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
28602014
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
10612015
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
8722017
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
5512011
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
3152018
Recovering complete and draft population genomes from metagenome datasets
N Sangwan, F Xia, JA Gilbert
Microbiome 4 (1), 1-11, 2016
1792016
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
1462012
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), 1-12, 2016
1222016
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
1052007
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
862020
Population genomic analysis of 1,777 extended-spectrum beta-lactamase-producing Klebsiella pneumoniae isolates, Houston, Texas: unexpected abundance of clonal group 307
SW Long, RJ Olsen, TN Eagar, SB Beres, P Zhao, JJ Davis, T Brettin, ...
MBio 8 (3), 2017
832017
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
832013
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), 1-11, 2018
692018
The DOE systems biology knowledgebase (KBase)
AP Arkin, RL Stevens, RW Cottingham, S Maslov, CS Henry, P Dehal, ...
BioRxiv, 096354, 2016
522016
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
502019
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, 79-101, 2018
422018
Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models
JP Faria, R Overbeek, F Xia, M Rocha, I Rocha, CS Henry
Briefings in bioinformatics 15 (4), 592-611, 2014
402014
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 (18), 59-69, 2018
392018
Genomes of the class Erysipelotrichia clarify the firmicute origin of the class Mollicutes
JJ Davis, F Xia, RA Overbeek, GJ Olsen
International journal of systematic and evolutionary microbiology 63 (Pt 7 …, 2013
392013
Connecting genotype to phenotype in the era of high-throughput sequencing
CS Henry, R Overbeek, F Xia, AA Best, E Glass, J Gilbert, P Larsen, ...
Biochimica et Biophysica Acta (BBA)-General Subjects 1810 (10), 967-977, 2011
392011
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