Bioinformatics Research and Applications

by Mandoiu, Ion; Zelikovsky, Alexander

• ISBN13: 9783540720300
• ISBN10: 3540720308
• Format: Paperback
• Copyright: 2007-06-01
• Publisher: Springer-Verlag New York Inc

Summary

This book constitutes the refereed proceedings of the Third International Symposium on Bioinformatics Research and Applications, ISBRA 2007, held in Atlanta, GA, USA in May 2007.The 55 revised full papers presented together with 3 invited talks were carefully reviewed and selected from a total of 146 submissions. The papers cover a wide range of topics, including clustering and classification, gene expression analysis, gene networks, genome analysis, motif finding, pathways, protein structure prediction, protein domain interactions, phylogenetics, and software tools.

Table of Contents

GFBA : a biclustering algorithm for discovering value-coherent biclusters	p. 1
Significance analysis of time-course gene expression profiles	p. 13
Data-driven smoothness enhanced variance ratio test to unearth responsive genes in 0-time normalized time-course microarray data	p. 25
Efficiently finding the most parsimonious phylogenetic tree via linear programming	p. 37
A multi-stack based phylogenetic tree building method	p. 49
A new linear-time heuristic algorithm for computing the parsimony score of phylogenetic networks : theoretical bounds and empirical performance	p. 61
A bootstrap correspondence analysis for factorial microarray experiments with replications	p. 73
Clustering algorithms optimizer : a framework for large datasets	p. 85
Ranking function based on higher order statistics (RF-HOS) for two-sample microarray experiments	p. 97
Searching for recombinant donors in a phylogenetic network of serial samples	p. 109
Algorithm for haplotype inferring via galled-tree networks with simple galls	p. 121
Estimating bacterial diversity from environmental DNA : a maximum likelihood approach	p. 133
Invited talk : modern homology search	p. 145
Statistical absolute evaluation of gene ontology terms with gene expression data	p. 146
Discovering relations among GO-annotated clusters by graph kernel methods	p. 158
An empirical comparison of dimensionality reduction methods for classifying gene and protein expression datasets	p. 170
NEURONgrid : a toolkit for generating parameter-space maps using NEURON in a grid environment	p. 182
An adaptive resolution tree visualization of large influenza virus sequence datasets	p. 192
Wavelet image interpolation (WII) : a wavelet-based approach to enhancement of digital mammography images	p. 203
High level programming environment system for protein structure data	p. 215
Finding minimal sets of informative genes in microarray data	p. 227
Noise-based feature perturbation as a selection method for microarray data	p. 237
Efficient generation of biologically relevant enriched gene sets	p. 248
Space and time efficient algorithms to discover endogenous RNAi patterns in complete genome data	p. 260
A fast approximate covariance-model-based database search method for non-coding RNA	p. 270
Extensions of naive Bayes and their applications to bioinformatics	p. 282
The solution space of sorting by reversals	p. 293
A fast and exact algorithm for the perfect reversal median problem	p. 305
Genomic signatures from DNA word graphs	p. 317
Enhancing motif refinement by incorporating comparative genomics data	p. 329
Mining discriminative distance context of transcription factor binding sites on ChIP enriched regions	p. 338
Enhanced prediction of cleavage in bovine precursor sequences	p. 350
Invited talk : a computational study of bidirectional promoters in the human genome	p. 361
The identification of antisense gene pairs through available software	p. 372
Inferring weak adaptations and selection biases in proteins from composition and substitution matrices	p. 382
Markov model variants for appraisal of coding potential in plant DNA	p. 394
Predicting palmitoylation sites using a regularised bio-basis function neural network	p. 406
A novel kernel-based approach for predicting binding peptides for HLA class II molecules	p. 418
A database for prediction of unique peptide motifs as linear epitopes	p. 430
A novel greedy algorithm for the minimum common string partition problem	p. 441
An efficient algorithm for finding gene-specific probes for DNA microarrays	p. 453
Multiple sequence local alignment using Monte Carlo EM algorithm	p. 465
Cancer class discovery using non-negative matrix factorization based on alternating non-negativity-constrained least squares	p. 477
A support vector machine ensemble for cancer classification using gene expression data	p. 488
Combining SVM classifiers using genetic fuzzy systems based on AUC for gene expression data analysis	p. 496
A BP-SCFG based approach for RNA secondary structure prediction with consecutive bases dependency and their relative positions information	p. 506
Delta : a toolset for the structural analysis of biological sequences on a 3D triangular lattice	p. 518
Statistical estimate for the size of the protein structural vocabulary	p. 530
Coclustering based parcellation of human brain cortex using diffusion tensor MRI	p. 539
An algorithm for hierarchical classification of genes of prokaryotic genomes	p. 551
Using multi level nearest neighbor classifiers for G-protein coupled receptor sub-families prediction	p. 564
Invited talk : ab initio gene finding engines : what is under the hood	p. 577
Reconstruction of 3D structures from protein contact maps	p. 578
A feature selection algorithm based on graph theory and random forests for protein secondary structure prediction	p. 590
DNA sites buried in nucleosome become accessible at room temperature : a discrete-event-simulation based modeling approach	p. 601
Comparative analysis of gene-coexpression networks across species	p. 615
Comparative pathway prediction via unified graph modeling of genomic structure information	p. 627
Extending the calculus of looping sequences to model protein interaction at the domain level	p. 638
Table of Contents provided by Blackwell. All Rights Reserved.