Using graph theory to analyze biological networks

GA Pavlopoulos, M Secrier, CN Moschopoulos… - BioData mining, 2011 - Springer
Understanding complex systems often requires a bottom-up analysis towards a systems
biology approach. The need to investigate a system, not only as individual components but …

Predicting protein function from sequence and structure

D Lee, O Redfern, C Orengo - Nature reviews molecular cell biology, 2007 - nature.com
While the number of sequenced genomes continues to grow, experimentally verified
functional annotation of whole genomes remains patchy. Structural genomics projects are …

High-quality binary protein interaction map of the yeast interactome network

H Yu, P Braun, MA Yıldırım, I Lemmens, K Venkatesan… - Science, 2008 - science.org
Current yeast interactome network maps contain several hundred molecular complexes with
limited and somewhat controversial representation of direct binary interactions. We carried …

Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system

DJ Hogan, DP Riordan, AP Gerber, D Herschlag… - PLoS …, 2008 - journals.plos.org
RNA-binding proteins (RBPs) have roles in the regulation of many post-transcriptional steps
in gene expression, but relatively few RBPs have been systematically studied. We searched …

Identification of essential proteins based on edge clustering coefficient

J Wang, M Li, H Wang, Y Pan - IEEE/ACM Transactions on …, 2011 - ieeexplore.ieee.org
Identification of essential proteins is key to understanding the minimal requirements for
cellular life and important for drug design. The rapid increase of available protein-protein …

The BioGRID interaction database: 2008 update

BJ Breitkreutz, C Stark, T Reguly, L Boucher… - Nucleic acids …, 2007 - academic.oup.com
Abstract The Biological General Repository for Interaction Datasets (BioGRID) database
(http://www. thebiogrid. org) was developed to house and distribute collections of protein …

Natural history and evolutionary principles of gene duplication in fungi

I Wapinski, A Pfeffer, N Friedman, A Regev - Nature, 2007 - nature.com
Gene duplication and loss is a powerful source of functional innovation. However, the
general principles that govern this process are still largely unknown. With the growing …

CORUM: the comprehensive resource of mammalian protein complexes

A Ruepp, B Brauner, I Dunger-Kaltenbach… - Nucleic acids …, 2007 - academic.oup.com
Protein complexes are key molecular entities that integrate multiple gene products to
perform cellular functions. The CORUM (http://mips. gsf. de/genre/proj/corum/index. html) …

A new essential protein discovery method based on the integration of protein-protein interaction and gene expression data

M Li, H Zhang, J Wang, Y Pan - BMC systems biology, 2012 - Springer
Background Identification of essential proteins is always a challenging task since it requires
experimental approaches that are time-consuming and laborious. With the advances in high …

Interaction landscape of membrane-protein complexes in Saccharomyces cerevisiae

M Babu, J Vlasblom, S Pu, X Guo, C Graham… - Nature, 2012 - nature.com
Macromolecular assemblies involving membrane proteins (MPs) serve vital biological roles
and are prime drug targets in a variety of diseases. Large-scale affinity purification studies of …