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James Taylor
James Taylor
Professor of Biology and Computer Science, Johns Hopkins University
Verified email at jhu.edu - Homepage
Title
Cited by
Cited by
Year
An integrated encyclopedia of DNA elements in the human genome
ENCODE Project Consortium
Nature 489 (7414), 57-74, 2012
119582012
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
E Birney, JA Stamatoyannopoulos, A Dutta, R Guigó, TR Gingeras, ...
Nature 447 (7146), 799-816, 2007
56812007
Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
J Goecks, A Nekrutenko, J Taylor
Genome Biol 11 (8), R86, 2010
39912010
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update
E Afgan, D Baker, B Batut, M van den Beek, D Bouvier, M Čech, J Chilton, ...
Nucleic acids research 46 (W1), W537-W544, 2018
39762018
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
LDW Hillier, W Miller, E Birney, W Warren, RC Hardison, CP Ponting, ...
Nature 432 (7018), 695-716, 2004
27082004
Galaxy: a platform for interactive large-scale genome analysis
B Giardine, C Riemer, RC Hardison, R Burhans, L Elnitski, P Shah, ...
Genome research 15 (10), 1451-1455, 2005
24042005
Genome sequence of the Brown Norway rat yields insights into mammalian evolution
RA Gibbs, GM Weinstock, ML Metzker, DM Muzny, EJ Sodergren, ...
Nature 428 (6982), 493-521, 2004
23932004
Initial sequence of the chimpanzee genome and comparison with the human genome
TC Sequencing, Analysis Consortium
Nature 437 (7055), 69-87, 2005
21552005
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update
E Afgan, D Baker, M Van den Beek, D Blankenberg, D Bouvier, M Čech, ...
Nucleic acids research 44 (W1), W3-W10, 2016
17662016
Galaxy: a web‐based genome analysis tool for experimentalists
D Blankenberg, GV Kuster, N Coraor, G Ananda, R Lazarus, M Mangan, ...
Current protocols in molecular biology 89 (1), 19.10. 1-19.10. 21, 2010
17022010
A comparative encyclopedia of DNA elements in the mouse genome
F Yue, Y Cheng, A Breschi, J Vierstra, W Wu, T Ryba, R Sandstrom, Z Ma, ...
Nature 515 (7527), 355-364, 2014
15722014
Architectural protein subclasses shape 3D organization of genomes during lineage commitment
JE Phillips-Cremins, MEG Sauria, A Sanyal, TI Gerasimova, BR Lajoie, ...
Cell 153 (6), 1281-1295, 2013
11152013
Topologically associating domains are stable units of replication-timing regulation
BD Pope, T Ryba, V Dileep, F Yue, W Wu, O Denas, DL Vera, Y Wang, ...
Nature 515 (7527), 402-405, 2014
7902014
Genome analysis of the platypus reveals unique signatures of evolution
WC Warren, LDW Hillier, JAM Graves, E Birney, CP Ponting, F Grützner, ...
Nature 453 (7192), 175-183, 2008
7482008
Manipulation of FASTQ data with Galaxy
D Blankenberg, A Gordon, G Von Kuster, N Coraor, J Taylor, ...
Bioinformatics 26 (14), 1783-1785, 2010
7062010
Ten Simple Rules for Reproducible Computational Research
GK Sandve, A Nekrutenko, J Taylor, E Hovig
PLOS Computational Biology 9 (10), e1003285, 2013
6812013
MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis
GV Uritskiy, J DiRuggiero, J Taylor
Microbiome 6 (1), 158, 2018
5232018
An encyclopedia of mouse DNA elements (Mouse ENCODE)
JA Stamatoyannopoulos, M Snyder, R Hardison, B Ren, T Gingeras, ...
Genome biology 13 (8), 418, 2012
3442012
Next-generation sequencing data interpretation: enhancing reproducibility and accessibility
A Nekrutenko, J Taylor
Nature Reviews Genetics 13 (9), 667-672, 2012
3232012
The genome sequence of the leaf-cutter ant Atta cephalotes reveals insights into its obligate symbiotic lifestyle
G Suen, C Teiling, L Li, C Holt, E Abouheif, E Bornberg-Bauer, P Bouffard, ...
PLoS genetics 7 (2), e1002007, 2011
3062011
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