This book constitutes the refereed proceedings of the 9th International Symposium on Bioinformatics Research and Applications, ISBRA 2013, held in Charlotte, NC, USA, in May 2013. The 25 revised full papers presented together with 4 invited talks were carefully reviewed and selected from 46 submissions. The papers cover a wide range of biomedical databases and data integration, high-performance bio-computing, biomolecular imaging, high-throughput sequencing data analysis, bio-ontologies, molecular evolution, comparative genomics and phylogenomics, molecular modeling and simulation, pattern discovery and classification, computational proteomics, population genetics, data mining and visualization, software tools and applications.
Author(s): Bin Ma (auth.), Zhipeng Cai, Oliver Eulenstein, Daniel Janies, Daniel Schwartz (eds.)
Series: Lecture Notes in Computer Science 7875
Edition: 1
Publisher: Springer-Verlag Berlin Heidelberg
Year: 2013
Language: English
Pages: 312
Tags: Computational Biology/Bioinformatics; Data Mining and Knowledge Discovery; Information Systems Applications (incl. Internet); Algorithm Analysis and Problem Complexity; Pattern Recognition; Computer Appl. in Life Sciences
Front Matter....Pages -
Peptide Identification from Mass Spectrometry....Pages 1-1
Identifying Critical Transitions of Biological Processes by Dynamical Network Biomarkers....Pages 2-2
Computational Behavioral Ecology....Pages 3-3
Unusual RNA Structures: Information Content in RNAs from the “Prebiotic Ribosome” to Modern Viruses....Pages 4-4
The Radiation Hybrid Map Construction Problem Is FPT....Pages 5-16
Reconstructing Ancestral Genomic Orders Using Binary Encoding and Probabilistic Models....Pages 17-27
Computational Methods for the Parallel 3D Simulation of Biochemical Kinetics at the Microscopic Scale....Pages 28-39
A Tool for Non-binary Tree Reconciliation....Pages 40-51
Patterns of Chromatin-Modifications Discriminate Different Genomic Features in Arabidopsis ....Pages 52-63
Inferring Time-Delayed Gene Regulatory Networks Using Cross-Correlation and Sparse Regression....Pages 64-75
A Simulation of Synthetic agr System in E.coli ....Pages 76-86
Gene Regulatory Networks from Gene Ontology....Pages 87-98
Partitioning Biological Networks into Highly Connected Clusters with Maximum Edge Coverage....Pages 99-111
Reconstructing k -Reticulated Phylogenetic Network from a Set of Gene Trees....Pages 112-124
LCR_Finder: A de Novo Low Copy Repeat Finder for Human Genome....Pages 125-136
Heuristic Algorithms for the Protein Model Assignment Problem....Pages 137-148
Alignment of DNA Mass-Spectral Profiles Using Network Flows....Pages 149-160
A Context-Driven Gene Prioritization Method for Web-Based Functional Genomics....Pages 161-172
Exploiting Dependencies of Patterns in Gene Expression Analysis Using Pairwise Comparisons....Pages 173-184
Cloud Computing for De Novo Metagenomic Sequence Assembly....Pages 185-198
Protein Closed Loop Prediction from Contact Probabilities....Pages 199-210
A Graph Approach to Bridge the Gaps in Volumetric Electron Cryo-microscopy Skeletons....Pages 211-223
Measure the Semantic Similarity of GO Terms Using Aggregate Information Content....Pages 224-236
Scalable and Versatile k -mer Indexing for High-Throughput Sequencing Data....Pages 237-248
POMAGO : Multiple Genome-Wide Alignment Tool for Bacteria....Pages 249-260
Effect of Incomplete Lineage Sorting on Tree-Reconciliation-Based Inference of Gene Duplication....Pages 261-272
Ellipsoid-Weighted Protein Conformation Alignment....Pages 273-285
Construction of Uncertain Protein-Protein Interaction Networks and Its Applications....Pages 286-297
Does Accurate Scoring of Ligands against Protein Targets Mean Accurate Ranking?....Pages 298-310
Back Matter....Pages -
