Suzanne Paley
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View article: The EcoCyc database (2025)
The EcoCyc database (2025) Open
EcoCyc is a bioinformatics database (DB) available at EcoCyc.org that describes the genome and the biochemical machinery of Escherichia coli K-12 MG1655. The long-term goal of the project was to describe the complete molecular catalog of t…
View article: Revisiting the y-ome of <i>Escherichia coli</i>
Revisiting the y-ome of <i>Escherichia coli</i> Open
The model organism Escherichia coli K-12 has one of the most extensively annotated genomes in terms of functional characterization, yet a significant number of genes, ∼35%, are still considered poorly characterized. Initially genes without…
View article: Visual analysis of multi-omics data
Visual analysis of multi-omics data Open
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 …
View article: The Comparative Genome Dashboard
The Comparative Genome Dashboard Open
The Comparative Genome Dashboard is a web-based software tool for interactive exploration of the similarities and differences in gene functions between organisms. It provides a high-level graphical survey of cellular functions, and enables…
View article: The Comparative Genome Dashboard
The Comparative Genome Dashboard Open
The Comparative Genome Dashboard is a web-based software tool for interactive exploration of the similarities and differences in gene functions between organisms. It provides a high-level graphical survey of cellular functions, and enables…
View article: Visual Analysis of Multi-Omics Data
Visual Analysis of Multi-Omics Data Open
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 …
View article: CyanoCyc cyanobacterial web portal
CyanoCyc cyanobacterial web portal Open
CyanoCyc is a web portal that integrates an exceptionally rich database collection of information about cyanobacterial genomes with an extensive suite of bioinformatics tools. It was developed to address the needs of the cyanobacterial res…
View article: The Omics Dashboard for Interactive Exploration of Metabolomics and Multi-Omics Data
The Omics Dashboard for Interactive Exploration of Metabolomics and Multi-Omics Data Open
The Omics Dashboard is a software tool for interactive exploration and analysis of metabolomics, transcriptomics, proteomics, and multi-omics datasets. Organized as a hierarchy of cellular systems, the Dashboard at its highest level contai…
View article: The EcoCyc Database (2023)
The EcoCyc Database (2023) Open
EcoCyc is a bioinformatics database available online at http://www.EcoCyc.org that describes the genome and the biochemical machinery of Escherichia coli K-12 MG1655. The long-term goal of the project is to describe the complete molecular …
View article: Erratum for Proctor et al., “Resources To Facilitate Use of the Altered Schaedler Flora (ASF) Mouse Model To Study Microbiome Function”
Erratum for Proctor et al., “Resources To Facilitate Use of the Altered Schaedler Flora (ASF) Mouse Model To Study Microbiome Function” Open
Volume 7, no. 5, e00293-22, 2022, https://doi.org/10.1128/mSystems.00293-22. In Table S1 in the supplemental material, the gBlock sequence for ASF# 492 is given incorrectly. The actual sequence is given in the revised file below.
View article: Resources to Facilitate Use of the Altered Schaedler Flora (ASF) Mouse Model to Study Microbiome Function
Resources to Facilitate Use of the Altered Schaedler Flora (ASF) Mouse Model to Study Microbiome Function Open
Improved experimental systems are needed to advance our understanding of how the gut microbiome influences processes of the mammalian host as well as microbial community structure and function. An approach that is receiving considerable at…
View article: Pathway Tools Management of Pathway/Genome Data for Microbial Communities
Pathway Tools Management of Pathway/Genome Data for Microbial Communities Open
The Pathway Tools (PTools) software provides a suite of capabilities for storing and analyzing integrated collections of genomic and metabolic information in the form of organism-specific Pathway/Genome Databases (PGDBs). A microbial commu…
View article: Plant Metabolic Network 15: A resource of genome‐wide metabolism databases for 126 plants and algae
Plant Metabolic Network 15: A resource of genome‐wide metabolism databases for 126 plants and algae Open
To understand and engineer plant metabolism, we need a comprehensive and accurate annotation of all metabolic information across plant species. As a step towards this goal, we generated genome‐scale metabolic pathway databases of 126 algal…
View article: The EcoCyc Database in 2021
The EcoCyc Database in 2021 Open
The EcoCyc model-organism database collects and summarizes experimental data for Escherichia coli K-12. EcoCyc is regularly updated by the manual curation of individual database entries, such as genes, proteins, and metabolic pathways, and…
View article: The BioCyc Metabolic Network Explorer
The BioCyc Metabolic Network Explorer Open
Background 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. Any metabolic network visualization tool must by ne…
View article: Plant Metabolic Network: A multi-species resource of plant metabolic information
Plant Metabolic Network: A multi-species resource of plant metabolic information Open
Plant metabolism is a pillar of our ecosystem, food security, and economy. To understand and engineer plant metabolism, we first need a comprehensive and accurate annotation of all metabolic information across plant species. As a step towa…
View article: Leveraging Curation Among Escherichia coli Pathway/Genome Databases Using Ortholog-Based Annotation Propagation
Leveraging Curation Among Escherichia coli Pathway/Genome Databases Using Ortholog-Based Annotation Propagation Open
Updating genome databases to reflect newly published molecular findings for an organism was hard enough when only a single strain of a given organism had been sequenced. With multiple sequenced strains now available for many organisms, the…
View article: Pathway Tools Visualization of Organism-Scale Metabolic Networks
Pathway Tools Visualization of Organism-Scale Metabolic Networks Open
Metabolomics, synthetic biology, and microbiome research demand information about organism-scale metabolic networks. The convergence of genome sequencing and computational inference of metabolic networks has enabled great progress toward s…
View article: The MetaCyc database of metabolic pathways and enzymes - a 2019 update
The MetaCyc database of metabolic pathways and enzymes - a 2019 update Open
MetaCyc (MetaCyc.org) is a comprehensive reference database of metabolic pathways and enzymes from all domains of life. It contains 2749 pathways derived from more than 60 000 publications, making it the largest curated collection of metab…
View article: Pathway Tools version 23.0 update: software for pathway/genome informatics and systems biology
Pathway Tools version 23.0 update: software for pathway/genome informatics and systems biology Open
Motivation Biological systems function through dynamic interactions among genes and their products, regulatory circuits and metabolic networks. Our development of the Pathway Tools software was motivated by the need to construct biological…
View article: The MultiOmics Explainer: explaining omics results in the context of a pathway/genome database
The MultiOmics Explainer: explaining omics results in the context of a pathway/genome database Open
The MultiOmics Explainer is a valuable tool that helps researchers understand and interpret the results of their omics experiments in the context of what is known about an organism's metabolic and regulatory network. It showcases the rich …
View article: A Comparison of Microbial Genome Web Portals
A Comparison of Microbial Genome Web Portals Open
Microbial genome web portals have a broad range of capabilities that address a number of information-finding and analysis needs for scientists. This article compares the capabilities of the major microbial genome web portals to aid researc…
View article: The EcoCyc Database
The EcoCyc Database Open
EcoCyc is a bioinformatics database available at EcoCyc.org that describes the genome and the biochemical machinery of Escherichia coli K-12 MG1655. The long-term goal of the project is to describe the complete molecular catalog of the E. …
View article: A Comparison of Microbial Genome Web Portals
A Comparison of Microbial Genome Web Portals Open
Microbial genome web portals have a broad range of capabilities that address a number of information-finding and analysis needs for scientists. This article compares the capabilities of the major microbial genome web portals to aid researc…
View article: The MetaCyc database of metabolic pathways and enzymes
The MetaCyc database of metabolic pathways and enzymes Open
MetaCyc (https://MetaCyc.org) is a comprehensive reference database of metabolic pathways and enzymes from all domains of life. It contains more than 2570 pathways derived from >54 000 publications, making it the largest curated collection…
View article: The Omics Dashboard for interactive exploration of gene-expression data
The Omics Dashboard for interactive exploration of gene-expression data Open
The Omics Dashboard is a software tool for interactive exploration and analysis of gene-expression datasets. The Omics Dashboard is organized as a hierarchy of cellular systems. At the highest level of the hierarchy the Dashboard contains …
View article: The BioCyc collection of microbial genomes and metabolic pathways
The BioCyc collection of microbial genomes and metabolic pathways Open
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. BioCy…
View article: Update notifications for the BioCyc collection of databases
Update notifications for the BioCyc collection of databases Open
https://BioCyc.org , https://EcoCyc.org , https://MetaCyc.org.