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Accepted Papers
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  Regular Papers  
  B207 "Fuzzy C-means method with empirical mode decomposition for clustering microarray data"
     Yan-Fei Wang, Zu-Guo Yu, and Vo Anh

B219 "A New Method for Measuring the Semantic Similarity on Gene Ontology"
     Ying Shen, Shaohong Zhang, and Hau-San Wong

B235 "Examining the sublineage structure of Mycobacterium tuberculosis complex strains with multiple-biomarker tensors"
     Cagri Ozcaglar, Amina Shabbeer, Scott Vandenberg, Bulent Yener, and Kristin P. Bennett

B238 "SoyMetDB: The Soybean Metabolome Database"
     Trupti Joshi, Qiuming Yao, Levi D. Franklin, Laurent Brechenmacher, Babu Valliyodan, Gary Stacey, Henry Nguyen, and Dong Xu

B249 "Protein-protein Interaction Prediction using Desolvation Energies and Interface Properties"
     Luis Rueda, Sridip Banerjee, Md. Mominul Aziz, and Mohammad Raza

B270 "Prediction of Protein-DNA Interactions based on Alpha Shape Modeling"
     Weiqiang Zhou and Hong Yan

B277 "Gene Cluster Profile Vectors: A Novel Method to Infer Functional Coupling Using Both Gene Proximity and Co-occurrence Profiles"
     Vikas Pejaver and Sun Kim

B279 "Identification of Critical Location on A Microstructural Bone Network"
     Taehyong Kim, Jaehan Koh, Kang Li, Murali Ramanathan, and Aidong Zhang

B293 "Iterative Correction of Suppressed Peptide Profiles from FTMS Measurements"
     Xuepo Ma, Travis Hestilow, Jian Cui, and Jianqiu Zhang

B304 "A Fast and Noise-Adaptive Rough-Fuzzy Hybrid Algorithm for Medical Image Segmentation"
     Arpit Srivastava, Abhinav Asati, and Mahua Bhattacharya

B314 "Peptide Charge State Determination of Tandem Mass Spectra from Low-Resolution Collision Induced Dissociation"
     Jinhong Shi and Fang-Xiang Wu

B316 "Accurate Prediction of ATP-binding Residues Using Sequence and Sequence-derived Structural Descriptors"
     Ke Chen, Marcin Mizianty, and Lukasz Kurgan

B318 "Link-Based Cluster Ensembles for Heterogeneous Biological Data Analysis"
     Natthakan Iam-On, Tossapon Boongoen, Simon Garrett, and Chris Price

B322 "FluRF, an automated flu virus reassortment finder based on phylogenetic trees"
     Alisa Yurovsky and Bernard M.E. Moret

B323 "Finding Optimal Control Policy in Probabilistic Boolean Networks with Hard Constraints by Using Integer Programming and Dynamic Programming"
     Xi Chen, Tatsuya Akutsu, Takeyuki Tamura, and Wai-Ki Ching

B326 "Semi-supervised learning Protein Complexes from Protein Interaction Networks"
     Lei Shi and Aidong Zhang

B337 "Discovering Functional Gene Pathways Associated with Cancer Heterogeneity via Sparse Supervised Learning"
     Shuichi Kawano, Teppei Shimamura, Atsushi Niida, Seiya Imoto, Rui Yamaguchi, Masao Nagasaki, Ryo Yoshida, Cristin Print, and Satoru Miyano

B345 "Prediction of Human Protein Kinase Substrate Specificities"
     Javad Safaei, Jano Manuch, Arvind Gupta, Ladislav Stacho, and Steven Pelech

B347 "Improving Robustness of Gene Ranking by Resampling and Permutation Based Score Correction and Normalization"
     Feng Yang and Kezhi Mao

B359 "Autoregressive Modeling of DNA Features for Short Exon Recognition"
     Yu Song and Hong Yan

B361 "Protein-protein Interaction Prediction via Collective Matrix Factorization"
     Qian Xu, Wei Xiang, and Qiang Yang

B369 "A Two-Stage Machine Learning Approach for Pathway Analysis"
     Wei Zhang, Scott Emrich, and Erliang Zeng

B379 "Concurrent Analysis of Copy Number Variations and Expression Profiles to Identify Genes Associated with Tumorigenesis and Survival Outcome in Lung Adenocarcinoma"
     Tzu-Pin Lu, Pei-Chun Chen, Liang-Chuan Lai, Mong-Hsun Tsai, Chuhsing Hsiao, and Eric Y Chuang

B384 "Ontology integration to identify protein complex in protein interaction networks"
     Bo Xu, Hongfei Lin, and Zhihao Yang

B403 "Predicting Human microRNA-disease Associations Based on Support Vector Machine"
     Qinghua Jiang, Guohua Wang, Tianjiao Zhang, and Yadong Wang

B404 "CEO: A Cloud Epistasis cOmputing model in GWAS"
     Zhengkui Wang, Yue Wang, Kian-Lee Tan, Limsoon Wong, and Divyakant Agrawal

B405 "A sparse regulatory network of copy-number driven expression reveals putative breast cancer oncogenes"
     yinyin yuan, Christina Curtis, Carlos Caldas, and Florian Markowetz

B408 "A Procedure for Identifying Master Regulators in Conjunction with Network Screening and Inference"
     Shigeru Saito, Xinrong Zhou, and Katsuhisa Horimoto

B410 "Robust hidden semi-Markov modeling of array CGH data"
     Jiarui Ding

B411 "Network-Based Identification of Smoking-Associated Gene Signature for Lung Cancer"
     Ying-Wooi Wan, Changchang Xiao, and Nancy Guo

B419 "Stochastic Gene Expression Modeling with Hill Function for Switch-like Gene Responses"
     Haseong Kim and Erol Gelenbe

B422 "Taxonomic Profiling for Metagenomic Sequences"
     Bo Liu, Theodore Gibbons, Mohammadreza Ghodsi, and Mihai Pop

B439 "Protein 8-class Secondary Structure Prediction Using Conditional Neural Fields"
     Zhiyong Wang, Feng Zhao, Jian Peng, and Jinbo Xu

B441 "IsoKEGG: A Logic based System for Querying Biological Pathways in KEGG"
     Kazi Zakia Sultana and Hasan Jamil

B442 "Truncation of Protein Sequences for Fast Profile Alignment with Application to Subcellular Localization"
     Man-Wai Mak, Wei Wang, and Sun-Yuan Kung

B444 "Multi-Objective Evolutionary Algorithms based Interpretable Fuzzy Models for Cancer Microarray Gene Expression Data Analysis"
     Zhenyu Wang and Vasile Plade

B445 "Feature Selection for Graph Kernels"
     Mehmet Tan, Faruk Polat, and Reda Alhajj

B446 "CAMBer: An Approach to Support Comparative Analysis of Multiple Bacterial Strains"
     Michal Wozniak, Limsoon Wong, and Jerzy Tiuryn

B448 "A Gene Ranking Method Using Text-Mining for the Identification of Disease Related Genes"
     Hyungmin Lee, Miyoung Shin, and Munpyo Hong

B462 "A Novel Reinforcement Learning Framework for Online Adaptive Seizure Prediction"
     Shouyi Wang, Wanpracha Chaovalitwongse, and Stephen Wong

B463 "An Evolutionary Monte Carlo Algorithm for Identifying Short Adjacent Repeats in Multiple Sequences"
     Jin Xu, Qiwei Li, Xiaodan Fan, Victor O. K. Li, and Shuo-Yen Robert Li

B467 "A Supervised Learning Approach to the Unsupervised Clustering of Genes"
     Andrew Rider, Geoffrey Siwo, Scott Emrich, Michael Ferdig, and Nitesh Chawla

B468 "Structure Identification and Parameter Estimation of Biological S-systems"
     Li-Zhi Liu, Fang-Xiang Wu, Li-Li Han, and Wenjun Zhang

B472 "Template-based Scoring Functions for Visualizing Biological Insights of H-2Kb–peptide–TCR Complexes"
     I-Hsin Liu, Yu-Shu Lo, and Jinn-Moon Yang

B477 "Gene Expression Rule Discovery with a Multi-objective Neural-Genetic Hybrid"
     Ed Keedwell and Ajit Narayanan

B480 "An Iterated Conditional Mode Solution for Bayesian Factor Modeling of Transcriptional Regulatory Networks"
     Jia Meng, Jianqiu Zhang, yidong chen, and Yufei Huang

B483 "NetLoc: Network Based Protein Localization Prediction Using Protein-Protein Interaction and Co-expression Networks"
     Ananda Mondal and Jianjun Hu

B488 "Predicting ligand binding residues using multi-positional correlations and kernel canonical correlation analysis"
     Alvaro Gonzalez, Li Liao, and Cathy Wu

B496 "Represented Indicator Measurement and Corpus Distillation on Focus Species Detection"
     Chih-Hsuan Wei and Hung-Yu Kao

B497 "PSI-RA: A parallel sparse index for read alignment on genomes"
     Muhammed Oguzhan Kulekci, Wing-Kai Hon, Rahul Shah, Jeffrey Scott Vitter, and Bojian Xu

B510 "Intracranial Pressure Level Prediction in Traumatic Brain Injury by Extracting Features from Multiple Sources and Using Machine Learning Methods"
     Wenan Chen, Charles Cockrell, Kevin Ward, and Kayvan Najarian

B513 "A New Method for Alignment of LC-MALDI-TOF Data"
     Zhiqun Tang, Lihua Zhang, Amrita Cheema, and Habtom Ressom

B516 "A Graph-based Elastic Net for Variable Selection and Module Identification for Genomic Data Analysis"
     Zheng Xia and Xiaobo Zhou

B518 "Computational Prediction of Toxicity"
     Meenakshi Mishra, Hongliang Fei, and Jun Huan

B525 "Detection of splicing events and multiread locations from RNA-seq data based on a geometric-tail (GT) distribution of intron length"
     Shao-Ke LOU, Jing-Woei LI, Hao QIN, Aldrin Kay-Yuen YIM, Leung Yau Lo, Bing Ni, Kwong Sak Leung, Stephen Kwok-Wing TSUI, and Ting-Fung CHAN

B526 "Evaluation of Short Read Metagenomic Assembly."
     Anveshi Charuvaka and Huzefa Rangwala

B530 "A Probabilistic Framework for Inferring Ancestral Genomic Orders"
     Jian Ma

B531 "Cis-regulatory Module Detection using Constraint Programming"
     Tias Guns, Hong Sun, Siegfried Nijssen, Kathleen Marchal, and Luc De Raedt

B535 "Predicting DNA-binding Locations and Orientation on Proteins Using Knowledge-based Learning of Geometric Properties"
     Chien-Chih Wang and Chien-Yu Chen

B544 "Eigenspectra, A Robust Regression Method For Multiplexed Raman Spectra Analysis"
     Shuo Li, Jean Gao, James Nyagilo, and Digant Dave

B550 "Integrated Analysis of the various types of microarray data using linear-mixed effects models"
     Sung Gon Yi and Taesung Park
  Short Papers  
  B218 "Classification of Genome-wide Copy Number Variations and Their Associated SNP and Gene Networks Analysis"
     Yang Liu, Yiu Fai Lee, and Michael K. Ng

B220 "A Parameterless Automatic Spot Detection Method in cDNA Microarray Images"
     Luis Rueda and Iman Rezaeian

B230 "seGOsa: Software Environment for Gene Ontology-driven Similarity Assessment"
     Haiying Wang, Francisco Azuaje, and Huiru Zheng

B231 "An accurate, automatic method for markerless alignment of electron tomographic images"
     Qi Chu, Fa Zhang, Kai Zhang, Xiaohua Wan, Mingwei Chen, and Zhiyong Liu

B234 "Overcoming Drug Resistance by Co-Targeting"
     Marzieh Ayati, Golnaz Taheri, Shahriar Arab, Limsoon Wong, and Changiz Eslahchi

B239 "Two-stage clustering based effective sample selection for classification of pre-miRNAs"
     Ping Xuan, Mao-zu Guo, Lei-lei Shi, Jun Wang, Wen-bin Li, and Ying-peng Han

B240 "Machine Learning Approaches for the Investigation of Features beyond Seed Matches Affecting miRNA Binding"
     Cen Gao and Jing Li

B241 "Prediction of Low Coverage Prone Regions for Illumina Sequencing Projects using a Support Vector Machine"
     Zejun Zheng, Guillaume Bourque, and Bertil Schmidt

B243 "Spatially Constrained Fuzzy Hyper-Prototype Clustering with Application to Brain Tissue Segmentation"
     Jin Liu, Tuan Pham, Wei Wen, and Perminer Sachdev

B245 "Exploring matrix factorization techniques for significant genes identification of microarray dataset"
     Wei Kong, Xiaoyang Mou, and Xiaohua Hu

B255 "A Non-parameter Ising Model for Network-based Identification of Differentially Expressed Genes"
     Xumeng Li, Zijun Wang, and Feng Luo

B257 "Hybrid SVM/CART Classification of Pathogenic Species of Bacterial Meningitis with Surface-Enhanced Raman Scattering"
     Chung-Yueh Huang, Tsung-Heng Tsai, Bing-Cheng Wen, Chia-Wen Chung, Li-Li Lie, Juen-Kai Wang, Yuh-Lin Wang, Chi-Hung Lin, Wen-Jie Lin, and Da-Wei Wang

B258 "Utilizing Cox Regression Model to Assess the Relations between Predefined Gene Sets and the Survival Outcome of Lung Adenocarcinoma"
     Jo-Yang Lu, Chuhsing Hsiao, Mong-Hsun Tsai, Pei-Chun Chen, Eric Y. Chuang, and Liang-Chuan Lai

B274 "Biomedical Concept Extraction using Concept Graphs and Ontology-based Mapping"
     Said Bleik, Wei Xiong, Yiran Wang, and Min Song

B292 "Pylogenetic Reconstruction with Gene Rearrangements and Gene Losses"
     Yiwei Zhang, Fei Hu, and Jijun Tang

B297 "Differences in outcomes of gene association analysis of cancer microarray data performed by different pre-processing algorithms"
     N Baskaran, Chee Keong Kwoh, and Kam Hui

B303 "Detecting SNPs-disease Associations Using Bayesian Networks"
     Bing Han and Xue-wen Chen

B306 "Sparse Canonical Correlation Analysis Applied to fMRI and Genetic Data Fusion"
     David Boutte and Jingyu Liu

B313 "An Automatic Procedure to Search Highly Repetitive Sequences in Genome as Fluorescence in Situ Hybridization Probes and Its Application on Brachypodium Distachyon"
     Qiwei Li, Tong Liang, Xiaodan Fan, Chunhui Xu, Weichang Yu, and Shuo-Yen Robert Li

B315 "Exploratory Analysis of the BioAssay Network with Implications to Therapeutic Discovery"
     Jintao Zhang, Gerlad Lushington, and Jun Huan

B325 "Decomposing protein interactome networks by graph entropy"
     Hao Lian, Chengsen Song, and Young-Rae Cho

B327 "Prediction of Intrinsic Disorder in Proteins by Unsupervised Learning from Multiple Predictors"
     Ping Zhang and Zoran Obradovic

B331 "Solving Training Issues in the Application of the Wavelet Transform to Precisely Analyze Human Body Acceleration Signals"
     E Martin

B336 "Sequence and Structural features of binding site residues in protein-protein complexes"
     Gromiha Michael, Saranya N., Selvaraj S., Jayaram B., and Kazuhiko Fukui

B341 "A Naïve Bayes Classifier for Differential Diagnosis of Long QT Syndrome in Children"
     Long Qu, Victoria Vetter, Geoffrey Bird, Haijun Qiu, and Pete White

B343 "Non-negative Matrix and Tensor Factorization Based Classification of Clinical Microarray Gene Expression Data"
     Yifeng Li and Alioune Ngom

B348 "Sparse Nonnegative Matrix Factorization with the Elastic Net"
     Weixiang Liu

B351 "Structural parsimony: reductions in sequence space"
     Roberto Blanco

B353 "NWE: Node-Weighted Expansion for Protein Complex Prediction Using Random Walk Distances"
     Osamu Maruyama and Ayaka Chihara

B356 "Unsupervised Pattern Discovery of Gene Expression Data"
     Gene P.K Wu, Keith C.C. Chan, Andrew K.C. Wong, and Bin Wu

B368 "Characterization of Structural Features for Small Regulatory RNAs in Escherichia coli Genomes"
     Shu-Yun Le and Bruce Shapiro

B372 "Decomposing PPI Networks for Complex Discovery"
     Guimei Liu, Chern Han Yong, Hon Nian Chua, and Limsoon Wong

B376 "Prediction of Protein-RNA Interaction Site Using SVM-KNN Algorithm with Spatial Information"
     Wei Chen, Shaowu Zhang, Yongmei Cheng, and Quan Pan

B381 "Enhanced Reference Guided Assembly"
     Francesco Vezzi, Alberto Policriti, and Federica Cattonaro

B385 "Hierarchical Decomposition of Vessel Skeletons for Graph Creation and Feature Extraction"
     Klaus Drechsler and Cristina Oyarzun Laura

B392 "A Possible Mutation that Enables H1N1 Influenza A Virus to Escape Antibody Recognition"
     Tran To Chinh Su, Stephanus Daniel Handoko, Christian Schönbach, Xiaoli Li, and Chee Keong Kwoh

B394 "Ranking SVM for Multiple Kernels Output Combination in Protein-Protein Interaction Extraction from Biomedical Literature"
     Zhihao Yang, Yuan Lin, Jiajin Wu, Nan Tang, Hongfei Lin, and Yanpeng Li

B401 "Semi-¬Supervised Feature Learning from Clinical Text"
     Zhuoran Wang, John Shawe-Taylor, and Anoop Shah

B406 "Concurrent Analysis of Copy Number Variation and Gene Expression: Application in Paired Non-Smoking Female Lung Cancer Patients"
     Jung-Chih Chang, Tzu-Pin Lu, Liang-Chuan Lai, Mong-Hsun Tsai, Chuhsing Hsiao, Eric Y. Chuang, and Pei-Chun Chen

B413 "A New Perspective of Integrative Genome-wide Association Analysis"
     Junho Kim and Doheon Lee

B415 "Detection and Application of CagA Sequence Markers for Assessing Risk Factor of Gastric Cancer Caused by Helicobacter pylori"
     Chao Zhang, Shunfu Xu, and Dong Xu

B416 "Computational Modeling of Phagocyte Transmigration during Biomaterial-Mediated Foreign Body Responses"
     Mingon Kang, Jean Gao, and Liping Tang

B418 "Rex: A Toolset for Reproducing Software Experiments"
     Somu Perianayagam, Gregory Andrews, and John Hartman

B423 "Discovering negative correlated gene sets from integrative gene expression data sets for cancer prognosis"
     Tao Zeng, Xuan Guo, and Juan Liu

B427 "A Comparative Study of Two Matrix Factorization Methods Applied to the Classification of Gene Expression Data"
     Vladimir Nikulin, Tian-Hsiang Huang, and Geoffrey McLachlan

B433 "MiRNAs as Promising Phylogenetic Markers for Inferring Deep Metazoan Phylogeny and in Support of Olfactores Hypothesis"
     Xiaoyan Zhang, Qingqing Cai, and Zuofeng Li

B434 "Time- and Space-efficient Maximal Repeat Finding Using Burrows-Wheeler Transform and Wavelet Trees"
     Muhammed Oguzhan Kulekci, Jeffrey Scott Vitter, and Bojian Xu

B437 "Searchable, Filterable Alignment Format"
     Ross Ka Kit Leung and Stephen Kwok-Wing TSUI

B447 "An ensemble method for querying gene expression compendia with experimental lists"
     Riet De Smet and Kathleen Marchal

B452 "Toward Automatically Drawn Metabolic Pathway Atlas with Peripheral Node Abstraction Algorithm"
     Myungha Jang, Arang Rhie, and Hyun S. Park

B458 "Correlating CpG islands, motifs, and sequence variants in human chromosome 21"
     Leah Spontaneo and Nick Cercone

B481 "An algorithm for mapping short reads to a dynamically changing genomic sequence"
     Solon Pissis, Costas Iliopoulos, Jan Holub, and Tomas Flouri

B482 "A Parallel Multi-objective Ab initio Approach for Protein Structure Prediction"
     David Becerra, Angelica Sandoval, Daniel Restrepo-Montoya, and Luis Nino

B485 "Probabilistic Topic Modeling for Genomic Data Interpretation"
     Xin Chen, Xiaohua Hu, Xiajiong Shen, and Gail Rosen

B486 "Identification and quantification of abundant species from pyrosequences of 16S rRNA by consensus alignment"
     Yuzhen Ye

B489 "Global Analysis of miRNA Target Genes in Colon Rectal Cancer"
     Meeta Pradhan, Lakenvia Ledford, Yogesh Pandit, and Mathew Palakal

B499 "Exploring a Multi-Source Fusion Approach for Genomics Information Retrieval"
     Qinmin Hu, Jimmy Huang, and Jun Miao

B500 "GPU-based Triangulations of the van der Waals Surface"
     Sergio Dias and Abel Gomes

B502 "Metabolomic profiling for biomarker discovery in pancreatic cancer"
     Prabhjit Kaur, Kathryn Sheikh, Alexander Kirilyuk, Ksenia Kirilyuk, Bhaskar Kallakury, Habtom Ressom, and Amrita Cheema

B507 "A Comparative Study on Gene Selection by Lasso and Dantzig Selector for Linear Classifiers"
     Songfeng Zheng and Weixiang Liu

B508 "Scalable, Updatable Predictive Models for Sequence Data"
     Neeraj Koul, Ngot Bui, and Vasant Honavar

B512 "Exploitation of 3D Stereotactic Surface Projection for Automated Classification of Alzheimer’s Disease according to Dementia Levels"
     Murat Ayhan, Ryan Benton, Vijay Raghavan, and Suresh Choubey

B515 "Module-Based Biomarker Discovery in Breast Cancer"
     Yuji Zhang, Jason Xuan, Robert Clarke, and Habtom Ressom

B528 "Gene Selection Using 1-Norm Regularization for Multi-Class Microarray Data"
     Xiaofei Nan, Nan Wang, Ping Gong, Chaoyang Zhang, Yixin Chen, and Dawn Wilkins

B534 "A Relevance-Novelty Combined Model for Genomics Search Result Diversification"
     Xiaoshi Yin, Zhoujun Li, Jimmy Huang, and Xiaohua Hu

B536 "Gene Clustering by Structural Prior based Local Factor Analysis Model under Bayesian Ying-Yang Harmony Learning"
     Lei Shi and Shikui Tu

B541 "A Generalized Sequence Pattern Matching Algorithm Using Dual-Seeding"
     Bing Ni, Leung Yau Lo, and Kwong Sak Leung

B551 "A Semi-Qualitative Model for Learning Gene Regulatory Networks"
     Zina Ibrahim, Alioune Ngom, and Ahmed Tawfik

B552 "An accurate classification of native and non-native protein-protein interactions using supervised and semi-supervised learning approaches"
     Nan Zhao, Bin Pang, Chi-Ren Shyu, and Dmitry Korkin