SK
Sergey Koren
genomicsbioinformaticsSoftwareGenomeGenome, HumanGenomicsAlgorithmsEvolution, MolecularDiploidyGenetic Variation
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
158 papers in the corpus · 2008–2026Generating 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
Telomere-to-telomere genome assembly and a pangenome for the rat.42561951 · Li, Kai, Ciosek, Julia L, Koren, Sergey et al.2026 · 1 citationCell genomics. 2026;6(8):101281
Automatic generation of model sequences for complex regions in assembly graphs with TTT.42561952 · Antipov, Dmitry, Chen, Ying, Sollitto, Marco et al.2026 · 0 citationsCell genomics. 2026;6(8):101323
Phased T2T horse and donkey assemblies from a mule reveal peculiar equid centromere evolution.42561953 · Li, Kai, Cappelletti, Eleonora, Dessaix, Carey et al.2026 · 2 citationsCell genomics. 2026;6(8):101307
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
Population-scale Y chromosome assemblies reveal recurrent remodeling within constrained architectures.42282846 · Hallast, Pille, Rhie, Arang, Loftus, Mark et al.2026 · 1 citationbioRxiv : the preprint server for biology. 2026
A complete human pancreatic cancer genome.42146349 · Wagner, Justin, Keskus, Ayse G, Oshima, Keisuke K et al.2026 · 4 citationsbioRxiv : the preprint server for biology. 2026
Biobank-scale genotyping of Robertsonian translocations reveals hidden structural variation on the human acrocentric chromosomes.41959047 · Rhie, Arang, Kim, Juhyun, Rodriguez-Algarra, Francisco et al.2026 · 1 citationbioRxiv : the preprint server for biology. 2026
The complete genome of the KOLF2.1J reference iPSC line.42051295 · Jerez, Pilar Alvarez, Rhie, Arang, Kim, Juhyun et al.2026 · 3 citationsbioRxiv : the preprint server for biology. 2026
Automatic Generation of Model Sequences for Complex Regions in Assembly Graphs.41959269 · Antipov, Dmitry, Chen, Ying, Sollitto, Marco et al.2026 · 1 citationbioRxiv : the preprint server for biology. 2026
Fully Phased Telomere-to-Telomere Assemblies for Thoroughbred Horse and Donkey Haplotypes derived from a Mule Illuminate the Peculiar Evolution of Equid Centromeres.42051287 · Li, Kai, Cappelletti, Eleonora, Dessaix, Carey et al.2026 · 1 citationbioRxiv : the preprint server for biology. 2026
Origin and evolution of acrocentric chromosomes in human and great apes.41497641 · Solar, Steven J, Hebbar, Prajna, de Lima, Leonardo Gomes et al.2026 · 0 citationsbioRxiv : the preprint server for biology. 2025
A trio-binned, haplotype-resolved genome sequence of the zebrafish, Danio rerio Hamilton 1822, SAT strain.41783605 · Howe, Kerstin, Rhie, Arang, Koren, Sergey et al.2026 · 1 citationWellcome open research. 2025;10:682
Complete genomes of a multi-generational pedigree to expand studies of genetic and epigenetic inheritance.41473289 · Cechova, Monika, Potapova, Tamara A, Rechtsteiner, Andreas et al.2026 · 4 citationsbioRxiv : the preprint server for biology. 2025
Finishing a complete giraffe genome from telomere to telomere with Verkko-Fillet.41256564 · Kim, Juhyun, Rosen, Benjamin D, Fumagalli, Sarah E et al.2026 · 2 citationsbioRxiv : the preprint server for biology. 2025
Complete de novo assembly and re-annotation of the zebrafish genome.41332591 · Okendo, Javan, Koren, Sergey, Rhie, Arang et al.2025 · 6 citationsbioRxiv : the preprint server for biology. 2025
The complete genome of a songbird.41480146 · Formenti, Giulio, Jain, Nivesh, Medico, Jack A et al.2026 · 9 citationsbioRxiv : the preprint server for biology. 2025
Bighorn sheep T2T genome assembly reveals differences in immune genes: a potential cause of high morbidity due to respiratory pathogens.41473269 · Olagunju, Temitayo A, Pospelova, Mariia, Schwartz, John C et al.2026 · 2 citationsbioRxiv : the preprint server for biology. 2025
Reference-guided assembly of metagenomes with MetaCompass.41015028 · Luan, Tu, Cepeda-Espinoza, Victoria P, Liu, Bo et al.2025 · 5 citationsCell reports methods. 2025;5(10):101186
A complete diploid human genome benchmark for personalized genomics.41000953 · Hansen, Nancy F, Dwarshuis, Nathan, Ji, Hyun Joo et al.2026 · 42 citationsbioRxiv : the preprint server for biology. 2025
Analysis of a Novel Human Protein, ORF3, Encoded by Spacer rDNA.40970945 · Chen, Yaohui, Kim, Jung-Hyun, Lee, Hee-Sheung et al.2025 · 1 citationJournal of molecular evolution. 2025;93(5):650-664
Author Correction: Complex genetic variation in nearly complete human genomes.40858940 · Logsdon, Glennis A, Ebert, Peter, Audano, Peter A et al.2026 · 3 citationsNature. 2025;645(8081):E6
Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding.40389285 · Antipov, Dmitry, Rautiainen, Mikko, Nurk, Sergey et al.2025 · 32 citationsGenome research. 2025;35(7):1583-1594
Verkko2: Integrating proximity ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding10.1101/2024.12.20.629807v2 · Phillippy, A. M., Koren, S., Antipov, D. et al.2024 · 7 citationsbioRxiv
Complete sequencing of ape genomes.39131277 · Yoo, DongAhn, Rhie, Arang, Hebbar, Prajna et al.2026 · 157 citationsbioRxiv : the preprint server for biology. 2024
The formation and propagation of human Robertsonian chromosomes.39386535 · de Lima, Leonardo Gomes, Guarracino, Andrea, Koren, Sergey et al.2025 · 32 citationsbioRxiv : the preprint server for biology. 2024
Complex genetic variation in nearly complete human genomes.39372794 · Logsdon, Glennis A, Ebert, Peter, Audano, Peter A et al.2026 · 137 citationsbioRxiv : the preprint server for biology. 2024
The Ruminant Telomere-to-Telomere (RT2T) Consortium.39103649 · Kalbfleisch, Theodore S, McKay, Stephanie D, Murdoch, Brenda M et al.2024 · 32 citationsNature genetics. 2024;56(8):1566-1573
Phasing Diploid Genome Assembly Graphs with Single-Cell Strand Sequencing.38529499 · Henglin, Mir, Ghareghani, Maryam, Harvey, William et al.2024 · 11 citationsbioRxiv : the preprint server for biology. 2024
Whole-genome sequence of Mucor velutinosus NIH1002, a strain associated with disseminated disease.38899875 · Conlan, Sean, Subramanian, Poorani, Plata Barril, Beatriz et al.2026 · 2 citationsMicrobiology resource announcements. 2024;13(7):e0006224
The reference genome of Macropodus opercularis (the paradise fish).38796485 · Fodor, Erika, Okendo, Javan, Szabó, Nóra et al.2024 · 6 citationsScientific data. 2024;11(1):540
The genome of the colonial hydroid Hydractinia reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals.38508693 · Schnitzler, Christine E, Chang, E Sally, Waletich, Justin et al.2024 · 15 citationsGenome research. 2024;34(3):498-513
The first complete T2T Assemblies of Cattle and Sheep Y-Chromosomes uncover remarkable divergence in structure and gene content.38712074 · Smith, Timothy, Olagunju, Temitayo, Rosen, Benjamin et al.2025 · 32 citationsResearch square. 2024
Gapless assembly of complete human and plant chromosomes using only nanopore sequencing.38529488 · Koren, Sergey, Bao, Zhigui, Guarracino, Andrea et al.2026 · 52 citationsbioRxiv : the preprint server for biology. 2024
MetaCompass: Reference-guided Assembly of Metagenomes2403.01578v1 · Tu Luan, Victoria Cepeda, Bo Liu et al.2024 · 25 citationsarXiv
Graph-based variant discovery reveals novel dynamics in the human microbiome2403.01610v1 · Harihara Subrahmaniam Muralidharan, Jacquelyn S Michaelis, Jay Ghurye et al.2024 · 2 citationsarXiv
MetaCompass: Reference-guided Assembly of Metagenomes.38903742 · Luan, Tu, Cepeda, Victoria, Liu, Bo et al.2025 · 25 citationsArXiv. 2024
The Genome of the Yellow Mealworm, Tenebrio molitor: It's Bigger Than You Think.38137031 · Oppert, Brenda, Dossey, Aaron T, Chu, Fu-Chyun et al.2023 · 28 citationsGenes. 2023;14(12)
The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes.38077089 · Makova, Kateryna D, Pickett, Brandon D, Harris, Robert S et al.2026 · 120 citationsbioRxiv : the preprint server for biology. 2023
Improved sequence mapping using a complete reference genome and lift-over.38036856 · Chen, Nae-Chyun, Paulin, Luis F, Sedlazeck, Fritz J et al.2024 · 29 citationsNature methods. 2024;21(1):41-49
The genome of the colonial hydroid Hydractinia reveals their stem cells utilize a toolkit of evolutionarily shared genes with all animals.37786714 · Schnitzler, Christine E, Chang, E Sally, Waletich, Justin et al.2025 · 2 citationsbioRxiv : the preprint server for biology. 2023
The complete sequence of a human Y chromosome.37612512 · Rhie, Arang, Nurk, Sergey, Cechova, Monika et al.2023 · 476 citationsNature. 2023;621(7978):344-354
The reference genome of the paradise fish (Macropodus opercularis).37609174 · Fodor, Erika, Okendo, Javan, Szabó, Nóra et al.2026 · 3 citationsbioRxiv : the preprint server for biology. 2023
Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph.37332563 · Cheng, Haoyu, Asri, Mobin, Lucas, Julian et al.2024 · 203 citationsArXiv. 2023
The variation and evolution of complete human centromeres.37398417 · Logsdon, Glennis A, Rozanski, Allison N, Ryabov, Fedor et al.2026 · 208 citationsbioRxiv : the preprint server for biology. 2023
Recombination between heterologous human acrocentric chromosomes.37165241 · Guarracino, Andrea, Buonaiuto, Silvia, de Lima, Leonardo Gomes et al.2023 · 135 citationsNature. 2023;617(7960):335-343
A draft human pangenome reference.37165242 · Liao, Wen-Wei, Asri, Mobin, Ebler, Jana et al.2023 · 1,170 citationsNature. 2023;617(7960):312-324
Reference genomes of channel catfish and blue catfish reveal multiple pericentric chromosome inversions.37013528 · Waldbieser, Geoffrey C, Liu, Shikai, Yuan, Zihao et al.2023 · 16 citationsBMC biology. 2023;21(1):67
Genome and Genetic Engineering of the House Cricket (Acheta domesticus): A Resource for Sustainable Agriculture.37189337 · Dossey, Aaron T, Oppert, Brenda, Chu, Fu-Chyun et al.2023 · 34 citationsBiomolecules. 2023;13(4)
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