BioCyc and Pathway Tools Publications

If you use BioCyc databases or the Pathway Tools software in your research, we ask that you cite relevant publications from the following list.

Like to learn more? View one or more BioCyc Web seminars.

Publications on the Full BioCyc Database Collection

[BioCyc19] Karp, P.D., et al., The BioCyc collection of microbial genomes and metabolic pathways
Briefings in Bioinformatics (2019).

Publications on the EcoCyc Database

[EcoCyc21] Keseler, I.M., Gama-Castro, S., Mackie, A., Billington, R., Billington, R., Caspi, R., Kothari, A., Krummenacker, M., Midford, P., Muñiz-Rascado, L., Ong, W., Paley, S., Santos-Zavaleta, A., Subhraveti, P., Tierrafria, V., Wolfe, A., Collado-Vides, J., Paulsen, I., and Karp, P.D.
The EcoCyc database in 2021
Front Microbiol 2021; 12: 711077.

[EcoCyc18] P.D.Karp, W.K.Ong, S.Paley, S.Billington, R.Caspi, C.Fulcher, A.Kothari, M.Krummenacker, M.Latendresse, P.E.Midford, P.Subhraveti., S.Gama-Castro, L. Muniz-Rascado., C.Bonavides-Martinez., A.Santos-Zavaleta, A.Mackie, J.Collado-Vides., I.M.Keseler., and I.Paulsen.
The EcoCyc Database
EcoSal Plus doi:10.1128/ecosalplus.ESP-0006-2018

See also: The EcoCyc publications page.

Publications on the MetaCyc Database

[MetaCyc20] R.Caspi, R.Billington, I.M. Keseler, A.Kothari, M.Krummenacker, P.E.Midford, W.K. Ong, S.Paley, P.Subhraveti, P.D. Karp The MetaCyc database of metabolic pathways and enzymes - a 2019 update
Nucleic Acids Res48(D1):D445-D453.doi: 10.1093/nar/gkz862.(2020)

[MetaCyc13] Caspi R., Dreher K., and Karp P.D. The challenge of constructing, classifying, and representing metabolic pathways.
FEMS Microbiol Lett. doi: 10.1111/1574-6968.12194. (2013)

[MetaCyc11] Karp P.D., and Caspi R., A survey of metabolic databases emphasizing the MetaCyc family
Archives of Toxicology 85:1015-33 (2011)

Publications on the HumanCyc Database

[HumanCyc04] P.Romero., J.Wagg., M.L.Green., D.Kaiser., M.Krummenacker., and P.D.Karp
Computational prediction of human metabolic pathways from the complete human genome,
Genome Biology 6:R2 R2.1-17 (2004)

Publications on the Pathway Tools Software Behind BioCyc

Latest Comprehensive Description of Pathway Tools:
[PTools19Survey] Karp, P.D. and Midford, P.E. and Paley, S.M. and Krummenacker, M. and Billington, R. and Kothari, A. and Ong, W.K. and Subhraveti, P. and Keseler, I.M. and Caspi, R.,
Pathway Tools version 23.0: Integrated Software for Pathway/Genome Informatics and Systems Biology,
arXiv 1-111 (2019).

Overviews of Pathway Tools:
[PTools19] Karp P.D., Midford, P.E., Billington, R., Kothari A., Krummenacker M., Latendresse, M., Ong, W.K., Subhraveti P., Caspi R., Fulcher C.A., Keseler I.M., Paley S.M.
Pathway Tools version 23.0 update: software for pathway/genome informatics and systems biology
Briefings in Bioinformatics doi: 10.1093/bib/bbz104. (2019)

[PTools15] Karp P.D., Latendresse M., Paley S.M., Krummenacker M., Ong Q., Billington R., Kothari A., Weaver D., Lee T., Subhraveti P., Spaulding A., Fulcher C.A., Keseler I.M., Caspi R.
Pathway Tools version 19.0: Integrated Software for Pathway/Genome Informatics and Systems Biology
Briefings in Bioinformatics doi: 10.1093/bib/bbv079. (2015)

[PTools10] P.D.Karp., S.M.Paley., M. Krummenacker. et al
Pathway Tools version 13.0: Integrated Software for Pathway/Genome Informatics and Systems Biology
Briefings in Bioinformatics 11:40-79 (2010)

Transcription Data Analysis:
[PTools17] Suzanne Paley, Karen Parker, Aaron Spaulding, Jean-Francois Tomb, Paul O'Maille, and Peter Karp.
The Omics Dashboard for interactive exploration of gene-expression data,
Nucleic Acids Research 45:12113-24 doi:10.1093/nar/gkx910 (2017)

[PTools06] S.M. Paley and P.D. Karp.
The Pathway Tools Cellular Overview Diagram and Omics Viewer,
Nucleic Acids Research 34:3771-8 (2006)

Metabolomics Data Analysis:
[PTools15] P.D. Karp., Billington. R., Holland. T.A., Kothari. A., Krummenacker. M., Weaver. D., M. Latendresse., Paley. S.
Computational Metabolomics Operations at BioCyc.org,
DATABASE - Metabolites — Open Access Metabolism & Metabolomics Journal , doi: 10.3390/metabo5020291, (2015)

SmartTables(Groups):
[PTools13] Mike Travers., S.M Paley., J.Shrager., T.A Holland., and Peter Karp
Groups:knowledge spreadsheets for symbolic biocomputing
Database, doi:10.1093/database/bat061 (2013)

Flux balance analysis (FBA) and multiple gap-filling:
[PTools22] M. Latendresse, W.K. Ong, P.D. Karp
Metabolic Modeling with MetaFlux
Methods Mol Biol doi: 10.1007/978-1-0716-1585-0_12 (2022) [PTools20] W.K. Ong, P.E. Midford, P.D. Karp
Taxonomic weighting improves the accuracy of a gap-filling algorithm for metabolic models
Bioinformatics36(6):1823-1830 doi: 10.1093/bioinformatics/btz813 (2020)

[PTool18]P.D. Karp, D. Weaver, M.Latendresse
How accurate is automated gap filling of metabolic models
BMC Syst Biol12(1):73 doi: 10.1186/s12918-018-0593-7 (2018)

[PTools14] Mario Latendresse,
Efficiently Gap-Filling Reaction Networks,
BMC Bioinformatics, 15:225, doi:10.1186/1471-2105-15-225, (June 2014)

[PTools12] Mario Latendresse, Markus Krummenacker, Miles Trupp, and Peter Karp
Construction and Completion of Flux-Balance Models from Pathway Databases
Bioinformatics, doi: 10.1093/bioinformatics/btr681, (2012)

Metabolic and Regulatory Network Visualization:
[PTools21] Suzanne Paley and Peter D. Karp
The BioCyc Metabolic Network Explorer,
BMC Bioinformatics 22:208, (2021)

[PTools21] S. Paley, R. Billington, J. Herson, M. Krummenacker and P. D. Karp
Pathway Tools Visualization of Organism-Scale Metabolic Networks,
Metabolites 11:64, (2021)

[PTools11] Suzanne M Paley, Mario Latendresse and Peter D. Karp
Regulatory network operations in the Pathway Tools software,
BMC Bioinformatics 13:243, (2012)

[PTools11]Mario Latendresse and Peter D. Karp
Web-based metabolic network visualization with a zooming user interface,
BMC Bioinformatics 12:176, (2011)

Metabolic Route Search:
[PTools19] M. Krummenacker, M. Latendresse, P.D. Karp
Metabolic route computation in organism communities
Microbiome7(1):89. doi: 10.1186/s40168-019-0706-6. (2019)

[PTools14] M. Latendresse, M.Krummenacker, P.D. Karp
Optimal metabolic route search based on atom mappings
Bioinformatics30(14) doi: 10.1093/bioinformatics/btu150.(2014)

Atom Mapping:
[PTools12] Mario Latendresse, Jeremiah P. Malerich, Mike Travers, and Peter D. Karp
Accurate Atom-Mapping Computation for Biochemical Reactions
DATABASE - The Journal of Chemical Information and Modelling(ACS)doi:10.1021/ci3002217, (2012)

Biological Database Querying:
[PTools10b] Mario Latendresse and Peter D. Karp
An advanced web query interface for biological databases
DATABASE - The Journal of Biological Databases and Curation doi: 10.1093/database/baq006, (2010)

Pathway Tools APIs:
[PTools05] M. Krummenacker., S. Paley., L. Mueller., T. Yan., and P.D. Karp.
Querying and Computing with BioCyc Databases,
Bioinformatics 21:3454-5 (2005)

Pathway Drawing Algorithms:
[PTools16] S.Paley, P.E.O'Maille, D.Weaver and P.D. Karp Pathway collages: personalized multi-pathway diagrams
BMC Bioinformatics17(1):529 doi: 10.1186/s12859-016-1382-1.(2016)

The Pathway Tools Cellular Overview Diagram and Omics Viewer,
Nucleic Acids Research 34:3771-8 2006. [PTools94] P.D. Karp and S.M. Paley

Automated drawing of metabolic pathways [PDF] [PS]
Proceedings of the Third International Conference on Bioinformatics and Genome Research, pp225-38 (1994)

Pathway Prediction/Metabolic Reconstruction:
[PTools14]N.W. Hanson, K.M. Konwar, A.K. Hawley, T. Altman, P.D. Karp, S.J. Hallam.
Metabolic pathways for the whole community
BMC Genomics15(1) :619. doi: 10.1186/1471-2164-15-619. (2014)

[PTools11] P.D. Karp., M. Latendresse., R. Caspi.
The Pathway Tools pathway prediction algorithm.
Standards in Genomic Sciences5(3): 424–429. doi: 10.4056/sigs.1794338 (2011)

[PTools10a] J.M Dale., L. Popescu., and P.D. Karp
Machine learning methods for metabolic pathway prediction.
BMC Bioinformatics 8:15 (2010)

[PTools02a] S.M.Paley and P.D.Karp
Evaluation of computational metabolic-pathway predictions for H. pylori
Bioinformatics 18:715-24 (2002)

Pathway Hole Filling Algorithm:
[PTools04] M.Green and P.D.Karp
A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases.
BMC Bioinformatics 5:76 (2004)

Operon Predictor:
[PTools04a] P.Romero and P.D.Karp
Using functional and organizational information to improve genome-wide computational prediction of transcription units on pathway/genome databases.
Bioinformatics (2004)

Predictor of Transport Reactions:
[PTools08] T.J.Lee., I. Paulsen., and P.D.Karp
Annotation-based inference of transporter function.
Bioinformatics 24:i259-67 (2008)

Publications on the Pathway Tools Ontology

[PTools04b] P.D.Karp., S. Paley., C.J. Krieger., and Zhang P.
An Evidence Ontology for use in Pathway/Genome Databases.
Pacific Symposium on Biocomputing 9:190-201 (2004)

[PTools00] P.D.Karp
An ontology for biological function based on molecular interactions.
Bioinformatics 16:269-85 (2000)

[PTools94a] P. Karp and S. Paley
Representations of metabolic knowledge: Pathways
in Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology. (Altman, R. and Brutlag, D. and Karp, P. and Lathrop, R. and Searls, D. eds.), (Menlo Park, CA), AAAI Press, (1994)

[PTools93] P. Karp and M. Riley
Representations of metabolic knowledge
in Proceedings of the First International Conference on Intelligent Systems for Molecular Biology. (L. Hunter, D. Searls, and J. Shavlik, eds.), (Menlo Park, CA), pp. 207-215, AAAI Press, (1993)

Publications on the Ocelot Object-Oriented DBMS Underlying Pathway Tools

[Ocelot99] P.D.Karp, V.K.Chaudhri, and S.M Paley
A collaborative environment for authoring large knowledge bases
J Intelligent Information Systems. 13:155-94 (1999)

Other Pathway Bioinformatics Publications

[Pathway05] M.L.Green and P.D. Karp
Genome Annotation Errors in Pathway Databases Due to Semantic Ambiguity in Partial EC Numbers.
Nucleic Acids Research 33:4035-9 (2005)

[Pathway06] M.L Green and P.D. Karp
The outcomes of pathway database computations depend on pathway ontology.
Nucleic Acids Research 34:3687-97 (2006)