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Benedict Paten

University of California

95H-index
355Paper Count
5.1WCitation Count
Published Papers 93
Publication Date
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Harmonizing standards and resources for the medical genome
errNature
IF48.5
err2026-07-01
err0
PREAI
errEuan A. Ashley; Ash A. Alizadeh; Hanae Armitage; Ami S. Bhatt; Yair Blumenfeld; Andrew Carroll; R. Martin Chavez; Petros Giannikopoulos; Megan E. Grove; Meghan C. Halley; Kiran Khush; Niall J. Lennon; Samantha Maragh; Alexander Marson; Benedict Paten; Adam M. Phillippy; Matthew H. Porteus; Heidi L. Rehm; Bradley R. Ringeisen; Julia Salzman; Valerie A. Schneider; Fritz J. Sedlazeck; Lars M. Steinmetz; Fyodor D. Urnov; Stacia K. Wyman; Justin M. Zook; Lloyd B. Minor; Jennifer A. Doudna
errShare
errSave
Accessing medically relevant complex regions with a pangenome graph of 20 near-complete Japanese haplotypes
errNature Communications
IF15.7
err2026-05-27
err0
errOAAI
errYoshihiko Suzuki; Chie Owa; Haruka Kobayashi; Ryo Nakabayashi; Brandy McNulty; Ivo Violich; Benedict Paten; Karen H. Miga; Shinichi Morishita
errShare
errSave
Lancet2: Improved and accelerated somatic variant calling with joint multi-sample local assembly graphs
errNAR Genomics and Bioinformatics
IF2.8
err2026-04-07
err0
errOAAI
errRajeeva Lochan Musunuri; Bryan Zhu; Wayne E Clarke; William Hooper; Timothy Chu; Jennifer Shelton; André Corvelo; Dickson Chung; Shreya Sundar; Adam M Novak; Benedict Paten; Michael C Zody; Nicolas Robine; Giuseppe Narzisi
errShare
errSave
Accurate somatic small variant discovery for multiple sequencing technologies with DeepSomatic
errNature Biotechnology
IF41.7
err2025-10-16
err0
PREAI
errJimin Park; Daniel E. Cook; Pi-Chuan Chang; Alexey Kolesnikov; Lucas Brambrink; Juan Carlos Mier; Joshua Gardner; Brandy McNulty; Samuel Sacco; Ayse G. Keskus; Asher Bryant; Tanveer Ahmad; Jyoti Shetty; Yongmei Zhao; Bao Tran; Giuseppe Narzisi; Adrienne Helland; Byunggil Yoo; Irina Pushel; Lisa A. Lansdon; Chengpeng Bi; Adam Walter; Margaret Gibson; Tomi Pastinen; Rebecca Reiman; Sharvari Mankame; T. Rhyker Ranallo-Benavidez; Christine Brown; Nicolas Robine; Floris P. Barthel; Midhat S. Farooqi; Karen H. Miga; Andrew Carroll; Mikhail Kolmogorov; Benedict Paten; Kishwar Shafin
errShare
errSave
Author Correction: Complex genetic variation in nearly complete human genomes
errNature
IF48.5
err2025-08-26
err0
errOAAI
errGlennis A. Logsdon; Peter Ebert; Peter A. Audano; Mark Loftus; David Porubsky; Jana Ebler; Feyza Yilmaz; Pille Hallast; Timofey Prodanov; DongAhn Yoo; Carolyn A. Paisie; William T. Harvey; Xuefang Zhao; Gianni V. Martino; Mir Henglin; Katherine M. Munson; Keon Rabbani; Chen-Shan Chin; Bida Gu; Hufsah Ashraf; Stephan Scholz; Olanrewaju Austine-Orimoloye; Parithi Balachandran; Marc Jan Bonder; Haoyu Cheng; Zechen Chong; Jonathan Crabtree; Mark Gerstein; Lisbeth A. Guethlein; Patrick Hasenfeld; Glenn Hickey; Kendra Hoekzema; Sarah E. Hunt; Matthew Jensen; Yunzhe Jiang; Sergey Koren; Youngjun Kwon; Chong Li; Heng Li; Jiaqi Li; Paul J. Norman; Keisuke K. Oshima; Benedict Paten; Adam M. Phillippy; Nicholas R. Pollock; Tobias Rausch; Mikko Rautiainen; Yuwei Song; Arda Söylev; Arvis Sulovari; Likhitha Surapaneni; Vasiliki Tsapalou; Weichen Zhou; Ying Zhou; Qihui Zhu; Michael C. Zody; Ryan E. Mills; Scott E. Devine; Xinghua Shi; Michael E. Talkowski; Mark J. P. Chaisson; Alexander T. Dilthey; Miriam K. Konkel; Jan O. Korbel; Charles Lee; Christine R. Beck; Evan E. Eichler; Tobias Marschall
errShare
errSave
Correction: Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair
errScientific Data
IF6.9
err2025-08-08
err0
errOAAI
errJennifer H. McDaniel; Vaidehi Patel; Nathan D. Olson; Hua-Jun He; Zhiyong He; Kenneth D. Cole; Alexander A. Gooden; Anthony Schmitt; Kristin Sikkink; Fritz J. Sedlazeck; Harsha Doddapaneni; Shalini N. Jhangiani; Donna M. Muzny; Marie-Claude Gingras; Heer Mehta; Sairam Behera; Luis F. Paulin; Alex R. Hastie; Hung-Chun Yu; Victor Weigman; Alison Rojas; Katie Kennedy; Jamie Remington; Isai Salas-González; Mitch Sudkamp; Kelly Wiseman; Bryan R. Lajoie; Shawn Levy; Miten Jain; Stuart Akeson; Giuseppe Narzisi; Zoe Steinsnyder; Catherine Reeves; Jennifer Shelton; Sarah B. Kingan; Christine Lambert; Primo Baybayan; Aaron M. Wenger; Ian J. McLaughlin; Aaron Adamson; Christopher Kingsley; Melanie Wescott; Young Kim; Benedict Paten; Jimin Park; Ivo Violich; Karen H. Miga; Joshua Gardner; Brandy McNulty; Gail L. Rosen; Rajiv McCoy; Francesco Brundu; Erfan Sayyari; Konrad Scheffler; Sean Truong; Severine Catreux; Lesley Chapman Hannah; Doron Lipson; Hila Benjamin; Nika Iremadze; Ilya Soifer; Gat Krieger; Stephen Eacker; Mary Wood; Erin Cross; Greg Husar; Stephen Gross; Michael Vernich; Mikhail Kolmogorov; Tanveer Ahmad; Ayse G. Keskus; Asher Bryant; Francoise Thibaud-Nissen; Jonathan Trow; Jacqueline Proszynski; Jeremy Wain Hirschberg; Krista Ryon; Christopher E. Mason; Mital S. Bhakta; J. Zachary Sanborn; Elizabeth M. Munding; Justin Wagner; Chunlin Xiao; Andrew S. Liss; Justin M. Zook
errShare
errSave
Complex genetic variation in nearly complete human genomes
errNature
IF48.5
err2025-07-23
err0
errOAAI
errGlennis A. Logsdon; Peter Ebert; Peter A. Audano; Mark Loftus; David Porubsky; Jana Ebler; Feyza Yilmaz; Pille Hallast; Timofey Prodanov; DongAhn Yoo; Carolyn A. Paisie; William T. Harvey; Xuefang Zhao; Gianni V. Martino; Mir Henglin; Katherine M. Munson; Keon Rabbani; Chen-Shan Chin; Bida Gu; Hufsah Ashraf; Stephan Scholz; Olanrewaju Austine-Orimoloye; Parithi Balachandran; Marc Jan Bonder; Haoyu Cheng; Zechen Chong; Jonathan Crabtree; Mark Gerstein; Lisbeth A. Guethlein; Patrick Hasenfeld; Glenn Hickey; Kendra Hoekzema; Sarah E. Hunt; Matthew Jensen; Yunzhe Jiang; Sergey Koren; Youngjun Kwon; Chong Li; Heng Li; Jiaqi Li; Paul J. Norman; Keisuke K. Oshima; Benedict Paten; Adam M. Phillippy; Nicholas R. Pollock; Tobias Rausch; Mikko Rautiainen; Yuwei Song; Arda Söylev; Arvis Sulovari; Likhitha Surapaneni; Vasiliki Tsapalou; Weichen Zhou; Ying Zhou; Qihui Zhu; Michael C. Zody; Ryan E. Mills; Scott E. Devine; Xinghua Shi; Michael E. Talkowski; Mark J. P. Chaisson; Alexander T. Dilthey; Miriam K. Konkel; Jan O. Korbel; Charles Lee; Christine R. Beck; Evan E. Eichler; Tobias Marschall
errShare
errSave
Adaptive radiation and social evolution of the ants
errCell
IF42.5
err2025-06-16
err0
errOAAI
errJoel Vizueta; Zijun Xiong; Guo Ding; Rasmus S. Larsen; Hao Ran; Qionghua Gao; Josefin Stiller; Wei Dai; Wei Jiang; Jie Zhao; Chunxue Guo; Xiafang Zhang; Dashuang Zuo; Wenjiang Zhong; Morten Schiøtt; Chengyuan Liu; Hailin Zhang; Xueqin Dai; Ignasi Andreu; Yue Shi; Sandra Tretter; Ding He; Shubham Gautam; Zelin Li; Glenn Hickey; Aniek B.F. Ivens; Marie-Pierre Meurville; Francisco Hita-Garcia; Jamie M. Kass; Benoit Guénard; Corrie Moreau; Benedict Paten; Adria C. LeBoeuf; Evan P. Economo; Michel Chapuisat; Jonathan Z. Shik; Philip S. Ward; Jürgen Heinze; Ted R. Schultz; Qiye Li; Robert R. Dunn; Nathan J. Sanders; Weiwei Liu; Lukas Schrader; Jacobus J. Boomsma; Guojie Zhang
errShare
errSave
Severus detects somatic structural variation and complex rearrangements in cancer genomes using long-read sequencing
errNATURE BIOTECHNOLOGY
IF41.7
err2025-04-04
err1
PREAI
errKeskus, Ayse G.; Bryant, Asher; Ahmad, Tanveer; Yoo, Byunggil; Aganezov, Sergey; Goretsky, Anton; Donmez, Ataberk; Lansdon, Lisa A.; Rodriguez, Isabel; Park, Jimin; Liu, Yuelin; Cui, Xiwen; Gardner, Joshua; McNulty, Brandy; Sacco, Samuel; Shetty, Jyoti; Zhao, Yongmei; Tran, Bao; Narzisi, Giuseppe; Helland, Adrienne; Cook, Daniel E.; Chang, Pi-Chuan; Kolesnikov, Alexey; Carroll, Andrew; Molloy, Erin K.; Bi, Chengpeng; Walter, Adam; Gibson, Margaret; Pushel, Irina; Guest, Erin; Pastinen, Tomi; Shafin, Kishwar; Miga, Karen H.; Malikic, Salem; Day, Chi-Ping; Robine, Nicolas; Sahinalp, Cenk; Dean, Michael; Farooqi, Midhat S.; Paten, Benedict; Kolmogorov, Mikhail
errShare
errSave
Advancing long-read nanopore genome assembly and accurate variant calling for rare disease detection
errAMERICAN JOURNAL OF HUMAN GENETICS
IF8.1
err2025-02-01
err1
PREAI
errNegi, Shloka; Stenton, Sarah L.; Berger, Seth I.; Canigiula, Paolo; Mcnulty, Brandy; Violich, Ivo; Gardner, Joshua; Hillaker, Todd; O'Rourke, Sara M.; O'Leary, Melanie C.; Carbonell, Elizabeth; Austin-Tse, Christina; Lemire, Gabrielle; Serrano, Jillian; Mangilog, Brian; Vannoy, Grace; Kolmogorov, Mikhail; Vilain, Eric; O'Donnell-Luria, Anne; Delot, Emmanuele; Miga, Karen H.; Monlong, Jean; Paten, Benedict
errShare
errSave
A phenome-wide association study of methylated GC-rich repeats identifies a GCC repeat expansion in AFF3 associated with intellectual disability
errNATURE GENETICS
IF31.8
err2024-09-23
err1
PREAI
errJadhav, Bharati; Garg, Paras; van Vugt, Joke J. F. A.; Ibanez, Kristina; Gagliardi, Delia; Lee, William; Shadrina, Mariya; Mokveld, Tom; Dolzhenko, Egor; Martin-Trujillo, Alejandro; Gies, Scott J.; Altman, Gabrielle; Rocca, Clarissa; Barbosa, Mafalda; Jain, Miten; Lahiri, Nayana; Lachlan, Katherine; Houlden, Henry; Paten, Benedict; Veldink, Jan; Tucci, Arianna; Sharp, Andrew J.
errShare
errSave
Personalized pangenome references
errNATURE METHODS
IF32.1
err2024-09-11
err1
PREAI
errSiren, Jouni; Eskandar, Parsa; Ungaro, Matteo Tommaso; Hickey, Glenn; Eizenga, Jordan M.; Novak, Adam M.; Chang, Xian; Chang, Pi-Chuan; Kolmogorov, Mikhail; Carroll, Andrew; Monlong, Jean; Paten, Benedict
errShare
errSave
Beyond the Human Genome Project: The Age of Complete Human Genome Sequences and Pangenome References
errannual review of genetics
IF7.9
err2024-08-27
err1
errOAAI
errTaylor, Dylan J.; Eizenga, Jordan M.; Li, Qiuhui; Das, Arun; Jenike, Katharine M.; Kenny, Eimear E.; Miga, Karen H.; Monlong, Jean; Mccoy, Rajiv C.; Paten, Benedict; Schatz, Michael C.
errShare
errSave
Local read haplotagging enables accurate long-read small variant calling
errNATURE COMMUNICATIONS
IF15.7
err2024-07-13
err0
errOAAI
errKolesnikov, Alexey; Cook, Daniel; Nattestad, Maria; Brambrink, Lucas; McNulty, Brandy; Gorzynski, John; Goenka, Sneha; Ashley, Euan A.; Jain, Miten; Miga, Karen H.; Paten, Benedict; Chang, Pi-Chuan; Carroll, Andrew; Shafin, Kishwar
errShare
errSave
SIMS: A deep-learning label transfer tool for single-cell RNA sequencing analysis
errCELL GENOMICS
IF9
err2024-06-01
err1
errOAAI
errGonzalez-Ferrer, Jesus; Lehrer, Julian; O'Farrell, Ash; Paten, Benedict; Teodorescu, Mircea; Haussler, David; Jonsson, Vanessa D.; Mostajo-Radji, Mohammed A.
errShare
errSave
Phased nanopore assembly with Shasta and modular graph phasing with GFAse
errGENOME RESEARCH
IF5.5
err2024-04-16
err3
errOAAI
errLorig-Roach, Ryan; Meredith, Melissa; Monlong, Jean; Jain, Miten; Olsen, Hugh E.; Mcnulty, Brandy; Porubsky, David; Montague, Tessa G.; Lucas, Julian K.; Condon, Chris; Eizenga, Jordan M.; Juul, Sissel; Mckenzie, Sean K.; Simmonds, Sara E.; Park, Jimin; Asri, Mobin; Koren, Sergey; Eichler, Evan E.; Axel, Richard; Martin, Bruce; Carnevali, Paolo; Miga, Karen H.; Paten, Benedict
errShare
errSave
A region of suppressed recombination misleads neoavian phylogenomics
errPROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
IF9.1
err2024-04-01
err3
errOAAI
errMirarab, Siavash; Rivas-Gonzalez, Iker; Feng, Shaohong; Stiller, Josefin; Fang, Qi; Mai, Uyen; Hickey, Glenn; Chen, Guangji; Brajuka, Nadolina; Fedrigo, Olivier; Formenti, Giulio; Wolf, Jochen B. W.; Howe, Kerstin; Antunes, Agostinho; Schierup, Mikkel H.; Paten, Benedict; Jarvis, Erich D.; Zhang, Guojie; Braun, Edward L.
errShare
errSave
Benchmarking long- and short-read somatic structural variation callers using a multi-technology panel of six tumor/normal cell lines
errCANCER RESEARCH
IF16.6
err2024-03-22
err0
PREAI
errKeskus, Ayse; Bryant, Asher; Ahmad, Tanveer; Donmez, Ataberk; Rodriguez, Isabel; Rossi, Nicole; Xie, Yi; Yoo, Byunggil; Milano, Rose; Lou, Hong; Park, Jimin; Gardner, Joshua; McNulty, Brandy; Miga, Karen; Dean, Mike; Farooqi, Midhat; Paten, Benedict; Kolmogorov, Mikhail
errShare
errSave
LungMAP Portal Ecosystem Systems-level Exploration of the Lung
errAMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY
IF5.3
err2024-02-01
err11
errOAAI
errGaddis, Nathan; Fortriede, Joshua; Guo, Minzhe; Bardes, Eric E.; Kouril, Michal; Tabar, Scott; Burns, Kevin; Ardini-Poleske, Maryanne E.; Loos, Stephanie; Schnell, Daniel; Jin, Kang; Iyer, Balaji; Du, Yina; Huo, Bing-Xing; Bhattacharjee, Anukana; Korte, Jeff; Munshi, Ruchi; Smith, Victoria; Herbst, Andrew; Kitzmiller, Joseph A.; Clair, Geremy C.; Carson, James P.; Adkins, Joshua; Morrisey, Edward E.; Pryhuber, Gloria S.; Misra, Ravi; Whitsett, Jeffrey A.; Sun, Xin; Heathorn, Trevor; Paten, Benedict; Prasath, V. B. Surya; Xu, Yan; Tickle, Tim; Aronow, Bruce J.; Salomonis, Nathan
errShare
errSave
The UCSC Genome Browser database: 2024 update
errNUCLEIC ACIDS RESEARCH
IF13.1
err2023-11-11
err44
errOAAI
errRaney, Brian J.; Barber, Galt P.; Benet-Pages, Anna; Casper, Jonathan; Clawson, Hiram; Cline, Melissa S.; Diekhans, Mark; Fischer, Clayton; Gonzalez, Jairo Navarro; Hickey, Glenn; Hinrichs, Angie S.; Kuhn, Robert M.; Lee, Brian T.; Lee, Christopher M.; Le Mercier, Phillipe; Miga, KarenH; Nassar, Luis R.; Nejad, Parisa; Paten, Benedict; Perez, Gerardo; Schmelter, Daniel; Speir, Matthew L.; Wick, Brittney D.; Zweig, Ann S.; Haussler, David; Kent, W. James; Haeussler, Maximilian
errShare
errSave

Research Directions

No research directions
Co-authors
Cooperation Journals
M
M Snyder
H-index: 210 · Papers: 3.3K
E
Evan E. Eichler
H-index: 191 · Papers: 864
M
Mark Gerstein
H-index: 191 · Papers: 1.2K
D
David Haussler
H-index: 175 · Papers: 720
J
Jay Shendure
H-index: 167 · Papers: 662
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