Publications by authors named "Tim Massingham"

19Publications

More on the Best Evolutionary Rate for Phylogenetic Analysis.

Syst Biol 2017 Sep;66(5):769-785

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK.

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http://dx.doi.org/10.1093/sysbio/syx051DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5790136PMC
September 2017

An improved protocol for sequencing of repetitive genomic regions and structural variations using mutagenesis and next generation sequencing.

PLoS One 2012 17;7(8):e43359. Epub 2012 Aug 17.

European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0043359PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3422288PMC
March 2013

Error-correcting properties of the SOLiD Exact Call Chemistry.

BMC Bioinformatics 2012 Jun 22;13:145. Epub 2012 Jun 22.

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK.

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http://dx.doi.org/10.1186/1471-2105-13-145DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3464616PMC
June 2012

All Your Base: a fast and accurate probabilistic approach to base calling.

Genome Biol 2012 Feb 29;13(2):R13. Epub 2012 Feb 29.

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1RQ, UK.

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http://genomebiology.biomedcentral.com/articles/10.1186/gb-2
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http://dx.doi.org/10.1186/gb-2012-13-2-r13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053729PMC
February 2012

Experimental design in phylogenetics: testing predictions from expected information.

Syst Biol 2012 Jul 10;61(4):661-74. Epub 2012 Feb 10.

Department of Zoology, The Natural History Museum, Cromwell Road, London SW7 5BD, UK.

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http://dx.doi.org/10.1093/sysbio/sys028DOI Listing
July 2012

A high-resolution map of human evolutionary constraint using 29 mammals.

Nature 2011 Oct 12;478(7370):476-82. Epub 2011 Oct 12.

Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA.

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http://dx.doi.org/10.1038/nature10530DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3207357PMC
October 2011

PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment.

BMC Bioinformatics 2011 Apr 19;12:104. Epub 2011 Apr 19.

EMBL-European Bioinformatics Institute, Hinxton, UK.

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http://dx.doi.org/10.1186/1471-2105-12-104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3102636PMC
April 2011

Experimental design in caecilian systematics: phylogenetic information of mitochondrial genomes and nuclear rag1.

Syst Biol 2009 Aug 18;58(4):425-38. Epub 2009 Aug 18.

Department of Zoology, The Natural History Museum, Cromwell Road, London SW7 5BD, UK.

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http://dx.doi.org/10.1093/sysbio/syp043DOI Listing
August 2009

Genomic DNA k-mer spectra: models and modalities.

Genome Biol 2009 8;10(10):R108. Epub 2009 Oct 8.

School of Computer Science, Tel Aviv University, Klausner St, Ramat-Aviv, Tel-Aviv 39040, Israel.

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http://dx.doi.org/10.1186/gb-2009-10-10-r108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2784323PMC
January 2010

Rapidly evolving human promoter regions.

Nat Genet 2008 Nov;40(11):1262-3; author reply 1263-4

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http://dx.doi.org/10.1038/ng1108-1262DOI Listing
November 2008

Detecting the presence and location of selection in proteins.

Authors:
Tim Massingham

Methods Mol Biol 2008 ;452:311-29

European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK.

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http://dx.doi.org/10.1007/978-1-60327-159-2_15DOI Listing
July 2008

Determination and validation of principal gene products.

Bioinformatics 2008 Jan 15;24(1):11-7. Epub 2007 Nov 15.

Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre, Madrid, Spain.

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http://dx.doi.org/10.1093/bioinformatics/btm547DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2734078PMC
January 2008

Experimental design criteria in phylogenetics: where to add taxa.

Syst Biol 2007 Aug;56(4):609-22

Laboratory of Plant Systematics, KU Leuven, Belgium.

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http://dx.doi.org/10.1080/10635150701499563DOI Listing
August 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

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.

Genome Res 2007 Jun;17(6):760-74

Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.

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http://mendel.stanford.edu/sidowlab/pdfs/2007EncodeGR.pdf
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http://www.genome.org/cgi/doi/10.1101/gr.6034307
Publisher Site
http://dx.doi.org/10.1101/gr.6034307DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1891336PMC
June 2007

Relating tissue specialization to the differentiation of expression of singleton and duplicate mouse proteins.

Genome Biol 2006 9;7(10):R89. Epub 2006 Oct 9.

EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK.

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http://dx.doi.org/10.1186/gb-2006-7-10-r89DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1794571PMC
March 2007

Detecting amino acid sites under positive selection and purifying selection.

Genetics 2005 Mar 16;169(3):1753-62. Epub 2005 Jan 16.

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK.

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http://dx.doi.org/10.1534/genetics.104.032144DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1449526PMC
March 2005