Abstract. We describe a probabilistic model, implemented as a dynamic Bayesian network, that can be used to predict nucleosome positioning along a chromosome based on one or more g...
Sheila M. Reynolds, Zhiping Weng, Jeff A. Bilmes, ...
Background: Genome sequences vary strongly in their repetitiveness and the causes for this are still debated. Here we propose a novel measure of genome repetitiveness, the index o...
Background: Identifying functional elements, such as transcriptional factor binding sites, is a fundamental step in reconstructing gene regulatory networks and remains a challengi...
Weichun Huang, David M. Umbach, Uwe Ohler, Leping ...
We develop a new framework for inferring models of transcriptional regulation. The models in this approach, which we call physical models, are constructed on the basis of verifiab...
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...