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» Revisiting the Sequence Constraint
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BMCBI
2008
90views more  BMCBI 2008»
15 years 2 months ago
Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation
Background: The rate of mRNA transcription is controlled by transcription factors that bind to specific DNA motifs in promoter regions upstream of protein coding genes. Recent res...
Jakub Orzechowski Westholm, Feifei Xu, Hans Ronne,...
BMCBI
2007
109views more  BMCBI 2007»
15 years 2 months ago
A cis-regulatory logic simulator
Background: A major goal of computational studies of gene regulation is to accurately predict the expression of genes based on the cis-regulatory content of their promoters. The d...
Robert D. Zeigler, Jason Gertz, Barak A. Cohen
BMCBI
2008
142views more  BMCBI 2008»
15 years 2 months ago
Strategies for measuring evolutionary conservation of RNA secondary structures
Background: Evolutionary conservation of RNA secondary structure is a typical feature of many functional non-coding RNAs. Since almost all of the available methods used for predic...
Andreas R. Gruber, Stephan H. F. Bernhart, Ivo L. ...
MP
2006
138views more  MP 2006»
15 years 1 months ago
A new ILP-based refinement heuristic for Vehicle Routing Problems
In the paper we address the Distance-Constrained Capacitated Vehicle Routing Problem (DCVRP), where k minimum-cost routes through a central depot have to be constructed so as to co...
Roberto De Franceschi, Matteo Fischetti, Paolo Tot...
TSE
2008
107views more  TSE 2008»
15 years 1 months ago
Interface Grammars for Modular Software Model Checking
We propose an interface specification language based on grammars for modular software model checking. In our interface specification language, component interfaces are specified a...
Graham Hughes, Tevfik Bultan