Peter Midford
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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: Improved BioCyc Operon Prediction: Revisiting the Operon Prediction Problem
Improved BioCyc Operon Prediction: Revisiting the Operon Prediction Problem Open
Introduction Operon prediction is a valuable component of microbial-genome annotation because operon organization can yield inferences about gene function, and because knowledge of operon structure can aid the interpretation of gene expres…
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: 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: Taxonomic weighting improves the accuracy of a gap-filling algorithm for metabolic models
Taxonomic weighting improves the accuracy of a gap-filling algorithm for metabolic models Open
Motivation The increasing availability of annotated genome sequences enables construction of genome-scale metabolic networks, which are useful tools for studying organisms of interest. However, due to incomplete genome annotations, draft m…
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: The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes
The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes Open
Background A hierarchical taxonomy of organisms is a prerequisite for semantic integration of biodiversity data. Ideally, there would be a single, expansive, authoritative taxonomy that includes extinct and extant taxa, information on syno…
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: Using Pathway Covering to Explore Connections among Metabolites
Using Pathway Covering to Explore Connections among Metabolites Open
Interpreting changes in metabolite abundance in response to experimental treatments or disease states remains a major challenge in metabolomics. Pathway Covering is a new algorithm that takes a list of metabolites (compounds) and determine…
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 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: ISA Talk on Spider Behavior Ontology
ISA Talk on Spider Behavior Ontology Open
PDF export of slides from a talk about building an ontology for spider behavior given at the 2016 International Congress of Arachnology.
View article: An Ontology For Spider Behavior
An Ontology For Spider Behavior Open
PDF export of slides from a talk about building an ontology for spider behavior given at the 2016 International Congress of Arachnology.