https://biorxiv.org This feed contains articles for bioRxiv Channel "Biology of Genomes 2016 #BOG16 " bioRxiv https://biorxiv.org https://biorxiv.org/cgi/content/short/036434v1?rss=1" Priya Moorjani Carlos Eduardo G. Amorim Peter F. Arndt Molly Przeworski 2016-01-11 doi:10.1101/036434 Cold Spring Harbor Laboratory Press 2016-01-11 https://biorxiv.org/cgi/content/short/045260v1?rss=1" Alvaro Barbeira Scott P Dickinson Jason M Torres Eric S Torstenson Jiamao Zheng Heather E Wheeler Kaanan P Shah Todd Edwards GTEx Consortium Dan Nicolae Nancy J Cox Hae Kyung Im 2016-03-23 doi:10.1101/045260 Cold Spring Harbor Laboratory Press 2016-03-23 https://biorxiv.org/cgi/content/short/043653v1?rss=1" Heather E Wheeler Kaanan P Shah Jonathon Brenner Tzintzuni Garcia Keston Aquino-Michaels GTEx Consortium Nancy J Cox Dan L Nicolae Hae Kyung Im 2016-03-15 doi:10.1101/043653 Cold Spring Harbor Laboratory Press 2016-03-15 https://biorxiv.org/cgi/content/short/043752v1?rss=1" Kaanan Shah Heather E Wheeler Eric R Gamazon Dan L Nicolae Nancy J Cox Hae Kyung Im 2016-03-15 doi:10.1101/043752 Cold Spring Harbor Laboratory Press 2016-03-15 https://biorxiv.org/cgi/content/short/049130v1?rss=1" 700 kb of noncoding sequence in an unbiased manner surrounding three genes (NF1, NF2, and CUL3) involved in resistance to the BRAF inhibitor vemurafenib in the BRAF-mutant melanoma cell line A375. We identify specific noncoding locations near genes that modulate drug resistance when mutated. These sites have predictive hallmarks of noncoding function, such as physical interaction with gene promoters, evolutionary conservation and tissue-specific chromatin accessibility. At a subset of identified elements at the CUL3 locus, we show that engineered mutations lead to a loss of gene expression associated with changes in transcription factor occupancy and in long-range and local epigenetic environments, implicating these sites in gene regulation and chemotherapeutic resistance. This demonstration of an unbiased mutagenesis screen across large noncoding regions expands the potential of pooled CRISPR screens for fundamental genomic discovery and for elucidating biologically relevant mechanisms of gene regulation. ]]> Neville E Sanjana Jason Wright Kaijie Zheng Ophir Shalem Pierre Fontanillas Julia Joung Christine Cheng Aviv Regev Feng Zhang 2016-04-18 doi:10.1101/049130 Cold Spring Harbor Laboratory Press 2016-04-18 https://biorxiv.org/cgi/content/short/047464v1?rss=1" Georg Stricker Alexander Engelhardt Daniel Schulz Matthias Schmid Achim Tresch Julien Gagneur 2016-04-06 doi:10.1101/047464 Cold Spring Harbor Laboratory Press 2016-04-06 https://biorxiv.org/cgi/content/short/041020v1?rss=1" Benedikt Zacher Margaux Michel Bjoern Schwalb Patrick Cramer Achim Tresch Julien Gagneur 2016-02-23 doi:10.1101/041020 Cold Spring Harbor Laboratory Press 2016-02-23 https://biorxiv.org/cgi/content/short/048819v1?rss=1" Jaleal Sanjak Anthony D Long Kevin R Thornton 2016-04-15 doi:10.1101/048819 Cold Spring Harbor Laboratory Press 2016-04-15 https://biorxiv.org/cgi/content/short/038463v1?rss=1" John A Lees Minna Vehkala Niko Välimäki Simon R Harris Claire Chewapreecha Nicholas J Croucher Pekka Marttinen Mark R Davies Andrew C Steer Stephen Y C Tong Antti Honkela Julian Parkhill Stephen D Bentley Jukka Corander 2016-02-02 doi:10.1101/038463 Cold Spring Harbor Laboratory Press 2016-02-02 https://biorxiv.org/cgi/content/short/019166v1?rss=1" Xun Lan Jonathan K Pritchard 2015-05-10 doi:10.1101/019166 Cold Spring Harbor Laboratory Press 2015-05-10 https://biorxiv.org/cgi/content/short/019067v1?rss=1" Abhinav Nellore Leonardo Collado-Torres Andrew E Jaffe José Alquicira-Hernández Jacob Pritt James Morton Jeffrey T Leek Ben Langmead 2015-05-07 doi:10.1101/019067 Cold Spring Harbor Laboratory Press 2015-05-07 https://biorxiv.org/cgi/content/short/051557v1?rss=1" Irwin Jungreis Clara S Chan Robert M Waterhouse Gabriel Fields Michael F Lin Manolis Kellis 2016-05-03 doi:10.1101/051557 Cold Spring Harbor Laboratory Press 2016-05-03 https://biorxiv.org/cgi/content/short/044925v1?rss=1" Maria Nattestad Michael C Schatz 2016-03-20 doi:10.1101/044925 Cold Spring Harbor Laboratory Press 2016-03-20 https://biorxiv.org/cgi/content/short/035287v1?rss=1" Abhinav Nellore Christopher Wilks Kasper D Hansen Jeffrey T Leek Ben Langmead 2015-12-24 doi:10.1101/035287 Cold Spring Harbor Laboratory Press 2015-12-24 https://biorxiv.org/cgi/content/short/038224v1?rss=1" Abhinav Nellore Andrew E Jaffe Jean-Philippe Fortin José Alquicira-Hernández Leonardo Collado-Torres Siruo Wang Robert A Phillips Nishika Karbhari Kasper D Hansen Ben Langmead Jeffrey T Leek 2016-01-29 doi:10.1101/038224 Cold Spring Harbor Laboratory Press 2016-01-29 https://biorxiv.org/cgi/content/short/039297v1?rss=1" Mikhail V Pogorelyy Yuval Elhanati Quentin Marcou Anastasia L Sycheva Ekaterina A Komech Vadim I Nazarov Olga V Britanova Dmitriy M Chudakov Ilgar Z Mamedov Yuri B Lebedev Thierry Mora Aleksandra M Walczak 2016-02-09 doi:10.1101/039297 Cold Spring Harbor Laboratory Press 2016-02-09 https://biorxiv.org/cgi/content/short/052084v1?rss=1" Yair Field Evan A Boyle Natalie Telis Ziyue Gao Kyle J Gaulton David Golan Loic Yengo Ghislain Rocheleau Philippe Froguel Mark I McCarthy Jonathan K Pritchard 2016-05-07 doi:10.1101/052084 Cold Spring Harbor Laboratory Press 2016-05-07 https://biorxiv.org/cgi/content/short/030338v1?rss=1" Exome Aggregation Consortium Monkol Lek Konrad Karczewski Eric Minikel Kaitlin Samocha Eric Banks Timothy Fennell Anne O'Donnell-Luria James Ware Andrew Hill Beryl Cummings Taru Tukiainen Daniel Birnbaum Jack Kosmicki Laramie Duncan Karol Estrada Fengmei Zhao James Zou Emma Pierce-Hoffman Joanne Berghout David Cooper Nicole Deflaux Mark DePristo Ron Do Jason Flannick Menachem Fromer Laura Gauthier Jackie Goldstein Namrata Gupta Daniel Howrigan Adam Kiezun Mitja Kurki Ami Levy Moonshine Pradeep Natarajan Lorena Orozco Gina Peloso Ryan Poplin Manuel Rivas Valentin Ruano-Rubio Samuel Rose Douglas 2015-10-30 doi:10.1101/030338 Cold Spring Harbor Laboratory Press 2015-10-30 https://biorxiv.org/cgi/content/short/039529v1?rss=1" Stephane E Castel Pejman Mohammadi Wendy K Chung Yufeng Shen Tuuli Lappalainen 2016-02-12 doi:10.1101/039529 Cold Spring Harbor Laboratory Press 2016-02-12 https://biorxiv.org/cgi/content/short/030486v1?rss=1" Balaji Sundararaman Lijun Zhan Steven Blue Rebecca Stanton Keri Elkins Sara Olson Xintao Wei Eric L Van Nostrand Stephanie C Huelga Brendan M Smalec Xiaofeng Wang Eurie L Hong Jean M Davidson Eric Lecuyer Brenton R Graveley Gene W Yeo 2015-11-03 doi:10.1101/030486 Cold Spring Harbor Laboratory Press 2015-11-03 https://biorxiv.org/cgi/content/short/041863v1?rss=1" 85,000 variants per second) with 50 attributes from 17 commonly used genome annotation resources.nnConclusionsVcfanno is a flexible software package that provides researchers with the ability to annotate genetic variation with a wide range of datasets and reference databases in diverse genomic formats.nnAvailabilityThe vcfanno source code is available at https://github.com/brentp/vcfanno under the MIT license, and platform-specific binaries are available at https://github.com/brentp/vcfanno/releases. Detailed documentation is available at http://brentp.github.io/vcfanno/, and the code underlying the analyses presented can be found at https://github.com/brentp/vcfanno/tree/master/scripts/paper. ]]> Brent Pedersen Ryan Layer Aaron Quinlan 2016-02-29 doi:10.1101/041863 Cold Spring Harbor Laboratory Press 2016-02-29 https://biorxiv.org/cgi/content/short/052571v1?rss=1" Juan Du Amy Leung Candi Trac Brian W. Parks Aldons J. Lusis Rama Natarajan Dustin E. Schones 2016-05-10 doi:10.1101/052571 Cold Spring Harbor Laboratory Press 2016-05-10 https://biorxiv.org/cgi/content/short/052225v1?rss=1" Bo Wang Junjie Zhu Emma Pierson Daniele Ramazzotti Serafim Batzoglou 2016-05-09 doi:10.1101/052225 Cold Spring Harbor Laboratory Press 2016-05-09 https://biorxiv.org/cgi/content/short/010934v1?rss=1" Simon Gravel 2014-10-30 doi:10.1101/010934 Cold Spring Harbor Laboratory Press 2014-10-30