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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 DatabaseCollection

[Caspi10] Caspi R, Altman T, Dale JM, Dreher K, Fulcher CA, Gilham F, Kaipa P, Karthikeyan AS, Kothari A, Krummenacker M, Latendresse M, Mueller LA, Paley S, Popescu L, Pujar A, Shearer AG, Zhang P, Karp PD.
"The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases,"
Nucleic Acids Research 38:D473-9 2010.

Publications on the EcoCyc Database

[EcoCyc11] Keseler, I.M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A.G., Mackie, A., Paulsen, I., Gunsalus, R.P., and Karp, P.D.
EcoCyc: a comprehensive database of Escherichia coli biology
Nucleic Acids Research 39:D583-590 2011.

[EcoCyc12] Keseler, I.M., Mackie, A., Peralta-Gil, M., Santos-Zavaleta, A., Gama-Castro, S., Bonavides-Martinez, C., Fulcher, C., Huerta, A.M., Kothari, A., Krummenacker, M., Latendresse, M., Muniz-Rascado, L., Ong, Q., Paley, S., Schroder, I., Shearer, A., Subhraveti, P., Travers, M., Weerasinghe, D., Weiss, V., Collado-Vides, J., Gunsalus, R.P., Paulsen, I., and Karp, P.D.,
EcoCyc: fusing model organism databases with systems biology
Nucleic Acids Research 2012.

See also: The EcoCyc publications page.

Publications on the MetaCyc Database

[Karp11] Karp, PD, and Caspi, R. "A survey of metabolic databases emphasizing the MetaCyc family" Archives of Toxicology 85:1015-33 2011.

[Caspi12] Caspi R, Altman T, Dreher K, Fulcher CA, Subhraveti P, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Mueller LA,Ong Q, Paley S, Pujar A, Shearer AG, Travers M, Weerasinghe D, Zhang P,Karp PD.
"The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases,"
Nucleic Acids Research 40:D742-53 2011.

See also: The MetaCyc User's Guide.

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

Overviews of Pathway Tools:
[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.

[PTools02] P. Karp, S. Paley, and P. Romero
"The Pathway Tools Software,"
Bioinformatics 18:S225-32 2002. [PTools01] Karp, P.D.
Pathway Databases: A Case Study in Computational Symbolic Theories
Science 293:2040-4, 2001.

[PTools99] Karp, P.D., Krummenacker, M., Paley, S., and Wagg, J.
Integrated pathway/genome databases and their role in drug discovery,
Trends in Biotechnology 17:275, 1999.

[PTools96] P. Karp and S. Paley
Integrated access to metabolic and genomic data,
Journal of Computational Biology, 3(1):191-212 1996.

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

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 Curationdoi: 10.1093/database/baq006, 2010.

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

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:
[PTools06] S.M. Paley and P.D. Karp.
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 predictor:
[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.