Author: Suzanne Paley

  • Revisiting the y-ome of Escherichia coli

    EcoCyc.org, the most comprehensive curated genome database for the model microorganism E. coli K-12, has implemented a new categorization schema that indicates the degree to which a gene has been characterized: well-characterized (54%), partially (26%) and uncharacterized (16%). This searchable category adds to the wealth of information and bioinformatics tools in EcoCyc aiding research decisions…

  • Visual Analysis of Multi-Omics Data

    Abstract We present a tool for multi-omics data analysis that enables simultaneous visualization of up to four types of omics data on organism-scale metabolic network diagrams. The tool’s interactive web-based metabolic charts depict the metabolic reactions, pathways, and metabolites of a single organism as described in a metabolic pathway database for that organism; the charts…

  • The Comparative Genome Dashboard

    The Comparative Genome Dashboard is a web-based software tool for interactive exploration of the similarities and differences in gene functions between organisms.

  • CyanoCyc Cyanobacterial Web Portal

    CyanoCyc is a web portal that integrates an exceptionally rich database collection of information about cyanobacterial genomes with an extensive suite of bioinformatics tools.

  • The Omics Dashboard for Interactive Exploration of Metabolomics and Multi-Omics Data

    The Omics Dashboard is a software tool for interactive exploration and analysis of metabolomics, transcriptomics, proteomics, and multi-omics datasets.

  • The EcoCyc Database (2023)

    The long-term goal of the project is to describe the complete molecular catalog of the E. coli cell, as well as the functions of each of its molecular parts, to facilitate a system-level understanding of E. coli.

  • Pathway Tools Management of Pathway/Genome Data for Microbial Communities

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

  • The EcoCyc Database in 2021

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

  • The BioCyc Metabolic Network Explorer

    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.

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

    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.

  • Pathway Tools Visualization of Organism-Scale Metabolic Networks

    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.

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

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