Automatic Generation of Predictive Dynamic Models Reveals Nuclear Phosphorylation as the Key Msn2 Control Mechanism

Tunable Signal Processing Through Modular Control of Transcription Factor Translocation

(2013) N. Hao et al.   SCIENCE

An integrated image analysis platform to quantify signal transduction in single cells

(2012) Serge Pelet et al.   Integrative Biology

Cellular Noise Regulons Underlie Fluctuations in Saccharomyces cerevisiae

(2012) Jacob Stewart-Ornstein et al.   MOLECULAR CELL

Computational Approaches for Analyzing Information Flow in Biological Networks

(2012) B. Kholodenko et al.   Science Signaling

A Dynamic Network Model of mTOR Signaling Reveals TSC-Independent mTORC2 Regulation

(2012) P. Dalle Pezze et al.   Science Signaling

How Do Control-Based Approaches Enter into Biology?

(2011) Philip R LeDuc et al.   Annual Review of Biomedical Engineering

A simple work flow for biologically inspired model reduction - application to early JAK-STAT signaling

(2011) Tom Quaiser et al.   BMC Systems Biology

A method for zooming of nonlinear models of biochemical systems

(2011) Mikael Sunnåker et al.   BMC Systems Biology

Efficient characterization of high-dimensional parameter spaces for systems biology

(2011) Elías Zamora-Sillero et al.   BMC Systems Biology

Signal-dependent dynamics of transcription factor translocation controls gene expression

(2011) Nan Hao et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Geometry of nonlinear least squares with applications to sloppy models and optimization

(2011) Mark K. Transtrum et al.   PHYSICAL REVIEW E

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments

(2010) Brendan MacLean et al.   BIOINFORMATICS

Understanding the temporal codes of intra-cellular signals

(2010) Marcelo Behar et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Cytosolic pH is a second messenger for glucose and regulates the PKA pathway through V-ATPase

(2010) Reinhard Dechant et al.   EMBO JOURNAL

Classic and contemporary approaches to modeling biochemical reactions

(2010) W. W. Chen et al.   GENES & DEVELOPMENT

Inferring Signaling Pathway Topologies from Multiple Perturbation Measurements of Specific Biochemical Species

(2010) T.-R. Xu et al.   Science Signaling

Parameter Estimation and Model Selection in Computational Biology

(2010) Gabriele Lillacci et al.   PLoS Computational Biology

Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood

(2009) A. Raue et al.   BIOINFORMATICS

Differential localization to cytoplasm, nucleus or P-bodies of yeast PKA subunits under different growth conditions

(2009) V. Tudisca et al.   EUROPEAN JOURNAL OF CELL BIOLOGY

Systems analysis of cellular networks under uncertainty

(2009) Hans-Michael Kaltenbach et al.   FEBS LETTERS

‘Glocal’ Robustness Analysis and Model Discrimination for Circadian Oscillators

(2009) Marc Hafner et al.   PLoS Computational Biology

Complexity reduction of biochemical rate expressions

(2008) Henning Schmidt et al.   BIOINFORMATICS

Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems

(2008) T. Toni et al.   Journal of the Royal Society Interface

Selected reaction monitoring for quantitative proteomics: a tutorial

(2008) Vinzenz Lange et al.   Molecular Systems Biology

Frequency-modulated nuclear localization bursts coordinate gene regulation

(2008) Long Cai et al.   NATURE