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Jared Simpson
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A global reference for human genetic variation
1000 Genomes Project Consortium
Nature 526 (7571), 68, 2015
118772015
ABySS: a parallel assembler for short read sequence data
JT Simpson, K Wong, SD Jackman, JE Schein, SJM Jones, I Birol
Genome research 19 (6), 1117-1123, 2009
39112009
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
15352018
Real-time, portable genome sequencing for Ebola surveillance
J Quick, NJ Loman, S Duraffour, JT Simpson, E Severi, L Cowley, JA Bore, ...
Nature 530 (7589), 228-232, 2016
12502016
Shotgun metagenomics, from sampling to analysis
C Quince, AW Walker, JT Simpson, NJ Loman, N Segata
Nature biotechnology 35 (9), 833-844, 2017
11382017
A complete bacterial genome assembled de novo using only nanopore sequencing data
NJ Loman, J Quick, JT Simpson
Nature methods 12 (8), 733-735, 2015
11262015
Pan-cancer analysis of whole genomes
Nature 578 (7793), 82-93, 2020
10542020
Complex landscapes of somatic rearrangement in human breast cancer genomes
PJ Stephens, DJ McBride, ML Lin, I Varela, ED Pleasance, JT Simpson, ...
Nature 462 (7276), 1005-1010, 2009
9692009
Efficient de novo assembly of large genomes using compressed data structures
JT Simpson, R Durbin
Genome research 22 (3), 549-556, 2012
8972012
Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples
J Quick, ND Grubaugh, ST Pullan, IM Claro, AD Smith, K Gangavarapu, ...
Nature protocols 12 (6), 1261-1276, 2017
7822017
Insights into hominid evolution from the gorilla genome sequence
A Scally, JY Dutheil, LDW Hillier, GE Jordan, I Goodhead, J Herrero, ...
Nature 483 (7388), 169-175, 2012
7592012
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
7452013
Detecting DNA cytosine methylation using nanopore sequencing
JT Simpson, RE Workman, PC Zuzarte, M David, LJ Dursi, W Timp
Nature Methods 14 (4), 407, 2017
7062017
Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly
VA Schneider, T Graves-Lindsay, K Howe, N Bouk, HC Chen, PA Kitts, ...
Genome research 27 (5), 849-864, 2017
6102017
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
5952011
Establishment and cryptic transmission of Zika virus in Brazil and the Americas
NR Faria, J Quick, IM Claro, J Theze, JG de Jesus, M Giovanetti, ...
Nature 546 (7658), 406-410, 2017
5462017
A renewed model of pancreatic cancer evolution based on genomic rearrangement patterns
F Notta, M Chan-Seng-Yue, M Lemire, Y Li, GW Wilson, AA Connor, ...
Nature 538 (7625), 378-382, 2016
4822016
Nanopore native RNA sequencing of a human poly (A) transcriptome
RE Workman, AD Tang, PS Tang, M Jain, JR Tyson, R Razaghi, ...
Nature methods 16 (12), 1297-1305, 2019
3762019
Trait variation in yeast is defined by population history
J Warringer, E Zörgö, FA Cubillos, A Zia, A Gjuvsland, JT Simpson, ...
PLoS genetics 7 (6), e1002111, 2011
3422011
Efficient construction of an assembly string graph using the FM-index
JT Simpson, R Durbin
Bioinformatics 26 (12), i367-i373, 2010
3322010
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