Durbin, Richard
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
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Iron Age and Anglo-Saxon genomes from East England reveal British migration history.
Nature communications 2016;7;10408
PUBMED: 26783965; PMC: 4735688; DOI: 10.1038/ncomms10408
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Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake.
Science (New York, N.Y.) 2015;350;6267;1493-1498
PUBMED: 26680190; PMC: 4700518; DOI: 10.1126/science.aac9927
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The UK10K project identifies rare variants in health and disease.
Nature 2015;526;7571;82-90
PUBMED: 26367797; PMC: 4773891; DOI: 10.1038/nature14962
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A global reference for human genetic variation.
Nature 2015;526;7571;68-74
PUBMED: 26432245; PMC: 4750478; DOI: 10.1038/nature15393
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Inferring human population size and separation history from multiple genome sequences.
Nature genetics 2014;46;8;919-25
PUBMED: 24952747; PMC: 4116295; DOI: 10.1038/ng.3015
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Genetic interactions affecting human gene expression identified by variance association mapping.
eLife 2014;3;e01381
PUBMED: 24771767; PMC: 4017648; DOI: 10.7554/eLife.01381
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Efficient haplotype matching and storage using the positional Burrows-Wheeler transform (PBWT).
Bioinformatics (Oxford, England) 2014;30;9;1266-72
PUBMED: 24413527; PMC: 3998136; DOI: 10.1093/bioinformatics/btu014
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Revising the human mutation rate: implications for understanding human evolution.
Nature reviews. Genetics 2012;13;10;745-53
PUBMED: 22965354; DOI: 10.1038/nrg3295
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Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses.
Nature protocols 2012;7;3;500-7
PUBMED: 22343431; PMC: 3398141; DOI: 10.1038/nprot.2011.457
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Efficient de novo assembly of large genomes using compressed data structures.
Genome research 2012;22;3;549-56
PUBMED: 22156294; PMC: 3290790; DOI: 10.1101/gr.126953.111
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Inference of human population history from individual whole-genome sequences.
Nature 2011;475;7357;493-6
PUBMED: 21753753; PMC: 3154645; DOI: 10.1038/nature10231
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Insights into hominid evolution from the gorilla genome sequence.
Nature 2012;483;7388;169-75
PUBMED: 22398555; PMC: 3303130; DOI: 10.1038/nature10842
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Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci.
Nature genetics 2018;50;11;1574-1583
PUBMED: 30275530; PMC: 6205630; DOI: 10.1038/s41588-018-0223-8
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Detecting archaic introgression using an unadmixed outgroup.
PLoS genetics 2018;14;9;e1007641
PUBMED: 30226838; DOI: 10.1371/journal.pgen.1007641
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Variation graph toolkit improves read mapping by representing genetic variation in the reference.
Nature biotechnology 2018
PUBMED: 30125266; DOI: 10.1038/nbt.4227
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Did Our Species Evolve in Subdivided Populations across Africa, and Why Does It Matter?
Trends in ecology & evolution 2018;33;8;582-594
PUBMED: 30007846; PMC: 6092560; DOI: 10.1016/j.tree.2018.05.005
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Crumble: reference free lossy compression of sequence quality values.
Bioinformatics (Oxford, England) 2018
PUBMED: 29992288; DOI: 10.1093/bioinformatics/bty608
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A graph-based approach to diploid genome assembly.
Bioinformatics (Oxford, England) 2018;34;13;i105-i114
PUBMED: 29949989; DOI: 10.1093/bioinformatics/bty279
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Estimating the human mutation rate from autozygous segments reveals population differences in human mutational processes.
Nature communications 2017;8;1;303
PUBMED: 28827725; DOI: 10.1038/s41467-017-00323-y
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De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms.
Scientific reports 2017;7;1;3935
PUBMED: 28638050; PMC: 5479803; DOI: 10.1038/s41598-017-03996-z
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Common genetic variation drives molecular heterogeneity in human iPSCs.
Nature 2017;546;7658;370-375
PUBMED: 28489815; PMC: 5524171; DOI: 10.1038/nature22403
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Contrasting evolutionary genome dynamics between domesticated and wild yeasts.
Nature genetics 2017;49;6;913-924
PUBMED: 28416820; PMC: 5446901; DOI: 10.1038/ng.3847
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Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly.
Genome research 2017;27;5;849-864
PUBMED: 28396521; PMC: 5411779; DOI: 10.1101/gr.213611.116
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Whole-genome view of the consequences of a population bottleneck using 2926 genome sequences from Finland and United Kingdom.
European journal of human genetics : EJHG 2017;25;4;477-484
PUBMED: 28145424; PMC: 5346294; DOI: 10.1038/ejhg.2016.205
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Whole-exome sequencing of 228 patients with sporadic Parkinson's disease.
Scientific reports 2017;7;41188
PUBMED: 28117402; DOI: 10.1038/srep41188
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Reference-based phasing using the Haplotype Reference Consortium panel.
Nature genetics 2016;48;11;1443-1448
PUBMED: 27694958; PMC: 5096458; DOI: 10.1038/ng.3679
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A genomic history of Aboriginal Australia.
Nature 2016;538;7624;207-214
PUBMED: 27654914; DOI: 10.1038/nature18299
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A reference panel of 64,976 haplotypes for genotype imputation.
Nature genetics 2016;48;10;1279-83
PUBMED: 27548312; PMC: 5388176; DOI: 10.1038/ng.3643
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Whole-exome sequencing in an isolated population from the Dalmatian island of Vis.
European journal of human genetics : EJHG 2016;24;10;1479-87
PUBMED: 27049301; PMC: 4950961; DOI: 10.1038/ejhg.2016.23
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TTC25 Deficiency Results in Defects of the Outer Dynein Arm Docking Machinery and Primary Ciliary Dyskinesia with Left-Right Body Asymmetry Randomization.
American journal of human genetics 2016;99;2;460-9
PUBMED: 27486780; PMC: 4974089; DOI: 10.1016/j.ajhg.2016.06.014
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DNAH11 Localization in the Proximal Region of Respiratory Cilia Defines Distinct Outer Dynein Arm Complexes.
American journal of respiratory cell and molecular biology 2016;55;2;213-24
PUBMED: 26909801; PMC: 4979367; DOI: 10.1165/rcmb.2015-0353OC
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Deficient methylation and formylation of mt-tRNA(Met) wobble cytosine in a patient carrying mutations in NSUN3.
Nature communications 2016;7;12039
PUBMED: 27356879; PMC: 4931328; DOI: 10.1038/ncomms12039
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GENOMICS. A federated ecosystem for sharing genomic, clinical data.
Science (New York, N.Y.) 2016;352;6291;1278-80
PUBMED: 27284183; DOI: 10.1126/science.aaf6162
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BCFtools/RoH: a hidden Markov model approach for detecting autozygosity from next-generation sequencing data.
Bioinformatics (Oxford, England) 2016;32;11;1749-51
PUBMED: 26826718; PMC: 4892413; DOI: 10.1093/bioinformatics/btw044
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Health and population effects of rare gene knockouts in adult humans with related parents.
Science (New York, N.Y.) 2016;352;6284;474-7
PUBMED: 26940866; PMC: 4985238; DOI: 10.1126/science.aac8624
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A high-content platform to characterise human induced pluripotent stem cell lines.
Methods (San Diego, Calif.) 2016;96;85-96
PUBMED: 26608109; PMC: 4773406; DOI: 10.1016/j.ymeth.2015.11.012
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Bi-allelic Truncating Mutations in TANGO2 Cause Infancy-Onset Recurrent Metabolic Crises with Encephalocardiomyopathy.
American journal of human genetics 2016;98;2;358-62
PUBMED: 26805782; PMC: 4746337; DOI: 10.1016/j.ajhg.2015.12.009
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Iron Age and Anglo-Saxon genomes from East England reveal British migration history.
Nature communications 2016;7;10408
PUBMED: 26783965; PMC: 4735688; DOI: 10.1038/ncomms10408
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A Method for Checking Genomic Integrity in Cultured Cell Lines from SNP Genotyping Data.
PloS one 2016;11;5;e0155014
PUBMED: 27176002; PMC: 4866717; DOI: 10.1371/journal.pone.0155014
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Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake.
Science (New York, N.Y.) 2015;350;6267;1493-1498
PUBMED: 26680190; PMC: 4700518; DOI: 10.1126/science.aac9927
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A global reference for human genetic variation.
Nature 2015;526;7571;68-74
PUBMED: 26432245; PMC: 4750478; DOI: 10.1038/nature15393
-
The UK10K project identifies rare variants in health and disease.
Nature 2015;526;7571;82-90
PUBMED: 26367797; PMC: 4773891; DOI: 10.1038/nature14962
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Homozygous loss-of-function variants in European cosmopolitan and isolate populations.
Human molecular genetics 2015;24;19;5464-74
PUBMED: 26173456; PMC: 4572071; DOI: 10.1093/hmg/ddv272
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Immunofluorescence Analysis and Diagnosis of Primary Ciliary Dyskinesia with Radial Spoke Defects.
American journal of respiratory cell and molecular biology 2015;53;4;563-73
PUBMED: 25789548; PMC: 5306451; DOI: 10.1165/rcmb.2014-0483OC
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Whole-genome sequencing identifies EN1 as a determinant of bone density and fracture.
Nature 2015;526;7571;112-7
PUBMED: 26367794; PMC: 4755714; DOI: 10.1038/nature14878
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Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel.
Nature communications 2015;6;8111
PUBMED: 26368830; PMC: 4579394; DOI: 10.1038/ncomms9111
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POPULATION GENETICS. Genomic evidence for the Pleistocene and recent population history of Native Americans.
Science (New York, N.Y.) 2015;349;6250;aab3884
PUBMED: 26198033; PMC: 4733658; DOI: 10.1126/science.aab3884
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Tracing the route of modern humans out of Africa by using 225 human genome sequences from Ethiopians and Egyptians.
American journal of human genetics 2015;96;6;986-91
PUBMED: 26027499; PMC: 4457944; DOI: 10.1016/j.ajhg.2015.04.019
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Deficiency of ECHS1 causes mitochondrial encephalopathy with cardiac involvement.
Annals of clinical and translational neurology 2015;2;5;492-509
PUBMED: 26000322; PMC: 4435704; DOI: 10.1002/acn3.189
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Pathway-based factor analysis of gene expression data produces highly heritable phenotypes that associate with age.
G3 (Bethesda, Md.) 2015;5;5;839-47
PUBMED: 25758824; PMC: 4426370; DOI: 10.1534/g3.114.011411
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Whole-genome sequence-based analysis of thyroid function.
Nature communications 2015;6;5681
PUBMED: 25743335; PMC: 4366514; DOI: 10.1038/ncomms6681
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The genomic and phenotypic diversity of Schizosaccharomyces pombe.
Nature genetics 2015;47;3;235-41
PUBMED: 25665008; PMC: 4645456; DOI: 10.1038/ng.3215
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Extending reference assembly models.
Genome biology 2015;16;13
PUBMED: 25651527; PMC: 4305238; DOI: 10.1186/s13059-015-0587-3
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Gene-gene and gene-environment interactions detected by transcriptome sequence analysis in twins.
Nature genetics 2015;47;1;88-91
PUBMED: 25436857; PMC: 4643454; DOI: 10.1038/ng.3162
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Estimation of epistatic variance components and heritability in founder populations and crosses.
Genetics 2014;198;4;1405-16
PUBMED: 25326236; PMC: 4256760; DOI: 10.1534/genetics.114.170795
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Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association.
PLoS genetics 2014;10;11;e1004798
PUBMED: 25411781; PMC: 4238955; DOI: 10.1371/journal.pgen.1004798
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A rare variant in APOC3 is associated with plasma triglyceride and VLDL levels in Europeans.
Nature communications 2014;5;4871
PUBMED: 25225788; PMC: 4167609; DOI: 10.1038/ncomms5871
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Managing clinically significant findings in research: the UK10K example.
European journal of human genetics : EJHG 2014;22;9;1100-4
PUBMED: 24424120; PMC: 4026295; DOI: 10.1038/ejhg.2013.290
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Inferring human population size and separation history from multiple genome sequences.
Nature genetics 2014;46;8;919-25
PUBMED: 24952747; PMC: 4116295; DOI: 10.1038/ng.3015
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Distribution and medical impact of loss-of-function variants in the Finnish founder population.
PLoS genetics 2014;10;7;e1004494
PUBMED: 25078778; PMC: 4117444; DOI: 10.1371/journal.pgen.1004494
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Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences.
Genome biology 2014;15;6;R88
PUBMED: 24980144; PMC: 4197830; DOI: 10.1186/gb-2014-15-6-r88
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Efficient haplotype matching and storage using the positional Burrows-Wheeler transform (PBWT).
Bioinformatics (Oxford, England) 2014;30;9;1266-72
PUBMED: 24413527; PMC: 3998136; DOI: 10.1093/bioinformatics/btu014
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Estimating telomere length from whole genome sequence data.
Nucleic acids research 2014;42;9;e75
PUBMED: 24609383; PMC: 4027178; DOI: 10.1093/nar/gku181
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Genetic interactions affecting human gene expression identified by variance association mapping.
eLife 2014;3;e01381
PUBMED: 24771767; PMC: 4017648; DOI: 10.7554/eLife.01381
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A high-definition view of functional genetic variation from natural yeast genomes.
Molecular biology and evolution 2014;31;4;872-88
PUBMED: 24425782; PMC: 3969562; DOI: 10.1093/molbev/msu037
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High-resolution mapping of complex traits with a four-parent advanced intercross yeast population.
Genetics 2013;195;3;1141-55
PUBMED: 24037264; PMC: 3813843; DOI: 10.1534/genetics.113.155515
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The anatomy of successful computational biology software.
Nature biotechnology 2013;31;10;894-7
PUBMED: 24104757; PMC: 4166496; DOI: 10.1038/nbt.2721
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A genome-wide survey of genetic variation in gorillas using reduced representation sequencing.
PloS one 2013;8;6;e65066
PUBMED: 23750230; PMC: 3672199; DOI: 10.1371/journal.pone.0065066
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An integrated map of genetic variation from 1,092 human genomes.
Nature 2012;491;7422;56-65
PUBMED: 23128226; PMC: 3498066; DOI: 10.1038/nature11632
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Mapping cis- and trans-regulatory effects across multiple tissues in twins.
Nature genetics 2012;44;10;1084-9
PUBMED: 22941192; PMC: 3784328; DOI: 10.1038/ng.2394
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The 1000 Genomes Project: data management and community access.
Nature methods 2012;9;5;459-62
PUBMED: 22543379; PMC: 3340611; DOI: 10.1038/nmeth.1974
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High levels of RNA-editing site conservation amongst 15 laboratory mouse strains.
Genome biology 2012;13;4;26
PUBMED: 22524474; PMC: 3446300; DOI: 10.1186/gb-2012-13-4-r26
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WormBase: Annotating many nematode genomes.
Worm 2012;1;1;15-21
PUBMED: 24058818; PMC: 3670165; DOI: 10.4161/worm.19574
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Dindel: accurate indel calls from short-read data.
Genome research 2011;21;6;961-73
PUBMED: 20980555; PMC: 3106329; DOI: 10.1101/gr.112326.110
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Ensembl 2011.
Nucleic acids research 2011;39;Database issue;D800-6
PUBMED: 21045057; PMC: 3013672; DOI: 10.1093/nar/gkq1064
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A map of human genome variation from population-scale sequencing.
Nature 2010;467;7319;1061-73
PUBMED: 20981092; PMC: 3042601; DOI: 10.1038/nature09534
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A Bayesian framework to account for complex non-genetic factors in gene expression levels greatly increases power in eQTL studies.
PLoS computational biology 2010;6;5;e1000770
PUBMED: 20463871; PMC: 2865505; DOI: 10.1371/journal.pcbi.1000770
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Systematic analysis of human protein complexes identifies chromosome segregation proteins.
Science (New York, N.Y.) 2010;328;5978;593-9
PUBMED: 20360068; PMC: 2989461; DOI: 10.1126/science.1181348
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Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes.
Nature 2010;464;7289;721-7
PUBMED: 20360735; PMC: 3108885; DOI: 10.1038/nature08869
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Copy number variant detection in inbred strains from short read sequence data.
Bioinformatics (Oxford, England) 2010;26;4;565-7
PUBMED: 20022973; PMC: 2820678; DOI: 10.1093/bioinformatics/btp693
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Ensembl's 10th year.
Nucleic acids research 2010;38;Database issue;D557-62
PUBMED: 19906699; PMC: 2808936; DOI: 10.1093/nar/gkp972
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Prepublication data sharing.
Nature 2009;461;7261;168-70
PUBMED: 19741685; PMC: 3073843; DOI: 10.1038/461168a
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The Sequence Alignment/Map format and SAMtools.
Bioinformatics (Oxford, England) 2009;25;16;2078-9
PUBMED: 19505943; PMC: 2723002; DOI: 10.1093/bioinformatics/btp352
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The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes.
Genome research 2009;19;7;1316-23
PUBMED: 19498102; PMC: 2704439; DOI: 10.1101/gr.080531.108
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Population genomics of domestic and wild yeasts.
Nature 2009;458;7236;337-41
PUBMED: 19212322; PMC: 2659681; DOI: 10.1038/nature07743
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Inferring selection on amino acid preference in protein domains.
Molecular biology and evolution 2009;26;3;527-36
PUBMED: 19095755; PMC: 2716081; DOI: 10.1093/molbev/msn286
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Ensembl 2009.
Nucleic acids research 2009;37;Database issue;D690-7
PUBMED: 19033362; PMC: 2686571; DOI: 10.1093/nar/gkn828
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A large genome center's improvements to the Illumina sequencing system.
Nature methods 2008;5;12;1005-10
PUBMED: 19034268; PMC: 2610436; DOI: 10.1038/nmeth.1270
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Accurate whole human genome sequencing using reversible terminator chemistry.
Nature 2008;456;7218;53-9
PUBMED: 18987734; PMC: 2581791; DOI: 10.1038/nature07517
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Mapping short DNA sequencing reads and calling variants using mapping quality scores.
Genome research 2008;18;11;1851-8
PUBMED: 18714091; PMC: 2577856; DOI: 10.1101/gr.078212.108
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A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis.
Nature biotechnology 2008;26;7;779-85
PUBMED: 18612301; PMC: 2644410; DOI: 10.1038/nbt1414
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Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing.
Nature genetics 2008;40;6;722-9
PUBMED: 18438408; PMC: 2705838; DOI: 10.1038/ng.128
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BAC TransgeneOmics: a high-throughput method for exploration of protein function in mammals.
Nature methods 2008;5;5;409-15
PUBMED: 18391959; PMC: 2871289; DOI: 10.1038/nmeth.1199
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Ensembl 2008.
Nucleic acids research 2008;36;Database issue;D707-14
PUBMED: 18000006; PMC: 2238821; DOI: 10.1093/nar/gkm988
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TreeFam: 2008 Update.
Nucleic acids research 2008;36;Database issue;D735-40
PUBMED: 18056084; PMC: 2238856; DOI: 10.1093/nar/gkm1005
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Genomix: a method for combining gene-finders' predictions, which uses evolutionary conservation of sequence and intron-exon structure.
Bioinformatics (Oxford, England) 2007;23;12;1468-75
PUBMED: 17483502; PMC: 2880447; DOI: 10.1093/bioinformatics/btm133
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Ensembl 2007.
Nucleic acids research 2007;35;Database issue;D610-7
PUBMED: 17148474; PMC: 1761443; DOI: 10.1093/nar/gkl996
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Mapping trait loci by use of inferred ancestral recombination graphs.
American journal of human genetics 2006;79;5;910-22
PUBMED: 17033967; PMC: 1698562; DOI: 10.1086/508901
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The DNA sequence and biological annotation of human chromosome 1.
Nature 2006;441;7091;315-21
PUBMED: 16710414; DOI: 10.1038/nature04727
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Ensembl 2006.
Nucleic acids research 2006;34;Database issue;D556-61
PUBMED: 16381931; PMC: 1347495; DOI: 10.1093/nar/gkj133
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TreeFam: a curated database of phylogenetic trees of animal gene families.
Nucleic acids research 2006;34;Database issue;D572-80
PUBMED: 16381935; PMC: 1347480; DOI: 10.1093/nar/gkj118
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The DNA sequence of the human X chromosome.
Nature 2005;434;7031;325-37
PUBMED: 15772651; PMC: 2665286; DOI: 10.1038/nature03440
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Ensembl 2005.
Nucleic acids research 2005;33;Database issue;D447-53
PUBMED: 15608235; PMC: 540092; DOI: 10.1093/nar/gki138
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Improved techniques for the identification of pseudogenes.
Bioinformatics (Oxford, England) 2004;20 Suppl 1;i94-100
PUBMED: 15262786; DOI: 10.1093/bioinformatics/bth942
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The DNA sequence and comparative analysis of human chromosome 10.
Nature 2004;429;6990;375-81
PUBMED: 15164054; DOI: 10.1038/nature02462
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DNA sequence and analysis of human chromosome 9.
Nature 2004;429;6990;369-74
PUBMED: 15164053; PMC: 2734081; DOI: 10.1038/nature02465
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An overview of Ensembl.
Genome research 2004;14;5;925-8
PUBMED: 15078858; PMC: 479121; DOI: 10.1101/gr.1860604
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The DNA sequence and analysis of human chromosome 13.
Nature 2004;428;6982;522-8
PUBMED: 15057823; PMC: 2665288; DOI: 10.1038/nature02379
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Genome sequence of the Brown Norway rat yields insights into mammalian evolution.
Nature 2004;428;6982;493-521
PUBMED: 15057822; DOI: 10.1038/nature02426
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Ensembl 2004.
Nucleic acids research 2004;32;Database issue;D468-70
PUBMED: 14681459; PMC: 308772; DOI: 10.1093/nar/gkh038
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The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics.
PLoS biology 2003;1;2;E45
PUBMED: 14624247; PMC: 261899; DOI: 10.1371/journal.pbio.0000045
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The DNA sequence and analysis of human chromosome 6.
Nature 2003;425;6960;805-11
PUBMED: 14574404; DOI: 10.1038/nature02055
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Systematic functional analysis of the Caenorhabditis elegans genome using RNAi.
Nature 2003;421;6920;231-7
PUBMED: 12529635; DOI: 10.1038/nature01278
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Ensembl 2002: accommodating comparative genomics.
Nucleic acids research 2003;31;1;38-42
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QuickTree: building huge Neighbour-Joining trees of protein sequences.
Bioinformatics (Oxford, England) 2002;18;11;1546-7
PUBMED: 12424131
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Comparative ab initio prediction of gene structures using pair HMMs.
Bioinformatics (Oxford, England) 2002;18;10;1309-18
PUBMED: 12376375
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GAZE: a generic framework for the integration of gene-prediction data by dynamic programming.
Genome research 2002;12;9;1418-27
PUBMED: 12213779; PMC: 186661; DOI: 10.1101/gr.149502
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The Ensembl genome database project.
Nucleic acids research 2002;30;1;38-41
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Initial sequencing and analysis of the human genome.
Nature 2001;409;6822;860-921
PUBMED: 11237011; DOI: 10.1038/35057062