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BRANE Cut: Biologically-Related Apriori Network Enhancement with Graph cuts

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[ BRANE Cut featured on RNA-Seq blog ][ Omic tools ][ bioRxiv preprint ][ PubMed/Biomed Central ][ BRANE Cut code ][ BRANE Omics ] Gene regulatory networks are somehow difficult to infer. This first work from an on-going work on BRANE Omics (termed BRANE *, for B iologically R elated A priori N etwok E nhancement) introduces an optimization method (based on Graph cuts, borrowed from computer vision/image processing) to infer graphs based on biologically-related a priori (including sparsity). It is succesfully tested on DREAM challenge data and an Escherichia coli network, with a specific work to derive optimization parameters from gene network cardinality properties. And it is quite fast. BRANE Cut: Biologically-Related Apriori Network Enhancement with Graph cuts for Gene Regulatory Network inference ( doi , BRANE Cut webpage , preprint ) Background : Inferring gene networks from high-throughput data constitutes an important step in the discovery of relevant regulat