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» Topology and prediction of RNA pseudoknots
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BMCBI
2010
175views more  BMCBI 2010»
13 years 4 months ago
Towards high performance computing for molecular structure prediction using IBM Cell Broadband Engine - an implementation perspe
Background: RNA structure prediction problem is a computationally complex task, especially with pseudo-knots. The problem is well-studied in existing literature and predominantly ...
S. P. T. Krishnan, Sim Sze Liang, Bharadwaj Veerav...
TCBB
2010
114views more  TCBB 2010»
13 years 3 months ago
Cache-Oblivious Dynamic Programming for Bioinformatics
— We present efficient cache-oblivious algorithms for some well-studied string problems in bioinformatics including the longest common subsequence, global pairwise sequence alig...
Rezaul Alam Chowdhury, Hai-son Le, Vijaya Ramachan...
BMCBI
2006
82views more  BMCBI 2006»
13 years 4 months ago
Selection of antisense oligonucleotides based on multiple predicted target mRNA structures
Background: Local structures of target mRNAs play a significant role in determining the efficacies of antisense oligonucleotides (ODNs), but some structure-based target site selec...
Xiaochen Bo, Shaoke Lou, Daochun Sun, Wenjie Shu, ...
RECOMB
2007
Springer
14 years 5 months ago
Reconstructing the Topology of Protein Complexes
Abstract. Recent advances in high-throughput experimental techniques have enabled the production of a wealth of protein interaction data, rich in both quantity and variety. While t...
Allister Bernard, David S. Vaughn, Alexander J. Ha...
BMCBI
2010
118views more  BMCBI 2010»
13 years 4 months ago
Bacillus anthracis genome organization in light of whole transcriptome sequencing
Emerging knowledge of whole prokaryotic transcriptomes could validate a number of theoretical concepts introduced in the early days of genomics. What are the rules connecting gene...
Jeffrey Martin, Wenhan Zhu, Karla D. Passalacqua, ...