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Fangfang Xia
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The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)
R Overbeek, R Olson, GD Pusch, GJ Olsen, JJ Davis, T Disz, RA Edwards, ...
Nucleic acids research 42 (D1), D206-D214, 2014
43712014
RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes
T Brettin, JJ Davis, T Disz, RA Edwards, S Gerdes, GJ Olsen, R Olson, ...
Scientific reports 5 (1), 1-6, 2015
23052015
Improvements to PATRIC, the all-bacterial bioinformatics database and analysis resource center
AR Wattam, JJ Davis, R Assaf, S Boisvert, T Brettin, C Bun, N Conrad, ...
Nucleic acids research 45 (D1), D535-D542, 2017
14752017
KBase: the United States department of energy systems biology knowledgebase
AP Arkin, RW Cottingham, CS Henry, NL Harris, RL Stevens, S Maslov, ...
Nature biotechnology 36 (7), 566-569, 2018
10242018
The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities
JJ Davis, AR Wattam, RK Aziz, T Brettin, R Butler, RM Butler, P Chlenski, ...
Nucleic acids research 48 (D1), D606-D612, 2020
8222020
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
6312011
Recovering complete and draft population genomes from metagenome datasets
N Sangwan, F Xia, JA Gilbert
Microbiome 4, 1-11, 2016
2702016
Introducing the bacterial and viral bioinformatics resource center (BV-BRC): a resource combining PATRIC, IRD and ViPR
RD Olson, R Assaf, T Brettin, N Conrad, C Cucinell, JJ Davis, ...
Nucleic acids research 51 (D1), D678-D689, 2023
2632023
SEED servers: high-performance access to the SEED genomes, annotations, and metabolic models
RK Aziz, S Devoid, T Disz, RA Edwards, CS Henry, GJ Olsen, R Olson, ...
PloS one 7 (10), e48053, 2012
2232012
Antimicrobial resistance prediction in PATRIC and RAST
JJ Davis, S Boisvert, T Brettin, RW Kenyon, C Mao, R Olson, R Overbeek, ...
Scientific reports 6 (1), 27930, 2016
2172016
Developing an in silico minimum inhibitory concentration panel test for Klebsiella pneumoniae
M Nguyen, T Brettin, SW Long, JM Musser, RJ Olsen, R Olson, M Shukla, ...
Scientific reports 8 (1), 421, 2018
1652018
Population Genomic Analysis of 1,777 Extended-Spectrum Beta-Lactamase-Producing Klebsiella pneumoniae Isolates, Houston, Texas: Unexpected Abundance …
SW Long, RJ Olsen, TN Eagar, SB Beres, P Zhao, JJ Davis, T Brettin, ...
MBio 8 (3), 10.1128/mbio. 00489-17, 2017
1522017
Converting tabular data into images for deep learning with convolutional neural networks
Y Zhu, T Brettin, F Xia, A Partin, M Shukla, H Yoo, YA Evrard, ...
Scientific reports 11 (1), 11325, 2021
1242021
Predicting tumor cell line response to drug pairs with deep learning
F Xia, M Shukla, T Brettin, C Garcia-Cardona, J Cohn, JE Allen, S Maslov, ...
BMC bioinformatics 19, 71-79, 2018
1212018
The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation
LK McNeil, C Reich, RK Aziz, D Bartels, M Cohoon, T Disz, RA Edwards, ...
Nucleic acids research 35 (suppl_1), D347-D353, 2007
1212007
Building the repertoire of dispensable chromosome regions in Bacillus subtilis entails major refinement of cognate large-scale metabolic model
K Tanaka, CS Henry, JF Zinner, E Jolivet, MP Cohoon, F Xia, V Bidnenko, ...
Nucleic acids research 41 (1), 687-699, 2013
1092013
PATRIC as a unique resource for studying antimicrobial resistance
DA Antonopoulos, R Assaf, RK Aziz, T Brettin, C Bun, N Conrad, JJ Davis, ...
Briefings in bioinformatics 20 (4), 1094-1102, 2019
1052019
Assembly, annotation, and comparative genomics in PATRIC, the all bacterial bioinformatics resource center
AR Wattam, T Brettin, JJ Davis, S Gerdes, R Kenyon, D Machi, C Mao, ...
Comparative genomics: Methods and protocols, 79-101, 2018
912018
CANDLE/Supervisor: A workflow framework for machine learning applied to cancer research
JM Wozniak, R Jain, P Balaprakash, J Ozik, NT Collier, J Bauer, F Xia, ...
BMC bioinformatics 19, 59-69, 2018
872018
The DOE systems biology knowledgebase (KBase)
AP Arkin, RL Stevens, RW Cottingham, S Maslov, CS Henry, P Dehal, ...
BioRxiv, 096354, 2016
772016
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