Publications by authors named "Simon Whelan"

35Publications

Estimating Phylogenies from Shape and Similar Multidimensional Data: Why It Is Not Reliable.

Syst Biol 2020 Sep;69(5):863-883

School of Biological Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK.

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http://dx.doi.org/10.1093/sysbio/syaa003DOI Listing
September 2020

Identifying Clusters of High Confidence Homologies in Multiple Sequence Alignments.

Mol Biol Evol 2019 10;36(10):2340-2351

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.

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http://dx.doi.org/10.1093/molbev/msz142DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6933875PMC
October 2019

Physicochemical Amino Acid Properties Better Describe Substitution Rates in Large Populations.

Mol Biol Evol 2019 04;36(4):679-690

Evolutionary Biology Center, Uppsala University, Uppsala, Sweden.

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https://academic.oup.com/mbe/advance-article/doi/10.1093/mol
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http://dx.doi.org/10.1093/molbev/msz003DOI Listing
April 2019

PREQUAL: detecting non-homologous characters in sets of unaligned homologous sequences.

Bioinformatics 2018 11;34(22):3929-3930

Department of Organismal Biology, Program in Systematic Biology, Uppsala University, Uppsala, Sweden.

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http://dx.doi.org/10.1093/bioinformatics/bty448DOI Listing
November 2018

Inferring Trees.

Methods Mol Biol 2017 ;1525:349-377

Department of Organism Biology, Uppsala University, Uppsala, Sweden.

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http://dx.doi.org/10.1007/978-1-4939-6622-6_14DOI Listing
January 2018

Phylogenetic Tree Estimation With and Without Alignment: New Distance Methods and Benchmarking.

Syst Biol 2017 Mar;66(2):218-231

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden.

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http://dx.doi.org/10.1093/sysbio/syw074DOI Listing
March 2017

Evidence of Statistical Inconsistency of Phylogenetic Methods in the Presence of Multiple Sequence Alignment Uncertainty.

Genome Biol Evol 2015 Jul 1;7(8):2102-16. Epub 2015 Jul 1.

Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Sweden

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http://dx.doi.org/10.1093/gbe/evv127DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4558847PMC
July 2015

Covariation Is a Poor Measure of Molecular Coevolution.

Mol Biol Evol 2015 Sep 4;32(9):2456-68. Epub 2015 May 4.

Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom Evolutionary Biology Centre, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden.

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http://dx.doi.org/10.1093/molbev/msv109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4540965PMC
September 2015

GeLL: a generalized likelihood library for phylogenetic models.

Bioinformatics 2015 Jul 27;31(14):2391-3. Epub 2015 Feb 27.

Department of Evolutionary Biology, Uppsala University, Uppsala, 75236, Sweden.

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http://dx.doi.org/10.1093/bioinformatics/btv126DOI Listing
July 2015

ModelOMatic: fast and automated model selection between RY, nucleotide, amino acid, and codon substitution models.

Syst Biol 2015 Jan 9;64(1):42-55. Epub 2014 Sep 9.

Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala 75236, Sweden and Faculty of Life Sciences, University of Manchester, Manchester, UK.

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http://dx.doi.org/10.1093/sysbio/syu062DOI Listing
January 2015

Impact of deep coalescence and recombination on the estimation of phylogenetic relationships among species using AFLP markers.

Mol Phylogenet Evol 2014 Jul 13;76:102-9. Epub 2014 Mar 13.

Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, 36310 Vigo, Spain. Electronic address:

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http://dx.doi.org/10.1016/j.ympev.2014.03.001DOI Listing
July 2014

Assessing the state of substitution models describing noncoding RNA evolution.

Genome Biol Evol 2014 Jan;6(1):65-75

Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom.

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http://dx.doi.org/10.1093/gbe/evt206DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3914692PMC
January 2014

Class of multiple sequence alignment algorithm affects genomic analysis.

Mol Biol Evol 2013 Mar 9;30(3):642-53. Epub 2012 Nov 9.

Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom.

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http://dx.doi.org/10.1093/molbev/mss256DOI Listing
March 2013

Protein Phylogenetic Analysis of Ca(2+)/cation Antiporters and Insights into their Evolution in Plants.

Front Plant Sci 2012 13;3. Epub 2012 Jan 13.

Faculty of Life Sciences, University of Manchester Manchester, UK.

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http://dx.doi.org/10.3389/fpls.2012.00001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3355786PMC
August 2012

Measuring the distance between multiple sequence alignments.

Bioinformatics 2012 Feb 23;28(4):495-502. Epub 2011 Dec 23.

Computational and Evolutionary Biology, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK.

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http://dx.doi.org/10.1093/bioinformatics/btr701DOI Listing
February 2012

Characterizing the phylogenetic tree-search problem.

Syst Biol 2012 Mar 10;61(2):228-39. Epub 2011 Nov 10.

Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK.

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http://dx.doi.org/10.1093/sysbio/syr097DOI Listing
March 2012

Determining the evolutionary history of gene families.

Bioinformatics 2012 Jan 28;28(1):48-55. Epub 2011 Oct 28.

Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PL, UK.

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http://dx.doi.org/10.1093/bioinformatics/btr592DOI Listing
January 2012

Dynamic expression patterns of 6-O endosulfatases during zebrafish development suggest a subfunctionalisation event for sulf2.

Dev Dyn 2010 Dec;239(12):3312-23

Cardiovascular Medicine, Faculty of Medical and Human Sciences, University of Manchester, Manchester, United Kingdom.

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http://dx.doi.org/10.1002/dvdy.22456DOI Listing
December 2010

Phylogenetic substitution models for detecting heterotachy during plastid evolution.

Mol Biol Evol 2011 Jan 19;28(1):449-58. Epub 2010 Aug 19.

Computational and Evolutionary Biology, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom.

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http://dx.doi.org/10.1093/molbev/msq215DOI Listing
January 2011

The prevalence of multifurcations in tree-space and their implications for tree-search.

Mol Biol Evol 2010 Dec 28;27(12):2674-7. Epub 2010 Jun 28.

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http://dx.doi.org/10.1093/molbev/msq163DOI Listing
December 2010

The genetic code can cause systematic bias in simple phylogenetic models.

Authors:
Simon Whelan

Philos Trans R Soc Lond B Biol Sci 2008 Dec;363(1512):4003-11

Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK.

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http://rstb.royalsocietypublishing.org/cgi/doi/10.1098/rstb.
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http://dx.doi.org/10.1098/rstb.2008.0171DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2607415PMC
December 2008

Inferring trees.

Authors:
Simon Whelan

Methods Mol Biol 2008 ;452:287-309

Faculty of Life Sciences, University of Manchester, Manchester, UK.

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http://dx.doi.org/10.1007/978-1-60327-159-2_14DOI Listing
July 2008

Spatial and temporal heterogeneity in nucleotide sequence evolution.

Authors:
Simon Whelan

Mol Biol Evol 2008 Aug 22;25(8):1683-94. Epub 2008 May 22.

Faculty of Life Sciences, University of Manchester, Michael Smith Building, Manchester M13 9PT, United Kingdom.

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http://dx.doi.org/10.1093/molbev/msn119DOI Listing
August 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

New approaches to phylogenetic tree search and their application to large numbers of protein alignments.

Authors:
Simon Whelan

Syst Biol 2007 Oct;56(5):727-40

Faculty of Life Sciences, Michael Smith Building, University of Manchester, Oxford Road, Manchester, UK.

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http://dx.doi.org/10.1080/10635150701611134DOI 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

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
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http://dx.doi.org/10.1101/gr.6034307DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1891336PMC
June 2007

PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees.

Nucleic Acids Res 2006 Jan;34(Database issue):D327-31

EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

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http://dx.doi.org/10.1093/nar/gkj087DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347450PMC
January 2006

Phylogenetics by likelihood: evolutionary modeling as a tool for understanding the genome.

J Biomed Inform 2006 Feb 15;39(1):51-61. Epub 2005 Sep 15.

EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1016/j.jbi.2005.08.003DOI Listing
February 2006

Estimating the frequency of events that cause multiple-nucleotide changes.

Genetics 2004 Aug;167(4):2027-43

EMBL-European Bioinformatics Institute, Hinxton CB10 1SD, United Kingdom.

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http://dx.doi.org/10.1534/genetics.103.023226DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1470989PMC
August 2004

Pandit: a database of protein and associated nucleotide domains with inferred trees.

Bioinformatics 2003 Aug;19(12):1556-63

Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.

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http://dx.doi.org/10.1093/bioinformatics/btg188DOI Listing
August 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

A novel use of equilibrium frequencies in models of sequence evolution.

Mol Biol Evol 2002 Nov;19(11):1821-31

Department of Zoology, University of Cambridge, UK.

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https://www-fourier.ujf-grenoble.fr/~dpiau/cdem/1821.pdf
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http://dx.doi.org/10.1093/oxfordjournals.molbev.a004007DOI Listing
November 2002