Webb Miller

Webb Miller

UNVERIFIED PROFILE

Are you Webb Miller?   Register this Author

Register author
Webb Miller

Webb Miller

Publications by authors named "Webb Miller"

Are you Webb Miller?   Register this Author

100Publications

2728Reads

16Profile Views

Genomic Variants Among Threatened Corals.

G3 (Bethesda) 2019 05 7;9(5):1633-1646. Epub 2019 May 7.

208 Mueller Lab, Biology Department, The Pennsylvania State University, University Park PA 16802

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1534/g3.119.400125DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6505131PMC
May 2019

Sex determination by SRY PCR and sequencing of Tasmanian devil facial tumour cell lines reveals non-allograft transmission.

Biochem Biophys Res Commun 2016 05 13;474(1):29-34. Epub 2016 Apr 13.

Division of Avian Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin, China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.bbrc.2016.04.052DOI Listing
May 2016

Elephantid Genomes Reveal the Molecular Bases of Woolly Mammoth Adaptations to the Arctic.

Cell Rep 2015 Jul 2;12(2):217-28. Epub 2015 Jul 2.

Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, 506B Wartik Lab, University Park, PA 16802, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.celrep.2015.06.027DOI Listing
July 2015

Comparative and population mitogenomic analyses of Madagascar's extinct, giant 'subfossil' lemurs.

J Hum Evol 2015 Feb 16;79:45-54. Epub 2014 Dec 16.

Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA; Department of Biology, Pennsylvania State University, University Park, PA 16802, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jhevol.2014.06.016DOI Listing
February 2015

Identification of indels in next-generation sequencing data.

BMC Bioinformatics 2015 Feb 13;16:42. Epub 2015 Feb 13.

Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, 506, Wartik Laboratory, University Park, PA, 16802, USA.

View Article

Download full-text PDF

Source
https://bmcbioinformatics.biomedcentral.com/articles/10.1186
Publisher Site
http://dx.doi.org/10.1186/s12859-015-0483-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4339746PMC
February 2015

Khoisan hunter-gatherers have been the largest population throughout most of modern-human demographic history.

Nat Commun 2014 Dec 4;5:5692. Epub 2014 Dec 4.

1] Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, 310 Wartik Lab, University Park, Pennsylvania 16802, USA [2] Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, SBS-01N-27, Singapore 637551, Singapore.

View Article

Download full-text PDF

Source
http://www.nature.com/articles/ncomms6692
Publisher Site
http://dx.doi.org/10.1038/ncomms6692DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4268704PMC
December 2014

Updates of the HbVar database of human hemoglobin variants and thalassemia mutations.

Nucleic Acids Res 2014 Jan 16;42(Database issue):D1063-9. Epub 2013 Oct 16.

The Pennsylvania State University, Center for Comparative Genomics and Bioinformatics, University Park, PA, USA, Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida, Malta, MGC-Department of Cell Biology and Genetics, Erasmus MC, Faculty of Medicine and Health Sciences, Rotterdam, The Netherlands, Department of Computer Engineering and Informatics, University of Patras, Faculty of Engineering, Patras, Greece, Department of Pharmacy, University of Patras, School of Health Sciences, Patras, Greece, Department of Medical Genetics, Laboratory of Cytogenetics, Institute of Biology, Nantes, France, Hôpital Edouard Herriot, Unité de Pathologie Moléculaire du Globule Rouge, Lyon, France, Department of Computer and Informatics Engineering, Technological Educational Institute of Western Greece, Patras, Greece, INSERM U955, CHU Henri Mondor, Creteil, France and Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.

View Article

Download full-text PDF

Source
http://nar.oxfordjournals.org/content/early/2013/10/16/nar.g
Web Search
http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkt911
Publisher Site
http://dx.doi.org/10.1093/nar/gkt911DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3964999PMC
January 2014

Galaxy tools to study genome diversity.

Gigascience 2013 Dec 30;2(1):17. Epub 2013 Dec 30.

Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, PA 16802, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/2047-217X-2-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3877877PMC
December 2013

Optimization methods for selecting founder individuals for captive breeding or reintroduction of endangered species.

Pac Symp Biocomput 2010 :43-53

Center for Comparative Genomics and Bioinformatics, Penn State, University Park, PA 16802, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1142/9789814295291_0006DOI Listing
November 2013

Some phenotype association tools in Galaxy: looking for disease SNPs in a full genome.

Curr Protoc Bioinformatics 2012 Sep;Chapter 15:Unit15.2

Pennsylvania State University, University Park, PA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/0471250953.bi1502s39DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3548453PMC
September 2012

Genome-wide identification of conserved regulatory function in diverged sequences.

Genome Res 2011 Jul 31;21(7):1139-49. Epub 2011 May 31.

Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.119016.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3129256PMC
July 2011

Conversion events in gene clusters.

BMC Evol Biol 2011 Jul 28;11:226. Epub 2011 Jul 28.

Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, PA 16802 USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2148-11-226DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3161012PMC
July 2011

Evaluation of methods for detecting conversion events in gene clusters.

BMC Bioinformatics 2011 Feb 15;12 Suppl 1:S45. Epub 2011 Feb 15.

Center for Comparative Genomics and Bioinformatics, 506 Wartik Lab, Pennsylvania State University, University Park, PA 16802, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2105-12-S1-S45DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3044302PMC
February 2011

Comparative and demographic analysis of orang-utan genomes.

Authors:
Devin P Locke LaDeana W Hillier Wesley C Warren Kim C Worley Lynne V Nazareth Donna M Muzny Shiaw-Pyng Yang Zhengyuan Wang Asif T Chinwalla Pat Minx Makedonka Mitreva Lisa Cook Kim D Delehaunty Catrina Fronick Heather Schmidt Lucinda A Fulton Robert S Fulton Joanne O Nelson Vincent Magrini Craig Pohl Tina A Graves Chris Markovic Andy Cree Huyen H Dinh Jennifer Hume Christie L Kovar Gerald R Fowler Gerton Lunter Stephen Meader Andreas Heger Chris P Ponting Tomas Marques-Bonet Can Alkan Lin Chen Ze Cheng Jeffrey M Kidd Evan E Eichler Simon White Stephen Searle Albert J Vilella Yuan Chen Paul Flicek Jian Ma Brian Raney Bernard Suh Richard Burhans Javier Herrero David Haussler Rui Faria Olga Fernando Fleur Darré Domènec Farré Elodie Gazave Meritxell Oliva Arcadi Navarro Roberta Roberto Oronzo Capozzi Nicoletta Archidiacono Giuliano Della Valle Stefania Purgato Mariano Rocchi Miriam K Konkel Jerilyn A Walker Brygg Ullmer Mark A Batzer Arian F A Smit Robert Hubley Claudio Casola Daniel R Schrider Matthew W Hahn Victor Quesada Xose S Puente Gonzalo R Ordoñez Carlos López-Otín Tomas Vinar Brona Brejova Aakrosh Ratan Robert S Harris Webb Miller Carolin Kosiol Heather A Lawson Vikas Taliwal André L Martins Adam Siepel Arindam Roychoudhury Xin Ma Jeremiah Degenhardt Carlos D Bustamante Ryan N Gutenkunst Thomas Mailund Julien Y Dutheil Asger Hobolth Mikkel H Schierup Oliver A Ryder Yuko Yoshinaga Pieter J de Jong George M Weinstock Jeffrey Rogers Elaine R Mardis Richard A Gibbs Richard K Wilson

Nature 2011 Jan;469(7331):529-33

The Genome Center at Washington University, Washington University School of Medicine, 4444 Forest Park Avenue, Saint Louis, Missouri 63108, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature09687DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3060778PMC
January 2011

CAGE: Combinatorial Analysis of Gene-cluster Evolution.

J Comput Biol 2010 Sep;17(9):1227-42

Center for Comparative Genomics and Bioinformatics, Penn State University, University Park, PA 16802, USA.

View Article

Download full-text PDF

Source
http://www.bx.psu.edu/miller_lab/dist/CAGE.pdf
Web Search
http://www.liebertonline.com/doi/abs/10.1089/cmb.2010.0094
Publisher Site
http://dx.doi.org/10.1089/cmb.2010.0094DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3122889PMC
September 2010

MultiPipMaker: a comparative alignment server for multiple DNA sequences.

Curr Protoc Bioinformatics 2010 Jun;Chapter 10:Unit10.4

The Pennsylvania State University, University Park, Pennsylvania, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/0471250953.bi1004s30DOI Listing
June 2010

Calling SNPs without a reference sequence.

BMC Bioinformatics 2010 Mar 15;11:130. Epub 2010 Mar 15.

Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2105-11-130DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2851604PMC
March 2010

Interpretation of custom designed Illumina genotype cluster plots for targeted association studies and next-generation sequence validation.

BMC Res Notes 2010 Feb 22;3:39. Epub 2010 Feb 22.

Cancer Genetics Group, Children's Cancer Institute Australia for Medical Research, Sydney Children's Hospital, High Street, Randwick, NSW 2031, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1756-0500-3-39DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2848685PMC
February 2010

Evolutionary history reconstruction for Mammalian complex gene clusters.

J Comput Biol 2009 Aug;16(8):1051-70

Center for Comparative Genomics and Bioinformatics, Penn State University , University Park, PA 16802, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1089/cmb.2009.0040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2879273PMC
August 2009

Simultaneous history reconstruction for complex gene clusters in multiple species.

Pac Symp Biocomput 2009 :162-73

Department of Statistics, 326 Thomas Building, Penn State University, University Park, PA 16802, USA.

View Article

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2758231PMC
March 2009

CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets.

Bioinformatics 2009 Jan 18;25(1):130-1. Epub 2008 Nov 18.

Department of Computer Science and Engineering and Department of Biology, Pennsylvania State University, University Park, PA 16802, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btn604DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3202307PMC
January 2009

Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif.

Genome Res 2008 Dec 25;18(12):1896-905. Epub 2008 Sep 25.

Center for Comparative Genomics and Bioinformatics of the Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

View Article

Download full-text PDF

Source
http://www.genome.org/cgi/doi/10.1101/gr.083089.108
Publisher Site
http://dx.doi.org/10.1101/gr.083089.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2593580PMC
December 2008

DUPCAR: reconstructing contiguous ancestral regions with duplications.

J Comput Biol 2008 Oct;15(8):1007-27

Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1089/cmb.2008.0069DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3205822PMC
October 2008

The infinite sites model of genome evolution.

Proc Natl Acad Sci U S A 2008 Sep 11;105(38):14254-61. Epub 2008 Sep 11.

Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.0805217105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2533685PMC
September 2008

Phylogenomic resources at the UCSC Genome Browser.

Methods Mol Biol 2008 ;422:133-44

Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/978-1-59745-581-7_9DOI Listing
August 2008

Computational reconstruction of ancestral DNA sequences.

Methods Mol Biol 2008 ;422:171-84

McGill Centre for Bioinformatics, McGill University, Montreal, Canada.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/978-1-59745-581-7_11DOI Listing
August 2008

Genome analysis of the platypus reveals unique signatures of evolution.

Authors:
Wesley C Warren LaDeana W Hillier Jennifer A Marshall Graves Ewan Birney Chris P Ponting Frank Grützner Katherine Belov Webb Miller Laura Clarke Asif T Chinwalla Shiaw-Pyng Yang Andreas Heger Devin P Locke Pat Miethke Paul D Waters Frédéric Veyrunes Lucinda Fulton Bob Fulton Tina Graves John Wallis Xose S Puente Carlos López-Otín Gonzalo R Ordóñez Evan E Eichler Lin Chen Ze Cheng Janine E Deakin Amber Alsop Katherine Thompson Patrick Kirby Anthony T Papenfuss Matthew J Wakefield Tsviya Olender Doron Lancet Gavin A Huttley Arian F A Smit Andrew Pask Peter Temple-Smith Mark A Batzer Jerilyn A Walker Miriam K Konkel Robert S Harris Camilla M Whittington Emily S W Wong Neil J Gemmell Emmanuel Buschiazzo Iris M Vargas Jentzsch Angelika Merkel Juergen Schmitz Anja Zemann Gennady Churakov Jan Ole Kriegs Juergen Brosius Elizabeth P Murchison Ravi Sachidanandam Carly Smith Gregory J Hannon Enkhjargal Tsend-Ayush Daniel McMillan Rosalind Attenborough Willem Rens Malcolm Ferguson-Smith Christophe M Lefèvre Julie A Sharp Kevin R Nicholas David A Ray Michael Kube Richard Reinhardt Thomas H Pringle James Taylor Russell C Jones Brett Nixon Jean-Louis Dacheux Hitoshi Niwa Yoko Sekita Xiaoqiu Huang Alexander Stark Pouya Kheradpour Manolis Kellis Paul Flicek Yuan Chen Caleb Webber Ross Hardison Joanne Nelson Kym Hallsworth-Pepin Kim Delehaunty Chris Markovic Pat Minx Yucheng Feng Colin Kremitzki Makedonka Mitreva Jarret Glasscock Todd Wylie Patricia Wohldmann Prathapan Thiru Michael N Nhan Craig S Pohl Scott M Smith Shunfeng Hou Mikhail Nefedov Pieter J de Jong Marilyn B Renfree Elaine R Mardis Richard K Wilson

Nature 2008 May;453(7192):175-83

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/nature06936DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2803040PMC
May 2008

Human-macaque comparisons illuminate variation in neutral substitution rates.

Genome Biol 2008 Apr 30;9(4):R76. Epub 2008 Apr 30.

Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, PA 16802, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/gb-2008-9-4-r76DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2643947PMC
April 2008

Comparative genomic analysis using the UCSC genome browser.

Methods Mol Biol 2007 ;395:17-34

UCSC Genome Bioinformatics Group, Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/978-1-59745-514-5_2DOI Listing
March 2008

Molecular and genomic data identify the closest living relative of primates.

Science 2007 Nov;318(5851):792-4

Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1126/science.1147555DOI Listing
November 2007

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

Finding cis-regulatory elements using comparative genomics: some lessons from ENCODE data.

Genome Res 2007 Jun;17(6):775-86

Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

View Article

Download full-text PDF

Source
http://www.genome.org/cgi/doi/10.1101/gr.5592107
Publisher Site
http://dx.doi.org/10.1101/gr.5592107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1891337PMC
June 2007

A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly.

Genome Res 2007 Jun;17(6):960-4

Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania 16802, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.5578007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1891355PMC
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

Using genomic data to unravel the root of the placental mammal phylogeny.

Genome Res 2007 Apr 23;17(4):413-21. Epub 2007 Feb 23.

Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.5918807DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1832088PMC
April 2007

Evolutionary and biomedical insights from the rhesus macaque genome.

Authors:
Richard A Gibbs Jeffrey Rogers Michael G Katze Roger Bumgarner George M Weinstock Elaine R Mardis Karin A Remington Robert L Strausberg J Craig Venter Richard K Wilson Mark A Batzer Carlos D Bustamante Evan E Eichler Matthew W Hahn Ross C Hardison Kateryna D Makova Webb Miller Aleksandar Milosavljevic Robert E Palermo Adam Siepel James M Sikela Tony Attaway Stephanie Bell Kelly E Bernard Christian J Buhay Mimi N Chandrabose Marvin Dao Clay Davis Kimberly D Delehaunty Yan Ding Huyen H Dinh Shannon Dugan-Rocha Lucinda A Fulton Ramatu Ayiesha Gabisi Toni T Garner Jennifer Godfrey Alicia C Hawes Judith Hernandez Sandra Hines Michael Holder Jennifer Hume Shalini N Jhangiani Vandita Joshi Ziad Mohid Khan Ewen F Kirkness Andrew Cree R Gerald Fowler Sandra Lee Lora R Lewis Zhangwan Li Yih-Shin Liu Stephanie M Moore Donna Muzny Lynne V Nazareth Dinh Ngoc Ngo Geoffrey O Okwuonu Grace Pai David Parker Heidie A Paul Cynthia Pfannkoch Craig S Pohl Yu-Hui Rogers San Juana Ruiz Aniko Sabo Jireh Santibanez Brian W Schneider Scott M Smith Erica Sodergren Amanda F Svatek Teresa R Utterback Selina Vattathil Wesley Warren Courtney Sherell White Asif T Chinwalla Yucheng Feng Aaron L Halpern Ladeana W Hillier Xiaoqiu Huang Pat Minx Joanne O Nelson Kymberlie H Pepin Xiang Qin Granger G Sutton Eli Venter Brian P Walenz John W Wallis Kim C Worley Shiaw-Pyng Yang Steven M Jones Marco A Marra Mariano Rocchi Jacqueline E Schein Robert Baertsch Laura Clarke Miklós Csürös Jarret Glasscock R Alan Harris Paul Havlak Andrew R Jackson Huaiyang Jiang Yue Liu David N Messina Yufeng Shen Henry Xing-Zhi Song Todd Wylie Lan Zhang Ewan Birney Kyudong Han Miriam K Konkel Jungnam Lee Arian F A Smit Brygg Ullmer Hui Wang Jinchuan Xing Richard Burhans Ze Cheng John E Karro Jian Ma Brian Raney Xinwei She Michael J Cox Jeffery P Demuth Laura J Dumas Sang-Gook Han Janet Hopkins Anis Karimpour-Fard Young H Kim Jonathan R Pollack Tomas Vinar Charles Addo-Quaye Jeremiah Degenhardt Alexandra Denby Melissa J Hubisz Amit Indap Carolin Kosiol Bruce T Lahn Heather A Lawson Alison Marklein Rasmus Nielsen Eric J Vallender Andrew G Clark Betsy Ferguson Ryan D Hernandez Kashif Hirani Hildegard Kehrer-Sawatzki Jessica Kolb Shobha Patil Ling-Ling Pu Yanru Ren David Glenn Smith David A Wheeler Ian Schenck Edward V Ball Rui Chen David N Cooper Belinda Giardine Fan Hsu W James Kent Arthur Lesk David L Nelson William E O'brien Kay Prüfer Peter D Stenson James C Wallace Hui Ke Xiao-Ming Liu Peng Wang Andy Peng Xiang Fan Yang Galt P Barber David Haussler Donna Karolchik Andy D Kern Robert M Kuhn Kayla E Smith Ann S Zwieg

Science 2007 Apr;316(5822):222-34

Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1126/science.1139247DOI Listing
April 2007

Mobile DNA in Old World monkeys: a glimpse through the rhesus macaque genome.

Science 2007 Apr;316(5822):238-40

Department of Biological Sciences, Biological Computation and Visualization Center, Center for Bio-Modular Multi-Scale Systems, Louisiana State University, Baton Rouge, LA 70803, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1126/science.1139462DOI Listing
April 2007

Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis.

Nucleic Acids Res 2007 18;35(1):1-10. Epub 2006 Aug 18.

Center for Ancient Genetics, Niels Bohr Institute and Biological Institutes, The University of Copenhagen, Juliane Maries vej 30, DK-2100 Copenhagen Ø, Denmark.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkl483DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1802572PMC
February 2007

HbVar database of human hemoglobin variants and thalassemia mutations: 2007 update.

Hum Mutat 2007 Feb;28(2):206

The Pennsylvania State University, Center for Comparative Genomics and Bioinformatics, University Park, Pennsylvania, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/humu.9479DOI Listing
February 2007

Reconstructing contiguous regions of an ancestral genome.

Genome Res 2006 Dec 18;16(12):1557-65. Epub 2006 Sep 18.

Center for Comparative Genomics and Bioinformatics, Penn State University, University Park, Pennsylvania 16802, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.5383506DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1665639PMC
December 2006

Experimental validation of predicted mammalian erythroid cis-regulatory modules.

Genome Res 2006 Dec 12;16(12):1480-92. Epub 2006 Oct 12.

Center for Comparative Genomics and Bioinformatics of the Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.5353806DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1665632PMC
December 2006

ESPERR: learning strong and weak signals in genomic sequence alignments to identify functional elements.

Genome Res 2006 Dec 19;16(12):1596-604. Epub 2006 Oct 19.

Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

View Article

Download full-text PDF

Source
http://www.genome.org/cgi/doi/10.1101/gr.4537706
Publisher Site
http://dx.doi.org/10.1101/gr.4537706DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1665643PMC
December 2006

Identification and classification of conserved RNA secondary structures in the human genome.

PLoS Comput Biol 2006 Apr 21;2(4):e33. Epub 2006 Apr 21.

Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.0020033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1440920PMC
April 2006

Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA.

Science 2006 Jan 20;311(5759):392-4. Epub 2005 Dec 20.

McMaster Ancient DNA Center, McMaster University, 1280 Main Street West, Hamilton ON, L8S 4L9 Canada.

View Article

Download full-text PDF

Source
http://www.sciencemag.org/cgi/doi/10.1126/science.1123360
Publisher Site
http://dx.doi.org/10.1126/science.1123360DOI Listing
January 2006

Galaxy: a platform for interactive large-scale genome analysis.

Genome Res 2005 Oct 16;15(10):1451-5. Epub 2005 Sep 16.

Center for Comparative Genomics and Bioinformatics, Huck Institutes for Life Sciences, Penn State University, University Park, Pennsylvania 16802, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.4086505DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240089PMC
October 2005

Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences.

Genome Res 2005 Aug 15;15(8):1051-60. Epub 2005 Jul 15.

Center for Comparative Genomics and Bioinformatics, Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.3642605DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1182217PMC
August 2005

Generation and annotation of the DNA sequences of human chromosomes 2 and 4.

Authors:
Ladeana W Hillier Tina A Graves Robert S Fulton Lucinda A Fulton Kymberlie H Pepin Patrick Minx Caryn Wagner-McPherson Dan Layman Kristine Wylie Mandeep Sekhon Michael C Becker Ginger A Fewell Kimberly D Delehaunty Tracie L Miner William E Nash Colin Kremitzki Lachlan Oddy Hui Du Hui Sun Holland Bradshaw-Cordum Johar Ali Jason Carter Matt Cordes Anthony Harris Amber Isak Andrew van Brunt Christine Nguyen Feiyu Du Laura Courtney Joelle Kalicki Philip Ozersky Scott Abbott Jon Armstrong Edward A Belter Lauren Caruso Maria Cedroni Marc Cotton Teresa Davidson Anu Desai Glendoria Elliott Thomas Erb Catrina Fronick Tony Gaige William Haakenson Krista Haglund Andrea Holmes Richard Harkins Kyung Kim Scott S Kruchowski Cynthia Madsen Strong Neenu Grewal Ernest Goyea Shunfang Hou Andrew Levy Scott Martinka Kelly Mead Michael D McLellan Rick Meyer Jennifer Randall-Maher Chad Tomlinson Sara Dauphin-Kohlberg Amy Kozlowicz-Reilly Neha Shah Sharhonda Swearengen-Shahid Jacqueline Snider Joseph T Strong Johanna Thompson Martin Yoakum Shawn Leonard Charlene Pearman Lee Trani Maxim Radionenko Jason E Waligorski Chunyan Wang Susan M Rock Aye-Mon Tin-Wollam Rachel Maupin Phil Latreille Michael C Wendl Shiaw-Pyng Yang Craig Pohl John W Wallis John Spieth Tamberlyn A Bieri Nicolas Berkowicz Joanne O Nelson John Osborne Li Ding Rekha Meyer Aniko Sabo Yoram Shotland Prashant Sinha Patricia E Wohldmann Lisa L Cook Matthew T Hickenbotham James Eldred Donald Williams Thomas A Jones Xinwei She Francesca D Ciccarelli Elisa Izaurralde James Taylor Jeremy Schmutz Richard M Myers David R Cox Xiaoqiu Huang John D McPherson Elaine R Mardis Sandra W Clifton Wesley C Warren Asif T Chinwalla Sean R Eddy Marco A Marra Ivan Ovcharenko Terrence S Furey Webb Miller Evan E Eichler Peer Bork Mikita Suyama David Torrents Robert H Waterston Richard K Wilson

Nature 2005 Apr;434(7034):724-31

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/nature03466DOI Listing
April 2005

MultiPipMaker: comparative alignment server for multiple DNA sequences.

Curr Protoc Bioinformatics 2005 Apr;Chapter 10:Unit10.4

The Pennsylvania State University, University Park, Pennsylvania, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/0471250953.bi1004s9DOI Listing
April 2005

An initial strategy for the systematic identification of functional elements in the human genome by low-redundancy comparative sequencing.

Proc Natl Acad Sci U S A 2005 Mar 18;102(13):4795-800. Epub 2005 Mar 18.

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.0409882102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC555705PMC
March 2005

Mulan: multiple-sequence local alignment and visualization for studying function and evolution.

Genome Res 2005 Jan 8;15(1):184-94. Epub 2004 Dec 8.

Energy, Environment, Biology and Institutional Computing, Lawrence Livermore National Laboratory, Livermore, California 94550, USA.

View Article

Download full-text PDF

Source
http://www.genome.org/cgi/doi/10.1101/gr.3007205
Publisher Site
http://dx.doi.org/10.1101/gr.3007205DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC540288PMC
January 2005

Evolution and functional classification of vertebrate gene deserts.

Genome Res 2005 Jan 8;15(1):137-45. Epub 2004 Dec 8.

Energy, Environment, Biology, and Institutional Computing, Lawrence Livermore National Laboratory, Livermore, California 94550, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.3015505DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC540279PMC
January 2005

Reconstructing large regions of an ancestral mammalian genome in silico.

Genome Res 2004 Dec;14(12):2412-23

Howard Hughes Medical Institute, University of California, Santa Cruz, California 95064, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.2800104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC534665PMC
December 2004

EST clustering error evaluation and correction.

Bioinformatics 2004 Nov 9;20(17):2973-84. Epub 2004 Jun 9.

Department of Statistics, Northwestern University, Evanston, IL 60208, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/bth342DOI Listing
November 2004

Comparative genomics.

Annu Rev Genomics Hum Genet 2004 ;5:15-56

The Center for Comparative Genomics and Bioinformatics, The Huck Institutes of Life Sciences, Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1146/annurev.genom.5.061903.180057DOI Listing
November 2004

The structure and evolution of centromeric transition regions within the human genome.

Nature 2004 Aug;430(7002):857-64

Department of Genetics, Center for Computational Genomics and the Center for Human Genetics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, Ohio 44106, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature02806DOI Listing
August 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

View Article

Download full-text PDF

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

Patterns of insertions and their covariation with substitutions in the rat, mouse, and human genomes.

Genome Res 2004 Apr;14(4):517-27

Department of Biochemistry and Molecular Biology, Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.1984404DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC383295PMC
April 2004

Regulatory potential scores from genome-wide three-way alignments of human, mouse, and rat.

Genome Res 2004 Apr;14(4):700-7

Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.1976004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC383316PMC
April 2004

Significance of interspecies matches when evolutionary rate varies.

Authors:
Jia Li Webb Miller

J Comput Biol 2003 ;10(3-4):537-54

Statistics Department, Penn State, University Park, PA 16802, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1089/10665270360688174DOI Listing
March 2004

zPicture: dynamic alignment and visualization tool for analyzing conservation profiles.

Genome Res 2004 Mar;14(3):472-7

Energy, Environment, Biology and Institutional Computing, Lawrence Livermore National Laboratory, Livermore, California 94550, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.2129504DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC353235PMC
March 2004

Dancing with complement C4 and the RP-C4-CYP21-TNX (RCCX) modules of the major histocompatibility complex.

Prog Nucleic Acid Res Mol Biol 2003 ;75:217-92

Center for Molecular and Human Genetics, Columbus Children's Research Institute, 700 Children's Drive, Columbus, OH 43205-2696, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/s0079-6603(03)75007-7DOI Listing
February 2004

Improvements in the HbVar database of human hemoglobin variants and thalassemia mutations for population and sequence variation studies.

Nucleic Acids Res 2004 Jan;32(Database issue):D537-41

MGC-Department of Cell Biology and Genetics, Erasmus MC, Faculty of Medicine and Health Sciences, PO Box 1738, 3000 DR, Rotterdam, The Netherlands.

View Article

Download full-text PDF

Source
https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
Publisher Site
http://dx.doi.org/10.1093/nar/gkh006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC308741PMC
January 2004

Gene length and proximity to neighbors affect genome-wide expression levels.

Genome Res 2003 Dec 12;13(12):2602-8. Epub 2003 Nov 12.

Department of Statistics and Department of Health Evaluation Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.1169203DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC403802PMC
December 2003

A combinatorial network of evolutionarily conserved myelin basic protein regulatory sequences confers distinct glial-specific phenotypes.

J Neurosci 2003 Nov;23(32):10214-23

Royal Victoria Hospital, Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec H3A 1A1, Canada.

View Article

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6741010PMC
November 2003

Multispecies comparative analysis of a mammalian-specific genomic domain encoding secretory proteins.

Genomics 2003 Oct;82(4):417-32

Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/s0888-7543(03)00114-9DOI Listing
October 2003

Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes.

Proc Natl Acad Sci U S A 2003 Sep 19;100(20):11484-9. Epub 2003 Sep 19.

Center for Biomolecular Science and Engineering and Howard Hughes Medical Institute, Department of Computer Science, University of California, Santa Cruz, CA 95064, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1932072100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784PMC
September 2003

MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences.

Nucleic Acids Res 2003 Jul;31(13):3518-24

Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA 16802, USA.

View Article

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC168985PMC
http://dx.doi.org/10.1093/nar/gkg579DOI Listing
July 2003

EnteriX 2003: Visualization tools for genome alignments of Enterobacteriaceae.

Nucleic Acids Res 2003 Jul;31(13):3527-32

Informatics Research, Celera/Applied Biosystems, 45 W. Gude Drive, Rockville, MD 20850, USA.

View Article

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC168958PMC
http://dx.doi.org/10.1093/nar/gkg551DOI Listing
July 2003

GALA, a database for genomic sequence alignments and annotations.

Genome Res 2003 Apr;13(4):732-41

Department of Computer Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.603103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC430176PMC
April 2003

PipMaker: a World Wide Web server for genomic sequence alignments.

Curr Protoc Bioinformatics 2003 Feb;Chapter 10:Unit 10.2

The Pennsylvania State University, University Park, Pennsylvania, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/0471250953.bi1002s00DOI Listing
February 2003