Genome-scale model of metabolism and gene expression provides a multi-scale description of acid stress responses in Escherichia coli

COBRAme: A computational framework for genome-scale models of metabolism and gene expression

(2018) Colton J. Lloyd et al.   PLoS Computational Biology

iML1515, a knowledgebase that computes Escherichia coli traits

(2017) Jonathan M Monk et al.   NATURE BIOTECHNOLOGY

solveME: fast and reliable solution of nonlinear ME models

(2016) Laurence Yang et al.   BMC BIOINFORMATICS

Identification of Genes Required for Growth of Escherichia coli MG1655 at Moderately Low pH

(2016) Bram Vivijs et al.   Frontiers in Microbiology

Principles of proteome allocation are revealed using proteomic data and genome-scale models

(2016) Laurence Yang et al.   Scientific Reports

The quantitative and condition-dependent Escherichia coli proteome

(2015) Alexander Schmidt et al.   NATURE BIOTECHNOLOGY

HdeB chaperone activity is coupled to its intrinsic dynamic properties

(2015) Jienv Ding et al.   Scientific Reports

Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale

(2014) Joanne K Liu et al.   BMC Systems Biology

Expanded microbial genome coverage and improved protein family annotation in the COG database

(2014) Michael Y. Galperin et al.   NUCLEIC ACIDS RESEARCH

Mechanisms of Acid Resistance inEscherichia coli

(2013) Usheer Kanjee et al.   Annual Review of Microbiology

Adaptive laboratory evolution – principles and applications for biotechnology

(2013) Martin Dragosits et al.   Microbial Cell Factories

Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction

(2013) E. J. O{middle dot}Brien et al.   Molecular Systems Biology

Consistent Estimation of Gibbs Energy Using Component Contributions

(2013) Elad Noor et al.   PLoS Computational Biology

Dissecting theEscherichia coliperiplasmic chaperone network using differential proteomics

(2012) Katleen Denoncin et al.   PROTEOMICS

Chaperone-dependent mechanisms for acid resistance in enteric bacteria

(2012) Weizhe Hong et al.   TRENDS IN MICROBIOLOGY

Molecular aspects of bacterial pH sensing and homeostasis

(2011) Terry A. Krulwich et al.   NATURE REVIEWS MICROBIOLOGY

Physical limits of cells and proteomes

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

Small RNAs and Small Proteins Involved in Resistance to Cell Envelope Stress and Acid Shock in Escherichia coli: Analysis of a Bar-Coded Mutant Collection

(2009) E. C. Hobbs et al.   JOURNAL OF BACTERIOLOGY

SURVIVAL AND GROWTH OF ACID ADAPTEDESCHERICHIA COLISTRAINS IN BROTH AT DIFFERENT PH LEVELS

(2009) BHEKISISA C. DLAMINI et al.   JOURNAL OF FOOD SAFETY

Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli

(2009) Bryson D Bennett et al.   Nature Chemical Biology

Computing protein stabilities from their chain lengths

(2009) K. Ghosh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interplay Between Intestinal pH, Transit Time and Feed Status on the In Vivo Performance of pH Responsive Ileo-Colonic Release Systems

(2008) Valentine C. Ibekwe et al.   PHARMACEUTICAL RESEARCH