2013

Inferring hierarchical orthologous groups from orthologous gene pairs
Altenhoff, A. M., Gil M., Gonnet G. H., and Dessimoz C.
PLoS ONE. Volume 8, (2013), p.e53786
SMIM1 underlies the Vel blood group and influences red blood cell traits
Cvejic, A., Haer-Wigman L., Stephens J.C., Kostadima M., Smethurst P.A., Frontini M., van den Akker E., Bertone P., Bielczyk-Maczyńska E., Farrow S., et al.
Nat Genet. May, Volume 45, (2013), p.542–545 doi:
Towards practical, high-capacity, low-maintenance information storage in synthesized DNA
Goldman, N., Bertone P., Chen S., Dessimoz C., LeProust E. M., Sipos B., and Birney E.
Nature. Volume 494, (2013), p.77-80
Approximate Bayesian computation
Sunnåker, M., Busetto A. G., Numminen E., Corander J., Foll M., and Dessimoz C.
PLoS Computational Biology. Volume 9, (2013), p.e1002803

2012

Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm
Löytynoja, A., Vilella A. J., and Goldman N.
Bioinformatics. Volume 28, (2012), p.1684-1691
Genome content of uncultivated marine _Roseobacters_ in the surface ocean
Luo, H., Löytynoja A., and Moran M. A.
Environmental Microbiology. Volume 14, (2012), p.41-51
Looking for Darwin in genomic sequences –- validity and success of statistical methods
Zhai, W., Nielsen R., Goldman N., and Yang Z.
Molecular Biology and Evolution. Volume 29, (2012), p.2889-2893
Resolving the ortholog conjecture: orthologs tend to be weakly, but significantly, more similar in function than paralogs
Altenhoff, A. M., Studer R. A., Robinson-Rechavi M., and Dessimoz C.
PLoS Computational Biology. Volume 8, (2012), p.e1002514
Alignment methods: strategies, challenges, benchmarking, and comparative overview
Löytynoja, A.
Evolutionary Genomics: Statistical and Computational Methods. Volume 1, (2012), New York, p.203-235
All your base: a fast and accurate probabilistic approach to base calling
Massingham, T., and Goldman N.
Genome Biology. Volume 13, (2012), p.R13
Error-correcting properties of the SOLiD Exact Call Chemistry
Massingham, T., and Goldman N.
BMC Bioinformatics. Volume 13, (2012), p.145
Experimental design in phylogenetics: testing predictions from expected information
San Mauro, D., Gower D. J., Cotton J. A., Zardoya R., Wilkinson M., and Massingham T.
Systematic Biology. Volume 61, (2012), p.661-674
An improved protocol for sequencing of repetitive genomic regions and structural variations using mutagenesis and Next Generation Sequencing
Sipos, B., Massingham T., Stütz A. M., and Goldman N.
PLoS ONE. Volume 7, (2012), p.e43359
Quality of computationally inferred Gene Ontology annotations
Škunca, N., Altenhoff A., and Dessimoz C.
PLoS Computational Biology. Volume 8, (2012), p.e1002533
Insights into hominid evolution from the gorilla genome sequence
Scally, Aylwyn, Dutheil Julien Y., Hillier LaDeana W., Jordan Gregory E., Goodhead Ian, Herrero Javier, Hobolth Asger, Lappalainen Tuuli, Mailund Thomas, Marques-Bonet Tomas, et al.
Nature. Volume 483, (2012), p.169-175
Foreword
Goldman, N., and Yang Z.
Codon Evolution. (2012), Oxford, p.ix-x
Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages
Schroder, K., Irvine K. M., Taylor M. S., Bokil N. J., Cao K. - A. L., Masterman K. - A., Labzin L. I., Semple C. A., Kapetanovic R., Fairbairn L., et al.
Proceedings of the National Academy of Sciences U.S.A.. Volume 109, (2012), p.E944-E953
The effects of alignment error and alignment filtering on the sitewise detection of positive selection
Jordan, G., and Goldman N.
Molecular Biology and Evolution. Volume 29, (2012), p.1125-1139

2011

Addressing inter-gene heterogeneity in maximum likelihood phylogenomic analysis: yeasts revisited
Hess, J., and Goldman N.
PLoS ONE. Volume 6, (2011), p.e22783
What's in a likelihood? Simple models of protein evolution and the contribution of structurally viable reconstructions to the likelihood
Lakner, C., Holder M. T., Goldman N., and Naylor G. J. P.
Systematic Biology. Volume 60, (2011), p.161-174
A high-resolution map of human evolutionary constraint using 29 mammals
Lindblad-Toh, Kerstin, Garber Manuel, Zuk Or, Lin Michael F., Parker Brian J., Washietl Stefan, Kheradpour Pouya, Ernst Jason, Jordan Gregory, Mauceli Evan, et al.
Nature. Volume 478, (2011), p.476-482
Exome sequencing identifies NBEAL2 as the causative gene for gray platelet syndrome
Albers, C. A., Cvejic A., Favier R., Bouwmans E. E., Alessi M. - C., Bertone P., Jordan G., Kettleborough R. N. W., Kiddle G., KOSTADIMA M., et al.
Nature Genetics. Volume 43, (2011), p.735-737
Markovian and non-Markovian protein sequence evolution: aggregated Markov process models
Kosiol, C., and Goldman N.
Journal of Molecular Biology. Volume 411, (2011), p.910-923
RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data
Washietl, S., Findeiß S., Müller S. A., Kalkhof S., von Bergen M., Hofacker I. L., Stadler P. F., and Goldman N.
RNA. Volume 17, (2011), p.578-594
Mitochondrial genes support a common origin of rodent malaria parasites and Plasmodium falciparum’s relatives infecting great apes
Blanquart, S., and Gascuel O.
BMC Evolutionary Biology. Volume 11, (2011), p.70
PhyloSim – Monte Carlo simulation of sequence evolution in the R statistical computing environment
Sipos, B., Massingham T., Jordan G. E., and Goldman N.
BMC Bioinformatics. Volume 12, (2011), p.104
Analysis of alignment error and sitewise constraint in mammalian comparative genomics
Jordan, G.
(2011),

2010

webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser
Löytynoja, A., and Goldman N.
BMC Bioinformatics. Volume 11, (2010), p.579
Approximate maximum parsimony and ancestral maximum likelihood
Alon, N., Chor B., Pardi F., and Rapoport A.
IEEE/ACM Transactions on Computational Biology and Bioinformatics. Volume 7, (2010), p.183-187
Graph representations and algorithms in computational biology of RNA secondary structure
Washietl, S., and Gesell T.
Structural Analysis of Complex Networks. (2010), p.421-438
Ensembl's 10th year
Flicek, P., Aken BL, Ballester B., Beal K., Bragin E., Brent S., Chen Y., Clapham P., Coates G., Fairley S., et al.
Nucleic Acids Research. Volume 38, (2010), p.D557-D562
Robustness of phylogenetic inference based on minimum evolution
Pardi, F., Guillemot S., and Gascuel O.
Bulletin of Mathematical Biology. Volume 72, (2010), p.1820-1839
Sequence and structure analysis of noncoding RNAs
Washietl, S.
Methods in Molecular Biology. Volume 609, (2010), p.285-306
Nucleic acid sequence and structure databases
Washietl, S., and Hofacker I. L.
Methods in Molecular Biology. Volume 609, (2010), p.3-15
The (non)malignancy of cancerous amino acidic substitutions
Talavera, D., Taylor M. S., and Thornton J. M.
Proteins. Volume 78, (2010), p.518-529
Evolution of the transcription factor repertoires in the Saccharomycotina
Hess, J.
(2010),

2009

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line
consortium, FANTOM, and the Riken Omics Science Center The
Nature Genetics. Volume 41, (2009), p.553-562
Algorithms on Phylogenetic Trees
Pardi, F.
(2009),
Uniting alignments and trees
Löytynoja, A., and Goldman N.
Science. Volume 324, (2009), p.1528-1529
In defense of statistical methods for detecting positive selection
Yang, Z., Nielsen R., and Goldman N.
Proceedings of the National Academy of Sciences U.S.A.. Volume 106, (2009), p.E95
Assigning strains to bacterial species via the internet
Bishop, C. J., Aanensen D. M., Jordan G. E., Kilian M., Hanage W. P., and Spratt B. G.
BMC Biology. Volume 7, (2009), p.3
Experimental design in caecilian systematics: phylogenetic information of mitochondrial genomes and nuclear rag1
San Mauro, D., Gower D. J., Massingham T., Wilkinson M., Zardoya R., and Cotton J. A.
Systematic Biology. Volume 58, (2009), p.425-438
The structure of change
Semple, C. A. M., and Taylor M. S.
Science. Volume 323, (2009), p.347-348
Genomic DNA $k$-mer spectra: models and modalities
Chor, B., Horn D., Levy Y., Goldman N., and Massingham T.
Genome Biology. Volume 10, (2009), p.R108
Budgeted phylogenetic diversity on circular split systems
Minh, B. Q., Pardi F., Klaere S., and von Haeseler A.
IEEE/ACM Transactions on Computational Biology and Bioinformatics. Volume 6, (2009), p.22-29
High resolution mapping of expression QTLs in heterogeneous stock mice in multiple tissues
Huang, G. J., Shifman S., Valdar W., Johannesson M., Yalcin B., Taylor M. S., Taylor J. M., Mott R., and Flint J.
Genome Research. Volume 19, (2009), p.1133-1140
Comparative genomics and mammalian promoter evolution
Taylor, M. S., Jordan G. E., and Semple C. A. M.
Cap-Analysis Gene Expression (CAGE). (2009), Singapore, p.209-222

2008

Rapidly evolving human promoter regions
Taylor, M. S., Massingham T., Hayashizaki Y., Carninci P., Goldman N., and Semple C. A. M.
Nature Genetics. Volume 40, (2008), p.1262-1263
Inferring trees
Whelan, S.
Bioinformatics. Volume I: Data, Sequence Analysis and Evolution, (2008), Totowa, NJ, USA, p.287-309
Singleton SNPs in the human genome and implications for genome-wide association studies
Ke, X., Taylor M. S., and Cardon L. R.
European Journal of Human Genetics. Volume 16, (2008), p.506-515
Distribution of phylogenetic diversity under random extinction
Faller, B., Pardi F., and Steel M.
Journal of Theoretical Biology. Volume 251, (2008), p.286-296
Profile Comparer: a program for scoring and aligning profile hidden Markov models
Madera, Martin
Bioinformatics. Volume 24, (2008), p.2630-2631
Determination and validation of principal gene products
Tress, M. L., Wesselink J. - J., Frankish A., Lopez G., Goldman N., Löytynoja A., Massingham T., Pardi F., Whelan S., Harrow J., et al.
Bioinformatics. Volume 24, (2008), p.11-17
The genome of the simian and human malaria parasite Plasmodium knowlesi
Pain, A., Bohme U., Berry A. E., Mungall K., Finn R. D., Jackson A. P., Mourier T., Mistry J., Pasini E. M., Aslett M. A., et al.
Nature. Volume 455, (2008), p.799-803
Detecting the presence and location of selection in proteins
Massingham, T.
Bioinformatics. Volume I: Data, Sequence Analysis and Evolution, (2008), Totowa, NJ, USA, p.311-329
Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis
Löytynoja, A., and Goldman N.
Science. Volume 320, (2008), p.1632-1635
Dinucleotide controlled null models for comparative RNA gene prediction
Gesell, T., and Washietl S.
BMC Bioinformatics. Volume 9, (2008), p.248
A model of evolution and structure for multiple sequence alignment
Löytynoja, A., and Goldman N.
Philosophical Transactions of the Royal Society of London. Volume B 363, (2008), p.3913-3919
Statistical and computational challenges in molecular phylogenetics and evolution
Goldman, N., and Yang Z.
Philosophical Transactions of the Royal Society of London. Volume B 363, (2008), p.3889-3892
Strategies for measuring evolutionary conservation of RNA secondary structures
Gruber, A. R., Bernhart S. H., Hofacker I. L., and Washietl S.
BMC Bioinformatics. Volume 9, (2008), p.122
Evolutionary footprints of nucleosome positions in yeast
Washietl, S., Machné R., and Goldman N.
Trends in Genetics. Volume 24, (2008), p.583-587
Development and evaluation of a real-time PCR assay for detection of Pneumocystis jirovecii DNA in bronchoalveolar lavage fluid of HIV-infected patients
Huggett, J. F., Taylor M. S., Kocjan G., Evans H. E., Morris-Jones S., Gant V., Novak T., Costello A. M., Zumla A., and Miller R. F.
Thorax. Volume 63, (2008), p.154-159
PhyloWidget: web-based visualizations for the tree of life
Jordan, G. E., and Piel W. H.
Bioinformatics. Volume 24, (2008), p.1641-1642

2007

New approaches to phylogenetic tree search and their application to large numbers of protein alignments
Whelan, S.
Systematic Biology. Volume 56, (2007), p.727-740
MATLIGN: a motif clustering, comparison and matching tool
Kankainen, M., and Löytynoja A.
BMC Bioinformatics. Volume 8, (2007), p.189
Probabilistic models for the study of protein evolution
Thorne, J. L., and Goldman N.
Handbook of Statistical Genetics. Volume 1, (2007), Chichester, UK, p.439-459
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
ENCODE Project Consortium, The
Nature. Volume 447, (2007), p.799-816
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
Margulies, Elliott H., Cooper Gregory M., Asimenos George, Thomas Daryl J., Dewey Colin N., Siepel Adam, Birney Ewan, Keefe Damian, Schwartz Ariel S., Hou Minmei, et al.
Genome Research. Volume 17, (2007), p.760-774
Resource aware taxon selection for maximizing phylogenetic diversity
Pardi, F., and Goldman N.
Systematic Biology. Volume 56, (2007), p.431-444
Statistics of the log-det estimator
Massingham, T., and Goldman N.
Molecular Biology and Evolution. Volume 24, (2007), p.2277-2285
Experimental design criteria in phylogenetics: where to add taxa
Geuten, K., Massingham T., Darius P., Smets E., and Goldman N.
Systematic Biology. Volume 56, (2007), p.609-622
Variation in evolutionary processes at different codon positions
Bofkin, L., and Goldman N.
Molecular Biology and Evolution. Volume 24, (2007), p.513-521
Properties of the log-det estimator
Kuhn, S.
(2007),
An empirical codon model for protein sequence evolution
Kosiol, C., Holmes I., and Goldman N.
Molecular Biology and Evolution. Volume 24, (2007), p.1464-1479
Management, presentation and interpretation of genome scans using GSCANDB
Taylor, M., Valdar W., Kumar A., Flint J., and Mott R.
Bioinformatics. Volume 23, (2007), p.1545-1549

2006

XRate: a fast prototyping, training and annotation tool for phylo-grammars
Klosterman, P. S., Uzilov A. V., Bendana Y. R., Bradley R. K., Chao S., Kosiol C., Goldman N., and Holmes I.
BMC Bioinformatics. Volume 7, (2006), p.428
PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees
Whelan, S., de Bakker P. I. W., Quevillon E., Rodriguez N., and Goldman N.
Nucleic Acids Research. Volume 34, (2006), p.D327-D331
Markov Models for Protein Sequence Evolution
Kosiol, C.
(2006),
Phylogenetics by likelihood: evolutionary modeling as a tool for understanding the genome
Kosiol, C., Bofkin L., and Whelan S.
Journal of Biomedical Informatics. Volume 39, (2006), p.51-61
The Causes and Consequences of Variation in Evolutionary Processes Acting on DNA Sequences
Bofkin, L.
(2006),
A high-resolution map of transcription in the yeast genome
David, L., Huber W., Granovskaia M., Toedling J., Palm C. J., Bofkin L., Jones T., Davis R. W., and Steinmetz L. M.
Proceedings of the National Academy of Sciences U.S.A.. Volume 103, (2006), p.5320-5325

2005

A linear memory algorithm for Baum-Welch training
Miklós, I., and Meyer I. M.
BMC Bioinformatics. Volume 6, (2005), p.231
Different versions of the Dayhoff rate matrix
Kosiol, C., and Goldman N.
Molecular Biology and Evolution. Volume 22, (2005), p.193-199
Species choice for comparative genomics: being greedy works
Pardi, F., and Goldman N.
PLoS Genetics. Volume 1, (2005), p.e71
Detecting amino acid sites under positive and purifying selection
Massingham, T., and Goldman N.
Genetics. Volume 169, (2005), p.1753-1762
An algorithm for progressive multiple alignment of sequences with insertions
Löytynoja, A., and Goldman N.
Proceedings of the National Academy of Sciences U.S.A.. Volume 102, (2005), p.10557-10562
Statistical evidence for conserved, local secondary structure in the coding regions of eukaryotic mRNAs and pre-mRNAs
Meyer, I. M., and Miklós I.
Nucleic Acids Research. Volume 33, (2005), p.6338-6348
Moments of the Boltzmann distribution for RNA secondary structures
Miklós, I., Meyer I. M., and Nagy B.
Bulletin of Mathematical Biology. Volume 67, (2005), p.1031-1047

2004

Estimating the frequency of events that cause multiple nucleotide changes
Whelan, S., and Goldman N.
Genetics. Volume 167, (2004), p.2027-2043
Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites
Wong, W. S. W., Yang Z., Goldman N., and Nielsen R.
Genetics. Volume 168, (2004), p.1041-1051
Phylogenomics and bioinformatics of SARS-CoV
Liò, P., and Goldman N.
Trends in Microbiology. Volume 12, (2004), p.106-111
Functional needles in a genomic haystack
Bofkin, L., and Whelan S.
Heredity. Volume 92, (2004), p.363-364
A new criterion and method for amino acid classification
Kosiol, C., Goldman N., and Buttimore N. H.
Journal of Theoretical Biology. Volume 228, (2004), p.97-106

2003

Probabilistic models for the study of protein evolution
Thorne, J. L., and Goldman N.
Handbook of Statistical Genetics. Volume 1, (2003), Chichester, UK, p.209-226
Pandit: a database of protein and associated nucleotide domains with inferred trees
Whelan, S., de Bakker P. I. W., and Goldman N.
Bioinformatics. Volume 19, (2003), p.1556-1563
Dimensionality and dependence problems in statistical genomics
Liò, P.
Briefings in Bioinformatics. Volume 4, (2003), p.168-177
Statistical bioinformatic methods in microbial genome analysis
Liò, P.
BioEssays. Volume 25, (2003), p.266-273
Wavelets in bioinformatics and computational biology: state of art and perspectives
Liò, P.
Bioinformatics. Volume 19, (2003), p.2-9
Investigating the evolution and structure of chemokine receptors
Liò, P., and Vannucci M.
Gene. Volume 317, (2003), p.29-37
Protein evolution with dependence among codons due to tertiary structure
Robinson, D. M., Jones D. T., Kishino H., Goldman N., and Thorne J. L.
Molecular Biology and Evolution. Volume 20, (2003), p.1692-1704
Co-variation in frequencies of substitution, deletion, transposition and recombination during eutherian evolution
Hardison, R. C., Roskin K. M., Yang S., Diekhans M., Kent W. J., Weber R., Elnitski L., Li J., O'Connor M., Kolbe D., et al.
Genome Research. Volume 13, (2003), p.13-26

2002

Initial sequencing and comparative analysis of the mouse genome
Waterston, R. H., Lindblad-Toh K., Birney E., Rogers J., ..., Goldman N., ..., Whelan S., ..., authors)of(total 222, et al.
Nature. Volume 420, (2002), p.520-562