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» Theoretical and Experimental DNA Computation
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BMCBI
2010
116views more  BMCBI 2010»
13 years 11 months ago
Predicting success of oligomerized pool engineering (OPEN) for zinc finger target site sequences
Background: Precise and efficient methods for gene targeting are critical for detailed functional analysis of genomes and regulatory networks and for potentially improving the eff...
Jeffry D. Sander, Deepak Reyon, Morgan L. Maeder, ...
SOFSEM
2012
Springer
12 years 6 months ago
Iterated Hairpin Completions of Non-crossing Words
Abstract. Iterated hairpin completion is an operation on formal languages that is inspired by the hairpin formation in DNA biochemistry. Iterated hairpin completion of a word (or m...
Lila Kari, Steffen Kopecki, Shinnosuke Seki
ICCS
2009
Springer
14 years 5 months ago
GPU Accelerated RNA Folding Algorithm
Many bioinformatics studies require the analysis of RNA or DNA structures. More specifically, extensive work is done to elaborate efficient algorithms able to predict the 2-D fold...
Guillaume Rizk, Dominique Lavenier
RECOMB
2005
Springer
14 years 11 months ago
An Interaction-Dependent Model for Transcription Factor Binding
Transcriptional regulation is accomplished by several transcription factor proteins that bind to specific DNA elements in the relative vicinity of the gene, and interact with each ...
Li-San Wang, Shane T. Jensen, Sridhar Hannenhalli
IPPS
2006
IEEE
14 years 4 months ago
Phylogenetic models of rate heterogeneity: a high performance computing perspective
Inference of phylogenetic trees using the maximum likelihood (ML) method is NP-hard. Furthermore, the computation of the likelihood function for huge trees of more than 1,000 orga...
Alexandros Stamatakis