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Construction and completion of flux balance models from pathway databases.

Bioinformatics (Oxford, England)

Latendresse M, Krummenacker M, Trupp M, Karp PD.
PMID: 22262672
Bioinformatics. 2012 Feb 01;28(3):388-96. doi: 10.1093/bioinformatics/btr681. Epub 2012 Jan 18.

MOTIVATION: Flux balance analysis (FBA) is a well-known technique for genome-scale modeling of metabolic flux. Typically, an FBA formulation requires the accurate specification of four sets: biochemical reactions, biomass metabolites, nutrients and secreted metabolites. The development of FBA models...

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Latendresse M, Krummenacker M, Trupp M, et al. Construction and completion of flux balance models from pathway databases. Bioinformatics. 2012;28(3):388-96doi: 10.1093/bioinformatics/btr681.
Latendresse, M., Krummenacker, M., Trupp, M., & Karp, P. D. (2012). Construction and completion of flux balance models from pathway databases. Bioinformatics (Oxford, England), 28(3), 388-96. https://doi.org/10.1093/bioinformatics/btr681
Latendresse, Mario, et al. "Construction and completion of flux balance models from pathway databases." Bioinformatics (Oxford, England) vol. 28,3 (2012): 388-96. doi: https://doi.org/10.1093/bioinformatics/btr681
Latendresse M, Krummenacker M, Trupp M, Karp PD. Construction and completion of flux balance models from pathway databases. Bioinformatics. 2012 Feb 01;28(3):388-96. doi: 10.1093/bioinformatics/btr681. Epub 2012 Jan 18. PMID: 22262672; PMCID: PMC3268246.
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The BioCyc collection of microbial genomes and metabolic pathways.

Briefings in bioinformatics

Karp PD, Billington R, Caspi R, Fulcher CA, Latendresse M, Kothari A, Keseler IM, Krummenacker M, Midford PE, Ong Q, Ong WK, Paley SM, Subhraveti P.
PMID: 29447345
Brief Bioinform. 2019 Jul 19;20(4):1085-1093. doi: 10.1093/bib/bbx085.

BioCyc.org is a microbial genome Web portal that combines thousands of genomes with additional information inferred by computer programs, imported from other databases and curated from the biomedical literature by biologist curators. BioCyc also provides an extensive range of...

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Karp PD, Billington R, Caspi R, et al. The BioCyc collection of microbial genomes and metabolic pathways. Brief Bioinform. 2019;20(4):1085-1093doi: 10.1093/bib/bbx085.
Karp, P. D., Billington, R., Caspi, R., Fulcher, C. A., Latendresse, M., Kothari, A., Keseler, I. M., Krummenacker, M., Midford, P. E., Ong, Q., Ong, W. K., Paley, S. M., & Subhraveti, P. (2019). The BioCyc collection of microbial genomes and metabolic pathways. Briefings in bioinformatics, 20(4), 1085-1093. https://doi.org/10.1093/bib/bbx085
Karp, Peter D, et al. "The BioCyc collection of microbial genomes and metabolic pathways." Briefings in bioinformatics vol. 20,4 (2019): 1085-1093. doi: https://doi.org/10.1093/bib/bbx085
Karp PD, Billington R, Caspi R, Fulcher CA, Latendresse M, Kothari A, Keseler IM, Krummenacker M, Midford PE, Ong Q, Ong WK, Paley SM, Subhraveti P. The BioCyc collection of microbial genomes and metabolic pathways. Brief Bioinform. 2019 Jul 19;20(4):1085-1093. doi: 10.1093/bib/bbx085. PMID: 29447345; PMCID: PMC6781571.
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Can we replace curation with information extraction software?.

Database : the journal of biological databases and curation

Karp PD.
PMID: 28025341
Database (Oxford). 2016 Dec 26;2016. doi: 10.1093/database/baw150. Print 2016.

Can we use programs for automated or semi-automated information extraction from scientific texts as practical alternatives to professional curation? I show that error rates of current information extraction programs are too high to replace professional curation today. Furthermore, current...

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Karp PD. Can we replace curation with information extraction software?. Database (Oxford). 2016;2016doi: 10.1093/database/baw150.
Karp, P. D. (2016). Can we replace curation with information extraction software?. Database : the journal of biological databases and curation, 2016. https://doi.org/10.1093/database/baw150
Karp, Peter D. "Can we replace curation with information extraction software?." Database : the journal of biological databases and curation vol. 2016 (2016). doi: https://doi.org/10.1093/database/baw150
Karp PD. Can we replace curation with information extraction software?. Database (Oxford). 2016 Dec 26;2016. doi: 10.1093/database/baw150. Print 2016. PMID: 28025341; PMCID: PMC5199131.
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The EcoCyc Database.

EcoSal Plus

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.
PMID: 26442933
EcoSal Plus. 2014 May;6(1). doi: 10.1128/ecosalplus.ESP-0009-2013.

EcoCyc is a bioinformatics database available at EcoCyc.org that describes the genome and the biochemical machinery of Escherichia coli K-12 MG1655. The long-term goal of the project is to describe the complete molecular catalog of the E. coli cell,...

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Karp PD, Weaver D, Paley S, et al. The EcoCyc Database. EcoSal Plus. 2014;6(1)doi: 10.1128/ecosalplus.ESP-0009-2013.
Karp, P. D., Weaver, D., Paley, S., Fulcher, C., Kubo, A., Kothari, A., Krummenacker, M., Subhraveti, P., Weerasinghe, D., Gama-Castro, S., Huerta, A. M., Muñiz-Rascado, L., Bonavides-Martinez, C., Weiss, V., Peralta-Gil, M., Santos-Zavaleta, A., Schröder, I., Mackie, A., Gunsalus, R., Collado-Vides, J., Keseler, I. M., & Paulsen, I. (2014). The EcoCyc Database. EcoSal Plus, 6(1), . https://doi.org/10.1128/ecosalplus.ESP-0009-2013
Karp, Peter D, et al. "The EcoCyc Database." EcoSal Plus vol. 6,1 (2014). doi: https://doi.org/10.1128/ecosalplus.ESP-0009-2013
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. The EcoCyc Database. EcoSal Plus. 2014 May;6(1). doi: 10.1128/ecosalplus.ESP-0009-2013. PMID: 26442933; PMCID: PMC4243172.
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Crowd-sourcing and author submission as alternatives to professional curation.

Database : the journal of biological databases and curation

Karp PD.
PMID: 28025340
Database (Oxford). 2016 Dec 26;2016. doi: 10.1093/database/baw149. Print 2016.

Can we decrease the costs of database curation by crowd-sourcing curation work or by offloading curation to publication authors? This perspective considers the significant experience accumulated by the bioinformatics community with these two alternatives to professional curation in the...

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Karp PD. Crowd-sourcing and author submission as alternatives to professional curation. Database (Oxford). 2016;2016doi: 10.1093/database/baw149.
Karp, P. D. (2016). Crowd-sourcing and author submission as alternatives to professional curation. Database : the journal of biological databases and curation, 2016. https://doi.org/10.1093/database/baw149
Karp, Peter D. "Crowd-sourcing and author submission as alternatives to professional curation." Database : the journal of biological databases and curation vol. 2016 (2016). doi: https://doi.org/10.1093/database/baw149
Karp PD. Crowd-sourcing and author submission as alternatives to professional curation. Database (Oxford). 2016 Dec 26;2016. doi: 10.1093/database/baw149. Print 2016. PMID: 28025340; PMCID: PMC5199147.
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Leveraging Curation Among .

Frontiers in microbiology

Paley S, Keseler IM, Krummenacker M, Karp PD.
PMID: 33763039
Front Microbiol. 2021 Mar 08;12:614355. doi: 10.3389/fmicb.2021.614355. eCollection 2021.

Updating genome databases to reflect newly published molecular findings for an organism was hard enough when only a single strain of a given organism had been sequenced. With multiple sequenced strains now available for many organisms, the challenge has...

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Paley S, Keseler IM, Krummenacker M, et al. Leveraging Curation Among . Front Microbiol. 2021;12:614355doi: 10.3389/fmicb.2021.614355.
Paley, S., Keseler, I. M., Krummenacker, M., & Karp, P. D. (2021). Leveraging Curation Among . Frontiers in microbiology, 12614355. https://doi.org/10.3389/fmicb.2021.614355
Paley, Suzanne, et al. "Leveraging Curation Among ." Frontiers in microbiology vol. 12 (2021): 614355. doi: https://doi.org/10.3389/fmicb.2021.614355
Paley S, Keseler IM, Krummenacker M, Karp PD. Leveraging Curation Among . Front Microbiol. 2021 Mar 08;12:614355. doi: 10.3389/fmicb.2021.614355. eCollection 2021. PMID: 33763039; PMCID: PMC7982652.
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Showing 1 to 6 of 6 entries