Publications by authors named "Douglas B Rusch"

72Publications

Complete Genome Sequence of Vibrio coralliilyticus OCN008.

Microbiol Resour Announc 2020 Jul 23;9(30). Epub 2020 Jul 23.

Biology Department, Indiana University, Bloomington, Indiana, USA

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http://dx.doi.org/10.1128/MRA.00323-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7378022PMC
July 2020

Increased microbiota diversity associated with higher FEV in infants.

Pediatr Pulmonol 2020 01 5;55(1):27-29. Epub 2019 Nov 5.

Department of Pediatrics, University of North Carolina School of Medicine, Chapel Hill, North Carolina.

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http://dx.doi.org/10.1002/ppul.24559DOI Listing
January 2020

Diversity in Natural Transformation Frequencies and Regulation across Species.

mBio 2019 12 17;10(6). Epub 2019 Dec 17.

Department of Biology, Indiana University, Bloomington, Indiana, USA

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http://dx.doi.org/10.1128/mBio.02788-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6918086PMC
December 2019

Global H-NS counter-silencing by LuxR activates quorum sensing gene expression.

Nucleic Acids Res 2020 01;48(1):171-183

Department of Biology, Indiana University, Bloomington, IN, USA.

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http://dx.doi.org/10.1093/nar/gkz1089DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145609PMC
January 2020

The neurogenomic transition from territory establishment to parenting in a territorial female songbird.

BMC Genomics 2019 Nov 7;20(1):819. Epub 2019 Nov 7.

Department of Biology, Indiana University, Bloomington, IN, 47405, USA.

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http://dx.doi.org/10.1186/s12864-019-6202-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6836416PMC
November 2019

Transcriptome Profiling Reveals Matrisome Alteration as a Key Feature of Ovarian Cancer Progression.

Cancers (Basel) 2019 Oct 9;11(10). Epub 2019 Oct 9.

Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN 46202, USA.

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http://dx.doi.org/10.3390/cancers11101513DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6826756PMC
October 2019

Destabilization of the Tumor-Inducing Plasmid from an Octopine-Type Lineage Drives a Large Deletion in the Co-resident At Megaplasmid.

G3 (Bethesda) 2019 10 7;9(10):3489-3500. Epub 2019 Oct 7.

Department of Biology, Indiana University, Bloomington, Indiana.

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http://dx.doi.org/10.1534/g3.119.400554DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6778807PMC
October 2019

DNA methyltransferase inhibition reduces inflammation-induced colon tumorigenesis.

Epigenetics 2019 12 26;14(12):1209-1223. Epub 2019 Jun 26.

Medical Sciences, Indiana University School of Medicine , Bloomington , IN , USA.

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http://dx.doi.org/10.1080/15592294.2019.1634986DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6791707PMC
December 2019

Co-occurring genomic capacity for anaerobic methane and dissimilatory sulfur metabolisms discovered in the Korarchaeota.

Nat Microbiol 2019 04 4;4(4):614-622. Epub 2019 Mar 4.

Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA.

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http://dx.doi.org/10.1038/s41564-019-0362-4DOI Listing
April 2019

Flagellar Mutants Have Reduced Pilus Synthesis in .

J Bacteriol 2019 09 22;201(18). Epub 2019 Aug 22.

Department of Biology, Indiana University, Bloomington, Indiana, USA

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http://dx.doi.org/10.1128/JB.00031-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6707913PMC
September 2019

Redefining the Small Regulatory RNA Transcriptome in Streptococcus pneumoniae Serotype 2 Strain D39.

J Bacteriol 2019 07 21;201(14). Epub 2019 Jun 21.

Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, USA

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http://dx.doi.org/10.1128/JB.00764-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6597385PMC
July 2019

Microbial mechanisms and ecosystem flux estimation for aerobic NO emissions from deciduous forest soils.

Proc Natl Acad Sci U S A 2019 02 18;116(6):2138-2145. Epub 2019 Jan 18.

Integrated Program in the Environment, Indiana University, Bloomington, IN 47405;

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http://dx.doi.org/10.1073/pnas.1814632116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6369794PMC
February 2019

Marsarchaeota are an aerobic archaeal lineage abundant in geothermal iron oxide microbial mats.

Nat Microbiol 2018 06 14;3(6):732-740. Epub 2018 May 14.

Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA.

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http://dx.doi.org/10.1038/s41564-018-0163-1DOI Listing
June 2018

In children, the microbiota of the nasopharynx and bronchoalveolar lavage fluid are both similar and different.

Pediatr Pulmonol 2018 04 6;53(4):475-482. Epub 2018 Feb 6.

Section of Pediatric Pulmonology, Allergy and Sleep Medicine, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana.

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http://dx.doi.org/10.1002/ppul.23953DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6542268PMC
April 2018

RNA polymerases IV and V influence the 3' boundaries of Polymerase II transcription units in Arabidopsis.

RNA Biol 2018 02 21;15(2):269-279. Epub 2017 Dec 21.

b Center for Genomics and Bioinformatics, Indiana University , Bloomington , Indiana , USA.

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http://dx.doi.org/10.1080/15476286.2017.1409930DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5798951PMC
February 2018

Genes linked to species diversity in a sexually dimorphic communication signal in electric fish.

J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2018 01 20;204(1):93-112. Epub 2017 Oct 20.

Department of Biology, Indiana University, Jordan Hall, 1001 E. 3rd St., Bloomington, IN, 47405, USA.

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http://dx.doi.org/10.1007/s00359-017-1223-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5817889PMC
January 2018

Complete Genome Sequence of the Pathogenic Type Strain ATCC 27562.

Genome Announc 2017 Aug 31;5(35). Epub 2017 Aug 31.

Center for Genomics and Bioinformatics, Indiana University Bloomington, Bloomington, Indiana, USA

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http://dx.doi.org/10.1128/genomeA.00907-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5578856PMC
August 2017

Complete Transcriptome RNA-Seq.

Methods Mol Biol 2017 ;1513:141-162

Medical Sciences Program, Indiana University School of Medicine, 1001 East 3rd Street, Bloomington, IN, 47405, USA.

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http://dx.doi.org/10.1007/978-1-4939-6539-7_10DOI Listing
January 2018

Speciation and ecological success in dimly lit waters: horizontal gene transfer in a green sulfur bacteria bloom unveiled by metagenomic assembly.

ISME J 2017 01 8;11(1):201-211. Epub 2016 Jul 8.

Integrative Freshwater Ecology Group, Centro de Estudios Avanzados de Blanes, CEAB-CSIC. Accés Cala Sant Francesc, Girona, Spain.

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http://dx.doi.org/10.1038/ismej.2016.93DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5315485PMC
January 2017

Metagenomic Analysis of the Indian Ocean Picocyanobacterial Community: Structure, Potential Function and Evolution.

PLoS One 2016 19;11(5):e0155757. Epub 2016 May 19.

Science for Life Laboratory, Department of Ecology, Environment and Plant Sciences, Stockholm University, Box 1031, 171 21 Solna, Sweden.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0155757PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4890579PMC
July 2017

The distribution, diversity and function of predominant Thermoproteales in high-temperature environments of Yellowstone National Park.

Environ Microbiol 2016 12 30;18(12):4755-4769. Epub 2016 May 30.

Department of Land Resources and Environmental Sciences and Thermal Biology Institute, Montana State University, Bozeman, MT, 59175-3120, USA.

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http://dx.doi.org/10.1111/1462-2920.13366DOI Listing
December 2016

Ecophysiology of an uncultivated lineage of Aigarchaeota from an oxic, hot spring filamentous 'streamer' community.

ISME J 2016 Jan 3;10(1):210-24. Epub 2015 Jul 3.

Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA.

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http://dx.doi.org/10.1038/ismej.2015.83DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4681859PMC
January 2016

Concordance of bacterial communities of two tick species and blood of their shared rodent host.

Mol Ecol 2015 May 22;24(10):2566-79. Epub 2015 Apr 22.

Institute of Evolutionary Biology & Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, EH9 3JT, UK; Department of Biology, Indiana University, 1001 E 3rd St, Bloomington, IN, 47405, USA.

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http://dx.doi.org/10.1111/mec.13187DOI Listing
May 2015

Stranded Whole Transcriptome RNA-Seq for All RNA Types.

Curr Protoc Hum Genet 2015 Jan 20;84:11.14.1-11.14.23. Epub 2015 Jan 20.

Medical Sciences, Indiana University School of Medicine, Bloomington, Indiana.

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http://dx.doi.org/10.1002/0471142905.hg1114s84DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4337225PMC
January 2015

Effects of the endocrine-disrupting chemical DDT on self-renewal and differentiation of human mesenchymal stem cells.

Environ Health Perspect 2015 Jan 11;123(1):42-8. Epub 2014 Jul 11.

Center for Stem Cell Research and Regenerative Medicine, Tulane University School of Medicine, New Orleans, Louisiana, USA.

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http://dx.doi.org/10.1289/ehp.1408188DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286277PMC
January 2015

Saccharide breakdown and fermentation by the honey bee gut microbiome.

Environ Microbiol 2015 Mar 8;17(3):796-815. Epub 2014 Jul 8.

Department of Biology, Indiana University, Bloomington, IN, 47405, USA.

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http://dx.doi.org/10.1111/1462-2920.12526DOI Listing
March 2015

Community structure and function of high-temperature chlorophototrophic microbial mats inhabiting diverse geothermal environments.

Front Microbiol 2013 3;4:106. Epub 2013 Jun 3.

Department of Land Resources and Environmental Sciences, Montana State University , Bozeman, MT , USA ; Thermal Biology Institute, Montana State University , Bozeman, MT , USA.

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http://dx.doi.org/10.3389/fmicb.2013.00106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3669762PMC
June 2013

Phylogenetic and Functional Analysis of Metagenome Sequence from High-Temperature Archaeal Habitats Demonstrate Linkages between Metabolic Potential and Geochemistry.

Front Microbiol 2013 15;4:95. Epub 2013 May 15.

Department of Land Resources and Environmental Sciences, Montana State University Bozeman, MT, USA ; Thermal Biology Institute, Montana State University Bozeman, MT, USA.

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http://dx.doi.org/10.3389/fmicb.2013.00095DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3654217PMC
May 2013

The YNP Metagenome Project: Environmental Parameters Responsible for Microbial Distribution in the Yellowstone Geothermal Ecosystem.

Front Microbiol 2013 6;4:67. Epub 2013 May 6.

Department of Land Resources and Environmental Sciences, Montana State University Bozeman MT, USA ; Thermal Biology Institute, Montana State University Bozeman MT, USA.

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http://dx.doi.org/10.3389/fmicb.2013.00067DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3644721PMC
May 2013

Metatranscriptomic analyses of chlorophototrophs of a hot-spring microbial mat.

ISME J 2011 Aug 23;5(8):1279-90. Epub 2011 Jun 23.

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

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http://www.nature.com/articles/ismej201137
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http://dx.doi.org/10.1038/ismej.2011.37DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3146272PMC
August 2011

Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic trees.

PLoS One 2011 Mar 18;6(3):e18011. Epub 2011 Mar 18.

Department of Evolution and Ecology, University of California Davis 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.0018011PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3060911PMC
March 2011

Characterization of Prochlorococcus clades from iron-depleted oceanic regions.

Proc Natl Acad Sci U S A 2010 Sep 23;107(37):16184-9. Epub 2010 Aug 23.

J Craig Venter Institute, Rockville, MD 20855, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.1009513107
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http://dx.doi.org/10.1073/pnas.1009513107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2941326PMC
September 2010

A catalog of reference genomes from the human microbiome.

Science 2010 May;328(5981):994-9

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http://dx.doi.org/10.1126/science.1183605DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2940224PMC
May 2010

Distribution of microbial terpenoid lipid cyclases in the global ocean metagenome.

ISME J 2009 Mar 27;3(3):352-63. Epub 2008 Nov 27.

Department of Earth and Planetary Sciences, Harvard University, 20 Oxford Street, Cambridge, MA 02138, USA.

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http://www.nature.com/articles/ismej2008116
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http://dx.doi.org/10.1038/ismej.2008.116DOI Listing
March 2009

The dog genome: survey sequencing and comparative analysis.

Science 2003 Sep;301(5641):1898-903

The Institute for Genomic Research, Rockville, MD 20850, USA.

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http://dx.doi.org/10.1126/science.1086432DOI Listing
September 2003

The genome sequence of the malaria mosquito Anopheles gambiae.

Authors:
Robert A Holt G Mani Subramanian Aaron Halpern Granger G Sutton Rosane Charlab Deborah R Nusskern Patrick Wincker Andrew G Clark José M C Ribeiro Ron Wides Steven L Salzberg Brendan Loftus Mark Yandell William H Majoros Douglas B Rusch Zhongwu Lai Cheryl L Kraft Josep F Abril Veronique Anthouard Peter Arensburger Peter W Atkinson Holly Baden Veronique de Berardinis Danita Baldwin Vladimir Benes Jim Biedler Claudia Blass Randall Bolanos Didier Boscus Mary Barnstead Shuang Cai Angela Center Kabir Chaturverdi George K Christophides Mathew A Chrystal Michele Clamp Anibal Cravchik Val Curwen Ali Dana Art Delcher Ian Dew Cheryl A Evans Michael Flanigan Anne Grundschober-Freimoser Lisa Friedli Zhiping Gu Ping Guan Roderic Guigo Maureen E Hillenmeyer Susanne L Hladun James R Hogan Young S Hong Jeffrey Hoover Olivier Jaillon Zhaoxi Ke Chinnappa Kodira Elena Kokoza Anastasios Koutsos Ivica Letunic Alex Levitsky Yong Liang Jhy-Jhu Lin Neil F Lobo John R Lopez Joel A Malek Tina C McIntosh Stephan Meister Jason Miller Clark Mobarry Emmanuel Mongin Sean D Murphy David A O'Brochta Cynthia Pfannkoch Rong Qi Megan A Regier Karin Remington Hongguang Shao Maria V Sharakhova Cynthia D Sitter Jyoti Shetty Thomas J Smith Renee Strong Jingtao Sun Dana Thomasova Lucas Q Ton Pantelis Topalis Zhijian Tu Maria F Unger Brian Walenz Aihui Wang Jian Wang Mei Wang Xuelan Wang Kerry J Woodford Jennifer R Wortman Martin Wu Alison Yao Evgeny M Zdobnov Hongyu Zhang Qi Zhao Shaying Zhao Shiaoping C Zhu Igor Zhimulev Mario Coluzzi Alessandra della Torre Charles W Roth Christos Louis Francis Kalush Richard J Mural Eugene W Myers Mark D Adams Hamilton O Smith Samuel Broder Malcolm J Gardner Claire M Fraser Ewan Birney Peer Bork Paul T Brey J Craig Venter Jean Weissenbach Fotis C Kafatos Frank H Collins Stephen L Hoffman

Science 2002 Oct;298(5591):129-49

Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA.

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http://ccb.jhu.edu/people/salzberg/docs/Anopheles-gambiae-re
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http://www.sciencemag.org/cgi/doi/10.1126/science.1076181
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http://dx.doi.org/10.1126/science.1076181DOI Listing
October 2002

A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome.

Authors:
Richard J Mural Mark D Adams Eugene W Myers Hamilton O Smith George L Gabor Miklos Ron Wides Aaron Halpern Peter W Li Granger G Sutton Joe Nadeau Steven L Salzberg Robert A Holt Chinnappa D Kodira Fu Lu Lin Chen Zuoming Deng Carlos C Evangelista Weiniu Gan Thomas J Heiman Jiayin Li Zhenya Li Gennady V Merkulov Natalia V Milshina Ashwinikumar K Naik Rong Qi Bixiong Chris Shue Aihui Wang Jian Wang Xin Wang Xianghe Yan Jane Ye Shibu Yooseph Qi Zhao Liansheng Zheng Shiaoping C Zhu Kendra Biddick Randall Bolanos Arthur L Delcher Ian M Dew Daniel Fasulo Michael J Flanigan Daniel H Huson Saul A Kravitz Jason R Miller Clark M Mobarry Knut Reinert Karin A Remington Qing Zhang Xiangqun H Zheng Deborah R Nusskern Zhongwu Lai Yiding Lei Wenyan Zhong Alison Yao Ping Guan Rui-Ru Ji Zhiping Gu Zhen-Yuan Wang Fei Zhong Chunlin Xiao Chia-Chien Chiang Mark Yandell Jennifer R Wortman Peter G Amanatides Suzanne L Hladun Eric C Pratts Jeffery E Johnson Kristina L Dodson Kerry J Woodford Cheryl A Evans Barry Gropman Douglas B Rusch Eli Venter Mei Wang Thomas J Smith Jarrett T Houck Donald E Tompkins Charles Haynes Debbie Jacob Soo H Chin David R Allen Carl E Dahlke Robert Sanders Kelvin Li Xiangjun Liu Alexander A Levitsky William H Majoros Quan Chen Ashley C Xia John R Lopez Michael T Donnelly Matthew H Newman Anna Glodek Cheryl L Kraft Marc Nodell Feroze Ali Hui-Jin An Danita Baldwin-Pitts Karen Y Beeson Shuang Cai Mark Carnes Amy Carver Parris M Caulk Angela Center Yen-Hui Chen Ming-Lai Cheng My D Coyne Michelle Crowder Steven Danaher Lionel B Davenport Raymond Desilets Susanne M Dietz Lisa Doup Patrick Dullaghan Steven Ferriera Carl R Fosler Harold C Gire Andres Gluecksmann Jeannine D Gocayne Jonathan Gray Brit Hart Jason Haynes Jeffery Hoover Tim Howland Chinyere Ibegwam Mena Jalali David Johns Leslie Kline Daniel S Ma Steven MacCawley Anand Magoon Felecia Mann David May Tina C McIntosh Somil Mehta Linda Moy Mee C Moy Brian J Murphy Sean D Murphy Keith A Nelson Zubeda Nuri Kimberly A Parker Alexandre C Prudhomme Vinita N Puri Hina Qureshi John C Raley Matthew S Reardon Megan A Regier Yu-Hui C Rogers Deanna L Romblad Jakob Schutz John L Scott Richard Scott Cynthia D Sitter Michella Smallwood Arlan C Sprague Erin Stewart Renee V Strong Ellen Suh Karena Sylvester Reginald Thomas Ni Ni Tint Christopher Tsonis Gary Wang George Wang Monica S Williams Sherita M Williams Sandra M Windsor Keriellen Wolfe Mitchell M Wu Jayshree Zaveri Kabir Chaturvedi Andrei E Gabrielian Zhaoxi Ke Jingtao Sun Gangadharan Subramanian J Craig Venter Cynthia M Pfannkoch Mary Barnstead Lisa D Stephenson

Science 2002 May;296(5573):1661-71

Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA.

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http://dx.doi.org/10.1126/science.1069193DOI Listing
May 2002