Invited Keynote Talk: Set-Level Analyses for Genome-Wide Association Data (Abstract) / Dan L. Nicolae ; Omar De la Cruz ; William Wen ; Baoguan Ke ; Minsun Song |
Hierarchical Clustering Using Constraints / Mariana Kant ; Maurice LeBon ; David Sankoff |
The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI Based Local Searches / Mukul S. Bansal ; Oliver Eulenstein |
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 |
An Approach for Determining Evolutionary Distance in Network-Based Phylogenetic Analysis / Tingting Zhou ; Keith C.C. Chan ; Yi Pan ; Zhenghua Wang |
Pairwise Statistical Significance Versus Database Statistical Significance for Local Alignment of Protein Sequences / Ankit Agrawal ; Volker Brendel ; Xiaoqiu Huang |
Estimating Pairwise Statistical Significance of Protein Local Alignments Using a Clustering-Classification Approach Based on Amino Acid Composition / Arka Ghosh |
Gapped Extension for Local Multiple Alignment of Interspersed DNA Repeats / Todd J. Treangen ; Aaron E. Darling ; Mark A. Ragan ; Xavier Messeguer |
Improved Alignment of Protein Sequences Based on Common Parts / David Hoksza |
Invited Keynote Talk: Computing P-Values for Peptide Identifications in Mass Spectrometry / Nikita Arnold ; Tema Fridman ; Robert M. Day ; Andrey A. Gorin |
PFP: A Computational Framework for Phylogenetic Footprinting in Prokaryotic Genomes / Dongsheng Che ; Guojun Li ; Shane T. Jensen ; Jun S. Liu ; Ying Xu |
Accelerating the Neighbor-Joining Algorithm Using the Adaptive Bucket Data Structure / Leonid Zaslavsky ; Tatiana A. Tatusova |
Generalized Gene Adjacencies, Graph Bandwidth and Clusters in Yeast Evolution / Qian Zhu ; Zaky Adam ; Vicky Choi |
Physicochemical Correlation between Amino Acid Sites in Short Sequences under Selective Pressure / David Campo ; Zoya Dimitrova ; Yuri Khudyakov |
HCV Quasispecies Assembly Using Network Flows / Kelly Westbrooks ; Irina Astrovskaya ; Piotr Berman ; Alex Zelikovsky |
A Dynamic Programming Algorithm for De Novo Peptide Sequencing with Variable Scoring / Matthew A. Goto ; Eric J. Schwabe |
Invited Keynote Talk: Haplotype Sharing for Genome-Wide Case-Control Association Studies (Abstract) / Andrew S. Allen |
Incorporating Literature Knowledge in Bayesian Network for Inferring Gene Networks with Gene Expression Data / Eyad Almasri ; Peter Larsen ; Guanrao Chen ; Yang Dai |
Integrative Network Component Analysis for Regulatory Network Reconstruction / Chen Wang ; Jianhua Xuan ; Li Chen ; Po Zhao ; Yue Wang ; Robert Clarke ; Eric P. Hoffman |
A Graph-Theoretic Method for Mining Overlapping Functional Modules in Protein Interaction Networks / Min Li ; Jianxin Wang ; Jianer Chen |
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 |
Mean Squared Residue Based Biclustering Algorithms / Stefan Gremalschi ; Gulsah Altun |
Sparse Decomposition of Gene Expression Data to Infer Transcriptional Modules Guided by Motif Information / Ting Gong ; Rebecca B. Riggins |
A Novel Metric for Redundant Gene Elimination Based on Discriminative Contribution / Xue-Qiang Zeng ; Guo-Zheng Li ; Jack Y. Yang ; Mary Qu Yang |
Network-Based Inference of Cancer Progression from Microarray Data / Yongjin Park ; Stanley Shackney ; Russell Schwartz |
Invited Keynote Talk: Quiet Revolution: Connectivity in the Cancer Research Community (Abstract) / Kenneth Buetow |
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. Ruggeri ; Brani Vidakovic |
Accurate Inverse Consistent Non-rigid Image Registration and Its Application on Automatic Re-contouring / Qingguo Zeng ; Yunmei Chen |
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 |
Pattern Matching in RNA Structures / Kejie Li ; Reazur Rahman ; Aditi Gupta ; Prasad Siddavatam ; Michael Gribskov |
The Use of a Conformational Alphabet for Fast Alignment of Protein Structures / Wei-Mou Zheng |
On-the-Fly Rotamer Pair Energy Evaluation in Protein Design / Andrew Leaver-Fay ; Jack Snoeyink ; Brian Kuhlman |
Invited Keynote Talk: Integrative Viral Molecular Epidemiology: Hepatitis C Virus Modeling / James Lara |
Multiple Kernel Support Vector Regression for siRNA Efficacy Prediction / Shibin Qiu ; Terran Lane |
Hierarchical Clustering Support Vector Machines for Classifying Type-2 Diabetes Patients / Wei Zhong ; Rick Chow ; Richard Stolz ; Jieyue He ; Marsha Dowell |
Computational Mutagenesis of E. Coli Lac Repressor: Insight into Structure-Function Relationships and Accurate Prediction of Mutant Activity / Majid Masso ; Kahkeshan Hijazi ; Nida Parvez ; Iosif I. Vaisman |
Evaluating Genetic Algorithms in Protein-Ligand Docking / Rafael Ordog ; Vince Grolmusz |
A Hidden Markov Model Approach for Prediction of Genomic Alterations from Gene Expression Profiling / Huimin Geng ; Hesham H. Ali ; Wing C. Chan |
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 |
Incorporating Knowledge of Topology Improves Reconstruction of Interaction Networks from Microarray Data |
Invited Keynote Talk: Data Mining and Statistical Methods for Analyzing Microarray Experiments (Abstract) / Shin-Lian Lo ; Kwok-Leung Tsui ; Benjamin Barwick |
Seven Variations of an Alignment Workflow - An Illustration of Agile Process Design and Management in Bio-jETI / Anna-Lena Lamprecht ; Tiziana Margaria ; Bernhard Steffen |
Supporting Computational Systems Science: Genomic Analysis Tool Federations Using Aspects and AOP / David Stotts ; Keith Lee ; Ivan Rusyn |
BioDQ: Data Quality Estimation and Management for Genomics Databases / Alexandra Martinez ; Joachim Hammer ; Sanjay Ranka |
Stepped Linear Regression to Accurately Assess Statistical Significance in Batch Confounded Differential Expression Analysis / Juntao Li ; Jianhua Liu ; R. Krishna Murthy Karuturi |
Bagging Multiple Comparisons from Microarray Data / Dimitris N. Politis |
Human Blood-Brain Differential Gene-Expression Correlates with Dipeptide Frequency of Gene Products / Shandar Ahmad |
Author Index |
Invited Keynote Talk: Set-Level Analyses for Genome-Wide Association Data (Abstract) / Dan L. Nicolae ; Omar De la Cruz ; William Wen ; Baoguan Ke ; Minsun Song |
Hierarchical Clustering Using Constraints / Mariana Kant ; Maurice LeBon ; David Sankoff |
The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI Based Local Searches / Mukul S. Bansal ; Oliver Eulenstein |