Publications

Publications

2018

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RAFTS³G – An efficient and versatile clustering software to analyses in large protein datasets
NICHIO BTD, de Oliveira AMR, de Pierri CR, Santos LGC, Vialle RA, Marchaukoski JN, Pedrosa FdO, Raittz RT. Preprint DOI: 10.1101/407437
SKEMPI 2.0: An updated benchmark of changes in protein-protein binding energy, kinetics and thermodynamics upon mutation.
Jankauskaite J, Jiménez-García B, Dapkunas J, Fernández-Recio J, Moal IH. Bioinformatics (Oxford, England) (2018) DOI: 10.1093/bioinformatics/bty635
Alignment Modulates Ancestral Sequence Reconstruction Accuracy.
Vialle RA, Tamuri AU, Goldman N. Molecular biology and evolution Volume 35 (2018) p.1783-1797 DOI: 10.1093/molbev/msy055
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SKEMPI 2.0: An updated benchmark of changes in protein-protein binding energy, kinetics and thermodynamics upon mutation
Jankauskaite J, Jimenez-Garcia B, Dapkunas J, Fernandez-Recio J, Moal IH. Preprint DOI: 10.1101/341735
Improving communication for interdisciplinary teams working on storage of digital information in DNA.
Hesketh EE, Sayir J, Goldman N. F1000Research Volume 7 (2018) p.39 DOI: 10.12688/f1000research.13482.1

2017

More on the Best Evolutionary Rate for Phylogenetic Analysis.
Klopfstein S, Massingham T, Goldman N. Systematic biology Volume 66 (2017) p.769-785 DOI: 10.1093/sysbio/syx051
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Computational approaches for discovery of mutational signatures in cancer.
Baez-Ortega A, Gori K. Briefings in bioinformatics (2017) DOI: 10.1093/bib/bbx082
A systematic analysis of scoring functions in rigid-body protein docking: The delicate balance between the predictive rate improvement and the risk of overtraining.
Barradas-Bautista D, Moal IH, Fernández-Recio J. Proteins Volume 85 (2017) p.1287-1297 DOI: 10.1002/prot.25289
Short template switch events explain mutation clusters in the human genome.
Löytynoja A, Goldman N. Genome research Volume 27 (2017) p.1039-1049 DOI: 10.1101/gr.214973.116
Modeling Protein Conformational Transition Pathways Using Collective Motions and the LASSO Method.
Hayes TW, Moal IH. Journal of chemical theory and computation Volume 13 (2017) p.1401-1410 DOI: 10.1021/acs.jctc.6b01110

2016

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PASP - a whole-transcriptome poly(A) tail length determination assay for the Illumina platform
Sipos B, Stütz AM, Slodkowicz G, Massingham T, Korbel J, Goldman N. Preprint DOI: 10.1101/060004
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RAFTS3: Rapid Alignment-Free Tool for Sequence Similarity Search
Vialle RA, Pedrosa FO, Weiss VA, Guizelini D, Tibaes JH, Marchaukoski JN, de Souza EM, Raittz RT. Preprint DOI: 10.1101/055269
Clustering Genes of Common Evolutionary History.
Gori K, Suchan T, Alvarez N, Goldman N, Dessimoz C. Molecular biology and evolution Volume 33 (2016) p.1590-1605 DOI: 10.1093/molbev/msw038
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Short template switch events explain mutation clusters in the human genome
Löytynoja A, Goldman N. Preprint DOI: 10.1101/038380
ALVIS: interactive non-aggregative visualization and explorative analysis of multiple sequence alignments.
Schwarz RF, Tamuri AU, Kultys M, King J, Godwin J, Florescu AM, Schultz J, Goldman N. Nucleic acids research Volume 44 (2016) p.e77 DOI: 10.1093/nar/gkw022

2015

Maximum Likelihood Phylogenetic Inference is Consistent on Multiple Sequence Alignments, with or without Gaps.
Truszkowski J, Goldman N. Systematic biology Volume 65 (2016) p.328-333 DOI: 10.1093/sysbio/syv089
Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference.
Tan G, Muffato M, Ledergerber C, Herrero J, Goldman N, Gil M, Dessimoz C. Systematic biology Volume 64 (2015) p.778-791 DOI: 10.1093/sysbio/syv033
Simple chained guide trees give poorer multiple sequence alignments than inferred trees in simulation and phylogenetic benchmarks.
Tan G, Gil M, Löytynoja AP, Goldman N, Dessimoz C. Proceedings of the National Academy of Sciences of the United States of America Volume 112 (2015) p.E99-100 DOI: 10.1073/pnas.1417526112
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The human blood DNA methylome displays a highly distinctive profile compared with other somatic tissues.
Lowe R, Slodkowicz G, Goldman N, Rakyan VK. Epigenetics Volume 10 (2015) p.274-281 DOI: 10.1080/15592294.2014.1003744

2014

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The structural basis for enhancer-dependent assembly and activation of the AAA transcriptional activator NorR.
Bush M, Ghosh T, Sawicka M, Moal IH, Bates PA, Dixon R, Zhang X. Molecular microbiology Volume 95 (2015) p.17-30 DOI: 10.1111/mmi.12844
The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease.
Peng X, Alföldi J, Gori K, Eisfeld AJ, Tyler SR, Tisoncik-Go J, Brawand D, Law GL, Skunca N, Hatta M, Gasper DJ, Kelly SM, Chang J, Thomas MJ, Johnson J, Berlin AM, Lara M, Russell P, Swofford R, Turner-Maier J, Young S, Hourlier T, Aken B, Searle S, Sun X, Yi Y, Suresh M, Tumpey TM, Siepel A, Wisely SM, Dessimoz C, Kawaoka Y, Birren BW, Lindblad-Toh K, Di Palma F, Engelhardt JF, Palermo RE, Katze MG. Nature biotechnology Volume 32 (2014) p.1250-1255 DOI: 10.1038/nbt.3079
The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements.
Altenhoff AM, Škunca N, Glover N, Train CM, Sueki A, Piližota I, Gori K, Tomiczek B, Müller S, Redestig H, Gonnet GH, Dessimoz C. Nucleic acids research Volume 43 (2015) p.D240-9 DOI: 10.1093/nar/gku1158
Transcriptional diversity during lineage commitment of human blood progenitors.
Chen L, Kostadima M, Martens JHA, Canu G, Garcia SP, Turro E, Downes K, Macaulay IC, Bielczyk-Maczynska E, Coe S, Farrow S, Poudel P, Burden F, Jansen SBG, Astle WJ, Attwood A, Bariana T, de Bono B, Breschi A, Chambers JC, Consortium B, Choudry FA, Clarke L, Coupland P, van der Ent M, Erber WN, Jansen JH, Favier R, Fenech ME, Foad N, Freson K, van Geet C, Gomez K, Guigo R, Hampshire D, Kelly AM, Kerstens HHD, Kooner JS, Laffan M, Lentaigne C, Labalette C, Martin T, Meacham S, Mumford A, Nürnberg S, Palumbo E, van der Reijden BA, Richardson D, Sammut SJ, Slodkowicz G, Tamuri AU, Vasquez L, Voss K, Watt S, Westbury S, Flicek P, Loos R, Goldman N, Bertone P, Read RJ, Richardson S, Cvejic A, Soranzo N, Ouwehand WH, Stunnenberg HG, Frontini M, Rendon A. Science (New York, N.Y.) Volume 345 (2014) p.1251033 DOI: 10.1126/science.1251033
Sequence Bundles: a novel method for visualising, discovering and exploring sequence motifs.
Kultys M, Nicholas L, Schwarz R, Goldman N, King J. BMC proceedings Volume 8 (2014) p.S8 DOI: 10.1186/1753-6561-8-S2-S8
Maximum likelihood inference of small trees in the presence of long branches.
Parks SL, Goldman N. Systematic biology Volume 63 (2014) p.798-811 DOI: 10.1093/sysbio/syu044
Genome sequencing of normal cells reveals developmental lineages and mutational processes.
Behjati S, Huch M, van Boxtel R, Karthaus W, Wedge DC, Tamuri AU, Martincorena I, Petljak M, Alexandrov LB, Gundem G, Tarpey PS, Roerink S, Blokker J, Maddison M, Mudie L, Robinson B, Nik-Zainal S, Campbell P, Goldman N, van de Wetering M, Cuppen E, Clevers H, Stratton MR. Nature Volume 513 (2014) p.422-425 DOI: 10.1038/nature13448
Phylogenetic quantification of intra-tumour heterogeneity.
Schwarz RF, Trinh A, Sipos B, Brenton JD, Goldman N, Markowetz F. PLoS computational biology Volume 10 (2014) p.e1003535 DOI: 10.1371/journal.pcbi.1003535
A penalized-likelihood method to estimate the distribution of selection coefficients from phylogenetic data.
Tamuri AU, Goldman N, dos Reis M. Genetics Volume 197 (2014) p.257-271 DOI: 10.1534/genetics.114.162263
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Who watches the watchmen? An appraisal of benchmarks for multiple sequence alignment.
Iantorno S, Gori K, Goldman N, Gil M, Dessimoz C. Methods in molecular biology (Clifton, N.J.) Volume 1079 (2014) p.59-73 DOI: 10.1007/978-1-62703-646-7_4

2013

Amino acid changes in disease-associated variants differ radically from variants observed in the 1000 genomes project dataset.
de Beer TA, Laskowski RA, Parks SL, Sipos B, Goldman N, Thornton JM. PLoS computational biology Volume 9 (2013) p.e1003382 DOI: 10.1371/journal.pcbi.1003382
Systematic evaluation of spliced alignment programs for RNA-seq data.
Engström PG, Steijger T, Sipos B, Grant GR, Kahles A, Rätsch G, Goldman N, Hubbard TJ, Harrow J, Guigó R, Bertone P, RGASP Consortium. Nature methods Volume 10 (2013) p.1185-1191 DOI: 10.1038/nmeth.2722
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Genetic and archaeological perspectives on the initial modern human colonization of southern Asia.
Mellars P, Gori KC, Carr M, Soares PA, Richards MB. Proceedings of the National Academy of Sciences of the United States of America Volume 110 (2013) p.10699-10704 DOI: 10.1073/pnas.1306043110
SMIM1 underlies the Vel blood group and influences red blood cell traits.
Cvejic A, Haer-Wigman L, Stephens JC, Kostadima M, Smethurst PA, Frontini M, van den Akker E, Bertone P, Bielczyk-Maczyńska E, Farrow S, Fehrmann RS, Gray A, de Haas M, Haver VG, Jordan G, Karjalainen J, Kerstens HH, Kiddle G, Lloyd-Jones H, Needs M, Poole J, Soussan AA, Rendon A, Rieneck K, Sambrook JG, Schepers H, Silljé HHW, Sipos B, Swinkels D, Tamuri AU, Verweij N, Watkins NA, Westra HJ, Stemple D, Franke L, Soranzo N, Stunnenberg HG, Goldman N, van der Harst P, van der Schoot CE, Ouwehand WH, Albers CA. Nature genetics Volume 45 (2013) p.542-545 DOI: 10.1038/ng.2603
Towards practical, high-capacity, low-maintenance information storage in synthesized DNA.
Goldman N, Bertone P, Chen S, Dessimoz C, LeProust EM, Sipos B, Birney E. Nature Volume 494 (2013) p.77-80 DOI: 10.1038/nature11875

2012

An improved protocol for sequencing of repetitive genomic regions and structural variations using mutagenesis and next generation sequencing.
Sipos B, Massingham T, Stütz AM, Goldman N. PloS one Volume 7 (2012) p.e43359 DOI: 10.1371/journal.pone.0043359
Error-correcting properties of the SOLiD Exact Call Chemistry.
Massingham T, Goldman N. BMC bioinformatics Volume 13 (2012) p.145 DOI: 10.1186/1471-2105-13-145
Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm.
Löytynoja A, Vilella AJ, Goldman N. Bioinformatics (Oxford, England) Volume 28 (2012) p.1684-1691 DOI: 10.1093/bioinformatics/bts198
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Looking for Darwin in genomic sequences--validity and success of statistical methods.
Zhai W, Nielsen R, Goldman N, Yang Z. Molecular biology and evolution Volume 29 (2012) p.2889-2893 DOI: 10.1093/molbev/mss104
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Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages.
Schroder K, Irvine KM, Taylor MS, Bokil NJ, Le Cao KA, Masterman KA, Labzin LI, Semple CA, Kapetanovic R, Fairbairn L, Akalin A, Faulkner GJ, Baillie JK, Gongora M, Daub CO, Kawaji H, McLachlan GJ, Goldman N, Grimmond SM, Carninci P, Suzuki H, Hayashizaki Y, Lenhard B, Hume DA, Sweet MJ. Proceedings of the National Academy of Sciences of the United States of America Volume 109 (2012) p.E944-53 DOI: 10.1073/pnas.1110156109
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Insights into hominid evolution from the gorilla genome sequence.
Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I, Herrero J, Hobolth A, Lappalainen T, Mailund T, Marques-Bonet T, McCarthy S, Montgomery SH, Schwalie PC, Tang YA, Ward MC, Xue Y, Yngvadottir B, Alkan C, Andersen LN, Ayub Q, Ball EV, Beal K, Bradley BJ, Chen Y, Clee CM, Fitzgerald S, Graves TA, Gu Y, Heath P, Heger A, Karakoc E, Kolb-Kokocinski A, Laird GK, Lunter G, Meader S, Mort M, Mullikin JC, Munch K, O'Connor TD, Phillips AD, Prado-Martinez J, Rogers AS, Sajjadian S, Schmidt D, Shaw K, Simpson JT, Stenson PD, Turner DJ, Vigilant L, Vilella AJ, Whitener W, Zhu B, Cooper DN, de Jong P, Dermitzakis ET, Eichler EE, Flicek P, Goldman N, Mundy NI, Ning Z, Odom DT, Ponting CP, Quail MA, Ryder OA, Searle SM, Warren WC, Wilson RK, Schierup MH, Rogers J, Tyler-Smith C, Durbin R. Nature Volume 483 (2012) p.169-175 DOI: 10.1038/nature10842
All Your Base: a fast and accurate probabilistic approach to base calling.
Massingham T, Goldman N. Genome biology Volume 13 (2012) p.R13 DOI: 10.1186/gb-2012-13-2-r13
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Foreword
Goldman N, Yang Z. Codon Evolution: Mechanisms and Models Oxford University Press

2011

The effects of alignment error and alignment filtering on the sitewise detection of positive selection.
Jordan G, Goldman N. Molecular biology and evolution Volume 29 (2012) p.1125-1139 DOI: 10.1093/molbev/msr272
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A high-resolution map of human evolutionary constraint using 29 mammals.
Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, Alföldi J, Beal K, Chang J, Clawson H, Cuff J, Di Palma F, Fitzgerald S, Flicek P, Guttman M, Hubisz MJ, Jaffe DB, Jungreis I, Kent WJ, Kostka D, Lara M, Martins AL, Massingham T, Moltke I, Raney BJ, Rasmussen MD, Robinson J, Stark A, Vilella AJ, Wen J, Xie X, Zody MC, Broad Institute Sequencing Platform and Whole Genome Assembly Team, Baldwin J, Bloom T, Chin CW, Heiman D, Nicol R, Nusbaum C, Young S, Wilkinson J, Worley KC, Kovar CL, Muzny DM, Gibbs RA, Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Cree A, Dihn HH, Fowler G, Jhangiani S, Joshi V, Lee S, Lewis LR, Nazareth LV, Okwuonu G, Santibanez J, Warren WC, Mardis ER, Weinstock GM, Wilson RK, Genome Institute at Washington University, Delehaunty K, Dooling D, Fronik C, Fulton L, Fulton B, Graves T, Minx P, Sodergren E, Birney E, Margulies EH, Herrero J, Green ED, Haussler D, Siepel A, Goldman N, Pollard KS, Pedersen JS, Lander ES, Kellis M. Nature Volume 478 (2011) p.476-482 DOI: 10.1038/nature10530
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Addressing inter-gene heterogeneity in maximum likelihood phylogenomic analysis: yeasts revisited.
Hess J, Goldman N. PloS one Volume 6 (2011) p.e22783 DOI: 10.1371/journal.pone.0022783
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Markovian and non-Markovian protein sequence evolution: aggregated Markov process models.
Kosiol C, Goldman N. Journal of molecular biology Volume 411 (2011) p.910-923 DOI: 10.1016/j.jmb.2011.06.005
PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment.
Sipos B, Massingham T, Jordan GE, Goldman N. BMC bioinformatics Volume 12 (2011) p.104 DOI: 10.1186/1471-2105-12-104
RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data.
Washietl S, Findeiss S, Müller SA, Kalkhof S, von Bergen M, Hofacker IL, Stadler PF, Goldman N. RNA (New York, N.Y.) Volume 17 (2011) p.578-594 DOI: 10.1261/rna.2536111
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What's in a likelihood? Simple models of protein evolution and the contribution of structurally viable reconstructions to the likelihood.
Lakner C, Holder MT, Goldman N, Naylor GJ. Systematic biology Volume 60 (2011) p.161-174 DOI: 10.1093/sysbio/syq088

2010

webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser.
Löytynoja A, Goldman N. BMC bioinformatics Volume 11 (2010) p.579 DOI: 10.1186/1471-2105-11-579

2009

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Genomic DNA k-mer spectra: models and modalities.
Chor B, Horn D, Goldman N, Levy Y, Massingham T. Genome biology Volume 10 (2009) p.R108 DOI: 10.1186/gb-2009-10-10-r108
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In defense of statistical methods for detecting positive selection.
Yang Z, Nielsen R, Goldman N. Proceedings of the National Academy of Sciences of the United States of America Volume 106 (2009) p.E95; author reply E96 DOI: 10.1073/pnas.0904550106
Evolution. Uniting alignments and trees.
Löytynoja A, Goldman N. Science (New York, N.Y.) Volume 324 (2009) p.1528-1529 DOI: 10.1126/science.1175949

2008

A model of evolution and structure for multiple sequence alignment.
Löytynoja A, Goldman N. Philosophical transactions of the Royal Society of London. Series B, Biological sciences Volume 363 (2008) p.3913-3919 DOI: 10.1098/rstb.2008.0170
Introduction. Statistical and computational challenges in molecular phylogenetics and evolution.
Goldman N, Yang Z. Philosophical transactions of the Royal Society of London. Series B, Biological sciences Volume 363 (2008) p.3889-3892 DOI: 10.1098/rstb.2008.0182
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Rapidly evolving human promoter regions.
Taylor MS, Massingham T, Hayashizaki Y, Carninci P, Goldman N, Semple CA. Nature genetics Volume 40 (2008) p.1262-3; author reply 1263-4 DOI: 10.1038/ng1108-1262
Evolutionary footprints of nucleosome positions in yeast.
Washietl S, Machné R, Goldman N. Trends in genetics : TIG Volume 24 (2008) p.583-587 DOI: 10.1016/j.tig.2008.09.003
Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis.
Löytynoja A, Goldman N. Science (New York, N.Y.) Volume 320 (2008) p.1632-1635 DOI: 10.1126/science.1158395

2007

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Determination and validation of principal gene products.
Tress ML, Wesselink JJ, Frankish A, López G, Goldman N, Löytynoja A, Massingham T, Pardi F, Whelan S, Harrow J, Valencia A. Bioinformatics (Oxford, England) Volume 24 (2008) p.11-17 DOI: 10.1093/bioinformatics/btm547
Probabilistic models for the study of protein evolution
Thorne JL, Goldman N. Handbook of Statistical Genetics John Wiley and Sons (3 edition) DOI: 10.1002/9780470061619.ch14
Statistics of the log-det estimator.
Massingham T, Goldman N. Molecular biology and evolution Volume 24 (2007) p.2277-2285 DOI: 10.1093/molbev/msm160
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Experimental design criteria in phylogenetics: where to add taxa.
Geuten K, Massingham T, Darius P, Smets E, Goldman N. Systematic biology Volume 56 (2007) p.609-622 DOI: 10.1080/10635150701499563
Resource-aware taxon selection for maximizing phylogenetic diversity.
Pardi F, Goldman N. Systematic biology Volume 56 (2007) p.431-444 DOI: 10.1080/10635150701411279
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA, NISC Comparative Sequencing Program, Baylor College of Medicine Human Genome Sequencing Center, Washington University Genome Sequencing Center, Broad Institute, Children's Hospital Oakland Research Institute, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ. Nature Volume 447 (2007) p.799-816 DOI: 10.1038/nature05874
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Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.
Margulies EH, Cooper GM, Asimenos G, Thomas DJ, Dewey CN, Siepel A, Birney E, Keefe D, Schwartz AS, Hou M, Taylor J, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Brown JB, Bickel P, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Stone EA, Rosenbloom KR, Kent WJ, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Hinrichs A, Trumbower H, Clawson H, Zweig A, Kuhn RM, Barber G, Harte R, Karolchik D, Field MA, Moore RA, Matthewson CA, Schein JE, Marra MA, Antonarakis SE, Batzoglou S, Goldman N, Hardison R, Haussler D, Miller W, Pachter L, Green ED, Sidow A. Genome research Volume 17 (2007) p.760-774 DOI: 10.1101/gr.6034307
An empirical codon model for protein sequence evolution.
Kosiol C, Holmes I, Goldman N. Molecular biology and evolution Volume 24 (2007) p.1464-1479 DOI: 10.1093/molbev/msm064

2006

Variation in evolutionary processes at different codon positions.
Bofkin L, Goldman N. Molecular biology and evolution Volume 24 (2007) p.513-521 DOI: 10.1093/molbev/msl178
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XRate: a fast prototyping, training and annotation tool for phylo-grammars.
Klosterman PS, Uzilov AV, Bendaña YR, Bradley RK, Chao S, Kosiol C, Goldman N, Holmes I. BMC bioinformatics Volume 7 (2006) p.428 DOI: 10.1186/1471-2105-7-428
PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees.
Whelan S, de Bakker PI, Quevillon E, Rodriguez N, Goldman N. Nucleic acids research Volume 34 (2006) p.D327-31 DOI: 10.1093/nar/gkj087

2005

Species choice for comparative genomics: being greedy works.
Pardi F, Goldman N. PLoS genetics Volume 1 (2005) p.e71 DOI: 10.1371/journal.pgen.0010071
An algorithm for progressive multiple alignment of sequences with insertions.
Löytynoja A, Goldman N. Proceedings of the National Academy of Sciences of the United States of America Volume 102 (2005) p.10557-10562 DOI: 10.1073/pnas.0409137102
Detecting amino acid sites under positive selection and purifying selection.
Massingham T, Goldman N. Genetics Volume 169 (2005) p.1753-1762 DOI: 10.1534/genetics.104.032144

2004

Different versions of the Dayhoff rate matrix.
Kosiol C, Goldman N. Molecular biology and evolution Volume 22 (2005) p.193-199 DOI: 10.1093/molbev/msi005
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Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites.
Wong WS, Yang Z, Goldman N, Nielsen R. Genetics Volume 168 (2004) p.1041-1051 DOI: 10.1534/genetics.104.031153
Estimating the frequency of events that cause multiple-nucleotide changes.
Whelan S, Goldman N. Genetics Volume 167 (2004) p.2027-2043 DOI: 10.1534/genetics.103.023226
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A new criterion and method for amino acid classification.
Kosiol C, Goldman N, Buttimore NH. Journal of theoretical biology Volume 228 (2004) p.97-106 DOI: 10.1016/j.jtbi.2003.12.010
Phylogenomics and bioinformatics of SARS-CoV.
Liò P, Goldman N. Trends in microbiology Volume 12 (2004) p.106-111 DOI: 10.1016/j.tim.2004.01.005

2003

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Pandit: a database of protein and associated nucleotide domains with inferred trees.
Whelan S, de Bakker PI, Goldman N. Bioinformatics (Oxford, England) Volume 19 (2003) p.1556-1563 DOI: 10.1093/bioinformatics/btg188
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Protein evolution with dependence among codons due to tertiary structure.
Robinson DM, Jones DT, Kishino H, Goldman N, Thorne JL. Molecular biology and evolution Volume 20 (2003) p.1692-1704 DOI: 10.1093/molbev/msg184
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Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution.
Hardison RC, Roskin KM, Yang S, Diekhans M, Kent WJ, Weber R, Elnitski L, Li J, O'Connor M, Kolbe D, Schwartz S, Furey TS, Whelan S, Goldman N, Smit A, Miller W, Chiaromonte F, Haussler D. Genome research Volume 13 (2003) p.13-26 DOI: 10.1101/gr.844103
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Probabilistic models for the study of protein evolution
Thorne JL, Goldman N. Handbook of Statistical Genetics John Wiley and Sons (2 edition)

2002

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Initial sequencing and comparative analysis of the mouse genome.
Mouse Genome Sequencing Consortium, Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, Botcherby M, Bray N, Brent MR, Brown DG, Brown SD, Bult C, Burton J, Butler J, Campbell RD, Carninci P, Cawley S, Chiaromonte F, Chinwalla AT, Church DM, Clamp M, Clee C, Collins FS, Cook LL, Copley RR, Coulson A, Couronne O, Cuff J, Curwen V, Cutts T, Daly M, David R, Davies J, Delehaunty KD, Deri J, Dermitzakis ET, Dewey C, Dickens NJ, Diekhans M, Dodge S, Dubchak I, Dunn DM, Eddy SR, Elnitski L, Emes RD, Eswara P, Eyras E, Felsenfeld A, Fewell GA, Flicek P, Foley K, Frankel WN, Fulton LA, Fulton RS, Furey TS, Gage D, Gibbs RA, Glusman G, Gnerre S, Goldman N, Goodstadt L, Grafham D, Graves TA, Green ED, Gregory S, Guigó R, Guyer M, Hardison RC, Haussler D, Hayashizaki Y, Hillier LW, Hinrichs A, Hlavina W, Holzer T, Hsu F, Hua A, Hubbard T, Hunt A, Jackson I, Jaffe DB, Johnson LS, Jones M, Jones TA, Joy A, Kamal M, Karlsson EK, Karolchik D, Kasprzyk A, Kawai J, Keibler E, Kells C, Kent WJ, Kirby A, Kolbe DL, Korf I, Kucherlapati RS, Kulbokas EJ, Kulp D, Landers T, Leger JP, Leonard S, Letunic I, Levine R, Li J, Li M, Lloyd C, Lucas S, Ma B, Maglott DR, Mardis ER, Matthews L, Mauceli E, Mayer JH, McCarthy M, McCombie WR, McLaren S, McLay K, McPherson JD, Meldrim J, Meredith B, Mesirov JP, Miller W, Miner TL, Mongin E, Montgomery KT, Morgan M, Mott R, Mullikin JC, Muzny DM, Nash WE, Nelson JO, Nhan MN, Nicol R, Ning Z, Nusbaum C, O'Connor MJ, Okazaki Y, Oliver K, Overton-Larty E, Pachter L, Parra G, Pepin KH, Peterson J, Pevzner P, Plumb R, Pohl CS, Poliakov A, Ponce TC, Ponting CP, Potter S, Quail M, Reymond A, Roe BA, Roskin KM, Rubin EM, Rust AG, Santos R, Sapojnikov V, Schultz B, Schultz J, Schwartz MS, Schwartz S, Scott C, Seaman S, Searle S, Sharpe T, Sheridan A, Shownkeen R, Sims S, Singer JB, Slater G, Smit A, Smith DR, Spencer B, Stabenau A, Stange-Thomann N, Sugnet C, Suyama M, Tesler G, Thompson J, Torrents D, Trevaskis E, Tromp J, Ucla C, Ureta-Vidal A, Vinson JP, Von Niederhausern AC, Wade CM, Wall M, Weber RJ, Weiss RB, Wendl MC, West AP, Wetterstrand K, Wheeler R, Whelan S, Wierzbowski J, Willey D, Williams S, Wilson RK, Winter E, Worley KC, Wyman D, Yang S, Yang SP, Zdobnov EM, Zody MC, Lander ES. Nature Volume 420 (2002) p.520-562 DOI: 10.1038/nature01262