Table of Contents

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