Publications by authors named "Michael Seringhaus"

17Publications

Getting started in text mining: part two.

PLoS Comput Biol 2009 Jul 31;5(7):e1000411. Epub 2009 Jul 31.

University of Chicago, Chicago, Illinois, United States of America.

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http://dx.plos.org/10.1371/journal.pcbi.1000411
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http://dx.doi.org/10.1371/journal.pcbi.1000411DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2709911PMC
July 2009

Mismatch oligonucleotides in human and yeast: guidelines for probe design on tiling microarrays.

BMC Genomics 2008 Dec 31;9:635. Epub 2008 Dec 31.

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1186/1471-2164-9-635DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2642824PMC
December 2008

Seeking a new biology through text mining.

Cell 2008 Jul;134(1):9-13

University of Chicago, Chicago, IL 60637, USA.

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http://dx.doi.org/10.1016/j.cell.2008.06.029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2735884PMC
July 2008

Personalized genomic medicine with a patchwork, partially owned genome.

Yale J Biol Med 2007 Dec;80(4):145-51

Program on Neurogenetics, Yale University Medical School, New Haven, Connecticut 06511, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2347364PMC
December 2007

Manually structured digital abstracts: a scaffold for automatic text mining.

FEBS Lett 2008 Apr 6;582(8):1170. Epub 2008 Mar 6.

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http://dx.doi.org/10.1016/j.febslet.2008.02.073DOI Listing
April 2008

Uncovering trends in gene naming.

Genome Biol 2008 Jan 31;9(1):401. Epub 2008 Jan 31.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1186/gb-2008-9-1-401DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2395243PMC
January 2008

Divergence of transcription factor binding sites across related yeast species.

Science 2007 Aug;317(5839):815-9

Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA.

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http://dx.doi.org/10.1126/science.1140748DOI Listing
August 2007

Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms.

Funct Integr Genomics 2007 Oct 19;7(4):335-45. Epub 2007 Jul 19.

Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA.

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http://dx.doi.org/10.1007/s10142-007-0054-7DOI Listing
October 2007

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Authors:
Ewan Birney John A Stamatoyannopoulos Anindya Dutta Roderic Guigó Thomas R Gingeras Elliott H Margulies Zhiping Weng Michael Snyder Emmanouil T Dermitzakis Robert E Thurman Michael S Kuehn Christopher M Taylor Shane Neph Christoph M Koch Saurabh Asthana Ankit Malhotra Ivan Adzhubei Jason A Greenbaum Robert M Andrews Paul Flicek Patrick J Boyle Hua Cao Nigel P Carter Gayle K Clelland Sean Davis Nathan Day Pawandeep Dhami Shane C Dillon Michael O Dorschner Heike Fiegler Paul G Giresi Jeff Goldy Michael Hawrylycz Andrew Haydock Richard Humbert Keith D James Brett E Johnson Ericka M Johnson Tristan T Frum Elizabeth R Rosenzweig Neerja Karnani Kirsten Lee Gregory C Lefebvre Patrick A Navas Fidencio Neri Stephen C J Parker Peter J Sabo Richard Sandstrom Anthony Shafer David Vetrie Molly Weaver Sarah Wilcox Man Yu Francis S Collins Job Dekker Jason D Lieb Thomas D Tullius Gregory E Crawford Shamil Sunyaev William S Noble Ian Dunham France Denoeud Alexandre Reymond Philipp Kapranov Joel Rozowsky Deyou Zheng Robert Castelo Adam Frankish Jennifer Harrow Srinka Ghosh Albin Sandelin Ivo L Hofacker Robert Baertsch Damian Keefe Sujit Dike Jill Cheng Heather A Hirsch Edward A Sekinger Julien Lagarde Josep F Abril Atif Shahab Christoph Flamm Claudia Fried Jörg Hackermüller Jana Hertel Manja Lindemeyer Kristin Missal Andrea Tanzer Stefan Washietl Jan Korbel Olof Emanuelsson Jakob S Pedersen Nancy Holroyd Ruth Taylor David Swarbreck Nicholas Matthews Mark C Dickson Daryl J Thomas Matthew T Weirauch James Gilbert Jorg Drenkow Ian Bell XiaoDong Zhao K G Srinivasan Wing-Kin Sung Hong Sain Ooi Kuo Ping Chiu Sylvain Foissac Tyler Alioto Michael Brent Lior Pachter Michael L Tress Alfonso Valencia Siew Woh Choo Chiou Yu Choo Catherine Ucla Caroline Manzano Carine Wyss Evelyn Cheung Taane G Clark James B Brown Madhavan Ganesh Sandeep Patel Hari Tammana Jacqueline Chrast Charlotte N Henrichsen Chikatoshi Kai Jun Kawai Ugrappa Nagalakshmi Jiaqian Wu Zheng Lian Jin Lian Peter Newburger Xueqing Zhang Peter Bickel John S Mattick Piero Carninci Yoshihide Hayashizaki Sherman Weissman Tim Hubbard Richard M Myers Jane Rogers Peter F Stadler Todd M Lowe Chia-Lin Wei Yijun Ruan Kevin Struhl Mark Gerstein Stylianos E Antonarakis Yutao Fu Eric D Green Ulaş Karaöz Adam Siepel James Taylor Laura A Liefer Kris A Wetterstrand Peter J Good Elise A Feingold Mark S Guyer Gregory M Cooper George Asimenos Colin N Dewey Minmei Hou Sergey Nikolaev Juan I Montoya-Burgos Ari Löytynoja Simon Whelan Fabio Pardi Tim Massingham Haiyan Huang Nancy R Zhang Ian Holmes James C Mullikin Abel Ureta-Vidal Benedict Paten Michael Seringhaus Deanna Church Kate Rosenbloom W James Kent Eric A Stone Serafim Batzoglou Nick Goldman Ross C Hardison David Haussler Webb Miller Arend Sidow Nathan D Trinklein Zhengdong D Zhang Leah Barrera Rhona Stuart David C King Adam Ameur Stefan Enroth Mark C Bieda Jonghwan Kim Akshay A Bhinge Nan Jiang Jun Liu Fei Yao Vinsensius B Vega Charlie W H Lee Patrick Ng Atif Shahab Annie Yang Zarmik Moqtaderi Zhou Zhu Xiaoqin Xu Sharon Squazzo Matthew J Oberley David Inman Michael A Singer Todd A Richmond Kyle J Munn Alvaro Rada-Iglesias Ola Wallerman Jan Komorowski Joanna C Fowler Phillippe Couttet Alexander W Bruce Oliver M Dovey Peter D Ellis Cordelia F Langford David A Nix Ghia Euskirchen Stephen Hartman Alexander E Urban Peter Kraus Sara Van Calcar Nate Heintzman Tae Hoon Kim Kun Wang Chunxu Qu Gary Hon Rosa Luna Christopher K Glass M Geoff Rosenfeld Shelley Force Aldred Sara J Cooper Anason Halees Jane M Lin Hennady P Shulha Xiaoling Zhang Mousheng Xu Jaafar N S Haidar Yong Yu Yijun Ruan Vishwanath R Iyer Roland D Green Claes Wadelius Peggy J Farnham Bing Ren Rachel A Harte Angie S Hinrichs Heather Trumbower Hiram Clawson Jennifer Hillman-Jackson Ann S Zweig Kayla Smith Archana Thakkapallayil Galt Barber Robert M Kuhn Donna Karolchik Lluis Armengol Christine P Bird Paul I W de Bakker Andrew D Kern Nuria Lopez-Bigas Joel D Martin Barbara E Stranger Abigail Woodroffe Eugene Davydov Antigone Dimas Eduardo Eyras Ingileif B Hallgrímsdóttir Julian Huppert Michael C Zody Gonçalo R Abecasis Xavier Estivill Gerard G Bouffard Xiaobin Guan Nancy F Hansen Jacquelyn R Idol Valerie V B Maduro Baishali Maskeri Jennifer C McDowell Morgan Park Pamela J Thomas Alice C Young Robert W Blakesley Donna M Muzny Erica Sodergren David A Wheeler Kim C Worley Huaiyang Jiang George M Weinstock Richard A Gibbs Tina Graves Robert Fulton Elaine R Mardis Richard K Wilson Michele Clamp James Cuff Sante Gnerre David B Jaffe Jean L Chang Kerstin Lindblad-Toh Eric S Lander Maxim Koriabine Mikhail Nefedov Kazutoyo Osoegawa Yuko Yoshinaga Baoli Zhu Pieter J de Jong
June 2007

Structured digital abstract makes text mining easy.

Nature 2007 May;447(7141):142

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http://dx.doi.org/10.1038/447142aDOI Listing
May 2007

Publishing perishing? Towards tomorrow's information architecture.

BMC Bioinformatics 2007 Jan 19;8:17. Epub 2007 Jan 19.

Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1186/1471-2105-8-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1781953PMC
January 2007

Chemistry Nobel rich in structure.

Science 2007 Jan;315(5808):40-1

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http://dx.doi.org/10.1126/science.315.5808.40DOI Listing
January 2007

Predicting essential genes in fungal genomes.

Genome Res 2006 Sep 9;16(9):1126-35. Epub 2006 Aug 9.

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA.

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http://dx.doi.org/10.1101/gr.5144106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1557763PMC
September 2006

Genomic analysis of insertion behavior and target specificity of mini-Tn7 and Tn3 transposons in Saccharomyces cerevisiae.

Nucleic Acids Res 2006 Apr 28;34(8):e57. Epub 2006 Apr 28.

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1093/nar/gkl184DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1450332PMC
April 2006

Analyzing cellular biochemistry in terms of molecular networks.

Annu Rev Biochem 2004 ;73:1051-87

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA.

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http://dx.doi.org/10.1146/annurev.biochem.73.011303.073950DOI Listing
October 2004