Ebook: Bioinformatics Research and Applications: 8th International Symposium, ISBRA 2012, Dallas, TX, USA, May 21-23, 2012. Proceedings

This book constitutes the refereed proceedings of the International Symposium on Bioinformatics Research and Applications, ISBRA 2012, held in Dallas, Texas, USA, in May 2012. The 26 revised full papers presented together with five invited talks were carefully reviewed and selected from 66 submissions. The papers address issues on various aspects of bioinformatics and computational biology and their applications.

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This book constitutes the refereed proceedings of the International Symposium on Bioinformatics Research and Applications, ISBRA 2012, held in Dallas, Texas, USA, in May 2012. The 26 revised full papers presented together with five invited talks were carefully reviewed and selected from 66 submissions. The papers address issues on various aspects of bioinformatics and computational biology and their applications.

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This book constitutes the refereed proceedings of the International Symposium on Bioinformatics Research and Applications, ISBRA 2012, held in Dallas, Texas, USA, in May 2012. The 26 revised full papers presented together with five invited talks were carefully reviewed and selected from 66 submissions. The papers address issues on various aspects of bioinformatics and computational biology and their applications.
Content:
Front Matter....Pages -
Trie-based Apriori Motif Discovery Approach....Pages 1-12
Inapproximability of (1,2)-Exemplar Distance....Pages 13-23
A Mixed Integer Programming Model for the Parsimonious Loss of Heterozygosity Problem....Pages 24-35
Reconstruction of Transcription Regulatory Networks by Stability-Based Network Component Analysis....Pages 36-47
A Transcript Perspective on Evolution....Pages 48-59
A Fast Algorithm for Computing the Quartet Distance for Large Sets of Evolutionary Trees....Pages 60-71
Error Propagation in Sparse Linear Systems with Peptide-Protein Incidence Matrices....Pages 72-83
Models and Algorithmic Tools for Computational Processes in Cellular Biology: Recent Developments and Future Directions....Pages 84-86
Identifying Rogue Taxa through Reduced Consensus: NP-Hardness and Exact Algorithms....Pages 87-98
Analytics Approaches for the Era of 10,000* Genomes *and Counting....Pages 99-101
GTP Supertrees from Unrooted Gene Trees: Linear Time Algorithms for NNI Based Local Searches....Pages 102-114
A Robinson-Foulds Measure to Compare Unrooted Trees with Rooted Trees....Pages 115-126
P-Binder: A System for the Protein-Protein Binding Sites Identification....Pages 127-138
Non-identifiable Pedigrees and a Bayesian Solution....Pages 139-152
Iterative Piecewise Linear Regression to Accurately Assess Statistical Significance in Batch Confounded Differential Expression Analysis....Pages 153-164
Reconstruction of Network Evolutionary History from Extant Network Topology and Duplication History....Pages 165-176
POPE: Pipeline of Parentally-Biased Expression....Pages 177-188
On Optimizing the Non-metric Similarity Search in Tandem Mass Spectra by Clustering....Pages 189-200
On the Comparison of Sets of Alternative Transcripts....Pages 201-212
MURPAR: A Fast Heuristic for Inferring Parsimonious Phylogenetic Networks from Multiple Gene Trees....Pages 213-224
Large Scale Ranking and Repositioning of Drugs with Respect to DrugBank Therapeutic Categories....Pages 225-236
Score Based Aggregation of microRNA Target Orderings....Pages 237-248
Modeling Complex Diseases Using Discriminative Network Fragments....Pages 249-249
Novel Multi-sample Scheme for Inferring Phylogenetic Markers from Whole Genome Tumor Profiles....Pages 250-262
Algorithms for Knowledge-Enhanced Supertrees....Pages 263-274
Improvement of BLASTp on the FPGA-Based High-Performance Computer RIVYERA....Pages 275-286
A Polynomial Time Solution for Protein Chain Pair Simplification under the Discrete Frechet Distance....Pages 287-298
Designing RNA Secondary Structures in Coding Regions....Pages 299-314
Phylogenetic Tree Reconstruction with Protein Linkage....Pages 315-327
Protein Structure Prediction and Clustering Using MUFOLD....Pages 328-329
Computational Modeling of Mammalian Promoters....Pages 330-330
Back Matter....Pages -

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This book constitutes the refereed proceedings of the International Symposium on Bioinformatics Research and Applications, ISBRA 2012, held in Dallas, Texas, USA, in May 2012. The 26 revised full papers presented together with five invited talks were carefully reviewed and selected from 66 submissions. The papers address issues on various aspects of bioinformatics and computational biology and their applications.
Content:
Front Matter....Pages -
Trie-based Apriori Motif Discovery Approach....Pages 1-12
Inapproximability of (1,2)-Exemplar Distance....Pages 13-23
A Mixed Integer Programming Model for the Parsimonious Loss of Heterozygosity Problem....Pages 24-35
Reconstruction of Transcription Regulatory Networks by Stability-Based Network Component Analysis....Pages 36-47
A Transcript Perspective on Evolution....Pages 48-59
A Fast Algorithm for Computing the Quartet Distance for Large Sets of Evolutionary Trees....Pages 60-71
Error Propagation in Sparse Linear Systems with Peptide-Protein Incidence Matrices....Pages 72-83
Models and Algorithmic Tools for Computational Processes in Cellular Biology: Recent Developments and Future Directions....Pages 84-86
Identifying Rogue Taxa through Reduced Consensus: NP-Hardness and Exact Algorithms....Pages 87-98
Analytics Approaches for the Era of 10,000* Genomes *and Counting....Pages 99-101
GTP Supertrees from Unrooted Gene Trees: Linear Time Algorithms for NNI Based Local Searches....Pages 102-114
A Robinson-Foulds Measure to Compare Unrooted Trees with Rooted Trees....Pages 115-126
P-Binder: A System for the Protein-Protein Binding Sites Identification....Pages 127-138
Non-identifiable Pedigrees and a Bayesian Solution....Pages 139-152
Iterative Piecewise Linear Regression to Accurately Assess Statistical Significance in Batch Confounded Differential Expression Analysis....Pages 153-164
Reconstruction of Network Evolutionary History from Extant Network Topology and Duplication History....Pages 165-176
POPE: Pipeline of Parentally-Biased Expression....Pages 177-188
On Optimizing the Non-metric Similarity Search in Tandem Mass Spectra by Clustering....Pages 189-200
On the Comparison of Sets of Alternative Transcripts....Pages 201-212
MURPAR: A Fast Heuristic for Inferring Parsimonious Phylogenetic Networks from Multiple Gene Trees....Pages 213-224
Large Scale Ranking and Repositioning of Drugs with Respect to DrugBank Therapeutic Categories....Pages 225-236
Score Based Aggregation of microRNA Target Orderings....Pages 237-248
Modeling Complex Diseases Using Discriminative Network Fragments....Pages 249-249
Novel Multi-sample Scheme for Inferring Phylogenetic Markers from Whole Genome Tumor Profiles....Pages 250-262
Algorithms for Knowledge-Enhanced Supertrees....Pages 263-274
Improvement of BLASTp on the FPGA-Based High-Performance Computer RIVYERA....Pages 275-286
A Polynomial Time Solution for Protein Chain Pair Simplification under the Discrete Frechet Distance....Pages 287-298
Designing RNA Secondary Structures in Coding Regions....Pages 299-314
Phylogenetic Tree Reconstruction with Protein Linkage....Pages 315-327
Protein Structure Prediction and Clustering Using MUFOLD....Pages 328-329
Computational Modeling of Mammalian Promoters....Pages 330-330
Back Matter....Pages -
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