Network‐based prediction of protein function

R Sharan, I Ulitsky, R Shamir - Molecular systems biology, 2007 - embopress.org
Functional annotation of proteins is a fundamental problem in the post‐genomic era. The
recent availability of protein interaction networks for many model species has spurred on the …

Large‐scale map** of human protein–protein interactions by mass spectrometry

RM Ewing, P Chu, F Elisma, H Li, P Taylor… - Molecular systems …, 2007 - embopress.org
Map** protein–protein interactions is an invaluable tool for understanding protein
function. Here, we report the first large‐scale study of protein–protein interactions in human …

KIT and RAS signalling pathways in testicular germ cell tumours: new data and a review of the literature

NC Goddard, A McIntyre, B Summersgill… - … journal of andrology, 2007 - Wiley Online Library
Testicular germ cell tumours (TGCTs) are the leading cause of cancer deaths in young male
Caucasians. Identifying changes in DNA copy number can pinpoint genes involved in …

Identification of functional modules using network topology and high-throughput data

I Ulitsky, R Shamir - BMC systems biology, 2007 - Springer
Background With the advent of systems biology, biological knowledge is often represented
today by networks. These include regulatory and metabolic networks, protein-protein …

Global networks of functional coupling in eukaryotes from comprehensive data integration

A Alexeyenko, ELL Sonnhammer - Genome research, 2009 - genome.cshlp.org
No single experimental method can discover all connections in the interactome. A
computational approach can help by integrating data from multiple, often unrelated …

HAPPI: an online database of comprehensive human annotated and predicted protein interactions

JY Chen, SR Mamidipalli, T Huan - BMC genomics, 2009 - Springer
Background Human protein-protein interaction (PPIs) data are the foundation for
understanding molecular signalling networks and the functional roles of biomolecules …

Resampling methods for parameter-free and robust feature selection with mutual information

D François, F Rossi, V Wertz, M Verleysen - Neurocomputing, 2007 - Elsevier
Combining the mutual information criterion with a forward feature selection strategy offers a
good trade-off between optimality of the selected feature subset and computation time …

Activation of the osteopontin/matrix metalloproteinase-9 pathway correlates with prostate cancer progression

G Castellano, G Malaponte, MC Mazzarino… - Clinical Cancer …, 2008 - aacrjournals.org
Purpose: Prostate cancer remains the second most frequent cause of tumor-related deaths
in the Western world. Additional markers for the identification of prostate cancer …

Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression

S De Bodt, S Proost, K Vandepoele, P Rouzé… - BMC genomics, 2009 - Springer
Background Large-scale identification of the interrelationships between different
components of the cell, such as the interactions between proteins, has recently gained great …

Dosage sensitivity shapes the evolution of copy-number varied regions

B Schuster-Böckler, D Conrad, A Bateman - PloS one, 2010 - journals.plos.org
Dosage sensitivity is an important evolutionary force which impacts on gene dispensability
and duplicability. The newly available data on human copy-number variation (CNV) allow an …