Benedict Paten
Benedict Paten
Associate Professor; Associate Director, UC Santa Cruz Genomics Institute, University of California
Verified email at ucsc.edu - Homepage
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
53742007
Genetic effects on gene expression across human tissues
GTEx Consortium
Nature 550 (7675), 204, 2017
13912017
A userís guide to the encyclopedia of DNA elements (ENCODE)
ENCODE Project Consortium
PLoS Biol 9 (4), e1001046, 2011
12412011
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
10352018
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
9602019
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
9362015
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
7772016
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
6682007
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
6522013
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
5632015
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
5522011
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
3862016
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
3362017
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
3302008
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
3182014
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
3012015
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
2962014
Long-read sequence assembly of the gorilla genome
D Gordon, J Huddleston, MJP Chaisson, CM Hill, ZN Kronenberg, ...
Science 352 (6281), aae0344, 2016
2732016
Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs
RE Green, EL Braun, J Armstrong, D Earl, N Nguyen, G Hickey, ...
Science 346 (6215), 2014
2702014
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
2682017
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