Paley, S. M., & Karp, P. D. (2006). The Pathway Tools cellular overview diagram and Omics Viewer. Nucleic Acids Res, 34(13), 3771-3778.
Green, M. L., & Karp, P. D. (2006). The outcomes of pathway database computations depend on pathway ontology. Nucleic Acids Res, 34(13), 3687-3697.
Lee, T. J., Pouliot, Y., Wagner, V., Gupta, P., Stringer-Calvert, D. W., Tenenbaum, J. D., et al. (2006). BioWarehouse: a bioinformatics database warehouse toolkit. BMC Bioinformatics, 7, 170.
Caspi, R., Foerster, H., Fulcher, C. A., Hopkinson, R., Ingraham, J., Kaipa, P., et al. (2006). MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res, 34(Database issue), D511-516.
Karp, P. D., Ouzounis, C. A., Moore-Kochlacs, C., Goldovsky, L., Kaipa, P., Ahren, D., et al. (2005). Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res, 33(19), 6083-6089.
Green, M. L., & Karp, P. D. (2005). Genome annotation errors in pathway databases due to semantic ambiguity in partial EC numbers. Nucleic Acids Res, 33(13), 4035-4039.
Krummenacker, M., Paley, S., Mueller, L., Yan, T., & Karp, P. D. (2005). Querying and computing with BioCyc databases. Bioinformatics, 21(16), 3454-3455.
Romero, P., Wagg, J., Green, M. L., Kaiser, D., Krummenacker, M., & Karp, P. D. (2005). Computational prediction of human metabolic pathways from the complete human genome. Genome Biol, 6(1), R2.
Keseler, I. M., Collado-Vides, J., Gama-Castro, S., Ingraham, J., Paley, S., Paulsen, I. T., et al. (2005). EcoCyc: a comprehensive database resource for Escherichia coli. Nucleic Acids Res, 33(Database issue), D334-337.
Green, M. L., & Karp, P. D. (2004). A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases. BMC Bioinformatics, 5, 76.
Karp, P. D., Paley, S., Krieger, C. J., & Zhang, P. (2004). An evidence ontology for use in pathway/genome databases. Pac Symp Biocomput, 190-201.
Romero, P. R., & Karp, P. D. (2004). Using functional and organizational information to improve genome-wide computational prediction of transcription units on pathway-genome databases. Bioinformatics, 20(5), 709-717.
Krieger, C. J., Zhang, P., Mueller, L. A., Wang, A., Paley, S., Arnaud, M., et al. (2004). MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res, 32(Database issue), D438-442.
Romero, P., & Karp, P. (2003). PseudoCyc, a pathway-genome database for Pseudomonas aeruginosa. J Mol Microbiol Biotechnol, 5(4), 230-239.
Karp, P. D. (2003). What database management system(s) should be employed in bioinformatics applications? Omics, 7(1), 35-36.
Karp, P. D., Paley, S., & Romero, P. (2002). The Pathway Tools software. Bioinformatics, 18 Suppl 1, S225-232.
Paley, S. M., & Karp, P. D. (2002). Evaluation of computational metabolic-pathway predictions for Helicobacter pylori. Bioinformatics, 18(5), 715-724.
Ouzounis, C. A., & Karp, P. D. (2002). The past, present and future of genome-wide re-annotation. Genome Biol, 3(2), COMMENT2001.
Karp, P. D., Riley, M., Paley, S. M., & Pellegrini-Toole, A. (2002). The MetaCyc Database. Nucleic Acids Res, 30(1), 59-61.
Karp, P. D., Riley, M., Saier, M., Paulsen, I. T., Collado-Vides, J., Paley, S. M., et al. (2002). The EcoCyc Database. Nucleic Acids Res, 30(1), 56-58.
Karp, P. D. (2001). Pathway databases: a case study in computational symbolic theories. Science, 293(5537), 2040-2044.
Karp, P. D., Paley, S., & Zhu, J. (2001). Database verification studies of SWISS-PROT and GenBank. Bioinformatics, 17(6), 526-532; discussion 533-524.
Romero, P. R., & Karp, P. (2001). Nutrient-related analysis of pathway/genome databases. Pac Symp Biocomput, 471-482.
Karp, P. D. (2000). An ontology for biological function based on molecular interactions. Bioinformatics, 16(3), 269-285.
Karp, P. D., Riley, M., Saier, M., Paulsen, I. T., Paley, S. M., & Pellegrini-Toole, A. (2000). The EcoCyc and MetaCyc databases. Nucleic Acids Res, 28(1), 56-59.
Karp, P. D., Riley, M., Paley, S. M., Pellegrini-Toole, A., & Krummenacker, M. (1998). EcoCyc: Encyclopedia of Escherichia coli genes and metabolism. Nucleic Acids Res, 26(1), 50-53.
des Jardins, M., Karp, P. D., Krummenacker, M., Lee, T. J., & Ouzounis, C. A. (1997). Prediction of enzyme classification from protein sequence without the use of sequence similarity. Proc Int Conf Intell Syst Mol Biol, 5, 92-99.
Karp, P. D., Riley, M., Paley, S. M., Pellegrini-Toole, A., & Krummenacker, M. (1997). EcoCyc: Enyclopedia of Escherichia coli Genes and Metabolism. Nucleic Acids Res, 25(1), 43-51.
Karp, P. D. (1996). Database links are a foundation for interoperability. Trends Biotechnol, 14(8), 273-279.
Paley, S. M., & Karp, P. D. (1996). Adapting EcoCyc for use on the World Wide Web. Gene, 172(1), GC43-50.
Karp, P. D. (1996). A protocol for maintaining multidatabase referential integrity. Pac Symp Biocomput, 438-445.
Karp, P. D., Ouzounis, C., & Paley, S. (1996). HinCyc: a knowledge base of the complete genome and metabolic pathways of H. influenzae. Proc Int Conf Intell Syst Mol Biol, 4, 116-124.
Karp, P. D., & Paley, S. (1996). Integrated access to metabolic and genomic data. J Comput Biol, 3(1), 191-212.
Karp, P. D., Riley, M., Paley, S. M., & Pelligrini-Toole, A. (1996). EcoCyc: an encyclopedia of Escherichia coli genes and metabolism. Nucleic Acids Res, 24(1), 32-39.
Karp, P. D. (1995). A strategy for database interoperation. J Comput Biol, 2(4), 573-586.
Karp, P. D., & Paley, S. M. (1994). Representations of metabolic knowledge: pathways. Proc Int Conf Intell Syst Mol Biol, 2, 203-211.
Karp, P. D., & Riley, M. (1993). Representations of metabolic knowledge. Proc Int Conf Intell Syst Mol Biol, 1, 207-215.
Karp, P. D. (1992). A knowledge base of the chemical compounds of intermediary metabolism. Comput Appl Biosci, 8(4), 347-357.
Other References on Metabolic Pathway Analysis
Gerrard, J. A., A. D. Sparrow and J. A. Wells (2001). Metabolic databases - what next? Trends Biochem Sci 26(2): 137-40.
Gribskov, M. (1999). The new biological literature. Bioinformatics 15(5): 347.
Juty, N. S., H. D. Spence, H. R. Hotz, et al. (2001). Simultaneous modelling of metabolic, genetic and product-interaction networks. Brief Bioinform 2(3): 223-32.
Mori, H., K. Isono, T. Horiuchi, et al. (2000). Functional genomics of Escherichia coli in Japan. Res Microbiol 151(2): 121-8.
Ogata, H., W. Fujibuchi, S. Goto, et al. (2000). A heuristic graph comparison algorithm and its application to detect functionally related enzyme clusters. Nucleic Acids Res 28(20): 4021-8.
Ogata, H., S. Goto, K. Sato, et al. (1999). KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 27(1): 29-34.
Perriere, G. and C. Gautier (1993). ColiGene: object-centered representation for the study of E coli gene expressivity by sequence analysis. Biochimie 75(5): 415-22.
Rechenmann, F. (2000). From data to knowledge. Bioinformatics 16(5): 411.
Saqi, M. A. and M. J. Sternberg (2001). A structural census of metabolic networks for E. coli. J Mol Biol 313(5): 1195-206.
Sugden, A. and E. Pennisi (2000). Diversity digitized. Science 289(5488): 2305.
Thomas, G. H. (1999). Completing the E. coli proteome: a database of gene products characterised since the completion of the genome sequence. Bioinformatics 15(10): 860-1.
Tsoka, S. and C. A. Ouzounis (2001). Functional versatility and molecular diversity of the metabolic map of Escherichia coli. Genome Res 11(9): 1503-10.
VanBogelen, R. A., K. D. Greis, R. M. Blumenthal, et al. (1999). Mapping regulatory networks in microbial cells. Trends Microbiol 7(8): 320-8.
Wittig, U. and A. De Beuckelaer (2001). Analysis and comparison of metabolic pathway databases. Brief Bioinform 2(2): 126-42.
Wood, D. W., J. C. Setubal, R. Kaul, et al. (2001). The genome of the natural genetic engineer Agrobacterium tumefaciens C58. Science 294(5550): 2317-23.
Back to Lecture
Back to Syllabus
