We define a new fixpoint modal logic, the visibly pushdown ?-calculus (VP-?), as an extension of the modal ?-calculus. The models of this logic are execution trees of structured p...
Abstract. With ever increasing amount of available data on protein-protein interaction (PPI) networks and research revealing that these networks evolve at a modular level, discover...
Abstract. In order to guarantee that the optimal motif is found, traditional pattern-driven approaches perform an exhaustive search over all candidate motifs of length l. We develo...
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, ...
motif discovery problem abstracts the task of discovering short, conserved sites in genomic DNA. Pevzner and Sze recently described a precise combinatorial formulation of motif di...