Plato's Cave Algorithm: Inferring Functional Signaling Networks from Early Gene Expression Shadows

How to Understand the Cell by Breaking It: Network Analysis of Gene Perturbation Screens

(2010) Florian Markowetz   PLoS Computational Biology

Analysis of Genetic Toggle Switch Systems Encoded on Plasmids

(2009) Adiel Loinger et al.   PHYSICAL REVIEW LETTERS

Stochastic Analysis of the SOS Response in Escherichia coli

(2009) Yishai Shimoni et al.   PLoS One

Genome-Scale Reconstruction of Escherichia coli's Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its Functional Characterization

(2009) Ines Thiele et al.   PLoS Computational Biology

Models from experiments: combinatorial drug perturbations of cancer cells

(2008) Sven Nelander et al.   Molecular Systems Biology

Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks

(2008) Jun Zhu et al.   NATURE GENETICS

Characterization of microRNA-regulated protein-protein interaction network

(2008) Chun-Wei Hsu et al.   PROTEOMICS