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Publications Search Results

The following are sorted by reverse chronological order of publication.

33 publications found:

  • Caspi R, Altman T, Billington R, Dreher K, Foerster H, Fulcher CA, Holland TA, Keseler IM, Kothari A, Kubo A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Subhraveti P, Weaver DS, Weerasinghe D, Zhang P, Karp PD. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res., vol. 42, no. 1, pp. D459-D471, 2014.  [PDF, Details]

  • 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 Res, vol. 40, no. D1, pp. D742-D753, 2012.  [PDF, Details]

  • 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 Adics Research, vol. 39, pp. D583-90, 2011.  [PDF, Details]

  • 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 Res, vol. 38, pp. D473-D479, 2010.  [PDF, Details]

  • Karp PD, Paley SM, Krummenacker M, Latendresse M, Dale JM, Lee TJ, Kaipa P, Gilham F, Spaulding A, Popescu L, Altman T, Paulsen I, Keseler IM, Caspi R. Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology.. Brief Bioinform., vol. 11, no. 1, pp. 40-79, Jan 2010.  [PDF, Details]

  • Keseler, I.M. and Bonavides-Martinez, C. and Collado-Vides, J. and Gama-Castro, S. and Gunsalus, R.P. and Johnson, D.A. and Krummenacker, M., and Nolan, L.M. and Paley, S. and Paulsen, I.T. and Peralta-Gil, M. and Santos-Zavaleta, A. and Shearer, A.G. and Karp, P.D. EcoCyc: a comprehensive view of Escherichia coli biology. Nucleic Acids Research, vol. 37, pp. D464-D470, Jan 2009.  [PDF, Details]

  • Caspi R, Foerster H, Fulcher C. A, Kaipa P, Krummenacker M, Latendresse M, Paley S, Rhee S. Y, Shearer A. G, Tissier C, Walk T. C, Zhang P, Karp P. D. The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Research, vol. 36, pp. D623-D631, 2007.  [PDF, Details]

  • Karp, P.D. and Keseler, I.M. and Shearer, A. and Latendresse, M. and Krummenacker, M. and Paley, S.M. and Paulsen, I. and Collado-Vides, J. and Gama-Castro, S. and Peralta-Gil, M. and Santos-Zavaleta, A. and Penaloza-Spinola, M.I. and Bonavides-Martinez, C. and Ingraham, J. Multidimensional annotation of the Escherichia coli K-12 genome. Nucleic Acids Research, vol. 35, no. 22, pp. 7577-7590, 2007.  [PDF, Details]

  • Caspi, R. and Foerster, H. and Fulcher, C.A. and Hopkinson, R. and Ingraham, J. and Kaipa, P. and Krummenacker, M. and Paley, S. and Pick, J. and Rhee, S.Y. and Tissier, C. and Zhang, P. and Karp, P.D. MetaCyc: a multiorganism database of metabolic pathways and enzymes.. Nucleic Acids Research, vol. 34, pp. D511-D516, Jan 2006.  [PDF, Details]

  • Keseler, I.M. and Collado-Vides, J. and Gama-Castro, S. and Ingraham, J. and Paley, S. and Paulsen, I.T. and Peralta-Gil, M. and Karp, P.D. EcoCyc: a comprehensive database resource for Escherichia coli. Nucleic Acids Research, vol. 33, pp. D334-D337, Jan 2005.  [PDF, Details]

  • Krummenacker, M., Paley, S., Mueller, L., Yan, T., and Karp, P.D. Querying and Computing with BioCyc Databases. Bioinformatics, vol. 21, pp. 3454-5, 2005.  [Details]

  • Zhang, P., Foerster, H., Tissier, C.P., Mueller, L., Paley, S., Karp,. MetaCyc and AraCyc. Metabolic Pathway Databases for Plant Resarch. Plant Physiol, vol. 138, no. 1, pp. 27–37, 2005.  [Details]

  • Krieger, C. J. and Zhang, P and Mueller, L. A. and Wang, A. and Paley, S. and Arnaud, M. and Pick, J. and Rhee, S. Y. and Karp, P. D. MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Research, vol. 32, pp. D438-D442, 2004.  [Details]

  • Paley, S. and Karp, P.D. Evaluation of computational metabolic-pathway predictions for Helicobacter pylori.. Bioinformatics, vol. 18, no. 5, pp. 715-24, May 2002.  [Details]

  • Karp, P.D. and Paley, S. and Romero, P. The Pathway Tools Software. Bioinformatics, vol. 18, pp. S225-S232, 2002.  [Details]

  • Karp, P.D., Riley, M., Paley, S., and Pellegrini-Toole, A. The MetaCyc Database. Nucleic Acids Research, vol. 30, no. 1, pp. 59-61, 2002.  [Details]

  • Karp, P.D., Riley, M., Saier, M., Paulsen, I.T., Collado-Vides, J., Paley, S., Pellegrini-Toole, A., Bonavides, C., and Gama-Castro, S. The EcoCyc Database. Nucleic Acids Research, vol. 30, no. 1, pp. 56-58, 2002.  [PDF, Details]

  • Karp, P.D., Riley, M., Paulsen, I.T., Paley, S., Pellegrini-Toole, A. The EcoCyc and MetaCyc Databases. Nucleic Acids Research, vol. 28, no. 1, pp. 56-59, 2000.  [PDF, Details]

  • Karp, P.D., Krummenacker, M., Paley, S., and Wagg, J. Integrated Pathway/Genome Databases and Their Role in Drug Discovery. Trends in Biotechnology, vol. 17, no. 7, pp. 275-281, 1999.  [PS, Details]

  • Karp, Peter D. and Chaudhri, Vinay K. and Paley, Suzanne M. A Collaborative Environment for Authoring Large Knowledge Bases. Journal of Intelligent Information Systems, vol. 13, pp. 155-194, 1999.  [PDF, Details]

  • Karp, Peter D. and Chaudhri, Vinay K. and Paley, Suzanne M. A Collaborative Environment for Authoring Large Knowledge Bases. , Apr 1997.  [PS, Details]

  • Karp, P. and Riley, M. and Paley, S. and Pellegrini-Toole, A. and Krummenacker, M. EcoCyc: Electronic Encyclopedia of E. coli Genes and Metabolism. Nuc. Acids Res., vol. 25, no. 1, 1997.  [PDF, Details]

  • Paley, S.M., Lowrance, J.D., and Karp, P.D. A Generic Knowledge-Base Browser and Editor, in Proceedings of the 1997 National Conference on Artificial Intelligence, 1997.  [PS, Details]

  • Karp, P. and Riley, M. and Paley, S. and Pellegrini-Toole, A. EcoCyc: Electronic Encyclopedia of E. coli Genes and Metabolism. Nuc. Acids Res., vol. 24, no. 1, pp. 32–39, 1996.  [PDF, Details]

  • Karp, P. D. and Ouzounis, C. and Paley, S. M. HinCyc: A Knowledge Base of the Complete Genome and Metabolic Pathways of H. influenzae, in Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology, AAAI Press, 1996.  [PS, Details]

  • Karp, P.D. and Paley, S. Integrated Access to Metabolic and Genomic Data. Journal of Computational Biology, vol. 3, no. 1, pp. 191-212, 1996.  [PS, Details]

  • Paley, S. and Karp, P.D. Adapting EcoCyc for Use on the World Wide Web. Gene, vol. 172, no. 1, pp. GC43-50, 1996.  [PDF, Details]

  • Karp, P. D. and Paley, S. M. Knowledge Representation in the Large, in Proceedings of the 1995 International Joint Conference on Artificial Intelligence, pp. 751-758, 1995.  [PS, Details]

  • Paley, S. M. and Karp, P. D. Adapting CLIM Applications for Use on the World Wide Web, in Proceedings of the Association of Lisp Users Meeting and Workshop, pp. 1-9, 1995.  [PS, Details]

  • Karp, Peter D., Paley, Suzanne M., and Greenberg, Ira. A Storage System for Scalable Knowledge Representation, Technical Note 547. AI Center, SRI International, 333 Ravenswood Ave, Menlo Park, CA 94025, Aug 1994.  [PDF, Details]

  • Karp, P. and Paley, S. M. Representations of Metabolic Knowledge: Pathways, in Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, AAAI Press, 1994.  [PS, Details]

  • Karp, P. and Paley, S. M. Automated Drawing of Metabolic Pathways, in Third International Conference on Bioinformatics and Genome Research, 1994.  [PS, Details]

  • Karp, P. D. and Paley, S. M. and Greenberg, I. A Storage System for Scalable Knowledge Representation, in Proceedings of the Third International Conference on Information and Knowledge Management, 1994.  [PS, Details]

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