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

[BioCyc17] Karp, P.D., et al., The BioCyc collection of microbial genomes and metabolic pathways
Briefings in Bioinformatics (2017).

[MetaCyc16] Caspi R., et al., The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases
Nucleic Acids Research 44(D1):D471-80. (2016).

Publications on the EcoCyc Database

[EcoCyc17] Keseler I.M., et al., The EcoCyc database: Reflecting new knowledge about Escherichia coli K-12
Nucleic Acids Research 41:D605-612.(2012)

[EcoCyc18] P.D.Karp., D.Weaver., S.Paley., C.Fulcher., A.Kubo., A.Kothari., M.Krummenacker., P.Subhraveti., D.Weerasinghe., S.Gama-Castro., A.M.Huerta., L. Muniz-Rascado., C.Bonavides-Martinez., V.Weiss., M.Peralta-Gil., A.Santos-Zavaleta, I.Schroder., A.Mackie., R.Gunsalus., J.Collado-Vides., I.M.Keseler., and I.Paulsen.
The EcoCyc Database
EcoSal Plus doi:10.1128/ecosalplus.ESP-0009-2014

See also: The EcoCyc publications page.

Publications on the MetaCyc Database

[MetaCyc18] Caspi R., et al., The MetaCyc database of metabolic pathways and enzymes
Nucleic Acids Research 46(D1):D633-9.(2018)

[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

Overviews of Pathway Tools:
[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)

[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)

Omics 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)

[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)

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

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:
[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)

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

Metabolic and Regulatory Network Visualization:
[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)

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:
[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:
[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)