Modelling microbial metabolic rewiring during growth in a complex medium

Metabolic network architecture and carbon source determine metabolite production costs

(2016) Silvio Waschina et al.   FEBS Journal

Insights into pH-induced metabolic switch by flux balance analysis

(2015) Marija Ivarsson et al.   BIOTECHNOLOGY PROGRESS

In silico evolution of diauxic growth

(2015) Dominique F. Chu   BMC EVOLUTIONARY BIOLOGY

Predicting internal cell fluxes at sub-optimal growth

(2015) André Schultz et al.   BMC Systems Biology

The MEME Suite

(2015) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Genome-scale metabolic reconstruction and constraint-based modelling of the Antarctic bacteriumPseudoalteromonas haloplanktis TAC125

(2014) Marco Fondi et al.   ENVIRONMENTAL MICROBIOLOGY

DMINDA: an integrated web server for DNA motif identification and analyses

(2014) Qin Ma et al.   NUCLEIC ACIDS RESEARCH

The Central Metabolism Regulator EIIA Glc Switches Salmonella from Growth Arrest to Acute Virulence through Activation of Virulence Factor Secretion

(2014) Alain Mazé et al.   Cell Reports

Saccharopolyspora erythraea’s genome is organised in high-order transcriptional regions mediated by targeted degradation at the metabolic switch

(2013) Esteban Marcellin et al.   BMC GENOMICS

RegTransBase – a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes

(2013) Michael J Cipriano et al.   BMC GENOMICS

RegPrecise 3.0 – A resource for genome-scale exploration of transcriptional regulation in bacteria

(2013) Pavel S Novichkov et al.   BMC GENOMICS

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

(2013) Ali Ebrahim et al.   BMC Systems Biology

CollecTF: a database of experimentally validated transcription factor-binding sites in Bacteria

(2013) Sefa Kılıç et al.   NUCLEIC ACIDS RESEARCH

Unconventional microbial systems for the cost-efficient production of high-quality protein therapeutics

(2012) José Luis Corchero et al.   BIOTECHNOLOGY ADVANCES

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

(2011) Jan Schellenberger et al.   Nature Protocols

Metabolomic analysis of a synthetic metabolic switch in Streptomyces coelicolor A3(2)

(2011) Andris Jankevics et al.   PROTEOMICS

Cytoplasmic and Periplasmic Proteomic Signatures of Exponentially Growing Cells of the Psychrophilic BacteriumPseudoalteromonas haloplanktisTAC125

(2010) Boris Wilmes et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor

(2010) Mohammad T Alam et al.   BMC GENOMICS

Fed-batch process for the psychrotolerant marine bacterium Pseudoalteromonas haloplanktis

(2010) Boris Wilmes et al.   Microbial Cell Factories

A metabolic switch is involved in lifestyle decisions in Photorhabdus luminescens

(2010) Lea Lango et al.   MOLECULAR MICROBIOLOGY

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

(2010) D. Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

DOOR: a database for prokaryotic operons

(2008) Fenglou Mao et al.   NUCLEIC ACIDS RESEARCH

PRODORIC (release 2009): a database and tool platform for the analysis of gene regulation in prokaryotes

(2008) A. Grote et al.   NUCLEIC ACIDS RESEARCH