List of works by Peter D. Karp

A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases

scientific article

A framework for application of metabolic modeling in yeast to predict the effects of nsSNV in human orthologs

scientific article (publication date: 3 June 2014)

A genome-scale metabolic flux model of Escherichia coli K-12 derived from the EcoCyc database

scientific article

A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information

scientific article (publication date: 2007)

A knowledge base of the chemical compounds of intermediary metabolism ⬇️

scientific article published on August 1, 1992

A protocol for maintaining multidatabase referential integrity.

scientific article published on January 1996

A strategy for database interoperation

scientific article published on January 1995

A survey of metabolic databases emphasizing the MetaCyc family

scientific article

A survey of orphan enzyme activities

scientific article

A systematic comparison of the MetaCyc and KEGG pathway databases

scientific article

A systematic study of genome context methods: calibration, normalization and combination

scientific article

Accurate atom-mapping computation for biochemical reactions

scientific article published on 15 October 2012

Adapting EcoCyc for use on the World Wide Web.

scientific article published on June 1996

Addition of Escherichia coli K-12 growth observation and gene essentiality data to the EcoCyc database

scientific article

An advanced web query interface for biological databases

scientific article

An evaluation of ontology exchange languages for bioinformatics.

scientific article published on January 2000

An evidence ontology for use in pathway/genome databases.

scientific article published on January 2004

An ontology for biological function based on molecular interactions

scientific article published on March 2000

Annotation-based inference of transporter function

scientific article published on July 2008

Artificial intelligence methods for theory representation and hypothesis formation.

scientific article published on July 1991

Beyond the genome (BTG) is a (PGDB) pathway genome database: HumanCyc.

scientific article

BioWarehouse: a bioinformatics database warehouse toolkit

scientific article

Browsing metabolic and regulatory networks with BioCyc

scientific article published on January 2012

Call for an enzyme genomics initiative

scientific article

Changes to NIH Grant System May Backfire

scientific article

Computational analysis of Plasmodium falciparum metabolism: organizing genomic information to facilitate drug discovery

scientific article published on 12 April 2004

Computational prediction of human metabolic pathways from the complete human genome

scientific article published in 2005

Computer-assisted three-dimensional and two-dimensional reconstructions of autoradiographic images of the cerebral cortex

scientific article published on 01 March 1984

Computing minimal nutrient sets from metabolic networks via linear constraint solving

scientific article

Construction and completion of flux balance models from pathway databases

scientific article (publication date: 18 January 2012)

Corrigendum: The BioPAX community standard for pathway data sharing

correction; published 7 December 2010

Creation of a genome-wide metabolic pathway database for Populus trichocarpa using a new approach for reconstruction and curation of metabolic pathways for plants

scientific article published on 03 June 2010

Curation accuracy of model organism databases

scientific article

Data mining in the MetaCyc family of pathway databases

scientific article

Database links are a foundation for interoperability

scientific article published on August 1996

Database verification studies of SWISS-PROT and GenBank

scientific article

Dead end metabolites--defining the known unknowns of the E. coli metabolic network

scientific article

Discovering novel subsystems using comparative genomics

scientific article

Eco Cyc: encyclopedia of Escherichia coli genes and metabolism

scientific article published on January 1999

EcoCyc: Encyclopedia of Escherichia coli genes and metabolism

scientific article

EcoCyc: Enyclopedia of Escherichia coli Genes and Metabolism

scientific article

EcoCyc: a comprehensive database of Escherichia coli biology

scientific article

EcoCyc: a comprehensive database resource for Escherichia coli

scientific article

EcoCyc: a comprehensive view of Escherichia coli biology

scientific article published on 30 October 2008

EcoCyc: an encyclopedia of Escherichia coli genes and metabolism

scientific article

EcoCyc: fusing model organism databases with systems biology

scientific article

Erratum: Corrigendum: The BioPAX community standard for pathway data sharing

scholarly article published in Nature Biotechnology

Erratum: The complete genome sequence of the gastric pathogen Helicobacter pylori

scientific article published in Nature

Estimation of equilibrium constants using automated group contribution methods.

scientific article

Evaluation of computational metabolic-pathway predictions for Helicobacter pylori

scientific article

Evidence supporting predicted metabolic pathways for Vibrio cholerae: gene expression data and clinical tests

scientific article

Expansion of the BioCyc collection of pathway/genome databases to 160 genomes

scientific article

Genome annotation errors in pathway databases due to semantic ambiguity in partial EC numbers

scientific article

Global properties of the metabolic map of Escherichia coli

scientific article

Groups: knowledge spreadsheets for symbolic biocomputing

scientific article published on 14 September 2013

HinCyc: a knowledge base of the complete genome and metabolic pathways of H. influenzae

article by P D Karp et al published 1996 in Proceedings. International Conference on Intelligent Systems for Molecular Biology

How accurate is automated gap filling of metabolic models?

scientific article

Integrated access to metabolic and genomic data

scientific article

Integrated pathway–genome databases and their role in drug discovery

scientific article published on 01 July 1999

Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO).

scientific article published on January 2003

Machine learning methods for metabolic pathway prediction

scientific article

Many Genbank entries for complete microbial genomes violate the Genbank standard

scientific article published on January 2001

MetaCyc and AraCyc. Metabolic pathway databases for plant research

scientific article published on May 2005

MetaCyc: a multiorganism database of metabolic pathways and enzymes

scientific article

MetaCyc: a multiorganism database of metabolic pathways and enzymes.

scientific article

Metabolic databases

scientific article published on 01 March 1998

Metabolic pathways for the whole community

scientific article

Metabolomics reveals amino acids contribute to variation in response to simvastatin treatment

scientific article

Multidimensional annotation of the Escherichia coli K-12 genome

scientific article

Nutrient-related analysis of pathway/genome databases

scientific article published in January 2001

Optimal metabolic route search based on atom mappings

scientific article published on 17 March 2014

Pathway Tools Visualization of Organism-Scale Metabolic Networks

scientific article

Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology

scientific article

Pathway collages: personalized multi-pathway diagrams

scientific article

Pathway databases: a case study in computational symbolic theories

scientific article published on September 2001

PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools.

scientific article

Prediction of enzyme classification from protein sequence without the use of sequence similarity.

scientific article

PseudoCyc, a pathway-genome database for Pseudomonas aeruginosa

scientific article published in January 2003

Querying and computing with BioCyc databases

scientific article

Regulatory network operations in the Pathway Tools software

scientific article

Representations of metabolic knowledge.

scientific article

Representations of metabolic knowledge: pathways.

scientific article published in January 1994

Simultaneous cross-evaluation of heterogeneous E. coli datasets via mechanistic simulation

scientific article

The BioPAX community standard for pathway data sharing

scientific article (publication date: September 2010)

The COMBREX project: design, methodology, and initial results

scientific article

The EcoCyc Database

scientific article

The EcoCyc and MetaCyc databases

scientific article

The MetaCyc Database

scientific article

The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

scientific article (publication date: 2008)

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

scientific article published on 12 November 2013

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

scientific article

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases ⬇️

scientific article (publication date: 2012)

The Pathway Tools cellular overview diagram and Omics Viewer

scientific article

The Pathway Tools software

scientific article (publication date: 2002)

The challenge of constructing, classifying, and representing metabolic pathways

scientific article

The complete genome sequence of Francisella tularensis, the causative agent of tularemia

scientific article

The complete genome sequence of the gastric pathogen Helicobacter pylori

scientific article

The comprehensive updated regulatory network of Escherichia coli K-12.

scientific article

The genome of the natural genetic engineer Agrobacterium tumefaciens C58

scientific article

The outcomes of pathway database computations depend on pathway ontology

scientific article

The past, present and future of genome-wide re-annotation

scientific article

The pathway tools pathway prediction algorithm

scientific article

Using Pathway Covering to Explore Connections among Metabolites.

scientific article

Using functional and organizational information to improve genome-wide computational prediction of transcription units on pathway-genome databases

scientific article published on 29 January 2004

Using genome-context data to identify specific types of functional associations in pathway/genome databases

scientific article

Using the MetaCyc pathway database and the BioCyc database collection

scientific article published in December 2007

Web-based metabolic network visualization with a zooming user interface

scientific article

What database management system(s) should be employed in bioinformatics applications?

scientific article published in January 2003

What we can learn about Escherichia coli through application of Gene Ontology

scientific article (publication date: July 2009)

What we do not know about sequence analysis and sequence databases

scientific article published on 01 January 1998

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