Bioinformatics Research and Applications: 5th International Symposium, ISBRA 2009 Fort Lauderdale, FL, USA, May 13-16, 2009, Proceedings / Edition 1

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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.

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Table of Contents

Evolution of Regulatory Systems in Bacteria (Invited Keynote Talk) Mikhail S. Gelfand Alexei E. Kazakov Yuri D. Korostelev Olga N. Laikova Andrei A. Mironov Alexandra B. Rakhmaninova Dmitry A. Ravcheev Dmitry A. Rodionov Alexei G. Vitreschak 1

Integrating Multiple-Platform Expression Data through Gene Set Features Mat&echeck;j Holec Filip &Zcheck;elezný Ji&rcheck;í Kléma Jakub Tolar 5

Practical Quality Assessment of Microarray Data by Simulation of Differential Gene Expression Brian E. Howard Beate Sick Steffen Heber 18

Mean Square Residue Biclustering with Missing Data and Row Inversions Stefan Gremalschi Gulsah Altun Irina Astrovskaya Alexander Zelikovsky 28

Using Gene Expression Modeling to Determine Biological Relevance of Putative Regulatory Networks Peter Larsen Yang Dai 40

Querying Protein-Protein Interaction Networks Guillaume Blin Florian Sikora Stéphane Vialette 52

Integrative Approach for Combining TNF α-NF κB Mathematical Model to a Protein Interaction Connectivity Map Mahesh Visvanathan Bernhard Pfeifer Christian Baumgartner Bernhard Tilg Gerald Henry Lushington 63

Hierarchical Organization of Functional Modules in Weighted Protein Interaction Networks Using Clustering Coefficient Min Li Jianxin Wang Jianer Chen Yi Pan 75

Bioinformatics Challenges in Translational Research (Invited Keynote Talk) Nicholas F. Tsinoremas 87

Untangling Tanglegrams: Comparing Trees by Their Drawings Balaji Venkatachalam Jim Apple Katherine St. John Dan Gusfield 88

An Experimental Analysis of Consensus Tree Algorithms for Large-Scale Tree Collections Seung-Jin Sul Tiffani L. Williams 100

Counting Faces in Split Networks Lichen BaoSergey Bereg 112

Relationship between Amino Acids Sequences and Protein Structures: Folding Patterns and Sequence Patterns Alexander Kister 124

Improved Algorithms for Parsing ESLTAGs: A Grammatical Model Suitable for RNA Pseudoknots Sanguthevar Rajasekaran Sahar Al Seesi Reda Ammar 135

Efficient Algorithms for Self Assembling Triangular and Other Nano Structures Vamsi Kundeti Sanguthevar Rajasekaran 148

Motif Construction from High-Throughput SELEX Data (Invited Keynote Talk) Esko Ukkonen 159

Rearrangement Phylogeny of Genomes in Contig Form Adriana Muñoz David Sankoff 160

Prediction of Contiguous Regions in the Amniote Ancestral Genome A&iumlet;da Ouangraoua Frédéric Boyer Andrew McPherson Éric Tannier Cedric Chauve 173

Pure Parsimony Xor Haplotyping Paola Bonizzoni Gianluca Della Vedova Riccardo Dondi Yuri Pirola Romeo Rizzi 186

A Decomposition of the Pure Parsimony Haplotyping Problem Allen Holder Thomas Langley 198

Exact Computation of Coalescent Likelihood under the Infinite Sites Model Yufeng Wu 209

Imputation-Based Local Ancestry Inference in Admixed Populations Bogdan Pa&scidle;aniuc Justin Kennedy Ion M&acheck;ndoiu 221

Interpreting Population Sequencing Data (Invited Keynote Talk) Shamil R. Sunyaev 234

Modeling and Visualizing Heterogeneity of Spatial Patterns of Protein-DNA Interaction from High-Density Chromatin Precipitation Mapping Data Juntao Li Fajrian Yunus Zhu Lei Majid Eshaghi Jianhua Liu R. Krishna Murthy Karuturi 236

A Linear-Time Algorithm for Analyzing Array CGH Data Using Log Ratio Triangulation Matthew Hayes Jing Li 248

Mining of cis-Regulatory Motifs Associated with Tissue-Specific Alternative Splicing Jihye Kim Sihui Zhao Brian E. Howard Steffen Heber 260

Analysis of Cis-Regulatory Motifs in Cassette Exons by Incorporating Exon Skipping Rates Sihui Zhao Jihye Kim Steffen Heber 272

A Class of Evolution-Based Kernels for Protein Homology Analysis: A Generalization of the PAM Model Valentina Sulimova Vadim Mottl Boris Mirkin Ilya Muchnik Casimir Kulikowski 284

Irreplaceable Amino Acids and Reduced Alphabets in Short-Term and Directed Protein Evolution Miguel A. Jiménez-Montaño Matthew He 297

A One-Class Classification Approach for Protein Sequences and Structures András Bánhalmi Róbert Busa-Fekete Balázs Kégl 310

Prediction and Classification of Real and Pseudo MicroRNA Precursors via Data Fuzzification and Fuzzy Decision Trees Na'el Abu-halaweh Robert Harrison 323

Author Index 335

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