Publications by authors named "Michael C Wendl"

67Publications

Integrated transcriptomic-genomic tool Texomer profiles cancer tissues.

Nat Methods 2019 05 15;16(5):401-404. Epub 2019 Apr 15.

Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

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http://dx.doi.org/10.1038/s41592-019-0388-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7337246PMC
May 2019

Systematic Analysis of Splice-Site-Creating Mutations in Cancer.

Cell Rep 2018 04;23(1):270-281.e3

Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Division of Oncology, Washington University in St. Louis, St. Louis, MO 63110, USA; Department of Genetics, Washington University in St. Louis, St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2018.03.052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6055527PMC
April 2018

Driver Fusions and Their Implications in the Development and Treatment of Human Cancers.

Cell Rep 2018 04;23(1):227-238.e3

Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Department of Genetics, Washington University in St. Louis, St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2018.03.050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5916809PMC
April 2018

Units: Don't tamper with SI-unit consistency.

Authors:
Michael C Wendl

Nature 2017 09;549(7671):160

Washington University, St Louis, Missouri, USA.

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http://dx.doi.org/10.1038/549160dDOI Listing
September 2017

Pseudonymous fame.

Authors:
Michael C Wendl

Science 2016 Mar;351(6280):1406

McDonnell Genome Institute and Departments of Mathematics and Genetics, Washington University, St. Louis, MO 63108, USA.

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http://dx.doi.org/10.1126/science.351.6280.1406DOI Listing
March 2016

Optimizing cancer genome sequencing and analysis.

Cell Syst 2015 Sep;1(3):210-223

The McDonnell Genome Institute, Washington University, St. Louis, MO, USA, 63108 ; Department of Genetics, Washington University, St. Louis, MO, USA, 63108 ; Siteman Cancer Center, Washington University, St. Louis, MO, USA, 63108 ; Department of Medicine, Washington University, St. Louis, MO, USA, 63108.

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http://dx.doi.org/10.1016/j.cels.2015.08.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4669575PMC
September 2015

Age-related mutations associated with clonal hematopoietic expansion and malignancies.

Nat Med 2014 Dec 19;20(12):1472-8. Epub 2014 Oct 19.

1] The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, USA. [2] Department of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA. [3] Department of Genetics, Washington University in St. Louis, St. Louis, Missouri, USA. [4] Siteman Cancer Center, Washington University in St. Louis, St. Louis, Missouri, USA.

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http://dx.doi.org/10.1038/nm.3733DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4313872PMC
December 2014

Expanding the computational toolbox for mining cancer genomes.

Nat Rev Genet 2014 Aug 8;15(8):556-70. Epub 2014 Jul 8.

Department of Computer Science and Center for Computational Molecular Biology, Brown University, 115 Waterman Street, Providence, Rhode Island 02912, USA.

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http://www.nature.com/articles/nrg3767
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http://dx.doi.org/10.1038/nrg3767DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4168012PMC
August 2014

Integrated analysis of germline and somatic variants in ovarian cancer.

Nat Commun 2014 ;5:3156

1] The Genome Institute, Washington University, St. Louis, Missouri 63108, USA [2] Department of Genetics, Washington University, St. Louis, Missouri 63108, USA [3] Siteman Cancer Center, Washington University, St. Louis, Missouri 63108, USA [4] Department of Medicine, Washington University, St. Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1038/ncomms4156DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4025965PMC
March 2016

MSIsensor: microsatellite instability detection using paired tumor-normal sequence data.

Bioinformatics 2014 Apr 25;30(7):1015-6. Epub 2013 Dec 25.

Departments of Genetics and Mathematics, The Genome Institute, Department of Genetics, Division of Statistical Genomics, Department of Medicine and Siteman Cancer Center, Washington University in St. Louis, MO 63108, USA.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btt755DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3967115PMC
April 2014

Differences that matter in cancer genomics.

Nat Biotechnol 2013 Oct;31(10):892-3

1] The Genome Institute, Washington University, St. Louis, Missouri, USA. [2] Department of Genetics, Washington University, St. Louis, Missouri, USA. [3] Department of Medicine, Washington University, St. Louis, Missouri, USA. [4] Siteman Cancer Center, Washington University, St. Louis, Missouri, USA.

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http://dx.doi.org/10.1038/nbt.2715DOI Listing
October 2013

Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia.

N Engl J Med 2013 05 1;368(22):2059-74. Epub 2013 May 1.

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http://dx.doi.org/10.1056/NEJMoa1301689DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3767041PMC
May 2013

Advances for studying clonal evolution in cancer.

Cancer Lett 2013 Nov 23;340(2):212-9. Epub 2013 Jan 23.

Department of Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, MO 63110, USA; The Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S03043835130003
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http://dx.doi.org/10.1016/j.canlet.2012.12.028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3783624PMC
November 2013

Coverage theories for metagenomic DNA sequencing based on a generalization of Stevens' theorem.

J Math Biol 2013 Nov 11;67(5):1141-61. Epub 2012 Sep 11.

The Genome Institute, Washington University, St. Louis, MO, 63108, USA,

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http://dx.doi.org/10.1007/s00285-012-0586-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3795925PMC
November 2013

Analysis of next-generation genomic data in cancer: accomplishments and challenges.

Hum Mol Genet 2010 Oct 15;19(R2):R188-96. Epub 2010 Sep 15.

Department of Genetics, The Genome Center at Washington University School of Medicine, 4444 Forest Park Blvd., St Louis, MO 63108, USA.

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http://dx.doi.org/10.1093/hmg/ddq391DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2953747PMC
October 2010

The theory of discovering rare variants via DNA sequencing.

BMC Genomics 2009 Oct 20;10:485. Epub 2009 Oct 20.

The Genome Center and Department of Genetics, Washington University, St Louis, MO 63108, USA.

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http://dx.doi.org/10.1186/1471-2164-10-485DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2778663PMC
October 2009

Statistical aspects of discerning indel-type structural variation via DNA sequence alignment.

BMC Genomics 2009 Aug 5;10:359. Epub 2009 Aug 5.

The Genome Center and Department of Genetics, Washington University, St Louis, MO 63108, USA.

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http://dx.doi.org/10.1186/1471-2164-10-359DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2748092PMC
August 2009

Technology takes on deadlines for fetal human rights.

Authors:
Michael C Wendl

Nature 2009 Apr;458(7240):831

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http://dx.doi.org/10.1038/458831cDOI Listing
April 2009

Somatic mutations affect key pathways in lung adenocarcinoma.

Nature 2008 Oct;455(7216):1069-75

The Genome Center at Washington University, Department of Genetics, Washington University School of Medicine, St Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1038/nature07423DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2694412PMC
October 2008

Aspects of coverage in medical DNA sequencing.

BMC Bioinformatics 2008 May 16;9:239. Epub 2008 May 16.

Genome Sequencing Center and Department of Genetics, Washington University, St Louis MO 63108, USA.

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http://dx.doi.org/10.1186/1471-2105-9-239DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2430974PMC
May 2008

H-index: however ranked, citations need context.

Authors:
Michael C Wendl

Nature 2007 Sep;449(7161):403

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http://dx.doi.org/10.1038/449403bDOI Listing
September 2007

Algebraic correction methods for computational assessment of clone overlaps in DNA fingerprint mapping.

Authors:
Michael C Wendl

BMC Bioinformatics 2007 Apr 18;8:127. Epub 2007 Apr 18.

Genome Sequencing Center, Washington University, St. Louis, MO 63108, USA.

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http://dx.doi.org/10.1186/1471-2105-8-127DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1868038PMC
April 2007

PolyScan: an automatic indel and SNP detection approach to the analysis of human resequencing data.

Genome Res 2007 May 6;17(5):659-66. Epub 2007 Apr 6.

Genome Sequencing Center, Washington University School of Medicine, St. Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1101/gr.6151507DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855178PMC
May 2007

A general coverage theory for shotgun DNA sequencing.

Authors:
Michael C Wendl

J Comput Biol 2006 Jul-Aug;13(6):1177-96

Genome Sequencing Center, Washington University, St. Louis, Missouri 63108, USA.

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http://www.liebertpub.com/doi/10.1089/cmb.2006.13.1177
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http://dx.doi.org/10.1089/cmb.2006.13.1177DOI Listing
October 2006

Occupancy modeling of coverage distribution for whole genome shotgun DNA sequencing.

Authors:
Michael C Wendl

Bull Math Biol 2006 Jan 24;68(1):179-96. Epub 2006 Mar 24.

Genome Sequencing Center, Washington University, 4444 Forest Park Boulevard, Campus Box 8501, St. Louis, MO 63108, USA.

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http://dx.doi.org/10.1007/s11538-005-9021-4DOI Listing
January 2006

Extension of Lander-Waterman theory for sequencing filtered DNA libraries.

BMC Bioinformatics 2005 Oct 10;6:245. Epub 2005 Oct 10.

Genome Sequencing Center, Washington University, St. Louis, MO 63108, USA.

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http://dx.doi.org/10.1186/1471-2105-6-245DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1280921PMC
October 2005

Bioweapons could kill more in one strike than guns.

Authors:
Michael C Wendl

Nature 2005 Sep;437(7056):192

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http://dx.doi.org/10.1038/437192bDOI Listing
September 2005

The question of forbidden knowledge.

Authors:
Michael C Wendl

Science 2005 Jun;308(5728):1549-50; author reply 1549-50

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June 2005

Probabilistic assessment of clone overlaps in DNA fingerprint mapping via a priori models.

Authors:
Michael C Wendl

J Comput Biol 2005 Apr;12(3):283-97

Genome Sequencing Center, Washington University, St. Louis, MO 63108, USA.

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http://dx.doi.org/10.1089/cmb.2005.12.283DOI Listing
April 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.

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http://dx.doi.org/10.1038/nature03466DOI Listing
April 2005

Gap statistics for whole genome shotgun DNA sequencing projects.

Bioinformatics 2004 Jul 12;20(10):1527-34. Epub 2004 Feb 12.

Genome Sequencing Center, Washington University School of Medicine, Box 8501, 4444 Forest Park Blvd., Saint Louis, MO 63108 USA.

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http://dx.doi.org/10.1093/bioinformatics/bth120DOI Listing
July 2004

Open-source answer to bibliography problem.

Nature 2003 Aug;424(6952):995

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http://www.nature.com/articles/424995c
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http://dx.doi.org/10.1038/424995cDOI Listing
August 2003

The DNA sequence of human chromosome 7.

Authors:
Ladeana W Hillier Robert S Fulton Lucinda A Fulton Tina A Graves Kymberlie H Pepin Caryn Wagner-McPherson Dan Layman Jason Maas Sara Jaeger Rebecca Walker Kristine Wylie Mandeep Sekhon Michael C Becker Michelle D O'Laughlin Mark E Schaller Ginger A Fewell Kimberly D Delehaunty Tracie L Miner William E Nash Matt Cordes Hui Du Hui Sun Jennifer Edwards Holland Bradshaw-Cordum Johar Ali Stephanie Andrews Amber Isak Andrew Vanbrunt Christine Nguyen Feiyu Du Betty Lamar Laura Courtney Joelle Kalicki Philip Ozersky Lauren Bielicki Kelsi Scott Andrea Holmes Richard Harkins Anthony Harris Cynthia Madsen Strong Shunfang Hou Chad Tomlinson Sara Dauphin-Kohlberg Amy Kozlowicz-Reilly Shawn Leonard Theresa Rohlfing Susan M Rock Aye-Mon Tin-Wollam Amanda Abbott Patrick Minx Rachel Maupin Catrina Strowmatt Phil Latreille Nancy Miller Doug Johnson Jennifer Murray Jeffrey P Woessner Michael C Wendl Shiaw-Pyng Yang Brian R Schultz John W Wallis John Spieth Tamberlyn A Bieri Joanne O Nelson Nicolas Berkowicz Patricia E Wohldmann Lisa L Cook Matthew T Hickenbotham James Eldred Donald Williams Joseph A Bedell Elaine R Mardis Sandra W Clifton Stephanie L Chissoe Marco A Marra Christopher Raymond Eric Haugen Will Gillett Yang Zhou Rose James Karen Phelps Shawn Iadanoto Kerry Bubb Elizabeth Simms Ruth Levy James Clendenning Rajinder Kaul W James Kent Terrence S Furey Robert A Baertsch Michael R Brent Evan Keibler Paul Flicek Peer Bork Mikita Suyama Jeffrey A Bailey Matthew E Portnoy David Torrents Asif T Chinwalla Warren R Gish Sean R Eddy John D McPherson Maynard V Olson Evan E Eichler Eric D Green Robert H Waterston Richard K Wilson

Nature 2003 Jul;424(6945):157-64

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/nature01782DOI Listing
July 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

Generalized gap model for bacterial artificial chromosome clone fingerprint mapping and shotgun sequencing.

Genome Res 2002 Dec;12(12):1943-9

Washington University School of Medicine, St. Louis, Missouri 63108, USA.

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http://www.genome.org/cgi/doi/10.1101/gr.655102
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http://dx.doi.org/10.1101/gr.655102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC187573PMC
December 2002