Colin Dewey

Colin Dewey

UNVERIFIED PROFILE

Are you Colin Dewey?   Register this Author

Register author
Colin Dewey

Colin Dewey

Publications by authors named "Colin Dewey"

Are you Colin Dewey?   Register this Author

41Publications

1310Reads

21Profile Views

Whole-Genome Alignment.

Authors:
Colin N Dewey

Methods Mol Biol 2019 ;1910:121-147

Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/978-1-4939-9074-0_4DOI Listing
January 2020

Genome-wide effects on transcription from ppGpp binding to its two sites on RNA polymerase.

Proc Natl Acad Sci U S A 2019 Apr 10;116(17):8310-8319. Epub 2019 Apr 10.

Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706;

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1819682116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6486775PMC
April 2019

Zebrafish zic2 controls formation of periocular neural crest and choroid fissure morphogenesis.

Dev Biol 2017 09 6;429(1):92-104. Epub 2017 Jul 6.

Department of Integrative Biology, University of Wisconsin, Madison, WI 53706, USA; Department of Neuroscience, University of Wisconsin, Madison, WI 53706, USA; McPherson Eye Research Institute, University of Wisconsin, Madison, WI, 53706, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ydbio.2017.07.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5603172PMC
September 2017

GATA Factor-Regulated Samd14 Enhancer Confers Red Blood Cell Regeneration and Survival in Severe Anemia.

Dev Cell 2017 08;42(3):213-225.e4

Department of Cell and Regenerative Biology, UW-Madison Blood Research Program, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.devcel.2017.07.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5578808PMC
August 2017

Analysis of embryonic development in the unsequenced axolotl: Waves of transcriptomic upheaval and stability.

Dev Biol 2017 06 28;426(2):143-154. Epub 2016 Jul 28.

Regenerative Biology, Morgridge Institute for Research, Madison, WI, United States. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ydbio.2016.05.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5272911PMC
June 2017

Integrative analysis with ChIP-seq advances the limits of transcript quantification from RNA-seq.

Genome Res 2016 08 12;26(8):1124-33. Epub 2016 Jul 12.

Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, Wisconsin 53706, USA; Department of Computer Sciences, University of Wisconsin, Madison, Wisconsin 53706, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.199174.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4971760PMC
August 2016

Mechanism governing heme synthesis reveals a GATA factor/heme circuit that controls differentiation.

EMBO Rep 2016 Feb 23;17(2):249-65. Epub 2015 Dec 23.

Department of Cell and Regenerative Biology, UW-Madison Blood Research Program, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA

View Article

Download full-text PDF

Source
http://dx.doi.org/10.15252/embr.201541465DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5290819PMC
February 2016

Perm-seq: Mapping Protein-DNA Interactions in Segmental Duplication and Highly Repetitive Regions of Genomes with Prior-Enhanced Read Mapping.

PLoS Comput Biol 2015 Oct 20;11(10):e1004491. Epub 2015 Oct 20.

Department of Statistics, University of Wisconsin, Madison, Wisconsin, United States of America; Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, Wisconsin, United States of America.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1004491DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4618727PMC
October 2015

Cis-regulatory mechanisms governing stem and progenitor cell transitions.

Sci Adv 2015 Sep 4;1(8):e1500503. Epub 2015 Sep 4.

Carbone Cancer Center, Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA. ; University of Wisconsin-Madison Blood Research Program, Madison, WI 53705, USA.

View Article

Download full-text PDF

Source
http://advances.sciencemag.org/cgi/doi/10.1126/sciadv.150050
Publisher Site
http://dx.doi.org/10.1126/sciadv.1500503DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4643771PMC
September 2015

EBSeq-HMM: a Bayesian approach for identifying gene-expression changes in ordered RNA-seq experiments.

Bioinformatics 2015 Aug 5;31(16):2614-22. Epub 2015 Apr 5.

Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btv193DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4528625PMC
August 2015

Hematopoietic Signaling Mechanism Revealed from a Stem/Progenitor Cell Cistrome.

Mol Cell 2015 Jul 11;59(1):62-74. Epub 2015 Jun 11.

Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA; UW-Madison Blood Research Program, Madison, WI 53706, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.molcel.2015.05.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4499333PMC
July 2015

Gata2 cis-element is required for hematopoietic stem cell generation in the mammalian embryo.

J Exp Med 2013 Dec 2;210(13):2833-42. Epub 2013 Dec 2.

Department of Cell and Regenerative Biology, Carbone Cancer Center, and 2 McArdle Laboratory for Cancer Research, 3 UW-Madison Blood Research Program; and 4 Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1084/jem.20130733DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3865483PMC
December 2013

Inference of alternative splicing from RNA-Seq data with probabilistic splice graphs.

Bioinformatics 2013 Sep 11;29(18):2300-10. Epub 2013 Jul 11.

Department of Computer Sciences, University of Wisconsin, Madison, WI 53706, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btt396DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3753571PMC
September 2013

Rbm20 regulates titin alternative splicing as a splicing repressor.

Nucleic Acids Res 2013 Feb 9;41(4):2659-72. Epub 2013 Jan 9.

Muscle Biology Laboratory, Department of Animal Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gks1362DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3575840PMC
February 2013

Whole-genome alignment.

Authors:
Colin N Dewey

Methods Mol Biol 2012 ;855:237-57

Biostatistics and Medical Informatics and Computer Sciences, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA.

View Article

Download full-text PDF

Source
http://link.springer.com/10.1007/978-1-61779-582-4_8
Publisher Site
http://dx.doi.org/10.1007/978-1-61779-582-4_8DOI Listing
July 2012

Sequence Surveyor: leveraging overview for scalable genomic alignment visualization.

IEEE Trans Vis Comput Graph 2011 Dec;17(12):2392-401

University of Wisconsin-Madison, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1109/TVCG.2011.232DOI Listing
December 2011

Positional orthology: putting genomic evolutionary relationships into context.

Authors:
Colin N Dewey

Brief Bioinform 2011 Sep 24;12(5):401-12. Epub 2011 Jun 24.

Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, 5785 Medical Sciences Center, 1300 University Ave, Madison, WI 53706, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bib/bbr040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3178058PMC
September 2011

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome.

Authors:
Bo Li Colin N Dewey

BMC Bioinformatics 2011 Aug 4;12:323. Epub 2011 Aug 4.

Department of Computer Sciences, University of Wisconsin-Madison, Madison, WI, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2105-12-323DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3163565PMC
August 2011

BUCKy: gene tree/species tree reconciliation with Bayesian concordance analysis.

Bioinformatics 2010 Nov 21;26(22):2910-1. Epub 2010 Sep 21.

Department of Statistics, University of Wisconsin-Madison, WI 53706, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btq539DOI Listing
November 2010

RNA-Seq gene expression estimation with read mapping uncertainty.

Bioinformatics 2010 Feb 18;26(4):493-500. Epub 2009 Dec 18.

Department of Computer Sciences, University of Wisconsin, Madison, WI 53706, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btp692DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2820677PMC
February 2010

Fine-scale phylogenetic discordance across the house mouse genome.

PLoS Genet 2009 Nov 20;5(11):e1000729. Epub 2009 Nov 20.

Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin, United States of America.

View Article

Download full-text PDF

Source
http://dx.plos.org/10.1371/journal.pgen.1000729
Publisher Site
http://dx.doi.org/10.1371/journal.pgen.1000729DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2770633PMC
November 2009

Fast statistical alignment.

PLoS Comput Biol 2009 May 29;5(5):e1000392. Epub 2009 May 29.

Department of Mathematics, University of California Berkeley, Berkeley, California, United States of America.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1000392DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2684580PMC
May 2009

Aligning multiple whole genomes with Mercator and MAVID.

Authors:
Colin N Dewey

Methods Mol Biol 2007 ;395:221-36

Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/978-1-59745-514-5_14DOI Listing
March 2008

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.

Genome Res 2007 Jun;17(6):760-74

Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.

View Article

Download full-text PDF

Source
http://mendel.stanford.edu/sidowlab/pdfs/2007EncodeGR.pdf
Web Search
http://www.genome.org/cgi/doi/10.1101/gr.6034307
Publisher Site
http://dx.doi.org/10.1101/gr.6034307DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1891336PMC
June 2007

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Authors:
Ewan Birney John A Stamatoyannopoulos Anindya Dutta Roderic Guigó Thomas R Gingeras Elliott H Margulies Zhiping Weng Michael Snyder Emmanouil T Dermitzakis Robert E Thurman Michael S Kuehn Christopher M Taylor Shane Neph Christoph M Koch Saurabh Asthana Ankit Malhotra Ivan Adzhubei Jason A Greenbaum Robert M Andrews Paul Flicek Patrick J Boyle Hua Cao Nigel P Carter Gayle K Clelland Sean Davis Nathan Day Pawandeep Dhami Shane C Dillon Michael O Dorschner Heike Fiegler Paul G Giresi Jeff Goldy Michael Hawrylycz Andrew Haydock Richard Humbert Keith D James Brett E Johnson Ericka M Johnson Tristan T Frum Elizabeth R Rosenzweig Neerja Karnani Kirsten Lee Gregory C Lefebvre Patrick A Navas Fidencio Neri Stephen C J Parker Peter J Sabo Richard Sandstrom Anthony Shafer David Vetrie Molly Weaver Sarah Wilcox Man Yu Francis S Collins Job Dekker Jason D Lieb Thomas D Tullius Gregory E Crawford Shamil Sunyaev William S Noble Ian Dunham France Denoeud Alexandre Reymond Philipp Kapranov Joel Rozowsky Deyou Zheng Robert Castelo Adam Frankish Jennifer Harrow Srinka Ghosh Albin Sandelin Ivo L Hofacker Robert Baertsch Damian Keefe Sujit Dike Jill Cheng Heather A Hirsch Edward A Sekinger Julien Lagarde Josep F Abril Atif Shahab Christoph Flamm Claudia Fried Jörg Hackermüller Jana Hertel Manja Lindemeyer Kristin Missal Andrea Tanzer Stefan Washietl Jan Korbel Olof Emanuelsson Jakob S Pedersen Nancy Holroyd Ruth Taylor David Swarbreck Nicholas Matthews Mark C Dickson Daryl J Thomas Matthew T Weirauch James Gilbert Jorg Drenkow Ian Bell XiaoDong Zhao K G Srinivasan Wing-Kin Sung Hong Sain Ooi Kuo Ping Chiu Sylvain Foissac Tyler Alioto Michael Brent Lior Pachter Michael L Tress Alfonso Valencia Siew Woh Choo Chiou Yu Choo Catherine Ucla Caroline Manzano Carine Wyss Evelyn Cheung Taane G Clark James B Brown Madhavan Ganesh Sandeep Patel Hari Tammana Jacqueline Chrast Charlotte N Henrichsen Chikatoshi Kai Jun Kawai Ugrappa Nagalakshmi Jiaqian Wu Zheng Lian Jin Lian Peter Newburger Xueqing Zhang Peter Bickel John S Mattick Piero Carninci Yoshihide Hayashizaki Sherman Weissman Tim Hubbard Richard M Myers Jane Rogers Peter F Stadler Todd M Lowe Chia-Lin Wei Yijun Ruan Kevin Struhl Mark Gerstein Stylianos E Antonarakis Yutao Fu Eric D Green Ulaş Karaöz Adam Siepel James Taylor Laura A Liefer Kris A Wetterstrand Peter J Good Elise A Feingold Mark S Guyer Gregory M Cooper George Asimenos Colin N Dewey Minmei Hou Sergey Nikolaev Juan I Montoya-Burgos Ari Löytynoja Simon Whelan Fabio Pardi Tim Massingham Haiyan Huang Nancy R Zhang Ian Holmes James C Mullikin Abel Ureta-Vidal Benedict Paten Michael Seringhaus Deanna Church Kate Rosenbloom W James Kent Eric A Stone Serafim Batzoglou Nick Goldman Ross C Hardison David Haussler Webb Miller Arend Sidow Nathan D Trinklein Zhengdong D Zhang Leah Barrera Rhona Stuart David C King Adam Ameur Stefan Enroth Mark C Bieda Jonghwan Kim Akshay A Bhinge Nan Jiang Jun Liu Fei Yao Vinsensius B Vega Charlie W H Lee Patrick Ng Atif Shahab Annie Yang Zarmik Moqtaderi Zhou Zhu Xiaoqin Xu Sharon Squazzo Matthew J Oberley David Inman Michael A Singer Todd A Richmond Kyle J Munn Alvaro Rada-Iglesias Ola Wallerman Jan Komorowski Joanna C Fowler Phillippe Couttet Alexander W Bruce Oliver M Dovey Peter D Ellis Cordelia F Langford David A Nix Ghia Euskirchen Stephen Hartman Alexander E Urban Peter Kraus Sara Van Calcar Nate Heintzman Tae Hoon Kim Kun Wang Chunxu Qu Gary Hon Rosa Luna Christopher K Glass M Geoff Rosenfeld Shelley Force Aldred Sara J Cooper Anason Halees Jane M Lin Hennady P Shulha Xiaoling Zhang Mousheng Xu Jaafar N S Haidar Yong Yu Yijun Ruan Vishwanath R Iyer Roland D Green Claes Wadelius Peggy J Farnham Bing Ren Rachel A Harte Angie S Hinrichs Heather Trumbower Hiram Clawson Jennifer Hillman-Jackson Ann S Zweig Kayla Smith Archana Thakkapallayil Galt Barber Robert M Kuhn Donna Karolchik Lluis Armengol Christine P Bird Paul I W de Bakker Andrew D Kern Nuria Lopez-Bigas Joel D Martin Barbara E Stranger Abigail Woodroffe Eugene Davydov Antigone Dimas Eduardo Eyras Ingileif B Hallgrímsdóttir Julian Huppert Michael C Zody Gonçalo R Abecasis Xavier Estivill Gerard G Bouffard Xiaobin Guan Nancy F Hansen Jacquelyn R Idol Valerie V B Maduro Baishali Maskeri Jennifer C McDowell Morgan Park Pamela J Thomas Alice C Young Robert W Blakesley Donna M Muzny Erica Sodergren David A Wheeler Kim C Worley Huaiyang Jiang George M Weinstock Richard A Gibbs Tina Graves Robert Fulton Elaine R Mardis Richard K Wilson Michele Clamp James Cuff Sante Gnerre David B Jaffe Jean L Chang Kerstin Lindblad-Toh Eric S Lander Maxim Koriabine Mikhail Nefedov Kazutoyo Osoegawa Yuko Yoshinaga Baoli Zhu Pieter J de Jong
June 2007

Compensatory relationship between splice sites and exonic splicing signals depending on the length of vertebrate introns.

BMC Genomics 2006 Dec 8;7:311. Epub 2006 Dec 8.

National Center for Biotechnology Information NLM, National Institutes of Health, Bethesda, MD 20894, USA.

View Article

Download full-text PDF

Source
http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2
Publisher Site
http://dx.doi.org/10.1186/1471-2164-7-311DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1713244PMC
December 2006

Parametric alignment of Drosophila genomes.

PLoS Comput Biol 2006 Jun 23;2(6):e73. Epub 2006 Jun 23.

Department of Electrical Engineering and Computer Sciences, University of California Berkeley, Berkeley, California, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.0020073DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1480539PMC
June 2006

Evolution at the nucleotide level: the problem of multiple whole-genome alignment.

Hum Mol Genet 2006 Apr;15 Spec No 1:R51-6

Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA 94720, USA.

View Article

Download full-text PDF

Source
http://statweb.stanford.edu/~nzhang/345_web/papers/Sequence/
Web Search
http://www.hmg.oxfordjournals.org/cgi/doi/10.1093/hmg/ddl056
Publisher Site
http://dx.doi.org/10.1093/hmg/ddl056DOI Listing
April 2006

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.

View Article

Download full-text PDF

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

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

View Article

Download full-text PDF

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

Accurate identification of novel human genes through simultaneous gene prediction in human, mouse, and rat.

Genome Res 2004 Apr;14(4):661-4

Department of Electrical Engineering, University of California-Berkeley, Berkeley, California 94720, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.1939804DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC383310PMC
April 2004

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.

View Article

Download full-text PDF

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