Using graph theory to analyze biological networks

Computational approaches for detecting protein complexes from protein interaction networks: a survey

(2010) Xiaoli Li et al.   BMC GENOMICS

Generalized walks-based centrality measures for complex biological networks

(2010) Ernesto Estrada   JOURNAL OF THEORETICAL BIOLOGY

Network medicine: a network-based approach to human disease

(2010) Albert-László Barabási et al.   NATURE REVIEWS GENETICS

Signalling ballet in space and time

(2010) Boris N. Kholodenko et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

A reference guide for tree analysis and visualization

(2010) Georgios A Pavlopoulos et al.   BioData Mining

jClust: a clustering and visualization toolbox

(2009) G. A. Pavlopoulos et al.   BIOINFORMATICS

GIBA: a clustering tool for detecting protein complexes

(2009) Charalampos N Moschopoulos et al.   BMC BIOINFORMATICS

Markov clustering versus affinity propagation for the partitioning of protein interaction graphs

(2009) James Vlasblom et al.   BMC BIOINFORMATICS

The powerful law of the power law and other myths in network biology

(2009) Gipsi Lima-Mendez et al.   Molecular BioSystems

Evolution of biomolecular networks — lessons from metabolic and protein interactions

(2009) Takuji Yamada et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

CLUSTERING ALGORITHMS FOR DETECTING FUNCTIONAL MODULES IN PROTEIN INTERACTION NETWORKS

(2009) LIN GAO et al.   Journal of Bioinformatics and Computational Biology

Identifying gene-disease associations using centrality on a literature mined gene-interaction network

(2008) A. Ozgur et al.   BIOINFORMATICS

DroID: the Drosophila Interactions Database, a comprehensive resource for annotated gene and protein interactions

(2008) Jingkai Yu et al.   BMC GENOMICS

Arena3D: visualization of biological networks in 3D

(2008) Georgios A Pavlopoulos et al.   BMC Systems Biology

Survival of the sparsest: robust gene networks are parsimonious

(2008) Robert D Leclerc   Molecular Systems Biology

Teasing out the missing links

(2008) Sid Redner   NATURE

Reconstruction of biochemical networks in microorganisms

(2008) Adam M. Feist et al.   NATURE REVIEWS MICROBIOLOGY

Centrality, Network Capacity, and Modularity as Parameters to Analyze the Core-Periphery Structure in Metabolic Networks

(2008) M.R. da Silva et al.   PROCEEDINGS OF THE IEEE

Linear Motif Atlas for Phosphorylation-Dependent Signaling

(2008) M. L. Miller et al.   Science Signaling

Network Hubs Buffer Environmental Variation in Saccharomyces cerevisiae

(2008) Sasha F Levy et al.   PLOS BIOLOGY

Why Do Hubs in the Yeast Protein Interaction Network Tend To Be Essential: Reexamining the Connection between the Network Topology and Essentiality

(2008) Elena Zotenko et al.   PLoS Computational Biology

A survey of visualization tools for biological network analysis

(2008) Georgios A Pavlopoulos et al.   BioData Mining