Publications by authors named "Ian Korf"

61Publications

Low-Pass Whole Genome Bisulfite Sequencing of Neonatal Dried Blood Spots Identifies a Role for RUNX1 in Down Syndrome DNA Methylation Profiles.

Hum Mol Genet 2020 Oct 1. Epub 2020 Oct 1.

Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA, 95616, USA.

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http://dx.doi.org/10.1093/hmg/ddaa218DOI Listing
October 2020

Pre- and post-sequencing recommendations for functional annotation of human fecal metagenomes.

BMC Bioinformatics 2020 Feb 24;21(1):74. Epub 2020 Feb 24.

USDA ARS Western Human Nutrition Research Center, Davis, CA, 95616, USA.

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http://dx.doi.org/10.1186/s12859-020-3416-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7041091PMC
February 2020

Fecal metatranscriptomics and glycomics suggest that bovine milk oligosaccharides are fully utilized by healthy adults.

J Nutr Biochem 2020 05 17;79:108340. Epub 2020 Jan 17.

Genome Center, University of California-Davis, Davis, California, United States; Foods for Health Institute, University of California, Davis, California, United States; USDA ARS Western Human Nutrition Research Center, Davis, California, United States. Electronic address:

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http://dx.doi.org/10.1016/j.jnutbio.2020.108340DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7233280PMC
May 2020

The collaborative effect of scientific meetings: A study of the International Milk Genomics Consortium.

PLoS One 2018 22;13(8):e0201637. Epub 2018 Aug 22.

Genome Center, University of California Davis, Davis, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0201637PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6104928PMC
January 2019

SAMSA2: a standalone metatranscriptome analysis pipeline.

BMC Bioinformatics 2018 05 21;19(1):175. Epub 2018 May 21.

Genome Center, University of California, Davis, California, USA.

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http://dx.doi.org/10.1186/s12859-018-2189-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5963165PMC
May 2018

Autosomal Trisomy and Triploidy Are Corrected During Female Meiosis in .

Genetics 2017 11 7;207(3):911-922. Epub 2017 Sep 7.

Department of Molecular and Cellular Biology, University of California, Davis, California 95616

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http://dx.doi.org/10.1534/genetics.117.300259DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5676225PMC
November 2017

Dental Pulp Stem Cells Model Early Life and Imprinted DNA Methylation Patterns.

Stem Cells 2017 04 19;35(4):981-988. Epub 2017 Jan 19.

Medical Microbiology and Immunology, UC Davis, Davis, California, USA.

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http://dx.doi.org/10.1002/stem.2563DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5367950PMC
April 2017

Cumulative Impact of Polychlorinated Biphenyl and Large Chromosomal Duplications on DNA Methylation, Chromatin, and Expression of Autism Candidate Genes.

Cell Rep 2016 12;17(11):3035-3048

Medical Microbiology and Immunology, UC Davis, Davis, CA 95616, USA; Genome Center, UC Davis, Davis, CA 95616, USA; MIND Institute, UC Davis, Davis, CA 95616, USA; Center for Children's Environmental Health, UC Davis, Davis, CA 95616, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2016.11.058DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5206988PMC
December 2016

SAMSA: a comprehensive metatranscriptome analysis pipeline.

BMC Bioinformatics 2016 Sep 29;17(1):399. Epub 2016 Sep 29.

Genome Center, University of California - Davis, Davis, CA, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5041328PMC
http://dx.doi.org/10.1186/s12859-016-1270-8DOI Listing
September 2016

Intron sequences that stimulate gene expression in Arabidopsis.

Plant Mol Biol 2016 Oct 5;92(3):337-46. Epub 2016 Aug 5.

Department of Molecular and Cellular Biology, University of California, 1 Shields Avenue, Davis, CA, 95616, USA.

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http://dx.doi.org/10.1007/s11103-016-0516-1DOI Listing
October 2016

GC skew is a conserved property of unmethylated CpG island promoters across vertebrates.

Nucleic Acids Res 2015 Nov 7;43(20):9729-41. Epub 2015 Aug 7.

Department of Molecular and Cellular Biology and Genome Center, University of California, Davis, CA 95616, United States

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http://dx.doi.org/10.1093/nar/gkv811DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4787789PMC
November 2015

Comparative Proteomics of Human and Macaque Milk Reveals Species-Specific Nutrition during Postnatal Development.

J Proteome Res 2015 May 6;14(5):2143-57. Epub 2015 Apr 6.

⊥Department of Human Evolutionary Biology, Harvard University, 11 Divinity Avenue, Cambridge, Massachusetts 02138, United States.

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http://pubs.acs.org/doi/10.1021/pr501243m
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http://dx.doi.org/10.1021/pr501243mDOI Listing
May 2015

The functional significance of common polymorphisms in zinc finger transcription factors.

G3 (Bethesda) 2014 Jun 26;4(9):1647-55. Epub 2014 Jun 26.

Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, California 95616

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http://dx.doi.org/10.1534/g3.114.012195DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4169156PMC
June 2014

StochHMM: a flexible hidden Markov model tool and C++ library.

Bioinformatics 2014 Jun 30;30(11):1625-6. Epub 2014 Jan 30.

Genome Center, One Shields Ave., University of California, Davis, CA 95616, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4029032PMC
June 2014

Genomics: the state of the art in RNA-seq analysis.

Authors:
Ian Korf

Nat Methods 2013 Dec;10(12):1165-6

UC Davis Genome Center, University of California, Davis, Davis, California, USA.

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http://dx.doi.org/10.1038/nmeth.2735DOI Listing
December 2013

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.

Gigascience 2013 Jul 22;2(1):10. Epub 2013 Jul 22.

Genome Center, UC, Davis, CA 95616, USA.

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http://dx.doi.org/10.1186/2047-217X-2-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3844414PMC
July 2013

The human placenta methylome.

Proc Natl Acad Sci U S A 2013 Apr 25;110(15):6037-42. Epub 2013 Mar 25.

Department of Medical Microbiology and Immunology, UC Davis School of Medicine, Davis, CA 95616, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.1215145110
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http://dx.doi.org/10.1073/pnas.1215145110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3625261PMC
April 2013

The effects of a stimulating intron on the expression of heterologous genes in Arabidopsis thaliana.

Plant Biotechnol J 2013 Jun 24;11(5):555-63. Epub 2013 Jan 24.

Molecular and Cellular Biology, University of California, Davis, CA, USA.

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http://dx.doi.org/10.1111/pbi.12043DOI Listing
June 2013

Comparative genomics of carp herpesviruses.

J Virol 2013 Mar 26;87(5):2908-22. Epub 2012 Dec 26.

MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom.

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http://jvi.asm.org/cgi/doi/10.1128/JVI.03206-12
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http://dx.doi.org/10.1128/JVI.03206-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3571366PMC
March 2013

G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes.

BMC Bioinformatics 2012 Sep 28;13:253. Epub 2012 Sep 28.

Genome Center, University of California Davis, 451 Health Science Dr, Davis, CA, 95616, United States of America.

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http://dx.doi.org/10.1186/1471-2105-13-253DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3575404PMC
September 2012

Guiding the design of synthetic DNA-binding molecules with massively parallel sequencing.

J Am Chem Soc 2012 Oct 10;134(42):17814-22. Epub 2012 Oct 10.

Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA.

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http://dx.doi.org/10.1021/ja308888cDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3483022PMC
October 2012

Holocentric chromosomes: convergent evolution, meiotic adaptations, and genomic analysis.

Chromosome Res 2012 Jul;20(5):579-93

Department of Molecular and Cell Biology and Genome Center, University of California, Davis, CA, USA.

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http://dx.doi.org/10.1007/s10577-012-9292-1DOI Listing
July 2012

R-loop formation is a distinctive characteristic of unmethylated human CpG island promoters.

Mol Cell 2012 Mar 1;45(6):814-25. Epub 2012 Mar 1.

Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA.

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http://dx.doi.org/10.1016/j.molcel.2012.01.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3319272PMC
March 2012

Myc and Miz-1 have coordinate genomic functions including targeting Hox genes in human embryonic stem cells.

Epigenetics Chromatin 2011 Nov 4;4:20. Epub 2011 Nov 4.

Department of Cell Biology and Human Anatomy, University of California Davis School of Medicine, Sacramento, CA, USA.

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http://dx.doi.org/10.1186/1756-8935-4-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3226433PMC
November 2011

Breadth by depth: expanding our understanding of the repair of transposon-induced DNA double strand breaks via deep-sequencing.

DNA Repair (Amst) 2011 Oct 1;10(10):1023-33. Epub 2011 Sep 1.

Department of Plant Biology, University of California, Davis, CA 95616, USA.

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http://dx.doi.org/10.1016/j.dnarep.2011.07.011DOI Listing
October 2011

Large-scale methylation domains mark a functional subset of neuronally expressed genes.

Genome Res 2011 Oct 22;21(10):1583-91. Epub 2011 Jul 22.

School of Medicine, Medical Microbiology and Immunology, University of California Davis, Davis, California 95616, USA.

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http://dx.doi.org/10.1101/gr.119131.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3202276PMC
October 2011

Comparative and functional analysis of intron-mediated enhancement signals reveals conserved features among plants.

Nucleic Acids Res 2011 Jul 22;39(13):5328-37. Epub 2011 Mar 22.

Genome Center and Molecular and Cellular Biology, University of California, Davis, CA 95616, USA.

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http://dx.doi.org/10.1093/nar/gkr043DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141229PMC
July 2011

Evidence for a DNA-Based Mechanism of Intron-Mediated Enhancement.

Front Plant Sci 2011 13;2:98. Epub 2011 Dec 13.

Molecular and Cellular Biology, University of California Davis, CA, USA.

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http://dx.doi.org/10.3389/fpls.2011.00098DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3355757PMC
August 2012

Bind-n-Seq: high-throughput analysis of in vitro protein-DNA interactions using massively parallel sequencing.

Nucleic Acids Res 2009 Dec;37(22):e151

Genome Center, University of California, Davis, CA 95616, USA.

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http://dx.doi.org/10.1093/nar/gkp802DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2794170PMC
December 2009

Applying word-based algorithms: the IMEter.

Methods Mol Biol 2009 ;553:287-301

Genome Center and Section of Molecular and Cellular Biology, University of California, Davis, CA, USA.

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http://dx.doi.org/10.1007/978-1-60327-563-7_14DOI Listing
January 2010

Assessing the gene space in draft genomes.

Nucleic Acids Res 2009 Jan 28;37(1):289-97. Epub 2008 Nov 28.

UC Davis Genome Center, University of California Davis, Davis, CA, USA.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkn916DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2615622PMC
January 2009

Longer first introns are a general property of eukaryotic gene structure.

PLoS One 2008 Aug 29;3(8):e3093. Epub 2008 Aug 29.

Genome Center, University of California Davis, Davis, California, USA.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0003093PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2518113PMC
August 2008

Promoter-proximal introns in Arabidopsis thaliana are enriched in dispersed signals that elevate gene expression.

Plant Cell 2008 Mar 4;20(3):543-51. Epub 2008 Mar 4.

Molecular and Cellular Biology, University of California, Davis, California 95616, USA.

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http://dx.doi.org/10.1105/tpc.107.057190DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2329928PMC
March 2008

Draft genome of the filarial nematode parasite Brugia malayi.

Science 2007 Sep;317(5845):1756-60

Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA.

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http://www.sciencemag.org/cgi/doi/10.1126/science.1145406
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http://dx.doi.org/10.1126/science.1145406DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2613796PMC
September 2007

CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes.

Bioinformatics 2007 May 1;23(9):1061-7. Epub 2007 Mar 1.

UC Davis Genome Center, University of California Davis, Davis, CA 95616, USA.

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http://dx.doi.org/10.1093/bioinformatics/btm071DOI Listing
May 2007

A probabilistic model of 3' end formation in Caenorhabditis elegans.

Nucleic Acids Res 2004 24;32(11):3392-9. Epub 2004 Jun 24.

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.

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http://dx.doi.org/10.1093/nar/gkh656DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC443532PMC
July 2004

Gene finding in novel genomes.

Authors:
Ian Korf

BMC Bioinformatics 2004 May 14;5:59. Epub 2004 May 14.

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.

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http://dx.doi.org/10.1186/1471-2105-5-59DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC421630PMC
May 2004

Serial BLAST searching.

Authors:
Ian Korf

Bioinformatics 2003 Aug;19(12):1492-6

The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK.

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http://dx.doi.org/10.1093/bioinformatics/btg199DOI Listing
August 2003

Leveraging the mouse genome for gene prediction in human: from whole-genome shotgun reads to a global synteny map.

Genome Res 2003 Jan;13(1):46-54

Department of Computer Science and Engineering, Washington University, St. Louis, Missouri 63130, USA.

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http://dx.doi.org/10.1101/gr.830003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC430948PMC
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