The DOI matches its Crossref record; 7 of the 7 references it cites were found in a registry or an index.
Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology
Open accessAbstract
Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer and comparative-genomics operations. It offers metabolic-informatics tools, such as metabolic reconstruction, quantitative metabolic modeling, prediction of reaction atom mappings and metabolic route search. Pathway Tools also provides regulatory-informatics tools, such as the ability to represent and visualize a wide range of regulatory interactions. This article outlines the advances in Pathway Tools in the past 5 years. Major additions include components for metabolic modeling, metabolic route search, computation of atom mappings and estimation of compound Gibbs free energies of formation; addition of editors for signaling pathways, for genome sequences and for cellular architecture; storage of gene essentiality data and phenotype data; display of multiple alignments, and of signaling and electron-transport pathways; and development of Python and web-services application programming interfaces. Scientists around the world have created more than 9800 Pathway/Genome Databases by using Pathway Tools, many of which are curated databases for important model organisms.
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Caspi, R., Billington, R., Ferrer, L., Foerster, H., Fulcher, C. A., Keseler, I. M., Kothari, A., Krummenacker, M., Latendresse, M., Mueller, L. A., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1164 · Cited by 3,395
Self-citationQuantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0
Schellenberger, J., Que, R., Fleming, R. M. T., Thiele, I., Orth, J. D., Feist, A. M., Zielinski, D. C., Bordbar, A., Lewis, N. E., Rahmanian, S., et al. (2011) · Nature Protocols · doi:10.1038/nprot.2011.308 · Cited by 1,835
A protocol for generating a high-quality genome-scale metabolic reconstruction
Thiele, I., & Palsson, B. Ø. (2010) · Nature Protocols · doi:10.1038/nprot.2009.203 · Cited by 1,789
The BioPAX community standard for pathway data sharing
Demir, E., Cary, M. P., Paley, S., Fukuda, K., Lemer, C., Vastrik, I., Wu, G., D'Eustachio, P., Schaefer, C., Luciano, J., et al. (2010) · Nature Biotechnology · doi:10.1038/nbt.1666 · Cited by 745
Self-citationPathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology
Karp, P. D., Paley, S. M., Krummenacker, M., Latendresse, M., Dale, J. M., Lee, T. J., Kaipa, P., Gilham, F., Spaulding, A., Popescu, L., et al. (2010) · Briefings in Bioinformatics · doi:10.1093/bib/bbp043 · Cited by 694
Self-citationKarp, P. D., Paley, S., & Romero, P. (2002) · Bioinformatics · doi:10.1093/bioinformatics/18.suppl_1.s225 · Cited by 661
Self-citationLibSBML: an API Library for SBML
Bornstein, B. J., Keating, S. M., Jouraku, A., & Hucka, M. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn051 · Cited by 373
Cited by
Caspi, R., Billington, R., Ferrer, L., Foerster, H., Fulcher, C. A., Keseler, I. M., Kothari, A., Krummenacker, M., Latendresse, M., Mueller, L. A., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1164 · Cited by 3,395
Self-citationA Deep Learning Approach to Antibiotic Discovery
Stokes, J. M., Yang, K., Swanson, K., Jin, W., Cubillos-Ruiz, A., Donghia, N. M., MacNair, C. R., French, S., Carfrae, L. A., Bloom-Ackermann, Z., et al. (2020) · Cell · doi:10.1016/j.cell.2020.01.021 · Cited by 2,463
The MetaCyc database of metabolic pathways and enzymes
Caspi, R., Billington, R., Fulcher, C. A., Keseler, I. M., Kothari, A., Krummenacker, M., Latendresse, M., Midford, P. E., Ong, Q., Ong, W. K., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gkx935 · Cited by 894
Self-citationCurrent status and applications of genome-scale metabolic models
Gu, C., Kim, G. B., Kim, W. J., Kim, H. U., & Lee, S. Y. (2019) · Genome Biology · doi:10.1186/s13059-019-1730-3 · Cited by 785
Comparative genomics of the major parasitic worms
International Helminth Genomes Consortium (2019) · Nature Genetics · doi:10.1038/s41588-018-0262-1 · Cited by 560
Metadata
- Authors
- Karp, P. D., Latendresse, M., Paley, S. M., Krummenacker, M., Ong, Q. D., Billington, R., Kothari, A., Weaver, D., Lee, T., Subhraveti, P., Spaulding, A., Fulcher, C., Keseler, I. M., & Caspi, R.
- Venue
- Briefings in Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2015-10-10
- Volume
- 17
- Issue
- 5
- Pages
- 877-890
- ISSN
- 1467-5463 (ISSN-L)
- 1477-4054
- OpenAlex
- W4236875018
- Cited by
- 266
- References
- 7
- FWCI
- 9.78
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Karp, P. D., Latendresse, M., Paley, S. M., Krummenacker, M., Ong, Q. D., Billington, R., Kothari, A., Weaver, D., Lee, T., Subhraveti, P., Spaulding, A., Fulcher, C., Keseler, I. M., & Caspi, R. (2016). Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology. Briefings in Bioinformatics. https://doi.org/10.1093/bib/bbv079
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