Integrating literature-constrained and data-driven inference of signalling networks

Extending pathways and processes using molecular interaction networks to analyse cancer genome data

(2011) Enrico Glaab et al.   BMC BIOINFORMATICS

Inferring signalling networks from longitudinal data using sampling based approaches in the R-package 'ddepn'

(2011) Christian Bender et al.   BMC BIOINFORMATICS

Crowdsourcing Network Inference: The DREAM Predictive Signaling Network Challenge

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

A Directed Protein Interaction Network for Investigating Intracellular Signal Transduction

(2011) A. Vinayagam et al.   Science Signaling

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

Logic-Based Models for the Analysis of Cell Signaling Networks

(2010) Melody K. Morris et al.   BIOCHEMISTRY

Systems analysis of EGF receptor signaling dynamics with microwestern arrays

(2010) Mark F Ciaccio et al.   NATURE METHODS

Pathway Commons, a web resource for biological pathway data

(2010) E. G. Cerami et al.   NUCLEIC ACIDS RESEARCH

A Boolean Approach to Linear Prediction for Signaling Network Modeling

(2010) Federica Eduati et al.   PLoS One

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

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

(2010) Florian Markowetz   PLoS Computational Biology

Mathematical Modelling of Cell-Fate Decision in Response to Death Receptor Engagement

(2010) Laurence Calzone et al.   PLoS Computational Biology

Protein–Protein Interactions Essentials: Key Concepts to Building and Analyzing Interactome Networks

(2010) Javier De Las Rivas et al.   PLoS Computational 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

The Logic of EGFR/ErbB Signaling: Theoretical Properties and Analysis of High-Throughput Data

(2009) Regina Samaga et al.   PLoS Computational Biology

minet: A R/Bioconductor Package for Inferring Large Transcriptional Networks Using Mutual Information

(2008) Patrick E Meyer et al.   BMC BIOINFORMATICS

Logic models of pathway biology

(2008) Steven Watterson et al.   DRUG DISCOVERY TODAY

Protein networks in disease

(2008) T. Ideker et al.   GENOME RESEARCH

Network inference using informative priors

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

Protein networking: insights into global functional organization of proteomes

(2008) Enrico Pieroni et al.   PROTEOMICS

WikiPathways: Pathway Editing for the People

(2008) Alexander R Pico et al.   PLOS BIOLOGY