Bioinformatics publications
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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…
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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…
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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.
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The Genome Explorer Genome Browser
In this paper we report on a major update to our browser, Genome Explorer, that provides nearly instantaneous scaling and traversing of a genome, enabling users to quickly and easily…
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An Evaluation of ChatGPT and Bard (Gemini) in the Context of Biological Knowledge Retrieval
We evaluate the effectiveness of chatbots in retrieving biological knowledge for curation and research purposes.
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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.
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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.
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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…
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BioCyc: Metabolic Pathway Databases and Informatics Tools
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.
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Reviewing Knowledgebase and Database Grant Proposals in the Life Sciences: The Role of Innovation
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.
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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.
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Metabolic Modeling with MetaFlux
The MetaFlux software supports creating, executing, and solving quantitative metabolic flux models using flux balance analysis (FBA).