iML1515, a knowledgebase that computes Escherichia coli traits

Systems biology of the structural proteome

(2016) Elizabeth Brunk et al.   BMC Systems Biology

Strain-level microbial epidemiology and population genomics from shotgun metagenomics

(2016) Matthias Scholz et al.   NATURE METHODS

Using Genome-scale Models to Predict Biological Capabilities

(2015) Edward J. O’Brien et al.   CELL

Bio-based production of monomers and polymers by metabolically engineered microorganisms

(2015) Hannah Chung et al.   CURRENT OPINION IN BIOTECHNOLOGY

The quantitative and condition-dependent Escherichia coli proteome

(2015) Alexander Schmidt et al.   NATURE BIOTECHNOLOGY

Model-driven discovery of underground metabolic functions inEscherichia coli

(2015) Gabriela I. Guzmán et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbial Forensics: Predicting Phenotypic Characteristics and Environmental Conditions from Large-Scale Gene Expression Profiles

(2015) Minseung Kim et al.   PLoS Computational Biology

Colony-live —a high-throughput method for measuring microbial colony growth kinetics— reveals diverse growth effects of gene knockouts in Escherichia coli

(2014) Rikiya Takeuchi et al.   BMC MICROBIOLOGY

Large-scale genomic sequencing of extraintestinal pathogenicEscherichia colistrains

(2014) Stephen J. Salipante et al.   GENOME RESEARCH

Sulphoglycolysis in Escherichia coli K-12 closes a gap in the biogeochemical sulphur cycle

(2014) Karin Denger et al.   NATURE

Optimizing genome-scale network reconstructions

(2014) Jonathan Monk et al.   NATURE BIOTECHNOLOGY

Identification of enterotoxigenic Escherichia coli (ETEC) clades with long-term global distribution

(2014) Astrid von Mentzer et al.   NATURE GENETICS

Network-level architecture and the evolutionary potential of underground metabolism

(2014) R. A. Notebaart et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Antibacterial mechanisms identified through structural systems pharmacology

(2013) Roger L Chang et al.   BMC Systems Biology

Gut metagenome in European women with normal, impaired and diabetic glucose control

(2013) Fredrik H. Karlsson et al.   NATURE

Potentiating antibacterial activity by predictably enhancing endogenous microbial ROS production

(2013) Mark P Brynildsen et al.   NATURE BIOTECHNOLOGY

Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments

(2013) J. M. Monk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural Systems Biology Evaluation of Metabolic Thermotolerance in Escherichia coli

(2013) R. L. Chang et al.   SCIENCE

A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011

(2011) J. D. Orth et al.   Molecular Systems Biology

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

(2011) Jan Schellenberger et al.   Nature Protocols

Discovery of the curcumin metabolic pathway involving a unique enzyme in an intestinal microorganism

(2011) A. Hassaninasab et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systematizing the generation of missing metabolic knowledge

(2010) Jeffrey D. Orth et al.   BIOTECHNOLOGY AND BIOENGINEERING

Comparison of 61 Sequenced Escherichia coli Genomes

(2010) Oksana Lukjancenko et al.   MICROBIAL ECOLOGY

Update on the Keio collection of Escherichia coli single-gene deletion mutants

(2009) Natsuko Yamamoto et al.   Molecular Systems Biology

GrowMatch: An Automated Method for Reconciling In Silico/In Vivo Growth Predictions

(2009) Vinay Satish Kumar et al.   PLoS Computational Biology