BP
Benedict Paten
bioinformaticsgenomicsGenome, HumanSoftwareGenomeGenomicsEvolution, MolecularAlgorithmsGenetic VariationNanopores
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
206 papers in the corpus · 2005–2026Pangenome alignment reveals global diversity and evolution of human centromeric regions.42922605 · Eizenga, Jordan, Mastoras, Mira, Lucas, Julian K et al.2026 · 16 citationsbioRxiv : the preprint server for biology. 2026
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
GBZ-base and GAF-base: Indexed pangenome file formats.42465382 · Sirén, Jouni, Paten, Benedict, Human Pangenome Reference Consortium2026 · 0 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
Structural variant discovery and diagnostic impact in rare diseases from short-read and long-read sequencing.42396270 · Sanchis-Juan, Alba, Mostovoy, Yulia, Stenton, Sarah L et al.2026 · 1 citationmedRxiv : the preprint server for health sciences. 2026
A Pan-pangenome illuminates complex structural variation and selection in humans, chimpanzees, and bonobos.42327276 · Rocha, Joana, Lou, Runyang Nicolas, De Lima Adam, Carolina et al.2026 · 0 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
Accessing medically relevant complex regions with a pangenome graph of 20 near-complete Japanese haplotypes.42203797 · Suzuki, Yoshihiko, Owa, Chie, Kobayashi, Haruka et al.2026 · 0 citationsNature communications. 2026;17(1)
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
Haplotype-resolved genome assemblies of BJ and IMR-90 human fibroblast cell lines reveal extensive structural variation and enable reanalysis of historical sequencing data.42049241 · Ranallo-Benavidez, T Rhyker, Hao, Yue, Volpe, Emilia et al.2026 · 2 citationsNucleic acids research. 2026;54(8)
Lancet2: Improved and accelerated somatic variant calling with joint multi-sample local assembly graphs.41972010 · Musunuri, Rajeeva Lochan, Zhu, Bryan, Clarke, Wayne E et al.2026 · 3 citationsNAR genomics and bioinformatics. 2026;8(2):lqag036
A Complete Genome for the Common Marmoset.41929024 · Hebbar, Prajna, Potapova, Tamara, Loucks, Hailey 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
Evaluating genome assemblies with HMM-Flagger.41847002 · Asri, Mobin, Eizenga, Jordan M, Hebbar, Prajna et al.2026 · 4 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
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
Wakhan: reconstruction of chromosome-scale copy number profiles of tumor genomes with long-read sequencing10.64898/2025.12.11.25342098v1 · Ahmad, T., Keskus, A. G., Aganezov, S. et al.2025 · 1 citationmedRxiv
Making genomic data FAIR through effective Data Portals.41315456 · Speir, Matthew L, Teh, Wei Kheng, Perry, Marc D et al.2025 · 7 citationsScientific data. 2025;12(1):1872
Accurate somatic small variant discovery for multiple sequencing technologies with DeepSomatic.41102444 · Park, Jimin, Cook, Daniel E, Chang, Pi-Chuan et al.2026 · 29 citationsNature biotechnology. 2026;44(9):1569-1578
Rapid, accurate long- and short-read mapping to large pangenome graphs with vg Giraffe.41256518 · Chang, Xian, Novak, Adam M, Eizenga, Jordan M et al.2025 · 9 citationsbioRxiv : the preprint server for biology. 2025
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
Author Correction: Genetic regulation of TERT splicing affects cancer risk by altering cellular longevity and replicative potential.40877316 · Florez-Vargas, Oscar, Ho, Michelle, Hogshead, Maxwell H et al.2025 · 0 citationsNature communications. 2025;16(1):8035
Correction: Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair.40781089 · McDaniel, Jennifer H, Patel, Vaidehi, Olson, Nathan D et al.2026 · 0 citationsScientific data. 2025;12(1):1385
An Efficient Graph Algorithm for Diploid Local Ancestry Inference10.1101/2025.07.05.662656v1 · Jafarzadeh, N., Eizenga, J. M., Paten, B.2025 · 1 citationbioRxiv
Haplotype-Resolved DNA Methylation at the APOE Locus identifies Allele-Specific Epigenetic Signatures Relevant to Alzheimer's Disease Risk.40631171 · Genner, Rylee M, Meredith, Melissa, Moller, Abraham et al.2026 · 1 citationbioRxiv : the preprint server for biology. 2025
Adaptive radiation and social evolution of the ants.40527318 · Vizueta, Joel, Xiong, Zijun, Ding, Guo et al.2025 · 51 citationsCell. 2025;188(18):4828-4848.e25
Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair.39345378 · McDaniel, Jennifer H, Patel, Vaidehi, Olson, Nathan D et al.2026 · 21 citationsbioRxiv : the preprint server for biology. 2025
Pangenome-aware DeepVariant.40501862 · Asri, Mobin, Chang, Pi-Chuan, Mier, Juan Carlos et al.2026 · 9 citationsbioRxiv : the preprint server for biology. 2025
Lossless Pangenome Indexing Using Tag Arrays.40463112 · Eskandar, Parsa, Paten, Benedict, Sirén, Jouni2026 · 0 citationsbioRxiv : the preprint server for biology. 2025
Diploid genome assembly of human fibroblast cell lines enables clone specific variant calling, improved read mapping and accurate phasing.41030990 · Ranallo-Benavidez, T Rhyker, Hao, Yue, Volpe, Emilia et al.2025 · 3 citationsbioRxiv : the preprint server for biology. 2025
Assessing DNA methylation detection for primary human tissue using Nanopore sequencing.40054862 · Genner, Rylee, Akeson, Stuart, Meredith, Melissa et al.2025 · 13 citationsGenome research. 2025;35(4):632-643
Severus detects somatic structural variation and complex rearrangements in cancer genomes using long-read sequencing.40185952 · Keskus, Ayse G, Bryant, Asher, Ahmad, Tanveer et al.2026 · 40 citationsNature biotechnology. 2026;44(2):247-257
Genetic diversity and regulatory features of human-specific NOTCH2NL duplications.40166283 · Real, Taylor D, Hebbar, Prajna, Yoo, DongAhn et al.2026 · 5 citationsbioRxiv : the preprint server for biology. 2025
Genetic regulation of TERT splicing affects cancer risk by altering cellular longevity and replicative potential.39956830 · Florez-Vargas, Oscar, Ho, Michelle, Hogshead, Maxwell H et al.2025 · 17 citationsNature communications. 2025;16(1):1676
Long-read sequencing resolves the clinically relevant CYP21A2 locus, supporting a new clinical test for Congenital Adrenal Hyperplasia.39990550 · Monlong, Jean, Chen, Xiao, Barseghyan, Hayk et al.2025 · 2 citationsmedRxiv : the preprint server for health sciences. 2025
GENCODE 2025: reference gene annotation for human and mouse.39565199 · Mudge, Jonathan M, Carbonell-Sala, Sílvia, Diekhans, Mark et al.2025 · 423 citationsNucleic acids research. 2025;53(D1):D966-D975
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
Genetic regulation of TERT splicing contributes to reduced or elevated cancer risk by altering cellular longevity and replicative potential.39802763 · Florez-Vargas, Oscar, Ho, Michelle, Hogshead, Maxwell et al.2025 · 0 citationsmedRxiv : the preprint server for health sciences. 2024
GENCODE: massively expanding the lncRNA catalog through capture long-read RNA sequencing.39554180 · Kaur, Gazaldeep, Perteghella, Tamara, Carbonell-Sala, Sílvia et al.2025 · 26 citationsbioRxiv : the preprint server for biology. 2024
Efficient indexing and querying of annotations in a pangenome graph.39464141 · Novak, Adam M, Chung, Dickson, Hickey, Glenn et al.2026 · 5 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
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
A phenome-wide association study of methylated GC-rich repeats identifies a GCC repeat expansion in AFF3 associated with intellectual disability.39313615 · Jadhav, Bharati, Garg, Paras, van Vugt, Joke J F A et al.2024 · 16 citationsNature genetics. 2024;56(11):2322-2332
Highly accurate assembly polishing with DeepPolisher.39345401 · Mastoras, Mira, Asri, Mobin, Brambrink, Lucas et al.2025 · 16 citationsbioRxiv : the preprint server for biology. 2024
Advancing long-read nanopore genome assembly and accurate variant calling for rare disease detection.39228712 · Negi, Shloka, Stenton, Sarah L, Berger, Seth I et al.2025 · 51 citationsmedRxiv : the preprint server for health sciences. 2024
DeepSomatic: Accurate somatic small variant discovery for multiple sequencing technologies.39229187 · Park, Jimin, Cook, Daniel E, Chang, Pi-Chuan et al.2025 · 19 citationsbioRxiv : the preprint server for biology. 2024
Beyond the Human Genome Project: The Age of Complete Human Genome Sequences and Pangenome References.38663087 · Taylor, Dylan J, Eizenga, Jordan M, Li, Qiuhui et al.2024 · 48 citationsAnnual review of genomics and human genetics. 2024;25(1):77-104
A region of suppressed recombination misleads neoavian phylogenomics.38557186 · Mirarab, Siavash, Rivas-González, Iker, Feng, Shaohong et al.2024 · 37 citationsProceedings of the National Academy of Sciences of the United States of America. 2024;121(15):e2319506121
Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements.38422184 · Wirthlin, Morgan E, Schmid, Tobias A, Elie, Julie E et al.2024 · 40 citationsScience (New York, N.Y.). 2024;383(6690):eabn3263
Career total: at least 376 works. 206 are in this corpus.Showing the 50 most recent.
Profile built from the corpus for this byline.
Author records are still filling in while the Hub is in alpha. If this is your page, you'll be able to claim it soon. Spot a mistake? Tell us.