Unifying framework for data-driven pathway discovery

General info

Date from - to: 01 Jan 2004 - 20 Sep 2009
Project leader(s): Reinders, Marcel Prof. dr. ir.
Participant(s): Huynen, Martijn A. Prof. dr.; Holstege, Frank C.P. Prof. dr.; Wessels, Lodewyk Dr.

Abstract

This project concentrates on the development of generic tools that enable the discovery of (evolutionary conserved) pathways by exploiting the various ~omics data types. Besides integrating these different data, the project strives towards capturing pathways beyond the level of pair wise comparisons in order to find more complex relationships such as linear paths of interacting proteins (modelling signal transduction pathways) or dense clusters of interactions (modelling protein complexes). By studying which genes show co-occurrence, it is attempted to predict protein functions. Also the conservation of bi-directionally transcribed genes (in fungi) is used to yield insights in protein function.

Link to the end report of this project

Publications

Conservation of divergent transcription in fungi
M-PAS: a comprehensive and flexible metabolic pathway alignment and scoring method
Inference of logic networks from insertion and expression data
An integrative kernel method dealing with diverse measurement noise in classification
Discovering cooperating oncogenes by statistical co-occurence analysis
CCR4/NOT complex associates with the proteasome and regulates histone methylation
Evidence for emergence of diverse polioviruses from C-cluster coxsackie A viruses and implications for global poliovirus eradication
Classification in the presence of class noise using a probabilistic kernel fisher method
Integration of prior knowledge of measurement noise in kernel density classification
PhyloPat: an updated version of the phylogenetic pattern database contains gene neighborhood
Identification of cancer genes using a statistical framework for multiexperiment analysis of nondiscretized array CGH data
Evolution of closely linked gene pairs in vertebrate genomes
Towards a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae
Multiple sequence alignment
Biochemical characterization of arterivirus nonstructural protein 11 reveals the nidovirus-wide conservation of a replicative endoribonuclease
Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution
Protein complex prediction using an integrative bioinformatics approach
Asymmetric relationships between proteins shape genome evolution
Large-scale mutagenesis in p19(ARF)- and p53-deficient mice identifies cancer genes and their collaborative networks
Metabolic pathway alignment between species using a comprehensive and flexible similarity measure
BioVenn - a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams
Orthology prediction at scalable resolution by phylogenetic tree analysis
Testing statistical significance scores of sequence comparison methods with structure similarity
PhyloPat: phylogenetic pattern analysis of eukaryotic genes
Sequence similarity searches
Co-occurrence analysis of insertional mutagenesis data reveals cooperating oncogenes
Candidate cancer discovery using KC-SMART: a novel method for statistical multi-experiment aCGH data analysis
Sequence harmony: detecting functional specificity from alignments
The meaning of alignment: lessons from structural diversity