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Computational Metabolomics Operations at BioCyc.org.
Karp PD, Billington R, Holland TA, Kothari A, Krummenacker M, Weaver D, Latendresse M, Paley S. Karp PD, et al. Among authors: weaver d. Metabolites. 2015 May 22;5(2):291-310. doi: 10.3390/metabo5020291. Metabolites. 2015. PMID: 26011592 Free PMC article.
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases.
Caspi R, Billington R, Ferrer L, Foerster H, Fulcher CA, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Subhraveti P, Weaver DS, Karp PD. Caspi R, et al. Among authors: weaver ds. Nucleic Acids Res. 2016 Jan 4;44(D1):D471-80. doi: 10.1093/nar/gkv1164. Epub 2015 Nov 2. Nucleic Acids Res. 2016. PMID: 26527732 Free PMC article.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
Keseler IM, Mackie A, Santos-Zavaleta A, Billington R, Bonavides-Martínez C, Caspi R, Fulcher C, Gama-Castro S, Kothari A, Krummenacker M, Latendresse M, Muñiz-Rascado L, Ong Q, Paley S, Peralta-Gil M, Subhraveti P, Velázquez-Ramírez DA, Weaver D, Collado-Vides J, Paulsen I, Karp PD. Keseler IM, et al. Among authors: weaver d. Nucleic Acids Res. 2017 Jan 4;45(D1):D543-D550. doi: 10.1093/nar/gkw1003. Epub 2016 Nov 28. Nucleic Acids Res. 2017. PMID: 27899573 Free PMC article.
Pathway collages: personalized multi-pathway diagrams.
Paley S, O'Maille PE, Weaver D, Karp PD. Paley S, et al. Among authors: weaver d. BMC Bioinformatics. 2016 Dec 13;17(1):529. doi: 10.1186/s12859-016-1382-1. BMC Bioinformatics. 2016. PMID: 27964719 Free PMC article.
How accurate is automated gap filling of metabolic models?
Karp PD, Weaver D, Latendresse M. Karp PD, et al. Among authors: weaver d. BMC Syst Biol. 2018 Jun 19;12(1):73. doi: 10.1186/s12918-018-0593-7. BMC Syst Biol. 2018. PMID: 29914471 Free PMC article.
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases.
Caspi R, Altman T, Billington R, Dreher K, Foerster H, Fulcher CA, Holland TA, Keseler IM, Kothari A, Kubo A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Subhraveti P, Weaver DS, Weerasinghe D, Zhang P, Karp PD. Caspi R, et al. Among authors: weaver ds. Nucleic Acids Res. 2014 Jan;42(Database issue):D459-71. doi: 10.1093/nar/gkt1103. Epub 2013 Nov 12. Nucleic Acids Res. 2014. PMID: 24225315 Free PMC article.
The EcoCyc Database.
Karp PD, Weaver D, Paley S, Fulcher C, Kubo A, Kothari A, Krummenacker M, Subhraveti P, Weerasinghe D, Gama-Castro S, Huerta AM, Muñiz-Rascado L, Bonavides-Martinez C, Weiss V, Peralta-Gil M, Santos-Zavaleta A, Schröder I, Mackie A, Gunsalus R, Collado-Vides J, Keseler IM, Paulsen I. Karp PD, et al. Among authors: weaver d. EcoSal Plus. 2014 May;6(1):10.1128/ecosalplus.ESP-0009-2013. doi: 10.1128/ecosalplus.ESP-0009-2013. EcoSal Plus. 2014. PMID: 26442933 Free PMC article.
Simultaneous cross-evaluation of heterogeneous E. coli datasets via mechanistic simulation.
Macklin DN, Ahn-Horst TA, Choi H, Ruggero NA, Carrera J, Mason JC, Sun G, Agmon E, DeFelice MM, Maayan I, Lane K, Spangler RK, Gillies TE, Paull ML, Akhter S, Bray SR, Weaver DS, Keseler IM, Karp PD, Morrison JH, Covert MW. Macklin DN, et al. Among authors: weaver ds. Science. 2020 Jul 24;369(6502):eaav3751. doi: 10.1126/science.aav3751. Science. 2020. PMID: 32703847 Free PMC article.
1,590 results