| The MetaCyc database of metabolic pathways and enzymes-a 2019 update R Caspi, R Billington, IM Keseler, A Kothari, M Krummenacker, ... Nucleic acids research 48 (D1), D445-D453, 2020 | 1031 | 2020 |
| The MetaCyc database of metabolic pathways and enzymes R Caspi, R Billington, CA Fulcher, IM Keseler, A Kothari, ... Nucleic acids research 46 (D1), D633-D639, 2018 | 914 | 2018 |
| Pathway Tools version 24.0: Integrated Software for Pathway/Genome Informatics and Systems Biology PD Karp, SM Paley, PE Midford, M Krummenacker, R Billington, A Kothari, ... arXiv preprint arXiv:1510.03964, 2015 | 914* | 2015 |
| The BioCyc collection of microbial genomes and metabolic pathways PD Karp, R Billington, R Caspi, CA Fulcher, M Latendresse, A Kothari, ... Briefings in bioinformatics 20 (4), 1085-1093, 2019 | 902 | 2019 |
| The EcoCyc database in 2021 IM Keseler, S Gama-Castro, A Mackie, PE Midford, AJ Wolfe, ... Frontiers in microbiology 12, 711077, 2021 | 223 | 2021 |
| The EcoCyc Database 2018 PD Karp, WK Ong, S Paley, R Billington, R Caspi, C Fulcher, A Kothari, ... EcoSal Plus, 2018 | 207* | 2018 |
| Pathway Tools version 23.0 update: software for pathway/genome informatics and systems biology PD Karp, PE Midford, R Billington, A Kothari, M Krummenacker, ... Briefings in bioinformatics 22 (1), 109-126, 2021 | 179 | 2021 |
| Computational methods in metabolic engineering for strain design MR Long, WK Ong, JL Reed Current opinion in biotechnology 34, 135-141, 2015 | 143 | 2015 |
| Comparisons of Shewanella strains based on genome annotations, modeling, and experiments WK Ong, TT Vu, KN Lovendahl, JM Llull, MH Serres, MF Romine, JL Reed BMC systems biology 8, 1-11, 2014 | 47 | 2014 |
| Gene dispensability in Escherichia coli grown in thirty different carbon environments M Tong, S French, SS El Zahed, WK Ong, PD Karp, ED Brown MBio 11 (5), 10.1128/mbio. 02259-20, 2020 | 40 | 2020 |
| A comparison of microbial genome web portals PD Karp, N Ivanova, M Krummenacker, N Kyrpides, M Latendresse, ... Frontiers in microbiology, 208, 2019 | 26 | 2019 |
| Expression of phosphofructokinase is not sufficient to enable Embden-Meyerhof-Parnas glycolysis in Zymomonas mobilis ZM4 MM Felczak, TB Jacobson, WK Ong, D Amador-Noguez, MA TerAvest Frontiers in microbiology 10, 482826, 2019 | 17 | 2019 |
| Model-driven analysis of mutant fitness experiments improves genome-scale metabolic models of Zymomonas mobilis ZM4 WK Ong, DK Courtney, S Pan, RB Andrade, PJ Kiley, BF Pfleger, JL Reed PLOS Computational Biology 16 (8), e1008137, 2020 | 16 | 2020 |
| BioCyc: a genomic and metabolic web portal with multiple omics analytical tools R Caspi, R Billington, CA Fulcher, IM Keseler, A Kothari, ... The FASEB Journal 33 (S1), 473.2-473.2, 2019 | 11 | 2019 |
| Taxonomic weighting improves the accuracy of a gap-filling algorithm for metabolic models WK Ong, PE Midford, PD Karp Bioinformatics 36 (6), 1823-1830, 2020 | 7 | 2020 |
| Metabolic modeling with MetaFlux M Latendresse, WK Ong, PD Karp Microbial Systems Biology: Methods and Protocols, 259-289, 2022 | 5 | 2022 |
| Inventory control and LQG: connections and extensions WK Ong, EJ Durango-Cohen, DJ Chmielewski Proceedings of the 2010 American Control Conference, 4391-4396, 2010 | 2 | 2010 |
| MetaCyc: a database of enzymes and pathways with a broad coverage of natural products biosynthesis R Caspi, R Billington, I Keseler, A Kothari, M Krummenacker, P Midford, ... 3rd International Conference on Natural Products Discovery and Development …, 2020 | 1 | 2020 |
| Erratum for Tong et al.,“Gene Dispensability in Escherichia coli Grown in Thirty Different Carbon Environments” M Tong, S French, SS El Zahed, W Ong, PD Karp, ED Brown Mbio 11 (6), e02865-20, 2020 | | 2020 |
| Metabolic Reconstruction and Modeling From Sequenced Genomes PD Karp, R Caspi, WK Ong The FASEB Journal 34 (S1), 1-1, 2020 | | 2020 |
