Inna Dubchak

Inna Dubchak

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Inna Dubchak

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KBase: The United States Department of Energy Systems Biology Knowledgebase.

Nat Biotechnol 2018 07;36(7):566-569

Computer Science and Math, Computer Science Initiative, Brookhaven National Laboratory, Upton, New York, USA.

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http://dx.doi.org/10.1038/nbt.4163DOI Listing
July 2018

Strategic Integration of Multiple Bioinformatics Resources for System Level Analysis of Biological Networks.

Methods Mol Biol 2017 ;1613:85-99

Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL, 60637, USA.

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http://dx.doi.org/10.1007/978-1-4939-7027-8_5DOI Listing
May 2018

An integrative computational approach for prioritization of genomic variants.

PLoS One 2014 15;9(12):e114903. Epub 2014 Dec 15.

Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America; Computation Institute, University of Chicago/Argonne National Laboratory, Chicago, Illinois, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0114903PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4266634PMC
November 2015

σ54-dependent regulome in Desulfovibrio vulgaris Hildenborough.

BMC Genomics 2015 Nov 10;16:919. Epub 2015 Nov 10.

Lawrence Berkeley National Laboratory, Berkeley, CA, 94710, USA.

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http://dx.doi.org/10.1186/s12864-015-2176-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4641369PMC
November 2015

Functionally conserved enhancers with divergent sequences in distant vertebrates.

BMC Genomics 2015 Oct 30;16:882. Epub 2015 Oct 30.

Children's Hospital Oakland Research Institute, Oakland, CA, 94609, USA.

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http://dx.doi.org/10.1186/s12864-015-2070-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4628251PMC
October 2015

Elviz - exploration of metagenome assemblies with an interactive visualization tool.

BMC Bioinformatics 2015 Apr 28;16:130. Epub 2015 Apr 28.

Department of Energy, Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA.

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http://dx.doi.org/10.1186/s12859-015-0566-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4432942PMC
April 2015

Alignathon: a competitive assessment of whole-genome alignment methods.

Genome Res 2014 Dec 1;24(12):2077-89. Epub 2014 Oct 1.

Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA; Biomolecular Engineering Department, University of California Santa Cruz, Santa Cruz, California 95064, USA;

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http://dx.doi.org/10.1101/gr.174920.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4248324PMC
December 2014

GenomeVISTA--an integrated software package for whole-genome alignment and visualization.

Bioinformatics 2014 Sep 23;30(18):2654-5. Epub 2014 May 23.

US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA, Centre for Computational Medicine, Hospital for Sick Children, Toronto, ON M5G 1X8 Canada, Department of Computer Science, University of Toronto, Toronto, ON M5S 3G4 Canada and Genomics Division, LBNL, Berkeley, CA 94720, USA US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA, Centre for Computational Medicine, Hospital for Sick Children, Toronto, ON M5G 1X8 Canada, Department of Computer Science, University of Toronto, Toronto, ON M5S 3G4 Canada and Genomics Division, LBNL, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu355DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4155257PMC
September 2014

The genome of Eucalyptus grandis.

Nature 2014 Jun 11;510(7505):356-62. Epub 2014 Jun 11.

1] US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA [2] HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, Alabama 35801, USA.

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http://dx.doi.org/10.1038/nature13308DOI Listing
June 2014

High-throughput translational medicine: challenges and solutions.

Adv Exp Med Biol 2014 ;799:39-67

Computation Institute, University of Chicago/Argonne National Laboratory, 5735 S Ellis Ave, Chicago, IL, 60637, USA,

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http://dx.doi.org/10.1007/978-1-4614-8778-4_3DOI Listing
April 2014

The genome portal of the Department of Energy Joint Genome Institute: 2014 updates.

Nucleic Acids Res 2014 Jan 12;42(Database issue):D26-31. Epub 2013 Nov 12.

Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA.

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http://dx.doi.org/10.1093/nar/gkt1069DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965075PMC
January 2014

MycoCosm portal: gearing up for 1000 fungal genomes.

Nucleic Acids Res 2014 Jan 1;42(Database issue):D699-704. Epub 2013 Dec 1.

US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA.

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http://dx.doi.org/10.1093/nar/gkt1183DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965089PMC
January 2014

New family of tungstate-responsive transcriptional regulators in sulfate-reducing bacteria.

J Bacteriol 2013 Oct 2;195(19):4466-75. Epub 2013 Aug 2.

Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.

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http://dx.doi.org/10.1128/JB.00679-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3807478PMC
October 2013

VISTA Region Viewer (RViewer)--a computational system for prioritizing genomic intervals for biomedical studies.

Bioinformatics 2011 Sep 26;27(18):2595-7. Epub 2011 Jul 26.

Genomics Division, Lawrence Berkeley National Laboratory, MS 84-171, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1093/bioinformatics/btr440DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3167054PMC
September 2011

Tandem termination signal in plant mRNAs.

Gene 2011 Jul 22;481(1):1-6. Epub 2011 Apr 22.

Institute of Cytology and Genetics, Lavrentieva ave. 10, Novosibirsk, 630090, Russia.

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https://linkinghub.elsevier.com/retrieve/pii/S03781119110015
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http://dx.doi.org/10.1016/j.gene.2011.04.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105159PMC
July 2011

Comparative genomics of the dormancy regulons in mycobacteria.

J Bacteriol 2011 Jul 20;193(14):3446-52. Epub 2011 May 20.

Energy Bioscience Institute, University of California, Berkeley, California 94720, USA.

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http://jb.asm.org/cgi/doi/10.1128/JB.00179-11
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http://dx.doi.org/10.1128/JB.00179-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3133309PMC
July 2011

A cis-regulatory signature in ascidians and flies, independent of transcription factor binding sites.

Curr Biol 2010 May 29;20(9):792-802. Epub 2010 Apr 29.

Institut du Biologie de Développement de Marseille Luminy (IBDML, UMR 6216), CNRS, Université de la Méditerranée, Parc Scientifique de Luminy Case 907, F-13288, Marseille Cedex 9, France.

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http://dx.doi.org/10.1016/j.cub.2010.03.063DOI Listing
May 2010

Visualizing genomes: techniques and challenges.

Nat Methods 2010 Mar 25;7(3 Suppl):S5-S15. Epub 2010 Feb 25.

British Columbia Cancer Agency, Genome Sciences Centre, Vancouver, Canada.

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http://dx.doi.org/10.1038/nmeth.1422DOI Listing
March 2010

RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes.

Nucleic Acids Res 2010 Jan 1;38(Database issue):D111-8. Epub 2009 Nov 1.

Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, State Scientific Center GosNIIGenetika, Moscow 117545, Russia.

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http://dx.doi.org/10.1093/nar/gkp894DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808921PMC
January 2010

MicrobesOnline: an integrated portal for comparative and functional genomics.

Nucleic Acids Res 2010 Jan 11;38(Database issue):D396-400. Epub 2009 Nov 11.

Virtual Institute for Microbial Stress and Survival, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1093/nar/gkp919DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808868PMC
January 2010

Obtaining comparative genomic data with the VISTA family of computational tools.

Curr Protoc Bioinformatics 2009 Jun;Chapter 10:Unit 10.6

Lawrence Berkeley National Laboratory, Berkeley, California, USA.

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http://dx.doi.org/10.1002/0471250953.bi1006s26DOI Listing
June 2009

Multiple whole-genome alignments without a reference organism.

Genome Res 2009 Apr 28;19(4):682-9. Epub 2009 Jan 28.

Genome Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.

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http://genome.cshlp.org/cgi/doi/10.1101/gr.081778.108
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http://dx.doi.org/10.1101/gr.081778.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2665786PMC
April 2009

ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes.

Nucleic Acids Res 2009 Jan 9;37(Database issue):D448-54. Epub 2008 Oct 9.

Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1093/nar/gkn684DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686458PMC
January 2009

Trends in prokaryotic evolution revealed by comparison of closely related bacterial and archaeal genomes.

J Bacteriol 2009 Jan 31;191(1):65-73. Epub 2008 Oct 31.

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

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http://jb.asm.org/cgi/doi/10.1128/JB.01237-08
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http://dx.doi.org/10.1128/JB.01237-08DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2612427PMC
January 2009

Comparative analysis and visualization of genomic sequences using VISTA browser and associated computational tools.

Authors:
Inna Dubchak

Methods Mol Biol 2007 ;395:3-16

Lawrence Berkeley National Laboratory, USA.

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http://dx.doi.org/10.1007/978-1-59745-514-5_1DOI Listing
March 2008

IMG/M: a data management and analysis system for metagenomes.

Nucleic Acids Res 2008 Jan 11;36(Database issue):D534-8. Epub 2007 Oct 11.

Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, USA.

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http://dx.doi.org/10.1093/nar/gkm869DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238950PMC
January 2008

The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions.

Nucleic Acids Res 2008 Jan 12;36(Database issue):D528-33. Epub 2007 Oct 12.

Biological Data Management and Technology Center, Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, USA.

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http://dx.doi.org/10.1093/nar/gkm846DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238897PMC
January 2008

The Chlamydomonas genome reveals the evolution of key animal and plant functions.

Authors:
Sabeeha S Merchant Simon E Prochnik Olivier Vallon Elizabeth H Harris Steven J Karpowicz George B Witman Astrid Terry Asaf Salamov Lillian K Fritz-Laylin Laurence Maréchal-Drouard Wallace F Marshall Liang-Hu Qu David R Nelson Anton A Sanderfoot Martin H Spalding Vladimir V Kapitonov Qinghu Ren Patrick Ferris Erika Lindquist Harris Shapiro Susan M Lucas Jane Grimwood Jeremy Schmutz Pierre Cardol Heriberto Cerutti Guillaume Chanfreau Chun-Long Chen Valérie Cognat Martin T Croft Rachel Dent Susan Dutcher Emilio Fernández Hideya Fukuzawa David González-Ballester Diego González-Halphen Armin Hallmann Marc Hanikenne Michael Hippler William Inwood Kamel Jabbari Ming Kalanon Richard Kuras Paul A Lefebvre Stéphane D Lemaire Alexey V Lobanov Martin Lohr Andrea Manuell Iris Meier Laurens Mets Maria Mittag Telsa Mittelmeier James V Moroney Jeffrey Moseley Carolyn Napoli Aurora M Nedelcu Krishna Niyogi Sergey V Novoselov Ian T Paulsen Greg Pazour Saul Purton Jean-Philippe Ral Diego Mauricio Riaño-Pachón Wayne Riekhof Linda Rymarquis Michael Schroda David Stern James Umen Robert Willows Nedra Wilson Sara Lana Zimmer Jens Allmer Janneke Balk Katerina Bisova Chong-Jian Chen Marek Elias Karla Gendler Charles Hauser Mary Rose Lamb Heidi Ledford Joanne C Long Jun Minagawa M Dudley Page Junmin Pan Wirulda Pootakham Sanja Roje Annkatrin Rose Eric Stahlberg Aimee M Terauchi Pinfen Yang Steven Ball Chris Bowler Carol L Dieckmann Vadim N Gladyshev Pamela Green Richard Jorgensen Stephen Mayfield Bernd Mueller-Roeber Sathish Rajamani Richard T Sayre Peter Brokstein Inna Dubchak David Goodstein Leila Hornick Y Wayne Huang Jinal Jhaveri Yigong Luo Diego Martínez Wing Chi Abby Ngau Bobby Otillar Alexander Poliakov Aaron Porter Lukasz Szajkowski Gregory Werner Kemin Zhou Igor V Grigoriev Daniel S Rokhsar Arthur R Grossman

Science 2007 Oct;318(5848):245-50

Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA 90095, USA.

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http://dx.doi.org/10.1126/science.1143609DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2875087PMC
October 2007

Short sequence motifs, overrepresented in mammalian conserved non-coding sequences.

BMC Genomics 2007 Oct 18;8:378. Epub 2007 Oct 18.

Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1186/1471-2164-8-378DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2176071PMC
October 2007

Extensive parallelism in protein evolution.

Biol Direct 2007 Aug 16;2:20. Epub 2007 Aug 16.

Life Sciences Institute and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109-2216, USA.

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http://dx.doi.org/10.1186/1745-6150-2-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2020468PMC
August 2007

Multiple whole genome alignments and novel biomedical applications at the VISTA portal.

Nucleic Acids Res 2007 Jul 8;35(Web Server issue):W669-74. Epub 2007 May 8.

Department of Computer Science, Banting and Best Department of Medical Research, University of Toronto, 6 King's College Road, Toronto, ON, Canada M5S 3G4.

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http://dx.doi.org/10.1093/nar/gkm279DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933192PMC
July 2007

TreeQ-VISTA: an interactive tree visualization tool with functional annotation query capabilities.

Bioinformatics 2007 Mar 17;23(6):764-6. Epub 2007 Jan 17.

Institute for Data Analysis and Visualization (IDAV), Department of Computer Science, University of California, Davis, One Shields Ave., Davis, CA 95616, USA.

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http://dx.doi.org/10.1093/bioinformatics/btl643DOI Listing
March 2007

VISTA Enhancer Browser--a database of tissue-specific human enhancers.

Nucleic Acids Res 2007 Jan 27;35(Database issue):D88-92. Epub 2006 Nov 27.

Genomics Division, MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA.

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http://dx.doi.org/10.1093/nar/gkl822DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1716724PMC
January 2007

RegTransBase--a database of regulatory sequences and interactions in a wide range of prokaryotic genomes.

Nucleic Acids Res 2007 Jan 16;35(Database issue):D407-12. Epub 2006 Nov 16.

Institute for Information Transmission Problems, RAS. Bolshoi Karetny pereulok 19, Moscow, 127994, Russia.

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http://dx.doi.org/10.1093/nar/gkl865DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1669780PMC
January 2007

Conservation patterns in different functional sequence categories of divergent Drosophila species.

Genomics 2006 Oct 11;88(4):431-42. Epub 2006 May 11.

Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1016/j.ygeno.2006.03.012DOI Listing
October 2006

VISTA family of computational tools for comparative analysis of DNA sequences and whole genomes.

Methods Mol Biol 2006 ;338:69-89

Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.

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http://dx.doi.org/10.1385/1-59745-097-9:69DOI Listing
September 2006

The integrated microbial genomes (IMG) system.

Nucleic Acids Res 2006 Jan;34(Database issue):D344-8

Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, USA.

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http://dx.doi.org/10.1093/nar/gkj024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347387PMC
January 2006

SNP-VISTA: an interactive SNP visualization tool.

BMC Bioinformatics 2005 Dec 8;6:292. Epub 2005 Dec 8.

Institute for Data Analysis and Visualization, (IDAV), Department of Computer Science, University of California, Davis, One ShieldsAve., Davis, CA 95616, USA.

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http://dx.doi.org/10.1186/1471-2105-6-292DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1325058PMC
December 2005

Dissimilatory metabolism of nitrogen oxides in bacteria: comparative reconstruction of transcriptional networks.

PLoS Comput Biol 2005 Oct 28;1(5):e55. Epub 2005 Oct 28.

Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.

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http://dx.doi.org/10.1371/journal.pcbi.0010055DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1274295PMC
October 2005

Reconstruction of regulatory and metabolic pathways in metal-reducing delta-proteobacteria.

Genome Biol 2004 22;5(11):R90. Epub 2004 Oct 22.

Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoi Karetny per, 19, Moscow 127994, Russia.

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http://dx.doi.org/10.1186/gb-2004-5-11-r90DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC545781PMC
August 2005

The MicrobesOnline Web site for comparative genomics.

Genome Res 2005 Jul;15(7):1015-22

Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.

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http://dx.doi.org/10.1101/gr.3844805DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1172046PMC
July 2005

Gene expression patterns define key transcriptional events in cell-cycle regulation by cAMP and protein kinase A.

Proc Natl Acad Sci U S A 2005 Jun 6;102(24):8561-6. Epub 2005 Jun 6.

Gladstone Institute of Cardiovascular Disease, University of California, San Francisco, CA 94141, USA.

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http://dx.doi.org/10.1073/pnas.0503363102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1150853PMC
June 2005

The splicing regulatory element, UGCAUG, is phylogenetically and spatially conserved in introns that flank tissue-specific alternative exons.

Nucleic Acids Res 2005 3;33(2):714-24. Epub 2005 Feb 3.

Life Sciences Division and Genomics Division, Lawrence Berkeley National Laboratory Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1093/nar/gki210DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC548355PMC
February 2005

Glocal alignment: finding rearrangements during alignment.

Bioinformatics 2003 ;19 Suppl 1:i54-62

Department of Computer Science, Stanford University, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1093/bioinformatics/btg1005DOI Listing
October 2004

VISTA: computational tools for comparative genomics.

Nucleic Acids Res 2004 Jul;32(Web Server issue):W273-9

Perlegen Sciences, Inc., 2021 Stierlin Court, Mountain View, CA 94043, USA.

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http://dx.doi.org/10.1093/nar/gkh458DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC441596PMC
July 2004

Integrative annotation of 21,037 human genes validated by full-length cDNA clones.

Authors:
Tadashi Imanishi Takeshi Itoh Yutaka Suzuki Claire O'Donovan Satoshi Fukuchi Kanako O Koyanagi Roberto A Barrero Takuro Tamura Yumi Yamaguchi-Kabata Motohiko Tanino Kei Yura Satoru Miyazaki Kazuho Ikeo Keiichi Homma Arek Kasprzyk Tetsuo Nishikawa Mika Hirakawa Jean Thierry-Mieg Danielle Thierry-Mieg Jennifer Ashurst Libin Jia Mitsuteru Nakao Michael A Thomas Nicola Mulder Youla Karavidopoulou Lihua Jin Sangsoo Kim Tomohiro Yasuda Boris Lenhard Eric Eveno Yoshiyuki Suzuki Chisato Yamasaki Jun-ichi Takeda Craig Gough Phillip Hilton Yasuyuki Fujii Hiroaki Sakai Susumu Tanaka Clara Amid Matthew Bellgard Maria de Fatima Bonaldo Hidemasa Bono Susan K Bromberg Anthony J Brookes Elspeth Bruford Piero Carninci Claude Chelala Christine Couillault Sandro J de Souza Marie-Anne Debily Marie-Dominique Devignes Inna Dubchak Toshinori Endo Anne Estreicher Eduardo Eyras Kaoru Fukami-Kobayashi Gopal R Gopinath Esther Graudens Yoonsoo Hahn Michael Han Ze-Guang Han Kousuke Hanada Hideki Hanaoka Erimi Harada Katsuyuki Hashimoto Ursula Hinz Momoki Hirai Teruyoshi Hishiki Ian Hopkinson Sandrine Imbeaud Hidetoshi Inoko Alexander Kanapin Yayoi Kaneko Takeya Kasukawa Janet Kelso Paul Kersey Reiko Kikuno Kouichi Kimura Bernhard Korn Vladimir Kuryshev Izabela Makalowska Takashi Makino Shuhei Mano Regine Mariage-Samson Jun Mashima Hideo Matsuda Hans-Werner Mewes Shinsei Minoshima Keiichi Nagai Hideki Nagasaki Naoki Nagata Rajni Nigam Osamu Ogasawara Osamu Ohara Masafumi Ohtsubo Norihiro Okada Toshihisa Okido Satoshi Oota Motonori Ota Toshio Ota Tetsuji Otsuki Dominique Piatier-Tonneau Annemarie Poustka Shuang-Xi Ren Naruya Saitou Katsunaga Sakai Shigetaka Sakamoto Ryuichi Sakate Ingo Schupp Florence Servant Stephen Sherry Rie Shiba Nobuyoshi Shimizu Mary Shimoyama Andrew J Simpson Bento Soares Charles Steward Makiko Suwa Mami Suzuki Aiko Takahashi Gen Tamiya Hiroshi Tanaka Todd Taylor Joseph D Terwilliger Per Unneberg Vamsi Veeramachaneni Shinya Watanabe Laurens Wilming Norikazu Yasuda Hyang-Sook Yoo Marvin Stodolsky Wojciech Makalowski Mitiko Go Kenta Nakai Toshihisa Takagi Minoru Kanehisa Yoshiyuki Sakaki John Quackenbush Yasushi Okazaki Yoshihide Hayashizaki Winston Hide Ranajit Chakraborty Ken Nishikawa Hideaki Sugawara Yoshio Tateno Zhu Chen Michio Oishi Peter Tonellato Rolf Apweiler Kousaku Okubo Lukas Wagner Stefan Wiemann Robert L Strausberg Takao Isogai Charles Auffray Nobuo Nomura Takashi Gojobori Sumio Sugano

PLoS Biol 2004 Jun 20;2(6):e162. Epub 2004 Apr 20.

Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan.

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http://dx.doi.org/10.1371/journal.pbio.0020162DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC393292PMC
June 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

The DNA sequence and biology of human chromosome 19.

Nature 2004 Apr;428(6982):529-35

Stanford Human Genome Center, Department of Genetics, Stanford University School of Medicine, 975 California Avenue, Palo Alto, California 94304, USA.

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http://dx.doi.org/10.1038/nature02399DOI Listing
April 2004

Characterization of evolutionary rates and constraints in three Mammalian genomes.

Genome Res 2004 Apr;14(4):539-48

Department of Genetics, Stanford University, Stanford, California 94305, USA.

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http://dx.doi.org/10.1101/gr.2034704DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC383297PMC
April 2004

Multi-species sequence comparison: the next frontier in genome annotation.

Genome Biol 2003 27;4(12):122. Epub 2003 Nov 27.

Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

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http://genomebiology.biomedcentral.com/articles/10.1186/gb-2
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http://dx.doi.org/10.1186/gb-2003-4-12-122DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC329408PMC
March 2004

Phylo-VISTA: interactive visualization of multiple DNA sequence alignments.

Bioinformatics 2004 Mar 22;20(5):636-43. Epub 2004 Jan 22.

Center for Image Processing and Integrated Computing, Department of Computer Science, One Shields Avenue, University of California, Davis, CA 95616-8562, USA.

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http://dx.doi.org/10.1093/bioinformatics/btg459DOI Listing
March 2004

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

AVID: A global alignment program.

Genome Res 2003 Jan;13(1):97-102

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

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http://dx.doi.org/10.1101/gr.789803DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC430967PMC
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

rVista for comparative sequence-based discovery of functional transcription factor binding sites.

Genome Res 2002 May;12(5):832-9

Genome Sciences Department, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.

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http://dx.doi.org/10.1101/gr.225502DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC186580PMC
May 2002

Comparative genomics approaches to study organism similarities and differences.

J Biomed Inform 2002 Apr;35(2):142-50

Nexus Genomics, Inc., 229 Polaris Ave., Suite 6, Mountain View, CA 94043, USA.

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April 2002

The computational challenges of applying comparative-based computational methods to whole genomes.

Brief Bioinform 2002 Mar;3(1):18-22

Lawrence Berkeley National Laboratory, National Energy Resesarch Scientific Computing Center, CA 94720, USA.

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http://dx.doi.org/10.1093/bib/3.1.18DOI Listing
March 2002