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Bioinformatics Research and Applications

Fourth International Symposium, ISBRA 2008, Atlanta, GA, USA, May 6-9, 2008. Proceedings

  • Editors
  • Ion Măndoiu
  • Raj Sunderraman
  • Alexander Zelikovsky
Conference proceedings ISBRA 2008

Part of the Lecture Notes in Computer Science book series (LNCS, volume 4983)

Also part of the Lecture Notes in Bioinformatics book sub series (LNBI, volume 4983)

Table of contents

  1. Front Matter
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  2. Invited Keynote Talk: Set-Level Analyses for Genome-Wide Association Data
    Dan L. Nicolae, Omar De la Cruz, William Wen, Baoguan Ke, Minsun Song
    Pages 1-1
  3. Hierarchical Clustering Using Constraints
    Mariana Kant, Maurice LeBon, David Sankoff
    Pages 2-13
  4. The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI Based Local Searches
    Mukul S. Bansal, Oliver Eulenstein
    Pages 14-25
  5. A Distance-Based Method for Detecting Horizontal Gene Transfer in Whole Genomes
    Xintao Wei, Lenore Cowen, Carla Brodley, Arthur Brady, D. Sculley, Donna K. Slonim
    Pages 26-37
  6. An Approach for Determining Evolutionary Distance in Network-Based Phylogenetic Analysis
    Tingting Zhou, Keith C. C. Chan, Yi Pan, Zhenghua Wang
    Pages 38-49
  7. Pairwise Statistical Significance Versus Database Statistical Significance for Local Alignment of Protein Sequences
    Ankit Agrawal, Volker Brendel, Xiaoqiu Huang
    Pages 50-61
  8. Estimating Pairwise Statistical Significance of Protein Local Alignments Using a Clustering-Classification Approach Based on Amino Acid Composition
    Ankit Agrawal, Arka Ghosh, Xiaoqiu Huang
    Pages 62-73
  9. Gapped Extension for Local Multiple Alignment of Interspersed DNA Repeats
    Todd J. Treangen, Aaron E. Darling, Mark A. Ragan, Xavier Messeguer
    Pages 74-86
  10. Improved Alignment of Protein Sequences Based on Common Parts
    David Hoksza
    Pages 87-99
  11. Invited Keynote Talk: Computing P-Values for Peptide Identifications in Mass Spectrometry
    Nikita Arnold, Tema Fridman, Robert M. Day, Andrey A. Gorin
    Pages 100-109
  12. PFP: A Computational Framework for Phylogenetic Footprinting in Prokaryotic Genomes
    Dongsheng Che, Guojun Li, Shane T. Jensen, Jun S. Liu, Ying Xu
    Pages 110-121
  13. Accelerating the Neighbor-Joining Algorithm Using the Adaptive Bucket Data Structure
    Leonid Zaslavsky, Tatiana A. Tatusova
    Pages 122-133
  14. Generalized Gene Adjacencies, Graph Bandwidth and Clusters in Yeast Evolution
    Qian Zhu, Zaky Adam, Vicky Choi, David Sankoff
    Pages 134-145
  15. Physicochemical Correlation between Amino Acid Sites in Short Sequences under Selective Pressure
    David Campo, Zoya Dimitrova, Yuri Khudyakov
    Pages 146-158
  16. HCV Quasispecies Assembly Using Network Flows
    Kelly Westbrooks, Irina Astrovskaya, David Campo, Yury Khudyakov, Piotr Berman, Alex Zelikovsky
    Pages 159-170
  17. A Dynamic Programming Algorithm for De Novo Peptide Sequencing with Variable Scoring
    Matthew A. Goto, Eric J. Schwabe
    Pages 171-182
  18. Invited Keynote Talk: Haplotype Sharing for Genome-Wide Case-Control Association Studies
    Andrew S. Allen
    Pages 183-183
  19. Incorporating Literature Knowledge in Bayesian Network for Inferring Gene Networks with Gene Expression Data
    Eyad Almasri, Peter Larsen, Guanrao Chen, Yang Dai
    Pages 184-195
  20. Integrative Network Component Analysis for Regulatory Network Reconstruction
    Chen Wang, Jianhua Xuan, Li Chen, Po Zhao, Yue Wang, Robert Clarke et al.
    Pages 196-207
  21. A Graph-Theoretic Method for Mining Overlapping Functional Modules in Protein Interaction Networks
    Min Li, Jianxin Wang, Jianer Chen
    Pages 208-219
  22. Identification of Transcription Factor Binding Sites in Promoter Regions by Modularity Analysis of the Motif Co-occurrence Graph
    Alexandre P. Francisco, Arlindo L. Oliveira, Ana T. Freitas
    Pages 220-231
  23. Mean Squared Residue Based Biclustering Algorithms
    Stefan Gremalschi, Gulsah Altun
    Pages 232-243
  24. Sparse Decomposition of Gene Expression Data to Infer Transcriptional Modules Guided by Motif Information
    Ting Gong, Jianhua Xuan, Li Chen, Rebecca B. Riggins, Yue Wang, Eric P. Hoffman et al.
    Pages 244-255
  25. A Novel Metric for Redundant Gene Elimination Based on Discriminative Contribution
    Xue-Qiang Zeng, Guo-Zheng Li, Jack Y. Yang, Mary Qu Yang
    Pages 256-267
  26. Network-Based Inference of Cancer Progression from Microarray Data
    Yongjin Park, Stanley Shackney, Russell Schwartz
    Pages 268-279
  27. Invited Keynote Talk: Quiet Revolution: Connectivity in the Cancer Research Community
    Kenneth Buetow
    Pages 280-280
  28. Wavelet-Based 3-D Multifractal Spectrum with Applications in Breast MRI Images
    Gordana Derado, Kichun Lee, Orietta Nicolis, F. DuBois Bowman, Mary Newell, Fabrizio F. Rugger et al.
    Pages 281-292
  29. Accurate Inverse Consistent Non-rigid Image Registration and Its Application on Automatic Re-contouring
    Qingguo Zeng, Yunmei Chen
    Pages 293-304
  30. GlycoBrowser: A Tool for Contextual Visualization of Biological Data and Pathways Using Ontologies
    Matthew Eavenson, Maciej Janik, Shravya Nimmagadda, John A. Miller, Krys J. Kochut, William S. York
    Pages 305-316
  31. Pattern Matching in RNA Structures
    Kejie Li, Reazur Rahman, Aditi Gupta, Prasad Siddavatam, Michael Gribskov
    Pages 317-330
  32. The Use of a Conformational Alphabet for Fast Alignment of Protein Structures
    Wei-Mou Zheng
    Pages 331-342
  33. On-the-Fly Rotamer Pair Energy Evaluation in Protein Design
    Andrew Leaver-Fay, Jack Snoeyink, Brian Kuhlman
    Pages 343-354
  34. Invited Keynote Talk: Integrative Viral Molecular Epidemiology: Hepatitis C Virus Modeling
    James Lara, Zoya Dimitrova, Yuri Khudyakov
    Pages 355-366
  35. Multiple Kernel Support Vector Regression for siRNA Efficacy Prediction
    Shibin Qiu, Terran Lane
    Pages 367-378
  36. Hierarchical Clustering Support Vector Machines for Classifying Type-2 Diabetes Patients
    Wei Zhong, Rick Chow, Richard Stolz, Jieyue He, Marsha Dowell
    Pages 379-389
  37. Computational Mutagenesis of E. coliLac Repressor: Insight into Structure-Function Relationships and Accurate Prediction of Mutant Activity
    Majid Masso, Kahkeshan Hijazi, Nida Parvez, Iosif I. Vaisman
    Pages 390-401
  38. Evaluating Genetic Algorithms in Protein-Ligand Docking
    Rafael Ördög, Vince Grolmusz
    Pages 402-413
  39. A Hidden Markov Model Approach for Prediction of Genomic Alterations from Gene Expression Profiling
    Huimin Geng, Hesham H. Ali, Wing C. Chan
    Pages 414-425
  40. Evolutionary Algorithm for Feature Subset Selection in Predicting Tumor Outcomes Using Microarray Data
    Qihua Tan, Mads Thomassen, Kirsten M. Jochumsen, Jing Hua Zhao, Kaare Christensen, Torben A. Kruse
    Pages 426-433
  41. Incorporating Knowledge of Topology Improves Reconstruction of Interaction Networks from Microarray Data
    Peter Larsen, Eyad Almasri, Guanrao Chen, Yang Dai
    Pages 434-443
  42. Invited Keynote Talk: Data Mining and Statistical Methods for Analyzing Microarray Experiments
    Shin-Lian Lo, Kwok-Leung Tsui, Benjamin Barwick
    Pages 444-444
  43. Seven Variations of an Alignment Workflow - An Illustration of Agile Process Design and Management in Bio-jETI
    Anna-Lena Lamprecht, Tiziana Margaria, Bernhard Steffen
    Pages 445-456
  44. Supporting Computational Systems Science: Genomic Analysis Tool Federations Using Aspects and AOP
    David Stotts, Keith Lee, Ivan Rusyn
    Pages 457-468
  45. BioDQ: Data Quality Estimation and Management for Genomics Databases
    Alexandra Martinez, Joachim Hammer, Sanjay Ranka
    Pages 469-480
  46. Stepped Linear Regression to Accurately Assess Statistical Significance in Batch Confounded Differential Expression Analysis
    Juntao Li, Jianhua Liu, R. Krishna Murthy Karuturi
    Pages 481-491
  47. Bagging Multiple Comparisons from Microarray Data
    Dimitris N. Politis
    Pages 492-503
  48. Human Blood-Brain Differential Gene-Expression Correlates with Dipeptide Frequency of Gene Products
    Shandar Ahmad
    Pages 504-508
  49. Back Matter
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About these proceedings

Introduction

This book constitutes the refereed proceedings of the Fourth International Symposium on Bioinformatics Research and Applications, ISBRA 2008, held in Atlanta, GA, USA in May 2008.

The 35 revised full papers presented together with 6 workshop papers and 6 invited papers were carefully reviewed and selected from a total of 94 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.

Keywords

bioinformatics biological systems analysis cellular systems classification complexity computational biology computational life scienc computational systems biology data mining evolutionary biology feature selection genome genome analysis machine lear

Bibliographic information

  • DOI https://doi.org/10.1007/978-3-540-79450-9
  • Copyright Information Springer-Verlag Berlin Heidelberg 2008
  • Publisher Name Springer, Berlin, Heidelberg
  • eBook Packages Computer Science
  • Print ISBN 978-3-540-79449-3
  • Online ISBN 978-3-540-79450-9
  • Series Print ISSN 0302-9743
  • Series Online ISSN 1611-3349
  • Buy this book on publisher's site