Colin N Dewey

Colin N Dewey

UNVERIFIED PROFILE

Are you Colin N Dewey?   Register this Author

Register author
Colin N Dewey

Colin N Dewey

Publications by authors named "Colin N Dewey"

Are you Colin N Dewey?   Register this Author

35Publications

970Reads

7Profile Views

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

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 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

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

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