Publications by authors named "Nicolas Bray"

19Publications

Controlled Cycling and Quiescence Enables Efficient HDR in Engraftment-Enriched Adult Hematopoietic Stem and Progenitor Cells.

Cell Rep 2020 Sep;32(9):108093

Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA; Department of Biology, ETH Zürich, 8093 Zürich, Switzerland. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2020.108093DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7487781PMC
September 2020

Expression reflects population structure.

PLoS Genet 2018 12 19;14(12):e1007841. Epub 2018 Dec 19.

Division of Biology and Biological Engineering, California Institute of Technology, Padadena, California, United States of America.

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http://dx.plos.org/10.1371/journal.pgen.1007841
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http://dx.doi.org/10.1371/journal.pgen.1007841DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6317812PMC
December 2018

Gene-level differential analysis at transcript-level resolution.

Genome Biol 2018 04 12;19(1):53. Epub 2018 Apr 12.

Division of Biology and Biological Engineering, Caltech, Pasadena, CA, USA.

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http://dx.doi.org/10.1186/s13059-018-1419-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5896116PMC
April 2018

Disabling Cas9 by an anti-CRISPR DNA mimic.

Sci Adv 2017 07 12;3(7):e1701620. Epub 2017 Jul 12.

Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1126/sciadv.1701620DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5507636PMC
July 2017

Differential analysis of RNA-seq incorporating quantification uncertainty.

Nat Methods 2017 Jul 5;14(7):687-690. Epub 2017 Jun 5.

Division of Biology and Biological Engineering, Caltech, Pasadena, California, USA.

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http://dx.doi.org/10.1038/nmeth.4324DOI Listing
July 2017

The Lair: a resource for exploratory analysis of published RNA-Seq data.

BMC Bioinformatics 2016 Dec 1;17(1):490. Epub 2016 Dec 1.

Department of Computer Science, University of California, Berkeley, 387 Soda Hall, Berkeley, 94720, USA.

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http://dx.doi.org/10.1186/s12859-016-1357-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5131447PMC
December 2016

Selection-free genome editing of the sickle mutation in human adult hematopoietic stem/progenitor cells.

Sci Transl Med 2016 10;8(360):360ra134

Innovative Genomics Initiative, University of California, Berkeley, Berkeley, CA 94720, USA. Department of Molecular and Cellular Biology, University of California, Berkeley, Berkeley, CA 94720, USA.

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http://stm.sciencemag.org/content/scitransmed/8/360/360ra134
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http://dx.doi.org/10.1126/scitranslmed.aaf9336DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5500303PMC
October 2016

Near-optimal probabilistic RNA-seq quantification.

Nat Biotechnol 2016 05 4;34(5):525-7. Epub 2016 Apr 4.

Department of Computer Science, University of California, Berkeley, California, USA.

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http://dx.doi.org/10.1038/nbt.3519DOI Listing
May 2016

A high-resolution atlas of nucleosome occupancy in yeast.

Nat Genet 2007 Oct 16;39(10):1235-44. Epub 2007 Sep 16.

Department of Genetics, Stanford University School of Medicine, Stanford, California 94305-5120, USA.

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http://dx.doi.org/10.1038/ng2117DOI Listing
October 2007

A genome-wide map of conserved microRNA targets in C. elegans.

Curr Biol 2006 Mar 2;16(5):460-71. Epub 2006 Feb 2.

Center for Comparative Functional Genomics, Department of Biology, New York University, New York, New York 10003, USA.

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http://dx.doi.org/10.1016/j.cub.2006.01.050DOI Listing
March 2006

MAVID: constrained ancestral alignment of multiple sequences.

Genome Res 2004 Apr;14(4):693-9

Department of Mathematics, University of California at Berkeley, Berkeley, California 94720, USA.

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http://dx.doi.org/10.1101/gr.1960404DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC383315PMC
April 2004

Genome sequence of the Brown Norway rat yields insights into mammalian evolution.

Authors:
Richard A Gibbs George M Weinstock Michael L Metzker Donna M Muzny Erica J Sodergren Steven Scherer Graham Scott David Steffen Kim C Worley Paula E Burch Geoffrey Okwuonu Sandra Hines Lora Lewis Christine DeRamo Oliver Delgado Shannon Dugan-Rocha George Miner Margaret Morgan Alicia Hawes Rachel Gill Celera Robert A Holt Mark D Adams Peter G Amanatides Holly Baden-Tillson Mary Barnstead Soo Chin Cheryl A Evans Steve Ferriera Carl Fosler Anna Glodek Zhiping Gu Don Jennings Cheryl L Kraft Trixie Nguyen Cynthia M Pfannkoch Cynthia Sitter Granger G Sutton J Craig Venter Trevor Woodage Douglas Smith Hong-Mei Lee Erik Gustafson Patrick Cahill Arnold Kana Lynn Doucette-Stamm Keith Weinstock Kim Fechtel Robert B Weiss Diane M Dunn Eric D Green Robert W Blakesley Gerard G Bouffard Pieter J De Jong Kazutoyo Osoegawa Baoli Zhu Marco Marra Jacqueline Schein Ian Bosdet Chris Fjell Steven Jones Martin Krzywinski Carrie Mathewson Asim Siddiqui Natasja Wye John McPherson Shaying Zhao Claire M Fraser Jyoti Shetty Sofiya Shatsman Keita Geer Yixin Chen Sofyia Abramzon William C Nierman Paul H Havlak Rui Chen K James Durbin Amy Egan Yanru Ren Xing-Zhi Song Bingshan Li Yue Liu Xiang Qin Simon Cawley Kim C Worley A J Cooney Lisa M D'Souza Kirt Martin Jia Qian Wu Manuel L Gonzalez-Garay Andrew R Jackson Kenneth J Kalafus Michael P McLeod Aleksandar Milosavljevic Davinder Virk Andrei Volkov David A Wheeler Zhengdong Zhang Jeffrey A Bailey Evan E Eichler Eray Tuzun Ewan Birney Emmanuel Mongin Abel Ureta-Vidal Cara Woodwark Evgeny Zdobnov Peer Bork Mikita Suyama David Torrents Marina Alexandersson Barbara J Trask Janet M Young Hui Huang Huajun Wang Heming Xing Sue Daniels Darryl Gietzen Jeanette Schmidt Kristian Stevens Ursula Vitt Jim Wingrove Francisco Camara M Mar Albà Josep F Abril Roderic Guigo Arian Smit Inna Dubchak Edward M Rubin Olivier Couronne Alexander Poliakov Norbert Hübner Detlev Ganten Claudia Goesele Oliver Hummel Thomas Kreitler Young-Ae Lee Jan Monti Herbert Schulz Heike Zimdahl Heinz Himmelbauer Hans Lehrach Howard J Jacob Susan Bromberg Jo Gullings-Handley Michael I Jensen-Seaman Anne E Kwitek Jozef Lazar Dean Pasko Peter J Tonellato Simon Twigger Chris P Ponting Jose M Duarte Stephen Rice Leo Goodstadt Scott A Beatson Richard D Emes Eitan E Winter Caleb Webber Petra Brandt Gerald Nyakatura Margaret Adetobi Francesca Chiaromonte Laura Elnitski Pallavi Eswara Ross C Hardison Minmei Hou Diana Kolbe Kateryna Makova Webb Miller Anton Nekrutenko Cathy Riemer Scott Schwartz James Taylor Shan Yang Yi Zhang Klaus Lindpaintner T Dan Andrews Mario Caccamo Michele Clamp Laura Clarke Valerie Curwen Richard Durbin Eduardo Eyras Stephen M Searle Gregory M Cooper Serafim Batzoglou Michael Brudno Arend Sidow Eric A Stone J Craig Venter Bret A Payseur Guillaume Bourque Carlos López-Otín Xose S Puente Kushal Chakrabarti Sourav Chatterji Colin Dewey Lior Pachter Nicolas Bray Von Bing Yap Anat Caspi Glenn Tesler Pavel A Pevzner David Haussler Krishna M Roskin Robert Baertsch Hiram Clawson Terrence S Furey Angie S Hinrichs Donna Karolchik William J Kent Kate R Rosenbloom Heather Trumbower Matt Weirauch David N Cooper Peter D Stenson Bin Ma Michael Brent Manimozhiyan Arumugam David Shteynberg Richard R Copley Martin S Taylor Harold Riethman Uma Mudunuri Jane Peterson Mark Guyer Adam Felsenfeld Susan Old Stephen Mockrin Francis Collins

Nature 2004 Apr;428(6982):493-521

Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, Texas 77030, USA. http://www.hgsc.bcm.tmc.edu

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http://dx.doi.org/10.1038/nature02426DOI Listing
April 2004

MAVID multiple alignment server.

Nucleic Acids Res 2003 Jul;31(13):3525-6

Department of Mathematics, 970 Evans Hall, UC Berkeley, Berkeley, CA 94720, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC169029PMC
http://dx.doi.org/10.1093/nar/gkg623DOI Listing
July 2003

Strategies and tools for whole-genome alignments.

Genome Res 2003 Jan;13(1):73-80

Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.

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http://dx.doi.org/10.1101/gr.762503DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC430965PMC
January 2003

Initial sequencing and comparative analysis of the mouse genome.

Authors:
Robert H Waterston Kerstin Lindblad-Toh Ewan Birney Jane Rogers Josep F Abril Pankaj Agarwal Richa Agarwala Rachel Ainscough Marina Alexandersson Peter An Stylianos E Antonarakis John Attwood Robert Baertsch Jonathon Bailey Karen Barlow Stephan Beck Eric Berry Bruce Birren Toby Bloom Peer Bork Marc Botcherby Nicolas Bray Michael R Brent Daniel G Brown Stephen D Brown Carol Bult John Burton Jonathan Butler Robert D Campbell Piero Carninci Simon Cawley Francesca Chiaromonte Asif T Chinwalla Deanna M Church Michele Clamp Christopher Clee Francis S Collins Lisa L Cook Richard R Copley Alan Coulson Olivier Couronne James Cuff Val Curwen Tim Cutts Mark Daly Robert David Joy Davies Kimberly D Delehaunty Justin Deri Emmanouil T Dermitzakis Colin Dewey Nicholas J Dickens Mark Diekhans Sheila Dodge Inna Dubchak Diane M Dunn Sean R Eddy Laura Elnitski Richard D Emes Pallavi Eswara Eduardo Eyras Adam Felsenfeld Ginger A Fewell Paul Flicek Karen Foley Wayne N Frankel Lucinda A Fulton Robert S Fulton Terrence S Furey Diane Gage Richard A Gibbs Gustavo Glusman Sante Gnerre Nick Goldman Leo Goodstadt Darren Grafham Tina A Graves Eric D Green Simon Gregory Roderic Guigó Mark Guyer Ross C Hardison David Haussler Yoshihide Hayashizaki LaDeana W Hillier Angela Hinrichs Wratko Hlavina Timothy Holzer Fan Hsu Axin Hua Tim Hubbard Adrienne Hunt Ian Jackson David B Jaffe L Steven Johnson Matthew Jones Thomas A Jones Ann Joy Michael Kamal Elinor K Karlsson Donna Karolchik Arkadiusz Kasprzyk Jun Kawai Evan Keibler Cristyn Kells W James Kent Andrew Kirby Diana L Kolbe Ian Korf Raju S Kucherlapati Edward J Kulbokas David Kulp Tom Landers J P Leger Steven Leonard Ivica Letunic Rosie Levine Jia Li Ming Li Christine Lloyd Susan Lucas Bin Ma Donna R Maglott Elaine R Mardis Lucy Matthews Evan Mauceli John H Mayer Megan McCarthy W Richard McCombie Stuart McLaren Kirsten McLay John D McPherson Jim Meldrim Beverley Meredith Jill P Mesirov Webb Miller Tracie L Miner Emmanuel Mongin Kate T Montgomery Michael Morgan Richard Mott James C Mullikin Donna M Muzny William E Nash Joanne O Nelson Michael N Nhan Robert Nicol Zemin Ning Chad Nusbaum Michael J O'Connor Yasushi Okazaki Karen Oliver Emma Overton-Larty Lior Pachter Genís Parra Kymberlie H Pepin Jane Peterson Pavel Pevzner Robert Plumb Craig S Pohl Alex Poliakov Tracy C Ponce Chris P Ponting Simon Potter Michael Quail Alexandre Reymond Bruce A Roe Krishna M Roskin Edward M Rubin Alistair G Rust Ralph Santos Victor Sapojnikov Brian Schultz Jörg Schultz Matthias S Schwartz Scott Schwartz Carol Scott Steven Seaman Steve Searle Ted Sharpe Andrew Sheridan Ratna Shownkeen Sarah Sims Jonathan B Singer Guy Slater Arian Smit Douglas R Smith Brian Spencer Arne Stabenau Nicole Stange-Thomann Charles Sugnet Mikita Suyama Glenn Tesler Johanna Thompson David Torrents Evanne Trevaskis John Tromp Catherine Ucla Abel Ureta-Vidal Jade P Vinson Andrew C Von Niederhausern Claire M Wade Melanie Wall Ryan J Weber Robert B Weiss Michael C Wendl Anthony P West Kris Wetterstrand Raymond Wheeler Simon Whelan Jamey Wierzbowski David Willey Sophie Williams Richard K Wilson Eitan Winter Kim C Worley Dudley Wyman Shan Yang Shiaw-Pyng Yang Evgeny M Zdobnov Michael C Zody Eric S Lander

Nature 2002 Dec;420(6915):520-62

Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1038/nature01262DOI Listing
December 2002