Network-based approaches for analysis of complex biological systems.
Cells function and respond to changes in their environment by the coordinated activity of their molecular components, including mRNAs, proteins and metabolites. At the heart of proper cellular function are molecular networks connecting these components to process extra-cellular environmental signals and drive dynamic, context-specific cellular responses. Network-based computational approaches aim to systematically integrate measurements from high-throughput experiments to gain a global understanding of cellular function under changing environmental conditions. We provide an overview of recent methodological developments toward solving two major computational problems within this field in the past two years (2013-2015): network reconstruction and network-based interpretation. Looking forward, we envision development of methods that can predict phenotypes with high accuracy as well as provide biologically plausible mechanistic hypotheses.
Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, United States.
Deborah
D
Chasman
Department of Computer Sciences, University of Wisconsin-Madison, Madison, WI 53706, United States; Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, United States; Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53792, United States.
Alireza
A
Fotuhi Siahpirani
Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, United States; Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53792, United States; Department of Computer Sciences, University of Wisconsin-Madison, Madison, WI 53706, United States. Electronic address: sroy@biostat.wisc.edu.
Sushmita
S
Roy
D000818:Animals; D002468:Cell Physiological Phenomena; D019295:Computational Biology / Q000379:methods*; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D006801:Humans; D010641:Phenotype