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 ...
Background: Unraveling the mechanisms that regulate gene expression is a major challenge in biology. An important task in this challenge is to identify regulatory elements, especi...
In this paper we study a generalization of the classical notions of bordered and unbordered words, motivated by DNA computing. DNA strands can be viewed as finite strings over th...
Background: The discovery of cis-regulatory modules in metazoan genomes is crucial for understanding the connection between genes and organism diversity. It is important to quanti...
Saurabh Sinha, Mark D. Schroeder, Ulrich Unnerstal...
Abstract: With today’s available computer power, free energy calculations from equilibrium molecular dynamics simulations “via counting” become feasible for an increasing num...