Dr Richard Durbin | Senior Group Leader

I am involved in a wide variety of genomic genetics projects from a computational and mathematical perspective. Current interests include human genetic variation, evolutionary and population genetics and algorithms and software for high throughput sequencing.
 

I typically have a research group of around ten students, postdocs and staff scientists, and am also involved in a large number of collaborative projects.  Applicants for postdoc or visiting positions are welcome at any time; please email me with an outline of what you are interested in doing and why it would fit with my group.  A list of current projects can be found at my research group page.

In the past I have led a number of large scale genomics projects, including the 1000 Genomes Project (with David Altshuler at the Broad Institute) and the UK10K project, both of which completed in 2015, and the gorilla reference sequencing project.  Previously I worked on sequence analysis software including hidden Markov model (HMM) methods for gene finding and protein similarity detection, jointly authoring a book Biological Sequence analysis with Sean Eddy, Anders Krogh and Graeme Mitchison.  I also helped establish a number of reference genomic databases including WormBase for C.elegans biology (using the ACeDB software I co-developed with Jean Thierry-Mieg), Pfam, TreeFam and Ensembl.

Publications

  • Iron Age and Anglo-Saxon genomes from East England reveal British migration history.

    Schiffels S, Haak W, Paajanen P, Llamas B, Popescu E et al.

    Nature communications 2016;7;10408

  • Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake.

    Malinsky M, Challis RJ, Tyers AM, Schiffels S, Terai Y et al.

    Science (New York, N.Y.) 2015;350;6267;1493-8

  • The UK10K project identifies rare variants in health and disease.

    UK10K Consortium, Walter K, Min JL, Huang J, Crooks L et al.

    Nature 2015;526;7571;82-90

  • A global reference for human genetic variation.

    1000 Genomes Project Consortium, Auton A, Brooks LD, Durbin RM, Garrison EP et al.

    Nature 2015;526;7571;68-74

  • Inferring human population size and separation history from multiple genome sequences.

    Schiffels S and Durbin R

    Nature genetics 2014;46;8;919-25

  • Genetic interactions affecting human gene expression identified by variance association mapping.

    Brown AA, Buil A, Viñuela A, Lappalainen T, Zheng HF et al.

    eLife 2014;3;e01381

  • Efficient haplotype matching and storage using the positional Burrows-Wheeler transform (PBWT).

    Durbin R

    Bioinformatics (Oxford, England) 2014;30;9;1266-72

  • Revising the human mutation rate: implications for understanding human evolution.

    Scally A and Durbin R

    Nature reviews. Genetics 2012;13;10;745-53

  • Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses.

    Stegle O, Parts L, Piipari M, Winn J and Durbin R

    Nature protocols 2012;7;3;500-7

  • Efficient de novo assembly of large genomes using compressed data structures.

    Simpson JT and Durbin R

    Genome research 2012;22;3;549-56

  • Inference of human population history from individual whole-genome sequences.

    Li H and Durbin R

    Nature 2011;475;7357;493-6

  • Insights into hominid evolution from the gorilla genome sequence.

    Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I et al.

    Nature 2012;483;7388;169-75

  • Contrasting evolutionary genome dynamics between domesticated and wild yeasts.

    Yue JX, Li J, Aigrain L, Hallin J, Persson K et al.

    Nature genetics 2017

  • Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly.

    Schneider VA, Graves-Lindsay T, Howe K, Bouk N, Chen HC et al.

    Genome research 2017

  • Whole-genome view of the consequences of a population bottleneck using 2926 genome sequences from Finland and United Kingdom.

    Chheda H, Palta P, Pirinen M, McCarthy S, Walter K et al.

    European journal of human genetics : EJHG 2017

  • Whole-exome sequencing of 228 patients with sporadic Parkinson's disease.

    Sandor C, Honti F, Haerty W, Szewczyk-Krolikowski K, Tomlinson P et al.

    Scientific reports 2017;7;41188

  • Reference-based phasing using the Haplotype Reference Consortium panel.

    Loh PR, Danecek P, Palamara PF, Fuchsberger C, A Reshef Y et al.

    Nature genetics 2016;48;11;1443-1448

  • A reference panel of 64,976 haplotypes for genotype imputation.

    McCarthy S, Das S, Kretzschmar W, Delaneau O, Wood AR et al.

    Nature genetics 2016;48;10;1279-83

  • A genomic history of Aboriginal Australia.

    Malaspinas AS, Westaway MC, Muller C, Sousa VC, Lao O et al.

    Nature 2016

  • TTC25 Deficiency Results in Defects of the Outer Dynein Arm Docking Machinery and Primary Ciliary Dyskinesia with Left-Right Body Asymmetry Randomization.

    Wallmeier J, Shiratori H, Dougherty GW, Edelbusch C, Hjeij R et al.

    American journal of human genetics 2016;99;2;460-9

  • Deficient methylation and formylation of mt-tRNA(Met) wobble cytosine in a patient carrying mutations in NSUN3.

    Van Haute L, Dietmann S, Kremer L, Hussain S, Pearce SF et al.

    Nature communications 2016;7;12039

  • GENOMICS. A federated ecosystem for sharing genomic, clinical data.

    Global Alliance for Genomics and Health

    Science (New York, N.Y.) 2016;352;6291;1278-80

  • BCFtools/RoH: a hidden Markov model approach for detecting autozygosity from next-generation sequencing data.

    Narasimhan V, Danecek P, Scally A, Xue Y, Tyler-Smith C and Durbin R

    Bioinformatics (Oxford, England) 2016;32;11;1749-51

  • Health and population effects of rare gene knockouts in adult humans with related parents.

    Narasimhan VM, Hunt KA, Mason D, Baker CL, Karczewski KJ et al.

    Science (New York, N.Y.) 2016;352;6284;474-7

  • Whole-exome sequencing in an isolated population from the Dalmatian island of Vis.

    Jeroncic A, Memari Y, Ritchie GR, Hendricks AE, Kolb-Kokocinski A et al.

    European journal of human genetics : EJHG 2016

  • A high-content platform to characterise human induced pluripotent stem cell lines.

    Leha A, Moens N, Meleckyte R, Culley OJ, Gervasio MK et al.

    Methods (San Diego, Calif.) 2016;96;85-96

  • DNAH11 Localization in the Proximal Region of Respiratory Cilia Defines Distinct Outer Dynein Arm Complexes.

    Dougherty GW, Loges NT, Klinkenbusch JA, Olbrich H, Pennekamp P et al.

    American journal of respiratory cell and molecular biology 2016

  • Bi-allelic Truncating Mutations in TANGO2 Cause Infancy-Onset Recurrent Metabolic Crises with Encephalocardiomyopathy.

    Kremer LS, Distelmaier F, Alhaddad B, Hempel M, Iuso A et al.

    American journal of human genetics 2016;98;2;358-62

  • Iron Age and Anglo-Saxon genomes from East England reveal British migration history.

    Schiffels S, Haak W, Paajanen P, Llamas B, Popescu E et al.

    Nature communications 2016;7;10408

  • A Method for Checking Genomic Integrity in Cultured Cell Lines from SNP Genotyping Data.

    Danecek P, McCarthy SA, HipSci Consortium and Durbin R

    PloS one 2016;11;5;e0155014

  • Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake.

    Malinsky M, Challis RJ, Tyers AM, Schiffels S, Terai Y et al.

    Science (New York, N.Y.) 2015;350;6267;1493-8

  • A global reference for human genetic variation.

    1000 Genomes Project Consortium, Auton A, Brooks LD, Durbin RM, Garrison EP et al.

    Nature 2015;526;7571;68-74

  • The UK10K project identifies rare variants in health and disease.

    UK10K Consortium, Walter K, Min JL, Huang J, Crooks L et al.

    Nature 2015;526;7571;82-90

  • Homozygous loss-of-function variants in European cosmopolitan and isolate populations.

    Kaiser VB, Svinti V, Prendergast JG, Chau YY, Campbell A et al.

    Human molecular genetics 2015;24;19;5464-74

  • Immunofluorescence Analysis and Diagnosis of Primary Ciliary Dyskinesia with Radial Spoke Defects.

    Frommer A, Hjeij R, Loges NT, Edelbusch C, Jahnke C et al.

    American journal of respiratory cell and molecular biology 2015;53;4;563-73

  • Whole-genome sequencing identifies EN1 as a determinant of bone density and fracture.

    Zheng HF, Forgetta V, Hsu YH, Estrada K, Rosello-Diez A et al.

    Nature 2015;526;7571;112-7

  • Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel.

    Huang J, Howie B, McCarthy S, Memari Y, Walter K et al.

    Nature communications 2015;6;8111

  • POPULATION GENETICS. Genomic evidence for the Pleistocene and recent population history of Native Americans.

    Raghavan M, Steinrücken M, Harris K, Schiffels S, Rasmussen S et al.

    Science (New York, N.Y.) 2015;349;6250;aab3884

  • Tracing the route of modern humans out of Africa by using 225 human genome sequences from Ethiopians and Egyptians.

    Pagani L, Schiffels S, Gurdasani D, Danecek P, Scally A et al.

    American journal of human genetics 2015;96;6;986-91

  • Deficiency of ECHS1 causes mitochondrial encephalopathy with cardiac involvement.

    Haack TB, Jackson CB, Murayama K, Kremer LS, Schaller A et al.

    Annals of clinical and translational neurology 2015;2;5;492-509

  • Pathway-based factor analysis of gene expression data produces highly heritable phenotypes that associate with age.

    Anand Brown A, Ding Z, Viñuela A, Glass D, Parts L et al.

    G3 (Bethesda, Md.) 2015;5;5;839-47

  • Whole-genome sequence-based analysis of thyroid function.

    Taylor PN, Porcu E, Chew S, Campbell PJ, Traglia M et al.

    Nature communications 2015;6;5681

  • The genomic and phenotypic diversity of Schizosaccharomyces pombe.

    Jeffares DC, Rallis C, Rieux A, Speed D, Převorovský M et al.

    Nature genetics 2015;47;3;235-41

  • Extending reference assembly models.

    Church DM, Schneider VA, Steinberg KM, Schatz MC, Quinlan AR et al.

    Genome biology 2015;16;13

  • Gene-gene and gene-environment interactions detected by transcriptome sequence analysis in twins.

    Buil A, Brown AA, Lappalainen T, Viñuela A, Davies MN et al.

    Nature genetics 2015;47;1;88-91

  • Estimation of epistatic variance components and heritability in founder populations and crosses.

    Young AI and Durbin R

    Genetics 2014;198;4;1405-16

  • Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association.

    Ding Z, Ni Y, Timmer SW, Lee BK, Battenhouse A et al.

    PLoS genetics 2014;10;11;e1004798

  • A rare variant in APOC3 is associated with plasma triglyceride and VLDL levels in Europeans.

    Timpson NJ, Walter K, Min JL, Tachmazidou I, Malerba G et al.

    Nature communications 2014;5;4871

  • Managing clinically significant findings in research: the UK10K example.

    Kaye J, Hurles M, Griffin H, Grewal J, Bobrow M et al.

    European journal of human genetics : EJHG 2014;22;9;1100-4

  • Inferring human population size and separation history from multiple genome sequences.

    Schiffels S and Durbin R

    Nature genetics 2014;46;8;919-25

  • Distribution and medical impact of loss-of-function variants in the Finnish founder population.

    Lim ET, Würtz P, Havulinna AS, Palta P, Tukiainen T et al.

    PLoS genetics 2014;10;7;e1004494

  • Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences.

    Colonna V, Ayub Q, Chen Y, Pagani L, Luisi P et al.

    Genome biology 2014;15;6;R88

  • Efficient haplotype matching and storage using the positional Burrows-Wheeler transform (PBWT).

    Durbin R

    Bioinformatics (Oxford, England) 2014;30;9;1266-72

  • Estimating telomere length from whole genome sequence data.

    Ding Z, Mangino M, Aviv A, Spector T, Durbin R and UK10K Consortium

    Nucleic acids research 2014;42;9;e75

  • Genetic interactions affecting human gene expression identified by variance association mapping.

    Brown AA, Buil A, Viñuela A, Lappalainen T, Zheng HF et al.

    eLife 2014;3;e01381

  • A high-definition view of functional genetic variation from natural yeast genomes.

    Bergström A, Simpson JT, Salinas F, Barré B, Parts L et al.

    Molecular biology and evolution 2014;31;4;872-88

  • High-resolution mapping of complex traits with a four-parent advanced intercross yeast population.

    Cubillos FA, Parts L, Salinas F, Bergström A, Scovacricchi E et al.

    Genetics 2013;195;3;1141-55

  • The anatomy of successful computational biology software.

    Altschul S, Demchak B, Durbin R, Gentleman R, Krzywinski M et al.

    Nature biotechnology 2013;31;10;894-7

  • A genome-wide survey of genetic variation in gorillas using reduced representation sequencing.

    Scally A, Yngvadottir B, Xue Y, Ayub Q, Durbin R and Tyler-Smith C

    PloS one 2013;8;6;e65066

  • An integrated map of genetic variation from 1,092 human genomes.

    1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA et al.

    Nature 2012;491;7422;56-65

  • Mapping cis- and trans-regulatory effects across multiple tissues in twins.

    Grundberg E, Small KS, Hedman ÅK, Nica AC, Buil A et al.

    Nature genetics 2012;44;10;1084-9

  • The 1000 Genomes Project: data management and community access.

    Clarke L, Zheng-Bradley X, Smith R, Kulesha E, Xiao C et al.

    Nature methods 2012;9;5;459-62

  • High levels of RNA-editing site conservation amongst 15 laboratory mouse strains.

    Danecek P, Nellåker C, McIntyre RE, Buendia-Buendia JE, Bumpstead S et al.

    Genome biology 2012;13;4;26

  • WormBase: Annotating many nematode genomes.

    Howe K, Davis P, Paulini M, Tuli MA, Williams G et al.

    Worm 2012;1;1;15-21

  • Dindel: accurate indel calls from short-read data.

    Albers CA, Lunter G, MacArthur DG, McVean G, Ouwehand WH and Durbin R

    Genome research 2011;21;6;961-73

  • A map of human genome variation from population-scale sequencing.

    1000 Genomes Project Consortium, Abecasis GR, Altshuler D, Auton A, Brooks LD et al.

    Nature 2010;467;7319;1061-73

  • A Bayesian framework to account for complex non-genetic factors in gene expression levels greatly increases power in eQTL studies.

    Stegle O, Parts L, Durbin R and Winn J

    PLoS computational biology 2010;6;5;e1000770

  • Systematic analysis of human protein complexes identifies chromosome segregation proteins.

    Hutchins JR, Toyoda Y, Hegemann B, Poser I, Hériché JK et al.

    Science (New York, N.Y.) 2010;328;5978;593-9

  • Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes.

    Neumann B, Walter T, Hériché JK, Bulkescher J, Erfle H et al.

    Nature 2010;464;7289;721-7

  • Copy number variant detection in inbred strains from short read sequence data.

    Simpson JT, McIntyre RE, Adams DJ and Durbin R

    Bioinformatics (Oxford, England) 2010;26;4;565-7

  • Ensembl's 10th year.

    Flicek P, Aken BL, Ballester B, Beal K, Bragin E et al.

    Nucleic acids research 2010;38;Database issue;D557-62

  • Prepublication data sharing.

    Toronto International Data Release Workshop Authors, Birney E, Hudson TJ, Green ED, Gunter C et al.

    Nature 2009;461;7261;168-70

  • The Sequence Alignment/Map format and SAMtools.

    Li H, Handsaker B, Wysoker A, Fennell T, Ruan J et al.

    Bioinformatics (Oxford, England) 2009;25;16;2078-9

  • The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes.

    Pruitt KD, Harrow J, Harte RA, Wallin C, Diekhans M et al.

    Genome research 2009;19;7;1316-23

  • Population genomics of domestic and wild yeasts.

    Liti G, Carter DM, Moses AM, Warringer J, Parts L et al.

    Nature 2009;458;7236;337-41

  • Inferring selection on amino acid preference in protein domains.

    Moses AM and Durbin R

    Molecular biology and evolution 2009;26;3;527-36

  • Ensembl 2009.

    Hubbard TJ, Aken BL, Ayling S, Ballester B, Beal K et al.

    Nucleic acids research 2009;37;Database issue;D690-7

  • A large genome center's improvements to the Illumina sequencing system.

    Quail MA, Kozarewa I, Smith F, Scally A, Stephens PJ et al.

    Nature methods 2008;5;12;1005-10

  • Accurate whole human genome sequencing using reversible terminator chemistry.

    Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J et al.

    Nature 2008;456;7218;53-9

  • Mapping short DNA sequencing reads and calling variants using mapping quality scores.

    Li H, Ruan J and Durbin R

    Genome research 2008;18;11;1851-8

  • A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis.

    Down TA, Rakyan VK, Turner DJ, Flicek P, Li H et al.

    Nature biotechnology 2008;26;7;779-85

  • Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing.

    Campbell PJ, Stephens PJ, Pleasance ED, O'Meara S, Li H et al.

    Nature genetics 2008;40;6;722-9

  • BAC TransgeneOmics: a high-throughput method for exploration of protein function in mammals.

    Poser I, Sarov M, Hutchins JR, Hériché JK, Toyoda Y et al.

    Nature methods 2008;5;5;409-15

  • Genomix: a method for combining gene-finders' predictions, which uses evolutionary conservation of sequence and intron-exon structure.

    Coghlan A and Durbin R

    Bioinformatics (Oxford, England) 2007;23;12;1468-75

  • Mapping trait loci by use of inferred ancestral recombination graphs.

    Minichiello MJ and Durbin R

    American journal of human genetics 2006;79;5;910-22

  • The DNA sequence and biological annotation of human chromosome 1.

    Gregory SG, Barlow KF, McLay KE, Kaul R, Swarbreck D et al.

    Nature 2006;441;7091;315-21

  • Ensembl 2006.

    Birney E, Andrews D, Caccamo M, Chen Y, Clarke L et al.

    Nucleic acids research 2006;34;Database issue;D556-61

  • TreeFam: a curated database of phylogenetic trees of animal gene families.

    Li H, Coghlan A, Ruan J, Coin LJ, Hériché JK et al.

    Nucleic acids research 2006;34;Database issue;D572-80

  • The DNA sequence of the human X chromosome.

    Ross MT, Grafham DV, Coffey AJ, Scherer S, McLay K et al.

    Nature 2005;434;7031;325-37

  • Ensembl 2005.

    Hubbard T, Andrews D, Caccamo M, Cameron G, Chen Y et al.

    Nucleic acids research 2005;33;Database issue;D447-53

  • Improved techniques for the identification of pseudogenes.

    Coin L and Durbin R

    Bioinformatics (Oxford, England) 2004;20 Suppl 1;i94-100

  • The DNA sequence and comparative analysis of human chromosome 10.

    Deloukas P, Earthrowl ME, Grafham DV, Rubenfield M, French L et al.

    Nature 2004;429;6990;375-81

  • DNA sequence and analysis of human chromosome 9.

    Humphray SJ, Oliver K, Hunt AR, Plumb RW, Loveland JE et al.

    Nature 2004;429;6990;369-74

  • An overview of Ensembl.

    Birney E, Andrews TD, Bevan P, Caccamo M, Chen Y et al.

    Genome research 2004;14;5;925-8

  • The DNA sequence and analysis of human chromosome 13.

    Dunham A, Matthews LH, Burton J, Ashurst JL, Howe KL et al.

    Nature 2004;428;6982;522-8

  • Genome sequence of the Brown Norway rat yields insights into mammalian evolution.

    Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ et al.

    Nature 2004;428;6982;493-521

  • Ensembl 2004.

    Birney E, Andrews D, Bevan P, Caccamo M, Cameron G et al.

    Nucleic acids research 2004;32;Database issue;D468-70

  • The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics.

    Stein LD, Bao Z, Blasiar D, Blumenthal T, Brent MR et al.

    PLoS biology 2003;1;2;E45

  • The DNA sequence and analysis of human chromosome 6.

    Mungall AJ, Palmer SA, Sims SK, Edwards CA, Ashurst JL et al.

    Nature 2003;425;6960;805-11

  • Systematic functional analysis of the Caenorhabditis elegans genome using RNAi.

    Kamath RS, Fraser AG, Dong Y, Poulin G, Durbin R et al.

    Nature 2003;421;6920;231-7

  • Ensembl 2002: accommodating comparative genomics.

    Clamp M, Andrews D, Barker D, Bevan P, Cameron G et al.

    Nucleic acids research 2003;31;1;38-42

  • QuickTree: building huge Neighbour-Joining trees of protein sequences.

    Howe K, Bateman A and Durbin R

    Bioinformatics (Oxford, England) 2002;18;11;1546-7

  • Comparative ab initio prediction of gene structures using pair HMMs.

    Meyer IM and Durbin R

    Bioinformatics (Oxford, England) 2002;18;10;1309-18

  • GAZE: a generic framework for the integration of gene-prediction data by dynamic programming.

    Howe KL, Chothia T and Durbin R

    Genome research 2002;12;9;1418-27

  • The Ensembl genome database project.

    Hubbard T, Barker D, Birney E, Cameron G, Chen Y et al.

    Nucleic acids research 2002;30;1;38-41

  • Initial sequencing and analysis of the human genome.

    Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC et al.

    Nature 2001;409;6822;860-921

  • Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins.

    Bateman A, Birney E, Durbin R, Eddy SR, Finn RD and Sonnhammer EL

    Nucleic acids research 1999;27;1;260-2

Career/Research Highlights

Durbin, Richard
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Richard's Timeline
1992

Wellcome Trust Sanger Instititute: Senior Group Leader and various roles including Head of Informatics, Deputy Director, Joint Head of Human Genetics, Acting Head of Computational Genomics

1990

MRC Laboratory of Molecular Biology: staff member/junior group leader working on the C. elegans genome project

1988

Postdoc in neural networks at Stanford University

1987

PhD on the development and organisation of the C.elegans nervous system at MRC Laboratory of Molecular Biology

1983

Fulbright fellowship in biophysics at Harvard University

1982

BA in Mathematics at Cambridge University