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).
Publications on the EcoCyc Database
[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
[EcoCyc17]
Keseler I.M., et al.,
The EcoCyc database: Reflecting new knowledge about Escherichia coli K-12
Nucleic Acids Research 41:D605-612.(2012)
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 BiologyBriefings 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 BiologyBriefings 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)
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)
[PTools20] W.K. Ong, P.E. Midford, P.D. Karp
Taxonomic weighting improves the accuracy of a gap-filling algorithm for metabolic modelsBioinformatics36(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 modelsBMC 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)
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]
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)
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)
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:
[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)
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