Inference of Quantitative Models of Bacterial Promoters from Time-Series Reporter Gene Data

Mass Spectrometry-based Workflow for Accurate Quantification ofEscherichia coliEnzymes: How Proteomics Can Play a Key Role in Metabolic Engineering

(2014) Mathieu Trauchessec et al.   MOLECULAR & CELLULAR PROTEOMICS

Small Regulatory RNAs in the Control of Motility and Biofilm Formation in E. coli and Salmonella

(2013) Franziska Mika et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Repression of Flagellar Genes in Exponential Phase by CsgD and CpxR, Two Crucial Modulators of Escherichia coli Biofilm Formation

(2013) O. Dudin et al.   JOURNAL OF BACTERIOLOGY

Reverse engineering and identification in systems biology: strategies, perspectives and challenges

(2013) A. F. Villaverde et al.   Journal of the Royal Society Interface

Promoters maintain their relative activity levels under different growth conditions

(2013) L. Keren et al.   Molecular Systems Biology

Dissecting specific and global transcriptional regulation of bacterial gene expression

(2013) L. Gerosa et al.   Molecular Systems Biology

Shared control of gene expression in bacteria by transcription factors and global physiology of the cell

(2013) S. Berthoumieux et al.   Molecular Systems Biology

A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis

(2013) Paola Picotti et al.   NATURE

Revisiting Global Gene Expression Analysis

(2012) Jakob Lovén et al.   CELL

On the identifiability of metabolic network models

(2012) Sara Berthoumieux et al.   JOURNAL OF MATHEMATICAL BIOLOGY

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

Studying and modelling dynamic biological processes using time-series gene expression data

(2012) Ziv Bar-Joseph et al.   NATURE REVIEWS GENETICS

Bacterial growth laws and their applications

(2011) Matthew Scott et al.   CURRENT OPINION IN BIOTECHNOLOGY

Identification of genetic network dynamics with unate structure

(2010) Riccardo Porreca et al.   BIOINFORMATICS

Experimental and computational validation of models of fluorescent and luminescent reporter genes in bacteria

(2010) Hidde de Jong et al.   BMC Systems Biology

EcoCyc: a comprehensive database of Escherichia coli biology

(2010) I. M. Keseler et al.   NUCLEIC ACIDS RESEARCH

Fluorescent Proteins and Their Applications in Imaging Living Cells and Tissues

(2010) Dmitriy M. Chudakov et al.   PHYSIOLOGICAL REVIEWS

Revealing strengths and weaknesses of methods for gene network inference

(2010) D. Marbach et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells

(2010) Y. Taniguchi et al.   SCIENCE

Growth Rate-Dependent Global Effects on Gene Expression in Bacteria

(2009) Stefan Klumpp et al.   CELL

Systems biology: parameter estimation for biochemical models

(2009) Maksat Ashyraliyev et al.   FEBS Journal

Correlation of mRNA and protein in complex biological samples

(2009) Tobias Maier et al.   FEBS LETTERS

Integrated modeling and experimental approach for determining transcription factor profiles from fluorescent reporter data

(2008) Zuyi Huang et al.   BMC Systems Biology

Molecular Titration and Ultrasensitivity in Regulatory Networks

(2008) Nicolas E. Buchler et al.   JOURNAL OF MOLECULAR BIOLOGY

Coordinating assembly of a bacterial macromolecular machine

(2008) Fabienne F. V. Chevance et al.   NATURE REVIEWS MICROBIOLOGY

Growth-rate-dependent partitioning of RNA polymerases in bacteria

(2008) S. Klumpp et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mathematical Analysis and Quantification of Fluorescent Proteins as Transcriptional Reporters

(2007) Xiao Wang et al.   BIOPHYSICAL JOURNAL