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Computational Metabolomics Operations at BioCyc.org.

Metabolites

Karp PD, Billington R, Holland TA, Kothari A, Krummenacker M, Weaver D, Latendresse M, Paley S.
PMID: 26011592
Metabolites. 2015 May 22;5(2):291-310. doi: 10.3390/metabo5020291.

BioCyc.org is a genome and metabolic pathway web portal covering 5500 organisms, including Homo sapiens, Arabidopsis thaliana, Saccharomyces cerevisiae and Escherichia coli. These organism-specific databases have undergone variable degrees of curation. The EcoCyc (Escherichia coli Encyclopedia) database is the...

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Karp PD, Billington R, Holland TA, et al. Computational Metabolomics Operations at BioCyc.org. Metabolites. 2015;5(2):291-310doi: 10.3390/metabo5020291.
Karp, P. D., Billington, R., Holland, T. A., Kothari, A., Krummenacker, M., Weaver, D., Latendresse, M., & Paley, S. (2015). Computational Metabolomics Operations at BioCyc.org. Metabolites, 5(2), 291-310. https://doi.org/10.3390/metabo5020291
Karp, Peter D, et al. "Computational Metabolomics Operations at BioCyc.org." Metabolites vol. 5,2 (2015): 291-310. doi: https://doi.org/10.3390/metabo5020291
Karp PD, Billington R, Holland TA, Kothari A, Krummenacker M, Weaver D, Latendresse M, Paley S. Computational Metabolomics Operations at BioCyc.org. Metabolites. 2015 May 22;5(2):291-310. doi: 10.3390/metabo5020291. PMID: 26011592; PMCID: PMC4495374.
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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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A Comparison of Microbial Genome Web Portals.

Frontiers in microbiology

Karp PD, Ivanova N, Krummenacker M, Kyrpides N, Latendresse M, Midford P, Ong WK, Paley S, Seshadri R.
PMID: 30853946
Front Microbiol. 2019 Feb 22;10:208. doi: 10.3389/fmicb.2019.00208. eCollection 2019.

Microbial genome web portals have a broad range of capabilities that address a number of information-finding and analysis needs for scientists. This article compares the capabilities of the major microbial genome web portals to aid researchers in determining which...

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Karp PD, Ivanova N, Krummenacker M, et al. A Comparison of Microbial Genome Web Portals. Front Microbiol. 2019;10:208doi: 10.3389/fmicb.2019.00208.
Karp, P. D., Ivanova, N., Krummenacker, M., Kyrpides, N., Latendresse, M., Midford, P., Ong, W. K., Paley, S., & Seshadri, R. (2019). A Comparison of Microbial Genome Web Portals. Frontiers in microbiology, 10208. https://doi.org/10.3389/fmicb.2019.00208
Karp, Peter D, et al. "A Comparison of Microbial Genome Web Portals." Frontiers in microbiology vol. 10 (2019): 208. doi: https://doi.org/10.3389/fmicb.2019.00208
Karp PD, Ivanova N, Krummenacker M, Kyrpides N, Latendresse M, Midford P, Ong WK, Paley S, Seshadri R. A Comparison of Microbial Genome Web Portals. Front Microbiol. 2019 Feb 22;10:208. doi: 10.3389/fmicb.2019.00208. eCollection 2019. PMID: 30853946; PMCID: PMC6395428.
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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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The pathway tools pathway prediction algorithm.

Standards in genomic sciences

Karp PD, Latendresse M, Caspi R.
PMID: 22675592
Stand Genomic Sci. 2011 Dec 31;5(3):424-9. doi: 10.4056/sigs.1794338. Epub 2011 Dec 23.

The PathoLogic component of the Pathway Tools software performs prediction of metabolic pathways in sequenced and annotated genomes. This article provides a detailed presentation of the PathoLogic algorithm. The algorithm consists of two phases. The reactome inference phase infers...

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Karp PD, Latendresse M, Caspi R. The pathway tools pathway prediction algorithm. Stand Genomic Sci. 2011;5(3):424-9doi: 10.4056/sigs.1794338.
Karp, P. D., Latendresse, M., & Caspi, R. (2011). The pathway tools pathway prediction algorithm. Standards in genomic sciences, 5(3), 424-9. https://doi.org/10.4056/sigs.1794338
Karp, Peter D, et al. "The pathway tools pathway prediction algorithm." Standards in genomic sciences vol. 5,3 (2011): 424-9. doi: https://doi.org/10.4056/sigs.1794338
Karp PD, Latendresse M, Caspi R. The pathway tools pathway prediction algorithm. Stand Genomic Sci. 2011 Dec 31;5(3):424-9. doi: 10.4056/sigs.1794338. Epub 2011 Dec 23. PMID: 22675592; PMCID: PMC3368424.
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Pathway size matters: the influence of pathway granularity on over-representation (enrichment analysis) statistics.

BMC genomics

Karp PD, Midford PE, Caspi R, Khodursky A.
PMID: 33726670
BMC Genomics. 2021 Mar 16;22(1):191. doi: 10.1186/s12864-021-07502-8.

BACKGROUND: Enrichment or over-representation analysis is a common method used in bioinformatics studies of transcriptomics, metabolomics, and microbiome datasets. The key idea behind enrichment analysis is: given a set of significantly expressed genes (or metabolites), use that set to...

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Karp PD, Midford PE, Caspi R, et al. Pathway size matters: the influence of pathway granularity on over-representation (enrichment analysis) statistics. BMC Genomics. 2021;22(1):191doi: 10.1186/s12864-021-07502-8.
Karp, P. D., Midford, P. E., Caspi, R., & Khodursky, A. (2021). Pathway size matters: the influence of pathway granularity on over-representation (enrichment analysis) statistics. BMC genomics, 22(1), 191. https://doi.org/10.1186/s12864-021-07502-8
Karp, Peter D, et al. "Pathway size matters: the influence of pathway granularity on over-representation (enrichment analysis) statistics." BMC genomics vol. 22,1 (2021): 191. doi: https://doi.org/10.1186/s12864-021-07502-8
Karp PD, Midford PE, Caspi R, Khodursky A. Pathway size matters: the influence of pathway granularity on over-representation (enrichment analysis) statistics. BMC Genomics. 2021 Mar 16;22(1):191. doi: 10.1186/s12864-021-07502-8. PMID: 33726670; PMCID: PMC7967953.
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Pathway Tools Visualization of Organism-Scale Metabolic Networks.

Metabolites

Paley S, Billington R, Herson J, Krummenacker M, Karp PD.
PMID: 33499002
Metabolites. 2021 Jan 22;11(2). doi: 10.3390/metabo11020064.

Metabolomics, synthetic biology, and microbiome research demand information about organism-scale metabolic networks. The convergence of genome sequencing and computational inference of metabolic networks has enabled great progress toward satisfying that demand by generating metabolic reconstructions from the genomes of...

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Paley S, Billington R, Herson J, et al. Pathway Tools Visualization of Organism-Scale Metabolic Networks. Metabolites. 2021;11(2)doi: 10.3390/metabo11020064.
Paley, S., Billington, R., Herson, J., Krummenacker, M., & Karp, P. D. (2021). Pathway Tools Visualization of Organism-Scale Metabolic Networks. Metabolites, 11(2), . https://doi.org/10.3390/metabo11020064
Paley, Suzanne, et al. "Pathway Tools Visualization of Organism-Scale Metabolic Networks." Metabolites vol. 11,2 (2021). doi: https://doi.org/10.3390/metabo11020064
Paley S, Billington R, Herson J, Krummenacker M, Karp PD. Pathway Tools Visualization of Organism-Scale Metabolic Networks. Metabolites. 2021 Jan 22;11(2). doi: 10.3390/metabo11020064. PMID: 33499002; PMCID: PMC7911265.
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The BioCyc Metabolic Network Explorer.

BMC bioinformatics

Paley S, Karp PD.
PMID: 33882841
BMC Bioinformatics. 2021 Apr 21;22(1):208. doi: 10.1186/s12859-021-04132-5.

BACKGROUND: The Metabolic Network Explorer is a new addition to the BioCyc.org website and the Pathway Tools software suite that supports the interactive exploration of metabolic networks. Any metabolic network visualization tool must by necessity show only a subset...

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Paley S, Karp PD. The BioCyc Metabolic Network Explorer. BMC Bioinformatics. 2021;22(1):208doi: 10.1186/s12859-021-04132-5.
Paley, S., & Karp, P. D. (2021). The BioCyc Metabolic Network Explorer. BMC bioinformatics, 22(1), 208. https://doi.org/10.1186/s12859-021-04132-5
Paley, Suzanne, and Karp, Peter D. "The BioCyc Metabolic Network Explorer." BMC bioinformatics vol. 22,1 (2021): 208. doi: https://doi.org/10.1186/s12859-021-04132-5
Paley S, Karp PD. The BioCyc Metabolic Network Explorer. BMC Bioinformatics. 2021 Apr 21;22(1):208. doi: 10.1186/s12859-021-04132-5. PMID: 33882841; PMCID: PMC8060992.
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The Time Is Right to Focus on Model Organism Metabolomes.

Metabolites

Edison AS, Hall RD, Junot C, Karp PD, Kurland IJ, Mistrik R, Reed LK, Saito K, Salek RM, Steinbeck C, Sumner LW, Viant MR.
PMID: 26891337
Metabolites. 2016 Feb 15;6(1). doi: 10.3390/metabo6010008.

Model organisms are an essential component of biological and biomedical research that can be used to study specific biological processes. These organisms are in part selected for facile experimental study. However, just as importantly, intensive study of a small...

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Edison AS, Hall RD, Junot C, et al. The Time Is Right to Focus on Model Organism Metabolomes. Metabolites. 2016;6(1)doi: 10.3390/metabo6010008.
Edison, A. S., Hall, R. D., Junot, C., Karp, P. D., Kurland, I. J., Mistrik, R., Reed, L. K., Saito, K., Salek, R. M., Steinbeck, C., Sumner, L. W., & Viant, M. R. (2016). The Time Is Right to Focus on Model Organism Metabolomes. Metabolites, 6(1), . https://doi.org/10.3390/metabo6010008
Edison, Arthur S, et al. "The Time Is Right to Focus on Model Organism Metabolomes." Metabolites vol. 6,1 (2016). doi: https://doi.org/10.3390/metabo6010008
Edison AS, Hall RD, Junot C, Karp PD, Kurland IJ, Mistrik R, Reed LK, Saito K, Salek RM, Steinbeck C, Sumner LW, Viant MR. The Time Is Right to Focus on Model Organism Metabolomes. Metabolites. 2016 Feb 15;6(1). doi: 10.3390/metabo6010008. PMID: 26891337; PMCID: PMC4812337.
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Showing 1 to 9 of 9 entries