Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks

Integrated cellular network of transcription regulations and protein-protein interactions

(2012) Yu-Chao Wang et al.   BMC Systems Biology

Elementary signaling modes predict the essentiality of signal transduction network components

(2011) Rui-Sheng Wang et al.   BMC Systems Biology

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

A Bow-Tie Genetic Architecture for Morphogenesis Suggested by a Genome-Wide RNAi Screen in Caenorhabditis elegans

(2011) Matthew D. Nelson et al.   PLoS Genetics

Logic-Based Models for the Analysis of Cell Signaling Networks

(2010) Melody K. Morris et al.   BIOCHEMISTRY

Construction of a large scale integrated map of macrophage pathogen recognition and effector systems

(2010) Sobia Raza et al.   BMC Systems Biology

Caveolin-1 regulates EGFR signalling in MCF-7 breast cancer cells and enhances gefitinib-induced tumor cell inhibition

(2010) Sophia Agelaki et al.   CANCER BIOLOGY & THERAPY

EGF-induced MAPK Signaling Inhibits Hemidesmosome Formation through Phosphorylation of the Integrin β4

(2010) Evelyne Frijns et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Networks Inferred from Biochemical Data Reveal Profound Differences in Toll-like Receptor and Inflammatory Signaling between Normal and Transformed Hepatocytes

(2010) Leonidas G. Alexopoulos et al.   MOLECULAR & CELLULAR PROTEOMICS

Interactome under construction

(2010) Laura Bonetta   NATURE

The BioPAX community standard for pathway data sharing

(2010) Emek Demir et al.   NATURE BIOTECHNOLOGY

A human MAP kinase interactome

(2010) Sourav Bandyopadhyay et al.   NATURE METHODS

Pathway Commons, a web resource for biological pathway data

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

Automated Network Analysis Identifies Core Pathways in Glioblastoma

(2010) Ethan Cerami et al.   PLoS One

Event extraction for systems biology by text mining the literature

(2010) Sophia Ananiadou et al.   TRENDS IN BIOTECHNOLOGY

BowTieBuilder: modeling signal transduction pathways

(2009) Jochen Supper et al.   BMC Systems Biology

Defining Network Topologies that Can Achieve Biochemical Adaptation

(2009) Wenzhe Ma et al.   CELL

On the basic computational structure of gene regulatory networks

(2009) Carlos Rodríguez-Caso et al.   Molecular BioSystems

G-Protein Coupled Receptor Signaling Architecture of Mammalian Immune Cells

(2009) Natalia Polouliakh et al.   PLoS One

Integrating Proteomic, Transcriptional, and Interactome Data Reveals Hidden Components of Signaling and Regulatory Networks

(2009) S.-s. C. Huang et al.   Science Signaling

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

(2009) Regina Samaga et al.   PLoS Computational Biology

A global pathway crosstalk network

(2008) Yong Li et al.   BIOINFORMATICS

Pathways connecting inflammation and cancer

(2008) Paola Allavena et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Literature-curated protein interaction datasets

(2008) Michael E Cusick et al.   NATURE METHODS

STRING 8--a global view on proteins and their functional interactions in 630 organisms

(2008) L. J. Jensen et al.   NUCLEIC ACIDS RESEARCH

Evolution of Complex Modular Biological Networks

(2008) Arend Hintze et al.   PLoS Computational Biology

Emergent decision-making in biological signal transduction networks

(2008) T. Helikar 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

Core Signaling Pathways in Human Pancreatic Cancers Revealed by Global Genomic Analyses

(2008) S. Jones et al.   SCIENCE

An Integrated Genomic Analysis of Human Glioblastoma Multiforme

(2008) D. W. Parsons et al.   SCIENCE