Publications by authors named "Simon Cawley"

22Publications

Differential dropout among SNP genotypes and impacts on association tests.

Authors:
Ke Hao Simon Cawley

Hum Hered 2007 7;63(3-4):219-28. Epub 2007 Mar 7.

Algorithm and Data Analysis, Affymetrix, Inc., Santa Clara, CA 95051, USA.

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https://www.karger.com/Article/FullText/100480
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http://dx.doi.org/10.1159/000100480DOI Listing
June 2007

Alternative base calling method for resequencing microarrays.

Conf Proc IEEE Eng Med Biol Soc 2005;2005:2809-12

Affymetrix Inc., Santa Clara, CA.

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http://dx.doi.org/10.1109/IEMBS.2005.1617057DOI Listing
October 2012

Multiple testing methods for ChIP-Chip high density oligonucleotide array data.

J Comput Biol 2006 Apr;13(3):579-613

Department of Statistics, University of Wisconsin, Madison, Madison, WI 53706, USA.

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http://dx.doi.org/10.1089/cmb.2006.13.579DOI Listing
April 2006

ANOSVA: a statistical method for detecting splice variation from expression data.

Bioinformatics 2005 Jun;21 Suppl 1:i107-15

Affymetrix, Inc. 3380 Central Expressway, Santa Clara, CA 95051, USA.

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http://dx.doi.org/10.1093/bioinformatics/bti1010DOI Listing
June 2005

Accurate identification of novel human genes through simultaneous gene prediction in human, mouse, and rat.

Genome Res 2004 Apr;14(4):661-4

Department of Electrical Engineering, University of California-Berkeley, Berkeley, California 94720, USA.

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http://dx.doi.org/10.1101/gr.1939804DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC383310PMC
April 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

HMM sampling and applications to gene finding and alternative splicing.

Bioinformatics 2003 Oct;19 Suppl 2:ii36-41

Affymetrix, Emeryville, CA 94608, USA.

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http://dx.doi.org/10.1093/bioinformatics/btg1057DOI Listing
October 2003

SLAM web server for comparative gene finding and alignment.

Nucleic Acids Res 2003 Jul;31(13):3507-9

Affymetrix Inc., 6550 Vallejo St, Suite 100, Emeryville, CA 94608, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC168989PMC
http://dx.doi.org/10.1093/nar/gkg583DOI Listing
July 2003

SLAM: cross-species gene finding and alignment with a generalized pair hidden Markov model.

Genome Res 2003 Mar;13(3):496-502

Department of Statistics, University of California, Berkeley, California 94720, USA.

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http://www.genome.org/cgi/doi/10.1101/gr.424203
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http://dx.doi.org/10.1101/gr.424203DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC430255PMC
March 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

Applications of generalized pair hidden Markov models to alignment and gene finding problems.

J Comput Biol 2002 ;9(2):389-99

Department of Mathematics, University of California Berkeley, Berkeley, CA 94720, USA.

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http://www.liebertpub.com/doi/10.1089/10665270252935520
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http://dx.doi.org/10.1089/10665270252935520DOI Listing
October 2002

Large-scale transcriptional activity in chromosomes 21 and 22.

Science 2002 May;296(5569):916-9

Affymetrix, Santa Clara, CA 95051, USA., National Cancer Institute, Bethesda, MD 20892, USA.

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http://dx.doi.org/10.1126/science.1068597DOI Listing
May 2002