Perturbation Biology: Inferring Signaling Networks in Cellular Systems

Drug Synergy Screen and Network Modeling in Dedifferentiated Liposarcoma Identifies CDK4 and IGF1R as Synergistic Drug Targets

(2013) M. L. Miller et al.   Science Signaling

AKT Inhibition Relieves Feedback Suppression of Receptor Tyrosine Kinase Expression and Activity

(2011) Sarat Chandarlapaty et al.   CANCER CELL

Resistance to BRAF Inhibitors: Unraveling Mechanisms and Future Treatment Options

(2011) J. Villanueva et al.   CANCER RESEARCH

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

Abiraterone and Increased Survival in Metastatic Prostate Cancer

(2011) Johann S. de Bono et al.   NEW ENGLAND JOURNAL OF MEDICINE

Concurrent loss of the PTEN and RB1 tumor suppressors attenuates RAF dependence in melanomas harboring V600EBRAF

(2011) F Xing et al.   ONCOGENE

Crowdsourcing Network Inference: The DREAM Predictive Signaling Network Challenge

(2011) R. J. Prill et al.   Science Signaling

Component-based construction of bio-pathway models: The parameter estimation problem

(2011) Geoffrey Koh et al.   THEORETICAL COMPUTER SCIENCE

Training Signaling Pathway Maps to Biochemical Data with Constrained Fuzzy Logic: Quantitative Analysis of Liver Cell Responses to Inflammatory Stimuli

(2011) Melody K. Morris et al.   PLoS Computational Biology

Inference of sparse combinatorial-control networks from gene-expression data: a message passing approach

(2010) Marc Bailly-Bechet et al.   BMC BIOINFORMATICS

Protein Dynamics in Drug Combinations: a Linear Superposition of Individual-Drug Responses

(2010) Naama Geva-Zatorsky et al.   CELL

Ligand-Specific c-Fos Expression Emerges from the Spatiotemporal Control of ErbB Network Dynamics

(2010) Takashi Nakakuki et al.   CELL

Rb-Raf-1 Interaction Disruptor RRD-251 Induces Apoptosis in Metastatic Melanoma Cells and Synergizes with Dacarbazine

(2010) S. Singh et al.   MOLECULAR CANCER THERAPEUTICS

Clinical efficacy of a RAF inhibitor needs broad target blockade in BRAF-mutant melanoma

(2010) Gideon Bollag et al.   NATURE

COT drives resistance to RAF inhibition through MAP kinase pathway reactivation

(2010) Cory M. Johannessen et al.   NATURE

Melanomas acquire resistance to B-RAF(V600E) inhibition by RTK or N-RAS upregulation

(2010) Ramin Nazarian et al.   NATURE

Multifaceted polo-like kinases: drug targets and antitargets for cancer therapy

(2010) Klaus Strebhardt   NATURE REVIEWS DRUG DISCOVERY

Gene Regulatory Networks from Multifactorial Perturbations Using Graphical Lasso: Application to the DREAM4 Challenge

(2010) Patricia Menéndez et al.   PLoS One

A Mitotic Phosphorylation Feedback Network Connects Cdk1, Plk1, 53BP1, and Chk2 to Inactivate the G2/M DNA Damage Checkpoint

(2010) Marcel A. T. M. van Vugt et al.   PLOS BIOLOGY

Identification of Crosstalk between Phosphoprotein Signaling Pathways in RAW 264.7 Macrophage Cells

(2010) Shakti Gupta et al.   PLoS Computational Biology

GeNGe: systematic generation of gene regulatory networks

(2009) Hendrik Hache et al.   BIOINFORMATICS

Reconstructing nonlinear dynamic models of gene regulation using stochastic sampling

(2009) Johanna Mazur et al.   BMC BIOINFORMATICS

Computational modeling of the EGFR network elucidates control mechanisms regulating signal dynamics

(2009) Dennis YQ Wang et al.   BMC Systems Biology

Genetic network identification using convex programming

(2009) A. Julius et al.   IET Systems Biology

Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction

(2009) Julio Saez-Rodriguez et al.   Molecular Systems Biology

V600EBRAF is associated with disabled feedback inhibition of RAF-MEK signaling and elevated transcriptional output of the pathway

(2009) C. A. Pratilas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Development of a Second-Generation Antiandrogen for Treatment of Advanced Prostate Cancer

(2009) C. Tran et al.   SCIENCE

A Factor Graph Nested Effects Model To Identify Networks from Genetic Perturbations

(2009) Charles J. Vaske et al.   PLoS Computational Biology

Single-Agent and Combination Therapeutic Strategies to Inhibit Hepatocyte Growth Factor/MET Signaling in Cancer

(2008) L. Toschi et al.   CLINICAL CANCER RESEARCH

On the Sparse Reconstruction of Gene Networks

(2008) M. Andrecut et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Inference algorithms for gene networks: a statistical mechanics analysis

(2008) A Braunstein et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Survival of the sparsest: robust gene networks are parsimonious

(2008) Robert D Leclerc   Molecular Systems Biology

Models from experiments: combinatorial drug perturbations of cancer cells

(2008) Sven Nelander et al.   Molecular Systems Biology

PI3K pathway alterations in cancer: variations on a theme

(2008) T L Yuan et al.   ONCOGENE

Extended Kalman Filter for Estimation of Parameters in Nonlinear State-Space Models of Biochemical Networks

(2008) Xiaodian Sun et al.   PLoS One