David Shteynberg

David Shteynberg

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David Shteynberg

David Shteynberg

Publications by authors named "David Shteynberg"

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28Publications

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Flexible and Fast Mapping of Peptides to a Proteome with ProteoMapper.

J Proteome Res 2018 12 28;17(12):4337-4344. Epub 2018 Sep 28.

Institute for Systems Biology , 401 Terry Ave North , Seattle , Washington 98109 , United States.

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http://dx.doi.org/10.1021/acs.jproteome.8b00544DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6438762PMC
December 2018

An Open Data Format for Visualization and Analysis of Cross-Linked Mass Spectrometry Results.

J Am Soc Mass Spectrom 2016 11 28;27(11):1728-1734. Epub 2016 Jul 28.

Institute for Systems Biology, Seattle, Washington, 98109, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5061604PMC
http://dx.doi.org/10.1007/s13361-016-1435-8DOI Listing
November 2016

Tiered Human Integrated Sequence Search Databases for Shotgun Proteomics.

J Proteome Res 2016 11 12;15(11):4091-4100. Epub 2016 Sep 12.

Institute for Systems Biology , Seattle, Washington 98109, United States.

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http://dx.doi.org/10.1021/acs.jproteome.6b00445DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5096980PMC
November 2016

Opening a SWATH Window on Posttranslational Modifications: Automated Pursuit of Modified Peptides.

Mol Cell Proteomics 2016 Mar 24;15(3):1151-63. Epub 2015 Dec 24.

From the §Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109

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http://www.mcponline.org/lookup/doi/10.1074/mcp.M115.054478
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http://dx.doi.org/10.1074/mcp.M115.054478DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4813695PMC
March 2016

Processing shotgun proteomics data on the Amazon cloud with the trans-proteomic pipeline.

Mol Cell Proteomics 2015 Feb 23;14(2):399-404. Epub 2014 Nov 23.

From the ‡Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109.

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http://dx.doi.org/10.1074/mcp.O114.043380DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4350034PMC
February 2015

Combining results of multiple search engines in proteomics.

Mol Cell Proteomics 2013 Sep 29;12(9):2383-93. Epub 2013 May 29.

Institute for Systems Biology, Seattle, Washington 98109, USA.

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http://dx.doi.org/10.1074/mcp.R113.027797DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3769318PMC
September 2013

Software pipeline and data analysis for MS/MS proteomics: the trans-proteomic pipeline.

Methods Mol Biol 2011 ;694:169-89

Rosetta Biosoftware, Seattle, WA, USA.

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http://dx.doi.org/10.1007/978-1-60761-977-2_12DOI Listing
February 2011

Proteomic analyses using Grifola frondosa metalloendoprotease Lys-N.

J Proteome Res 2009 Mar;8(3):1415-22

Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, USA.

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http://dx.doi.org/10.1021/pr800774hDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2798736PMC
March 2009

Optimized peptide separation and identification for mass spectrometry based proteomics via free-flow electrophoresis.

J Proteome Res 2006 Sep;5(9):2241-9

Institute for Molecular Systems Molecular Biology, Swiss Federal Institute for Technology Zürich (ETH), Hoenggerberg 8093 Zürich, Switzerland.

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http://dx.doi.org/10.1021/pr0600632DOI Listing
September 2006

Gene finding in the chicken genome.

BMC Bioinformatics 2005 May 30;6:131. Epub 2005 May 30.

Institut Municipal d'Investigacio Medica, Universitat Pompeu Fabra, Centre de Regulacio Genomica, E08003 Barcelona, Catalonia, Spain.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-6-131DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1174864PMC
May 2005

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

Identification of rat genes by TWINSCAN gene prediction, RT-PCR, and direct sequencing.

Genome Res 2004 Apr;14(4):665-71

Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1101/gr.1959604DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC383311PMC
April 2004