RD
Richard Durbin
genomicsSoftwareGenomicsGenomeGenome, HumanAlgorithmsevolutionary biologygeneticsbioinformaticsEvolution, Molecular
On Valency
published · living versionsW_26xzgw86·v1 · currentpublished
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
with Keith R. Bradnam, Joseph N. Fass, Anton Alexandrov, Paul Baranay +86
1 version
Preprints & journals
304 papers in the corpus · 1985–2026Author Correction: Long-read sequencing reveals pre-meiotic gene conversion in sperm.42897286 · Schweiger, Regev, Lee, Sangjin, Zhou, Chenxi et al.2026 · 0 citationsNature. 2026
A Run-Length-Compressed Skiplist Data Structure for Dynamic GBWTs Supports Time- and Space-Efficient Pangenome Operations over Syncmers.42878135 · Durbin, Richard2026 · 1 citationJournal of computational biology : a journal of computational molecular cell biology. 2026:15578666261495122
Near-complete genomes for nine haplochromine cichlid fishes reveal a novel centromeric satellite structure organised around a pair of inverted elements.42855603 · Sierra, Pio, Zhou, Chenxi, Fischer, Bettina et al.2026 · 0 citationsChromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology. 2026;34(1)
Generating eukaryotic reference genome assemblies: Earth BioGenome Project quality standards and recommendations.42859441 · Howe, Kerstin, Agius, Dolores R, Alioto, Tyler et al.2026 · 0 citationsArXiv. 2026
Deep coalescent history of the hominin lineage.42821567 · Cousins, Trevor, Durbin, Richard, Schweiger, Regev2026 · 2 citationsGenetics. 2026
Long-read sequencing reveals pre-meiotic gene conversion in sperm.42649296 · Schweiger, Regev, Lee, Sangjin, Zhou, Chenxi et al.2026 · 1 citationNature. 2026;657(8133):981-987
HPRC2: A human pangenome reference with near-complete coverage of common genetic variation.42539208 · Lucas, Julian K, Hebbar, Prajna, Liao, Wen-Wei et al.2026 · 9 citationsbioRxiv : the preprint server for biology. 2026
The Vertebrate Genomes Project Phase I: A global reference genome resource.42395566 · Formenti, Giulio, Absolon, Dominic E, Abueg, Linelle Ann L et al.2026 · 10 citationsbioRxiv : the preprint server for biology. 2026
340 dipteran genomes reveal the origin of Muller elements and sex chromosomes in Diptera10.64898/2026.06.01.729285v1 · Gries, J., Ebdon, S., Bliznina, A. et al.2026 · 3 citationsbioRxiv
Cryptic Diversity and Impacts of Domestication in the Black Soldier Fly (Hermetia illucens) Genome.41984023 · Generalovic, Tomas N, Sandrock, Christoph, Roberts, Benjamin J et al.2026 · 15 citationsGenome biology and evolution. 2026;18(5)
A new phased assembly of the Antarctic spiny plunderfish provides novel insights into the evolution of the notothenioid radiation.42079040 · Martelossi, Jacopo, Krasheninnikova, Ksenia, Denton, Amy et al.2026 · 0 citationsbioRxiv : the preprint server for biology. 2026
Genetic architecture of cichlid brain morphology10.64898/2026.04.01.715931v1 · Morris, J., Rivas-Sanchez, D. F., Elkin, J. et al.2026 · 0 citationsbioRxiv
The Genomics of Convergent Adaptation to Intertidal Gravel Beaches in Mediterranean Clingfishes.41671394 · Wagner, Maximilian, Resl, Philipp, Klar, Nadine et al.2026 · 5 citationsGenome biology and evolution. 2026;18(3)
Phylogenomics of Cypriniformes, the most diverse order of freshwater fishes: consensus, challenges and limitations10.64898/2026.01.14.699467v1 · Sudasinghe, H., Britz, R., Matschiner, M. et al.2026 · 8 citationsbioRxiv
Pangenome-guided sequence assembly via binary optimization.41744226 · Cudby, Josh, Bonfield, James, Zhou, Chenxi et al.2026 · 1 citationBriefings in bioinformatics. 2026;27(1)
Somatic and germline mutational processes across the tree of life10.64898/2025.12.28.691837v1 · Lee, S., Wang, Y., Haynes, H. et al.2025 · 2 citationsbioRxiv
fgf8a signalling shapes brain divergence between Malawi cichlids10.1101/2025.10.13.682009v1 · Marconi, A., Morris, J., Sierra, P. et al.2025 · 0 citationsbioRxiv
FastGA: fast genome alignment.41262969 · Myers, Gene, Durbin, Richard, Zhou, Chenxi2025 · 6 citationsBioinformatics advances. 2025;5(1):vbaf238
WinPCA: a package for windowed principal component analysis.40981508 · Blumer, L Moritz, Good, Jeffrey M, Durbin, Richard2025 · 10 citationsBioinformatics (Oxford, England). 2025;41(10)
Pangenome-guided sequence assembly via binary optimisation2508.08200v2 · Josh Cudby, James Bonfield, Chenxi Zhou et al.2025 · 0 citationsarXiv
Oatk: a de novo assembly tool for complex plant organelle genomes.40775726 · Zhou, Chenxi, Brown, Max, Blaxter, Mark et al.2025 · 280 citationsGenome biology. 2025;26(1):235
Hi-reComb: constructing recombination maps from bulk gamete Hi-C sequencing.40161681 · Malinsky, Milan, Talbi, Marion, Zhou, Chenxi et al.2026 · 2 citationsbioRxiv : the preprint server for biology. 2025
Introgression dynamics of sex-linked chromosomal inversions shape the Malawi cichlid radiation.40504893 · Blumer, L M, Burskaia, V, Artiushin, I et al.2025 · 40 citationsScience (New York, N.Y.). 2025;388(6752):eadr9961
Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements.40210437 · Quah, Fu Xiang, Almeida, Miguel Vasconcelos, Blumer, Moritz et al.2025 · 17 citationsGenome research. 2025;35(5):1094-1107
Sparse haplotype-based fine-scale local ancestry inference at scale reveals recent selection on immune responses.40113767 · Yang, Yaoling, Durbin, Richard, Iversen, Astrid K N et al.2025 · 13 citationsNature communications. 2025;16(1):2742
A structured coalescent model reveals deep ancestral structure shared by all modern humans.40102687 · Cousins, Trevor, Scally, Aylwyn, Durbin, Richard2025 · 32 citationsNature genetics. 2025;57(4):856-864
MCHelper automatically curates transposable element libraries across eukaryotic species.39653419 · Orozco-Arias, Simon, Sierra, Pío, Durbin, Richard et al.2024 · 37 citationsGenome research. 2024;34(12):2256-2268
Genomic diversity of the African malaria vector Anopheles funestus.39763861 · Boddé, Marilou, Nwezeobi, Joachim, Korlević, Petra et al.2025 · 21 citationsbioRxiv : the preprint server for biology. 2024
Deep coalescent history of the hominin lineage10.1101/2024.10.17.618932v4 · Cousins, T., Durbin, R., Schweiger, R.2024 · 2 citationsbioRxiv
The Hypolimnas misippus Genome Supports a Common Origin of the W Chromosome in Lepidoptera.39475310 · Orteu, Anna, McCarthy, Shane A, Hornett, Emily A et al.2024 · 3 citationsGenome biology and evolution. 2024;16(10)
Genomic evidence reveals three W-autosome fusions in Heliconius butterflies.39024186 · Rueda-M, Nicol, Pardo-Diaz, Carolina, Montejo-Kovacevich, Gabriela et al.2024 · 8 citationsPLoS genetics. 2024;20(7):e1011318
Insights into non-crossover recombination from long-read sperm sequencing.39005338 · Schweiger, Regev, Lee, Sangjin, Zhou, Chenxi et al.2024 · 11 citationsbioRxiv : the preprint server for biology. 2024
Identification of transposable element families from pangenome polymorphisms.38926873 · Sierra, Pío, Durbin, Richard2026 · 25 citationsMobile DNA. 2024;15(1):13
Genetic and developmental divergence in the neural crest programme between cichlid fish species.38352436 · Marconi, Aleksandra, Vernaz, Grégoire, Karunaratna, Achira et al.2026 · 4 citationsbioRxiv : the preprint server for biology. 2024
Genome assembly in the telomere-to-telomere era.38649458 · Li, Heng, Durbin, Richard2024 · 235 citationsNature reviews. Genetics. 2024;25(9):658-670
The genome sequence of the Dracula fish, Danionella dracula (Britz, Conway & Rüber, 2009).39224769 · Rüber, Lukas, Britz, Ralf, Conway, Kevin et al.2024 · 3 citationsWellcome open research. 2024;9:194
Dynamic co-evolution of transposable elements and the piRNA pathway in African cichlid fishes.38617250 · Almeida, Miguel Vasconcelos, Blumer, Moritz, Yuan, Chengwei Ulrika et al.2026 · 10 citationsbioRxiv : the preprint server for biology. 2024
A pangenomic perspective of the Lake Malawi cichlid radiation reveals extensive structural variation driven by transposable elements10.1101/2024.03.28.587230v1 · Quah, F. X., Almeida, M. V., Blumer, M. et al.2024 · 8 citationsbioRxiv
Ancient genomes illuminate Eastern Arabian population history and adaptation against malaria.38417441 · Martiniano, Rui, Haber, Marc, Almarri, Mohamed A et al.2024 · 10 citationsCell genomics. 2024;4(3):100507
Publisher Correction: Population genomics of post-glacial western Eurasia.38238538 · Allentoft, Morten E, Sikora, Martin, Refoyo-Martínez, Alba et al.2026 · 0 citationsNature. 2024;626(7997):E3
The selection landscape and genetic legacy of ancient Eurasians.38200293 · Irving-Pease, Evan K, Refoyo-Martínez, Alba, Barrie, William et al.2024 · 153 citationsNature. 2024;625(7994):312-320
100 ancient genomes show repeated population turnovers in Neolithic Denmark.38200294 · Allentoft, Morten E, Sikora, Martin, Fischer, Anders et al.2024 · 114 citationsNature. 2024;625(7994):329-337
Population genomics of post-glacial western Eurasia.38200295 · Allentoft, Morten E, Sikora, Martin, Refoyo-Martínez, Alba et al.2024 · 208 citationsNature. 2024;625(7994):301-311
Rotate: A command-line program to rotate circular DNA sequences to start at a given position or string.38680652 · Durbin, Richard, De Sanctis, Bianca, Blumer, Moritz2025 · 18 citationsWellcome open research. 2023;8:401
A deep learning phenotyping method for genetic analysis of 3D micro-CT data10.1101/2023.08.24.554725v2 · Karshenas, A., Linderoth, T. P., Zatha, R. et al.2023 · 0 citationsbioRxiv
Genome assembly in the telomere-to-telomere era.37645045 · Li, Heng, Durbin, Richard2025 · 8 citationsArXiv. 2023
MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads.37464285 · Uliano-Silva, Marcela, Ferreira, João Gabriel R N, Krasheninnikova, Ksenia et al.2023 · 1,962 citationsBMC bioinformatics. 2023;24(1):288
Ultrafast genome-wide inference of pairwise coalescence times.37562965 · Schweiger, Regev, Durbin, Richard2023 · 14 citationsGenome research. 2023;33(7):1023-1031
Genomics of cold adaptations in the Antarctic notothenioid fish radiation.37296119 · Bista, Iliana, Wood, Jonathan M D, Desvignes, Thomas et al.2023 · 94 citationsNature communications. 2023;14(1):3412
Caecilian Genomes Reveal the Molecular Basis of Adaptation and Convergent Evolution of Limblessness in Snakes and Caecilians.37194566 · Ovchinnikov, Vladimir, Uliano-Silva, Marcela, Wilkinson, Mark et al.2023 · 21 citationsMolecular biology and evolution. 2023;40(5)
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