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Josť P. Faria
Josť P. Faria
Assistant Computational Biologist
Verified email at anl.gov - Homepage
Title
Cited by
Cited by
Year
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
679*2018
A genomic catalog of Earth’s microbiomes
S Nayfach, S Roux, R Seshadri, D Udwary, N Varghese, F Schulz, D Wu, ...
Nature biotechnology 39 (4), 499-509, 2021
2622021
MEMOTE for standardized genome-scale metabolic model testing
C Lieven, ME Beber, BG Olivier, FT Bergmann, M Ataman, P Babaei, ...
Nature biotechnology 38 (3), 272-276, 2020
234*2020
The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes
SMD Seaver, F Liu, Q Zhang, J Jeffryes, JP Faria, JN Edirisinghe, ...
Nucleic acids research 49 (D1), D575-D588, 2021
652021
Methods for automated genome-scale metabolic model reconstruction
JP Faria, M Rocha, I Rocha, CS Henry
Biochemical Society Transactions 46 (4), 931-936, 2018
432018
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, 2013
412013
A pathway for every product? Tools to discover and design plant metabolism
JG Jeffryes, SMD Seaver, JP Faria, CS Henry
Plant Science 273, 61-70, 2018
192018
Reconstruction of the Regulatory Network for Bacillus subtilis and Reconciliation with Gene Expression Data
JP Faria, R Overbeek, RC Taylor, N Conrad, V Vonstein, A Goelzer, ...
Frontiers in Microbiology 7, 275, 2016
162016
A review of methods for the reconstruction and analysis of integrated genome-scale models of metabolism and regulation
F Cruz, JP Faria, M Rocha, I Rocha, O Dias
Biochemical Society Transactions 48 (5), 1889-1903, 2020
112020
Constructing and analyzing metabolic flux models of microbial communities
JP Faria, T Khazaei, JN Edirisinghe, P Weisenhorn, S Seaver, N Conrad, ...
Hydrocarbon and Lipid Microbiology Protocols, 247-273, 2016
92016
Computing and applying atomic regulons to understand gene expression and regulation
JP Faria, JJ Davis, JN Edirisinghe, RC Taylor, P Weisenhorn, RD Olson, ...
Frontiers in microbiology 7, 1819, 2016
82016
TranSyT, the Transport Systems Tracker
D Lagoa, JP Faria, F Liu, E Cunha, CS Henry, O Dias
bioRxiv, 2021
62021
Draft Genome Sequence of Rhodococcus sp. Strain ATCC 49988, a Quinoline-Degrading Bacterium
N Gupta, KA Skinner, ZM Summers, JN Edirisinghe, JP Faria, ...
Microbiology resource announcements 8 (25), e00403-19, 2019
42019
Enabling comparative modeling of closely related genomes: example genus Brucella
JP Faria, JN Edirisinghe, JJ Davis, T Disz, A Hausmann, CS Henry, ...
3 Biotech 5 (1), 101-105, 2015
32015
Analysis of the effect of reversibility constraints on the predictions of genome-scale metabolic models
J Faria, M Rocha, R Stevens, C Henry
Advances in Bioinformatics, 209-215, 2010
32010
Application of the metabolic modeling pipeline in KBase to categorize reactions, predict essential genes, and predict pathways in an isolate genome
BH Allen, N Gupta, JN Edirisinghe, JP Faria, CS Henry
Microbial Systems Biology, 291-320, 2022
12022
TranSyT, an innovative framework for identifying transport systems
DRS Lagoa, JP Faria, F Liu, ER Cunha, CS Henry, O Dias
Cold Spring Harbor Laboratory, 2021
12021
Draft Genome Sequence of Pseudarthrobacter sp. Strain ATCC 49442 (Formerly Micrococcus luteus), a Pyridine-Degrading Bacterium
N Gupta, KA Skinner, ZM Summers, JN Edirisinghe, PB Weisenhorn, ...
Microbiology resource announcements 9 (38), e00299-20, 2020
12020
Reconstruction and analysis of central metabolism in microbes
JN Edirisinghe, JP Faria, NL Harris, BH Allen, CS Henry
Metabolic Network Reconstruction and Modeling, 111-129, 2018
12018
kb_DRAM: Annotating and functional profiling of genomes with DRAM in KBase
M Shaffer, MA Borton, B Bolduc, P Ghadermazi, J Edirisinghe, JP Faria, ...
bioRxiv, 2022
2022
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