Peter Karp

Summary

Affiliation: SRI International
Country: USA

Publications

  1. pmc EcoCyc: a comprehensive view of Escherichia coli biology
    Ingrid M Keseler
    SRI International, 333 Ravenswood Ave, Menlo Park, CA 94025, USA
    Nucleic Acids Res 37:D464-70. 2009
  2. pmc MetaCyc: a multiorganism database of metabolic pathways and enzymes
    Ron Caspi
    SRI International 333 Ravenswood, Menlo Park, CA 94025, USA
    Nucleic Acids Res 34:D511-6. 2006
  3. pmc EcoCyc: a comprehensive database resource for Escherichia coli
    Ingrid M Keseler
    SRI International, 333 Ravenswood Avenue, Menlo Park, CA 94025, USA
    Nucleic Acids Res 33:D334-7. 2005
  4. pmc The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases
    Ron Caspi
    SRI International, 333 Ravenswood, Menlo Park, CA 94025, USA
    Nucleic Acids Res 36:D623-31. 2008
  5. pmc The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
    Ron Caspi
    SRI International, 333 Ravenswood, Menlo Park, CA 94025, USA
    Nucleic Acids Res 38:D473-9. 2010
  6. pmc The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
    Ron Caspi
    SRI International, 333 Ravenswood, Menlo Park, CA 94025, USA, USA
    Nucleic Acids Res 40:D742-53. 2012
  7. pmc The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases
    Ron Caspi
    SRI International, 333 Ravenswood, Menlo Park, CA 94025, USA, Carnegie Institution, Department of Plant Biology, 260 Panama Street, Stanford, CA 94305, USA and Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, New York 14853 USA
    Nucleic Acids Res 42:D459-71. 2014
  8. pmc The outcomes of pathway database computations depend on pathway ontology
    M L Green
    Bioinformatics Research Group, Artificial Intelligence Center, SRI International, Menlo Park, CA 94025, USA
    Nucleic Acids Res 34:3687-97. 2006
  9. pmc Groups: knowledge spreadsheets for symbolic biocomputing
    Michael Travers
    Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA
    Database (Oxford) 2013:bat061. 2013
  10. pmc A systematic comparison of the MetaCyc and KEGG pathway databases
    Tomer Altman
    Bioinformatics Research Group, SRI International, Menlo Park, USA
    BMC Bioinformatics 14:112. 2013

Collaborators

Detail Information

Publications56

  1. pmc EcoCyc: a comprehensive view of Escherichia coli biology
    Ingrid M Keseler
    SRI International, 333 Ravenswood Ave, Menlo Park, CA 94025, USA
    Nucleic Acids Res 37:D464-70. 2009
    ..A new advanced query page guides users in interactively constructing complex database queries against EcoCyc. A Macintosh version of EcoCyc is now available. A series of Webinars is available to instruct users in the use of EcoCyc...
  2. pmc MetaCyc: a multiorganism database of metabolic pathways and enzymes
    Ron Caspi
    SRI International 333 Ravenswood, Menlo Park, CA 94025, USA
    Nucleic Acids Res 34:D511-6. 2006
    ..SRI and the European Bioinformatics Institute employed this tool to create pathway/genome databases (PGDBs) for 165 organisms, available at the BioCyc.org website. These PGDBs also include predicted operons and pathway hole fillers...
  3. pmc EcoCyc: a comprehensive database resource for Escherichia coli
    Ingrid M Keseler
    SRI International, 333 Ravenswood Avenue, Menlo Park, CA 94025, USA
    Nucleic Acids Res 33:D334-7. 2005
    ....
  4. pmc The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases
    Ron Caspi
    SRI International, 333 Ravenswood, Menlo Park, CA 94025, USA
    Nucleic Acids Res 36:D623-31. 2008
    ..The BioCyc PGDBs generated by SRI are offered for adoption by any interested party for the ongoing integration of metabolic and genome-related information about an organism...
  5. pmc The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
    Ron Caspi
    SRI International, 333 Ravenswood, Menlo Park, CA 94025, USA
    Nucleic Acids Res 38:D473-9. 2010
    ..The BioCyc PGDBs generated by SRI are offered for adoption by any party interested in curation of metabolic, regulatory, and genome-related information about an organism...
  6. pmc The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
    Ron Caspi
    SRI International, 333 Ravenswood, Menlo Park, CA 94025, USA, USA
    Nucleic Acids Res 40:D742-53. 2012
    ..New developments include a zoomable web interface for diagrams; flux-balance analysis model generation from PGDBs; web services; and a new tool called Web Groups...
  7. pmc The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases
    Ron Caspi
    SRI International, 333 Ravenswood, Menlo Park, CA 94025, USA, Carnegie Institution, Department of Plant Biology, 260 Panama Street, Stanford, CA 94305, USA and Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, New York 14853 USA
    Nucleic Acids Res 42:D459-71. 2014
    ....
  8. pmc The outcomes of pathway database computations depend on pathway ontology
    M L Green
    Bioinformatics Research Group, Artificial Intelligence Center, SRI International, Menlo Park, CA 94025, USA
    Nucleic Acids Res 34:3687-97. 2006
    ....
  9. pmc Groups: knowledge spreadsheets for symbolic biocomputing
    Michael Travers
    Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA
    Database (Oxford) 2013:bat061. 2013
    ..Database URL: BioCyc.org. ..
  10. pmc A systematic comparison of the MetaCyc and KEGG pathway databases
    Tomer Altman
    Bioinformatics Research Group, SRI International, Menlo Park, USA
    BMC Bioinformatics 14:112. 2013
    ..We devoted significant effort to computational and manual matching of these entities, and we evaluated the accuracy of the correspondences...
  11. pmc Computing minimal nutrient sets from metabolic networks via linear constraint solving
    Steven Eker
    Computer Science Laboratory, SRI International, Menlo Park, CA 94025, USA
    BMC Bioinformatics 14:114. 2013
    ..One type of phenotypic prediction is to determine sets of compounds that will support the growth of a bacterium from the metabolic network inferred from the genome sequence of that organism...
  12. pmc Data mining in the MetaCyc family of pathway databases
    Peter D Karp
    Bioinformatics Research Group, SRI International, Menlo Park, CA, USA
    Methods Mol Biol 939:183-200. 2013
    ..We present an overview of the Pathway Tools schema, an understanding of which is needed to query the DBs. The chapter also presents several interactive data mining tools within Pathway Tools for performing omics data analysis...
  13. pmc Regulatory network operations in the Pathway Tools software
    Suzanne M Paley
    Bioinformatics Research Group, SRI International 333 Ravenswood Ave, Menlo Park, CA 94025, USA
    BMC Bioinformatics 13:243. 2012
    ..Biologists are elucidating complex collections of genetic regulatory data for multiple organisms. Software is needed for such regulatory network data...
  14. pmc Computational prediction of human metabolic pathways from the complete human genome
    Pedro Romero
    Bioinformatics Research Group, SRI International, 333 Ravenswood Ave, Menlo Park, CA 94025, USA
    Genome Biol 6:R2. 2005
    ..Pathway assignments place genes in their larger biological context, and are a necessary first step toward quantitative modeling of metabolism...
  15. pmc Call for an enzyme genomics initiative
    Peter D Karp
    Genome Biol 5:401. 2004
    ..There are 1,437 enzyme activities for which Enzyme Commission (EC) numbers have been assigned but no sequence can be found in public protein-sequence databases...
  16. pmc A systematic study of genome context methods: calibration, normalization and combination
    Luciana Ferrer
    Artificial Intelligence Center, SRI International, Menlo Park, California, USA
    BMC Bioinformatics 11:493. 2010
    ..Much work has been done in the application of these methods to different bioinformatics tasks, but few papers present a systematic study of the methods and their combination necessary for their optimal use...
  17. pmc Machine learning methods for metabolic pathway prediction
    Joseph M Dale
    Bioinformatics Research Group, SRI International, 333 Ravenswood Ave, Menlo Park, CA 94025, USA
    BMC Bioinformatics 11:15. 2010
    ..One strategy for addressing this problem is to predict which metabolic pathways, from a reference database of known pathways, are present in the organism, based on the annotated genome of the organism...
  18. pmc Web-based metabolic network visualization with a zooming user interface
    Mario Latendresse
    Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA
    BMC Bioinformatics 12:176. 2011
    ..Displaying complex metabolic-map diagrams, for Web browsers, and allowing users to interact with them for querying and overlaying expression data over them is challenging...
  19. pmc The comprehensive updated regulatory network of Escherichia coli K-12
    Heladia Salgado
    Bioinformatics Research Group, SRI International, 333 Ravenswood Ave EK207, Menlo Park CA 94025 USA
    BMC Bioinformatics 7:5. 2006
    ..2002) have been added, making the RegulonDB and EcoCyc databases the largest comprehensive and constantly curated regulatory network of E. coli K-12...
  20. pmc A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases
    Michelle L Green
    Bioinformatics Research Group, SRI International, 333 Ravenswood Ave, Menlo Park, CA 94025, USA
    BMC Bioinformatics 5:76. 2004
    ..If a protein has not been assigned a specific function during the annotation process, any reaction catalyzed by that protein will appear as a missing enzyme or pathway hole in a Pathway/Genome database...
  21. pmc A survey of orphan enzyme activities
    Yannick Pouliot
    Bioinformatics Research Group, Artificial Intelligence Center, SRI International, Menlo Park, California 94025 3493, USA
    BMC Bioinformatics 8:244. 2007
    ..The survey was intended to determine whether sequences for these enzyme activities are truly unknown, or whether these sequences are absent from the public sequence databases but can be found in the literature...
  22. pmc BioWarehouse: a bioinformatics database warehouse toolkit
    Thomas J Lee
    Bioinformatics Research Group, SRI International, Menlo Park, USA
    BMC Bioinformatics 7:170. 2006
    ..This article addresses the problem of interoperation of heterogeneous bioinformatics databases...
  23. pmc Multidimensional annotation of the Escherichia coli K-12 genome
    Peter D Karp
    SRI International, 333 Ravenswood Ave EK207, Menlo Park, CA 94025, USA
    Nucleic Acids Res 35:7577-90. 2007
    ..coli, such as dead-end metabolites. EcoCyc provides a genome browser with novel properties, and a novel interactive display of transcriptional regulatory networks...
  24. ncbi request reprint Pathway databases: a case study in computational symbolic theories
    P D Karp
    Bioinformatics Research Group, SRI International, EK223, 333 Ravenswood Avenue, Menlo Park, CA 94025, USA
    Science 293:2040-4. 2001
    ..It is argued that by encoding scientific theories in symbolic form, we open new realms of analysis and understanding for theories that would otherwise be too large and complex for scientists to reason with effectively...
  25. pmc A survey of metabolic databases emphasizing the MetaCyc family
    Peter D Karp
    Bioinformatics Research Group, SRI International, 333 Ravenswood Ave, Menlo Park, CA, 94025, USA
    Arch Toxicol 85:1015-33. 2011
    ..These web sites also provide multiple tools for analysis of gene expression and metabolomics data, including visualization of those datasets on metabolic network diagrams and over-representation analysis of gene sets and metabolite sets...
  26. pmc Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology
    Peter D Karp
    Artificial Intelligence Center, SRI International, 333 Ravenswood Ave, AE206, Menlo Park, CA 94025, USA
    Brief Bioinform 11:40-79. 2010
    ..Those PGDBs can be exchanged using a peer-to-peer DB sharing system called the PGDB Registry...
  27. pmc Expansion of the BioCyc collection of pathway/genome databases to 160 genomes
    Peter D Karp
    Bioinformatics Research Group, SRI International EK207, 333 Ravenswood Avenue, Menlo Park, CA 94025, USA
    Nucleic Acids Res 33:6083-9. 2005
    ..Only by harnessing the expertise of many scientists we can hope to produce biological databases, which accurately reflect the depth and breadth of knowledge that the biomedical research community is producing...
  28. ncbi request reprint A strategy for database interoperation
    P D Karp
    Artificial Intelligence Center, SRI International, Menlo Park, CA 94025, USA
    J Comput Biol 2:573-86. 1995
    ..A number of the components are translators that bridge the heterogeneities that exist between biological DBs at several different levels, including the conceptual level, the data model, the query language, and data formats...
  29. ncbi request reprint The Pathway Tools software
    Peter D Karp
    Bioinformatics Research Group, SRI International, 333 Ravenswood Ave, Menlo Park, CA, 94025, USA
    Bioinformatics 18:S225-32. 2002
    ..Bioinformatics requires reusable software tools for creating model-organism databases (MODs)...
  30. pmc The past, present and future of genome-wide re-annotation
    Christos A Ouzounis
    Bioinformatics Research Group, AI Center, SRI International, Menlo Park, CA 94025, USA
    Genome Biol 3:COMMENT2001. 2002
    ..We define the process of annotating a previously annotated genome sequence as 're-annotation', and examine the strengths and weaknesses of current manual and automatic genome-wide re-annotation approaches...
  31. pmc The MetaCyc Database
    Peter D Karp
    Bioinformatics Research Group, SRI International, 333 Ravenswood Avenue EK207, Menlo Park, CA 94025, USA
    Nucleic Acids Res 30:59-61. 2002
    ..org/ecocyc/metacyc.html, and is available for local installation as a binary program for the PC and the Sun workstation, and as a set of flatfiles. Contact metacyc-info@ai.sri.com for information on obtaining a local copy of MetaCyc...
  32. pmc The EcoCyc Database
    Peter D Karp
    Bioinformatics Research Group, SRI International, 333 Ravenswood Avenue EK207, Menlo Park, CA 94025, USA
    Nucleic Acids Res 30:56-8. 2002
    ..EcoCyc is queried using the Pathway Tools graphical user interface, which provides a wide variety of query operations and visualization tools. EcoCyc is available at http://ecocyc.org/...
  33. ncbi request reprint Database verification studies of SWISS-PROT and GenBank
    P D Karp
    Bioinformatics Research Group, SRI International, EK223, 333 Ravenswood Ave, Menlo Park, CA 94025, USA
    Bioinformatics 17:526-32; discussion 533-4. 2001
    ..Second is to assess the consistency between translated GenBank sequences and sequences in SWISS-PROT and TrEMBL...
  34. ncbi request reprint An ontology for biological function based on molecular interactions
    P D Karp
    Bioinformatics Research Group, SRI International, EK223, 333 Ravenswood Avenue, Menlo Park, CA 94025, USA
    Bioinformatics 16:269-85. 2000
    ..Functional bioinformatics is an emerging subfield of bioinformatics that is concerned with developing ontologies and algorithms for computing with biological function...
  35. pmc The EcoCyc and MetaCyc databases
    P D Karp
    SRI International, 333 Ravenswood Avenue, EK223, Menlo Park, CA 94025, USA
    Nucleic Acids Res 28:56-9. 2000
    ..Both databases are queried using the Pathway Tools graphical user interface, which provides a wide variety of query operations and visualization tools. EcoCyc and MetaCyc are available at http://ecocyc.PangeaSystems.com/ecocyc/..
  36. pmc EcoCyc: Enyclopedia of Escherichia coli Genes and Metabolism
    P D Karp
    Artificial Intelligence Center, SRI International, 333 Ravenswood Avenue, Menlo Park, CA 94025, USA
    Nucleic Acids Res 25:43-51. 1997
    ..EcoCyc can be thought of as both an electronic review article because of its copious references to the primary literature, and as an in silicio model of E.coli metabolism that can be probed and analyzed through computational means...
  37. ncbi request reprint Database links are a foundation for interoperability
    P D Karp
    Artificial Intelligence Center, SRI International, Menlo Park, CA 94025, USA
    Trends Biotechnol 14:273-9. 1996
    ..This article provides an overview of the DB-interoperation problem, and offers several solutions. It discusses how links are used in molecular biology DBs, and describes the potential stumbling blocks when DB links are created and used...
  38. ncbi request reprint HinCyc: a knowledge base of the complete genome and metabolic pathways of H. influenzae
    P D Karp
    Artificial Intelligence Center, SRI International, Menlo Park, CA 94025, USA
    Proc Int Conf Intell Syst Mol Biol 4:116-24. 1996
    ..influenzae. HinCyc connects the predicted genes, enzymes, enzyme-catalyzed reactions, and biochemical pathways in a WWW-accessible knowledge base to allow scientists to explore this complex hypothesis...
  39. ncbi request reprint What database management system(s) should be employed in bioinformatics applications?
    Peter D Karp
    SRI International, Menlo Park, California 94025, USA
    OMICS 7:35-6. 2003
  40. pmc MetaCyc: a multiorganism database of metabolic pathways and enzymes
    Cynthia J Krieger
    SRI International, 333 Ravenswood, Menlo Park, CA 94025, USA
    Nucleic Acids Res 32:D438-42. 2004
    ..In the past 2 years the data content and the Pathway Tools software used to query, visualize and edit MetaCyc have been expanded significantly. These enhancements are described in this paper...
  41. ncbi request reprint Using the MetaCyc pathway database and the BioCyc database collection
    Ron Caspi
    SRI International, Menlo Park, California, USA
    Curr Protoc Bioinformatics . 2007
    ..The protocols in this unit introduce the user to the extensive data content available in MetaCyc and BioCyc, and to mechanisms for querying, visualizing, and analyzing these data using the Pathway Tools software...
  42. pmc Querying and computing with BioCyc databases
    Markus Krummenacker
    SRI International, Bioinformatics Research Group, EK207 Menlo Park, CA 94025, USA
    Bioinformatics 21:3454-5. 2005
    ....
  43. pmc Annotation-based inference of transporter function
    Thomas J Lee
    Artificial Intelligence Center, SRI International, Menlo Park, CA, USA
    Bioinformatics 24:i259-67. 2008
    ....
  44. ncbi request reprint Using genome-context data to identify specific types of functional associations in pathway/genome databases
    Michelle L Green
    Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA
    Bioinformatics 23:i205-11. 2007
    ..This algorithm performs with varying degrees of accuracy on each type of relationship, and performs best in predicting pathway and protein complex relationships...
  45. ncbi request reprint Evaluation of computational metabolic-pathway predictions for Helicobacter pylori
    Suzanne M Paley
    Bioinformatics Research Group, SRI International, EK207, 333 Ravenswood Ave, Menlo Park, CA 94025, USA
    Bioinformatics 18:715-24. 2002
    ....
  46. pmc An advanced web query interface for biological databases
    Mario Latendresse
    Bioinformatics Research Group, SRI International, 333 Ravenswood Avenue, Menlo Park, CA 94025, USA
    Database (Oxford) 2010:baq006. 2010
    ..The SAQP is part of the Pathway Tools software and is available as part of several bioinformatics web sites powered by Pathway Tools, including the BioCyc.org site that contains more than 500 Pathway/Genome DBs...
  47. pmc EcoCyc: a comprehensive database of Escherichia coli biology
    Ingrid M Keseler
    SRI International, 333 Ravenswood Ave, Menlo Park, CA 94025, USA
    Nucleic Acids Res 39:D583-90. 2011
    ..The graphical representation of signal transduction pathways has been updated, and the cellular and regulatory overviews were enhanced with new functionality. A specialized undergraduate teaching resource using EcoCyc is being developed...
  48. pmc The Pathway Tools cellular overview diagram and Omics Viewer
    Suzanne M Paley
    Bioinformatics Research Group, SRI International EK207, 333 Ravenswood Avenue, Menlo Park, CA 94025, USA
    Nucleic Acids Res 34:3771-8. 2006
    ....
  49. ncbi request reprint PseudoCyc, a pathway-genome database for Pseudomonas aeruginosa
    Pedro Romero
    Bioinformatics Research Group, SRI International, Menlo Park, Calif, USA
    J Mol Microbiol Biotechnol 5:230-9. 2003
    ..The finding of the probable location of the PCAI and PCAJ genes is but one example of the discoveries facilitated by such a PGDB. PseudoCyc, along with PGDBs for 12 other organisms, is available at http://BioCyc.org/...
  50. pmc Computational analysis of Plasmodium falciparum metabolism: organizing genomic information to facilitate drug discovery
    Iwei Yeh
    Department of Genetics, Stanford University, Stanford, California 94305, USA
    Genome Res 14:917-24. 2004
    ..A total of 87.5% of proposed drug targets with biological evidence in the literature are chokepoint reactions. Therefore, identifying chokepoint enzymes represents one systematic way to identify potential metabolic drug targets...
  51. pmc A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information
    Adam M Feist
    Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
    Mol Syst Biol 3:121. 2007
    ..The increased scope and computational capability using this new reconstruction is expected to broaden the spectrum of both basic biology and applied systems biology studies of E. coli metabolism...
  52. pmc MetaCyc and AraCyc. Metabolic pathway databases for plant research
    Peifen Zhang
    The Arabidopsis Information Resource, Department of Plant Biology, Carnegie Institution of Washington, Stanford, California 94305, USA
    Plant Physiol 138:27-37. 2005
    ....
  53. pmc Evidence supporting predicted metabolic pathways for Vibrio cholerae: gene expression data and clinical tests
    Jing Shi
    Biomedical Informatics Program, MC 5429, Stanford University, Stanford, CA 94305, USA
    Nucleic Acids Res 34:2438-44. 2006
    ..VchoCyc is available in the BioCyc database collection (http://BioCyc.org)...
  54. ncbi request reprint Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO)
    Iwei Yeh
    Department of Genetics, Stanford University, Stanford, CA 94305 5120, USA
    Bioinformatics 19:241-8. 2003
    ..In this paper, we assess the applicability of a Knowledge Base Management System (KBMS), Protégé-2000, to the maintenance and development of GO...
  55. ncbi request reprint The complete genome sequence of Francisella tularensis, the causative agent of tularemia
    Par Larsson
    Swedish Defence Research Agency, SE 901 82 Umea, Sweden
    Nat Genet 37:153-9. 2005
    ..tularensis is an obligate host-dependent bacterium in its natural life cycle. Our results have implications for our understanding of how highly virulent human pathogens evolve and will expedite strategies to combat them...

Research Grants35

  1. The MetaCyc Metabolic Pathway Database
    Peter Karp; Fiscal Year: 2005
    ....
  2. Robust Software Components for Model Organism Databases
    Peter Karp; Fiscal Year: 2007
    ..We will also interact with the community of developers of other MOD software components to ensure interoperability of our software components with components developed by other groups. ..
  3. Encyclopedia of E. Coli Genes and Metabolism
    Peter Karp; Fiscal Year: 2007
    ..coli. For 1 example, scientists who study drug-resistant bacteria, and bacteria that are the subjects of bioterrorism research, frequently turn to the comprehensive collection of information in EcoCyc to accelerate their research. ..
  4. The MetaCyc and BioCyc Pathway/Genome Databases
    Peter Karp; Fiscal Year: 2007
    ..It will speed the development of drugs that kill disease-causing bacteria by enabling identification of essential metabolic pathways for disruption. ..
  5. Pathway Prediction and Assessment Integrating Multiple Evidence Types
    Peter Karp; Fiscal Year: 2007
    ..We will search the MetaCyc reaction space (comprising almost 6000 reactions) for novel subpathways, explicitly constraining our search using organism-specific evidence (i.e., homology, experimental evidence, etc.) at each step. ..
  6. The MetaCyc and BioCyc Pathway/Genome Databases
    Peter Karp; Fiscal Year: 2008
    ..It will speed the development of drugs that kill disease-causing bacteria by enabling identification of essential metabolic pathways for disruption. ..
  7. Development and Support of the Pathway Tools Software
    Peter Karp; Fiscal Year: 2008
    ....
  8. Encyclopedia of E. Coli Genes and Metabolism
    Peter Karp; Fiscal Year: 2008
    ..coli. For 1 example, scientists who study drug-resistant bacteria, and bacteria that are the subjects of bioterrorism research, frequently turn to the comprehensive collection of information in EcoCyc to accelerate their research. ..
  9. Pathway Prediction and Assessment Integrating Multiple Evidence Types
    Peter Karp; Fiscal Year: 2008
    ..We will search the MetaCyc reaction space (comprising almost 6000 reactions) for novel subpathways, explicitly constraining our search using organism-specific evidence (i.e., homology, experimental evidence, etc.) at each step. ..
  10. Development and Support of the Pathway Tools Software
    Peter Karp; Fiscal Year: 2009
    ....
  11. The MetaCyc and BioCyc Pathway/Genome Databases
    Peter Karp; Fiscal Year: 2009
    ..It will speed the development of drugs that kill disease-causing bacteria by enabling identification of essential metabolic pathways for disruption. ..
  12. Pathway Prediction and Assessment Integrating Multiple Evidence Types
    Peter Karp; Fiscal Year: 2009
    ..We will search the MetaCyc reaction space (comprising almost 6000 reactions) for novel subpathways, explicitly constraining our search using organism-specific evidence (i.e., homology, experimental evidence, etc.) at each step. ..
  13. Development and Support of the Pathway Tools Software
    Peter D Karp; Fiscal Year: 2010
    ....
  14. The MetaCyc and BioCyc Pathway/Genome Databases
    Peter D Karp; Fiscal Year: 2010
    ..It will speed the development of drugs that kill disease-causing bacteria by enabling identification of essential metabolic pathways for disruption. ..
  15. Robust Software Components for Model Organism Databases
    Peter Karp; Fiscal Year: 2006
    ..We will also interact with the community of developers of other MOD software components to ensure interoperability of our software components with components developed by other groups. ..
  16. Encyclopedia of E. Coli Genes and Metabolism
    Peter Karp; Fiscal Year: 2005
    ..SRI further proposes to develop new bioinformatics methods for comparative genomics, and for predicting nutritional requirements and essential genes of an organism form its metabolic network. ..
  17. Robust Software Components for Model Organism Databases
    Peter Karp; Fiscal Year: 2005
    ..We will also interact with the community of developers of other MOD software components to ensure interoperability of our software components with components developed by other groups. ..
  18. ENCYCLOPEDIA OF E COLI GENES AND METABOLISM
    Peter Karp; Fiscal Year: 1992
    ..EcoCyc will also be useful to scientists who perform quantitative simulations of metabolic pathways, and to those who design variants of biochemical pathways for industrial applications...
  19. ENCYCLOPEDIA OF E COLI GENES AND METABOLISM
    Peter Karp; Fiscal Year: 1993
    ..EcoCyc will also be useful to scientists who perform quantitative simulations of metabolic pathways, and to those who design variants of biochemical pathways for industrial applications...
  20. ENCYCLOPEDIA OF E COLI GENES AND METABOLISM
    Peter Karp; Fiscal Year: 1999
    ..The database is also useful for designing variants of biochemical pathways for biotechnology applications, and for teaching biochemistry. ..
  21. ENCYCLOPEDIA OF E COLI GENES AND METABOLISM
    Peter Karp; Fiscal Year: 2000
    ..The database is also useful for designing variants of biochemical pathways for biotechnology applications, and for teaching biochemistry. ..
  22. DEVELOPMENT OF THE METACYC METABOLIC PATHWAY DATABASE
    Peter Karp; Fiscal Year: 2002
    ....
  23. Encyclopedia of E. Coli Genes and Metabolism
    Peter Karp; Fiscal Year: 2002
    ..SRI further proposes to develop new bioinformatics methods for comparative genomics, and for predicting nutritional requirements and essential genes of an organism form its metabolic network. ..
  24. ENCYCLOPEDIA OF E COLI GENES AND METABOLISM
    Peter Karp; Fiscal Year: 2001
    ..The database is also useful for designing variants of biochemical pathways for biotechnology applications, and for teaching biochemistry. ..
  25. Robust Software Components for Model Organism Databases
    Peter Karp; Fiscal Year: 2002
    ..Although Pathway Tools is particularly well adapted to microbial MODs, one goal of this application is to adapt the metabolic pathway part of Pathway Tools to work with MODs for higher organisms. ..
  26. Encyclopedia of E. Coli Genes and Metabolism
    Peter Karp; Fiscal Year: 2003
    ..SRI further proposes to develop new bioinformatics methods for comparative genomics, and for predicting nutritional requirements and essential genes of an organism form its metabolic network. ..
  27. DEVELOPMENT OF THE METACYC METABOLIC PATHWAY DATABASE
    Peter Karp; Fiscal Year: 2003
    ....
  28. Robust Software Components for Model Organism Databases
    Peter Karp; Fiscal Year: 2003
    ..Although Pathway Tools is particularly well adapted to microbial MODs, one goal of this application is to adapt the metabolic pathway part of Pathway Tools to work with MODs for higher organisms. ..
  29. Encyclopedia of E. Coli Genes and Metabolism
    Peter Karp; Fiscal Year: 2004
    ..SRI further proposes to develop new bioinformatics methods for comparative genomics, and for predicting nutritional requirements and essential genes of an organism form its metabolic network. ..
  30. Development and Support of the Pathway Tools Software
    Peter Karp; Fiscal Year: 2009
    ....