Simon Twigger

Simon Twigger

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Simon Twigger

Publications by authors named "Simon Twigger"

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Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder.

Nat Neurosci 2017 Apr 6;20(4):602-611. Epub 2017 Mar 6.

The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada.

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http://dx.doi.org/10.1038/nn.4524DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5501701PMC
April 2017

The Rat Genome Database pathway portal.

Database (Oxford) 2011 8;2011:bar010. Epub 2011 Apr 8.

Human and Molecular Genetics Center, Medical College of Wisconsin, WI, 53226-3548, USA.

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http://dx.doi.org/10.1093/database/bar010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072770PMC
September 2011

Using multiple ontologies to integrate complex biological data.

Comp Funct Genomics 2005 ;6(7-8):373-8

Human and Molecular Genetics Center Medical College of Wisconsin Milwaukee WI 53226 USA.

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http://dx.doi.org/10.1002/cfg.498DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447497PMC
July 2011

The rat genome database curators: who, what, where, why.

PLoS Comput Biol 2009 Nov 26;5(11):e1000582. Epub 2009 Nov 26.

Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.

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http://dx.doi.org/10.1371/journal.pcbi.1000582DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2775909PMC
November 2009

Low cost, scalable proteomics data analysis using Amazon's cloud computing services and open source search algorithms.

J Proteome Res 2009 Jun;8(6):3148-53

Biotechnology and Bioengineering Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, USA.

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http://dx.doi.org/10.1021/pr800970zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2691775PMC
June 2009

The Rat Genome Database 2009: variation, ontologies and pathways.

Nucleic Acids Res 2009 Jan 7;37(Database issue):D744-9. Epub 2008 Nov 7.

Department of Physiology and Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI, USA.

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http://dx.doi.org/10.1093/nar/gkn842DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686558PMC
January 2009

Big data: The future of biocuration.

Nature 2008 Sep;455(7209):47-50

The Zebrafish Information Network, 5291 University of Oregon, Eugene, Oregon 97403-5291, USA.

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http://www.nature.com/articles/455047a
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http://dx.doi.org/10.1038/455047aDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2819144PMC
September 2008

Comparative proteomic analysis of PAI-1 and TNF-alpha-derived endothelial microparticles.

Proteomics 2008 Jun;8(12):2430-46

Department of Surgery, Medical College of Wisconsin and Children's Research Institute, Milwaukee, WI 53226, USA.

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http://dx.doi.org/10.1002/pmic.200701029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4753841PMC
June 2008

Protein composition of plasminogen activator inhibitor type 1-derived endothelial microparticles.

Shock 2008 Apr;29(4):504-11

Department of Surgery, Medical College of Wisconsin and Children's Research Institute, Milwaukee, WIsconsin 53226, USA.

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http://dx.doi.org/10.1097/shk.0b013e3181454898DOI Listing
April 2008

The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts.

Authors:
Chisato Yamasaki Katsuhiko Murakami Yasuyuki Fujii Yoshiharu Sato Erimi Harada Jun-ichi Takeda Takayuki Taniya Ryuichi Sakate Shingo Kikugawa Makoto Shimada Motohiko Tanino Kanako O Koyanagi Roberto A Barrero Craig Gough Hong-Woo Chun Takuya Habara Hideki Hanaoka Yosuke Hayakawa Phillip B Hilton Yayoi Kaneko Masako Kanno Yoshihiro Kawahara Toshiyuki Kawamura Akihiro Matsuya Naoki Nagata Kensaku Nishikata Akiko Ogura Noda Shin Nurimoto Naomi Saichi Hiroaki Sakai Ryoko Sanbonmatsu Rie Shiba Mami Suzuki Kazuhiko Takabayashi Aiko Takahashi Takuro Tamura Masayuki Tanaka Susumu Tanaka Fusano Todokoro Kaori Yamaguchi Naoyuki Yamamoto Toshihisa Okido Jun Mashima Aki Hashizume Lihua Jin Kyung-Bum Lee Yi-Chueh Lin Asami Nozaki Katsunaga Sakai Masahito Tada Satoru Miyazaki Takashi Makino Hajime Ohyanagi Naoki Osato Nobuhiko Tanaka Yoshiyuki Suzuki Kazuho Ikeo Naruya Saitou Hideaki Sugawara Claire O'Donovan Tamara Kulikova Eleanor Whitfield Brian Halligan Mary Shimoyama Simon Twigger Kei Yura Kouichi Kimura Tomohiro Yasuda Tetsuo Nishikawa Yutaka Akiyama Chie Motono Yuri Mukai Hideki Nagasaki Makiko Suwa Paul Horton Reiko Kikuno Osamu Ohara Doron Lancet Eric Eveno Esther Graudens Sandrine Imbeaud Marie Anne Debily Yoshihide Hayashizaki Clara Amid Michael Han Andreas Osanger Toshinori Endo Michael A Thomas Mika Hirakawa Wojciech Makalowski Mitsuteru Nakao Nam-Soon Kim Hyang-Sook Yoo Sandro J De Souza Maria de Fatima Bonaldo Yoshihito Niimura Vladimir Kuryshev Ingo Schupp Stefan Wiemann Matthew Bellgard Masafumi Shionyu Libin Jia Danielle Thierry-Mieg Jean Thierry-Mieg Lukas Wagner Qinghua Zhang Mitiko Go Shinsei Minoshima Masafumi Ohtsubo Kousuke Hanada Peter Tonellato Takao Isogai Ji Zhang Boris Lenhard Sangsoo Kim Zhu Chen Ursula Hinz Anne Estreicher Kenta Nakai Izabela Makalowska Winston Hide Nicola Tiffin Laurens Wilming Ranajit Chakraborty Marcelo Bento Soares Maria Luisa Chiusano Yutaka Suzuki Charles Auffray Yumi Yamaguchi-Kabata Takeshi Itoh Teruyoshi Hishiki Satoshi Fukuchi Ken Nishikawa Sumio Sugano Nobuo Nomura Yoshio Tateno Tadashi Imanishi Takashi Gojobori

Nucleic Acids Res 2008 Jan 18;36(Database issue):D793-9. Epub 2007 Dec 18.

Japan Biological Information Research Center, Japan Biological Informatics Consortium, Japan.

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http://dx.doi.org/10.1093/nar/gkm999DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238988PMC
January 2008

Structures of proteins of biomedical interest from the Center for Eukaryotic Structural Genomics.

J Struct Funct Genomics 2007 Sep 6;8(2-3):73-84. Epub 2007 Sep 6.

Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.

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http://dx.doi.org/10.1007/s10969-007-9023-6DOI Listing
September 2007

The Rat Genome Database, update 2007--easing the path from disease to data and back again.

Nucleic Acids Res 2007 Jan 6;35(Database issue):D658-62. Epub 2006 Dec 6.

Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.

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https://nar.oxfordjournals.org/content/35/suppl_1/D658.full-
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http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkl988
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http://dx.doi.org/10.1093/nar/gkl988DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1761441PMC
January 2007

Exploring phenotypic data at the rat genome database.

Curr Protoc Bioinformatics 2006 Jul;Chapter 1:Unit 1.14

Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.

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http://dx.doi.org/10.1002/0471250953.bi0114s14DOI Listing
July 2006

A new method for identifying informative genetic markers in selectively bred rats.

Mamm Genome 2005 Oct 29;16(10):784-91. Epub 2005 Oct 29.

Department of Human Genetics, Emory University, Whitehead 301, 615 Michael Street, Atlanta, Georgia 30322, USA.

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http://dx.doi.org/10.1007/s00335-005-0047-6DOI Listing
October 2005

DeNovoID: a web-based tool for identifying peptides from sequence and mass tags deduced from de novo peptide sequencing by mass spectroscopy.

Nucleic Acids Res 2005 Jul;33(Web Server issue):W376-81

Bioinformatics Research Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53213, USA.

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http://dx.doi.org/10.1093/nar/gki461DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1160222PMC
July 2005

Simultaneous quantification and identification using 18O labeling with an ion trap mass spectrometer and the analysis software application "ZoomQuant".

J Am Soc Mass Spectrom 2005 Jun 15;16(6):916-25. Epub 2005 Apr 15.

National Proteomics Research Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53213, USA.

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http://dx.doi.org/10.1016/j.jasms.2005.02.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771642PMC
June 2005

Using Comparative Genomics to Leverage Animal Models in the Identification of Cancer Genes. Examples in Prostate Cancer.

Cancer Genomics Proteomics 2005 May-Jun;2(3):137-144. Epub 2005 May 1.

Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin, U.S.A.

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May 2005

ZoomQuant: an application for the quantitation of stable isotope labeled peptides.

J Am Soc Mass Spectrom 2005 Mar 13;16(3):302-6. Epub 2005 Jan 13.

Bioinformatics, Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53213, USA.

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http://dx.doi.org/10.1016/j.jasms.2004.11.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2793075PMC
March 2005

Peptide identification using peptide amino acid attribute vectors.

J Proteome Res 2004 Jul-Aug;3(4):813-20

Bioinformatics Research Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53213, USA.

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http://dx.doi.org/10.1021/pr0499444DOI Listing
January 2005

Of rats and men.

Authors:
Simon N Twigger

Genome Biol 2004 25;5(3):314. Epub 2004 Feb 25.

Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI 53211, USA.

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http://dx.doi.org/10.1186/gb-2004-5-3-314DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC395761PMC
October 2004

ProMoST (Protein Modification Screening Tool): a web-based tool for mapping protein modifications on two-dimensional gels.

Nucleic Acids Res 2004 Jul;32(Web Server issue):W638-44

Bioinformatics Research Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53213, USA.

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http://dx.doi.org/10.1093/nar/gkh356DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC441494PMC
July 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

ChromSorter PC: a database of chromosomal regions associated with human prostate cancer.

BMC Genomics 2004 Apr 28;5(1):27. Epub 2004 Apr 28.

Department of Pathology, Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA.

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http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2
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http://dx.doi.org/10.1186/1471-2164-5-27DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC416659PMC
April 2004

Phylogenetics of rat inbred strains.

Mamm Genome 2003 Jan;14(1):61-4

Bioinformatics Research Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, USA.

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http://link.springer.com/10.1007/s00335-002-2204-5
Publisher Site
http://dx.doi.org/10.1007/s00335-002-2204-5DOI Listing
January 2003

Rat Genome Database (RGD): mapping disease onto the genome.

Nucleic Acids Res 2002 Jan;30(1):125-8

Bioinformatics Research Center and Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC99132PMC
http://dx.doi.org/10.1093/nar/30.1.125DOI Listing
January 2002