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BMCBI
2006
116views more  BMCBI 2006»
15 years 6 months ago
Optimized mixed Markov models for motif identification
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 ...
BMCBI
2007
247views more  BMCBI 2007»
15 years 6 months ago
A survey of DNA motif finding algorithms
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...
Modan K. Das, Ho-Kwok Dai
IJFCS
2007
111views more  IJFCS 2007»
15 years 6 months ago
Involutively Bordered Words
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...
Lila Kari, Kalpana Mahalingam
BMCBI
2004
150views more  BMCBI 2004»
15 years 6 months ago
Cross-species comparison significantly improves genome-wide prediction of cis-regulatory modules in Drosophila
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...
JCC
2011
87views more  JCC 2011»
15 years 1 months ago
Determining equilibrium constants for dimerization reactions from molecular dynamics simulations
Abstract: With today’s available computer power, free energy calculations from equilibrium molecular dynamics simulations “via counting” become feasible for an increasing num...
Djurre H. De Jong, Lars V. Schäfer, Alex H. D...