Author: Richard Durbin

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Preprints

The complete sequence of a human genome

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  • Site-wide: 173

Population Genomics of Stone Age Eurasia

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  • Site-wide: 871
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Genome Graphs

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  • Site-wide: 1,358
  • In bioinformatics: 65
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  • Site-wide: 21,646

The population history of northeastern Siberia since the Pleistocene

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  • Site-wide: 3,648

Insights into human genetic variation and population history from 929 diverse genomes

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  • Site-wide: 1,620
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  • Site-wide: 15,213
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  • Site-wide: 21,846

Towards complete and error-free genome assemblies of all vertebrate species

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  • Site-wide: 2,436
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  • Site-wide: 7,425
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  • Site-wide: 6,966

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

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  • Site-wide: 2,522
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  • Site-wide: 194,295
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  • Site-wide: 145,837

Inferring human population size and separation history from multiple genome sequences

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  • Site-wide: 3,011
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  • Site-wide: 15,234
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  • Site-wide: 117,231

A reference panel of 64,976 haplotypes for genotype imputation

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  • Site-wide: 3,766
  • In genetics: 105
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  • Site-wide: 38,168
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  • Site-wide: 149,031

Sequence variation aware genome references and read mapping with the variation graph toolkit

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  • Site-wide: 4,550
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  • Site-wide: 37,178
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  • Site-wide: 200,186

souporcell: Robust clustering of single cell RNAseq by genotype and ambient RNA inference without reference genotypes

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  • Site-wide: 5,127
  • In bioinformatics: 462
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  • Site-wide: 180,481
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Efficiently inferring the demographic history of many populations with allele count data

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  • Site-wide: 5,387
  • In evolutionary biology: 87
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  • Site-wide: 37,216
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  • Site-wide: 15,858

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

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  • Site-wide: 5,887
  • In evolutionary biology: 100
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  • Site-wide: 100,145
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  • Site-wide: 95,013

Identifying and removing haplotypic duplication in primary genome assemblies

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  • Site-wide: 6,013
  • In bioinformatics: 552
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  • Site-wide: 15,238
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  • Site-wide: 15,839

Common genetic variation drives molecular heterogeneity in human iPSCs

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  • Site-wide: 7,364
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  • Site-wide: 105,477
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  • Site-wide: 152,458

Placing ancient DNA sequences into reference phylogenies

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  • Site-wide: 7,734
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  • Site-wide: 22,012
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  • Site-wide: 19,669

Reference-based phasing using the Haplotype Reference Consortium panel

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  • Site-wide: 12,599
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  • Site-wide: 31,740
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  • Site-wide: 76,013

Using reference-free compressed data structures to analyse sequencing reads from thousands of human genomes

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  • Site-wide: 13,155
  • In genomics: 1,188
• Year to date:
  • Site-wide: 174,987
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  • Site-wide: 60,414

Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph

• Downloaded 2,018 times
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  • Site-wide: 13,273
  • In genomics: 1,199
• Year to date:
  • Site-wide: 61,164
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  • Site-wide: 163,933

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

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  • Site-wide: 14,277
  • In genomics: 1,299
• Year to date:
  • Site-wide: 31,549
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  • Site-wide: 26,197

Multiple laboratory mouse reference genomes define strain specific haplotypes and novel functional loci

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  • Site-wide: 15,778
  • In genomics: 1,442
• Year to date:
  • Site-wide: 107,551
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  • Site-wide: 20,274

A High-Quality De Novo Genome Assembly from a Single Mosquito using PacBio Sequencing

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  • Site-wide: 15,838
  • In genomics: 1,431
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  • Site-wide: 139,979
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  • Site-wide: 198,625

A haplotype-aware de novo assembly of related individuals using pedigree graph

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  • Site-wide: 21,269
  • In bioinformatics: 2,337
• Year to date:
  • Site-wide: 142,145
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  • Site-wide: 148,854

Contrasting genome dynamics between domesticated and wild yeasts

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  • Site-wide: 21,751
  • In genomics: 1,893
• Year to date:
  • Site-wide: 105,539
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  • Site-wide: 92,483

trio-sga: facilitating de novo assembly of highly heterozygous genomes with parent-child trios

• Downloaded 1,316 times
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  • Site-wide: 26,054
  • In bioinformatics: 2,805
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  • Site-wide: 82,396
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  • Site-wide: 75,411

Identifying extrinsic versus intrinsic drivers of variation in cell behaviour in human iPS cell lines from healthy donors

• Downloaded 1,308 times
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  • Site-wide: 26,310
  • In cell biology: 911
• Year to date:
  • Site-wide: 102,839
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  • Site-wide: 118,052

Transcriptome Sequencing Reveals Widespread Gene-Gene and Gene-Environment Interactions

• Downloaded 1,301 times
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  • Site-wide: 26,533
  • In genomics: 2,248
• Year to date:
  • Site-wide: 174,929
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  • Site-wide: 151,779

A direct multi-generational estimate of the human mutation rate from autozygous segments seen in thousands of parentally related individuals

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  • Site-wide: 26,889
  • In genomics: 2,279
• Year to date:
  • Site-wide: 141,705
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  • Site-wide: 152,421

Narrow-sense heritability estimation of complex traits using identity-by-descent information.

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  • Site-wide: 27,350
  • In genetics: 1,093
• Year to date:
  • Site-wide: 47,590
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  • Site-wide: 178,066

Detecting archaic introgression without archaic reference genomes

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  • Site-wide: 28,032
  • In evolutionary biology: 947
• Year to date:
  • Site-wide: 105,381
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  • Site-wide: 197,915

The Selection Landscape and Genetic Legacy of Ancient Eurasians

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  • Site-wide: 29,191
  • In evolutionary biology: 1,267
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  • Site-wide: 1,336
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  • Site-wide: 2,737

Complete vertebrate mitogenomes reveal widespread gene duplications and repeats

• Downloaded 1,219 times
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  • Site-wide: 29,399
  • In genomics: 2,490
• Year to date:
  • Site-wide: 62,674
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  • Site-wide: 76,661

Recombination Suppression is Unlikely to Contribute to Speciation in Sympatric Heliconius Butterflies

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  • Site-wide: 30,561
  • In evolutionary biology: 1,094
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  • Site-wide: 180,405
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  • Site-wide: 175,809

Purging of deleterious variants due to drift and founder effect in Italian populations with extended autozygosity

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  • Site-wide: 32,458
  • In evolutionary biology: 1,173
• Year to date:
  • Site-wide: 142,931
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  • Site-wide: 153,774

The rate of false polymorphisms introduced when imputing genotypes from global imputation panels

• Downloaded 1,115 times
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  • Site-wide: 33,823
  • In genetics: 1,342
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  • Site-wide: 163,520
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  • Site-wide: 89,647

YaHS: yet another Hi-C scaffolding tool

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  • Site-wide: 37,076
  • In bioinformatics: 4,134
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  • Site-wide: 4,296
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  • Site-wide: 4,303

Substantial somatic genomic variation and selection for BCOR mutations in human induced pluripotent stem cells

• Downloaded 1,012 times
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  • Site-wide: 39,229
  • In genomics: 3,064
• Year to date:
  • Site-wide: 127,795
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  • Site-wide: 72,479

A high-quality, chromosome-level genome assembly of the Black Soldier Fly (Hermetia Illucens L.)

• Downloaded 972 times
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  • Site-wide: 41,814
  • In genomics: 3,214
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  • Site-wide: 132,469
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  • Site-wide: 65,165

Differential use of multiple genetic sex determination systems in divergent ecomorphs of an African crater lake cichlid

• Downloaded 939 times
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  • Site-wide: 44,041
  • In evolutionary biology: 1,781
• Year to date:
  • Site-wide: 45,177
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  • Site-wide: 28,485

Fast and scalable genome-wide inference of local tree topologies from large number of haplotypes based on tree consistent PBWT data structure

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  • Site-wide: 44,296
  • In genomics: 3,365
• Year to date:
  • Site-wide: 107,055
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  • Site-wide: 119,624

Haplotype-aware graph indexes

• Downloaded 934 times
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  • Site-wide: 44,419
  • In bioinformatics: 4,634
• Year to date:
  • Site-wide: 106,493
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  • Site-wide: 32,830

The methylomes of Lake Malawi cichlids reveal epigenetic variation associated with phenotypic diversification

• Downloaded 808 times
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  • Site-wide: 55,361
  • In evolutionary biology: 2,302
• Year to date:
  • Site-wide: 152,835
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  • Site-wide: 213,709

A haplotype-resolved, de novo genome assembly for the wood tiger moth (Arctia plantaginis) through trio binning

• Downloaded 772 times
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  • Site-wide: 59,273
  • In genomics: 4,154
• Year to date:
  • Site-wide: 181,861
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  • Site-wide: 127,924

Crumble: reference free lossy compression of sequence quality values

• Downloaded 770 times
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  • Site-wide: 59,514
  • In bioinformatics: 5,725
• Year to date:
  • Site-wide: 197,844
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  • Site-wide: 197,502

Caecilian genomes reveal molecular basis of adaptation and convergent evolution of limblessness in snakes and caecilians.

• Downloaded 747 times
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  • Site-wide: 62,283
  • In evolutionary biology: 2,701
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Genomics of cold adaptations in the Antarctic notothenioid fish radiation.

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  • Site-wide: 63,678
  • In genomics: 4,744
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  • Site-wide: 4,792
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  • Site-wide: 8,485

Genome sequence assembly evaluation using long-range sequencing data

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  • Site-wide: 68,581
  • In bioinformatics: 6,670
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  • Site-wide: 17,486
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Ancestral hybridisation facilitated species diversification in the Lake Malawi cichlid fish adaptive radiation

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  • Site-wide: 73,667
  • In evolutionary biology: 3,237
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  • Site-wide: 202,245

False gene and chromosome losses affected by assembly and sequence errors

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  • Site-wide: 74,964
  • In genomics: 4,975
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  • Site-wide: 127,215
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  • Site-wide: 28,624

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

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  • Site-wide: 91,297
  • In genomics: 5,665
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  • Site-wide: 199,049

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

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  • Site-wide: 95,598
  • In genetics: 3,621
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  • Site-wide: 202,118

Epigenetic Divergence during Early Stages of Speciation in an African Crater Lake Cichlid Fish

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  • Site-wide: 110,957
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  • Site-wide: 48,563

Ecological speciation promoted by divergent regulation of functional genes within African cichlid fishes

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  • Site-wide: 115,640
  • In evolutionary biology: 5,454
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  • Site-wide: 26,553

High resolution species assignment of Anopheles mosquitoes using k-mer distances on targeted sequences

• Downloaded 447 times
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  • Site-wide: 117,527
  • In evolutionary biology: 5,494
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  • Site-wide: 127,509
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  • Site-wide: 31,359

Ultra-fast genome-wide inference of pairwise coalescence times

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  • Site-wide: 152,338
  • In genetics: None
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  • Site-wide: 196
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MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio High Fidelity reads

• Downloaded 193 times
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  • Site-wide: 189,461
  • In bioinformatics: 15,327
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  • Site-wide: 2,616
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  • Site-wide: 1,545