Research Topics
| Peter KarpSummaryAffiliation: SRI International Country: USA Publications
Research Grants
| Collaborators
|
Detail Information
Publications
Computational prediction of human metabolic pathways from the complete human genomePedro 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...- Call for an enzyme genomics initiativePeter 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... - A systematic study of genome context methods: calibration, normalization and combinationLuciana 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... - Machine learning methods for metabolic pathway predictionJoseph 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... - Web-based metabolic network visualization with a zooming user interfaceMario 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... - The comprehensive updated regulatory network of Escherichia coli K-12Heladia 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... - A Bayesian method for identifying missing enzymes in predicted metabolic pathway databasesMichelle 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... - A survey of orphan enzyme activitiesYannick 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... - BioWarehouse: a bioinformatics database warehouse toolkitThomas 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... - The MetaCyc DatabasePeter 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... - Multidimensional annotation of the Escherichia coli K-12 genomePeter 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... - EcoCyc: Enyclopedia of Escherichia coli Genes and MetabolismP 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... - HinCyc: a knowledge base of the complete genome and metabolic pathways of H. influenzaeP 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... - Expansion of the BioCyc collection of pathway/genome databases to 160 genomesPeter 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... - The EcoCyc and MetaCyc databasesP 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/.. - Database verification studies of SWISS-PROT and GenBankP D Karp
Bioinformatics Research Group, SRI International, EK223, 333 Ravenswood Ave, Menlo Park, CA 94025, USA
Bioinformatics 17:526-32; discussion 533-4. 2001..Although many of these differences can be explained by the complexity of the DB, and by the curation processes used to create it, the scale of the differences is notable... - Database links are a foundation for interoperabilityP 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... - Pathway databases: a case study in computational symbolic theoriesP 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... - The EcoCyc DatabasePeter 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/... - Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biologyPeter 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... - The past, present and future of genome-wide re-annotationChristos 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... - A survey of metabolic databases emphasizing the MetaCyc familyPeter 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... - The Pathway Tools softwarePeter D Karp
Bioinformatics Research Group, SRI International, 333 Ravenswood Ave, Menlo Park, CA, 94025, USA
Bioinformatics 18:S225-32. 2002..The Pathway Tools makes use of the Ocelot object database system for data management services for PGDBs. The Pathway Tools has been used to build PGDBs for 13 organisms within SRI and by external users... - A strategy for database interoperationP 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... - 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 - An ontology for biological function based on molecular interactionsP 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... - The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databasesRon 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... - EcoCyc: a comprehensive database resource for Escherichia coliIngrid M Keseler
SRI International, 333 Ravenswood Avenue, Menlo Park, CA 94025, USA
Nucleic Acids Res 33:D334-7. 2005.... - EcoCyc: a comprehensive view of Escherichia coli biologyIngrid 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... - The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome DatabasesRon 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... - MetaCyc: a multiorganism database of metabolic pathways and enzymesCynthia 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... - Querying and computing with BioCyc databasesMarkus Krummenacker
SRI International, Bioinformatics Research Group, EK207 Menlo Park, CA 94025, USA
Bioinformatics 21:3454-5. 2005.... - Using the MetaCyc pathway database and the BioCyc database collectionRon 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... - MetaCyc: a multiorganism database of metabolic pathways and enzymesRon 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... - Annotation-based inference of transporter functionThomas J Lee
Artificial Intelligence Center, SRI International, Menlo Park, CA, USA
Bioinformatics 24:i259-67. 2008.... - EcoCyc: a comprehensive database of Escherichia coli biologyIngrid 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... - An advanced web query interface for biological databasesMario 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... - Evaluation of computational metabolic-pathway predictions for Helicobacter pyloriSuzanne M Paley
Bioinformatics Research Group, SRI International, EK207, 333 Ravenswood Ave, Menlo Park, CA 94025, USA
Bioinformatics 18:715-24. 2002.... - Using genome-context data to identify specific types of functional associations in pathway/genome databasesMichelle 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... - The Pathway Tools cellular overview diagram and Omics ViewerSuzanne M Paley
Bioinformatics Research Group, SRI International EK207, 333 Ravenswood Avenue, Menlo Park, CA 94025, USA
Nucleic Acids Res 34:3771-8. 2006.... - PseudoCyc, a pathway-genome database for Pseudomonas aeruginosaPedro 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/... - 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..AVAILABILITY: Gene Ontology in Protégé-2000 and the associated code are located at http://smi.stanford.edu/projects/helix/gokbms/. Protégé-2000 is available from http://protege.stanford.edu... - A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic informationAdam 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... - Computational analysis of Plasmodium falciparum metabolism: organizing genomic information to facilitate drug discoveryIwei 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... - MetaCyc and AraCyc. Metabolic pathway databases for plant researchPeifen Zhang
The Arabidopsis Information Resource, Department of Plant Biology, Carnegie Institution of Washington, Stanford, California 94305, USA
Plant Physiol 138:27-37. 2005.... - Evidence supporting predicted metabolic pathways for Vibrio cholerae: gene expression data and clinical testsJing 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)...
Research Grants
- The MetaCyc Metabolic Pathway DatabasePeter Karp; Fiscal Year: 2005....
- Robust Software Components for Model Organism DatabasesPeter 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. ..
- Encyclopedia of E. Coli Genes and MetabolismPeter 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. ..
- The MetaCyc and BioCyc Pathway/Genome DatabasesPeter 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. ..
- Pathway Prediction and Assessment Integrating Multiple Evidence TypesPeter 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. ..
- Pathway Prediction and Assessment Integrating Multiple Evidence TypesPeter 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. ..
- Development and Support of the Pathway Tools SoftwarePeter D Karp; Fiscal Year: 2010....
- The MetaCyc and BioCyc Pathway/Genome DatabasesPeter 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. ..
- Encyclopedia of E. Coli Genes and MetabolismPeter 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. ..
- ENCYCLOPEDIA OF E COLI GENES AND METABOLISMPeter 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...
- ENCYCLOPEDIA OF E COLI GENES AND METABOLISMPeter Karp; Fiscal Year: 2001..The database is also useful for designing variants of biochemical pathways for biotechnology applications, and for teaching biochemistry. ..
- DEVELOPMENT OF THE METACYC METABOLIC PATHWAY DATABASEPeter Karp; Fiscal Year: 2003....
- Robust Software Components for Model Organism DatabasesPeter 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. ..
- Development and Support of the Pathway Tools SoftwarePeter Karp; Fiscal Year: 2009....