Integrative approaches for finding modular structure in biological networks

K Mitra, AR Carvunis, SK Ramesh, T Ideker - Nature Reviews Genetics, 2013 - nature.com
A central goal of systems biology is to elucidate the structural and functional architecture of
the cell. To this end, large and complex networks of molecular interactions are being rapidly …

Principles and methods of integrative genomic analyses in cancer

VN Kristensen, OC Lingjærde, HG Russnes… - Nature Reviews …, 2014 - nature.com
Combined analyses of molecular data, such as DNA copy-number alteration, mRNA and
protein expression, point to biological functions and molecular pathways being deregulated …

pathfindR: an R package for comprehensive identification of enriched pathways in omics data through active subnetworks

E Ulgen, O Ozisik, OU Sezerman - Frontiers in genetics, 2019 - frontiersin.org
Pathway analysis is often the first choice for studying the mechanisms underlying a
phenotype. However, conventional methods for pathway analysis do not take into account …

Fundamentals of protein interaction network mapping

J Snider, M Kotlyar, P Saraon, Z Yao… - Molecular systems …, 2015 - embopress.org
Studying protein interaction networks of all proteins in an organism (“interactomes”) remains
one of the major challenges in modern biomedicine. Such information is crucial to …

Identifying functional modules in protein–protein interaction networks: an integrated exact approach

MT Dittrich, GW Klau, A Rosenwald, T Dandekar… - …, 2008 - academic.oup.com
Motivation: With the exponential growth of expression and protein–protein interaction (PPI)
data, the frontier of research in systems biology shifts more and more to the integrated …

Brain neurotrauma: molecular, neuropsychological, and rehabilitation aspects

FH Kobeissy - 2015 - books.google.com
With the contribution from more than one hundred CNS neurotrauma experts, this book
provides a comprehensive and up-to-date account on the latest developments in the area of …

Toward the dynamic interactome: it's about time

TM Przytycka, M Singh, DK Slonim - Briefings in bioinformatics, 2010 - academic.oup.com
Dynamic molecular interactions play a central role in regulating the functioning of cells and
organisms. The availability of experimentally determined large-scale cellular networks …

Protein–protein interactions: detection, reliability assessment and applications

X Peng, J Wang, W Peng, FX Wu… - Briefings in …, 2017 - academic.oup.com
Protein–protein interactions (PPIs) participate in all important biological processes in living
organisms, such as catalyzing metabolic reactions, DNA replication, DNA transcription …

[图书][B] Computational systems biology of cancer

E Barillot, L Calzone, P Hupe, JP Vert, A Zinovyev - 2013 - api.taylorfrancis.com
Cancer is a complex and heterogeneous disease that exhibits high levels of robustness
against various therapeutic interventions. It is a constellation of diverse and evolving …

An integrative-omics approach to identify functional sub-networks in human colorectal cancer

RK Nibbe, M Koyutürk, MR Chance - PLoS computational biology, 2010 - journals.plos.org
Emerging evidence indicates that gene products implicated in human cancers often cluster
together in “hot spots” in protein-protein interaction (PPI) networks. Additionally, small sub …