Benedict Paten

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David HausslerScientific Director, UC Santa Cruz Genomics Institute, University of California, Santa CruzVerified email at soe.ucsc.edu
Miten JainAssistant Professor, Northeastern UniversityVerified email at northeastern.edu
Jordan M EizengaPostdoctoral Researcher, Genomics Institute, University of California Santa CruzVerified email at ucsc.edu
Karen H MigaAssistant Professor; Associate Director, UC Santa Cruz Genomics Institute, University of CaliforniaVerified email at ucsc.edu
Mark DiekhansUniversity of California, Santa Cruz; UC Santa Cruz Genomics InstituteVerified email at soe.ucsc.edu
Mark AkesonProfessor of Biomolecular Engineering, UC Santa CruzVerified email at soe.ucsc.edu
Ian Fiddes10x GenomicsVerified email at 10xgenomics.com
Ewan BirneyDirector, EMBL-EBIVerified email at ebi.ac.uk
Daniel ZerbinoMosaic TherapeuticsVerified email at mosaic-tx.com
Dent EarlStaff Software Engineer at Google. Formerly of UCSC, UCLA.Verified email at soe.ucsc.edu
Ngan NguyenAtreca Inc.Verified email at atreca.com
W James KentUC Santa Cruz Genomics Institute, University of California Santa Cruz, UCSC Genome BrowserVerified email at soe.ucsc.edu
Paul FlicekThe Jackson Laboratory, University of CambridgeVerified email at jax.org
Ian HolmesProfessor, Computational Biology and Bioengineering, UC BerkeleyVerified email at berkeley.edu
laurence ettwiller, Ph.DNew England Biolabs, INCVerified email at neb.com
John St. JohnMachine Learning Scientist @ NvidiaVerified email at nvidia.com

Benedict Paten

Professor; Associate Director, UC Santa Cruz Genomics Institute, University of California

Verified email at ucsc.edu - Homepage

computational genomics sequence analysis genome comparison human variation cancer genomics


Title Sort by citations Sort by year Sort by title	Cited by Cited by	Year
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project Management Group Liefer Laura A. 51 Wetterstrand Kris A. 51 Good Peter J. 51 ... nature 447 (7146), 799-816, 2007	6074	2007
Genetic effects on gene expression across human tissues GT Consortium, DA Laboratory Nature 550 (7675), 204-213, 2017	3452*	2017
GENCODE reference annotation for the human and mouse genomes A Frankish, M Diekhans, AM Ferreira, R Johnson, I Jungreis, J Loveland, ... Nucleic acids research 47 (D1), D766-D773, 2019	2780	2019
The complete sequence of a human genome S Nurk, S Koren, A Rhie, M Rautiainen, AV Bzikadze, A Mikheenko, ... Science 376 (6588), 44-53, 2022	2205	2022
Nanopore sequencing and assembly of a human genome with ultra-long reads M Jain, S Koren, KH Miga, J Quick, AC Rand, TA Sasani, JR Tyson, ... Nature biotechnology 36 (4), 338-345, 2018	1948	2018
Towards complete and error-free genome assemblies of all vertebrate species A Rhie, SA McCarthy, O Fedrigo, J Damas, G Formenti, S Koren, ... Nature 592 (7856), 737-746, 2021	1806	2021
The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community M Jain, HE Olsen, B Paten, M Akeson Genome biology 17, 1-11, 2016	1709	2016
Expanded encyclopaedias of DNA elements in the human and mouse genomes JE Moore, MJ Purcaro, HE Pratt, CB Epstein, N Shoresh, J Adrian, T Kawli, ... Nature 583 (7818), 699-710, 2020	1353	2020
Toil enables reproducible, open source, big biomedical data analyses J Vivian, AA Rao, FA Nothaft, C Ketchum, J Armstrong, A Novak, J Pfeil, ... Nature biotechnology 35 (4), 314-316, 2017	1098	2017
The UCSC genome browser database: 2015 update KR Rosenbloom, J Armstrong, GP Barber, J Casper, H Clawson, ... Nucleic acids research 43 (D1), D670-D681, 2015	1090	2015
GENCODE 2021 A Frankish, M Diekhans, I Jungreis, J Lagarde, JE Loveland, JM Mudge, ... Nucleic acids research 49 (D1), D916-D923, 2021	919	2021
A user’s guide to the encyclopedia of DNA elements (ENCODE) ENCODE Project Consortium PLoS Biol 9 (4), e1001046, 2011	866	2011
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species KR Bradnam, JN Fass, A Alexandrov, P Baranay, M Bechner, I Birol, ... Gigascience 2 (1), 2047-217X-2-10, 2013	810	2013
Improved data analysis for the MinION nanopore sequencer M Jain, IT Fiddes, KH Miga, HE Olsen, B Paten, M Akeson Nature methods 12 (4), 351-356, 2015	800	2015
Telomere-to-telomere assembly of a complete human X chromosome KH Miga, S Koren, A Rhie, MR Vollger, A Gershman, A Bzikadze, ... Nature 585 (7823), 79-84, 2020	722	2020
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures A Stark, MF Lin, P Kheradpour, JS Pedersen, L Parts, JW Carlson, ... Nature 450 (7167), 219-232, 2007	717	2007
A user's guide to the encyclopedia of DNA elements (ENCODE) RM Myers, J Stamatoyannopoulos, M Snyder, I Dunham, RC Hardison, ... PLoS biology 9 (4), 2011	677	2011
Assemblathon 1: a competitive assessment of de novo short read assembly methods D Earl, K Bradnam, JS John, A Darling, D Lin, J Fass, HOK Yu, V Buffalo, ... Genome research 21 (12), 2224-2241, 2011	637	2011
Nanopore native RNA sequencing of a human poly (A) transcriptome (vol 16, pg, 1297, 2019) RE Workman, AD Tang, PS Tang, M Jain, JR Tyson, R Razaghi, ... NATURE METHODS 17 (1), 114-114, 2020	611*	2020
Variation graph toolkit improves read mapping by representing genetic variation in the reference E Garrison, J Sirén, AM Novak, G Hickey, JM Eizenga, ET Dawson, ... Nature biotechnology 36 (9), 875-879, 2018	603	2018

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