Author: Ron Caspi
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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 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…
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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 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…
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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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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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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.
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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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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.
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Pathway Size Matters: The Influence of Pathway Granularity on Over-Representation (Enrichment) Statistics
We show that alternative pathway definitions can alter enrichment p -values by up to nine orders of magnitude, whereas statistical corrections typically alter enrichment p -values by only two orders of magnitude.
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Prediction of Selected Biosynthetic Pathways for the Lipopolysaccharide Components in Porphyromonas gingivalis
We use bioinformatics tools to predict biosynthetic pathways for the production of the normal (O-type) lipopolysaccharide in the W50 strain Porphyromonas gingivalis and compare the pathway with other putative pathways in fully sequenced and completed genomes of other pathogenic strains.
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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.
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The MetaCyc database of metabolic pathways and enzymes
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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The EcoCyc Database: Reflecting New Knowledge About Escherichia Coli K-12
New experimental discoveries about gene products, their function and regulation, new metabolic pathways, enzymes and cofactors are regularly added to EcoCyc.