Transactions on Computational Systems Biology II
It gives me great pleasure to present the Special Issue of LNCS Transactions on Computational Systems Biology devoted to considerably extended versions of selected papers presented at the International Workshop on Bioinformatics Research and Applications (IWBRA 2005). The IWBRA workshop was a part of the International Conference on Computational Science (ICCS 2005) which took place in Emory University, Atlanta, Georgia, USA, May 22–24, 2005. See http://www.cs.gsu.edu/pan/ iwbra.htm for more details. The 10 papers selected for the special issue cover a wide range of bioinformatics research. The first papers are devoted to problems in RNA structure prediction: Blin et al. contribute to the arc-preserving subsequence problem and Liu et al. develop an efficient search of pseudoknots. The coding schemes and structural alphabets for protein structure prediction are discussed in the contributions of Lei and Dai, and Zheng and Liu, respectively. Song et al. propose a novel technique for efficient extraction of biomedical information. Nakhleh and Wang discuss introducing hybrid speciation and horizontal gene transfer in phylogenetic networks. Practical algorithms minimizing recombinations in pedigree phasing are proposed by Zhang et al. Kolliet al. propose a new parallel implementation in OpenMP for finding the edit distance between two signed gene permutations. The issue is concluded with two papers devoted to bioinformatics problems that arise in DNA microarrays: improved tag set design for universal tag arrays is suggested by Mandoiu et al. and a new method of gene selection is discussed by Xu and Zhang.
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What Makes the ArcPreserving Subsequence Problem Hard?
Proﬁling and Searching for RNA Pseudoknot Structures in Genomes
A Class of New Kernels Based on HighScored Pairs of kPeptides for SVMs and Its Application for Prediction of Protein Subcellular Localization
A Protein Structural Alphabet and Its Substitution Matrix CLESUM
An Effective Biomedical Information Extraction Technique Based on Mixture Hidden Markov Models
Properties and Relationship to Trees and Clusters
Minimum ParentOffspring Recombination Haplotype Inference in Pedigrees
Calculating Genomic Distances in Parallel Using OpenMP
Improved Tag Set Design and Multiplexing Algorithms for Universal Arrays
Using Correlations Between Genes to Select Informative Genes on Microarray Datasets
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a1 and a2 active terminal alignment amino acid APS problem arrays base G Bioinformatics biological BLOSUM c-tokens clade classification accuracy classifier cluster CM components complexity Computer construction contains denote experiments extraction feasible haplotype configurations feature selection Figure gene selection genome genotype Hidden Markov Models hybridization inheritance profile Intel C++ compiler k-MRHI k-peptide kernel KN,D KXtractor least one base Lemma matched matrix method MiHMM Min-Deg mixture model network node NP-C NP-complete nucleotides number of genes obtained OpenMP pairs pairwise virtual gene pedigree performance phylogenetic network polynomial prediction accuracy primer Primer-Del+ protein pseudoknot structures resp root S1xj S1xk sample secondary structures selection algorithms set is deleted Sexm single POS HMM Ssxi Ssxk subcellular localization substitution matrix substrings support vector machines T-decomposition tag set terminal edge terminal in S1xi text chunking tree node tree search algorithm virtual gene algorithm