The spatial clustering of genes across different genomes has been used to study important problems in comparative genomics, from identification of operons to detection of homologo...
— We present an integrative method for clustering coregulated genes and elucidating their underlying regulatory mechanisms. We use multi-state partition functions and thermodynam...
Background: There has been a lot of interest in recent years focusing on the modeling and simulation of Gene Regulatory Networks (GRNs). However, the evolutionary mechanisms that ...
Abstract. This paper considers piecewise affine models of genetic regulatory networks and focuses on the problem of detecting switches among different modes of operation in gene e...
We present a novel classification-based algorithm called GeneClass for learning to predict gene regulatory response. Our approach is motivated by the hypothesis that in simple orga...
Manuel Middendorf, Anshul Kundaje, Chris Wiggins, ...