Benedict Paten

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Citations	27662	18969
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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 EizengaPostdoctoral Researcher, Genomics Institute, University of California Santa CruzVerified 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 Professor; Associate Director, UC Santa Cruz Genomics Institute, University of CaliforniaVerified email at 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	5628	2007
Genetic effects on gene expression across human tissues. A Battle, CD Brown, BE Engelhardt, SB Montgomery Nature 550 (7675), 204-213, 2017	1847*	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	1564	2019
A user’s guide to the encyclopedia of DNA elements (ENCODE) ENCODE Project Consortium PLoS Biol 9 (4), e1001046, 2011	1328	2011
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	1298	2018
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	1005	2016
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	993	2015
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	700	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	690	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	650	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	572	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	510	2017
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	407	2020
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	406	2016
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	386	2020
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	372	2015
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	368	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	342	2008
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	341	2017
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	325	2018

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