Benedict Paten

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Citations	24881	17746
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David HausslerScientific Director, UC Santa Cruz Genomics Institute, University of California, Santa CruzVerified email at soe.ucsc.edu
Miten JainAssistant Research Scientist, UC Santa Cruz Genomics InstituteVerified email at ucsc.edu
Jordan M EizengaPhD Student in Bioinformatics, University of California Santa Cruz Genomics InstituteVerified email at ucsc.edu
Mark AkesonProfessor of Biomolecular Engineering, UC Santa CruzVerified email at soe.ucsc.edu
Mark DiekhansUniversity of California, Santa Cruz; UC Santa Cruz Genomics InstituteVerified email at soe.ucsc.edu
Ian FiddesInscriptaVerified email at inscripta.com
Karen H MigaAssistant Research Scientist, UC Santa Cruz Genomics InstituteVerified email at soe.ucsc.edu
Ewan BirneyDirector, EMBL-EBIVerified email at ebi.ac.uk
Daniel ZerbinoMosaic TherapeuticsVerified email at mosaic-tx.com
Ngan NguyenAtreca Inc.Verified email at atreca.com
Dent EarlStaff Software Engineer at Google. Formerly of UCSC, UCLA.Verified email at soe.ucsc.edu
W James KentUC Santa Cruz Genomics Institute, University of California Santa Cruz, UCSC Genome BrowserVerified email at soe.ucsc.edu
Ian HolmesProfessor, Computational Biology and Bioengineering, UC BerkeleyVerified email at berkeley.edu
Paul FlicekEMBL, European Bioinformatics Institute, Wellcome Sanger InstituteVerified email at ebi.ac.uk
laurence ettwiller, Ph.DNew England Biolabs, INCVerified email at neb.com
John St. JohnComputational Biologist - Modeling, FreenomeVerified email at freenome.com

Benedict Paten

Associate 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 ENCODE Project Consortium nature 447 (7146), 799, 2007	5507	2007
Genetic effects on gene expression across human tissues. A Battle, CD Brown, BE Engelhardt, SB Montgomery Nature 550 (7675), 204-213, 2017	1647	2017
A user’s guide to the encyclopedia of DNA elements (ENCODE) ENCODE Project Consortium PLoS Biol 9 (4), e1001046, 2011	1272	2011
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	1252	2019
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	1172	2018
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	975	2015
The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community M Jain, HE Olsen, B Paten, M Akeson Genome biology 17 (1), 1-11, 2016	892	2016
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	687	2013
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	678	2007
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	602	2015
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	565	2011
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	400	2017
The UCSC genome browser database: 2016 update ML Speir, AS Zweig, KR Rosenbloom, BJ Raney, B Paten, P Nejad, ... Nucleic acids research 44 (D1), D717-D725, 2016	394	2016
An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons FMJ Jacobs, D Greenberg, N Nguyen, M Haeussler, AD Ewing, ... Nature 516 (7530), 242-245, 2014	345	2014
Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs B Paten, J Herrero, K Beal, S Fitzgerald, E Birney Genome research 18 (11), 1814-1828, 2008	337	2008
The Matchmaker Exchange: a platform for rare disease gene discovery AA Philippakis, DR Azzariti, S Beltran, AJ Brookes, CA Brownstein, ... Human mutation 36 (10), 915-921, 2015	334	2015
Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser BJ Raney, TR Dreszer, GP Barber, H Clawson, PA Fujita, T Wang, ... Bioinformatics 30 (7), 1003-1005, 2014	315	2014
Dynamic landscape and regulation of RNA editing in mammals MH Tan, Q Li, R Shanmugam, R Piskol, J Kohler, AN Young, KI Liu, ... Nature 550 (7675), 249-254, 2017	308	2017
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	295	2020
Long-read sequence assembly of the gorilla genome D Gordon, J Huddleston, MJP Chaisson, CM Hill, ZN Kronenberg, ... Science 352 (6281), aae0344, 2016	295	2016

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