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Home » Archives for Ron Caspi
Ron Caspi

Ron Caspi

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Publications

Artificial intelligence publications March 1, 2023

BioCyc: Metabolic Pathway Databases and Informatics Tools

Peter Karp, Ron Caspi

This article describes a coordinated set of bioinformatics databases and software tools designed to solve multiple problems faced by metabolic engineers and microbiologists related to metabolic pathways.

Information & computer science publications July 1, 2021

The EcoCyc Database in 2021

Peter Karp, Suzanne Paley, Ron Caspi

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

Artificial intelligence publications March 1, 2021

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

Peter Karp, Ron Caspi

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

Prediction of Selected Biosynthetic Pathways for the Lipopolysaccharide Components in Porphyromonas gingivalis

Ron Caspi

We use bioinformatics tools to predict biosynthetic pathways for the production of the normal (O-type) lipopolysaccharide in the W50 strain Porphyromonas gingivalis and compare the pathway with other putative pathways in fully sequenced and completed genomes of other pathogenic strains.

Artificial intelligence publications October 5, 2019

The MetaCyc Database of Metabolic Pathways and Enzymes – A 2019 Update

Peter Karp, Suzanne Paley, Ron Caspi

This article provides an update on the developments in MetaCyc during September 2017 to August 2019, up to version 23.1.

Artificial intelligence publications January 1, 2018

The MetaCyc database of metabolic pathways and enzymes

Peter Karp, Suzanne Paley, Ron Caspi

This article provides an update on the developments in MetaCyc during the past two years, including the expansion of data and addition of new features.

Artificial intelligence publications January 1, 2017

The BioCyc collection of microbial genomes and metabolic pathways

Peter Karp, Suzanne Paley, Ron Caspi

BioCyc.org is a microbial genome Web portal that combines thousands of genomes with additional information inferred by computer programs, imported from other databases and curated from the biomedical literature by biologist curators.

Artificial intelligence publications January 1, 2017

The EcoCyc Database: Reflecting New Knowledge About Escherichia Coli K-12

David Weaver, Peter Karp, Suzanne Paley, Ron Caspi

New experimental discoveries about gene products, their function and regulation, new metabolic pathways, enzymes and cofactors are regularly added to EcoCyc.

Artificial intelligence publications January 1, 2016

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

David Weaver, Peter Karp, Suzanne Paley, Ron Caspi

The MetaCyc database (MetaCyc.org) is a freely accessible comprehensive database describing metabolic pathways and enzymes from all domains of life.

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