Durbin, Richard

richard.durbin@sanger.ac.uk

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

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

Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow.

Malinsky M, Svardal H, Tyers AM, Miska EA, Genner MJ et al.

Nature ecology & evolution 2018;2;12;1940-1955

PUBMED: 30455444; PMC: 6443041; DOI: 10.1038/s41559-018-0717-x
Variation graph toolkit improves read mapping by representing genetic variation in the reference.

Garrison E, Sirén J, Novak AM, Hickey G, Eizenga JM et al.

Nature biotechnology 2018;36;9;875-879

PUBMED: 30125266; PMC: 6126949; DOI: 10.1038/nbt.4227
The first horse herders and the impact of early Bronze Age steppe expansions into Asia.

de Barros Damgaard P, Martiniano R, Kamm J, Moreno-Mayar JV, Kroonen G et al.

Science (New York, N.Y.) 2018;360;6396

PUBMED: 29743352; PMC: 6748862; DOI: 10.1126/science.aar7711
Earth BioGenome Project: Sequencing life for the future of life.

Lewin HA, Robinson GE, Kress WJ, Baker WJ, Coddington J et al.

Proceedings of the National Academy of Sciences of the United States of America 2018;115;17;4325-4333

PUBMED: 29686065; PMC: 5924910; DOI: 10.1073/pnas.1720115115
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

PUBMED: 26940866; PMC: 4985238; DOI: 10.1126/science.aac8624
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

PUBMED: 26783965; PMC: 4735688; DOI: 10.1038/ncomms10408
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;1493-1498

PUBMED: 26680190; PMC: 4700518; DOI: 10.1126/science.aac9927
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

PUBMED: 26367797; PMC: 4773891; DOI: 10.1038/nature14962
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

PUBMED: 26432245; PMC: 4750478; DOI: 10.1038/nature15393
Efficient haplotype matching and storage using the positional Burrows-Wheeler transform (PBWT).

Durbin R

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

PUBMED: 24413527; PMC: 3998136; DOI: 10.1093/bioinformatics/btu014
Revising the human mutation rate: implications for understanding human evolution.

Scally A and Durbin R

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

PUBMED: 22965354; DOI: 10.1038/nrg3295
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

PUBMED: 22343431; PMC: 3398141; DOI: 10.1038/nprot.2011.457
Efficient de novo assembly of large genomes using compressed data structures.

Simpson JT and Durbin R

Genome research 2012;22;3;549-56

PUBMED: 22156294; PMC: 3290790; DOI: 10.1101/gr.126953.111
Inference of human population history from individual whole-genome sequences.

Li H and Durbin R

Nature 2011;475;7357;493-6

PUBMED: 21753753; PMC: 3154645; DOI: 10.1038/nature10231
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

PUBMED: 22398555; PMC: 3303130; DOI: 10.1038/nature10842

Ancestral hybridisation facilitated species diversification in the Lake Malawi cichlid fish adaptive radiation.

Svardal H, Quah FX, Malinsky M, Ngatunga BP, Miska EA et al.

Molecular biology and evolution 2019

PUBMED: 31821500; DOI: 10.1093/molbev/msz294
Haplotype-aware graph indexes.

Sirén J, Garrison E, Novak AM, Paten B and Durbin R

Bioinformatics (Oxford, England) 2019

PUBMED: 31406990; DOI: 10.1093/bioinformatics/btz575
Efficiently Inferring the Demographic History of Many Populations With Allele Count Data

Kamm J, Terhorst J, Durbin R and Song YS

Journal of the American Statistical Association 2019

DOI: 10.1080/01621459.2019.1635482
Viral coinfection analysis using a MinHash toolkit.

Dawson ET, Wagner S, Roberson D, Yeager M, Boland J et al.

BMC bioinformatics 2019;20;1;389

PUBMED: 31299914; PMC: 6626348; DOI: 10.1186/s12859-019-2918-y
The population history of northeastern Siberia since the Pleistocene.

Sikora M, Pitulko VV, Sousa VC, Allentoft ME, Vinner L et al.

Nature 2019;570;7760;182-188

PUBMED: 31168093; DOI: 10.1038/s41586-019-1279-z
Identifying Extrinsic versus Intrinsic Drivers of Variation in Cell Behavior in Human iPSC Lines from Healthy Donors.

Vigilante A, Laddach A, Moens N, Meleckyte R, Leha A et al.

Cell reports 2019;26;8;2078-2087.e3

PUBMED: 30784590; PMC: 6381787; DOI: 10.1016/j.celrep.2019.01.094
A High-Quality De novo Genome Assembly from a Single Mosquito Using PacBio Sequencing.

Kingan SB, Heaton H, Cudini J, Lambert CC, Baybayan P et al.

Genes 2019;10;1

PUBMED: 30669388; PMC: 6357164; DOI: 10.3390/genes10010062
Crumble: reference free lossy compression of sequence quality values.

Bonfield JK, McCarthy SA and Durbin R

Bioinformatics (Oxford, England) 2019;35;2;337-339

PUBMED: 29992288; PMC: 6330002; DOI: 10.1093/bioinformatics/bty608
GFAKluge: A C++ library and command line utilities for the Graphical Fragment Assembly formats.

Dawson ET and Durbin R

Journal of open source software 2019;4;33

PUBMED: 31535074; PMC: 6751074; DOI: 10.21105/joss.01083

Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow.

Malinsky M, Svardal H, Tyers AM, Miska EA, Genner MJ et al.

Nature ecology & evolution 2018;2;12;1940-1955

PUBMED: 30455444; PMC: 6443041; DOI: 10.1038/s41559-018-0717-x
Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci.

Lilue J, Doran AG, Fiddes IT, Abrudan M, Armstrong J et al.

Nature genetics 2018;50;11;1574-1583

PUBMED: 30275530; PMC: 6205630; DOI: 10.1038/s41588-018-0223-8
Variation graph toolkit improves read mapping by representing genetic variation in the reference.

Garrison E, Sirén J, Novak AM, Hickey G, Eizenga JM et al.

Nature biotechnology 2018;36;9;875-879

PUBMED: 30125266; PMC: 6126949; DOI: 10.1038/nbt.4227
Detecting archaic introgression using an unadmixed outgroup.

Skov L, Hui R, Shchur V, Hobolth A, Scally A et al.

PLoS genetics 2018;14;9;e1007641

PUBMED: 30226838; DOI: 10.1371/journal.pgen.1007641
Did Our Species Evolve in Subdivided Populations across Africa, and Why Does It Matter?

Scerri EML, Thomas MG, Manica A, Gunz P, Stock JT et al.

Trends in ecology & evolution 2018;33;8;582-594

PUBMED: 30007846; PMC: 6092560; DOI: 10.1016/j.tree.2018.05.005
A graph-based approach to diploid genome assembly.

Garg S, Rautiainen M, Novak AM, Garrison E, Durbin R and Marschall T

Bioinformatics (Oxford, England) 2018;34;13;i105-i114

PUBMED: 29949989; PMC: 6022571; DOI: 10.1093/bioinformatics/bty279
The first horse herders and the impact of early Bronze Age steppe expansions into Asia.

de Barros Damgaard P, Martiniano R, Kamm J, Moreno-Mayar JV, Kroonen G et al.

Science (New York, N.Y.) 2018;360;6396

PUBMED: 29743352; PMC: 6748862; DOI: 10.1126/science.aar7711
Earth BioGenome Project: Sequencing life for the future of life.

Lewin HA, Robinson GE, Kress WJ, Baker WJ, Coddington J et al.

Proceedings of the National Academy of Sciences of the United States of America 2018;115;17;4325-4333

PUBMED: 29686065; PMC: 5924910; DOI: 10.1073/pnas.1720115115

Estimating the human mutation rate from autozygous segments reveals population differences in human mutational processes.

Narasimhan VM, Rahbari R, Scally A, Wuster A, Mason D et al.

Nature communications 2017;8;1;303

PUBMED: 28827725; PMC: 5566399; DOI: 10.1038/s41467-017-00323-y
No evidence for maintenance of a sympatric Heliconius species barrier by chromosomal inversions.

Davey JW, Barker SL, Rastas PM, Pinharanda A, Martin SH et al.

Evolution letters 2017;1;3;138-154

PUBMED: 30283645; PMC: 6122123; DOI: 10.1002/evl3.12
Enrichment of low-frequency functional variants revealed by whole-genome sequencing of multiple isolated European populations.

Xue Y, Mezzavilla M, Haber M, McCarthy S, Chen Y et al.

Nature communications 2017;8;15927

PUBMED: 28643794; PMC: 5490002; DOI: 10.1038/ncomms15927
De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms.

Giordano F, Aigrain L, Quail MA, Coupland P, Bonfield JK et al.

Scientific reports 2017;7;1;3935

PUBMED: 28638050; PMC: 5479803; DOI: 10.1038/s41598-017-03996-z
Common genetic variation drives molecular heterogeneity in human iPSCs.

Kilpinen H, Goncalves A, Leha A, Afzal V, Alasoo K et al.

Nature 2017;546;7658;370-375

PUBMED: 28489815; PMC: 5524171; DOI: 10.1038/nature22403
Contrasting evolutionary genome dynamics between domesticated and wild yeasts.

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

Nature genetics 2017;49;6;913-924

PUBMED: 28416820; PMC: 5446901; DOI: 10.1038/ng.3847
Whole-Genome Sequencing Coupled to Imputation Discovers Genetic Signals for Anthropometric Traits.

Tachmazidou I, Süveges D, Min JL, Ritchie GRS, Steinberg J et al.

American journal of human genetics 2017;100;6;865-884

PUBMED: 28552196; PMC: 5473732; DOI: 10.1016/j.ajhg.2017.04.014
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;27;5;849-864

PUBMED: 28396521; PMC: 5411779; DOI: 10.1101/gr.213611.116
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;25;4;477-484

PUBMED: 28145424; PMC: 5346294; DOI: 10.1038/ejhg.2016.205
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

PUBMED: 28117402; DOI: 10.1038/srep41188

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

PUBMED: 27694958; PMC: 5096458; DOI: 10.1038/ng.3679
A genomic history of Aboriginal Australia.

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

Nature 2016;538;7624;207-214

PUBMED: 27654914; DOI: 10.1038/nature18299
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

PUBMED: 27548312; PMC: 5388176; DOI: 10.1038/ng.3643
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;24;10;1479-87

PUBMED: 27049301; PMC: 4950961; DOI: 10.1038/ejhg.2016.23
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

PUBMED: 27486780; PMC: 4974089; DOI: 10.1016/j.ajhg.2016.06.014
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;55;2;213-24

PUBMED: 26909801; PMC: 4979367; DOI: 10.1165/rcmb.2015-0353OC
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

PUBMED: 27356879; PMC: 4931328; DOI: 10.1038/ncomms12039
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

PUBMED: 27284183; DOI: 10.1126/science.aaf6162
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

PUBMED: 26826718; PMC: 4892413; DOI: 10.1093/bioinformatics/btw044
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

PUBMED: 26940866; PMC: 4985238; DOI: 10.1126/science.aac8624
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

PUBMED: 26608109; PMC: 4773406; DOI: 10.1016/j.ymeth.2015.11.012
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

PUBMED: 26805782; PMC: 4746337; DOI: 10.1016/j.ajhg.2015.12.009
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

PUBMED: 26783965; PMC: 4735688; DOI: 10.1038/ncomms10408
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

PUBMED: 27176002; PMC: 4866717; DOI: 10.1371/journal.pone.0155014

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;1493-1498

PUBMED: 26680190; PMC: 4700518; DOI: 10.1126/science.aac9927
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

PUBMED: 26432245; PMC: 4750478; DOI: 10.1038/nature15393
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

PUBMED: 26367797; PMC: 4773891; DOI: 10.1038/nature14962
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

PUBMED: 26173456; PMC: 4572071; DOI: 10.1093/hmg/ddv272
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

PUBMED: 25789548; PMC: 5306451; DOI: 10.1165/rcmb.2014-0483OC
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

PUBMED: 26367794; PMC: 4755714; DOI: 10.1038/nature14878
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

PUBMED: 26368830; PMC: 4579394; DOI: 10.1038/ncomms9111
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

PUBMED: 26198033; PMC: 4733658; DOI: 10.1126/science.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

PUBMED: 26027499; PMC: 4457944; DOI: 10.1016/j.ajhg.2015.04.019
Characterization of functional methylomes by next-generation capture sequencing identifies novel disease-associated variants.

Allum F, Shao X, Guénard F, Simon MM, Busche S et al.

Nature communications 2015;6;7211

PUBMED: 26021296; PMC: 4544751; DOI: 10.1038/ncomms8211
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

PUBMED: 26000322; PMC: 4435704; DOI: 10.1002/acn3.189
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

PUBMED: 25758824; PMC: 4426370; DOI: 10.1534/g3.114.011411
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

PUBMED: 25743335; PMC: 4366514; DOI: 10.1038/ncomms6681
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

PUBMED: 25665008; PMC: 4645456; DOI: 10.1038/ng.3215
Extending reference assembly models.

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

Genome biology 2015;16;13

PUBMED: 25651527; PMC: 4305238; DOI: 10.1186/s13059-015-0587-3
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

PUBMED: 25436857; PMC: 4643454; DOI: 10.1038/ng.3162

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

Young AI and Durbin R

Genetics 2014;198;4;1405-16

PUBMED: 25326236; PMC: 4256760; DOI: 10.1534/genetics.114.170795
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

PUBMED: 25411781; PMC: 4238955; DOI: 10.1371/journal.pgen.1004798
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

PUBMED: 25225788; PMC: 4167609; DOI: 10.1038/ncomms5871
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

PUBMED: 24424120; PMC: 4026295; DOI: 10.1038/ejhg.2013.290
Inferring human population size and separation history from multiple genome sequences.

Schiffels S and Durbin R

Nature genetics 2014;46;8;919-25

PUBMED: 24952747; PMC: 4116295; DOI: 10.1038/ng.3015
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

PUBMED: 25078778; PMC: 4117444; DOI: 10.1371/journal.pgen.1004494
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

PUBMED: 24980144; PMC: 4197830; DOI: 10.1186/gb-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

PUBMED: 24413527; PMC: 3998136; DOI: 10.1093/bioinformatics/btu014
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

PUBMED: 24609383; PMC: 4027178; DOI: 10.1093/nar/gku181
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

PUBMED: 24771767; PMC: 4017648; DOI: 10.7554/eLife.01381
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

PUBMED: 24425782; PMC: 3969562; DOI: 10.1093/molbev/msu037

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

PUBMED: 24037264; PMC: 3813843; DOI: 10.1534/genetics.113.155515
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

PUBMED: 24104757; PMC: 4166496; DOI: 10.1038/nbt.2721
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

PUBMED: 23750230; PMC: 3672199; DOI: 10.1371/journal.pone.0065066

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

PUBMED: 23128226; PMC: 3498066; DOI: 10.1038/nature11632
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

PUBMED: 22941192; PMC: 3784328; DOI: 10.1038/ng.2394
Revising the human mutation rate: implications for understanding human evolution.

Scally A and Durbin R

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

PUBMED: 22965354; DOI: 10.1038/nrg3295
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

PUBMED: 22543379; PMC: 3340611; DOI: 10.1038/nmeth.1974
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

PUBMED: 22524474; PMC: 3446300; DOI: 10.1186/gb-2012-13-4-r26
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

PUBMED: 22398555; PMC: 3303130; DOI: 10.1038/nature10842
Efficient de novo assembly of large genomes using compressed data structures.

Simpson JT and Durbin R

Genome research 2012;22;3;549-56

PUBMED: 22156294; PMC: 3290790; DOI: 10.1101/gr.126953.111
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

PUBMED: 22343431; PMC: 3398141; DOI: 10.1038/nprot.2011.457
WormBase: Annotating many nematode genomes.

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

Worm 2012;1;1;15-21

PUBMED: 24058818; PMC: 3670165; DOI: 10.4161/worm.19574

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

Li H and Durbin R

Nature 2011;475;7357;493-6

PUBMED: 21753753; PMC: 3154645; DOI: 10.1038/nature10231
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

PUBMED: 20980555; PMC: 3106329; DOI: 10.1101/gr.112326.110
Ensembl 2011.

Flicek P, Amode MR, Barrell D, Beal K, Brent S et al.

Nucleic acids research 2011;39;Database issue;D800-6

PUBMED: 21045057; PMC: 3013672; DOI: 10.1093/nar/gkq1064

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

PUBMED: 20981092; PMC: 3042601; DOI: 10.1038/nature09534
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

PUBMED: 20463871; PMC: 2865505; DOI: 10.1371/journal.pcbi.1000770
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

PUBMED: 20360068; PMC: 2989461; DOI: 10.1126/science.1181348
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

PUBMED: 20360735; PMC: 3108885; DOI: 10.1038/nature08869
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

PUBMED: 20022973; PMC: 2820678; DOI: 10.1093/bioinformatics/btp693
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

PUBMED: 19906699; PMC: 2808936; DOI: 10.1093/nar/gkp972

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

PUBMED: 19741685; PMC: 3073843; DOI: 10.1038/461168a
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

PUBMED: 19505943; PMC: 2723002; DOI: 10.1093/bioinformatics/btp352
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

PUBMED: 19498102; PMC: 2704439; DOI: 10.1101/gr.080531.108
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

PUBMED: 19212322; PMC: 2659681; DOI: 10.1038/nature07743
Inferring selection on amino acid preference in protein domains.

Moses AM and Durbin R

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

PUBMED: 19095755; PMC: 2716081; DOI: 10.1093/molbev/msn286
Deep short-read sequencing of chromosome 17 from the mouse strains A/J and CAST/Ei identifies significant germline variation and candidate genes that regulate liver triglyceride levels.

Sudbery I, Stalker J, Simpson JT, Keane T, Rust AG et al.

Genome biology 2009;10;10;R112

PUBMED: 19825173; PMC: 2784327; DOI: 10.1186/gb-2009-10-10-r112
Ensembl 2009.

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

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

PUBMED: 19033362; PMC: 2686571; DOI: 10.1093/nar/gkn828

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

PUBMED: 19034268; PMC: 2610436; DOI: 10.1038/nmeth.1270
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

PUBMED: 18987734; PMC: 2581791; DOI: 10.1038/nature07517
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

PUBMED: 18714091; PMC: 2577856; DOI: 10.1101/gr.078212.108
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

PUBMED: 18612301; PMC: 2644410; DOI: 10.1038/nbt1414
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

PUBMED: 18438408; PMC: 2705838; DOI: 10.1038/ng.128
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

PUBMED: 18391959; PMC: 2871289; DOI: 10.1038/nmeth.1199
Ensembl 2008.

Flicek P, Aken BL, Beal K, Ballester B, Caccamo M et al.

Nucleic acids research 2008;36;Database issue;D707-14

PUBMED: 18000006; PMC: 2238821; DOI: 10.1093/nar/gkm988
TreeFam: 2008 Update.

Ruan J, Li H, Chen Z, Coghlan A, Coin LJ et al.

Nucleic acids research 2008;36;Database issue;D735-40

PUBMED: 18056084; PMC: 2238856; DOI: 10.1093/nar/gkm1005

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

PUBMED: 17483502; PMC: 2880447; DOI: 10.1093/bioinformatics/btm133
Ensembl 2007.

Hubbard TJ, Aken BL, Beal K, Ballester B, Caccamo M et al.

Nucleic acids research 2007;35;Database issue;D610-7

PUBMED: 17148474; PMC: 1761443; DOI: 10.1093/nar/gkl996

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

PUBMED: 17033967; PMC: 1698562; DOI: 10.1086/508901
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

PUBMED: 16710414; DOI: 10.1038/nature04727
Ensembl 2006.

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

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

PUBMED: 16381931; PMC: 1347495; DOI: 10.1093/nar/gkj133
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

PUBMED: 16381935; PMC: 1347480; DOI: 10.1093/nar/gkj118

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

PUBMED: 15772651; PMC: 2665286; DOI: 10.1038/nature03440
Ensembl 2005.

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

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

PUBMED: 15608235; PMC: 540092; DOI: 10.1093/nar/gki138

Improved techniques for the identification of pseudogenes.

Coin L and Durbin R

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

PUBMED: 15262786; DOI: 10.1093/bioinformatics/bth942
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

PUBMED: 15164054; DOI: 10.1038/nature02462
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

PUBMED: 15164053; PMC: 2734081; DOI: 10.1038/nature02465
An overview of Ensembl.

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

Genome research 2004;14;5;925-8

PUBMED: 15078858; PMC: 479121; DOI: 10.1101/gr.1860604
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

PUBMED: 15057823; PMC: 2665288; DOI: 10.1038/nature02379
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

PUBMED: 15057822; DOI: 10.1038/nature02426
Ensembl 2004.

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

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

PUBMED: 14681459; PMC: 308772; DOI: 10.1093/nar/gkh038
Gene structure conservation aids similarity based gene prediction.

Meyer IM and Durbin R

Nucleic acids research 2004;32;2;776-83

PUBMED: 14764925; PMC: 373336; DOI: 10.1093/nar/gkh211

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

PUBMED: 14624247; PMC: 261899; DOI: 10.1371/journal.pbio.0000045
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

PUBMED: 14574404; DOI: 10.1038/nature02055
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

PUBMED: 12529635; DOI: 10.1038/nature01278
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

PUBMED: 12519943; PMC: 165530; DOI: 10.1093/nar/gkg083

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

Howe K, Bateman A and Durbin R

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

PUBMED: 12424131; DOI: 10.1093/bioinformatics/18.11.1546
Comparative ab initio prediction of gene structures using pair HMMs.

Meyer IM and Durbin R

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

PUBMED: 12376375; DOI: 10.1093/bioinformatics/18.10.1309
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

PUBMED: 12213779; PMC: 186661; DOI: 10.1101/gr.149502
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

PUBMED: 11752248; PMC: 99161; DOI: 10.1093/nar/30.1.38

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

PUBMED: 11237011; DOI: 10.1038/35057062

Career/Research Highlights

Whole genome sequence phylogeny of over 50 Lake Malawi cichlid species that we have sequenced, with illustrations of focal species for which we are collecting population samples. Speciation is very recent or even ongoing, with divergence between species of 0.1% to 0.3% compared to diversity within species of 0.05% to 0.1%.
Rarecoal uses rare segregating variants across a set of population samples to infer population separation times and mean effective population sizes, using a coalescent likelihood approximation.
The populations in the final Phase 3 1000 Genomes Project data set, with per sample diversity and number of singletons per population.

Dr Richard Durbin | Associate Faculty

Durbin, Richard

Publications

Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow.

Variation graph toolkit improves read mapping by representing genetic variation in the reference.

The first horse herders and the impact of early Bronze Age steppe expansions into Asia.

Earth BioGenome Project: Sequencing life for the future of life.

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

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

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

The UK10K project identifies rare variants in health and disease.

A global reference for human genetic variation.

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

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

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

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

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

Insights into hominid evolution from the gorilla genome sequence.

Ancestral hybridisation facilitated species diversification in the Lake Malawi cichlid fish adaptive radiation.

Haplotype-aware graph indexes.

Efficiently Inferring the Demographic History of Many Populations With Allele Count Data

Viral coinfection analysis using a MinHash toolkit.

The population history of northeastern Siberia since the Pleistocene.

Identifying Extrinsic versus Intrinsic Drivers of Variation in Cell Behavior in Human iPSC Lines from Healthy Donors.

A High-Quality De novo Genome Assembly from a Single Mosquito Using PacBio Sequencing.

Crumble: reference free lossy compression of sequence quality values.

GFAKluge: A C++ library and command line utilities for the Graphical Fragment Assembly formats.

Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow.

Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci.

Variation graph toolkit improves read mapping by representing genetic variation in the reference.

Detecting archaic introgression using an unadmixed outgroup.

Did Our Species Evolve in Subdivided Populations across Africa, and Why Does It Matter?

A graph-based approach to diploid genome assembly.

The first horse herders and the impact of early Bronze Age steppe expansions into Asia.

Earth BioGenome Project: Sequencing life for the future of life.

Estimating the human mutation rate from autozygous segments reveals population differences in human mutational processes.

No evidence for maintenance of a sympatric Heliconius species barrier by chromosomal inversions.

Enrichment of low-frequency functional variants revealed by whole-genome sequencing of multiple isolated European populations.

De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms.

Common genetic variation drives molecular heterogeneity in human iPSCs.

Contrasting evolutionary genome dynamics between domesticated and wild yeasts.

Whole-Genome Sequencing Coupled to Imputation Discovers Genetic Signals for Anthropometric Traits.

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

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

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

Reference-based phasing using the Haplotype Reference Consortium panel.

A genomic history of Aboriginal Australia.

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

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

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

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

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

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

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

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

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

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

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

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

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

A global reference for human genetic variation.

The UK10K project identifies rare variants in health and disease.

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

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

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

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

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

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

Characterization of functional methylomes by next-generation capture sequencing identifies novel disease-associated variants.

Deficiency of ECHS1 causes mitochondrial encephalopathy with cardiac involvement.

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

Whole-genome sequence-based analysis of thyroid function.

The genomic and phenotypic diversity of Schizosaccharomyces pombe.

Extending reference assembly models.

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

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

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

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

Managing clinically significant findings in research: the UK10K example.

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