| The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases R Caspi, T Altman, R Billington, K Dreher, H Foerster, CA Fulcher, ... Nucleic acids research 42 (D1), D459-D471, 2014 | 3523* | 2014 |
| EcoCyc: a comprehensive database of Escherichia coli biology IM Keseler, J Collado-Vides, A Santos-Zavaleta, M Peralta-Gil, ... Nucleic acids research 39 (suppl_1), D583-D590, 2010 | 652 | 2010 |
| Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology PD Karp, SM Paley, M Krummenacker, M Latendresse, JM Dale, TJ Lee, ... Briefings in bioinformatics 11 (1), 40-79, 2010 | 616 | 2010 |
| Petabase-scale sequence alignment catalyses viral discovery RC Edgar, B Taylor, V Lin, T Altman, P Barbera, D Meleshko, D Lohr, ... Nature 602 (7895), 142-147, 2022 | 399 | 2022 |
| A systematic comparison of the MetaCyc and KEGG pathway databases T Altman, M Travers, A Kothari, R Caspi, PD Karp BMC bioinformatics 14, 1-15, 2013 | 200 | 2013 |
| Metabolic pathways for the whole community NW Hanson, KM Konwar, AK Hawley, T Altman, PD Karp, SJ Hallam BMC genomics 15, 1-14, 2014 | 66 | 2014 |
| Beyond the genome (BTG) is a (PGDB) pathway genome database: HumanCyc M Trupp, T Altman, CA Fulcher, R Caspi, M Krummenacker, S Paley, ... Genome biology 11, 1-1, 2010 | 53 | 2010 |
| 56 BIBLIOGRAPHY Suzanne Paley, Pallavi Subhraveti, Daniel S. Weaver, Deepika Weerasinghe, Peifen Zhang, and Peter D. Karp. The MetaCyc database of metabolic pathways and … R Caspi, T Altman, R Billington, K Dreher, H Foerster, CA Fulcher, ... Nucleic acids research 42 (D1), D459-D471, 2014 | 50 | 2014 |
| A comparative evaluation of tools to predict metabolite profiles from microbiome sequencing data X Yin, T Altman, E Rutherford, KA West, Y Wu, J Choi, PL Beck, ... Frontiers in microbiology 11, 595910, 2020 | 27 | 2020 |
| Finding sequences for over 270 orphan enzymes AG Shearer, T Altman, CD Rhee PLoS One 9 (5), e97250, 2014 | 22 | 2014 |
| Data mining in the MetaCyc family of pathway databases PD Karp, S Paley, T Altman Data mining for systems biology: methods and protocols, 183-200, 2012 | 15 | 2012 |
| Methods and compositions for determining metabolic maps C Cutcliffe, JS Eid, JH Bullard, T Altman, F Perraudeau US Patent App. 15/945,705, 2018 | 13 | 2018 |
| Methods and compositions relating to isolated and purified microbes C Cutcliffe, JS Eid, JH Bullard, MF Schicklberger, AT Cheng, ... US Patent App. 16/431,257, 2020 | 10 | 2020 |
| A geographically-diverse collection of 418 human gut microbiome pathway genome databases AS Hahn, T Altman, KM Konwar, NW Hanson, D Kim, DA Relman, DL Dill, ... Scientific Data 4 (1), 1-12, 2017 | 9 | 2017 |
| Methods and compositions for treatment of microbiome-associated disorders C Cutcliffe, JS Eid, T Altman, OG Kolterman, JH Bullard US Patent 11,583,558, 2023 | 5 | 2023 |
| BioCyc: Microbial Genomes and Cellular Networks-The BioCyc system helps scientists navigate the greatly expanding information space of genomes and metabolic information PD Karp, IM Keseler, T Altman, R Caspi, CA Fulcher, P Subhraveti, ... Microbe 6 (4), 176, 2011 | 2 | 2011 |
| GutCyc: a Multi-Study Collection of Human Gut Microbiome Metabolic Models AS Hahn, T Altman, KM Konwar, NW Hanson, D Kim, DA Relman, DL Dill, ... BioRxiv, 055574, 2016 | 1 | 2016 |
| The Pathway Tools Software in 2009 PD Karp, SM Paley, M Krummenacker, M Latendresse, JM Dale, T Lee, ... S225–S232 p, 0 | 1 | |
| Methods and compositions for treatment of microbiome associated disorders C Cutcliffe, JS Eid, T Altman, OG Kolterman, JH Bullard US Patent 12,233,095, 2025 | | 2025 |
| MetaPathways v3. 5: Modularity and Scalability Improvements for Pathway Inference from Environmental Genomes RJ McLaughlin, TX Liu, T Altman, AN Nallan, AS Hahn, J Anstett, ... bioRxiv, 2024.06. 04.597460, 2024 | | 2024 |
Peter D. KarpDirector of the Bioinformatics Research Group, SRI InternationalVerified email at ai.sri.com
