This book constitutes the refereed proceedings of the 5th International Symposium on Bioinformatics Research and Applications, ISBRA 2009, held in Fort Lauderdale, FL, USA, in May 2009.
The 26 revised full papers presented together four invited papers were carefully reviewed and selected from a total of 55 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.
Author(s): Mikhail S. Gelfand, Alexei E. Kazakov (auth.), Ion Măndoiu, Giri Narasimhan, Yanqing Zhang (eds.)
Series: Lecture Notes in Computer Science 5542 : Lecture Notes in Bioinformatics
Edition: 1
Publisher: Springer-Verlag Berlin Heidelberg
Year: 2009
Language: English
Pages: 336
Tags: Computational Biology/Bioinformatics; Bioinformatics; Computer Appl. in Life Sciences; Pattern Recognition; Computer Imaging, Vision, Pattern Recognition and Graphics; Data Mining and Knowledge Discovery
Front Matter....Pages -
Evolution of Regulatory Systems in Bacteria (Invited Keynote Talk)....Pages 1-4
Integrating Multiple-Platform Expression Data through Gene Set Features....Pages 5-17
Practical Quality Assessment of Microarray Data by Simulation of Differential Gene Expression....Pages 18-27
Mean Square Residue Biclustering with Missing Data and Row Inversions....Pages 28-39
Using Gene Expression Modeling to Determine Biological Relevance of Putative Regulatory Networks....Pages 40-51
Querying Protein-Protein Interaction Networks....Pages 52-62
Integrative Approach for Combining TNFα-NFκB Mathematical Model to a Protein Interaction Connectivity Map....Pages 63-74
Hierarchical Organization of Functional Modules in Weighted Protein Interaction Networks Using Clustering Coefficient....Pages 75-86
Bioinformatics Challenges in Translational Research....Pages 87-87
Untangling Tanglegrams: Comparing Trees by Their Drawings....Pages 88-99
An Experimental Analysis of Consensus Tree Algorithms for Large-Scale Tree Collections....Pages 100-111
Counting Faces in Split Networks....Pages 112-123
Relationship between Amino Acids Sequences and Protein Structures: Folding Patterns and Sequence Patterns....Pages 124-134
Improved Algorithms for Parsing ESLTAGs: A Grammatical Model Suitable for RNA Pseudoknots....Pages 135-147
Efficient Algorithms for Self Assembling Triangular and Other Nano Structures....Pages 148-158
Motif Construction from High–Throughput SELEX Data....Pages 159-159
Rearrangement Phylogeny of Genomes in Contig Form....Pages 160-172
Prediction of Contiguous Regions in the Amniote Ancestral Genome....Pages 173-185
Pure Parsimony Xor Haplotyping....Pages 186-197
A Decomposition of the Pure Parsimony Haplotyping Problem....Pages 198-208
Exact Computation of Coalescent Likelihood under the Infinite Sites Model....Pages 209-220
Imputation-Based Local Ancestry Inference in Admixed Populations....Pages 221-233
Interpreting Population Sequencing Data....Pages 234-235
Modeling and Visualizing Heterogeneity of Spatial Patterns of Protein-DNA Interaction from High-Density Chromatin Precipitation Mapping Data....Pages 236-247
A Linear-Time Algorithm for Analyzing Array CGH Data Using Log Ratio Triangulation....Pages 248-259
Mining of cis -Regulatory Motifs Associated with Tissue-Specific Alternative Splicing....Pages 260-271
Analysis of Cis-Regulatory Motifs in Cassette Exons by Incorporating Exon Skipping Rates....Pages 272-283
A Class of Evolution-Based Kernels for Protein Homology Analysis: A Generalization of the PAM Model....Pages 284-296
Irreplaceable Amino Acids and Reduced Alphabets in Short-Term and Directed Protein Evolution....Pages 297-309
A One-Class Classification Approach for Protein Sequences and Structures....Pages 310-322
Prediction and Classification of Real and Pseudo MicroRNA Precursors via Data Fuzzification and Fuzzy Decision Trees....Pages 323-334
Back Matter....Pages -
