Network based elucidation of drug response: from modulators to targets

Transcriptional data: a new gateway to drug repositioning?

(2012) Francesco Iorio et al.   DRUG DISCOVERY TODAY

Id proteins synchronize stemness and anchorage to the niche of neural stem cells

(2012) Francesco Niola et al.   NATURE CELL BIOLOGY

Boolean modeling in systems biology: an overview of methodology and applications

(2012) Rui-Sheng Wang et al.   PHYSICAL BIOLOGY

Versatile pathway-centric approach based on high-throughput sequencing to anticancer drug discovery

(2012) H. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Using Functional Signatures to Identify Repositioned Drugs for Breast, Myelogenous Leukemia and Prostate Cancer

(2012) Daichi Shigemizu et al.   PLoS Computational Biology

Exploiting drug-disease relationships for computational drug repositioning

(2011) J. T. Dudley et al.   BRIEFINGS IN BIOINFORMATICS

mRNA Expression Signatures of Human Skeletal Muscle Atrophy Identify a Natural Compound that Increases Muscle Mass

(2011) Steven D. Kunkel et al.   Cell Metabolism

Transcriptional gene network inference from a massive dataset elucidates transcriptome organization and gene function

(2011) Vincenzo Belcastro et al.   NUCLEIC ACIDS RESEARCH

Dynamical and Structural Analysis of a T Cell Survival Network Identifies Novel Candidate Therapeutic Targets for Large Granular Lymphocyte Leukemia

(2011) Assieh Saadatpour et al.   PLoS Computational Biology

Identification of small molecules enhancing autophagic function from drug network analysis

(2010) Francesco Iorio et al.   Autophagy

Two additive mechanisms impair the differentiation of 'substrate-selective' p38 inhibitors from classical p38 inhibitors in vitro

(2010) Bart S Hendriks et al.   BMC Systems Biology

Identification of Optimal Drug Combinations Targeting Cellular Networks: Integrating Phospho-Proteomics and Computational Network Analysis

(2010) S. Iadevaia et al.   CANCER RESEARCH

Functional pathway pharmacology: chemical tools, pathway knowledge and mechanistic model-based interpretation of experimental data

(2010) Bart S Hendriks   CURRENT OPINION IN CHEMICAL BIOLOGY

Model-based method for transcription factor target identification with limited data

(2010) Antti Honkela et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Discovery of drug mode of action and drug repositioning from transcriptional responses

(2010) F. Iorio et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Modeling ERBB receptor-regulated G1/S transition to find novel targets for de novo trastuzumab resistance

(2009) Özgür Sahin et al.   BMC Systems Biology

Molecular networks as sensors and drivers of common human diseases

(2009) Eric E. Schadt   NATURE

The transcriptional network for mesenchymal transformation of brain tumours

(2009) Maria Stella Carro et al.   NATURE

Human Disease-Drug Network Based on Genomic Expression Profiles

(2009) Guanghui Hu et al.   PLoS One

Logic models of pathway biology

(2008) Steven Watterson et al.   DRUG DISCOVERY TODAY

Direct targets of the TRP63 transcription factor revealed by a combination of gene expression profiling and reverse engineering

(2008) G. Della Gatta et al.   GENOME RESEARCH

Drug Target Identification Using Side-Effect Similarity

(2008) M. Campillos et al.   SCIENCE