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Home » Archives for Suzanne Paley
Suzanne Paley

Suzanne Paley

Senior Computer Scientist, Artificial Intelligence Center
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Publications

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 .

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

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 October 5, 2019

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

Peter Karp, Suzanne Paley

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

Artificial intelligence publications July 1, 2019

The MultiOmics Explainer: Explaining Omics Results in the Context of a Pathway/Genome Database

Peter Karp, Suzanne Paley

We describe the MultiOmics Explainer, a new tool within the Pathway Tools software suite that leverages what is known about an organism’s metabolic and regulatory network to suggest explanations for the results of omics experiments.

Artificial intelligence publications February 1, 2019

A Comparison of Microbial Genome Web Portals

Peter Karp, Mario Latendresse, Suzanne Paley

This article compares the capabilities of the major microbial genome web portals to aid researchers in determining which portal(s) are best suited to their needs.

Artificial intelligence publications January 1, 2018

The MetaCyc database of metabolic pathways and enzymes

Mario Latendresse, Peter Karp, Suzanne Paley

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.

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