Bioinformatics Research and Applications: Third International Symposium,ISBRA 2007, Atlanta, GA, USA, May 7-10, 2007, ProceedingsIon Măndoiu, Alexander Zelikovsky 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 three invited talks 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. |
Contents
A Biclustering Algorithm for Discovering ValueCoherent Biclusters | 1 |
Significance Analysis of TimeCourse Gene Expression Profiles | 13 |
DataDriven Smoothness Enhanced Variance Ratio Test to Unearth Responsive Genes in 0Time Normalized TimeCourse Microarray Data | 25 |
Efficiently Finding the Most Parsimonious Phylogenetic Tree Via Linear Programming | 37 |
A MultiStack Based Phylogenetic Tree Building Method | 49 |
Theoretical Bounds and Empirical Performance | 61 |
A Bootstrap Correspondence Analysis for Factorial Microarray Experiments with Replications | 73 |
A Framework for Large Datasets | 85 |
Organization | vii |
Table of Contents | xi |
A Biclustering Algorithm for Discovering ValueCoherent Biclusters | 1 |
Significance Analysis of TimeCourse Gene Expression Profiles | 13 |
DataDriven Smoothness Enhanced Variance Ratio Test to Unearth Responsive Genes in 0Time Normalized TimeCourse Microarray Data | 25 |
Efficiently Finding the Most Parsimonious Phylogenetic Tree Via Linear Programming | 37 |
A MultiStack Based Phylogenetic Tree Building Method | 49 |
Theoretical Bounds and Empirical Performance | 61 |
Ranking Function Based on Higher Order Statistics RFHOS for TwoSample Microarray Experiments | 97 |
Searching for Recombinant Donors in a Phylogenetic Network of Serial Samples | 109 |
Algorithm for Haplotype Inferring Via GalledTree Networks with Simple Galls Extended Abstract | 121 |
A Maximum Likelihood Approach | 133 |
Modern Homology Search | 145 |
Statistical Absolute Evaluation of Gene Ontology Terms with Gene Expression Data | 146 |
Discovering Relations Among GOAnnotated Clusters by Graph Kernel Methods | 158 |
An Empirical Comparison of Dimensionality Reduction Methods for Classifying Gene and Protein Expression Datasets | 170 |
A Toolkit for Generating Parameter Space Maps Using NEURON in a Grid Environment | 182 |
An Adaptive Resolution Tree Visualization of Large Influenza Virus Sequence Datasets | 192 |
A WaveletBased Approach to Enhancement of Digital Mammography Images | 203 |
High Level Programming Environment System for Protein Structure Data | 215 |
Finding Minimal Sets of Informative Genes in Microarray Data | 227 |
NoiseBased Feature Perturbation as a Selection Method for Microarray Data | 237 |
Efficient Generation of Biologically Relevant Enriched Gene Sets | 248 |
Space and Time Efficient Algorithms to DiscoverEndogenous RNAi Patterns in Complete Genome Data | 260 |
A Fast Approximate CovarianceModelBased Database Search Method for Noncoding RNA | 270 |
Extensions of Naive Bayes and Their Applications to Bioinformatics | 282 |
The Solution Space of Sorting by Reversals | 293 |
A Fast and Exact Algorithm for the Perfect Reversal Median Problem | 305 |
Genomic Signatures from DNA Word Graphs | 317 |
Enhancing Motif Refinement by Incorporating Comparative Genomics Data | 329 |
Mining Discriminative Distance Context of Transcription Factor Binding Sites on ChIP Enriched Regions | 338 |
Enhanced Prediction of Cleavage in Bovine Precursor Sequences | 350 |
A Computational Study of Bidirectional Promoters in the Human Genome | 361 |
The Identification of Antisense Gene Pairs Through Available Software | 372 |
Inferring Weak Adaptations and Selection Biases in Proteins from Composition and Substitution Matrices | 382 |
Markov Model Variants for Appraisal of Coding Potential in Plant DNA | 394 |
Predicting Palmitoylation Sites Using a Regularised Biobasis Function Neural Network | 406 |
A Novel KernelBased Approach for Predicting BindingPeptides for HLA Class II Molecules | 418 |
A Database for Prediction of Unique Peptide Motifs as Linear Epitopes | 430 |
A Novel Greedy Algorithm for the Minimum Common String Partition Problem | 441 |
An Efficient Algorithm for Finding GeneSpecific Probes for DNA Microarrays | 453 |
Multiple Sequence Local Alignment Using Monte Carlo EM Algorithm | 465 |
Cancer Class Discovery Using Nonnegative Matrix Factorization Based on Alternating NonnegativityConstrained Least Squares | 477 |
A Support Vector Machine Ensemble for Cancer Classification Using Gene Expression Data | 488 |
Combining SVM Classifiers Using Genetic Fuzzy Systems Based on AUC for Gene Expression Data Analysis | 496 |
A BPSCFG Based Approach for RNA Secondary Structure Prediction with Consecutive Bases Dependency and Their Relative Positions Information | 506 |
A Toolset for the Structural Analysis of Biological Sequences on a 3D Triangular Lattice | 518 |
Statistical Estimate for the Size of the Protein Structural Vocabulary | 530 |
Coclustering Based Parcellation of Human Brain Cortex Using Diffusion Tensor MRI | 539 |
An Algorithm for Hierarchical Classification of Genes of Prokaryotic Genomes | 551 |
Using Multi Level Nearest Neighbor Classifiers for GProtein Coupled Receptor Subfamilies Prediction | 564 |
Ab Initio Gene Finding Engines What Is Under the Hood | 577 |
Reconstruction of 3D Structures from Protein Contact Maps | 578 |
A Feature Selection Algorithm Based on Graph Theory and Random Forests for Protein Secondary Structure Prediction | 590 |
A DiscreteEventSimulation Based Modeling Approach | 601 |
Comparative Analysis of GeneCoexpression Networks Across Species | 615 |
Comparative Pathway Prediction Via Unified Graph Modeling of Genomic Structure Information | 627 |
Extending the Calculus of Looping Sequences to Model Protein Interaction at the Domain Level | 638 |
Author Index | 650 |
Title Page | iii |
Preface | vi |
A Bootstrap Correspondence Analysis for Factorial Microarray Experiments with Replications | 73 |
A Framework for Large Datasets | 85 |
Ranking Function Based on Higher Order Statistics RFHOS for TwoSample Microarray Experiments | 97 |
Searching for Recombinant Donors in a Phylogenetic Network of Serial Samples | 109 |
Algorithm for Haplotype Inferring Via GalledTree Networks with Simple Galls Extended Abstract | 121 |
A Maximum Likelihood Approach | 133 |
Modern Homology Search | 145 |
Statistical Absolute Evaluation of Gene Ontology Terms with Gene Expression Data | 146 |
Discovering Relations Among GOAnnotated Clusters by Graph Kernel Methods | 158 |
An Empirical Comparison of Dimensionality Reduction Methods for Classifying Gene and Protein Expression Datasets | 170 |
A Toolkit for Generating Parameter Space Maps Using NEURON in a Grid Environment | 182 |
An Adaptive Resolution Tree Visualization of Large Influenza Virus Sequence Datasets | 192 |
A WaveletBased Approach to Enhancement of Digital Mammography Images | 203 |
High Level Programming Environment System for Protein Structure Data | 215 |
Finding Minimal Sets of Informative Genes in Microarray Data | 227 |
NoiseBased Feature Perturbation as a Selection Method for Microarray Data | 237 |
Efficient Generation of Biologically Relevant Enriched Gene Sets | 248 |
Space and Time Efficient Algorithms to DiscoverEndogenous RNAi Patterns in Complete Genome Data | 260 |
A Fast Approximate CovarianceModelBased Database Search Method for Noncoding RNA | 270 |
Extensions of Naive Bayes and Their Applications to Bioinformatics | 282 |
The Solution Space of Sorting by Reversals | 293 |
A Fast and Exact Algorithm for the Perfect Reversal Median Problem | 305 |
Genomic Signatures from DNA Word Graphs | 317 |
Enhancing Motif Refinement by Incorporating Comparative Genomics Data | 329 |
Mining Discriminative Distance Context of Transcription Factor Binding Sites on ChIP Enriched Regions | 338 |
Enhanced Prediction of Cleavage in Bovine Precursor Sequences | 350 |
A Computational Study of Bidirectional Promoters in the Human Genome | 361 |
The Identification of Antisense Gene Pairs Through Available Software | 372 |
Inferring Weak Adaptations and Selection Biases in Proteins from Composition and Substitution Matrices | 382 |
Markov Model Variants for Appraisal of Coding Potential in Plant DNA | 394 |
Predicting Palmitoylation Sites Using a Regularised Biobasis Function Neural Network | 406 |
A Novel KernelBased Approach for Predicting BindingPeptides for HLA Class II Molecules | 418 |
A Database for Prediction of Unique Peptide Motifs as Linear Epitopes | 430 |
A Novel Greedy Algorithm for the Minimum Common String Partition Problem | 441 |
An Efficient Algorithm for Finding GeneSpecific Probes for DNA Microarrays | 453 |
Multiple Sequence Local Alignment Using Monte Carlo EM Algorithm | 465 |
Cancer Class Discovery Using Nonnegative Matrix Factorization Based on Alternating NonnegativityConstrained Least Squares | 477 |
A Support Vector Machine Ensemble for Cancer Classification Using Gene Expression Data | 488 |
Combining SVM Classifiers Using Genetic Fuzzy Systems Based on AUC for Gene Expression Data Analysis | 496 |
A BPSCFG Based Approach for RNA Secondary Structure Prediction with Consecutive Bases Dependency and Their Relative Positions Information | 506 |
A Toolset for the Structural Analysis of Biological Sequences on a 3D Triangular Lattice | 518 |
Statistical Estimate for the Size of the Protein Structural Vocabulary | 530 |
Coclustering Based Parcellation of Human Brain Cortex Using Diffusion Tensor MRI | 539 |
An Algorithm for Hierarchical Classification of Genes of Prokaryotic Genomes | 551 |
Using Multi Level Nearest Neighbor Classifiers for GProtein Coupled Receptor Subfamilies Prediction | 564 |
Ab Initio Gene Finding Engines What Is Under the Hood | 577 |
Reconstruction of 3D Structures from Protein Contact Maps | 578 |
A Feature Selection Algorithm Based on Graph Theory and Random Forests for Protein Secondary Structure Prediction | 590 |
A DiscreteEventSimulation Based Modeling Approach | 601 |
Comparative Analysis of GeneCoexpression Networks Across Species | 615 |
Comparative Pathway Prediction Via Unified Graph Modeling of Genomic Structure Information | 627 |
Extending the Calculus of Looping Sequences to Model Protein Interaction at the Domain Level | 638 |
| 650 | |
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Common terms and phrases
algorithm alignment amino acid analysis antisense applied approach Berlin Heidelberg 2007 biclusters binding Bioinformatics biological cancer cell chromosome classification clusters compared components computed corresponding database dataset defined denote differentially expressed distance distribution DR methods dSEVRaT edge evaluate experimental false positive fuzzy gene expression data Gene Ontology gene sets genetic genome genome sequence GO terms graph Greedy algorithm haplotype i-trace identify input interaction ISBRA Isomap kernel length linear LNBI matrix median microarray data microcalcifications Molecular motif neural network normal nucleosome optimal p-value pairs parameter pathway patterns peptides performance permutations phylogenetic network phylogenetic tree phylogeny prediction accuracy prime node problem proposed protein pseudoknots random random forests recombination reversals samples score secondary structure selected simulation solution species statistical string substring subtree support vector machine Table TATA box threshold time-course values variance vector wavelet Zelikovsky Eds