| 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 | 1319 | 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 | 681 | 2021 |
| 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 | 456* | 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 | 201 | 2021 |
| Methods for automated genome-scale metabolic model reconstruction JP Faria, M Rocha, I Rocha, CS Henry Biochemical Society Transactions 46 (4), 931-936, 2018 | 65 | 2018 |
| 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 | 46 | 2013 |
| 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 | 26 | 2016 |
| 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 | 25 | 2018 |
| 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 | 19 | 2020 |
| TranSyT, an innovative framework for identifying transport systems E Cunha, D Lagoa, JP Faria, F Liu, CS Henry, O Dias Bioinformatics 39 (8), btad466, 2023 | 15* | 2023 |
| Constructing and analyzing metabolic flux models of microbial communities JP Faria, T Khazaei, JN Edirisinghe, P Weisenhorn, SMD Seaver, ... Hydrocarbon and Lipid Microbiology Protocols: Genetic, Genomic and System …, 2017 | 15 | 2017 |
| ModelSEED v2: High-throughput genome-scale metabolic model reconstruction with enhanced energy biosynthesis pathway prediction JP Faria, F Liu, JN Edirisinghe, N Gupta, SMD Seaver, AP Freiburger, ... bioRxiv, 2023.10. 04.556561, 2023 | 8 | 2023 |
| 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 | 8 | 2016 |
| 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), 10.1128/mra. 00403-19, 2019 | 6 | 2019 |
| 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: Methods and Protocols, 291-320, 2022 | 5 | 2022 |
| 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, 101-105, 2015 | 5 | 2015 |
| 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), 10.1128/mra. 00299-20, 2020 | 4 | 2020 |
| Reconstruction and analysis of central metabolism in microbes JN Edirisinghe, JP Faria, NL Harris, BH Allen, CS Henry Metabolic Network Reconstruction and Modeling: Methods and Protocols, 111-129, 2018 | 4 | 2018 |
| A functional microbiome catalogue crowdsourced from North American rivers MA Borton, BB McGivern, KR Willi, BJ Woodcroft, AC Mosier, ... Nature, 1-10, 2024 | 3 | 2024 |
| kb_DRAM: annotation and metabolic profiling of genomes with DRAM in KBase M Shaffer, MA Borton, B Bolduc, JP Faria, RM Flynn, P Ghadermazi, ... Bioinformatics 39 (4), btad110, 2023 | 3 | 2023 |
Christopher HenryComputational Biologist, Argonne National LaboratoryVerified email at mcs.anl.gov
