MicroScope—an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data

Distinct co-evolution patterns of genes associated to DNA polymerase III DnaE and PolC

(2012) Stefan Engelen et al.   BMC GENOMICS

Magnetosomes eliminate intracellular reactive oxygen species in Magnetospirillum gryphiswaldense MSR-1

(2012) Fang Fang Guo et al.   ENVIRONMENTAL MICROBIOLOGY

The Pathway Tools Pathway Prediction Algorithm

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

The CanOE Strategy: Integrating Genomic and Metabolic Contexts across Multiple Prokaryote Genomes to Find Candidate Genes for Orphan Enzymes

(2012) Adam Alexander Thil Smith et al.   PLoS Computational Biology

Chemical Evolution of a Bacterium’s Genome

(2011) Philippe Marlière et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Core and Panmetabolism in Escherichia coli

(2011) G. Vieira et al.   JOURNAL OF BACTERIOLOGY

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Rhea—a manually curated resource of biochemical reactions

(2011) Rafael Alcántara et al.   NUCLEIC ACIDS RESEARCH

InterPro in 2011: new developments in the family and domain prediction database

(2011) S. Hunter et al.   NUCLEIC ACIDS RESEARCH

Reorganizing the protein space at the Universal Protein Resource (UniProt)

(2011)   NUCLEIC ACIDS RESEARCH

NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

(2011) K. D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2011) R. Caspi et al.   NUCLEIC ACIDS RESEARCH

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Mutation Rate Inferred From Synonymous Substitutions in a Long-Term Evolution Experiment With Escherichia coli

(2011) Sébastien Wielgoss et al.   G3-Genes Genomes Genetics

Azospirillum Genomes Reveal Transition of Bacteria from Aquatic to Terrestrial Environments

(2011) Florence Wisniewski-Dyé et al.   PLoS Genetics

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

A protocol for generating a high-quality genome-scale metabolic reconstruction

(2010) Ines Thiele et al.   Nature Protocols

Structure, Function, and Evolution of the Thiomonas spp. Genome

(2010) Florence Arsène-Ploetze et al.   PLoS Genetics

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology

(2009) P. D. Karp et al.   BRIEFINGS IN BIOINFORMATICS

FIGfams: yet another set of protein families

(2009) Folker Meyer et al.   NUCLEIC ACIDS RESEARCH

MicroScope: a platform for microbial genome annotation and comparative genomics

(2009) D. Vallenet et al.   Database-The Journal of Biological Databases and Curation

NeMeSys: a biological resource for narrowing the gap between sequence and function in the human pathogen Neisseria meningitidis

(2009) Christophe Rusniok et al.   GENOME BIOLOGY

A complete collection of single-gene deletion mutants of Acinetobacter baylyi ADP1

(2008) Véronique de Berardinis et al.   Molecular Systems Biology