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BIBE
2007
IEEE
145views Bioinformatics» more  BIBE 2007»
14 years 5 months ago
Homomorphisms of Multisource Trees into Networks with Applications to Metabolic Pathways
Network mapping is a convenient tool for comparing and exploring biological networks; it can be used for predicting unknown pathways, fast and meaningful searching of databases, a...
Qiong Cheng, Robert W. Harrison, Alexander Zelikov...
BIBE
2007
IEEE
128views Bioinformatics» more  BIBE 2007»
14 years 5 months ago
QOMA2: Optimizing the alignment of many sequences
Abstract—We consider the problem of aligning multiple protein sequences with the goal of maximizing the SP (Sum-of-Pairs) score, when the number of sequences is large. The QOMA (...
Xu Zhang, Tamer Kahveci
BIBE
2007
IEEE
150views Bioinformatics» more  BIBE 2007»
14 years 5 months ago
Differential Scoring for Systolic Sequence Alignment
Systolic implementations of dynamic programming solutions that utilize a similarity matrix can achieve appreciable performance with both course- and fine-grain parallelization. A ...
Antonio E. de la Serna
BIBE
2007
IEEE
133views Bioinformatics» more  BIBE 2007»
14 years 5 months ago
Denoising of Array-Based DNA Copy Number Data Using The Dual-tree Complex Wavelet Transform
—Array-based comparative genomic hybridization (array CGH) is a highly efficient technique, allowing the simultaneous measurement of genomic DNA copy number at hundreds or thous...
Nha Nguyen, Heng Huang, Soontorn Oraintara, Yuhang...
BIBE
2007
IEEE
138views Bioinformatics» more  BIBE 2007»
14 years 5 months ago
A Flexible Stem-Based Local Search Algorithm for Predicting RNA Secondary Structures Including Pseudoknots
-We demonstrate a new algorithm named FlexStem to predict RNA secondary structures with pseudoknots. Our approach is based on the free energy minimization criterion, and utilizes a...
Xiang Chen, Simin He, Dongbo Bu, Runsheng Chen, We...
BIBE
2007
IEEE
195views Bioinformatics» more  BIBE 2007»
14 years 5 months ago
Finding Clusters of Positive and Negative Coregulated Genes in Gene Expression Data
— In this paper, we propose a system for finding partial positive and negative coregulated gene clusters in microarray data. Genes are clustered together if they show the same p...
Kerstin Koch, Stefan Schönauer, Ivy Jansen, J...
BIBE
2007
IEEE
147views Bioinformatics» more  BIBE 2007»
14 years 5 months ago
A New Alignment-Independent Algorithm for Clustering Protein Sequences
—The rapid burgeoning of available protein data makes the use of clustering within families of proteins increasingly important, the challenge is to identify subfamilies of evolut...
Abdellali Kelil, Shengrui Wang, Ryszard Brzezinski
BIBE
2007
IEEE
125views Bioinformatics» more  BIBE 2007»
14 years 5 months ago
Large-scale Discovery of Regulatory Motifs Involved in Alternative Splicing
Alternative splicing is a highly important process in many eukaryotic organisms, but surprisingly little is known about its regulation. Often, this process involves cis-regulatory ...
Sihui Zhao, Jihye Kim, Steffen Heber