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More About This Textbook
Overview
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.
Product Details
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 Aïet;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