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Home » Archives for Peter Karp
Peter Karp

Peter Karp

Technical Director, Artificial Intelligence Center
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Publications

Artificial intelligence publications December 15, 2022

Reviewing Knowledgebase and Database Grant Proposals in the Life Sciences: The Role of Innovation

Peter Karp

Abstract This article offers thoughts on reviewing grant proposals for biological knowledgebases and databases (KDs) in the hope of aiding grant reviewers and applicants in addressing the issue of innovation. Assessing such grant proposals involves a number of subtleties that are worthy of discussion, particularly for new reviewers and applicants. In part, this article is […]

Biomedical sciences publications April 1, 2022

Pathway Tools Management of Pathway/Genome Data for Microbial Communities

Peter Karp, Suzanne Paley

The Pathway Tools software provides a suite of capabilities for storing and analyzing collections of genomic and metabolic information .

Artificial intelligence publications October 31, 2021

Metabolic Modeling with MetaFlux 

Peter Karp, Mario Latendresse, Wai Kit Ong

The MetaFlux software supports creating, executing, and solving quantitative metabolic flux models using flux balance analysis (FBA).

Information & computer science publications July 1, 2021

The EcoCyc Database in 2021

Peter Karp, Suzanne Paley

This article highlights recent improvements to the curated data in the areas of metabolism, transport, DNA repair, and regulation of gene expression.

Information & computer science publications April 1, 2021

The BioCyc Metabolic Network Explorer

Peter Karp, Suzanne Paley

The Metabolic Network Explorer is a new addition to the BioCyc.org website and the Pathway Tools software suite that supports the interactive exploration of metabolic networks.

Artificial intelligence publications March 1, 2021

Pathway Size Matters: The Influence of Pathway Granularity on Over-Representation (Enrichment) Statistics

Peter Karp

We show that alternative pathway definitions can alter enrichment p -values by up to nine orders of magnitude, whereas statistical corrections typically alter enrichment p -values by only two orders of magnitude.

Artificial intelligence publications March 1, 2021

Leveraging Curation Among Escherichia coli Pathway/Genome Databases Using Ortholog-Based Annotation Propagation

Peter Karp, Suzanne Paley

We have developed a method to automatically propagate multiple types of curated knowledge from genes and proteins in one genome database to their orthologs in uncurated databases for related strains, imposing several quality-control filters to reduce the chances of introducing errors.

Artificial intelligence publications January 1, 2021

Pathway Tools Visualization of Organism-Scale Metabolic Networks

Peter Karp, Suzanne Paley

We have developed bioinformatics software tools that automatically generate a full metabolic-network diagram for an organism, and that enable searching and analyses of the network.

Artificial intelligence publications January 9, 2020

A Comparison of the Pathway Tools Software with the Reactome Software

Peter Karp

This document compares SRI’s Pathway Tools (PTools) software with the Reactome software. Both software systems serve the pathway bioinformatics area, including representation and analysis of metabolic pathways and signaling pathways.

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