Ron Caspi
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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: An evaluation of ChatGPT and Bard (Gemini) in the context of biological knowledge retrieval
An evaluation of ChatGPT and Bard (Gemini) in the context of biological knowledge retrieval Open
ChatGPT and Bard (now called Gemini), two conversational AI models developed by OpenAI and Google AI, respectively, have garnered considerable attention for their ability to engage in natural language conversations and perform various lang…
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: An Evaluation of ChatGPT and Bard (Gemini) in the Context of Biological Knowledge Retrieval
An Evaluation of ChatGPT and Bard (Gemini) in the Context of Biological Knowledge Retrieval Open
ChatGPT and Bard (now called Gemini), two conversational AI models developed by OpenAI and Google AI, respectively, have garnered considerable attention for their ability to engage in natural language conversations and perform various lang…
View article: An Evaluation of ChatGPT and Bard in the Context of Biological Knowledge Retrieval
An Evaluation of ChatGPT and Bard in the Context of Biological Knowledge Retrieval Open
ChatGPT and Bard, two conversational AI models developed by OpenAI and Google AI, respectively, have garnered considerable attention for their ability to engage in natural language conversations and perform various language-related tasks. …
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 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: 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: Prediction of Selected Biosynthetic Pathways for the Lipopolysaccharide Components in Porphyromonas gingivalis
Prediction of Selected Biosynthetic Pathways for the Lipopolysaccharide Components in Porphyromonas gingivalis Open
Porphyromonas gingivalis is an oral human pathogen. The bacterium destroys dental tissue and is a serious health problem worldwide. Experimental data and bioinformatic analysis revealed that the pathogen produces three types of lipopolysac…
View article: Additional file 2 of Pathway size matters: the influence of pathway granularity on over-representation (enrichment analysis) statistics
Additional file 2 of Pathway size matters: the influence of pathway granularity on over-representation (enrichment analysis) statistics Open
Additional file 2 R code to reproduce supplemental figures. Please set your R working directory (e.g., setwd()) to the location of the following two files. You may also need to load package matrixStat (e.g., library(matrixStat)) if this is…
View article: Additional file 4 of Pathway size matters: the influence of pathway granularity on over-representation (enrichment analysis) statistics
Additional file 4 of Pathway size matters: the influence of pathway granularity on over-representation (enrichment analysis) statistics Open
Additional file 4 Set of 69 similar KEGG and EcoCyc pathways, used to generate Supplement Figure S2.
View article: Additional file 3 of Pathway size matters: the influence of pathway granularity on over-representation (enrichment analysis) statistics
Additional file 3 of Pathway size matters: the influence of pathway granularity on over-representation (enrichment analysis) statistics Open
Additional file 3 Counts of EocCyc pathway genes used to generate supplement figures.
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 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: 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 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: The EcoCyc database: reflecting new knowledge about<i>Escherichia coli</i>K-12
The EcoCyc database: reflecting new knowledge about<i>Escherichia coli</i>K-12 Open
EcoCyc (EcoCyc.org) is a freely accessible, comprehensive database that collects and summarizes experimental data for Escherichia coli K-12, the best-studied bacterial model organism. New experimental discoveries about gene products, their…