 2017-12-22 <![CDATA[ High Frequency Actionable Pathogenic Exome Mutations in an Average-Risk Cohort ]]> https://biorxiv.org/cgi/content/short/151225v1?rss=1" Rego, S. Dagan-Rosenfeld, O. Zhou, W. Sailani, M. R. Limcaoco, P. Colbert, E. Avina, M. Wheeler, J. Craig, C. Salins, D. Rost, H. L. Dunn, J. McLaughlin, T. Steinmetz, L. M. Bernstein, J. A. Snyder, M. P. 2017-06-18 doi:10.1101/151225 Cold Spring Harbor Laboratory Press 2017-06-18 <![CDATA[ Two consecutive microtubule-based epithelial seaming events mediate dorsal closure in the scuttle fly Megaselia abdita ]]> https://biorxiv.org/cgi/content/short/229492v1?rss=1" Fraire-Zamora, J. J. Jaeger, J. Solon, J. 2017-12-05 doi:10.1101/229492 Cold Spring Harbor Laboratory Press 2017-12-05 <![CDATA[ Ecogenomics and biogeochemical impacts of uncultivated globally abundant ocean viruses ]]> https://biorxiv.org/cgi/content/short/053090v1?rss=1" Simon Roux Jennifer R Brum Bas E. Dutilh Shinichi Sunagawa Melissa B Duhaime Alexander Loy Bonnie T Poulos Natalie Solonenko Elena Lara Julie Poulain Stephane PESANT Stefanie Kandels-Lewis Céline Dimier Marc Picheral Sarah Searson Corinne Cruaud Adriana Alberti Carlos M. M Duarte Josep M M Gasol Dolors Vaqué Tara Oceans Coordinators Peer Bork Silvia G Acinas Patrick Wincker Matthew B Sullivan 2016-05-12 doi:10.1101/053090 Cold Spring Harbor Laboratory Press 2016-05-12 <![CDATA[ LiMMBo: a simple, scalable approach for linear mixed models in high-dimensional genetic association studies ]]> https://biorxiv.org/cgi/content/short/255497v1?rss=1" Hannah, M. V. Casale, F. P. Stegle, O. Birney, E. 2018-01-30 doi:10.1101/255497 Cold Spring Harbor Laboratory Press 2018-01-30 <![CDATA[ Short template switch events explain mutation clusters in the human genome ]]> https://biorxiv.org/cgi/content/short/038380v1?rss=1" Ari Löytynoja Nick Goldman 2016-02-01 doi:10.1101/038380 Cold Spring Harbor Laboratory Press 2016-02-01 <![CDATA[ Lipid metabolic perturbation is an early-onset phenotype in adult spin mutants: a Drosophila model for lysosomal storage disorders ]]> https://biorxiv.org/cgi/content/short/075556v1?rss=1" sarita hebbar Avinash Khandelwal Jayashree R Samantha J Hindle Yin Ning Chiang Joanne Yew Sean Sweeney Dominik Schwudke 2016-09-16 doi:10.1101/075556 Cold Spring Harbor Laboratory Press 2016-09-16 <![CDATA[ Power Analysis of Single Cell RNA‐Sequencing Experiments ]]> https://biorxiv.org/cgi/content/short/073692v1?rss=1" Valentine Svensson Kedar N Natarajan Lam-Ha Ly Ricardo J Miragaia Charlotte Labalette Iain C Macaulay Ana Cvejic Sarah A Teichmann 2016-09-08 doi:10.1101/073692 Cold Spring Harbor Laboratory Press 2016-09-08 <![CDATA[ SC3 - consensus clustering of single-cell RNA-Seq data ]]> https://biorxiv.org/cgi/content/short/036558v1?rss=1" Vladimir Yu. Kiselev Kristina Kirschner Michael T. Schaub Tallulah Andrews Andrew Yiu Tamir Chandra Kedar N Natarajan Wolf Reik Mauricio Barahona Anthony R Green Martin Hemberg 2016-01-13 doi:10.1101/036558 Cold Spring Harbor Laboratory Press 2016-01-13 <![CDATA[ Genome variation and conserved regulation identify genomic regions responsible for strain specific phenotypes in rat ]]> https://biorxiv.org/cgi/content/short/169748v1?rss=1" Martin-Galvez, D. Dunoyer-de-Segonzac, D. Ma, M. C. J. Kwitek, A. E. Thybert, D. Flicek, P. 2017-07-28 doi:10.1101/169748 Cold Spring Harbor Laboratory Press 2017-07-28 <![CDATA[ Interplay of cis and trans mechanisms driving transcription factor binding, chromatin, and gene expression evolution ]]> https://biorxiv.org/cgi/content/short/059873v1?rss=1" Emily S Wong Bianca M Schmitt Anastasiya Kazachenka David Thybert Aisling Redmond Frances Connor Tim F Rayner Christine Feig Anne C Ferguson-Smith John C Marioni Paul Flicek Duncan T Odom 2016-06-19 doi:10.1101/059873 Cold Spring Harbor Laboratory Press 2016-06-19 <![CDATA[ Cotranslational assembly imposes evolutionary constraints on homomeric proteins ]]> https://biorxiv.org/cgi/content/short/074963v1?rss=1" Eviatar Natan Tamaki Endoh Liora Haim-Vilmovsky Guilhem Chalancon Tilman Flock Jonathan TS Hopper Balint Kintses Lejla Daruka Gergely Fekete Csaba Pal Balazs Papp Peter Horvath Joseph A Marsh Adrian H Elcock M Madan Babu Carol V Robinson Naoki Sugimoto Sarah A Teichmann 2016-09-13 doi:10.1101/074963 Cold Spring Harbor Laboratory Press 2016-09-13 <![CDATA[ scater: pre-processing, quality control, normalisation and visualisation of single-cell RNA-seq data in R ]]> https://biorxiv.org/cgi/content/short/069633v1?rss=1" Davis J McCarthy Kieran R Campbell Aaron T L Lun Quin F Wills 2016-08-15 doi:10.1101/069633 Cold Spring Harbor Laboratory Press 2016-08-15 <![CDATA[ Excitability in the p53 network mediates robust signaling with tunable activation thresholds in single cells ]]> https://biorxiv.org/cgi/content/short/068668v1?rss=1" Gregor Moenke Elena Christiano Ana Finzel Dhana Friedrich Hanspeter Herzel Martin Falcke Alexander Loewer 2016-08-09 doi:10.1101/068668 Cold Spring Harbor Laboratory Press 2016-08-09 <![CDATA[ Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes. ]]> https://biorxiv.org/cgi/content/short/089581v1?rss=1" Sundaramoorthy, R. Hughes, A. L. Singh, V. Wiechens, N. Ryan, D. P. El-Mkami, H. Petoukhov, M. Svergun, D. I. Treuutlein, B. Fischer, M. Michaelis, J. Bottcher, B. Norman, D. G. Owen-Hughes, T. 2016-11-26 doi:10.1101/089581 Cold Spring Harbor Laboratory Press 2016-11-26 <![CDATA[ Gap gene regulatory dynamics evolve along a genotype network ]]> https://biorxiv.org/cgi/content/short/024471v1?rss=1" Anton Crombach Karl R Wotton Eva Jimenez-Guri Johannes Jaeger 2015-08-12 doi:10.1101/024471 Cold Spring Harbor Laboratory Press 2015-08-12 <![CDATA[ A survey of DNA methylation polymorphism identifies environmentally responsive co-regulated networks of epigenetic variation in the human genome ]]> https://biorxiv.org/cgi/content/short/189704v1?rss=1" Garg, P. Joshi, R. S. Watson, C. Sharp, A. J. 2017-09-15 doi:10.1101/189704 Cold Spring Harbor Laboratory Press 2017-09-15 <![CDATA[ GARFIELD - GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction ]]> https://biorxiv.org/cgi/content/short/085738v1?rss=1" Iotchkova, V. Ritchie, G. R. S. Geihs, M. Morganella, S. Min, J. L. Walter, K. Timpson, N. J. UK10K Consortium, Dunham, I. Birney, E. Soranzo, N. 2016-11-07 doi:10.1101/085738 Cold Spring Harbor Laboratory Press 2016-11-07 <![CDATA[ Computational Pan-Genomics: Status, Promises and Challenges ]]> https://biorxiv.org/cgi/content/short/043430v1?rss=1" Tobias Marschall Manja Marz Thomas Abeel Louis Dijkstra Bas E Dutilh Ali Ghaffaari Paul Kersey Wigard Kloosterman Veli Makinen Adam Novak Benedict Paten David Porubsky Eric RIVALS Can Alkan Jasmijn Baaijens Paul I. W. de Bakker Valentina Boeva Raoul J.P. Bonnal Francesca Chiaromonte Rayan Chikhi Francesca D. Ciccarelli Robin Cijvat Erwin Datema Cornelia M. Van Duijn Evan E. Eichler Corinna Ernst Eleazar Eskin Erik Garrison Mohammed El-Kebir Gunnar W. Klau Jan O Korbel Eric-Wubbo Lameijer Ben Langmead Marcel Martin Paul Medvedev John C. Mu Pieter Neerincx Klaasjan Ouwens Pierre Peterlongo Pisan 2016-03-12 doi:10.1101/043430 Cold Spring Harbor Laboratory Press 2016-03-12 <![CDATA[ Fibril branching dominates self-assembly of mutant huntingtin exon-1 aggregates in vitro ]]> https://biorxiv.org/cgi/content/short/195297v1?rss=1" Wagner, A. S. Politi, A. Z. Steinhof, A. Bravo-Rodriguez, K. Buntru, A. Strempel, N. U. Brusendorf, L. Haenig, C. Boeddrich, A. Plassmann, S. Ramirez-Anguita, J. M. Baum, K. Sanchez-Garcia, E. Wolf, J. Wanker, E. E. 2017-10-19 doi:10.1101/195297 Cold Spring Harbor Laboratory Press 2017-10-19 <![CDATA[ Csde1 binds transcripts involved in protein homeostasis and controls their expression in erythropoiesis ]]> https://biorxiv.org/cgi/content/short/203497v1?rss=1" Moore, K. S. Yagci, N. van Alphen, F. Paolini, N. A. horos, R. Held, N. M. Houtkooper, R. H. van den Akker, E. Meijer, A. B. 't Hoen, P. A. C. von Lindern, M. 2017-10-15 doi:10.1101/203497 Cold Spring Harbor Laboratory Press 2017-10-15 <![CDATA[ Genetic variation and gene expression across multiple tissues and developmental stages in a non-human primate ]]> https://biorxiv.org/cgi/content/short/092874v1?rss=1" Jasinska, A. J. Zelaya, I. Service, S. K. Peterson, C. Cantor, R. M. Choi, O.-W. DeYoung, J. Eskin, E. Fairbanks, L. A. Fears, S. Furterer, A. Huang, Y. S. Ramensky, V. Schmitt, C. A. Svardal, H. Jorgensen, M. J. Kaplan, J. R. Villar, D. Aken, B. L. Flicek, P. Nag, R. Wong, E. S. Blangero, J. Dyer, T. D. Bogomolov, M. Benjamini, Y. Weinstock, G. M. Dewar, K. Sabatti, C. Wilson, R. K. Jentsch, J. D. Warren, W. Coppola, G. Woods, R. P. Freimer, N. B. 2016-12-09 doi:10.1101/092874 Cold Spring Harbor Laboratory Press 2016-12-09 <![CDATA[ The human leukemia virus HTLV-1 alters the structure and transcription of host chromatin in cis ]]> https://biorxiv.org/cgi/content/short/277335v1?rss=1" 300 kb from the integration site. We conclude that HTLV-1 causes insertional mutagenesis up to the megabase range in the host genome in >104 persistently-maintained HTLV-1+ T-cell clones in vivo. ]]> Melamed, A. Yaguchi, H. Miura, M. Witkover, A. Fitzgerald, T. W. Birney, E. Bangham, C. R. M. 2018-03-07 doi:10.1101/277335 Cold Spring Harbor Laboratory Press 2018-03-07 <![CDATA[ Chromosomal rearrangements are commonly post-transcriptionally attenuated in cancer ]]> https://biorxiv.org/cgi/content/short/093369v1?rss=1" Goncalves, E. Fraguais, A. Garcia-Alonso, L. Cramer, T. Saez-Rodriguez, J. Beltrao, P. 2016-12-12 doi:10.1101/093369 Cold Spring Harbor Laboratory Press 2016-12-12 <![CDATA[ A high-resolution mRNA expression time course of embryonic development in zebrafish ]]> https://biorxiv.org/cgi/content/short/107631v1?rss=1" White, R. J. Collins, J. E. Sealy, I. M. Wali, N. Dooley, C. M. Digby, Z. Murphy, D. N. Hourlier, T. Fullgrabe, A. Davis, M. P. Enright, A. J. Busch-Nentwich, E. M. 2017-02-10 doi:10.1101/107631 Cold Spring Harbor Laboratory Press 2017-02-10 <![CDATA[ Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum functional genome and evolutionary origin of diatoms ]]> https://biorxiv.org/cgi/content/short/176024v1?rss=1" Rastogi, A. Maheswari, U. Dorrell, R. G. Maumus, F. Rocha Jimenez Vieira, F. Kustka, A. McCarthy, J. Allen, A. E. Kersey, P. Bowler, C. Tirichine, L. 2017-08-14 doi:10.1101/176024 Cold Spring Harbor Laboratory Press 2017-08-14 <![CDATA[ Tex19.1 Regulates Acetylated SMC3 Cohesin and Prevents Aneuploidy in Mouse Oocytes ]]> https://biorxiv.org/cgi/content/short/102285v1?rss=1" Reichmann, J. Dobie, K. Lister, L. M. Best, D. Crichton, J. H. MacLennan, M. Read, D. Raymond, E. S. Hung, C.-C. Boyle, S. Shirahige, K. Cooke, H. J. Bickmore, W. A. Herbert, M. Adams, I. R. 2017-02-07 doi:10.1101/102285 Cold Spring Harbor Laboratory Press 2017-02-07 <![CDATA[ Condensin’s ATPase Machinery Drives and Dampens Mitotic Chromosome Condensation ]]> https://biorxiv.org/cgi/content/short/216630v1?rss=1" Elbatsh, A. M. O. Raaijmakers, J. A. van der Weide, R. H. uit de Bos, J. Teunissen, H. Bravo, S. Medema, R. H. de Wit, E. Haering, C. H. Rowland, B. D. 2017-11-08 doi:10.1101/216630 Cold Spring Harbor Laboratory Press 2017-11-08 <![CDATA[ Re-evaluation of SNP heritability in complex human traits ]]> https://biorxiv.org/cgi/content/short/074310v1?rss=1" Doug Speed Na Cai The UCLEB Consortium Michael Johnson Sergey Nejentsev David Balding 2016-09-09 doi:10.1101/074310 Cold Spring Harbor Laboratory Press 2016-09-09 <![CDATA[ Functional regulatory evolution outside of the minimal even-skipped stripe 2 enhancer ]]> https://biorxiv.org/cgi/content/short/101311v1?rss=1" Crocker, J. Stern, D. L. 2017-01-18 doi:10.1101/101311 Cold Spring Harbor Laboratory Press 2017-01-18 <![CDATA[ A synthetic biology approach to probing nucleosome symmetry ]]> https://biorxiv.org/cgi/content/short/170811v1?rss=1" Ichikawa, Y. Connelly, C. F. Appleboim, A. Jacobi, H. Abshiru, N. A. Chou, H.-J. Chen, Y. Sharma, U. Zheng, Y. Thomas, P. M. Chen, H. V. Bajaj, V. Kelleher, N. L. Friedman, N. Bolon, D. N. Rando, O. J. Kaufman, P. D. 2017-07-31 doi:10.1101/170811 Cold Spring Harbor Laboratory Press 2017-07-31 <![CDATA[ Genomic rearrangements near genes leading to upregulation across a diverse subset of human cancers ]]> https://biorxiv.org/cgi/content/short/099861v1?rss=1" Creighton, C. Zhang, Y. Chen, F. 2017-01-12 doi:10.1101/099861 Cold Spring Harbor Laboratory Press 2017-01-12 <![CDATA[ A scored human protein-protein interaction network to catalyze genomic interpretation ]]> https://biorxiv.org/cgi/content/short/064535v1?rss=1" 4,700 cancer genomes and genes involved in neuropsychiatric diseases. ]]> Taibo Li Rasmus Wernersson Rasmus Borup Hansen Heiko Horn Johnathan M Mercer Greg Slodkowicz Christopher Workman Olga Regina Kristoffer Rapacki Hans-Henrik Staerfeldt Soren Brunak Thomas S Jensen Kasper Lage 2016-07-19 doi:10.1101/064535 Cold Spring Harbor Laboratory Press 2016-07-19 <![CDATA[ Systematic analysis of transcriptional and post-transcriptional regulation of metabolism in yeast ]]> https://biorxiv.org/cgi/content/short/057398v1?rss=1" Emanuel Gonçalves Zrinka Raguz Mattia Zampieri Omar Wagih David Ochoa Uwe Sauer Pedro Beltrao Julio Saez-Rodriguez 2016-06-23 doi:10.1101/057398 Cold Spring Harbor Laboratory Press 2016-06-23 <![CDATA[ Mutational signatures of DNA mismatch repair deficiency in C. elegans and human cancers ]]> https://biorxiv.org/cgi/content/short/149153v1?rss=1" NTG mutations in C. elegans, likely caused by the absence of cytosine (CpG) methylation in worms. The other two human MMR signatures may reflect the interaction between MMR deficiency and other mutagenic processes, but their exact cause remains unknown. In summary, combining information from genetically defined models and cancer samples allows for better aligning mutational signatures to causal mutagenic processes. ]]> Meier, B. Volkova, N. Hong, Y. Schofield, P. Campbell, P. J. Gerstung, M. Gartner, A. 2017-06-13 doi:10.1101/149153 Cold Spring Harbor Laboratory Press 2017-06-13 <![CDATA[ Patterns of structural variation in human cancer ]]> https://biorxiv.org/cgi/content/short/181339v1?rss=1" 2,500 cancer genomes. Nine signatures of structural variation emerged. Deletions have trimodal size distribution; assort unevenly across tumour types and patients; enrich in late-replicating regions; and correlate with inversions. Tandem duplications also have trimodal size distribution, but enrich in early-replicating regions, as do unbalanced translocations. Replication-based mechanisms of rearrangement generate varied chromosomal structures with low-level copy number gains and frequent inverted rearrangements. One prominent structure consists of 1-7 templates copied from distinct regions of the genome strung together within one locus. Such cycles of templated insertions correlate with tandem duplications, frequently activating the telomerase gene, TERT, in liver cancer. Cancers access many rearrangement processes, flexibly sculpting the genome to maximise oncogenic potential. ]]> Li, Y. Roberts, N. Weischenfeldt, J. Wala, J. A. Shapira, O. Schumacher, S. Khurana, E. Korbel, J. O. Imielinski, M. Beroukhim, R. Campbell, P. 2017-08-27 doi:10.1101/181339 Cold Spring Harbor Laboratory Press 2017-08-27 <![CDATA[ MAPseq: Improved Speed, Accuracy And Consistency In Ribosomal RNA Sequence Analysis ]]> https://biorxiv.org/cgi/content/short/126953v1?rss=1" Matias Rodrigues, J. F. Schmidt, T. S. Tackmann, J. von Mering, C. 2017-04-12 doi:10.1101/126953 Cold Spring Harbor Laboratory Press 2017-04-12 <![CDATA[ Overcoming confounding plate effects in differential expression analyses of single-cell RNA-seq data ]]> https://biorxiv.org/cgi/content/short/073973v1?rss=1" Aaron TL Lun John C Marioni 2016-09-08 doi:10.1101/073973 Cold Spring Harbor Laboratory Press 2016-09-08 <![CDATA[ Analysis of the human kinome and phosphatome reveals diseased signaling networks induced by overexpression ]]> https://biorxiv.org/cgi/content/short/314716v1?rss=1" Lun, X.-K. Szklarczyk, D. Gabor, A. Dobberstein, N. Zanotelli, V. R. T. Saez-Rodriguez, J. von Mering, C. Bodenmiller, B. 2018-05-04 doi:10.1101/314716 Cold Spring Harbor Laboratory Press 2018-05-04 <![CDATA[ Single-molecule dynamics and genome-wide transcriptomics reveal that NF-kB (p65)-DNA binding times can be decoupled from transcriptional activation ]]> https://biorxiv.org/cgi/content/short/255380v1?rss=1" Callegari, A. Sieben, C. Benke, A. Suter, D. Fierz, B. Mazza, D. Manley, S. 2018-01-28 doi:10.1101/255380 Cold Spring Harbor Laboratory Press 2018-01-28 <![CDATA[ Depolymerized lamins link nuclear envelope breakdown to mitotic transcriptional quiescence ]]> https://biorxiv.org/cgi/content/short/334110v1?rss=1" Ikegami, K. Secchia, S. Lieb, J. D. Moskowitz, I. P. 2018-05-30 doi:10.1101/334110 Cold Spring Harbor Laboratory Press 2018-05-30 <![CDATA[ The genome of the biting midge Culicoides sonorensis and gene expression analyses of vector competence for Bluetongue virus ]]> https://biorxiv.org/cgi/content/short/249482v1?rss=1" Morales Hojas, R. Hinsley, M. Armean, I. M. Silk, R. Harrup, L. E. Gonzalez-Uriarte, A. Veronesi, E. Campbell, L. Nayduch, D. Saski, C. Tabachnick, W. J. Kersey, P. Carpenter, S. Fife, M. 2018-01-17 doi:10.1101/249482 Cold Spring Harbor Laboratory Press 2018-01-17 <![CDATA[ The WYL domain of the Thermotoga elfii PIF1 helicase is an accessory single-stranded DNA binding module ]]> https://biorxiv.org/cgi/content/short/163188v1?rss=1" Andis, N. M. Sausen, C. W. Alladin, A. Bochman, M. 2017-07-13 doi:10.1101/163188 Cold Spring Harbor Laboratory Press 2017-07-13 <![CDATA[ Dissecting cancer resistance to therapies with cell-type-specific dynamic logic models ]]> https://biorxiv.org/cgi/content/short/094755v1?rss=1" Eduati, F. Doldan-Martelli, V. Klinger, B. Cokelaer, T. Sieber, A. Kogera, F. Dorel, M. Garnett, M. J. Bluthgen, N. Saez-Rodriguez, J. 2016-12-16 doi:10.1101/094755 Cold Spring Harbor Laboratory Press 2016-12-16 <![CDATA[ A functional landscape of chronic kidney disease entities from public transcriptomic data ]]> https://biorxiv.org/cgi/content/short/265447v1?rss=1" Tajti, F. Antoranz, A. Ibrahim, M. M. Kim, H. Ceccarelli, F. Kuppe, C. Alexopoulos, L. G. Kramann, R. Saez-Rodriguez, J. 2018-02-14 doi:10.1101/265447 Cold Spring Harbor Laboratory Press 2018-02-14 <![CDATA[ Multiple laboratory mouse reference genomes define strain specific haplotypes and novel functional loci ]]> https://biorxiv.org/cgi/content/short/235838v1?rss=1" Lilue, J. Doran, A. G. Fiddes, I. T. Abrudan, M. Armstrong, J. Bennett, R. Chow, W. Collins, J. Czechanski, A. Danecek, P. Diekhans, M. Dolle, D.-D. Dunn, M. Durbin, R. Earl, D. Ferguson-Smith, A. Flicek, P. Flint, J. Frankish, A. Fu, B. Gerstein, M. Gilbert, J. Goodstadt, L. Harrow, J. Howe, K. Kolmogorov, M. Koenig, S. Lelliott, C. Loveland, J. Mott, R. Muir, P. Navarro, F. Odom, D. Park, N. Pelan, S. Phan, S. K. Quail, M. Reinholdt, L. Romoth, L. Shirley, L. Sisu, C. Sjoberg-Herrera, M. Stanke, M. Steward, C. Thomas, M. Threadgold, G. Thybert, D 2018-02-12 doi:10.1101/235838 Cold Spring Harbor Laboratory Press 2018-02-12 <![CDATA[ Single cell transcriptomics of regulatory T cells reveals trajectories of tissue adaptation ]]> https://biorxiv.org/cgi/content/short/217489v1?rss=1" Miragaia, R. J. Gomes, T. Chomka, A. Jardine, L. Riedel, A. Hegazy, A. N. Lindeman, I. Emerton, G. Krausgruber, T. Shields, J. Haniffa, M. Powrie, F. Teichmann, S. A. 2017-11-22 doi:10.1101/217489 Cold Spring Harbor Laboratory Press 2017-11-22 <![CDATA[ Noise control is a primary function of microRNAs and post-transcriptional regulation ]]> https://biorxiv.org/cgi/content/short/168641v1?rss=1" Schmiedel, J. Marks, D. S. Lehner, B. Bluthgen, N. 2017-07-26 doi:10.1101/168641 Cold Spring Harbor Laboratory Press 2017-07-26 <![CDATA[ Flipping between Polycomb repressed and active transcriptional states introduces noise in gene expression ]]> https://biorxiv.org/cgi/content/short/117267v1?rss=1" Kar, G. Kim, J. K. Kolodziejczyk, A. A. Natarajan, K. N. Triglia, E. T. Mifsud, B. Elderkin, S. Marioni, J. C. Pombo, A. Teichmann, S. A. 2017-03-16 doi:10.1101/117267 Cold Spring Harbor Laboratory Press 2017-03-16 <![CDATA[ Structural basis for EarP-mediated arginine glycosylation of translation elongation factor EF-P ]]> https://biorxiv.org/cgi/content/short/116038v1?rss=1" Krafczyk, R. Macosek, J. Gast, D. Wunder, S. Jagtap, P. K. A. Mitra, P. Jha, A. K. Rohr, J. Hoffmann-Roeder, A. Jung, K. Hennig, J. Lassak, J. 2017-03-11 doi:10.1101/116038 Cold Spring Harbor Laboratory Press 2017-03-11 <![CDATA[ The IRE1a-XBP1 pathway promotes T helper cell differentiation by resolving secretory stress and accelerating proliferation ]]> https://biorxiv.org/cgi/content/short/235010v1?rss=1" Pramanik, J. Chen, X. Kar, G. Gomes, T. Henriksson, J. Miao, Z. Natarajan, K. McKenzie, A. N. J. Mahata, B. Teichmann, S. A. 2017-12-15 doi:10.1101/235010 Cold Spring Harbor Laboratory Press 2017-12-15 <![CDATA[ Crosslinkers both drive and brake cytoskeletal remodeling and furrowing in cytokinesis ]]> https://biorxiv.org/cgi/content/short/150813v1?rss=1" Descovich, C. P. Cortes, D. B. Ryan, S. Nash, J. Zhang, L. Maddox, P. S. Nedelec, F. Maddox, A. S. 2017-06-16 doi:10.1101/150813 Cold Spring Harbor Laboratory Press 2017-06-16 <![CDATA[ The contributions of the actin machinery to endocytic membrane bending and vesicle formation ]]> https://biorxiv.org/cgi/content/short/172072v1?rss=1" Picco, A. Kukulski, W. Manenschijn, H. E. Specht, T. Briggs, J. A. G. Kaksonen, M. 2017-08-03 doi:10.1101/172072 Cold Spring Harbor Laboratory Press 2017-08-03 <![CDATA[ The Nucleosome Remodelling and Deacetylation complex restricts Mediator access to enhancers to control transcription ]]> https://biorxiv.org/cgi/content/short/103192v1?rss=1" Xenophontos, M. Reynolds, N. Gharbi, S. Johnstone, E. Signolet, J. Floyd, R. Ralser, M. Borneloev, S. Dietmann, S. Loos, R. Bertone, P. Hendrich, B. 2017-01-25 doi:10.1101/103192 Cold Spring Harbor Laboratory Press 2017-01-25 <![CDATA[ A Critical Review on the Use of Support Values in Tree Viewers and Bioinformatics Toolkits ]]> https://biorxiv.org/cgi/content/short/035360v1?rss=1" Lucas Czech Jaime Huerta-Cepas Alexandros Stamatakis 2015-12-25 doi:10.1101/035360 Cold Spring Harbor Laboratory Press 2015-12-25 <![CDATA[ Sub-minute phosphoregulation of cell-cycle systems during Plasmodium gamete formation revealed by a high-resolution time course ]]> https://biorxiv.org/cgi/content/short/126276v1?rss=1" Invergo, B. Brochet, M. Yu, L. Choudhary, J. Beltrao, P. Billker, O. 2017-04-10 doi:10.1101/126276 Cold Spring Harbor Laboratory Press 2017-04-10 <![CDATA[ Population-level characterization of pathway alterations with SLAPenrich dissects heterogeneity of cancer hallmark acquisition ]]> https://biorxiv.org/cgi/content/short/077701v1?rss=1" Francesco Iorio Luz Garcia-Alonso Jonathan Brammeld Inigo Martincorena David R Wille Ultan McDermott Julio Saez-Rodriguez 2016-09-27 doi:10.1101/077701 Cold Spring Harbor Laboratory Press 2016-09-27 <![CDATA[ H2AFX AND MDC1 PROTECT GENOMIC INTEGRITY IN MALE GERM CELLS BY PROMOTING RECOMBINATION AND ACTIVATION OF THE RECOMBINATION-DEPENDENT CHECKPOINT ]]> https://biorxiv.org/cgi/content/short/235085v1?rss=1" Testa, E. Nardozi, D. Antinozzi, C. Faieta, M. Di Cecca, S. Caggiano, C. Fukuda, T. Bonanno, E. Zenkun, L. Maldonado, A. Roig, I. Di Giacomo, M. Barchi, M. 2017-12-15 doi:10.1101/235085 Cold Spring Harbor Laboratory Press 2017-12-15 <![CDATA[ Quantitative evaluation of two-photon calcium imaging modalities for high-speed volumetric calcium imaging in scattering brain tissue ]]> https://biorxiv.org/cgi/content/short/115659v1?rss=1" Weisenburger, S. Prevedel, R. Vaziri, A. 2017-03-10 doi:10.1101/115659 Cold Spring Harbor Laboratory Press 2017-03-10 <![CDATA[ Omics Discovery Index - Discovering and Linking Public Omics Datasets ]]> https://biorxiv.org/cgi/content/short/049205v1?rss=1" Yasset Perez-Riverol Mingze Bai Felipe Leprevost Silvano Squizzato Young Mi Park Ove Kenneth Haug Adam J. Carroll Dylan Spalding Justin Paschall Mingxun Wang Noemi del-Toro Tobias Ternent Peng Zhang Nicola Buso Nuno Bandeira Eric Deutsch David S. Campbell Ronald C. Beavis Reza Salek Alexey Nesvizhskii Susanna-Assunta Sansone Christoph Steinbeck Rodrigo Lopez Juan Antonio Vizcaino Peipei Ping Henning Hermjakob 2016-04-18 doi:10.1101/049205 Cold Spring Harbor Laboratory Press 2016-04-18 <![CDATA[ Functional interaction of low-homology FRPs from different cyanobacteria with Synechocystis OCP ]]> https://biorxiv.org/cgi/content/short/247882v1?rss=1" Slonimskiy, Y. B. Maksimov, E. G. Lukashev, E. P. Moldenhauer, M. Jeffries, C. M. Svergun, D. I. Friedrich, T. Sluchanko, N. N. 2018-01-15 doi:10.1101/247882 Cold Spring Harbor Laboratory Press 2018-01-15 <![CDATA[ Comprehensive variant effect predictions of single nucleotide variants in model organisms ]]> https://biorxiv.org/cgi/content/short/313031v1?rss=1" Wagih, O. Busby, B. Galardini, M. Memon, D. Typas, A. Beltrao, P. 2018-05-02 doi:10.1101/313031 Cold Spring Harbor Laboratory Press 2018-05-02 <![CDATA[ Cell type boundaries organize plant development ]]> https://biorxiv.org/cgi/content/short/126466v1?rss=1" Heisler, M. G. Caggiano, M. P. Yu, X. Bhatia, N. Larsson, A. Ram, H. Ohno, C. K. Sappl, P. Meyerowitz, E. M. Jonsson, H. 2017-04-11 doi:10.1101/126466 Cold Spring Harbor Laboratory Press 2017-04-11 <![CDATA[ A rapid and robust method for single cell chromatin accessibility profiling ]]> https://biorxiv.org/cgi/content/short/309831v1?rss=1" Chen, X. Natarajan, K. N. Teichmann, S. A. 2018-04-27 doi:10.1101/309831 Cold Spring Harbor Laboratory Press 2018-04-27 <![CDATA[ An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations. ]]> https://biorxiv.org/cgi/content/short/080796v1?rss=1" Clavijo, B. J. Venturini, L. Schudoma, C. Garcia Accinelli, G. Kaithakottil, G. Wright, J. Borrill, P. Kettleborough, G. Heavens, D. Chapman, H. Lipcombe, J. Barker, T. Lu, F.-H. McKenzie, N. Raats, D. Ramirez Gonzalez, R. H. Coince, A. Peel, N. Percival-Alwyn, L. Duncan, O. Trosch, J. Yu, G. Bolser, D. Naamati, G. Kerhornou, A. Spannagl, M. Gundlach, H. Haberer, G. Davey, R. P. Fosker, C. Di Palma, F. Phillips, A. Millar, A. H. Kersey, P. J. Uauy, C. Krasileva, K. V. Swarbreck, D. Bevan, M. W. Clark, M. D. 2016-10-13 doi:10.1101/080796 Cold Spring Harbor Laboratory Press 2016-10-13 <![CDATA[ Landscape and dynamics of transcription initiation in the malaria parasite Plasmodium falciparum ]]> https://biorxiv.org/cgi/content/short/024356v1?rss=1" Sophie Adjalley Christophe Chabbert Bernd Klaus Vicent Pelechano Lars Steinmetz 2015-08-10 doi:10.1101/024356 Cold Spring Harbor Laboratory Press 2015-08-10 <![CDATA[ Assessing The Reliability Of Spike-In Normalization For Analyses Of Single-Cell RNA Sequencing Data ]]> https://biorxiv.org/cgi/content/short/119784v1?rss=1" Lun, A. T. Calero-Nieto, F. J. Haim-Vilmovsky, L. Gottgens, B. Marioni, J. C. 2017-03-23 doi:10.1101/119784 Cold Spring Harbor Laboratory Press 2017-03-23 <![CDATA[ Dense And Accurate Whole-Chromosome Haplotyping Of Individual Genomes ]]> https://biorxiv.org/cgi/content/short/126136v1?rss=1" 95% of alleles to their parental haplotypes using as few as 10 Strand-seq libraries in combination with 10-fold coverage PacBio data or, alternatively, 10X Genomics linked-read sequencing data. We conclude that the combination of Strand-seq with different sequencing technologies represents an attractive solution to chart the unique genetic variation of diploid genomes. ]]> Porubsky, D. Garg, S. Sanders, A. D. Korbel, J. O. Guryev, V. Lansdorp, P. M. Marschall, T. 2017-04-10 doi:10.1101/126136 Cold Spring Harbor Laboratory Press 2017-04-10 <![CDATA[ Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes ]]> https://biorxiv.org/cgi/content/short/158659v1?rss=1" Thybert, D. Roller, M. Navarro, F. C. P. Fiddes, I. Streeter, I. Feig, C. Martin-Galvez, D. Kolmogorov, M. Janousek, V. Akanni, W. Aken, B. Aldridge, S. Chakrapani, V. Chow, W. Clarke, L. Cummins, C. Doran, A. Dunn, M. Goodstadt, L. Howe, K. Howell, M. Josselin, A.-A. Karn, R. C. Laukaitis, C. M. Jingtao, L. Martin, F. Muffato, M. Quail, M. A. Sisu, C. Stanke, M. Stefflova, K. Van Oosterhout, C. Veyrunes, F. Ward, B. Yang, F. Yazdanifar, G. Zadissa, A. Adams, D. Brazma, A. Gerstein, M. Paten, B. Pham, S. Keane, T. Odom, D. T. Flicek, P. 2017-07-02 doi:10.1101/158659 Cold Spring Harbor Laboratory Press 2017-07-02 <![CDATA[ Deciphering programs of transcriptional regulation by combined deconvolution of multiple omics layers ]]> https://biorxiv.org/cgi/content/short/199547v1?rss=1" Huebschmann, D. Kurzawa, N. Steinhauser, S. Rentzsch, P. Kraemer, S. Andresen, C. Park, J. Eils, R. Schlesner, M. Herrmann, C. 2017-10-08 doi:10.1101/199547 Cold Spring Harbor Laboratory Press 2017-10-08 <![CDATA[ Joint Profiling Of Chromatin Accessibility, DNA Methylation And Transcription In Single Cells ]]> https://biorxiv.org/cgi/content/short/138685v1?rss=1" Clark, S. J. Argelaguet, R. Kapourani, C.-A. Stubbs, T. M. Lee, H. J. Krueger, F. Sanguinetti, G. Kelsey, G. Marioni, J. C. Stegle, O. Reik, W. 2017-05-17 doi:10.1101/138685 Cold Spring Harbor Laboratory Press 2017-05-17 <![CDATA[ Prefrontal cortical control of a brainstem social behavior circuit ]]> https://biorxiv.org/cgi/content/short/073734v1?rss=1" Tamara B. Franklin Bianca A. Silva Zinaida Perova Livia Marrone Maria E. Masferrer Yang Zhan Angie Kaplan Louise Greetham Voilaine Verrechia Andreas Halman Sara Pagella Alexei L. Vyssotski Anna Illarianova Tiago Branco Cornelius T. Gross 2016-09-09 doi:10.1101/073734 Cold Spring Harbor Laboratory Press 2016-09-09 <![CDATA[ Integrating long-range connectivity information into de Bruijn graphs ]]> https://biorxiv.org/cgi/content/short/147777v1?rss=1" Turner, I. Garimella, K. V. Iqbal, Z. McVean, G. 2017-06-08 doi:10.1101/147777 Cold Spring Harbor Laboratory Press 2017-06-08 <![CDATA[ Modularity, criticality and evolvability of a developmental gene regulatory network ]]> https://biorxiv.org/cgi/content/short/413211v1?rss=1" Verd, B. Monk, N. A. Jaeger, J. 2018-09-10 doi:10.1101/413211 Cold Spring Harbor Laboratory Press 2018-09-10 <![CDATA[ Architecture of TAF11/TAF13/TBP complex suggests novel regulatory state in General Transcription Factor TFIID function ]]> https://biorxiv.org/cgi/content/short/168716v1?rss=1" Gupta, K. Watson, A. A. Baptista, T. Scheer, E. Chambers, A. L. Koehler, C. Zou, J. Obong-Ebong, I. Kandiah, E. Temblador, A. Round, A. Forest, E. Man, P. Bieniossek, C. Laue, E. D. Lemke, E. A. Rappsilber, J. Robinson, C. V. Devys, D. Tora, L. Berger, I. 2017-07-26 doi:10.1101/168716 Cold Spring Harbor Laboratory Press 2017-07-26 <![CDATA[ Mechanism of Nuclear Movements in a Multinucleated Cell ]]> https://biorxiv.org/cgi/content/short/095695v1?rss=1" Gibeaux, R. Politi, A. Philippsen, P. Nedelec, F. 2016-12-20 doi:10.1101/095695 Cold Spring Harbor Laboratory Press 2016-12-20 <![CDATA[ destiny – diffusion maps for large-scale single-cell data in R ]]> https://biorxiv.org/cgi/content/short/023309v1?rss=1" Philipp Angerer Laleh Haghverdi Maren Büttner Fabian Theis Carsten Marr Florian Buettner 2015-07-27 doi:10.1101/023309 Cold Spring Harbor Laboratory Press 2015-07-27 <![CDATA[ Genomics in healthcare: GA4GH looks to 2022 ]]> https://biorxiv.org/cgi/content/short/203554v1?rss=1" Birney, E. Vamathevan, J. Goodhand, P. 2017-10-15 doi:10.1101/203554 Cold Spring Harbor Laboratory Press 2017-10-15 <![CDATA[ Cell-specific modulation of nuclear pore complexes controls cell cycle entry during asymmetric division ]]> https://biorxiv.org/cgi/content/short/203232v1?rss=1" Kumar, A. Sharma, P. Shcheprova, Z. Daulny, A. Sanmartin, T. Matucci, I. Funaya, C. Beato, M. Mendoza, M. 2017-10-14 doi:10.1101/203232 Cold Spring Harbor Laboratory Press 2017-10-14 <![CDATA[ An Atlas of Human Kinase Regulation ]]> https://biorxiv.org/cgi/content/short/067900v1?rss=1" David Ochoa Mindaugas Jonikas Robert T Lawrence Bachir El Debs Joel Selkrig Athanasios Typas Judit Villen Silvia Santos Pedro Beltrao 2016-08-04 doi:10.1101/067900 Cold Spring Harbor Laboratory Press 2016-08-04 <![CDATA[ Benchmark and integration of resources for the estimation of human transcription factor activities ]]> https://biorxiv.org/cgi/content/short/337915v1?rss=1" Garcia-Alonso, L. Ibrahim, M. M. Turei, D. Saez-Rodriguez, J. 2018-06-03 doi:10.1101/337915 Cold Spring Harbor Laboratory Press 2018-06-03 <![CDATA[ On expert curation and sustainability: UniProtKB/Swiss-Prot as a case study ]]> https://biorxiv.org/cgi/content/short/094011v1?rss=1" Poux, S. Arighi, C. N. Magrane, M. Bateman, A. Wei, C.-H. Lu, Z. Boutet, E. Bye-A-Jee, H. Famiglietti, M. L. Roechert, B. 2016-12-14 doi:10.1101/094011 Cold Spring Harbor Laboratory Press 2016-12-14 <![CDATA[ Circadian protein regulation in the green lineage I. A phospho-dawn anticipates light onset before proteins peak in daytime. ]]> https://biorxiv.org/cgi/content/short/287862v1?rss=1" Noordally, Z. B. Hindle, M. M. Martin, S. F. Seaton, D. D. Simpson, I. Le Bihan, T. Millar, A. J. 2018-04-04 doi:10.1101/287862 Cold Spring Harbor Laboratory Press 2018-04-04 <![CDATA[ Genome-scale oscillations in DNA methylation during exit from pluripotency ]]> https://biorxiv.org/cgi/content/short/338822v1?rss=1" Rulands, S. Lee, H. J. Clark, S. J. Angermueller, C. Smallwood, S. A. Krueger, F. Mohammed, H. Dean, W. Nichols, J. Rugg-Gunn, P. Kelsey, G. Stegle, O. Simons, B. D. Reik, W. 2018-06-05 doi:10.1101/338822 Cold Spring Harbor Laboratory Press 2018-06-05 <![CDATA[ Post-catalytic spliceosome structure reveals mechanism of 3'-splice site selection ]]> https://biorxiv.org/cgi/content/short/212811v1?rss=1" Wilkinson, M. E. Fica, S. M. Galej, W. P. Norman, C. M. Newman, A. J. NAGAI, K. 2017-11-01 doi:10.1101/212811 Cold Spring Harbor Laboratory Press 2017-11-01 <![CDATA[ Promoter architecture determines co-translational regulation of mRNA ]]> https://biorxiv.org/cgi/content/short/192195v1?rss=1" Espinar Calvo, M. L. Schikora Tamarit, M. A. Domingo Espinos, J. Carey, L. B. 2017-09-22 doi:10.1101/192195 Cold Spring Harbor Laboratory Press 2017-09-22 <![CDATA[ The Hox Transcription Factor Ubx stabilizes Lineage Commitment by Suppressing Cellular Plasticity ]]> https://biorxiv.org/cgi/content/short/437947v1?rss=1" Domsch, K. Carnesecchi, J. Disela, V. Friedrich, J. Trost, N. Ermakova, O. Polychronidou, M. Lohmann, I. 2018-10-08 doi:10.1101/437947 Cold Spring Harbor Laboratory Press 2018-10-08 <![CDATA[ Real-time search of all bacterial and viral genomic data ]]> https://biorxiv.org/cgi/content/short/234955v1?rss=1" Bradley, P. den Bakker, H. Rocha, E. McVean, G. Iqbal, Z. 2017-12-15 doi:10.1101/234955 Cold Spring Harbor Laboratory Press 2017-12-15 <![CDATA[ Specificity of RNAi, LNA and CRISPRi as loss-of-function methods in transcriptional analysis ]]> https://biorxiv.org/cgi/content/short/234930v1?rss=1" Stojic, L. Lun, A. Mangei, J. Mascalchi, P. Quarantotti, V. Barr, A. Bakal, C. Marioni, J. Gergely, F. Odom, D. 2017-12-15 doi:10.1101/234930 Cold Spring Harbor Laboratory Press 2017-12-15 <![CDATA[ Nearly all new protein-coding predictions in the CHESS database are not protein-coding ]]> https://biorxiv.org/cgi/content/short/360602v1?rss=1" Jungreis, I. Tress, M. L. Mudge, J. Sisu, C. Hunt, T. Johnson, R. Uszczynska-Ratajczak, B. Lagarde, J. Wright, J. Muir, P. Gerstein, M. Guigo, R. Kellis, M. Frankish, A. Flicek, P. The GENCODE Consortium, 2018-07-02 doi:10.1101/360602 Cold Spring Harbor Laboratory Press 2018-07-02 <![CDATA[ A protein standard that emulates homology for the characterization of protein inference algorithms ]]> https://biorxiv.org/cgi/content/short/236471v1?rss=1" The, M. Edfors, F. Perez-Riverol, Y. Payne, S. H. Hoopmann, M. R. Palmblad, M. Forsström, B. Käll, L. 2017-12-19 doi:10.1101/236471 Cold Spring Harbor Laboratory Press 2017-12-19 <![CDATA[ Single-cell RNA-sequencing redefines blood cell type classification in mosquitoes ]]> https://biorxiv.org/cgi/content/short/234492v1?rss=1" Severo, M. S. Landry, J. J. M. Lindquist, R. L. Goosmann, C. Brinkmann, V. Collier, P. Hauser, A. E. Benes, V. Teichmann, S. A. Levashina, E. A. 2017-12-15 doi:10.1101/234492 Cold Spring Harbor Laboratory Press 2017-12-15 <![CDATA[ Terminal uridylyltransferases target RNA viruses as part of the innate immune system in animals ]]> https://biorxiv.org/cgi/content/short/209114v1?rss=1" Le Pen, J. Jiang, H. Di Domenico, T. Kneuss, E. Kosalka, J. Morgan, M. Much, C. Rudolph, K. L. M. Enright, A. J. O'Carroll, D. Wang, D. Miska, E. A. 2017-10-25 doi:10.1101/209114 Cold Spring Harbor Laboratory Press 2017-10-25 <![CDATA[ Correcting batch effects in single-cell RNA sequencing data by matching mutual nearest neighbours. ]]> https://biorxiv.org/cgi/content/short/165118v1?rss=1" Haghverdi, L. Lun, A. T. L. Morgan, M. D. Marioni, J. C. 2017-07-18 doi:10.1101/165118 Cold Spring Harbor Laboratory Press 2017-07-18 <![CDATA[ Distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data ]]> https://biorxiv.org/cgi/content/short/234872v1?rss=1" Lun, A. Riesenfeld, S. Andrews, T. Dao, T. P. Gomes, T. participants in the 1st Human Cell Atlas Jamboree, Marioni, J. 2018-04-04 doi:10.1101/234872 Cold Spring Harbor Laboratory Press 2018-04-04 <![CDATA[ A Balance Between Regulatory Constraints And Pathogen Pressure Shapes The Evolution Of Innate Immunity ]]> https://biorxiv.org/cgi/content/short/137992v1?rss=1" Hagai, T. Chen, X. Miragaia, R. J. Gomes, T. Rostom, R. Kunowska, N. Proserpio, V. Donati, G. Bossini-Castillo, L. Naamati, G. Emerton, G. Trynka, G. Kondova, I. Denis, M. Teichmann, S. 2017-05-15 doi:10.1101/137992 Cold Spring Harbor Laboratory Press 2017-05-15 <![CDATA[ The whole-genome panorama of cancer drivers ]]> https://biorxiv.org/cgi/content/short/190330v1?rss=1" Sabarinathan, R. Pich, O. Martincorena, I. Rubio-Perez, C. Juul, M. Wala, J. Schumacher, S. Shapira, O. Sidiropoulos, N. Waszak, S. Tamborero, D. Mularoni, L. Rheinbay, E. Hornshoj, H. Deu-Pons, J. Muinos, F. Bertl, J. Guo, Q. Weischenfeldt, J. Korbel, J. O. Getz, G. Campbell, P. J. Pedersen, J. S. Beroukhim, R. Perez-Gonzalez, A. Lopez-Bigas, N. PCAWG Drivers and Functional Interpretation Group, ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Net, 2017-09-20 doi:10.1101/190330 Cold Spring Harbor Laboratory Press 2017-09-20 <![CDATA[ Gene fusion between CDKN1A and RAB44 caused by exon skipping like mechanism due to disruption of a splice site ]]> https://biorxiv.org/cgi/content/short/111856v1?rss=1" Sun, H. Wu, J. Zhu, C. Aiyar, R. Jakob, P. Mueller, W. Wei, W. Steinmetz, L. 2017-03-02 doi:10.1101/111856 Cold Spring Harbor Laboratory Press 2017-03-02 <![CDATA[ Alpha-synuclein fibrils induce autophagy in microglial cells as a consequence of lysosomal damage. ]]> https://biorxiv.org/cgi/content/short/169375v1?rss=1" Bussi, C. Peralta Ramos, J. M. Arroyo, D. S. Gallea, J. I. Ronchi, P. Kolovou, A. Wang, J. M. Florey, O. Celej, M. S. Schwab, Y. Ktistakis, N. T. Iribarren, P. 2017-07-27 doi:10.1101/169375 Cold Spring Harbor Laboratory Press 2017-07-27 <![CDATA[ Mutation accumulation differentially impacts ageing in mammalian tissues ]]> https://biorxiv.org/cgi/content/short/247700v1?rss=1" Turan, Z. G. Parvizi, P. Donertas, H. M. Tung, J. Khaitovich, P. Somel, M. 2018-01-15 doi:10.1101/247700 Cold Spring Harbor Laboratory Press 2018-01-15 <![CDATA[ CELLector: Genomics Guided Selection of Cancer in vitro Models ]]> https://biorxiv.org/cgi/content/short/275032v1?rss=1" View larger version (41K): org.highwire.dtl.DTLVardef@11f46b1org.highwire.dtl.DTLVardef@5a207aorg.highwire.dtl.DTLVardef@10a57edorg.highwire.dtl.DTLVardef@12b332_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Najgebauer, H. Yang, M. Francies, H. Stronach, E. A. Garnett, M. J. Saez-Rodriguez, J. Iorio, F. 2018-03-03 doi:10.1101/275032 Cold Spring Harbor Laboratory Press 2018-03-03 <![CDATA[ Unraveling the polygenic architecture of complex traits using blood eQTL meta-analysis ]]> https://biorxiv.org/cgi/content/short/447367v1?rss=1" Vosa, U. Claringbould, A. Westra, H.-J. Bonder, M. J. Deelen, P. Zeng, B. Kirsten, H. Saha, A. Kreuzhuber, R. Kasela, S. Pervjakova, N. Alvaes, I. Fave, M.-J. Agbessi, M. Christiansen, M. Jansen, R. Seppälä, I. Tong, L. Teumer, A. Schramm, K. Hemani, G. Verlouw, J. Yaghootkar, H. Sönmez, R. Andrew, A. A. Kukushkina, V. Kalnapenkis, A. Rüeger, S. Porcu, E. Kronberg-Guzman, J. Kettunen, J. Powell, J. Lee, B. Zhang, F. Arindrarto, W. Beutner, F. BIOS Consortium, Brugge, H. i2QTL Consortium, Dmitrieva, J. Elansary, M. Fairfax, B. P. Georges, M. He 2018-10-19 doi:10.1101/447367 Cold Spring Harbor Laboratory Press 2018-10-19 <![CDATA[ An insulin, AMPK, and steroid hormone-mediated metabolic switch regulates the transition between growth and diapause in C. elegans ]]> https://biorxiv.org/cgi/content/short/323956v1?rss=1" Penkov, S. Erkut, C. Oertel, J. Galli, R. Vorkel, D. Verbavatz, J.-M. Koch, E. Fahmy, K. Kurzchalia, T. V. 2018-05-16 doi:10.1101/323956 Cold Spring Harbor Laboratory Press 2018-05-16 <![CDATA[ Multi-platform discovery of haplotype-resolved structural variation in human genomes ]]> https://biorxiv.org/cgi/content/short/193144v1?rss=1" Chaisson, M. J. P. Sanders, A. D. Zhao, X. Malhotra, A. Porubsky, D. Rausch, T. Gardner, E. J. Rodriguez, O. Guo, L. Collins, R. L. Fan, X. Wen, J. Handsaker, R. E. Fairley, S. Kronenberg, Z. N. Kong, X. Hormozdiari, F. Lee, D. Wenger, A. M. Hastie, A. Antaki, D. Audano, P. Brand, H. Cantsilieris, S. Cao, H. Cerveira, E. Chen, C. Chen, X. Chin, C.-S. Chong, Z. Chuang, N. T. Church, D. M. Clarke, L. Farrell, A. Flores, J. Galeev, T. David, G. Gujral, M. Guryev, V. Haynes-Heaton, W. Korlach, J. Kumar, S. Kwon, J. Y. Lee, J. E. Lee, J. Lee, W.-P. Lee, 2017-09-23 doi:10.1101/193144 Cold Spring Harbor Laboratory Press 2017-09-23 <![CDATA[ Accurate And Fast Feature Selection Workflow For High-Dimensional Omics Data ]]> https://biorxiv.org/cgi/content/short/144162v1?rss=1" Perez-Riverol, Y. Kun, M. Vizcaino, J. A. Hitz, M.-P. Audain, E. 2017-06-02 doi:10.1101/144162 Cold Spring Harbor Laboratory Press 2017-06-02 <![CDATA[ A positive feedback loop drives centrosome maturation in flies ]]> https://biorxiv.org/cgi/content/short/380907v1?rss=1" Alvarez Rodrigo, I. Conduit, P. T. Baumbach, J. Novak, Z. A. Aydogan, M. G. Wainman, A. Raff, J. W. 2018-07-31 doi:10.1101/380907 Cold Spring Harbor Laboratory Press 2018-07-31 <![CDATA[ In silico prioritization of transporter-drug relationships from drug sensitivity screens ]]> https://biorxiv.org/cgi/content/short/381335v1?rss=1" Cesar-Razquin, A. Girardi, E. Yang, M. Brehme, M. Saez-Rodriguez, J. Superti-Furga, G. 2018-07-31 doi:10.1101/381335 Cold Spring Harbor Laboratory Press 2018-07-31 <![CDATA[ Telomerecat: A Ploidy-Agnostic Method For Estimating Telomere Length From Whole Genome Sequencing Data ]]> https://biorxiv.org/cgi/content/short/139972v1?rss=1" Farmery, J. H. R. Smith, M. L. NIHR BioResource - Rare Diseases, Lynch, A. G. 2017-05-19 doi:10.1101/139972 Cold Spring Harbor Laboratory Press 2017-05-19 <![CDATA[ β-catenin has both conserved and novel functions in the sponge Ephydatia muelleri ]]> https://biorxiv.org/cgi/content/short/164012v1?rss=1" Schippers, K. J. Nichols, S. A. 2017-07-15 doi:10.1101/164012 Cold Spring Harbor Laboratory Press 2017-07-15 <![CDATA[ A High-Resolution Genetic Map for the Laboratory Rat ]]> https://biorxiv.org/cgi/content/short/268227v1?rss=1" Littrell, J. Tsaih, S.-W. Baud, A. Rastas, P. M. A. Solberg-Woods, L. Flister, M. 2018-02-20 doi:10.1101/268227 Cold Spring Harbor Laboratory Press 2018-02-20 <![CDATA[ In toto fluorescence live imaging in scuttle fly Megaselia abdita reveals gradual transitions towards a novel extraembryonic architecture. ]]> https://biorxiv.org/cgi/content/short/236364v1?rss=1" Caroti, F. Gonzalez Avalos, E. Gonzalez Avalos, P. Kromm, D. Noeske, V. Wosch, M. Schütz, L. Hufnagel, L. Lemke, S. 2017-12-18 doi:10.1101/236364 Cold Spring Harbor Laboratory Press 2017-12-18 <![CDATA[ Staged developmental mapping and X chromosome transcriptional dynamics during mouse spermatogenesis ]]> https://biorxiv.org/cgi/content/short/350868v1?rss=1" Ernst, C. Eling, N. Martinez-Jimenez, C. P. Marioni, J. C. Odom, D. T. 2018-06-20 doi:10.1101/350868 Cold Spring Harbor Laboratory Press 2018-06-20 <![CDATA[ PASP - a whole-transcriptome poly(A) tail length determination assay for the Illumina platform ]]> https://biorxiv.org/cgi/content/short/060004v1?rss=1" Botond Sipos Adrian M Stütz Greg Slodkowicz Tim Massingham Jan Korbel Nick Goldman 2016-06-21 doi:10.1101/060004 Cold Spring Harbor Laboratory Press 2016-06-21 <![CDATA[ SourceData - a semantic platform for curating and searching figures ]]> https://biorxiv.org/cgi/content/short/058529v1?rss=1" Robin Liechti Nancy George Sara El-Gebali Lou Götz Isaac Crespo Ioannis Xenarios Thomas Lemberger 2016-06-13 doi:10.1101/058529 Cold Spring Harbor Laboratory Press 2016-06-13 <![CDATA[ Beyond comparisons of means: understanding changes in gene expression at the single-cell level ]]> https://biorxiv.org/cgi/content/short/035949v1?rss=1" Catalina A Vallejos Sylvia Richardson John C Marioni 2016-01-05 doi:10.1101/035949 Cold Spring Harbor Laboratory Press 2016-01-05 <![CDATA[ Literature Evidence in Open Targets - a target validation platform ]]> https://biorxiv.org/cgi/content/short/124719v1?rss=1" 26 million PubMed abstracts and >1.2 million Open Access full text articles. Our comparative analyses on the current available evidence data in the platform revealed that 850179 of these associations are exclusively identified by literature mining.nnConclusionThis component helps the platforms users by providing the most relevant literature hits for a given target and disease. The text mining evidence along with the other types of evidence can be explored visually through https://www.targetvalidation.org and all the evidence data is available for download in json format from https://www.targetvalidation.org/downloads/data. ]]> Kafkas, S. Dunham, I. McEntyre, J. 2017-04-06 doi:10.1101/124719 Cold Spring Harbor Laboratory Press 2017-04-06 <![CDATA[ Molecular mechanism of the dual regulation of bacterial iron sulfur cluster biogenesis by CyaY and IscX ]]> https://biorxiv.org/cgi/content/short/212290v1?rss=1" Pastore, A. Adinolfi, S. Puglisi, R. Crack, J. Iannuzzi, C. Dal Piaz, F. Konarev, P. Svergun, D. Martin, S. Le Brun, N. 2017-11-03 doi:10.1101/212290 Cold Spring Harbor Laboratory Press 2017-11-03 <![CDATA[ The global distribution and spread of the mobilized colistin resistance gene mcr-1 ]]> https://biorxiv.org/cgi/content/short/220921v1?rss=1" Wang, R. van Dorp, L. Shaw, L. Bradley, P. Wang, Q. Wang, X. Jin, L. Zhang, Q. Liu, Y. Rieux, A. Dorai-Schneiders, T. Weinert, L. A. Iqbal, Z. Didelot, X. Wang, H. Balloux, F. 2017-11-17 doi:10.1101/220921 Cold Spring Harbor Laboratory Press 2017-11-17 <![CDATA[ SKEMPI 2.0: An updated benchmark of changes in protein-protein binding energy, kinetics and thermodynamics upon mutation ]]> https://biorxiv.org/cgi/content/short/341735v1?rss=1" Jankauskaite, J. Jimenez-Garcia, B. Dapkunas, J. Fernandez-Recio, J. Moal, I. H. 2018-06-07 doi:10.1101/341735 Cold Spring Harbor Laboratory Press 2018-06-07 <![CDATA[ BioJS-HGV Viewer: Genetic Variation Visualizer ]]> https://biorxiv.org/cgi/content/short/032573v1?rss=1" Saket Choudhary Leyla Garcia Andrew Nightingale Maria-Jesus Martin 2015-11-22 doi:10.1101/032573 Cold Spring Harbor Laboratory Press 2015-11-22 <![CDATA[ Hemodynamic forces tune the arrest, adhesion and extravasation of circulating tumor cells ]]> https://biorxiv.org/cgi/content/short/183046v1?rss=1" Follain, G. Osmani, N. Azevedo, S. Allio, G. Mercier, L. Karreman, M. Solecki, G. Fekonja, N. Hille, C. Chabannes, V. Dolle, G. Metivet, T. Prudhomme, C. Ruthensteiner, B. Kemmling, A. Siemonsen, S. Schneider, T. Fiehler, J. Glatzel, M. Winkler, F. Schwab, Y. Pantel, K. Harlepp, S. Goetz, J. G. 2017-08-31 doi:10.1101/183046 Cold Spring Harbor Laboratory Press 2017-08-31 <![CDATA[ Balance of microtubule stiffness and cortical tension determines the size of blood cells with marginal band across species ]]> https://biorxiv.org/cgi/content/short/086728v1?rss=1" Dmitrieff, S. Alsina, A. Mathur, A. Nedelec, F. 2016-11-09 doi:10.1101/086728 Cold Spring Harbor Laboratory Press 2016-11-09 <![CDATA[ Nodal and Eph signalling relay drives the transition between apical constriction and apico-basal shortening during ascidian endoderm invagination ]]> https://biorxiv.org/cgi/content/short/418988v1?rss=1" Fiuza, U.-M. Negishi, T. Rouan, A. Yasuo, H. Lemaire, P. 2018-09-15 doi:10.1101/418988 Cold Spring Harbor Laboratory Press 2018-09-15 <![CDATA[ Onset of differentiation is posttranscriptionally controlled in adult neural stem cells ]]> https://biorxiv.org/cgi/content/short/289868v1?rss=1" Baser, A. Dang, Y. Skabkin, M. Guelcueler Balta, G. Kalamakis, G. Kleber, S. Goepferich, M. Schefzik, R. Santos Lopez, A. Llorens Bobadilla, E. Schultz, C. Fischer, B. Martin-Villalba, A. 2018-03-27 doi:10.1101/289868 Cold Spring Harbor Laboratory Press 2018-03-27 <![CDATA[ Modelling cell-cell interactions from spatial molecular data with spatial variance component analysis ]]> https://biorxiv.org/cgi/content/short/265256v1?rss=1" Arnol, D. Schapiro, D. Bodenmiller, B. Saez-Rodriguez, J. Stegle, O. 2018-02-14 doi:10.1101/265256 Cold Spring Harbor Laboratory Press 2018-02-14 <![CDATA[ Dppa2 and Dppa4 directly regulate the Dux driven zygotic transcriptional programme ]]> https://biorxiv.org/cgi/content/short/431890v1?rss=1" Eckersley-Maslin, M. A. Alda-Catalinas, C. Blotenburg, M. Kreibich, E. Krueger, C. Reik, W. 2018-10-01 doi:10.1101/431890 Cold Spring Harbor Laboratory Press 2018-10-01 <![CDATA[ The cis-regulatory dynamics of embryonic development at single cell resolution ]]> https://biorxiv.org/cgi/content/short/166066v1?rss=1" Cusanovich, D. A. Reddington, J. P. Garfield, D. A. Daza, R. Marco-Ferreres, R. Christiansen, L. Qiu, X. Steemers, F. Trapnell, C. Shendure, J. Furlong, E. E. M. 2017-07-20 doi:10.1101/166066 Cold Spring Harbor Laboratory Press 2017-07-20 <![CDATA[ Interoperable and scalable metabolomics data analysis with microservices ]]> https://biorxiv.org/cgi/content/short/213603v1?rss=1" Emami Khoonsari, P. Moreno, P. Bergmann, S. Burman, J. Capuccini, M. Carone, M. Cascante, M. de Atauri, P. Foguet, C. Gonzalez-Beltran, A. Hankemeier, T. Haug, K. He, S. Herman, S. Johnson, D. Kale, N. Larsson, A. Neumann, S. Peters, K. Pireddu, L. Rocca-Serra, P. Roger, P. Rueedi, R. Ruttkies, C. Sadawi, N. Salek, R. M. Sansone, S.-A. Schober, D. Selivanov, V. Thevenot, E. A. van Vliet, M. Zanetti, G. Steinbeck, C. Kultima, K. Spjuth, O. 2017-11-03 doi:10.1101/213603 Cold Spring Harbor Laboratory Press 2017-11-03 <![CDATA[ The Image Data Resource: A Scalable Platform for Biological Image Data Access, Integration, and Dissemination ]]> https://biorxiv.org/cgi/content/short/089359v1?rss=1" Williams, E. Moore, J. Li, S. W. Rustici, G. Tarkowska, A. Chessel, A. Leo, S. Antal, B. Ferguson, R. K. Sarkans, U. Brazma, A. Carazo-Salas, R. E. Swedlow, J. 2016-11-24 doi:10.1101/089359 Cold Spring Harbor Laboratory Press 2016-11-24 <![CDATA[ Dual Function For Tango1 In Secretion Of Bulky Cargo And In ER-Golgi Morphology ]]> https://biorxiv.org/cgi/content/short/144923v1?rss=1" Rios-Barrera, L. D. Sigurbjornsdottir, S. Baer, M. Leptin, M. 2017-06-01 doi:10.1101/144923 Cold Spring Harbor Laboratory Press 2017-06-01 <![CDATA[ NAD(P)HX repair deficiency causes central metabolic perturbations in yeast and human cells ]]> https://biorxiv.org/cgi/content/short/302257v1?rss=1" Becker-Kettern, J. Paczia, N. Conrotte, J.-F. Zhu, C. Fiehn, O. Jung, P. P. Steinmetz, L. M. Linster, C. L. 2018-04-16 doi:10.1101/302257 Cold Spring Harbor Laboratory Press 2018-04-16 <![CDATA[ beachmat: a Bioconductor C++ API for accessing single-cell genomics data from a variety of R matrix types ]]> https://biorxiv.org/cgi/content/short/167445v1?rss=1" Lun, A. T. L. Pages, H. Smith, M. L. 2017-07-24 doi:10.1101/167445 Cold Spring Harbor Laboratory Press 2017-07-24 <![CDATA[ A global perspective on bioinformatics training needs ]]> https://biorxiv.org/cgi/content/short/098996v1?rss=1" Brazas, M. D. Brooksbank, C. Jimenez, R. C. Blackford, S. Palagi, P. M. De Las Rivas, J. Ouellette, B. F. F. Kumuthini, J. Korpelainen, E. Lewitter, F. van Gelder, C. W. G. Mulder, N. Corpas, M. Schneider, M. V. Tan, T. W. Clements, D. Davies, A. Attwood, T. K. 2017-02-27 doi:10.1101/098996 Cold Spring Harbor Laboratory Press 2017-02-27 <![CDATA[ Comprehensive genome and transcriptome analysis reveals genetic basis for gene fusions in cancer ]]> https://biorxiv.org/cgi/content/short/148684v1?rss=1" Fonseca, N. A. He, Y. Greger, L. - PCAWG-3, Brazma, A. Zhang, Z. 2017-06-12 doi:10.1101/148684 Cold Spring Harbor Laboratory Press 2017-06-12 <![CDATA[ Identifiers for the 21st century:How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data ]]> https://biorxiv.org/cgi/content/short/117812v1?rss=1" McMurry, J. Juty, N. Blomberg, N. Burdett, A. Conlin, T. Conte, N. Courtot, M. Deck, J. Dumontier, M. Fellows, D. Gonzalez-Beltran, A. Gormanns, P. Grethe, J. Hastings, J. Hermjakob, H. Heriche, J.-K. Ison, J. Jimenez, R. Jupp, S. Kunze, J. Laibe, C. Le Novere, N. Malone, J. R. Martin, M.-J. McEntyre, J. Morris, C. Muilu, J. Mueller, W. Rocca-Serra, P. Sansone, S.-A. Sariyar, M. Snoep, J. Stanford, N. J. Soiland-Reyes, S. Swainston, N. Washington, N. Williams, A. Wimalaratne, S. Winfree, L. Wolstencroft, K. Goble, C. Mungall, C. Haendel, M. Parkinson, 2017-03-20 doi:10.1101/117812 Cold Spring Harbor Laboratory Press 2017-03-20 <![CDATA[ Ciliary and rhabdomeric photoreceptor-cell circuits form a spectral depth gauge in marine zooplankton ]]> https://biorxiv.org/cgi/content/short/251686v1?rss=1" Veraszto, C. Guhmann, M. Jia, H. Rajan, V. B. V. Bezares-Calderon, L. A. Lopez, C. P. Randel, N. Shahidi, R. Michiels, N. K. Yokoyama, S. Tessmar-Raible, K. Jekely, G. 2018-01-22 doi:10.1101/251686 Cold Spring Harbor Laboratory Press 2018-01-22 <![CDATA[ Data-driven hypothesis weighting increases detection power in multiple testing ]]> https://biorxiv.org/cgi/content/short/034330v1?rss=1" Nikolaos Ignatiadis Bernd Klaus Judith Zaugg Wolfgang Huber 2015-12-13 doi:10.1101/034330 Cold Spring Harbor Laboratory Press 2015-12-13 <![CDATA[ Using the drug-protein interactome to identify anti-ageing compounds for humans ]]> https://biorxiv.org/cgi/content/short/438234v1?rss=1" Fuentealba Valenzuela, M. Donertas, H. M. Williams, R. Labbadia, J. Thornton, J. Partridge, L. 2018-10-08 doi:10.1101/438234 Cold Spring Harbor Laboratory Press 2018-10-08 <![CDATA[ A pan cancer analysis of promoter activity highlights the regulatory role of alternative transcription start sites and their association with noncoding mutations ]]> https://biorxiv.org/cgi/content/short/176487v1?rss=1" Demircioglu, D. Kindermans, M. Nandi, T. Cukuroglu, E. Calabrese, C. Fonseca, N. A. Kahles, A. Lehmann, K. Stegle, O. PCAWG-3, PCAWG-Network, Brazma, A. Brooks, A. Rätsch, G. Tan, P. Göke, J. 2017-08-15 doi:10.1101/176487 Cold Spring Harbor Laboratory Press 2017-08-15 <![CDATA[ The landscape of selection in 551 Esophageal Adenocarcinomas defines genomic biomarkers for the clinic ]]> https://biorxiv.org/cgi/content/short/310029v1?rss=1" Frankell, A. M. Jammula, S. Contino, G. Killcoyne, S. S. Abbas, S. Perner, J. Bower, L. Devonshire, G. Grehan, N. Mok, J. O'Donovan, M. Macrae, S. Tavare, S. Fitzgerald, R. C. the Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium, 2018-04-28 doi:10.1101/310029 Cold Spring Harbor Laboratory Press 2018-04-28 <![CDATA[ Combined single cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity ]]> https://biorxiv.org/cgi/content/short/328138v1?rss=1" Linker, S. M. Urban, L. Clark, S. Chhatriwala, M. Amatya, S. McCarthy, D. Ebersberger, I. Vallier, L. Reik, W. Stegle, O. Bonder, M. J. 2018-05-22 doi:10.1101/328138 Cold Spring Harbor Laboratory Press 2018-05-22 <![CDATA[ Modeling of DNA methylation in cis reveals principles of chromatin folding in vivo in the absence of crosslinking and ligation ]]> https://biorxiv.org/cgi/content/short/407031v1?rss=1" Redolfi, J. Zhan, Y. Valdes, C. Kryzhanovska, M. Misteli Guerreiro, I. Iesmantavicius, V. Tiana, G. Pollex, T. Kind, J. Smallwood, S. de Laat, W. Giorgetti, L. 2018-09-03 doi:10.1101/407031 Cold Spring Harbor Laboratory Press 2018-09-03 <![CDATA[ Structural Basis Of STAT2 Recognition By IRF9 Reveals Molecular Insights Into ISGF3 Function ]]> https://biorxiv.org/cgi/content/short/131714v1?rss=1" Rengachari, S. Groiss, S. Devos, J. Caron, E. Grandvaux, N. Panne, D. 2017-04-28 doi:10.1101/131714 Cold Spring Harbor Laboratory Press 2017-04-28 <![CDATA[ VarQ: a tool for the structural analysis of Human Protein Variants ]]> https://biorxiv.org/cgi/content/short/277491v1?rss=1" Radusky, L. Modenutti, C. P. Delgado, J. Bustamante, J. P. Vishnopolska, S. Kiel, C. Serrano, L. Marti, M. Turjanski, A. G. 2018-03-07 doi:10.1101/277491 Cold Spring Harbor Laboratory Press 2018-03-07 <![CDATA[ Reverse GWAS: Using Genetics to Identify and Model Phenotypic Subtypes ]]> https://biorxiv.org/cgi/content/short/446492v1?rss=1" Dahl, A. Cai, N. Ko, A. Laakso, M. Pajukanta, P. Flint, J. Zaitlen, N. 2018-10-17 doi:10.1101/446492 Cold Spring Harbor Laboratory Press 2018-10-17 <![CDATA[ Systematic Characterization of RhoGEF/RhoGAP Regulatory Proteins Reveals Organization Principles of Rho GTPase Signaling ]]> https://biorxiv.org/cgi/content/short/354316v1?rss=1" Rocks, O. Mueller, P. M. Rademacher, J. Bagshaw, R. D. Alp, K. M. Giudice, G. Heinrich, L. E. Barth, C. Eccles, R. L. Sanchez-Castro, M. Mbamalu, G. Tucholska, M. Spatt, L. Wortmann, C. Czajkowski, M. T. Welke, R. W. Zhang, S. Nguyen, V. Brandeburg, L. Rrustemi, T. Trnka, P. Freitag, K. Larsen, B. Popp, O. Colwill, K. Mertins, P. Gingras, A.-C. Bakal, C. Pertz, O. Roth, F. P. Pawson, T. Petsalaki, E. 2018-06-24 doi:10.1101/354316 Cold Spring Harbor Laboratory Press 2018-06-24 <![CDATA[ SpatialDE - Identification Of Spatially Variable Genes ]]> https://biorxiv.org/cgi/content/short/143321v1?rss=1" Svensson, V. Teichmann, S. A. Stegle, O. 2017-05-28 doi:10.1101/143321 Cold Spring Harbor Laboratory Press 2017-05-28 <![CDATA[ Epigallocatechin-3-Gallate Improves Facial Dysmorphology Associated with Down Syndrome ]]> https://biorxiv.org/cgi/content/short/276493v1?rss=1" Starbuck, J. Llambrich, S. Gonzalez, R. Albaiges, J. Sarle, A. Wouters, J. Gonzalez, A. Sevillano, X. Sharpe, J. de la Torre, R. Dierssen, M. Vande Velde, G. Martinez-Abadias, N. 2018-03-05 doi:10.1101/276493 Cold Spring Harbor Laboratory Press 2018-03-05 <![CDATA[ Placozoans are eumetazoans related to Cnidaria ]]> https://biorxiv.org/cgi/content/short/200972v1?rss=1" Laumer, C. E. Gruber-Vodicka, H. Hadfield, M. G. Pearse, V. B. Riesgo, A. Marioni, J. C. Giribet, G. 2017-10-11 doi:10.1101/200972 Cold Spring Harbor Laboratory Press 2017-10-11 <![CDATA[ A damped oscillator imposes temporal order on posterior gap gene expression in Drosophila ]]> https://biorxiv.org/cgi/content/short/068072v1?rss=1" Berta Verd Erik Clark Anton Crombach Johannes Jaeger 2016-08-05 doi:10.1101/068072 Cold Spring Harbor Laboratory Press 2016-08-05 <![CDATA[ The proBAM and proBed standard formats: enabling a seamless integration of genomics and proteomics data. ]]> https://biorxiv.org/cgi/content/short/152579v1?rss=1" Menschaert, G. Wang, X. Jones, A. R. Ghali, F. Fenyo, D. Olexiouk, V. Zhang, B. Deutsch, E. W. Ternent, T. Vizcaino, J. A. 2017-06-20 doi:10.1101/152579 Cold Spring Harbor Laboratory Press 2017-06-20 <![CDATA[ Ubiquitous abundance distribution of non-dominant plankton across the world’s ocean ]]> https://biorxiv.org/cgi/content/short/269068v1?rss=1" Ser-Giacomi, E. Zinger, L. Malviya, S. De Vargas, C. Karsenti, E. Bowler, C. De Monte, S. 2018-02-21 doi:10.1101/269068 Cold Spring Harbor Laboratory Press 2018-02-21 <![CDATA[ Transcript Isoform Differences Across Human Tissues Are Predominantly Driven By Alternative Start And Termination Sites Of Transcription ]]> https://biorxiv.org/cgi/content/short/127894v1?rss=1" Reyes, A. Huber, W. 2017-04-17 doi:10.1101/127894 Cold Spring Harbor Laboratory Press 2017-04-17 <![CDATA[ GDSCTools for Mining Pharmacogenomic Interactions in Cancer ]]> https://biorxiv.org/cgi/content/short/166223v1?rss=1" Cokelaer, T. Chen, E. Iorio, F. Menden, M. P. Lightfoot, H. Saez-Rodriguez, J. Mathew, G. J. 2017-07-20 doi:10.1101/166223 Cold Spring Harbor Laboratory Press 2017-07-20 <![CDATA[ A Theory That Predicts Behaviors Of Disordered Cytoskeletal Networks ]]> https://biorxiv.org/cgi/content/short/138537v1?rss=1" Belmonte, J. Leptin, M. Nedelec, F. 2017-05-16 doi:10.1101/138537 Cold Spring Harbor Laboratory Press 2017-05-16 <![CDATA[ The druggable genome and support for target identification and validation in drug development ]]> https://biorxiv.org/cgi/content/short/066027v1?rss=1" Chris Finan Anna Gaulton Felix Kruger Tom Lumbers Tina Shah Jorgen Engmann Luana Galver Ryan Kelly Anneli Karlsson Rita Santos John Overington Aroon Hingorani Juan Pablo Casas 2016-07-26 doi:10.1101/066027 Cold Spring Harbor Laboratory Press 2016-07-26 <![CDATA[ Super-resolution fight club: A broad assessment of 2D & 3D single-molecule localization microscopy software ]]> https://biorxiv.org/cgi/content/short/362517v1?rss=1" Sage, D. Pham, T.-A. Babcock, H. Lukes, T. Pengo, T. Velmurugan, R. Herbert, A. Agarwal, A. Colabrese, S. Wheeler, A. Archetti, A. Rieger, B. Ober, R. Hagen, G. M. Sibarita, J.-B. Ries, J. Henriques, R. Unser, M. Holden, S. 2018-07-04 doi:10.1101/362517 Cold Spring Harbor Laboratory Press 2018-07-04 <![CDATA[ Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm ]]> https://biorxiv.org/cgi/content/short/297960v1?rss=1" Bliven, S. E. Lafita, A. Rose, P. W. Capitani, G. Prlic, A. Bourne, P. 2018-04-09 doi:10.1101/297960 Cold Spring Harbor Laboratory Press 2018-04-09 <![CDATA[ Phenotype prediction in an Escherichia coli strain panel ]]> https://biorxiv.org/cgi/content/short/141879v1?rss=1" Galardini, M. Koumoutsi, A. Herrera-Dominguez, L. Cordero Varela, J. A. Telzerow, A. Wagih, O. Wartel, M. Clermont, O. Denamur, E. Typas, A. Beltrao, P. 2017-05-24 doi:10.1101/141879 Cold Spring Harbor Laboratory Press 2017-05-24 <![CDATA[ A genome-wide resource for high-throughput genomic tagging of yeast ORFs ]]> https://biorxiv.org/cgi/content/short/226811v1?rss=1" Meurer, M. Duan, Y. Sass, E. Kats, I. Herbst, K. Buchmuller, B. C. Dederer, V. Huber, F. Kirrmaier, D. Stefl, M. Van Laer, K. Dick, T. P. Lemberg, M. K. Khmelinskii, A. Levy, E. D. Knop, M. 2017-11-30 doi:10.1101/226811 Cold Spring Harbor Laboratory Press 2017-11-30 <![CDATA[ Alzheimer related genes show accelerated evolution ]]> https://biorxiv.org/cgi/content/short/114108v1?rss=1" Nitsche, A. Reiche, K. Ueberham, U. Arnold, C. Hackermueller, J. Horn, F. Stadler, P. F. Arendt, T. 2017-03-07 doi:10.1101/114108 Cold Spring Harbor Laboratory Press 2017-03-07 <![CDATA[ Tracing the Transitions from Pluripotency to Germ Cell Fate with CRISPR Screening ]]> https://biorxiv.org/cgi/content/short/269811v1?rss=1" Hackett, J. A. Huang, Y. Gunesdogan, U. Holm-Gretarsson, K. Kobayashi, T. Surani, A. M. 2018-02-22 doi:10.1101/269811 Cold Spring Harbor Laboratory Press 2018-02-22 <![CDATA[ A bromodomain-DNA interaction facilitates acetylation-dependent bivalent nucleosome recognition by the BET protein BRDT ]]> https://biorxiv.org/cgi/content/short/074773v1?rss=1" Thomas CR Miller Bernd Simon Vladimir Rybin Helga Grötsch Sandrine Curtet Saadi Khochbin Teresa Carlomagno Christoph W Müller 2016-09-12 doi:10.1101/074773 Cold Spring Harbor Laboratory Press 2016-09-12 <![CDATA[ Avoiding ascertainment bias in the maximum likelihood inference of phylogenies based on truncated data ]]> https://biorxiv.org/cgi/content/short/186478v1?rss=1" Tamuri, A. Goldman, N. 2017-09-09 doi:10.1101/186478 Cold Spring Harbor Laboratory Press 2017-09-09 <![CDATA[ Dynamics of ASC speck formation during skin inflammatory responses in vivo ]]> https://biorxiv.org/cgi/content/short/111542v1?rss=1" Kuri Rodriguez, P. S. Schieber, N. Thumberger, T. Wittbrodt, J. Schwab, Y. Leptin, M. 2017-02-27 doi:10.1101/111542 Cold Spring Harbor Laboratory Press 2017-02-27 <![CDATA[ Identifying accurate metagenome and amplicon software via a meta-analysis of benchmarking studies ]]> https://biorxiv.org/cgi/content/short/202077v1?rss=1" Gardner, P. P. Watson, R. J. Morgan, X. C. Draper, J. L. Finn, R. D. Morales, S. E. Stott, M. B. 2017-10-12 doi:10.1101/202077 Cold Spring Harbor Laboratory Press 2017-10-12 <![CDATA[ Rapid identification of optimal drug combinations for personalized cancer therapy using microfluidics ]]> https://biorxiv.org/cgi/content/short/093906v1?rss=1" Eduati, F. Utharala, R. Madhavan, D. Neumann, U. P. Cramer, T. Saez-Rodriguez, J. Merten, C. A. 2016-12-14 doi:10.1101/093906 Cold Spring Harbor Laboratory Press 2016-12-14 <![CDATA[ Targeting neuronal and glial cell types with synthetic promoter AAVs in mice, non-human primates, and humans ]]> https://biorxiv.org/cgi/content/short/434720v1?rss=1" Juettner, J. Szabo, A. Gross-Scherf, B. Morikawa, R. Rompani, S. Teixeira, M. Hantz, P. Szikra, T. Esposti, F. Cowan, C. Bharioke, A. Patino, C. Keles, O. Roth, C. Kusnyerik, A. Gerber-Hollbach, N. Azoulay, T. Hartl, D. Krebs, A. Schuebeler, D. Hajdu, R. Lukats, A. Nemeth, J. Nagy, Z. Wu, K.-C. Wu, R.-H. Xiang, L. Fang, X.-L. Jin, Z.-B. Goldblum, D. Hasler, P. Scholl, H. Krol, J. Roska, B. 2018-10-04 doi:10.1101/434720 Cold Spring Harbor Laboratory Press 2018-10-04 <![CDATA[ Kipoi: accelerating the community exchange and reuse of predictive models for genomics ]]> https://biorxiv.org/cgi/content/short/375345v1?rss=1" Avsec, Z. Kreuzhuber, R. Israeli, J. Xu, N. Cheng, J. Shrikumar, A. Banerjee, A. Kim, D. S. Urban, L. Kundaje, A. Stegle, O. Gagneur, J. 2018-07-24 doi:10.1101/375345 Cold Spring Harbor Laboratory Press 2018-07-24 <![CDATA[ Online resources for PCAWG data exploration, visualization, and discovery ]]> https://biorxiv.org/cgi/content/short/163907v1?rss=1" Goldman, M Zhang, J Fonseca, N Xiang, Q Craft, B Piñeiro-Yáñez, E O'Connor, B Bazant, W Barrera, E Muñoz, A Petryszak, R Füllgrabe, A Al-Shahrour, F Keays, M Haussler, D Weinstein, J Huber, W Valencia, A Papatheodorou, I Zhu, J Ferreti, V Vazquez, M 2017-07-14 doi:10.1101/163907 Cold Spring Harbor Laboratory Press 2017-07-14 <![CDATA[ Studying the fate of tumor extracellular vesicles at high spatio-temporal resolution using the zebrafish embryo ]]> https://biorxiv.org/cgi/content/short/380238v1?rss=1" Hyenne, V. Ghoroghi, S. Collot, M. Harlepp, S. Bauer, J. Mercier, L. Busnelli, I. Lefebvre, O. Fekonja, N. Machado, P. Bons, J. Delalande, F. Amor, A. I. Silva, S. G. Verweij, F. J. Van Niel, G. Schwab, Y. Peinado, H. Carapito, C. Klymchenko, A. S. Goetz, J. G. 2018-07-30 doi:10.1101/380238 Cold Spring Harbor Laboratory Press 2018-07-30 <![CDATA[ The USTC complex co-opts an ancient machinery to drive piRNA transcription in C. elegans ]]> https://biorxiv.org/cgi/content/short/377390v1?rss=1" Weng, C. Kosalka, A. Berkyurek, A. C. Stempor, P. Feng, X. Mao, H. Zeng, C. Li, W.-J. Yan, Y.-H. Dong, M.-Q. Zuliani, C. Barabas, O. Ahringer, J. Guang, S. Miska, E. 2018-07-25 doi:10.1101/377390 Cold Spring Harbor Laboratory Press 2018-07-25 <![CDATA[ Subdivision of ancestral scale genetic program underlies origin of feathers and avian scutate scales ]]> https://biorxiv.org/cgi/content/short/377358v1?rss=1" Musser, J. M. Wagner, G. P. Liang, C. Stabile, F. A. Cloutier, A. Baker, A. J. Prum, R. O. 2018-07-25 doi:10.1101/377358 Cold Spring Harbor Laboratory Press 2018-07-25 <![CDATA[ TET2 binding to enhancers facilitates transcription factor recruitment in hematopoietic cells ]]> https://biorxiv.org/cgi/content/short/336008v1?rss=1" Rasmussen, K. Berest, I. Kessler, S. Nishimura, K. Simon-Carrasco, L. Vassilou, G. S. Pedersen, M. T. Christensen, J. Zaugg, J. Helin, K. 2018-05-31 doi:10.1101/336008 Cold Spring Harbor Laboratory Press 2018-05-31 <![CDATA[ Drug repurposing for ageing research using model organisms ]]> https://biorxiv.org/cgi/content/short/095380v1?rss=1" Ziehm, M. Kaur, S. Ivanov, D. K. Ballester, P. J. Marcus, D. Partridge, L. Thornton, J. M. 2016-12-22 doi:10.1101/095380 Cold Spring Harbor Laboratory Press 2016-12-22 <![CDATA[ Condensin controls cellular RNA levels through the accurate segregation of chromosomes instead of directly regulating transcription ]]> https://biorxiv.org/cgi/content/short/330654v1?rss=1" Hocquet, C. Robellet, X. Modolo, L. Sun, X.-M. Burny, C. Cuylen-Haering, S. Toselli, E. Clauder-Münster, S. Steinmetz, L. Haering, C. H. Marguerat, S. Bernard, P. 2018-05-25 doi:10.1101/330654 Cold Spring Harbor Laboratory Press 2018-05-25 <![CDATA[ A Data Citation Roadmap for Scholarly Data Repositories ]]> https://biorxiv.org/cgi/content/short/097196v1?rss=1" Fenner, M. Crosas, M. Grethe, J. Kennedy, D. Hermjakob, H. Rocca-Serra, P. Berjon, R. Karcher, S. Martone, M. Clark, T. 2016-12-28 doi:10.1101/097196 Cold Spring Harbor Laboratory Press 2016-12-28 <![CDATA[ Assessing the Gene Regulatory Landscape in 1,188 Human Tumors ]]> https://biorxiv.org/cgi/content/short/225441v1?rss=1" Calabrese, C. Lehmann, K.-V. Urban, L. Liu, F. Erkek, S. Fonseca, N. Kahles, A. Kilpinen-Barrett, L. H. Markowski, J. PCAWG-3, Waszak, S. Korbel, J. Zhang, Z. Brazma, A. Raetsch, G. Schwarz, R. Stegle, O. 2017-11-29 doi:10.1101/225441 Cold Spring Harbor Laboratory Press 2017-11-29 <![CDATA[ Understanding trivial challenges of microbial genomics: An assembly example ]]> https://biorxiv.org/cgi/content/short/347625v1?rss=1" Lariviere, D. Mei, H. Freeberg, M. Taylor, J. Nekrutenko, A. 2018-06-14 doi:10.1101/347625 Cold Spring Harbor Laboratory Press 2018-06-14 <![CDATA[ Highly dynamic chromatin interactions drive neurogenesis through gene regulatory networks ]]> https://biorxiv.org/cgi/content/short/303842v1?rss=1" Malysheva, V. Mendoza-Parra, M. A. Blum, M. Gronemeyer, H. 2018-04-18 doi:10.1101/303842 Cold Spring Harbor Laboratory Press 2018-04-18 <![CDATA[ Robust expression variability testing reveals heterogeneous T cell responses ]]> https://biorxiv.org/cgi/content/short/237214v1?rss=1" Eling, N. Richard, A. C. Richardson, S. Marioni, J. C. Vallejos, C. A. 2017-12-21 doi:10.1101/237214 Cold Spring Harbor Laboratory Press 2017-12-21 <![CDATA[ Pan-cancer analysis of whole genomes ]]> https://biorxiv.org/cgi/content/short/162784v1?rss=1" Campbell, P. J. Getz, G. Stuart, J. M. Korbel, J. O. Stein, L. D. - ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Net, 2017-07-12 doi:10.1101/162784 Cold Spring Harbor Laboratory Press 2017-07-12 <![CDATA[ Tunneling nanotubes contribute to the stroma-mediated imatinib resistance of leukemic cells ]]> https://biorxiv.org/cgi/content/short/425041v1?rss=1" Kolba, M. D. Dudka, W. Zareba-Koziol, M. Kominek, A. Ronchi, P. Turos, L. Wlodarczyk, J. Schwab, Y. Cysewski, D. Srpan, K. Davis, D. M. Piwocka, K. 2018-09-25 doi:10.1101/425041 Cold Spring Harbor Laboratory Press 2018-09-25 <![CDATA[ MDM4 is an essential disease driver targeted by 1q gain in Burkitt lymphoma ]]> https://biorxiv.org/cgi/content/short/289363v1?rss=1" Huellein, J. Slabicki, M. Rosolowski, M. Jethwa, A. Habringer, S. Tomska, K. Kurilov, R. Lu, J. Scheinost, S. Wagener, R. Huang, Z. Lukas, M. Yavorska, O. Helferich, H. Scholtysik, R. Bonneau, K. Tedesco, D. Kueppers, R. Klapper, W. Pott, C. Stilgenbauer, S. Burkhardt, B. Loeffler, M. Truemper, L. Hummel, M. Brors, B. Zapatka, M. Siebert, R. Keller, U. Huber, W. Kreuz, M. Zenz, T. MMML consortium, 2018-04-09 doi:10.1101/289363 Cold Spring Harbor Laboratory Press 2018-04-09 <![CDATA[ Quantification of gene expression patterns to reveal the origins of abnormal morphogenesis ]]> https://biorxiv.org/cgi/content/short/246256v1?rss=1" Martinez-Abadias, N. Mateu Estivill, R. Sastre Tomas, J. Motch Perrine, S. Yoon, M. Robert-Moreno, A. Swoger, J. Russo, L. Kawasaki, K. Richtsmeier, J. Sharpe, J. 2018-01-11 doi:10.1101/246256 Cold Spring Harbor Laboratory Press 2018-01-11 <![CDATA[ Cardelino: Integrating whole exomes and single-cell transcriptomes to reveal phenotypic impact of somatic variants ]]> https://biorxiv.org/cgi/content/short/413047v1?rss=1" McCarthy, D. J. Rostom, R. Huang, Y. Kunz, D. J. Danecek, P. Bonder, M. J. Hagai, T. HipSci Consortium, Wang, W. Gaffney, D. J. Simons, B. D. Stegle, O. Teichmann, S. A. 2018-09-10 doi:10.1101/413047 Cold Spring Harbor Laboratory Press 2018-09-10 <![CDATA[ CONSTRUCTION OF WHOLE GENOMES FROM SCAFFOLDS USING SINGLE CELL STRAND-SEQ DATA ]]> https://biorxiv.org/cgi/content/short/271510v1?rss=1" Hills, M. Falconer, E. O'Neil, K. Sanders, A. Howe, K. Guryev, V. Lansdorp, P. M. 2018-02-26 doi:10.1101/271510 Cold Spring Harbor Laboratory Press 2018-02-26 <![CDATA[ Real-time detection of condensin-driven DNA compaction reveals a multistep binding mechanism ]]> https://biorxiv.org/cgi/content/short/149138v1?rss=1" Eeftens, J. M. Bisht, S. Kerssemakers, J. Haering, C. Dekker, C. 2017-06-15 doi:10.1101/149138 Cold Spring Harbor Laboratory Press 2017-06-15 <![CDATA[ Post-translational regulation of metabolism in fumarate hydratase deficient cancer cells ]]> https://biorxiv.org/cgi/content/short/149716v1?rss=1" Goncalves, E. Sciacovelli, M. Costa, A. S. H. Johnson, T. I. Machado, D. Frezza, C. Saez-Rodriguez, J. 2017-06-13 doi:10.1101/149716 Cold Spring Harbor Laboratory Press 2017-06-13 <![CDATA[ Microbial adaptation to venom is common in snakes and spiders ]]> https://biorxiv.org/cgi/content/short/348433v1?rss=1" Esmaeilishirazifard, E. Usher, L. Trim, C. Denise, H. Sangal, V. Tyson, G. H. Barlow, A. Redway, K. Taylor, J. D. Kremmyda-Vlachou, M. Loftus, T. D. Lock, M. M. G. Wright, K. Dalby, A. Snyder, L. A. S. Wuster, W. Trim, S. Moschos, S. A. 2018-06-16 doi:10.1101/348433 Cold Spring Harbor Laboratory Press 2018-06-16 <![CDATA[ RELION-3: new tools for automated high-resolution cryo-EM structure determination ]]> https://biorxiv.org/cgi/content/short/421123v1?rss=1" Zivanov, J. Nakane, T. Forsberg, B. Kimanius, D. Hagen, W. J. H. Lindahl, E. Scheres, S. H. W. 2018-09-19 doi:10.1101/421123 Cold Spring Harbor Laboratory Press 2018-09-19 <![CDATA[ IsoProt: A fully reproducible one-stop-shop for the analysis of iTRAQ/TMT data ]]> https://biorxiv.org/cgi/content/short/446070v1?rss=1" Griss, J. Vinterhalter, G. Schwaemmle, V. 2018-10-17 doi:10.1101/446070 Cold Spring Harbor Laboratory Press 2018-10-17 <![CDATA[ Mining therapeutic insights from large scale drug screenings with transfer learning ]]> https://biorxiv.org/cgi/content/short/225573v1?rss=1" Yang, M. Simm, J. Zakeri, P. Moreau, Y. Saez-Rodriguez, J. 2017-11-27 doi:10.1101/225573 Cold Spring Harbor Laboratory Press 2017-11-27 <![CDATA[ Harmonizing semantic annotations for computational models in biology ]]> https://biorxiv.org/cgi/content/short/246470v1?rss=1" Neal, M. L. König, M. Nickerson, D. Mısırlı, G. Kalbasi, R. Dräger, A. Atalag, K. Chelliah, V. Cooling, M. Cook, D. L. Crook, S. de Alba, M. Friedman, S. H. Garny, A. Gennari, J. H. Gleeson, P. Golebiewski, M. Hucka, M. Juty, N. Le Novere, N. Myers, C. Olivier, B. G. Sauro, H. M. Scharm, M. Snoep, J. L. Toure, V. Wipat, A. Wolkenhauer, O. Waltemath, D. 2018-01-23 doi:10.1101/246470 Cold Spring Harbor Laboratory Press 2018-01-23 <![CDATA[ Fluorescence-Based Detection of Fusion State on a Cryo-EM Grid using Correlated Cryo-Fluorescence and Cryo-Electron Microscopy ]]> https://biorxiv.org/cgi/content/short/388579v1?rss=1" Metskas, L. A. Briggs, J. A. G. 2018-08-10 doi:10.1101/388579 Cold Spring Harbor Laboratory Press 2018-08-10 <![CDATA[ The Human RNA-Binding Proteome and Its Dynamics During Arsenite-Induced Translational Arrest ]]> https://biorxiv.org/cgi/content/short/329995v1?rss=1" Trendel, J. Schwarzl, T. Prakash, A. Bateman, A. Hentze, M. W. Krijgsveld, J. 2018-05-30 doi:10.1101/329995 Cold Spring Harbor Laboratory Press 2018-05-30 <![CDATA[ clusterSeq: methods for identifying co-expression in high-throughput sequencing data ]]> https://biorxiv.org/cgi/content/short/188581v1?rss=1" Hardcastle, T. J. Papatheodorou, I. 2017-09-13 doi:10.1101/188581 Cold Spring Harbor Laboratory Press 2017-09-13 <![CDATA[ The Drosophila microbiome has a limited influence on sleep, activity, and courtship behaviors ]]> https://biorxiv.org/cgi/content/short/287045v1?rss=1" Selkrig, J. Mohammad, F. Ng, S. H. Chua, J. Y. Tumkaya, T. Ho, J. Chiang, Y. N. Rieger, D. Pettersson, S. Helfrich-Foerster, C. Yew, J. Claridge-Chang, A. 2018-03-22 doi:10.1101/287045 Cold Spring Harbor Laboratory Press 2018-03-22 <![CDATA[ Protein inference using PIA workflows and PSI standard file formats ]]> https://biorxiv.org/cgi/content/short/424473v1?rss=1" Uszkoreit, J. Perez-Riverol, Y. Eggers, B. Marcus, K. Eisenacher, M. 2018-09-23 doi:10.1101/424473 Cold Spring Harbor Laboratory Press 2018-09-23 <![CDATA[ Topological data analysis quantifies biological nano-structure from single molecule localization microscopy ]]> https://biorxiv.org/cgi/content/short/400275v1?rss=1" Pike, J. A. Khan, A. O. Pallini, C. Thomas, S. G. Mund, M. Ries, J. Poulter, N. S. Styles, I. B. 2018-08-26 doi:10.1101/400275 Cold Spring Harbor Laboratory Press 2018-08-26 <![CDATA[ Recent improvements to the automatic characterization and data collection algorithms on MASSIF-1 ]]> https://biorxiv.org/cgi/content/short/236596v1?rss=1" Svensson, O. Gilski, M. Nurizzo, D. Bowler, M. W. 2017-12-19 doi:10.1101/236596 Cold Spring Harbor Laboratory Press 2017-12-19 <![CDATA[ Raoult’s law revisited: accurately predicting equilibrium relative humidity points for humidity control experiments ]]> https://biorxiv.org/cgi/content/short/089094v1?rss=1" Bowler, M. G. Bowler, D. R. Bowler, M. W. 2016-11-22 doi:10.1101/089094 Cold Spring Harbor Laboratory Press 2016-11-22 <![CDATA[ Germline determinants of the somatic mutation landscape in 2,642 cancer genomes ]]> https://biorxiv.org/cgi/content/short/208330v1?rss=1" T mutagenesis at CpG dinucleotides, a ubiquitous mutational process acting across tissues. Analysis of somatic structural variation exposed complex rearrangement patterns, involving cycles of templated insertions and tandem duplications, in BRCA1-deficient tumours. Genome-wide association analysis implicated common genetic variation at the APOBEC3 gene cluster with reduced basal levels of somatic mutagenesis attributable to APOBEC cytidine deaminases across cancer types. We further inferred over a hundred polymorphic L1/LINE elements with somatic retrotransposition activity in cancer. Our study highlights the major impact of rare and common germline variants on mutational landscapes in cancer. ]]> Waszak, S. M. Tiao, G. Zhu, B. Rausch, T. Muyas, F. Rodriguez-Martin, B. Rabionet, R. Yakneen, S. Escaramis, G. Li, Y. Saini, N. Roberts, S. A. Demidov, G. M. Pitkanen, E. Delaneau, O. Heredia-Genestar, J. M. Weischenfeldt, J. Shringarpure, S. S. Chen, J. Nakagawa, H. Alexandrov, L. B. Drechsel, O. Dursi, L. J. Segre, A. V. Garrison, E. Erkek, S. Habermann, N. Urban, L. Khurana, E. Cafferkey, A. Hayashi, S. Imoto, S. Aaltonen, L. A. Alvarez, E. G. Baez-Ortega, A. Bailey, M. Bosio, M. Bruzos, A. L. Buchhalter, I. Bustamante, C. D. Calabrese, C. DiBiase, 2017-11-01 doi:10.1101/208330 Cold Spring Harbor Laboratory Press 2017-11-01 <![CDATA[ iProteinDB: an integrative database of Drosophila post-translational modifications ]]> https://biorxiv.org/cgi/content/short/386268v1?rss=1" Hu, Y. Sopko, R. Chung, V. Studer, R. A. Landry, S. D. Liu, D. Rabinow, L. Gnad, F. Beltrao, P. Perrimon, N. 2018-08-07 doi:10.1101/386268 Cold Spring Harbor Laboratory Press 2018-08-07 <![CDATA[ The Condensin Complex Is A Mechanochemical Motor That Translocates Along DNA ]]> https://biorxiv.org/cgi/content/short/137711v1?rss=1" Terekawa, T. Bisht, S. Eeftens, J. Dekker, C. Haering, C. Greene, E. 2017-05-13 doi:10.1101/137711 Cold Spring Harbor Laboratory Press 2017-05-13 <![CDATA[ Patterning of a telencephalon-like region in the adult brain of amphioxus ]]> https://biorxiv.org/cgi/content/short/307629v1?rss=1" Benito Gutierrez, E. Stemmer, M. Rohr, S. D. Schumacher, L. N. Tang, J. Marconi, A. Jekely, G. Arendt, D. 2018-04-25 doi:10.1101/307629 Cold Spring Harbor Laboratory Press 2018-04-25 <![CDATA[ Evolution of protein kinase substrate recognition at the active site ]]> https://biorxiv.org/cgi/content/short/443945v1?rss=1" Bradley, D. Beltrao, P. 2018-10-16 doi:10.1101/443945 Cold Spring Harbor Laboratory Press 2018-10-16 <![CDATA[ Postmitotic Nuclear Pore Assembly Proceeds By Radial Dilation Of Small ER Membrane Openings ]]> https://biorxiv.org/cgi/content/short/141150v1?rss=1" Otsuka, S. Steyer, A. M. Schorb, M. Heriche, J.-K. Hossain, M. J. Sethi, S. Schwab, Y. Beck, M. Ellenberg, J. 2017-05-23 doi:10.1101/141150 Cold Spring Harbor Laboratory Press 2017-05-23 <![CDATA[ ConfocalGN : a minimalistic confocal image simulator. ]]> https://biorxiv.org/cgi/content/short/088906v1?rss=1" Dmitrieff, S. Nedelec, F. 2016-11-21 doi:10.1101/088906 Cold Spring Harbor Laboratory Press 2016-11-21 <![CDATA[ Minimal phenotyping yields GWAS hits of low specificity for major depression ]]> https://biorxiv.org/cgi/content/short/440735v1?rss=1" Cai, N. Kendler, K. Flint, J. 2018-10-11 doi:10.1101/440735 Cold Spring Harbor Laboratory Press 2018-10-11 <![CDATA[ Contact-dependent cell communications drive morphological invariance during ascidian embryogenesis ]]> https://biorxiv.org/cgi/content/short/238741v1?rss=1" Guignard, L. Fiuza, U.-M. Leggio, B. Faure, E. Laussu, J. Hufnagel, L. Malandain, G. Godin, C. Lemaire, P. 2017-12-24 doi:10.1101/238741 Cold Spring Harbor Laboratory Press 2017-12-24 <![CDATA[ Utilisation of staphylococcal immune evasion protein Sbi as a novel vaccine adjuvant ]]> https://biorxiv.org/cgi/content/short/413294v1?rss=1" Yang, Y. Back, C. Graewert, M. Wahid, A. Denton, H. Kildani, R. Paulin, J. Woerner, K. Kaiser, W. Svergun, D. I. Sartbaeva, A. Watts, A. Marchbank, K. van den Elsen, J. M. 2018-09-10 doi:10.1101/413294 Cold Spring Harbor Laboratory Press 2018-09-10 <![CDATA[ In situ architecture of the algal nuclear pore complex ]]> https://biorxiv.org/cgi/content/short/232017v1?rss=1" Mosalaganti, S. Kosinski, J. Albert, S. Schaffer, M. Plitzko, J. M. Baumeister, W. Engel, B. D. Beck, M. 2017-12-10 doi:10.1101/232017 Cold Spring Harbor Laboratory Press 2017-12-10 <![CDATA[ Sperm chemotaxis is driven by the slope of the chemoattractant concentration field ]]> https://biorxiv.org/cgi/content/short/148650v1?rss=1" Ramirez-Gomez, H. V. Jimenez-Sabinina, V. Tuval, I. Velazquez-Perez, M. Beltran, C. Carneiro, J. Wood, C. Darszon, A. Guerrero, A. 2017-06-10 doi:10.1101/148650 Cold Spring Harbor Laboratory Press 2017-06-10 <![CDATA[ The small non-coding vault RNA1-1 acts as a riboregulator of autophagy ]]> https://biorxiv.org/cgi/content/short/177949v1?rss=1" Horos, R. Alleaume, A.-M. Kleinendorst, R. Tarafder, A. K. Schwarzl, T. Zielonka, E. M. Adak, A. Castello, A. Huber, W. Sachse, C. Hentze, M. W. 2017-08-18 doi:10.1101/177949 Cold Spring Harbor Laboratory Press 2017-08-18 <![CDATA[ Whole-head recording of chemosensory activity in the marine annelid Platynereis dumerilii ]]> https://biorxiv.org/cgi/content/short/391920v1?rss=1" nView larger version (74K):norg.highwire.dtl.DTLVardef@4384corg.highwire.dtl.DTLVardef@10c2563org.highwire.dtl.DTLVardef@6a8a32org.highwire.dtl.DTLVardef@96f06c_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Chartier, T. F. Deschamps, J. Duerichen, W. Jekely, G. Arendt, D. 2018-08-14 doi:10.1101/391920 Cold Spring Harbor Laboratory Press 2018-08-14 <![CDATA[ Differential encoding of predator fear in the ventromedial hypothalamus and periaqueductal grey ]]> https://biorxiv.org/cgi/content/short/283820v1?rss=1" Esteban Masferrer, M. Silva, B. A. Nomoto, K. Lima, S. Q. Gross, C. T. 2018-03-17 doi:10.1101/283820 Cold Spring Harbor Laboratory Press 2018-03-17 <![CDATA[ Molecule guided laser ablation as a novel therapeutic strategy to control itch. ]]> https://biorxiv.org/cgi/content/short/225391v1?rss=1" Nocchi, L. D'Attilia, M. Roy, N. Dhandapani, R. Traista, A. Maffei, M. Castaldi, L. Perlas, E. Heppenstall, P. A. 2017-11-27 doi:10.1101/225391 Cold Spring Harbor Laboratory Press 2017-11-27 <![CDATA[ Polarity sorting drives remodeling of actin-myosin networks ]]> https://biorxiv.org/cgi/content/short/314484v1?rss=1" Wollrab, V. Belmonte, J. M. Leptin, M. Nedelec, F. Koenderink, G. H. 2018-05-04 doi:10.1101/314484 Cold Spring Harbor Laboratory Press 2018-05-04 <![CDATA[ Microglia remodel synapses by presynaptic trogocytosis and spine head filopodia induction ]]> https://biorxiv.org/cgi/content/short/190975v1?rss=1" Weinhard, L. Neniskyte, U. di Bartolomei, G. Bolasco, G. Machado, P. Schieber, N. Exiga, M. Vadisiute, A. Raggioli, A. Schertel, A. Schwab, Y. Gross, C. T. 2017-09-19 doi:10.1101/190975 Cold Spring Harbor Laboratory Press 2017-09-19 <![CDATA[ Control of mechanical pain hypersensitivity through ligand-targeted photoablation of TrkB positive sensory neurons ]]> https://biorxiv.org/cgi/content/short/233452v1?rss=1" Dhandapani, R. Arokiaraj, C. M. Taberner, F. J. Pacifico, P. Raja, S. Nocchi, L. Portulano, C. Franciosa, F. Maffei, M. Hussain, A. F. Reis, F. d. C. Reymond, L. Perlas, E. Garcovich, S. Barth, S. Johnsson, K. Lechner, S. G. Heppenstall, P. A. 2017-12-13 doi:10.1101/233452 Cold Spring Harbor Laboratory Press 2017-12-13 <![CDATA[ Structural rearrangement of TFIIS- and TFIIF/TFIIE-like subunits in RNA polymerase I transcription complexes ]]> https://biorxiv.org/cgi/content/short/353136v1?rss=1" Tafur, L. Sadian, Y. Wetzel, R. Weis, F. Muller, C. W. 2018-07-03 doi:10.1101/353136 Cold Spring Harbor Laboratory Press 2018-07-03 <![CDATA[ Evolutionary changes in DNA accessibility and sequence predict divergence of transcription factor binding and enhancer activity ]]> https://biorxiv.org/cgi/content/short/319046v1?rss=1" Peng, P.-C. Khoueiry, P. Girardot, C. Reddington, J. P. Garfield, D. A. Furlong, E. E. M. Sinha, S. 2018-05-10 doi:10.1101/319046 Cold Spring Harbor Laboratory Press 2018-05-10 <![CDATA[ The Integrated Rapid Infectious Disease Analysis (IRIDA) Platform ]]> https://biorxiv.org/cgi/content/short/381830v1?rss=1" Matthews, T. C. Bristow, F. R. Griffiths, E. J. Petkau, A. Adam, J. Dooley, D. Kruczkiewicz, P. Curatcha, J. Cabral, J. Fornika, D. Winsor, G. L. Courtot, M. Bertelli, C. Roudgar, A. Feijao, P. Mabon, P. Enns, E. Thiessen, J. Keddy, A. Isaac-Renton, J. Gardy, J. L. Tang, P. The IRIDA Consortium, Carrico, J. A. Chindelevitch, L. Chauve, C. Graham, M. R. McArthur, A. G. Taboada, E. N. Beiko, R. G. Brinkman, F. S. Hsiao, W. W. Van Domselaar, G. 2018-07-31 doi:10.1101/381830 Cold Spring Harbor Laboratory Press 2018-07-31 <![CDATA[ pyseer: a comprehensive tool for microbial pangenome-wide association studies ]]> https://biorxiv.org/cgi/content/short/266312v1?rss=1" Lees, J. Galardini, M. Bentley, S. D. Weiser, J. N. Corander, J. 2018-02-15 doi:10.1101/266312 Cold Spring Harbor Laboratory Press 2018-02-15 <![CDATA[ Condensin II inactivation in interphase does not affect chromatin folding or gene expression ]]> https://biorxiv.org/cgi/content/short/437459v1?rss=1" Abdennur, N. Schwarzer, W. Pekowska, A. Shaltiel, I. A. Huber, W. Haering, C. H. Mirny, L. Spitz, F. 2018-10-07 doi:10.1101/437459 Cold Spring Harbor Laboratory Press 2018-10-07 <![CDATA[ Global analysis of specificity determinants in eukaryotic protein kinases ]]> https://biorxiv.org/cgi/content/short/195115v1?rss=1" Bradley, D. Vieitez, C. Rajeeve, V. Cutillas, P. R. Beltrao, P. 2017-09-27 doi:10.1101/195115 Cold Spring Harbor Laboratory Press 2017-09-27 <![CDATA[ Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper ]]> https://biorxiv.org/cgi/content/short/076331v1?rss=1" Jaime Huerta-Cepas Kristoffer Forslund Damian Szklarczyk Lars Juhl Jensen Christian von Mering Peer Bork 2016-09-22 doi:10.1101/076331 Cold Spring Harbor Laboratory Press 2016-09-22 <![CDATA[ Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite ]]> https://biorxiv.org/cgi/content/short/350991v1?rss=1" Lieven, C. Beber, M. E. Olivier, B. G. Bergmann, F. T. Babaei, P. Bartell, J. A. Blank, L. M. Chauhan, S. Correia, K. Diener, C. Dräger, A. Ebert, B. E. Edirisinghe, J. N. Fleming, R. M. T. Garcia-Jimenez, B. van Helvoirt, W. Henry, C. Hermjakob, H. Herrgard, M. J. Kim, H. U. King, Z. Koehorst, J. J. Klamt, S. Klipp, E. Lakshmanan, M. Le Novere, N. Lee, D.-Y. Lee, S. Y. Lee, S. Lewis, N. E. Ma, H. Machado, D. Mahadevan, R. Maia, P. Mardinoglu, A. Medlock, G. L. Monk, J. Nielsen, J. Nielsen, L. K. Nogales, J. Nookaew, I. Resendis, O. Palsson, B. 2018-06-21 doi:10.1101/350991 Cold Spring Harbor Laboratory Press 2018-06-21 <![CDATA[ Benchmarking substrate-based kinase activity inference using phosphoproteomic data ]]> https://biorxiv.org/cgi/content/short/080978v1?rss=1" Hernandez-Armenta, C. Ochoa, D. Goncalves, E. Saez-Rodriguez, J. Beltrao, P. 2016-10-14 doi:10.1101/080978 Cold Spring Harbor Laboratory Press 2016-10-14 <![CDATA[ Capturing variation impact on molecular interactions: the IMEx Consortium mutations data set ]]> https://biorxiv.org/cgi/content/short/346833v1?rss=1" The IMEx Consortium curators, del-Toro, N. Duesbury, M. Koch, M. Perfetto, L. Shrivastava, A. Ochoa, D. Wagih, O. Pinero, J. Kotlyar, M. Chiara, P. Beltrao, P. Furlong, L. I. Jurisica, I. Hermjakob, H. Orchard, S. Porras Millan, P. 2018-06-14 doi:10.1101/346833 Cold Spring Harbor Laboratory Press 2018-06-14 <![CDATA[ Structural variability of EspG chaperones from mycobacterial ESX-1, ESX-3 and ESX-5 type VII secretion systems ]]> https://biorxiv.org/cgi/content/short/250803v1?rss=1" Tuukkanen, A. T. Freire, D. Chan, S. Arbing, M. A. Reed, R. W. Evans, T. J. Zenkeviciute, G. Kim, J. Kahng, S. Sawaya, M. R. Wilmanns, M. Eisenberg, D. Parret, A. H. A. Korotkov, K. V. 2018-01-24 doi:10.1101/250803 Cold Spring Harbor Laboratory Press 2018-01-24 <![CDATA[ Quantification of differential transcription factor activity and multiomic-based classification into activators and repressors: diffTF ]]> https://biorxiv.org/cgi/content/short/368498v1?rss=1" Berest, I. Arnold, C. Reyes-Palomares, A. Palla, G. Rasmussen, K. D. Helin, K. Zaugg, J. 2018-07-13 doi:10.1101/368498 Cold Spring Harbor Laboratory Press 2018-07-13 <![CDATA[ Three-dimensional nanostructure of an intact microglia cell ]]> https://biorxiv.org/cgi/content/short/388538v1?rss=1" Bolasco, G. Weinhard, L. Boissonnet, T. Neujahr, R. Gross, C. T. 2018-08-09 doi:10.1101/388538 Cold Spring Harbor Laboratory Press 2018-08-09 <![CDATA[ Uniform Resolution of Compact Identifiers for Biomedical Data ]]> https://biorxiv.org/cgi/content/short/101279v1?rss=1" Wimalaratne, S. Juty, N. Kunze, J. Janee, G. McMurry, J. A. Beard, N. Jimenez, R. Grethe, J. Hermjakob, H. Clark, T. 2017-01-18 doi:10.1101/101279 Cold Spring Harbor Laboratory Press 2017-01-18 <![CDATA[ Bleaching-independent, whole-cell, 3D and multi-color STED imaging with exchangeable fluorophores ]]> https://biorxiv.org/cgi/content/short/420638v1?rss=1" Spahn, C. Grimm, J. B. Lavis, L. D. Lampe, M. Heilemann, M. 2018-09-18 doi:10.1101/420638 Cold Spring Harbor Laboratory Press 2018-09-18 <![CDATA[ The transcriptome-wide landscape and modalities of EJC binding in adult Drosophila ]]> https://biorxiv.org/cgi/content/short/459354v1?rss=1" Obrdlik, A. Lin, G. Haberman, N. Ule, J. Ephrussi, A. 2018-11-04 doi:10.1101/459354 Cold Spring Harbor Laboratory Press 2018-11-04 <![CDATA[ Iron deficiency affects early stages of embryonic hematopoiesis but not the endothelial to hematopoietic transition ]]> https://biorxiv.org/cgi/content/short/462978v1?rss=1" Shvartsman, M. Bilican, S. Lancrin, C. 2018-11-05 doi:10.1101/462978 Cold Spring Harbor Laboratory Press 2018-11-05 <![CDATA[ Lumen expansion facilitates epiblast-primitive endoderm fate specification in the mouse blastocyst formation. ]]> https://biorxiv.org/cgi/content/short/575282v1?rss=1" Ryan, A. Q. Chan, C. J. Graner, F. Hiiragi, T. 2019-03-12 doi:10.1101/575282 Cold Spring Harbor Laboratory Press 2019-03-12