AP
Adam M. Phillippy
genomicsbioinformaticsSoftwareGenomeGenome, HumanGenomicsEvolution, MolecularAlgorithmsSequence Analysis, DNAGenetic 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
181 papers in the corpus · 2003–2026Mapping long-read sequences to a complete reference genome reveals uncaptured variants across the β-Globin cluster in Africans with sickle cell disease.42693638 · Lurie, Pamela, Mahmoud, Medhat, Haldipur, Aparna et al.2026 · 0 citationsHGG advances. 2026;7(4):100669
Filling the holes in whole genomes: A vision for personalized genomics from telomere to telomere.42561910 · Phillippy, Adam M, Mao, Yafei, Kang, Yu et al.2026 · 0 citationsCell. 2026;189(16):4825-4828
Complex subtelomeric architectures in a complete rhesus macaque reference genome.42561916 · Zhang, Shilong, Xu, Ning, Lu, Yong et al.2026 · 0 citationsCell. 2026;189(16):4909-4921.e15
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
Harmonizing standards and resources for the medical genome.42387168 · Ashley, Euan A, Alizadeh, Ash A, Armitage, Hanae et al.2026 · 1 citationNature. 2026;655(8121):47-58
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 · 0 citationsbioRxiv : 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
Germline sequence variation within the ribosomal DNA is associated with human complex traits.41966685 · Rodriguez-Algarra, Francisco, Whittaker, Elliott, Cooper, Maia et al.2026 · 9 citationsCell genomics. 2026;6(6):101213
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 · 16 citationsbioRxiv : 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
AniAnn's: alignment-free annotation of tandem repeat arrays using fast average nucleotide identity estimates.41659693 · Sweeten, Alexander, Schatz, Michael C, Phillippy, Adam M2026 · 2 citationsbioRxiv : 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
Human acrocentric chromosome short arm de novo mutation and recombination.41446150 · Lin, Jiadong, Mastrorosa, F Kumara, Noyes, Michelle D et al.2026 · 2 citationsbioRxiv : the preprint server for biology. 2025
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
Protamine lacunae preserve the paternal chromatin landscape in sperm.41256633 · Tullius, Thomas W, Heuer, Rachel A, Bohaczuk, Stephanie C et al.2025 · 4 citationsbioRxiv : the preprint server for biology. 2025
Chromosome-specific epigenetic control and transmission of ribosomal DNA arrays in Hominidae genomes.41043432 · Potapova, Tamara A, Kostos, Paxton, McKinney, Sean et al.2025 · 11 citationsCell genomics. 2025;5(12):101031
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
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
A complete and near-perfect rhesus macaque reference genome: lessons from subtelomeric repeats and sequencing bias.41019632 · Zhang, Shilong, Xu, Ning, Lu, Yong et al.2026 · 1 citationbioRxiv : the preprint server for biology. 2025
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
Chromosome-level echidna genome illuminates evolution of multiple sex chromosome system in monotremes.39778707 · Zhou, Yang, Jin, Jiazheng, Li, Xuemei et al.2025 · 13 citationsGigaScience. 2025;14
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
Long-read sequencing of hundreds of diverse brains provides insight into the impact of structural variation on gene expression and DNA methylation.39764002 · Billingsley, Kimberley J, Meredith, Melissa, Daida, Kensuke et al.2026 · 16 citationsbioRxiv : the preprint server for biology. 2024
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
Epigenetic control and inheritance of rDNA arrays.39372739 · Potapova, Tamara, Kostos, Paxton, McKinney, Sean et al.2025 · 12 citationsbioRxiv : the preprint server for biology. 2024
ModDotPlot-rapid and interactive visualization of tandem repeats.39110522 · Sweeten, Alexander P, Schatz, Michael C, Phillippy, Adam M2024 · 63 citationsBioinformatics (Oxford, England). 2024;40(8)
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
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
ModDotPlot-Rapid and interactive visualization of complex repeats.38712106 · Sweeten, Alexander P, Schatz, Michael C, Phillippy, Adam M2024 · 10 citationsbioRxiv : the preprint server for biology. 2024
Comparative genomics of macaques and integrated insights into genetic variation and population history.38645259 · Zhang, Shilong, Xu, Ning, Fu, Lianting et al.2025 · 48 citationsbioRxiv : the preprint server for biology. 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
A High-Quality Blue Whale Genome, Segmental Duplications, and Historical Demography.38376487 · Bukhman, Yury V, Morin, Phillip A, Meyer, Susanne et al.2024 · 26 citationsMolecular biology and evolution. 2024;41(3)
Parsnp 2.0: Scalable Core-Genome Alignment for Massive Microbial Datasets.38352342 · Kille, Bryce, Nute, Michael G, Huang, Victor et al.2024 · 110 citationsbioRxiv : the preprint server for biology. 2024
High-quality metagenome assembly from long accurate reads with metaMDBG.38168989 · Benoit, Gaëtan, Raguideau, Sébastien, James, Robert et al.2024 · 197 citationsNature biotechnology. 2024;42(9):1378-1383
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
Low mutation rate in epaulette sharks is consistent with a slow rate of evolution in sharks.37857613 · Sendell-Price, Ashley T, Tulenko, Frank J, Pettersson, Mats et al.2023 · 46 citationsNature communications. 2023;14(1):6628
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