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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 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
[EcoCyc25]
Karp, P.D., Paley, S., Caspi, R., Kothari, A., Krummenacker, M., Midford, P., Moore, L.R., Subhraveti, P., Gama-Castro, S., Tierrafria, V., Paloma, L.,
Muñiz-Rascado, L., Bonavides-Martinez, C., Santos-Zavaleta, A., Mackie, A., Sun, G., Ahn-Horst, T.A., Choi, H., Covert, M.W., Collado-Vides, J.
and Paulsen, I.,
The EcoCyc database (2025)
EcoSal Plus doi:10.1128/ecosalplus.ESP-0019-2024
[EcoCyc24]
Moore, L.R.,Caspi, R., Boyd, D., Berkem, M., Mackie, A., Paley, S., Karp, P.D.
Revisiting the y-ome of Escherichia coli
Nucleic Acids Research doi::10.1093/nar/gkae857 (2024)
[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.
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.
[MetaCyc11]
Karp P.D., and Caspi R., [HumanCyc04] P.Romero., J.Wagg., M.L.Green., D.Kaiser., M.Krummenacker., and P.D.Karp [CyanoCyc04] Moore, L.R., Caspi, R., Campbell, D.A., Casey, J.R., Crevecoeur, S., Lea-Smith, D.J., Long, B., Omar, N.M., Paley, S.M., Schmelling, N.M., Torrado, A., Zehr, J.P., and P.D.Karp
The challenge of constructing, classifying, and representing metabolic pathways.
FEMS Microbiol Lett. doi: 10.1111/1574-6968.12194. (2013)
A survey of metabolic databases emphasizing the MetaCyc family
Archives of Toxicology 85:1015-33 (2011)Publications on the HumanCyc Database
Computational
prediction of human metabolic pathways from the complete human
genome,
Genome Biology 6:R2 R2.1-17 (2004)
Publications on the CyanoCyc Portal
CyanoCyc cyanobacterial web portal,
Front. Microbiol.,doi: 10.3389/fmicb.2024.1340413 (2024)
Publications on the Pathway Tools Software Behind BioCyc
Latest Comprehensive Description of Pathway Tools:[PTools24]P. D. Karp, S.M. Paley, M. Krummenacker, A. Kothari, P.E. Midford, P. Subhraveti, A. Swart, L. Moore, and R. Caspi.
Pathway Tools version 28.0: Integrated software for Pathway/Genome informatics and Systems Biology,
arXiv:1510.03964:1–107, 2024. doi: 10.48550/arXiv.1510.03964.
[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 (2020).
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)
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)
Genome Browser:
[PTools24]
Herson, J. , Krummenacker, M. , Spaulding, A. , O’Maille, P. and Karp,P.D.
The Genome Explorer genome browser,
mSystems doi:10.1128/msystems.00267-24 (2024)
Comparative Genome Dashboard and Omics Dashboard:
[PTools24]
Paley Suzanne , Caspi Ron , O'Maille Paul , Karp Peter D., .
The Comparative Genome Dashboard
Frontiers in Microbiology. doi:10.3389/fmicb.2024.1447632 (2024)
The Omics Dashboard for Interactive Exploration of Metabolomics and Multi-Omics Data
Metabolites. doi:10.3390/metabo14010065 (2024)
Transcriptomics Data Analysis:
[PTools17]
Austin Swart, Ron Caspi, Suzanne Paley and P.D. Karp.
Visual analysis of multi-omics data.
Frontiers in bioinformatics
doi: 10.3389/fbinf.2024.1395981 (2024).
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)
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)
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)
