4. ISBRA 2008: Atlanta, GA, USA

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

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