Nick Goldman

Nick Goldman

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Nick Goldman

Publications by authors named "Nick Goldman"

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Modeling Structural Constraints on Protein Evolution via Side-Chain Conformational States.

Mol Biol Evol 2019 09;36(9):2086-2103

European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridgeshire, United Kingdom.

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http://dx.doi.org/10.1093/molbev/msz122DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6736381PMC
September 2019

Alignment Modulates Ancestral Sequence Reconstruction Accuracy.

Mol Biol Evol 2018 07;35(7):1783-1797

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom.

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http://dx.doi.org/10.1093/molbev/msy055DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5995191PMC
July 2018

Improving communication for interdisciplinary teams working on storage of digital information in DNA.

F1000Res 2018 10;7:39. Epub 2018 Jan 10.

European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, CB10 1SD, UK.

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http://dx.doi.org/10.12688/f1000research.13482.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5883387PMC
January 2018

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

Short template switch events explain mutation clusters in the human genome.

Genome Res 2017 06 6;27(6):1039-1049. Epub 2017 Apr 6.

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

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http://dx.doi.org/10.1101/gr.214973.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5453318PMC
June 2017

Clustering Genes of Common Evolutionary History.

Mol Biol Evol 2016 06 17;33(6):1590-605. Epub 2016 Feb 17.

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Campus, Hinxton, United Kingdom Department of Ecology and Evolution, Biophore Building, UNIL-Sorge, University of Lausanne, Lausanne, Switzerland Department of Genetics, Evolution & Environment, University College London, London, United Kingdom Department of Computer Science, University College London, London, United Kingdom Centre for Integrative Genomics, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics, Biophore, Lausanne, Switzerland

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http://dx.doi.org/10.1093/molbev/msw038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4868114PMC
June 2016

ALVIS: interactive non-aggregative visualization and explorative analysis of multiple sequence alignments.

Nucleic Acids Res 2016 05 26;44(8):e77. Epub 2016 Jan 26.

European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK

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http://dx.doi.org/10.1093/nar/gkw022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4856975PMC
May 2016

Maximum Likelihood Phylogenetic Inference is Consistent on Multiple Sequence Alignments, with or without Gaps.

Syst Biol 2016 Mar 28;65(2):328-33. Epub 2015 Nov 28.

European Molecular Biology Laboratory, European Bioinformatics Institute Wellcome Genome Campus, Hinxton, CB10 1SD, UK;

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http://dx.doi.org/10.1093/sysbio/syv089DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4748752PMC
March 2016

The human blood DNA methylome displays a highly distinctive profile compared with other somatic tissues.

Epigenetics 2015 ;10(4):274-81

a The Blizard Institute; Barts and The London School of Medicine and Dentistry ; Queen Mary University of London ; London , UK.

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http://dx.doi.org/10.1080/15592294.2014.1003744DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4622544PMC
November 2015

Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference.

Syst Biol 2015 Sep 1;64(5):778-91. Epub 2015 Jun 1.

University College London, Gower St, London WC1E 6BT, UK; and European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK;

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http://dx.doi.org/10.1093/sysbio/syv033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4538881PMC
September 2015

Simple chained guide trees give poorer multiple sequence alignments than inferred trees in simulation and phylogenetic benchmarks.

Proc Natl Acad Sci U S A 2015 Jan 6;112(2):E99-100. Epub 2015 Jan 6.

European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom; and Department of Genetics, Evolution & Environment and Department of Computer Science, University College London, London WC1E 6BT, United Kingdom

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http://dx.doi.org/10.1073/pnas.1417526112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4299236PMC
January 2015

Maximum likelihood inference of small trees in the presence of long branches.

Syst Biol 2014 Sep 4;63(5):798-811. Epub 2014 Jul 4.

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

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http://dx.doi.org/10.1093/sysbio/syu044DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6371681PMC
September 2014

Sequence Bundles: a novel method for visualising, discovering and exploring sequence motifs.

BMC Proc 2014 28;8(Suppl 2 Proceedings of the 3rd Annual Symposium on Biologica):S8. Epub 2014 Aug 28.

Science Practice Ltd, London, 83-85 Paul Street, EC2A 4NQ, UK.

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http://dx.doi.org/10.1186/1753-6561-8-S2-S8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4155607PMC
September 2014

Amino acid changes in disease-associated variants differ radically from variants observed in the 1000 genomes project dataset.

PLoS Comput Biol 2013 12;9(12):e1003382. Epub 2013 Dec 12.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genomes Campus, Cambridge, Cambridgeshire, United Kingdom.

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http://dx.doi.org/10.1371/journal.pcbi.1003382DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3861039PMC
August 2014

Who watches the watchmen? An appraisal of benchmarks for multiple sequence alignment.

Methods Mol Biol 2014 ;1079:59-73

Wellcome Trust Sanger Institute, Cambridge, UK.

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http://dx.doi.org/10.1007/978-1-62703-646-7_4DOI Listing
May 2014

A penalized-likelihood method to estimate the distribution of selection coefficients from phylogenetic data.

Genetics 2014 May 14;197(1):257-71. Epub 2014 Feb 14.

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom.

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http://dx.doi.org/10.1534/genetics.114.162263DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4012484PMC
May 2014

Phylogenetic quantification of intra-tumour heterogeneity.

PLoS Comput Biol 2014 Apr 17;10(4):e1003535. Epub 2014 Apr 17.

University of Cambridge, Cambridge, United Kingdom; Cancer Research UK Cambridge Institute, Cambridge, United Kingdom.

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http://dx.doi.org/10.1371/journal.pcbi.1003535DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3990475PMC
April 2014

Systematic evaluation of spliced alignment programs for RNA-seq data.

Nat Methods 2013 Dec 3;10(12):1185-91. Epub 2013 Nov 3.

1] European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK. [2].

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http://dx.doi.org/10.1038/nmeth.2722DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4018468PMC
December 2013

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

Towards practical, high-capacity, low-maintenance information storage in synthesized DNA.

Nature 2013 Feb 23;494(7435):77-80. Epub 2013 Jan 23.

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

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http://dx.doi.org/10.1038/nature11875DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3672958PMC
February 2013

Looking for Darwin in genomic sequences--validity and success of statistical methods.

Mol Biol Evol 2012 Oct 3;29(10):2889-93. Epub 2012 Apr 3.

Center for Computational Biology and Laboratory of Disease Genomics and Individualized Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China.

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https://academic.oup.com/mbe/article-lookup/doi/10.1093/molb
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http://dx.doi.org/10.1093/molbev/mss104DOI Listing
October 2012

Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm.

Bioinformatics 2012 Jul 23;28(13):1684-91. Epub 2012 Apr 23.

EMBL-European Bioinformatics Institute, Hinxton, CB10 1SD, UK.

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http://dx.doi.org/10.1093/bioinformatics/bts198DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3381962PMC
July 2012

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

The effects of alignment error and alignment filtering on the sitewise detection of positive selection.

Mol Biol Evol 2012 Apr 1;29(4):1125-39. Epub 2011 Nov 1.

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom.

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http://dx.doi.org/10.1093/molbev/msr272DOI Listing
April 2012

Addressing inter-gene heterogeneity in maximum likelihood phylogenomic analysis: yeasts revisited.

PLoS One 2011 5;6(8):e22783. Epub 2011 Aug 5.

Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0022783PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3151265PMC
February 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

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

Markovian and non-Markovian protein sequence evolution: aggregated Markov process models.

J Mol Biol 2011 Aug 21;411(4):910-23. Epub 2011 Jun 21.

Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, A-1210 Wien, Austria.

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http://dx.doi.org/10.1016/j.jmb.2011.06.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3157587PMC
August 2011

RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data.

RNA 2011 Apr 28;17(4):578-94. Epub 2011 Feb 28.

EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB101SD, United Kingdom.

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http://dx.doi.org/10.1261/rna.2536111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3062170PMC
April 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

What's in a likelihood? Simple models of protein evolution and the contribution of structurally viable reconstructions to the likelihood.

Syst Biol 2011 Mar 12;60(2):161-74. Epub 2011 Jan 12.

Department of Biological Science, Section of Ecology and Evolution, Florida State University, Tallahassee, FL 32306-4120, USA.

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http://dx.doi.org/10.1093/sysbio/syq088DOI Listing
March 2011

webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser.

BMC Bioinformatics 2010 Nov 26;11:579. Epub 2010 Nov 26.

EMBL-European Bioinformatics Institute, Hinxton, Cambridgeshire, UK.

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http://dx.doi.org/10.1186/1471-2105-11-579DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3009689PMC
November 2010

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

In defense of statistical methods for detecting positive selection.

Proc Natl Acad Sci U S A 2009 Sep 31;106(36):E95; author reply E96. Epub 2009 Aug 31.

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http://dx.doi.org/10.1073/pnas.0904550106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2741286PMC
September 2009

Evolution. Uniting alignments and trees.

Science 2009 Jun;324(5934):1528-9

European Molecular Biology Laboratory European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK.

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http://dx.doi.org/10.1126/science.1175949DOI Listing
June 2009

Introduction. Statistical and computational challenges in molecular phylogenetics and evolution.

Philos Trans R Soc Lond B Biol Sci 2008 Dec;363(1512):3889-92

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

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http://dx.doi.org/10.1098/rstb.2008.0182DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2590901PMC
December 2008

A model of evolution and structure for multiple sequence alignment.

Philos Trans R Soc Lond B Biol Sci 2008 Dec;363(1512):3913-9

EMBL-European Bioinformatics Institute, Hinxton, UK.

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http://dx.doi.org/10.1098/rstb.2008.0170DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2592536PMC
December 2008

Evolutionary footprints of nucleosome positions in yeast.

Trends Genet 2008 Dec 24;24(12):583-7. Epub 2008 Oct 24.

European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.

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http://dx.doi.org/10.1016/j.tig.2008.09.003DOI Listing
December 2008

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

Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis.

Science 2008 Jun;320(5883):1632-5

European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK.

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http://dx.doi.org/10.1126/science.1158395DOI Listing
June 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

An empirical codon model for protein sequence evolution.

Mol Biol Evol 2007 Jul 30;24(7):1464-79. Epub 2007 Mar 30.

EMBL-European [corrected] Bioinformatics Institute, Hinxton, United Kingdom.

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http://i122server.vu-wien.ac.at/pop/Kosiol_website/pdfs/Kosi
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http://mbe.oxfordjournals.org/cgi/doi/10.1093/molbev/msm064
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http://dx.doi.org/10.1093/molbev/msm064DOI Listing
July 2007

Resource-aware taxon selection for maximizing phylogenetic diversity.

Syst Biol 2007 Jun;56(3):431-44

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

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http://dx.doi.org/10.1080/10635150701411279DOI Listing
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

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

Variation in evolutionary processes at different codon positions.

Mol Biol Evol 2007 Feb 21;24(2):513-21. Epub 2006 Nov 21.

European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, United Kingdom.

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http://dx.doi.org/10.1093/molbev/msl178DOI Listing
February 2007

XRate: a fast prototyping, training and annotation tool for phylo-grammars.

BMC Bioinformatics 2006 Oct 3;7:428. Epub 2006 Oct 3.

Department of Bioengineering, University of California, Berkeley CA, USA.

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http://dx.doi.org/10.1186/1471-2105-7-428DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1622757PMC
October 2006

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

Species choice for comparative genomics: being greedy works.

PLoS Genet 2005 Dec 2;1(6):e71. Epub 2005 Dec 2.

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

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http://dx.doi.org/10.1371/journal.pgen.0010071DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1298936PMC
December 2005

An algorithm for progressive multiple alignment of sequences with insertions.

Proc Natl Acad Sci U S A 2005 Jul 6;102(30):10557-62. Epub 2005 Jul 6.

European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton CB10 1SD, United Kingdom.

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http://dx.doi.org/10.1073/pnas.0409137102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1180752PMC
July 2005

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

Different versions of the Dayhoff rate matrix.

Mol Biol Evol 2005 Feb 13;22(2):193-9. Epub 2004 Oct 13.

EMBL-European Bioinformatics Institute, Hinxton, UK.

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http://dx.doi.org/10.1093/molbev/msi005DOI Listing
February 2005

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

A new criterion and method for amino acid classification.

J Theor Biol 2004 May;228(1):97-106

School of Mathematics, Trinity College, University of Dublin, Dublin 2, Ireland.

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http://dx.doi.org/10.1016/j.jtbi.2003.12.010DOI Listing
May 2004

Phylogenomics and bioinformatics of SARS-CoV.

Trends Microbiol 2004 Mar;12(3):106-11

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

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http://dx.doi.org/10.1016/j.tim.2004.01.005DOI Listing
March 2004

Protein evolution with dependence among codons due to tertiary structure.

Mol Biol Evol 2003 Oct 28;20(10):1692-704. Epub 2003 Jul 28.

Bioinformatics Research Center, North Carolina State University, USA.

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https://academic.oup.com/mbe/article-lookup/doi/10.1093/molb
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http://dx.doi.org/10.1093/molbev/msg184DOI Listing
October 2003

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

Modeling mitochondrial protein evolution using structural information.

J Mol Evol 2002 Apr;54(4):519-29

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

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http://dx.doi.org/10.1007/s00239001-0052-7DOI Listing
April 2002