Search result matching 66 Publications
Metabolic route computation in organism communities
SRI Authors: Mario Latendresse, Peter Karp
Journal Article June 3, 2019
How accurate is automated gap filling of metabolic models?
SRI Authors: Peter Karp, David Weaver, Mario Latendresse
Journal Article January 1, 2018
Evaluation of reaction gap-filling accuracy by randomization
SRI Authors: Mario Latendresse, Peter Karp
Journal Article January 1, 2018
The MetaCyc database of metabolic pathways and enzymes
SRI Authors: Mario Latendresse, Manish Kothari, Peter Karp
Journal Article January 1, 2018
The Omics Dashboard for interactive exploration of gene-expression data
SRI Authors: Peter Karp, Paul O’Maille
Journal Article October 13, 2017
Journal Article January 1, 2017
The BioCyc collection of microbial genomes and metabolic pathways
SRI Authors: Peter Karp, Mario Latendresse, Manish Kothari
Journal Article January 1, 2017
Update notifications for the BioCyc collection of databases
SRI Authors: Peter Karp
Article January 1, 2017
The EcoCyc database: reflecting new knowledge about em Escherichia coli K-12
SRI Authors: Manish Kothari, Mario Latendresse, David Weaver, Peter Karp
Article January 1, 2016
How the strengths of Lisp-family languages facilitate building complex and flexible bioinformatics applications
SRI Authors: Peter Karp
Article January 1, 2016
Representation and inference of cellular architecture for metabolic reconstruction and modeling
SRI Authors: Peter Karp
Article January 1, 2016
Crowd-sourcing and author submission as alternatives to professional curation
SRI Authors: Peter Karp
Article January 1, 2016
The Time Is Right to Focus on Model Organism Metabolomes
SRI Authors: Peter Karp
Article January 1, 2016
Pathway collages: personalized multi-pathway diagrams
SRI Authors: David Weaver, Peter Karp
Article January 1, 2016
Can we replace curation with information extraction software?
SRI Authors: Peter Karp
Article January 1, 2016
Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology
SRI Authors: Peter Karp, Mario Latendresse, Manish Kothari, David Weaver
Article January 1, 2016
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases.
SRI Authors: Mario Latendresse, David Weaver, Peter Karp
Article May 1, 2015
Computational Metabolomics Operations at Biocyc.Org
SRI Authors: Peter Karp, David Weaver
Article January 1, 2015
“Pathway Tools version 19.0 update: Software for Pathway/Genome Informatics and Systems Biology”
SRI Authors: Peter Karp, Mario Latendresse
Article July 1, 2014
Optimal Metabolic Route Search Based on Atom Mappings
SRI Authors: Mario Latendresse, Peter Karp
Article June 1, 2014
A Genome-Scale Metabolic Flux Model of Escherichia coli K-12 Derived from the EcoCyc Database
SRI Authors: David Weaver, Peter Karp
Article June 1, 2014
A Framework for Application of Metabolic Modeling in Yeast to Predict the Effects of Nssnv in Human Orthologs
SRI Authors: David Weaver, Peter Karp
Article March 1, 2014
Addition of Escherichia coli K-12 Growth Observation and Gene Essentiality Data to the Ecocyc Database
SRI Authors: Peter Karp
Article January 1, 2014
PortEco: A Resource for Exploring Bacterial Biology through High-Throughput Data and Analysis Tools
SRI Authors: Peter Karp
Article January 1, 2014
The Metacyc Database of Metabolic Pathways and Enzymes and the Biocyc Collection of Pathway/Genome Databases
SRI Authors: Mario Latendresse, Peter Karp
Article January 1, 2014
Addition of Escherichia coli K–12 Growth-Observation and Gene Essentiality Data to the EcoCyc database
SRI Authors: Peter Karp
Chapter October 1, 2013
Metabolic Reconstruction Databases and Their Application to Metabolomics Research
SRI Authors: Peter Karp
Article September 1, 2013
Dead End Metabolites – Defining the Known Unknowns of the E. coli Metabolic Network
SRI Authors: Peter Karp
Article August 1, 2013
The COMBREX Project: Design, Methodology, and Initial Results
SRI Authors: Peter Karp
Article July 1, 2013
Groups: Knowledge Spreadsheets for Symbolic Biocomputing
SRI Authors: Peter Karp
Article June 1, 2013
The Challenge of Constructing, Classifying, and Representing Metabolic Pathways
SRI Authors: Peter Karp
Article March 1, 2013
Computing Minimal Nutrient Sets from Metabolic Networks Via Linear Constraint Solving
SRI Authors: Carolyn Talcott, Peter Karp
Article March 1, 2013
A Systematic Comparison of the MetaCyc and Kegg Pathway Databases
SRI Authors: Peter Karp
Article January 1, 2013
Data Mining in the Metacyc Family of Pathway Databases
SRI Authors: Peter Karp
Article November 1, 2012
EcoCyc: Fusing Model Organism Databases with Systems Biology
SRI Authors: Mario Latendresse, Peter Karp, Peter Karp
Journal Article September 1, 2012
Accurate Atom-Mapping Computation for Biochemical Reactions
SRI Authors: Mario Latendresse, Jeremiah Malerich, Peter Karp
Journal Article September 1, 2011
A Survey of Metabolic Databases Emphasizing the Metacyc Family
SRI Authors: Peter Karp
Article July 1, 2011
Discovering Novel Subsystems Using Comparative Genomics
SRI Authors: Peter Karp
Article May 1, 2011
Web-Based Metabolic Network Visualization with a Zooming User Interface
SRI Authors: Mario Latendresse, Peter Karp
Article April 1, 2011
Biocyc: Microbial Genomes and Cellular Networks
SRI Authors: Mario Latendresse, Peter Karp
Conference Paper February 1, 2011
Using Cellular Network Diagrams to Interpret Large-Scale Datasets: Past Progress and Future Challenges
SRI Authors: Mario Latendresse, Peter Karp
Article January 1, 2011
Metabolic Pathway Databases for 1,000 Organisms
SRI Authors: Peter Karp
Article November 1, 2010
EcoCyc: a Comprehensive Database of Escherichia Coli Biology
SRI Authors: Peter Karp
Article October 1, 2010
Beyond the Genome (BTG) Is a (PGDB) Pathway Genome Database: Humancyc
SRI Authors: Peter Karp
Article October 1, 2010
A Systematic Study of Genome Context Methods: Calibration, Normalization and Combination
SRI Authors: Peter Karp
Journal Article September 1, 2010
The BioPAX Community Standard for Pathway Data Sharing
SRI Authors: Peter Karp
Article August 1, 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
SRI Authors: Peter Karp
Article January 1, 2010
An Advanced Web Query Interface for Biological Databases
SRI Authors: Mario Latendresse, Peter Karp
Article January 1, 2010
Machine Learning Methods for Metabolic Pathway Prediction
SRI Authors: Peter Karp
Article December 1, 2009
Pathway Tools Version 13.0: Integrated Software for Pathway/Genome Informatics and Systems Biology
SRI Authors: Mario Latendresse, Peter Karp
Journal Article July 1, 2009
What We Can Learn About Escherichia Coli Through Application of Gene Ontology
SRI Authors: Peter Karp
Article January 1, 2009
The Multiple Scientific Disciplines Served By EcoCyc
SRI Authors: Peter Karp
Journal Article November 1, 2008
Changes to NIH Grant System May Backfire
SRI Authors: Peter Karp, Keith R. Laderoute
Article October 1, 2008
EcoCyc: a Comprehensive View of Escherichia Coli Biology
SRI Authors: Peter Karp
Article July 1, 2008
Annotation-Based Inference of Transporter Function
SRI Authors: Peter Karp
Conference Paper January 1, 2008
Biowarehouse: Relational Integration of Eleven Bioinformatics Databases and Formats
SRI Authors: Peter Karp
Journal Article February 1, 2000
XOL: An XML-Based Ontology Exchange Language
SRI Authors: Peter Karp
Journal Article August 1, 1994
A Storage System for Scalable Knowledge Representation
SRI Authors: Peter Karp
Journal Article August 1, 1994
Distinguishing Knowledge Bases and Data Bases: Who’s on First and What’s on Second
SRI Authors: Peter Karp
Journal Article January 1, 1993
The Grasper-CL Graph Management System
SRI Authors: Peter Karp, John D. Lowrance
Journal Article October 1, 1992
The Design Space of Frame Knowledge Representation Systems
SRI Authors: Peter Karp