4.7 Review

Pathway Tools version 23.0 update: software for pathway/genome informatics and systems biology

Related references

Note: Only part of the references are listed.
Article Biotechnology & Applied Microbiology

Candidatus Prosiliicoccus vernus, a spring phytoplankton bloom associated member of the Flavobacteriaceae

T. Ben Francis et al.

SYSTEMATIC AND APPLIED MICROBIOLOGY (2019)

Review Microbiology

A Comparison of Microbial Genome Web Portals

Peter D. Karp et al.

FRONTIERS IN MICROBIOLOGY (2019)

Article Microbiology

Metabolic route computation in organism communities

Markus Krummenacker et al.

MICROBIOME (2019)

Article Biochemistry & Molecular Biology

Using Pathway Covering to Explore Connections among Metabolites

Peter E. Midford et al.

METABOLITES (2019)

Article Biochemical Research Methods

The BioCyc collection of microbial genomes and metabolic pathways

Peter D. Karp et al.

BRIEFINGS IN BIOINFORMATICS (2019)

Article Mathematical & Computational Biology

Differential metabolic activity and discovery of therapeutic targets using summarized metabolic pathway models

Cankut Cubuk et al.

NPJ SYSTEMS BIOLOGY AND APPLICATIONS (2019)

Article Biochemistry & Molecular Biology

Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species

Paul Julian Kersey et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Biochemical Research Methods

Evaluation of reaction gap-filling accuracy by randomization

Mario Latendresse et al.

BMC BIOINFORMATICS (2018)

Article Food Science & Technology

Metagenomic and metatranscriptomic analysis of the microbial community in Swiss-type Maasdam cheese during ripening

Ilhan Cem Duru et al.

INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY (2018)

Letter Biotechnology & Applied Microbiology

KBase: The United States Department of Energy Systems Biology Knowledgebase

Adam P. Arkin et al.

NATURE BIOTECHNOLOGY (2018)

Article Biotechnology & Applied Microbiology

Food Spoilage-Associated Leuconostoc, Lactococcus, and Lactobacillus Species Display Different Survival Strategies in Response to Competition

Margarita Andreevskaya et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2018)

Article Biochemistry & Molecular Biology

IMG/M: integrated genome and metagenome comparative data analysis system

I-Min A. Chen et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Biochemistry & Molecular Biology

KEGG: new perspectives on genomes, pathways, diseases and drugs

Minoru Kanehisa et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Biochemistry & Molecular Biology

Genomewide landscape of gene-metabolome associations in Escherichia coli

Tobias Fuhrer et al.

MOLECULAR SYSTEMS BIOLOGY (2017)

Article Biochemistry & Molecular Biology

The Omics Dashboard for interactive exploration of gene-expression data

Suzanne Paley et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Multidisciplinary Sciences

A geographically-diverse collection of 418 human gut microbiome pathway genome databases

Aria S. Hahn et al.

SCIENTIFIC DATA (2017)

Article Mathematical & Computational Biology

A genome-scale metabolic flux model of Escherichia coli K-12 derived from the EcoCyc database

Daniel S. Weaver et al.

BMC SYSTEMS BIOLOGY (2014)

Article Biochemistry & Molecular Biology

PATRIC, the bacterial bioinformatics database and analysis resource

Alice R. Wattam et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Genetics & Heredity

The Pathway Tools Pathway Prediction Algorithm

Peter D. Karp et al.

STANDARDS IN GENOMIC SCIENCES (2011)

Article Biochemical Research Methods

Machine learning methods for metabolic pathway prediction

Joseph M. Dale et al.

BMC BIOINFORMATICS (2010)

Article Biochemical Research Methods

A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases

ML Green et al.

BMC BIOINFORMATICS (2004)