Author: Peter Karp

  • 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.

  • 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 zoom into an area of interest.

  • 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.

  • 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.

  • 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.

  • 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.

  • 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.

  • Metabolic Modeling with MetaFlux 

    The MetaFlux software supports creating, executing, and solving quantitative metabolic flux models using flux balance analysis (FBA).