[Front cover]

Title Page i (PDF)

pp. i

Title Page iii (PDF)

pp. iii

[Copyright notice] (PDF)

pp. iv

Table of contents (PDF)

pp. v-xiv

Preface (PDF)

pp. xv-xvi

Committee Lists (PDF)

pp. xvii-xviii

Program Committee Members (PDF)

pp. xix-xxiv

Inferring Functional Groups from Microbial Gene Catalogue with Probabilistic Topic Models (Abstract)

Yuan An

pp. 3-9

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Stratified Random Forest for Genome-wide Association Study (Abstract)

pp. 10-15

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Structure-based RNA Function Prediction Using Elastic Shape Analysis (Abstract)

pp. 16-21

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VASP-S: A Volumetric Analysis and Statistical Model for Predicting Steric Influences on Protein-Ligand Binding Specificity (Abstract)

Brian Y. Chen

Soutir Bandyopadhyay

pp. 22-29

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Fast Algorithm for Clustering a Large Number of Protein Structural Decoys (Abstract)

Jingfen Zhang

Dong Xu

pp. 30-36

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Active Protein Interaction Network and Its Application on Protein Complex Detection (Abstract)

Jianxin Wang

Xiaoqing Peng

Min Li

Yong Luo

pp. 37-42

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Intrinsic Disorder in Putative Protein Sequences (Abstract)

Uros Midic

Zoran Obradovic

pp. 43-48

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Simplification Methods for Maximum Parsimony: A Relational View (Abstract)

Roberto Blanco

pp. 49-56

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Prediction of Trans-regulators of Recombination Hotspots in Mouse Genome (Abstract)

Min Wu

Jing Li

pp. 57-62

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A New Measurement for Evaluating Clusters in Protein Interaction Networks (Abstract)

Min Li

Xuehong Wu

Jianxin Wang

pp. 63-68

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Phylogenomic Analysis of the Phenylalanine Ammonia Lyase Gene Family in Loblolly Pine (Pinus Taeda L.) (Abstract)

Ujwal R. Bagal

James H. Leebens-Mack

W. Walter Lorenz

Jeffrey F.D. Dean

pp. 69-74

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Data-Driven Insights into Deletions of Mycobacterium tuberculosis Complex Chromosomal DR Region Using Spoligoforests (Abstract)

pp. 75-82

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Efficient and Fast Analysis for Detecting High Order Gene-by-Gene Interactions in a Genome-Wide Association Study (Abstract)

pp. 83-88

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Simultaneous Prediction of RNA Secondary Structure and Helix Coaxial Stacking (Abstract)

pp. 89-95

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Clustering PPI Data Based on Bacteria Foraging Optimization Algorithm (Abstract)

pp. 96-99

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imiRTP: An Integrated Method to Identifying miRNA-target Interactions in Arabidopsis thaliana (Abstract)

pp. 100-104

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Emulating Insertion and Deletion Events in Genome Rearrangement Analysis (Abstract)

William Arndt

Jijun Tang

pp. 105-108

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Benchmarking Short Sequence Mapping Tools (Abstract)

pp. 109-113

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Populating Local Minima in the Protein Conformational Space (Abstract)

Brian Olson

Amarda Shehu

pp. 114-117

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A Simple and Accurate Method for Rogue Taxon Identification (Abstract)

Andre J. Aberer

Alexandros Stamatakis

pp. 118-122

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An Improved Graph Entropy-based Method for Identifying Protein Complexes (Abstract)

Yan Yan

pp. 123-126

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Discovering Drug-Protein Interactions Based on their Fingerprints (Abstract)

Weimin Luo

Keith C.C. Chan

pp. 127-130

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Approximate Common Intervals in Multiple Genome Comparison (Abstract)

pp. 131-134

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Employing Weighted Biological Network Structure for Finding Disease Genetic Markers in SNP Association Studies (Abstract)

Jaeyoung Kim

Miyoung Shin

pp. 135-138

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mrNA: The MPI Randomized Numerical Aligner (Abstract)

pp. 139-142

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Prediction of Heme Binding Sites in Heme Proteins Using an Integrative Sequence Profile Coupling Evolutionary Information with Physicochemical Properties (Abstract)

pp. 143-146

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No-Reference Compression of Genomic Data Stored in FASTQ Format (Abstract)

Vishal Bhola

Ajit S. Bopardikar

Rangavittal Narayanan

Kyusang Lee

TaeJin Ahn

pp. 147-150

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Improved RNA-Seq Partitions in Linear Models for Isoform Quantification (Abstract)

pp. 151-154

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Chronology-Sensitive Hierarchical Clustering of Pyrosequenced DNA Samples of E. coli: A Case Study (Abstract)

pp. 155-159

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A Constraint Dynamic Graph Approach to Identify the Secondary Structure Topology from cryoEM Density Data in Presence of Errors (Abstract)

Dong Si

Jing He

pp. 160-163

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Stochastic Models for Studying the Degradation of mRNA Molecules (Abstract)

Tianhai Tian

pp. 167-172

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Generalized Adjacency in Genetic Networks and the Conservation of Functional Gene Clusters (Abstract)

Zhenyu Yang

David Sankoff

pp. 173-178

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Functional Gene Detection and Clustering from Seed Gene Sets (Abstract)

Alexander Senf

Xue-wen Chen

pp. 179-184

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Predicing Yeast Synthetic Lethal Genetic Interactions Using Short Polypeptide Clusters (Abstract)

Bo Li

pp. 185-190

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Improve Accuracy of Peptide Identification with Consistency between Peptides (Abstract)

pp. 191-196

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Delay-Dependent Stability for Genetic Regulatory Networks (Abstract)

Li-Ping Tian

Fang-Xiang Wu

pp. 197-201

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Reconstruction of Large-Scale Gene Regulatory Networks Using Bayesian Model Averaging (Abstract)

Haseong Kim

Erol Gelenbe

pp. 202-207

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Inferring Transcript Phylogenies (Abstract)

Yann Christinat

Bernard M.E. Moret

pp. 208-215

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Modeling Gene Regulatory Subnetworks from Time Course Gene Expression Data (Abstract)

pp. 216-221

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Evolutionary Conservation of Human Phosphorylation Sites (Abstract)

pp. 222-227

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Identifying Transcription Factors and microRNAs as Key Regulators of Pathways Using Bayesian Inference on Known Pathway Structures (Abstract)

pp. 228-233

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Global Network Alignment Based on Multiple Hub Seeds (Abstract)

Bingbo Wang

Lin Gao

pp. 234-237

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Employing Machine Learning Techniques for Data Enrichment: Increasing the Number of Samples for Effective Gene Expression Data Analysis (Abstract)

pp. 238-242

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Semi-supervised Learning of Alternatively Spliced Exons Using Co-training (Abstract)

Karthik Tangirala

Doina Caragea

pp. 243-246

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A Computational Pipeline for LC-MS/MS Based Metabolite Identification (Abstract)

pp. 247-251

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Stability Analysis of Feature Ranking Techniques on Biological Datasets (Abstract)

David Dittman

Taghi M. Khoshgoftaar

Randall Wald

Huanjing Wang

pp. 252-256

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Predicting Kinase-specific Phosphorylation Sites Using a Multitask Classification Framework (Abstract)

Shan Gao

Jianwen Fang

pp. 257-260

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Bayesian Alignment Model for LC-MS Data (Abstract)

pp. 261-264

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Biological Interpretation of Model-Reference Adaptive Control in a Mass Action Kinetics Metabolic Pathway Model (Abstract)

Chang F. Quo

May D. Wang

pp. 265-268

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Microarray Time-Series Data Clustering Using Rough-Fuzzy C-Means Algorithm (Abstract)

Pradipta Maji

Sushmita Paul

pp. 269-272

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Prediction and Evaluation of miRNA -- Target Gene Pairs Using K-means Clustering and Bipartite Graphs with Statistical Scoring (Abstract)

Kevin McCormick

Li Liao

pp. 273-277

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A Network Biology Approach to Predicting Drug Cardiotoxicity (Abstract)

Liang-Chin Huang

Jake Yue Chen

pp. 278-281

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Multi-label Learning for Protein Subcellular Location Prediction (Abstract)

pp. 282-285

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Deconvolution of Microarray Data Predicts Transcriptionally Regulated Protein Kinases of Plasmodium falciparum (Abstract)

pp. 286-289

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Systems Approach to Identifying Relevant Pathways from Phenotype Information in Dose-Dependent Time Series Microarray Data (Abstract)

Julian Dymacek

Nancy Lan Guo

pp. 290-293

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Identifying Ovarian Cancer Chemotherapy Response Relevant Gene Cliques (Abstract)

Bin Han

pp. 294-298

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Improved Quantification of Labeled LC-MS (Abstract)

Long Chen

Konstantinos Petritis

Tony Tegeler

Brianne Petritis

William E. Haskins

Jianqiu (Michelle) Zhang

pp. 299-303

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Formal Modeling and Analysis of Biological Regulatory Networks Using SPIN (Abstract)

pp. 304-308

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Learning Condition-Dependent Dynamical PPI Networks from Conflict-Sensitive Phosphorylation Dynamics (Abstract)

pp. 309-312

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Cardinal Multiridgelet-based Prostate Cancer Histological Image Classification for Gleason Grading (Abstract)

Hong-Jun Yoon

Ching-Chung Li

Christhunesa Christudass

pp. 315-320

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A Differential Evolution-Based System Supporting Medical Diagnosis through Automatic Knowledge Extraction from Databases (Abstract)

Ivanoe De Falco

pp. 321-326

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A Posture Scheduling Algorithm Using Constrained Shortest Path to Prevent Pressure Ulcers (Abstract)

pp. 327-332

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Computer-Based Image Analysis of Liver Steatosis with Large-Scale Microscopy Imagery and Correlation with Magnetic Resonance Imaging Lipid Analysis (Abstract)

pp. 333-338

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Predicting Malignancy from Mammography Findings and Surgical Biopsies (Abstract)

pp. 339-344

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PRIMEGENSw3: A Web-Based Tool for High-Throughput Primer and Probe Design (Abstract)

Garima Kushwaha

Gyan Prakash Srivastava

Dong Xu

pp. 345-351

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Coupling Oriented Hidden Markov Random Field Model with Local Clustering for Segmenting Blood Vessels and Measuring Spatial Structures in Images of Tumor Microenvironment (Abstract)

Wei Wei

pp. 352-357

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A Pattern Mining Approach for Classifying Multivariate Temporal Data (Abstract)

pp. 358-365

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3D Neuron Tip Detection in Volumetric Microscopy Images (Abstract)

Min Liu

Hanchuan Peng

Amit K. Roy-Chowdhury

Eugene Myers

pp. 366-371

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Automatic Summarization of Results from Clinical Trials (Abstract)

Rodney L. Summerscales

pp. 372-377

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Cell Resolution 3D Reconstruction of Developing Multilayer Tissues from Sparsely Sampled Volumetric Microscopy Images (Abstract)

Anirban Chakraborty

Ram Kishor Yadav

G. Venugopala Reddy

Amit K. Roy-Chowdhury

pp. 378-383

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Diagnostic Classification of Digital Mammograms by Wavelet-Based Spectral Tools: A Comparative Study (Abstract)

pp. 384-389

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Cost-Sensitive Classification on Pathogen Species of Bacterial Meningitis by Surface Enhanced Raman Scattering (Abstract)

pp. 390-393

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Classification of Schizophrenia Patients with Combined Analysis of SNP and fMRI Data Based on Sparse Representation (Abstract)

pp. 394-397

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A Novel Algorithm for Multi-class Cancer Diagnosis on MALDI-TOF Mass Spectra (Abstract)

Phuong Pham

Li Yu

Minh Nguyen

pp. 398-401

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Identification of Breast Cancer Gene Signature in Protein Interaction Network Using Graph Centrality (Abstract)

pp. 402-405

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Barbara Wisniowiecka-Kowalnik

Efficient Multiple Samples aCGH Analysis for Rare CNVs Detection (Abstract)

Pawel Stankiewicz

Anna Gambin

pp. 406-409

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Motion Artifact Correction in ASL images: An Improved Automated Procedure (Abstract)

pp. 410-413

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Object Segmentation by Comparison of Active Contour Snake and Level Set in Biomedical Applications (Abstract)

Muhammad Hameed Siddiqi

Sungyoung Lee

Young-Koo Lee

pp. 414-417

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Preserving Narratives in Electronic Health Records (Abstract)

pp. 418-421

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Histological Image Feature Mining Reveals Emergent Diagnostic Properties for Renal Cancer (Abstract)

pp. 422-425

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A Framework for Personalized Medicine with Reverse Phase Protein Array and Drug Sensitivity (Abstract)

pp. 426-429

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Mental Stress Detection Based on Soft Computing Techniques (Abstract)

F. Mokhayeri

M-R. Akbarzadeh-T

pp. 430-433

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Protein Structure Visualization by Dimension Reduction and Texture Mapping (Abstract)

pp. 437-442

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Detecting Pathway Cross-Talks by Analyzing Conserved Functional Modules across Multiple Phenotype-Expressing Organisms (Abstract)

Ye Jin

pp. 443-449

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Probabilistic Signal Network Models from Multiple Replicates of Sparse Time-Course Data (Abstract)

pp. 450-455

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Promoting Ranking Diversity for Biomedical Information Retrieval Based on LDA (Abstract)

pp. 456-461

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ENteric Immunity SImulator: A Tool for in silico Study of Gut Immunopathologies (Abstract)

Katherine V. Wendeldorf

Josep Bassaganya-Riera

pp. 462-469

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Essential Protein Discovery Based on Network Motif and Gene Ontology (Abstract)

Wooyoung Kim

Min Li

Jianxin Wang

pp. 470-475

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Multi-class Joint Rule Extraction and Feature Selection for Biological Data (Abstract)

Gang Fu

pp. 476-481

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Improving Prediction Accuracy of Protein-DNA Docking with GPU Computing (Abstract)

Bo Hong

Jiadong Wu

Jun-tao Guo

pp. 482-487

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Ontology Graph Based Query Expansion for Biomedical Information Retrieval (Abstract)

pp. 488-493

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BioVLAB-MMIA: A Reconfigurable Cloud Computing Environment for microRNA and mRNA Integrated Analysis (Abstract)

Patanachai Tangchaisin

Chathura Herath

Suresh Marru

Kenneth P. Nephew

Sun Kim

pp. 494-499

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An Artificial Neural Network Based Approach for Identification of Native Protein Structures Using an Extended Forcefield (Abstract)

Timothy Matthew Fawcett

pp. 500-505

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Finding Informative Genes from Multiple Microarray Experiments: A Graph-based Consensus Maximization Model (Abstract)

Liang Ge

Nan Du

Aidong Zhang

pp. 506-511

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Krishnaprasad Thirunarayan

Semantic Predications for Complex Information Needs in Biomedical Literature (Abstract)

pp. 512-519

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IDDI: The Integrated Domain-Domain Interaction Analysis System (Abstract)

Yul Kim

Bumki Min

Gwan-Su Yi

pp. 520-525

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Probabilistic Partial Least Square Regression: A Robust Model for Quantitative Analysis of Raman Spectroscopy Data (Abstract)

Shuo Li

pp. 526-531

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A Term Association Approach for Genomics Information Retrieval (Abstract)

pp. 532-537

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Protein Sequence Classification Using Feature Hashing (Abstract)

pp. 538-543

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Discriminative Application of String Similarity Methods to Chemical and Non-chemical Names for Biomedical Abbreviation Clustering (Abstract)

pp. 544-549

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ProKinO: A Framework for Protein Kinase Ontology (Abstract)

Gurinder Pal Singh Gosal

Natarajan Kannan

Krys J. Kochut

pp. 550-555

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Toward a Cooperative Natural Language Query Interface for Biological Databases (Abstract)

Hasan M. Jamil

pp. 556-561

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Supervised Link Discovery on Large-Scale Biomedical Concept Networks (Abstract)

pp. 562-568

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Assessment of Cluster Overlaps to Improve Accuracy of Module Detection from PPI Networks (Abstract)

Nicholas Soltau

Young-Rae Cho

pp. 569-573

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Internal Evaluation Measures as Proxies for External Indices in Clustering Gene Expression Data (Abstract)

pp. 574-577

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An Automatic System for Extracting Figures and Captions in Biomedical PDF Documents (Abstract)

pp. 578-581

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Identifying Protein Complexes from PPI Networks Using GO Semantic Similarity (Abstract)

pp. 582-585

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Visually Relating Gene Expression and in vivo DNA Binding Data (Abstract)

pp. 586-589

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Detection of Conflicts and Inconsistencies in Taxonomy-Based Authorization Policies (Abstract)

pp. 590-594

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Bayesian Classifiers for Chemical Toxicity Prediction (Abstract)

pp. 595-599

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Efficient Calculation of Structural Similarity Threshold for the SCAN Network Clustering Algorithm (Abstract)

pp. 600-603

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Hypergeometric Similarity Measure for Spatial Analysis in Tissue Imaging Mass Spectrometry (Abstract)

pp. 604-607

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Literature-based Evaluation of Microarray Normalization Procedures (Abstract)

pp. 608-612

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RNA2DMap: A Visual Exploration Tool of the Information in RNA's Higher-Order Structure (Abstract)

pp. 613-617

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R-PASS: A Fast Structure-Based RNA Sequence Alignment Algorithm (Abstract)

pp. 618-622

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Using Rules to Investigate the Differences in Partonomy between Biomedical Ontologies (Abstract)

Pengfei Sun

Songmao Zhang

pp. 623-626

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A Comparative Assessment of Conventional and Machine-Learning-Based Scoring Functions in Predicting Binding Affinities of Protein-Ligand Complexes (Abstract)

Hossam M. Ashtawy

Nihar R. Mahapatra

pp. 627-630

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Wavelet and PCA for Metabolic Network Comparison (Abstract)

pp. 633-638

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Mining Gene-centric Relationships from Literature to Support Drug Discovery (Abstract)

Ying Li

pp. 639-644

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Hypothesis Generation and Evaluation in Clinical Trial Design (Abstract)

Michael Liebman

Sabrina Molinaro

pp. 645-651

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Mining Protein Interactions and Gene Expression Data to Gain Insights into Drug-induced Toxicity Mechanisms (Abstract)

Kaushal Desai

David Brott

Xiaohua Hu

Anastasia Christianson

pp. 652-657

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Data Exploration in Secondary Use of Healthcare Data (Abstract)

Jian Wang

pp. 658

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Opening the Door to Electronic Medical Records: Using Informatics to Overcome Terabytes (Abstract)

pp. 659

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Uniting Data for Memory: Building Informatics against Alzheimer's (Abstract)

pp. 660

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Decision Support in Safety Intelligence Using Pharmaconnect Knowledgebase (Abstract)

pp. 661

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Generating More Knowledge from Our Data and More Value from Our Studies: The Value of Expert Information Science Skills (Abstract)

Anastasia M. Khoury Christianson

pp. 662

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Author Index (PDF)

pp. 663-668

[Roster page] (PDF)

pp. 670