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

A Comparison of Microbial Genome Web Portals

(2019) Peter D. Karp et al.   Frontiers in Microbiology

Metabolic route computation in organism communities

(2019) Markus Krummenacker et al.   Microbiome

Using Pathway Covering to Explore Connections among Metabolites

(2019) Peter E. Midford et al.   Metabolites

Evaluation of reaction gap-filling accuracy by randomization

(2018) Mario Latendresse et al.   BMC BIOINFORMATICS

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

(2018) Ilhan Cem Duru et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

KBase: The United States Department of Energy Systems Biology Knowledgebase

(2018) Adam P Arkin et al.   NATURE BIOTECHNOLOGY

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

(2018) Margarita Andreevskaya et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2018) T. Ben Francis et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris

(2017) Sarah Schatschneider et al.   MICROBIOLOGY-SGM

Genomewide landscape of gene–metabolome associations in Escherichia coli

(2017) Tobias Fuhrer et al.   Molecular Systems Biology

The Omics Dashboard for interactive exploration of gene-expression data

(2017) Suzanne Paley et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Paul Julian Kersey et al.   NUCLEIC ACIDS RESEARCH

Rapid Sampling of Escherichia coli After Changing Oxygen Conditions Reveals Transcriptional Dynamics

(2017) Joachim von Wulffen et al.   Genes

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

(2017) Aria S. Hahn et al.   Scientific Data

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

(2016) I-Min A. Chen et al.   NUCLEIC ACIDS RESEARCH

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

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report

(2016)   Microbiome

Metabolomics Workbench: An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools

(2015) Manish Sud et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Daniel S Weaver et al.   BMC Systems Biology

PATRIC, the bacterial bioinformatics database and analysis resource

(2013) Alice R. Wattam et al.   NUCLEIC ACIDS RESEARCH

The Pathway Tools Pathway Prediction Algorithm

(2012) Peter D. Karp et al.   Standards in Genomic Sciences

Machine learning methods for metabolic pathway prediction

(2010) Joseph M Dale et al.   BMC BIOINFORMATICS