Peter Karp

Q: What Schools Are Affiliated With Peter Karp

Peter Karp is affiliated with the following schools: Stanford University, Cornell University

Peter Karp 's AcademicInfluence.com Rankings

Peter Karp

Biology

#9093

World Rank

#12255

Historical Rank

Systems Biology

#31

World Rank

#31

Historical Rank

Bioinformatics

#126

World Rank

#128

Historical Rank

Computational Biology

#220

World Rank

#221

Historical Rank

biology Degrees

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Biology

Peter Karp 's Degrees

PhD Computer Science Stanford University
Masters Computer Science Stanford University
Bachelors Computer Science Stanford University

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Why Is Peter Karp Influential?

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According to Wikipedia, Peter D. Karp is director of the Bioinformatics Research Group at SRI International in Menlo Park, California. Karp leads the development of the BioCyc database collection . BioCyc databases combine genome, metabolic pathway, and regulatory information for thousands of organisms.

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Peter Karp 's Published Works

Number of citations in a given year to any of this author's works

Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author

Published Works

The complete genome sequence of the gastric pathogen Helicobacter pylori (1997) (3551)
A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information (2007) (1452)
The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases (2007) (1215)
The Genome of the Natural Genetic Engineer Agrobacterium tumefaciens C58 (2001) (817)
EcoCyc: a comprehensive database resource for Escherichia coli (2004) (757)
The Pathway Tools software (2002) (684)
Expansion of the BioCyc collection of pathway/genome databases to 160 genomes (2005) (669)
Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology (2015) (630)
The MetaCyc database of metabolic pathways and enzymes (2017) (615)
EcoCyc: fusing model organism databases with systems biology (2012) (607)
BioPAX – A community standard for pathway data sharing (2010) (594)
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases (2015) (570)
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases (2011) (561)
MetaCyc: a multiorganism database of metabolic pathways and enzymes (2005) (530)
The EcoCyc Database (2002) (517)
Computational prediction of human metabolic pathways from the complete human genome (2004) (514)
EcoCyc: a comprehensive database of Escherichia coli biology (2010) (491)
The complete genome sequence of Francisella tularensis, the causative agent of tularemia (2005) (474)
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12 (2016) (457)
The BioCyc collection of microbial genomes and metabolic pathways (2019) (406)
EcoCyc: A comprehensive view of Escherichia coli biology (2008) (401)
The MetaCyc Database (2002) (396)
The MetaCyc database of metabolic pathways and enzymes - a 2019 update (2019) (392)
OKBC: A Programmatic Foundation for Knowledge Base Interoperability (1998) (385)
MetaCyc: a multiorganism database of metabolic pathways and enzymes. (2004) (383)
The EcoCyc and MetaCyc databases (2000) (312)
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases (2013) (288)
A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases (2004) (284)
MetaCyc and AraCyc. Metabolic Pathway Databases for Plant Research1[w] (2005) (251)
Pathway Databases: A Case Study in Computational Symbolic Theories (2001) (244)
Computational analysis of Plasmodium falciparum metabolism: organizing genomic information to facilitate drug discovery. (2004) (242)
Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology (2016) (214)
BioWarehouse: a bioinformatics database warehouse toolkit (2006) (204)
An ontology for biological function based on molecular interactions (2000) (194)
EcoCyc: Encyclopedia of Escherichia coli genes and metabolism (1998) (193)
Multidimensional annotation of the Escherichia coli K-12 genome (2007) (186)
XOL: An XML-Based Ontology Exchange Language (2000) (177)
The Pathway Tools cellular overview diagram and Omics Viewer (2006) (172)
Integrated pathway-genome databases and their role in drug discovery. (1999) (172)
Machine learning methods for metabolic pathway prediction (2010) (157)
The COMBREX Project: Design, Methodology, and Initial Results (2013) (137)
A systematic comparison of the MetaCyc and KEGG pathway databases (2013) (131)
What we do not know about sequence analysis and sequence databases. (1998) (129)
A Strategy for Database Interoperation (1995) (125)
Creation of a Genome-Wide Metabolic Pathway Database for Populus trichocarpa Using a New Approach for Reconstruction and Curation of Metabolic Pathways for Plants1[W][OA] (2010) (119)
Corrigendum: The BioPAX community standard for pathway data sharing (2010) (114)
The past, present and future of genome-wide re-annotation (2002) (113)
The Pathway Tools Pathway Prediction Algorithm (2011) (111)
The Generic Frame Protocol (1995) (111)
Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO) (2003) (110)
Evaluation of computational metabolic-pathway predictions for Helicobacter pylori (2002) (106)
Global properties of the metabolic map of Escherichia coli. (2000) (101)
Construction and completion of flux balance models from pathway databases (2012) (101)
EcoCyc: an encyclopedia of Escherichia coli genes and metabolism (1996) (100)
Querying and computing with BioCyc databases (2005) (97)
Genome annotation errors in pathway databases due to semantic ambiguity in partial EC numbers (2005) (96)
The design space of frame knowledge representation systems (1992) (90)
Automated Drawing of Metabolic Pathways (2000) (89)
Metabolomics Reveals Amino Acids Contribute to Variation in Response to Simvastatin Treatment (2012) (87)
The outcomes of pathway database computations depend on pathway ontology (2006) (86)
Using functional and organizational information to improve genome-wide computational prediction of transcription units on pathway-genome databases (2004) (84)
Prediction of Enzyme Classification from Protein Sequence without the Use of Sequence Similarity (1997) (83)
Call for an enzyme genomics initiative (2004) (83)
Simultaneous cross-evaluation of heterogeneous E. coli datasets via mechanistic simulation (2019) (81)
Automated presentation planning of animation using task decomposition with heuristic reasoning (1993) (80)
Issues in the automated generation of animated presentations (1990) (77)
Detection and elimination of inference channels in multilevel relational database systems (1993) (74)
The comprehensive updated regulatory network of Escherichia coli K-12 (2006) (71)
The EcoCyc Database. (2014) (70)
Accurate Atom-Mapping Computation for Biochemical Reactions (2012) (70)
A survey of metabolic databases emphasizing the MetaCyc family (2011) (66)
Database links are a foundation for interoperability. (1996) (66)
HinCyc: A Knowledge Base of the Complete Genome and Metabolic Pathways of H. influenzae (1996) (66)
Integrated Access to Metabolic and Genomic Data (1996) (65)
Pathway Tools version 23.0 update: software for pathway/genome informatics and systems biology (2019) (64)
Metabolic pathways for the whole community (2014) (59)
The Time Is Right to Focus on Model Organism Metabolomes (2016) (55)
Representations of Metabolic Knowledge (1993) (52)
The challenge of constructing, classifying, and representing metabolic pathways. (2013) (52)
The EcoCyc Database in 2021 (2021) (51)
BioPAX - Biological Pathways Exchange Language Level 2, Version 1.0 Documentation (2005) (50)
Representations of Metabolic Knowledge: Pathways (1994) (49)
An Evaluation of Ontology Exchange Languages for Bioinformatics (2000) (49)
Eco Cyc: encyclopedia of Escherichia coli genes and metabolism (1999) (48)
Representing, analyzing, and synthesizing biochemical pathways (1994) (48)
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases (2009) (47)
A qualitative biochemistry and its application to the regulation of the tryptophan operon (1993) (47)
Database verification studies of SWISS-PROT and GenBank (2001) (46)
An Evidence Ontology for Use in Pathway/Genome Databases (2003) (46)
Annotation-based inference of transporter function (2008) (46)
Plant Metabolic Network 15: A resource of genome-wide metabolism databases for 126 plants and algae. (2021) (45)
A genome-scale metabolic flux model of Escherichia coli K–12 derived from the EcoCyc database (2014) (44)
Optimal metabolic route search based on atom mappings (2014) (44)
A survey of orphan enzyme activities (2007) (41)
The BioPAX community standard for pathway data sharing (Nature Biotechnology (2010) 28, (935-942)) (2012) (41)
PseudoCyc, A Pathway-Genome Database for Pseudomonas aeruginosa (2003) (37)
Web-based metabolic network visualization with a zooming user interface (2011) (36)
Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology (1996) (36)
Using genome-context data to identify specific types of functional associations in pathway/genome databases (2007) (35)
Beyond the genome (BTG) is a (PGDB) pathway genome database: HumanCyc (2010) (34)
The Omics Dashboard for interactive exploration of gene-expression data (2017) (34)
Browsing metabolic and regulatory networks with BioCyc. (2012) (34)
A Collaborative Environment for Authoring Large Knowledge Bases (1999) (34)
A systematic study of genome context methods: calibration, normalization and combination (2010) (33)
Nutrient-related analysis of pathway/genome databases. (2000) (33)
Pathway size matters: the influence of pathway granularity on over-representation (enrichment analysis) statistics (2021) (32)
The Grasper-CL graph management system (1994) (32)
A Generic Knowledge-Base Browser and Editor (1997) (31)
Fully Automated Chemical Synthesis: Toward the Universal Synthesizer (2020) (30)
How much does curation cost? (2016) (30)
Curation accuracy of model organism databases (2014) (30)
Metabolic databases. (1998) (27)
Can we replace curation with information extraction software? (2016) (26)
How accurate is automated gap filling of metabolic models? (2018) (26)
Hypothesis Formation and Qualitative Reasoning in Molecular Biology (1990) (26)
Dead End Metabolites - Defining the Known Unknowns of the E. coli Metabolic Network (2013) (25)
fusing model organism databases with systems biology. (2012) (25)
PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools (2013) (24)
Computational Metabolomics Operations at BioCyc.org (2015) (24)
Coordinating the use of qualitative and quantitative knowledge in declarative device modeling (1989) (23)
Knowledge Representation in the Large (1995) (21)
Groups: knowledge spreadsheets for symbolic biocomputing (2013) (20)
Pathway collages: personalized multi-pathway diagrams (2016) (20)
An analysis of the distinction between deep and shallow expert systems (1989) (19)
The EcoCyc Database. (2018) (19)
An advanced web query interface for biological databases (2010) (18)
Design Methods for Scientific Hypothesis Formation and Their Application to Molecular Biology (2004) (17)
Artificial intelligence methods for theory representation and hypothesis formation (1991) (16)
BioCyc: Online Resource for Genome and Metabolic Pathway Analysis (2016) (16)
EcoCyc: The Resource and the Lessons Learned (2002) (16)
A Comparison of Microbial Genome Web Portals (2018) (16)
A knowledge base of the chemical compounds of intermediary metabolism (1992) (15)
What we can learn about Escherichia coli through application of Gene Ontology. (2009) (15)
Evidence supporting predicted metabolic pathways for Vibrio cholerae: gene expression data and clinical tests (2006) (15)
Gene Dispensability in Escherichia coli Grown in Thirty Different Carbon Environments (2020) (15)
Regulatory network operations in the Pathway Tools software (2012) (14)
Data mining in the MetaCyc family of pathway databases. (2013) (14)
An Experimental Approach to Genome Annotation (2004) (14)
Estimation of equilibrium constants using automated group contribution methods (1997) (14)
Many Genbank Entries for Complete Microbial Genomes Violate the Genbank Standard (2001) (12)
Evaluation of reaction gap-filling accuracy by randomization (2018) (11)
Adapting EcoCyc for use on the World Wide Web. (1996) (11)
EcoCyc: Enyclopedia of Escherichia coli Genes and Metabolism (1997) (11)
Crowd-sourcing and author submission as alternatives to professional curation (2016) (10)
Addition of Escherichia coli K-12 Growth Observation and Gene Essentiality Data to the EcoCyc Database (2013) (10)
Discovering novel subsystems using comparative genomics (2011) (10)
A storage system for scalable knowledge representation (1994) (10)
Corrections: The complete genome sequence of the gastric pathogen Helicobacter pylori (1997) (9)
Update notifications for the BioCyc collection of databases (2017) (9)
BioCyc: A Genomic and Metabolic Web Portal with Multiple Omics Analytical Tools (2019) (7)
Computing minimal nutrient sets from metabolic networks via linear constraint solving (2013) (7)
A protocol for maintaining multidatabase referential integrity. (1996) (7)
The MetaCyc Metabolic Pathway Database (2002) (6)
Design methods for scientific hypothesis formation and their application to molecular biology (1993) (6)
Pathway Tools Visualization of Organism-Scale Metabolic Networks (2021) (5)
The MultiOmics Explainer: explaining omics results in the context of a pathway/genome database (2019) (5)
ISCB Ebola Award for Important Future Research on the Computational Biology of Ebola Virus (2015) (5)
The BioCyc Metabolic Network Explorer (2021) (4)
BioWarehouse: Relational Integration of Eleven Bioinformatics Databases and Formats (2008) (4)
Nutrition-Related Analysis of Pathway/Genome Databases (2001) (4)
Querying Schema Information (1997) (4)
How the strengths of Lisp-family languages facilitate building complex and flexible bioinformatics applications (2017) (4)
The Pathway Tools Software in 2009 (2009) (4)
PathwayTools version 13 . 0 : integrated software for pathway / genome informatics and systems biology (2010) (3)
A roadmap for the functional annotation of protein families: a community perspective (2022) (3)
Metabolic route computation in organism communities (2019) (3)
How the strengths of Lisp-family languages facilitate building complex and flexible bioinformatics applications (2016) (3)
PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools (2014) (3)
What Database Management System(s) Should Be Employed in Bioinformatics Applications? (2003) (3)
Using Pathway Covering to Explore Connections among Metabolites (2019) (2)
Leveraging Curation Among Escherichia coli Pathway/Genome Databases Using Ortholog-Based Annotation Propagation (2021) (2)
Changes to NIH Grant System May Backfire (2008) (2)
Erratum: The BioPAX community standard for pathway data sharing (Nat. Biotechnol. (2010) 28 (935-942) (2010) (2)
Identifying candidate genes using the BioWarehouse: a case study (2005) (2)
Using the EcoCyc Database (1997) (2)
Development of Large Scientific Knowledge Bases (2010) (2)
errata: The yeast genome directory (1997) (2)
Plant Metabolic Pathways in MetaCyc and SolCyc (2009) (2)
Knowledge Integration for Bio-Threat Response (2005) (2)
Bioinformatics computation of metabolic models from sequenced genomes (2015) (2)
ISCB Ebola Award for Important Future Research on the Computational Biology of Ebola Virus (2015) (1)
Regulatory network operations in the Pathway Tools software (2012) (1)
BioCyc: Microbial Genomes and Cellular Networks: The BioCyc system helps scientists navigate the greatly expanding information space of genomes and metabolic information (2011) (1)
Taxonomic weighting improves the accuracy of a gap-filling algorithm for metabolic models (2019) (1)
New Directions for Scientific Discovery Research (1995) (1)
A systematic comparison of the MetaCyc and KEGG pathway databases (2013) (1)
Pathway bioinformatics (2003) (1)
Using cellular network diagrams to interpret large-scale datasets: past progress and future challenges (2011) (1)
Metabolic pathways for the whole community (2014) (1)
Metabolic Modeling with MetaFlux. (2021) (1)
A framework for application of metabolic modeling in yeast to predict the effects of nsSNV in human orthologs (2014) (1)
Creating Fungal Pathway/Genome Databases Using Pathway Tools (2006) (1)
Software Demo: The Pathway Tools Software (2002) (1)
The Multiple Scientific Disciplines Served by EcoCyc (2009) (0)
SESSION ON GENOME, PATHWAY, AND INTERACTION BIOINFORMATICS INTRODUCTION (2000) (0)
A genome-scale metabolic flux model of Escherichiacoli K-12 derived from the EcoCyc (2014) (0)
Plaster Users' Guide (1982) (0)
Internet On-Ramp World Wide Web Resources for Microbiologists (1999) (0)
The Omics Dashboard for Metabolomics Data (2017) (0)
Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology, Halkidiki, Greece, June 21-26, 1997 (1997) (0)
The BioCyc Metabolic Network Explorer (2021) (0)
Pathway Databases: A Case Study in Computational (2009) (0)
Metabolic route computation in organism communities (2019) (0)
Pathway collages: personalized multi-pathway diagrams (2016) (0)
Computing minimal nutrient sets from metabolic networks via linear constraint solving (2013) (0)
Plaster Source Code (1982) (0)
Erratum for Proctor et al., “Resources To Facilitate Use of the Altered Schaedler Flora (ASF) Mouse Model To Study Microbiome Function” (2023) (0)
Symbolic Theories Pathway Databases : A Case Study in Computational (2001) (0)
Analyzing metabolomics data with smart tables (2014) (0)
Pathway Tools Management of Pathway/Genome Data for Microbial Communities (2022) (0)
for automated or semi-automated information extraction from scientific texts as practical alternatives to professional curation ? (2016) (0)
Report of the Workshop on Interconnection of Molecular Biology Databases (2014) (0)
Update notifications for biological databases (2017) (0)
Computing Metabolic Routes in the Human Microbiome (2018) (0)
Metabolism: Cellular Organization (2008) (0)
The Grasper-CL (1994) (0)
Databases and Algorithms for Pathway Bioinformatics (2010) (0)
Transitioning BioCyc to a Subscription Model (2017) (0)
Reviewing knowledgebase and database grant proposals in the life sciences: the role of innovation (2022) (0)
Prediction of Enzyme Classi cation from Protein Sequence without Homology (1998) (0)
Metabolomics applications of the MetaCyc family of metabolic databases (2013) (0)
Evaluation of reaction gap-filling accuracy by randomization (2018) (0)
Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, August 14-17, 1994, Stanford University, Stanford, California, USA (1994) (0)
Bioinformatics MetaCyc and AraCyc . Metabolic Pathway Databases for Plant Research 1 [ w ] (2005) (0)
Supporting Multiuser Access to Large-Scale Persistent Knowledge Bases. (1997) (0)
Current issues in BioCuration (2017) (0)
Computing Metabolic Routes in the Human Microbiome (2018) (0)
Pathway size matters: the influence of pathway granularity on over-representation (enrichment analysis) statistics (2021) (0)
Three Models of Gene Regulation in E.coli (1996) (0)
Genome, Pathway and Interaction Bioinformatics - Session Introduction (2001) (0)
Curation and Computational Design of Bioenergy-Related Metabolic Pathways (2014) (0)
GENOME, PATHWAY AND INTERACTIONS BIOINFORMATICS (2001) (0)
Resources to Facilitate Use of the Altered Schaedler Flora (ASF) Mouse Model to Study Microbiome Function (2022) (0)
Erratum for Tong et al., “Gene Dispensability in Escherichia coli Grown in Thirty Different Carbon Environments” (2020) (0)
The MultiOmics Explainer: explaining omics results in the context of a pathway/genome database (2019) (0)
World Wide Web Resources for Microbiologists (1999) (0)
The Grasper-CL (Trademark) Graph Management System (1993) (0)
Plant Metabolic Network: A multi-species resource of plant metabolic information (2021) (0)
Metabolic reconstruction databases and their application to metabolomics research (2013) (0)
Session on computation in biological pathways (1996) (0)
Representation and inference of cellular architecture for metabolic reconstruction and modeling (2016) (0)
A framework for application of metabolic modeling in yeast to predict the effects of nsSNV in human orthologs (2014) (0)
Novel Bioinformatics Tools for Omics Data Analysis and Visualization (2018) (0)
A Comparison of the Pathway Tools Software with the Reactome Software. (2020) (0)
Contents Vol. 5, 2003 (2003) (0)
Subject Index Vol. 5, 2003 (2003) (0)
The Pathway Tools Software for Metabolic Reconstruction and Modeling (2016) (0)
Addition of Escherichia coli K – 12 1 2 Growth-Observations and Gene Essentiality Data to 2 3 the EcoCyc Database (2013) (0)
Bioinformatics pathway representations, databases, and algorithms (2005) (0)

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What Schools Are Affiliated With Peter Karp ?

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Peter Karp 's Degrees

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Why Is Peter Karp Influential?

Peter Karp 's Published Works

Published Works

Other Resources About Peter Karp

What Schools Are Affiliated With Peter Karp ?

Peter Karp 's AcademicInfluence.com Rankings