The Community for Technology Leaders
2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) (2010)
Hong Kong China
Dec. 18, 2010 to Dec. 21, 2010
ISBN: 978-1-4244-8306-8
TABLE OF CONTENTS

Predicting DNA-binding locations and orientation on proteins using knowledge-based learning of geometric properties (PDF)

Chien-Chih Wang , Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei 106, Taiwan, R.O.C.
Chien-Yu Chen , Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei 106, Taiwan, R.O.C.
pp. 3-8

Classification of genome-wide copy number variations and their associated SNP and gene networks analysis (PDF)

Yang Liu , Department of Mathematics, Hong Kong Baptist University, Kowloon Tong, Hong Kong
Yiu Fai Lee , Department of Mathematics, Hong Kong Baptist University, Kowloon Tong, Hong Kong
K. Ng Michael , Centre for Mathematical Imaging and Vision, Hong Kong Baptist University, Kowloon Tong, Hong Kong
pp. 9-12

Prediction of low coverage prone regions for Illumina sequencing projects using a support vector machine (PDF)

Zejun Zheng , School of Computer Engineering, Nanyang Technological University, Singapore 639798
Bertil Schmidt , School of Computer Engineering, Nanyang Technological University, Singapore 639798
Guillaume Bourque , Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01., Singapore 138672
pp. 13-16

Protein-protein interaction prediction using desolvation energies and interface properties (PDF)

Luis Rueda , School of Computer Science University of Windsor, 401 Sunset Ave., Windsor, ON, N9B 3P4, Canada
Sridip Banerjee , School of Computer Science University of Windsor, 401 Sunset Ave., Windsor, ON, N9B 3P4, Canada
Md. Mominul Aziz , School of Computer Science University of Windsor, 401 Sunset Ave., Windsor, ON, N9B 3P4, Canada
Mohammad Raza , School of Computer Science University of Windsor, 401 Sunset Ave., Windsor, ON, N9B 3P4, Canada
pp. 17-22

Prediction of DNA-binding protein based on alpha shape modeling (PDF)

Weiqiang Zhou , Department of Electronic Engineering, City University of Hong Kong, Kowloon, Hong Kong
Hong Yan , Department of Electronic Engineering, City University of Hong Kong, Kowloon, Hong Kong
pp. 23-28

Gene cluster profile vectors: A novel method to infer functional coupling using both gene proximity and co-occurrence profiles (PDF)

Vikas Rao Pejaver , School of Informatics and Computing, Indiana University, Bloomington, USA
Sun Kim , School of Informatics and Computing, Indiana University, Bloomington, USA
pp. 29-34

Phylogenetic reconstruction with gene rearrangements and gene losses (PDF)

Yiwei Zhang , Department of Computer Science and Engineering, University of South Carolina, Columbia SC, USA
Fei Hu , Department of Computer Science and Engineering, University of South Carolina, Columbia SC, USA
Jijun Tang , Department of Computer Science and Engineering, University of South Carolina, Columbia SC, USA
pp. 35-38

Detecting SNPs-disease associations using Bayesian networks (PDF)

Bing Han , Electrical Engineering and Computer Science Department, The University of Kansas, Lawrence, KS 66045, USA
Xue-wen Chen , Electrical Engineering and Computer Science Department, The University of Kansas, Lawrence, KS 66045, USA
pp. 39-42

Accurate prediction of ATP-binding residues using sequence and sequence-derived structural descriptors (PDF)

Ke Chen , Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB, Canada
J. Mizianty Marcin , Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB, Canada
Lukasz Kurgan , Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB, Canada
pp. 43-48

Unsupervised integration of multiple protein disorder predictors (PDF)

Ping Zhang , Center for Information Science and Technology, Temple University, Philadelphia, PA 19122
Zoran Obradovic , Center for Information Science and Technology, Temple University, Philadelphia, PA 19122
pp. 49-52

Sequence and structural features of binding site residues in protein-protein complexes (PDF)

M. Michael Gromiha , Computational Biology Research Center (CBRC), National Institute of Advanced Industrial, Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
N. Saranya , Department of Bioinformatics, Bharathidasan University, Tiruchirapalli 620024, Tamilnadu, India
S. Selvaraj , Department of Bioinformatics, Bharathidasan University, Tiruchirapalli 620024, Tamilnadu, India
B. Jayaram , Department of Chemistry and Supercomputing Facility for Bioinformatics and Computational, Biology, Indian Institute of Technology Delhi, New Delhi 110016, India
Kazuhiko Fukui , Computational Biology Research Center (CBRC), National Institute of Advanced Industrial, Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
pp. 53-56

Structural parsimony: Reductions in sequence space (PDF)

Roberto Blanco , Department of Computer Science and Systems Engineering (DIIS), Aragon Institute of Engineering Research (I3A), Universidad de Zaragoza Zaragoza, Spain
pp. 57-61

Protein-protein interaction prediction via Collective Matrix Factorization (PDF)

Qian Xu , Bioengineering Program, HKUST, Hong Kong, China
Evan Wei Xiang , Dept. of Computer Science and Engineering, HKUST, Hong Kong, China
Qiang Yang , Dept. of Computer Science and Engineering, HKUST, Hong Kong, China
pp. 62-67

Characterization of structural features for small regulatory RNAs in Escherichia coli genomes (PDF)

Shu-Yun Le , Center for Cancer Research Nanobiology Program, National Cancer Institute, NIH
A. Shapiro Bruce , Center for Cancer Research Nanobiology Program, National Cancer Institute, NIH
pp. 68-72

Prediction of Protein-RNA interaction site using SVM-KNN algorithm with spatial information (PDF)

Wei Chen , College of Automation, Northwestern Polytechnical University, 710072, Xi'an, China
Shao-Wu Zhang , College of Automation, Northwestern Polytechnical University, 710072, Xi'an, China
Yong-Mei Cheng , College of Automation, Northwestern Polytechnical University, 710072, Xi'an, China
Quan Pan , College of Automation, Northwestern Polytechnical University, 710072, Xi'an, China
pp. 73-76

Enhanced reference guided assembly (PDF)

Federica Cattonaro , IGA Applied Genomics Institute, via Linussio, 51, 33100 Udine, Italy
Alberto Policriti , DIMI, University of Udine, via delle Scienze, 206, 33100 Udine, Italy
Francesco Vezzi , DIMI, University of Udine, via delle Scienze, 206, 33100 Udine, Italy
pp. 77-80

A possible mutation that enables H1N1 influenza a virus to escape antibody recognition (PDF)

T. T. Su Chinh , School of Computer Engineering, Nanyang Technological University, Singapore
D. Handoko Stephanus , School of Computer Engineering, Nanyang Technological University, Singapore
Chee-Keong Kwoh , School of Computer Engineering, Nanyang Technological University, Singapore
Christian Schonbach , Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Fukuoka, Japan
Xiaoli Li , Institute for Infocomm Research, Agency for Science, Technology and Research, Singapore
pp. 81-84

CEO a cloud epistasis computing model in GWAS (PDF)

Zhengkui Wang , NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore
Yue Wang , NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore
Kian-Lee Tan , School of Computing, National University of Singapore, Singapore
Limsoon Wong , School of Computing, National University of Singapore, Singapore
Divyakant Agrawal , Department of Computer Science, University of California, Santa Barbara, USA
pp. 85-90

A new perspective of integrative genome-wide association analysis considering trans eSNP effect (PDF)

Junho Kim , Department of Bio and Brain Engineering, KAIST, Daejeon, South Korea
Doheon Lee , Department of Bio and Brain Engineering, KAIST, Daejeon, South Korea
pp. 91-94

MetaPhyler: Taxonomic profiling for metagenomic sequences (PDF)

Bo Liu , Center for Bioinformatics and Computational Biology, UMIACS
Theodore Gibbons , Center for Bioinformatics and Computational Biology, UMIACS
Mohammad Ghodsi , Center for Bioinformatics and Computational Biology, UMIACS
Mihai Pop , Center for Bioinformatics and Computational Biology, UMIACS
pp. 95-100

MiRNAs as promising phylogenetic markers for inferring deep metazoan phylogeny and in support of Olfactores hypothesis (PDF)

Qingqing Cai , School of Life Sciences and Technology, Tongji University, Shanghai, 200092, P. R. China
Xiaoyan Zhang , School of Life Sciences and Technology, Tongji University, Shanghai, 200092, P. R. China
Zoufeng Li , Shanghai Center for Bioinformation Technology, Shanghai 200235, P. R. China
pp. 101-104

alns — A searchable and filterable sequence alignment format (PDF)

Ross K K Leung , Hong Kong Bioinformatics Centre and School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong
Stephen K W Tsui , Hong Kong Bioinformatics Centre and School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong
pp. 105-108

Protein 8-class secondary structure prediction using Conditional Neural Fields (PDF)

Zhiyong Wang , Toyota Technological Institute at Chicago, Chicago, IL, United States
Feng Zhao , Toyota Technological Institute at Chicago, Chicago, IL, United States
Jian Peng , Toyota Technological Institute at Chicago, Chicago, IL, United States
Jinbo Xu , Toyota Technological Institute at Chicago, Chicago, IL, United States
pp. 109-114

Truncation of protein sequences for fast profile alignment with application to subcellular localization (PDF)

Man-Wai Mak , Dept. of Electronic and Information Engineering, The Hong Kong Polytechnic University, Hung Hom, Hong Kong SAR
Wei Wang , Dept. of Electronic and Information Engineering, The Hong Kong Polytechnic University, Hung Hom, Hong Kong SAR
Sun-Yuan Kung , Dept. of Electrical Engineering, Princeton University, New Jersey, USA
pp. 115-120

CAMBer: An approach to support comparative analysis of multiple bacterial strains (PDF)

Michal Wozniak , Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Poland
Limsoon Wong , School of Computing, National University of Singapore, Singapore
Jerzy Tiuryn , Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Poland
pp. 121-126

Template-based scoring functions for visualizing biological insights of H-2Kb-peptide-TCR complexes (PDF)

I-Hsin Liu , Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 30050, Taiwan
Yu-Shu Lo , Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 30050, Taiwan
Jinn-Moon Yang , Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 30050, Taiwan
pp. 127-132

An algorithm for mapping short reads to a dynamically changing genomic sequence (PDF)

Tomas Flouri , Department of Theoretical Computer Science, Faculty of Information Technology, Czech Technical University in Prague, Czech Republic
Jan Holub , Department of Theoretical Computer Science, Faculty of Information Technology, Czech Technical University in Prague, Czech Republic
Costas Iliopoulos , Department of Computer Science, King's College London, London WC2R 2LS, UK
Solon Pissis , Department of Computer Science, King's College London, London WC2R 2LS, UK
pp. 133-136

A parallel multi-objective ab initio approach for protein structure prediction (PDF)

David Becerra , Intelligent Systems Research Laboratory (LISI) and the Algorithms and Combinatorics Research Group (ALGOS), National University of Colombia
Angelica Sandoval , Intelligent Systems Research Laboratory (LISI) and the Algorithms and Combinatorics Research Group (ALGOS), National University of Colombia
Daniel Restrepo-Montoya , Intelligent Systems Research Laboratory (LISI) and the Algorithms and Combinatorics Research Group (ALGOS), National University of Colombia
F. Nino Luis , Intelligent Systems Research Laboratory (LISI) and the Algorithms and Combinatorics Research Group (ALGOS), National University of Colombia
pp. 137-141

NetLoc: Network based protein localization prediction using protein-protein interaction and co-expression networks (PDF)

M. Mondal Ananda , Department of Computer Science and Engineering, University of South Carolina, 301 Main St, Columbia, SC, 29036
Jianjun Hu , Department of Computer Science and Engineering, University of South Carolina, 301 Main St, Columbia, SC, 29036
pp. 142-148

Probabilistic topic modeling for genomic data interpretation (PDF)

Xin Chen , College of Information Science and Technology, Drexel University, Philadelphia, PA, USA
Xiaohua Hu , College of Information Science and Technology, Drexel University, Philadelphia, PA, USA
Xiajiong Shen , College of Computer and Information Engineering, Henan University, Henan, China
Gail Rosen , Department of Electrical and Computer Engineering at Drexel University in Philadelphia, PA, USA
pp. 149-152

Identification and quantification of abundant species from pyrosequences of 16S rRNA by consensus alignment (PDF)

Yuzhen Ye , School of Informatics and Computing, Bloomington, IN 47408, U.S.A
pp. 153-157

Predicting ligand binding residues using multi-positional correlations and kernel canonical correlation analysis (PDF)

J. Gonzalez Alvaro , Department of Computer and Information Sciences, University of Delaware, 101 Smith Hall, Newark, DE 19716
Li Liao , Department of Computer and Information Sciences, University of Delaware, 101 Smith Hall, Newark, DE 19716
H. Wu Cathy , Department of Computer and Information Sciences, University of Delaware, 101 Smith Hall, Newark, DE 19716
pp. 158-163

Detection of splicing events and multiread locations from RNA-seq data based on a geometric-tail (GT) distribution of intron length (PDF)

Authors Shao-Ke Lou , The Chinese University of Hong Kong, Sha Tin, N.T., Hong Kong
Jing-Woei Li , The Chinese University of Hong Kong, Sha Tin, N.T., Hong Kong
Hao Qin , The Chinese University of Hong Kong, Sha Tin, N.T., Hong Kong
Aldrin Kay-Yuen Yim , The Chinese University of Hong Kong, Sha Tin, N.T., Hong Kong
Leung-Yau Lo , The Chinese University of Hong Kong, Sha Tin, N.T., Hong Kong
Bing Ni , The Chinese University of Hong Kong, Sha Tin, N.T., Hong Kong
Kwong-Sak Leung , The Chinese University of Hong Kong, Sha Tin, N.T., Hong Kong
Stephen Kwok-Wing Tsui , The Chinese University of Hong Kong, Sha Tin, N.T., Hong Kong
Ting-Fung Chan , The Chinese University of Hong Kong, Sha Tin, N.T., Hong Kong
pp. 164-170

Evaluation of short read metagenomic assembly (PDF)

Anveshi Charuvaka , Dept. of Computer Science George Mason University
Huzefa Rangwala , Dept. of Computer Science George Mason University
pp. 171-178

A probabilistic framework for inferring ancestral genomic orders (PDF)

Jian Ma , Department of Bioengineering and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, USA
pp. 179-184

An accurate classification of native and non-native protein-protein interactions using supervised and semi-supervised learning approaches (PDF)

Nan Zhao , Informatics Institute and Department of Computer Science, University of Missouri
Bin Pang , Informatics Institute and Department of Computer Science, University of Missouri
Chi-Ren Shyu , Informatics Institute and Department of Computer Science, University of Missouri
Dmitry Korkin , Informatics Institute and Department of Computer Science, University of Missouri
pp. 185-189

Fuzzy C-means method with empirical mode decomposition for clustering microarray data (PDF)

Yan-Fei Wang , Discipline of Mathematical Sciences, Faculty of Science and Technology, Queensland University of Technology, Brisbane, Q4001, Australia
Zu-Guo Yu , Discipline of Mathematical Sciences, Faculty of Science and Technology, Queensland University of Technology, Brisbane, Q4001, Australia
Vo Anh , Discipline of Mathematical Sciences, Faculty of Science and Technology, Queensland University of Technology, Brisbane, Q4001, Australia
pp. 192-197

Overcoming drug resistance by co-targeting (PDF)

Marzieh Ayati , Department of Computer Science, Sharif University of Technology, Iran
Golnaz Taheri , Department of Computer Science, Sharif University of Technology, Iran
Shahriar Arab , School of Computer Science, Institute for Research in Fundamental Sciences (IPM), Iran
Limsoon Wong , Department of Computer Science, National University of Singapore, Singapore
Changiz Eslahchi , Department of Mathematics, Shahid Beheshti University, Iran
pp. 198-202

SoyMetDB: The soybean metabolome database (PDF)

Trupti Joshi , Department of Computer Science; University of Missouri, Columbia, MO 65211-2060, USA
Qiuming Yao , Department of Computer Science; University of Missouri, Columbia, MO 65211-2060, USA
D. Franklin Levi , Department of Computer Science; University of Missouri, Columbia, MO 65211-2060, USA
Laurent Brechenmacher , Christopher S. Bond Life Sciences Center; University of Missouri, Columbia, MO 65211-2060, USA
Babu Valliyodan , Christopher S. Bond Life Sciences Center; University of Missouri, Columbia, MO 65211-2060, USA
Gary Stacey , Christopher S. Bond Life Sciences Center; University of Missouri, Columbia, MO 65211-2060, USA
Henry Nguyen , Christopher S. Bond Life Sciences Center; University of Missouri, Columbia, MO 65211-2060, USA
Dong Xu , Department of Computer Science; University of Missouri, Columbia, MO 65211-2060, USA
pp. 203-208

Machine learning approaches for the investigation of features beyond seed matches affecting miRNA binding (PDF)

Cen Gao , Department of Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, OH 44106, USA
Jing Li , Department of Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, OH 44106, USA
pp. 209-213

A non-parameter Ising model for network-based identification of differentially expressed genes in recurrent breast cancer patients (PDF)

Xumeng Li , School of Computing, Clemson University, Clemson, SC, 29634, USA
F. Alex Feltus , Department of Genetics and Biochemistry, Clemson University, Clemson, SC, 29634, USA
Xiaoqian Sun , Department of Mathematics Science, Clemson University, Clemson, SC, 29634, USA
Zijun Wang , School of Computing, Clemson University, Clemson, SC, 29634, USA
Feng Luo , School of Computing, Clemson University, Clemson, SC, 29634, USA
pp. 214-217

Utilizing Cox regression model to assess the relations between predefined gene sets and the survival outcome of lung adenocarcinoma (PDF)

Jo-Yang Lu , Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
Y Chuang Eric , Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
K. Hsiao Chuhsing , Department of Public Health, Institute of Epidemiology, National Taiwan University, Taipei, Taiwan
Mong-Hsun Tsai , Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
Liang-Chuan Lai , Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
Pei-Chun Chen , Department of Statistics and Bioinformatics Science, Providence University, Taichung, Taiwan
pp. 218-221

Iterative correction of suppressed peptide profiles from FTMS measurements (PDF)

Xuepo Ma , Department of Electrical and Computer Engineering, University of Texas at San Antonio, San Antonio, TX, USA
J. Hestilow Travis , Department of Electrical and Computer Engineering, University of Texas at San Antonio, San Antonio, TX, USA
Jian Cui , Department of Electrical and Computer Engineering, University of Texas at San Antonio, San Antonio, TX, USA
Jianqiu Zhang , Department of Electrical and Computer Engineering, University of Texas at San Antonio, San Antonio, TX, USA
pp. 222-227

Outcomes of gene association analysis of cancer microarray data are impacted by pre-processing algorithms (PDF)

N Baskaran , Division of Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Drive Singapore 169610
Chee Keong Kwoh , Division of Information Systems, School of Computer Engineering, Nanyang Technological University, Nanyang Avenue, Singapore 639798
M. Hui Kam , Division of Cellular and Molecular Research, National Cancer Centre Singapore, 11 Hospital Drive Singapore 169610
pp. 228-233

Peptide charge state determination of tandem mass spectra from low-resolution collision induced dissociation (PDF)

Jinhong Shi , Division of Biomedical Engineering, University of Saskatchewan, Saskatoon, Canada
Fang-Xiang Wu , Division of Biomedical Engineering, Department of Mechanical Engineering, University of Saskatchewan, Saskatoon, Canada
pp. 234-239

Finding optimal control policy in Probabilistic Boolean Networks with hard constraints by using integer programming and dynamic programming (PDF)

Xi Chen , AMAC Laboratory, Department of Mathematics, The University of Hong Kong, Hong Kong, China
Tatsuya Akutsu , Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto, Japan
Takeyuki Tamura , Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto, Japan
Wai-Ki Ching , AMAC Laboratory, Department of Mathematics, The University of Hong Kong, Hong Kong, China
pp. 240-246

Semi-supervised learning protein complexes from protein interaction networks (PDF)

Lei Shi , Computer Science & Engineering Department, State University of New York at Buffalo, Buffalo, NY 14260, USA
Aidong Zhang , Computer Science & Engineering Department, State University of New York at Buffalo, Buffalo, NY 14260, USA
pp. 247-252

Discovering functional gene pathways associated with cancer heterogeneity via sparse supervised learning (PDF)

Shuichi Kawano , Human Genome Center, Institute of Medical Science University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
Teppei Shimamura , Human Genome Center, Institute of Medical Science University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
Atsushi Niida , Human Genome Center, Institute of Medical Science University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
Seiya Imoto , Human Genome Center, Institute of Medical Science University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
Rui Yamaguchi , Human Genome Center, Institute of Medical Science University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
Masao Nagasaki , Human Genome Center, Institute of Medical Science University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
Ryo Yoshida , Human Genome Center, Institute of Medical Science University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
Cristin Printe , Human Genome Center, Institute of Medical Science University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
Satoru Miyano , Human Genome Center, Institute of Medical Science University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
pp. 253-258

Prediction of human protein kinase substrate specificities (Abstract)

Javad Safaei , Department of Computer Science, University of British Columbia, Vancouver, Canada
Jan Manuch , Department of Computer Science, University of British Columbia, Vancouver, Canada
Arvind Gupta , Department of Computer Science, University of British Columbia, Vancouver, Canada
Ladislav Stacho , Department of Mathematics, Simon Fraser University, Burnaby, Canada
Steven Pelech , Department of Medicine, University of British Columbia, Vancouver, Canada, Kinexus Bioinformatics Corporation, Vancouver, Canada
pp. 259-264

Sparse nonnegative matrix factorization with the elastic net (PDF)

Weixiang Liu , Department of Biomedical Engineering, School of Medicine, Shenzhen University, Shenzhen, China 518060
Songfeng Zheng , Department of Mathematics, Missouri State University Springfield, MO 65897, USA
Sen Jia , School of Computer Science, Shenzhen University, Shenzhen, China 518060
Linlin Shen , School of Computer Science, Shenzhen University, Shenzhen, China 518060
Xianghua Fu , School of Computer Science, Shenzhen University, Shenzhen, China 518060
pp. 265-268

Unsupervised discovery of fuzzy patterns in gene expression data (PDF)

P. K. Wu Gene , Department of Computing, The Hong Kong, Polytechnic University, Hong Kong SAR, China
C. C. Chan Keith , Department of Computing, The Hong Kong, Polytechnic University, Hong Kong SAR, China
K. C. Wong Andrew , Department of Systems Design Engineering, University of Waterloo, Waterloo, Ontario, Canada
Bin Wu , Department of Systems Design Engineering, University of Waterloo, Waterloo, Ontario, Canada
pp. 269-273

A two-stage machine learning approach for pathway analysis (PDF)

Wei Zhang , Deprtment of Computer Science and Engineering, University of Notre Dame, Notre Dame, USA
Scott Emrich , Deprtment of Computer Science and Engineering, University of Notre Dame, Notre Dame, USA
Erliang Zeng , Deprtment of Computer Science and Engineering, University of Notre Dame, Notre Dame, USA
pp. 274-279

Decomposing PPI networks for complex discovery (PDF)

Guimei Liu , School of Computing, National University of Singapore, Singapore
Chern Han Yong , School of Computing, National University of Singapore, Singapore
Limsoon Wong , School of Computing, National University of Singapore, Singapore
Hon Nian Chua , Data Mining Department, Institute for Infocomm Research, Singapore
pp. 280-283

Concurrent analysis of copy number variations and expression profiles to identify genes associated with tumorigenesis and survival outcome in lung adenocarcinoma (PDF)

Tzu-Pin Lu , Graduate Institute of Biomedical, Electronics and Bioinformatics, National Taiwan University
Liang-Chuan Lai , Graduate Institute of Physiology, National Taiwan University
K. Hsiao Chuhsing , Department of Public Health, Institute of Epidemiology, National Taiwan University
Pei-Chun Chen , Department of Statistics and Informatics Science, Providence University
Mong-Hsun Tsai , Institute of Biotechnology, National Taiwan University
Y Chuang Eric , Graduate Institute of Biomedical, Electronics and Bioinformatics, National Taiwan University
pp. 284-289

Ontology integration to identify protein complex in protein interaction networks (PDF)

Bo Xu , Department of Computer Science and Engineering, Dalian University of Technology, Dalian, China
Hongfei Lin , Department of Computer Science and Engineering, Dalian University of Technology, Dalian, China
Zhihao Yang , Department of Computer Science and Engineering, Dalian University of Technology, Dalian, China
pp. 290-295

A procedure for identifying master regulators in conjunction with network screening and inference (PDF)

Shigeru Saito , INFOCOM Corp
Xinrong Zhou , Tongji Hospital
Taejeong Bae , Seoul National University
Sunghoon Kim , Seoul National University
pp. 296-301

Stochastic gene expression modeling with hill function for switch-like gene responses (PDF)

Haseong Kim , Intelligent Systems and Networks Group, Department of Electrical and Electronic Engineering, Imperial College London, UK
Erol Gelenbe , Intelligent Systems and Networks Group, Department of Electrical and Electronic Engineering, Imperial College London, UK
pp. 302-307

Multi-objective evolutionary algorithms based Interpretable Fuzzy models for microarray gene expression data analysis (PDF)

Zhenyu Wang , Computing Laboratory, Oxford University, Oxford, OX1 3QD, UK
Vasile Palade , Computing Laboratory, Oxford University, Oxford, OX1 3QD, UK
pp. 308-313

An ensemble method for querying gene expression compendia with experimental lists (PDF)

Riet De Smet , Department of Microbial and Molecular systems, Katholieke Universiteit Leuven, Belgium
Kathleen Marchal , Department of Microbial and Molecular systems, Katholieke Universiteit Leuven, Belgium
pp. 3141-318

Correlating CpG islands, motifs, and sequence variants in human chromosome 21 (PDF)

Leah Spontaneo , Department of Computer Science and Engineering, York University, Toronto, Ontario, Canada
Nick Cercone , Department of Computer Science and Engineering, York University, Toronto, Ontario, Canada
pp. 319-322

A supervised learning approach to the unsupervised clustering of genes (PDF)

Andrew Rider , Department of Computer Science and Engineering
Geoffrey Siwo , Department of Biological Sciences
Scott Emrich , Department of Computer Science and Engineering
Michael Ferdig , Department of Biological Sciences
Nitesh V. Chawla Habtom , Department of Computer Science and Engineering
pp. 322-328

Structure identification and parameter estimation of biological s-systems (PDF)

Li-Zhi Liu , Department of Mechanical Engineering
Fang-Xiang Wu , Department of Mechanical Engineering
Li-Li Han , Department of Mechanical Engineering
W. J. Zhang , Department of Mechanical Engineering
pp. 329-334

An Iterated Conditional Modes solution for sparse Bayesian factor modeling of transcriptional regulatory networks (PDF)

Jia Meng , Department of Electrical and Computer Engineering, University of Texas at San Antonio, San Antonio Texas
Jianqiu Zhang , Department of Electrical and Computer Engineering, University of Texas at San Antonio, San Antonio Texas
Yidong Chen , Department of Epidemiology and Biostatistics, UT Health Science Center at San Antonio, San Antonio, Texas
Yufei Huang , Department of Electrical and Computer Engineering, University of Texas at San Antonio, San Antonio Texas
pp. 335-340

Global analysis of miRNA target genes in colon rectal cancer (PDF)

Meeta Pradhan , School of Informatics, Indiana University-Purdue University, Indianapolis, IN 46202
Lakenvia Ledford , School of Informatics, Indiana University-Purdue University, Indianapolis, IN 46202
Yogesh Pandit , School of Informatics, Indiana University-Purdue University, Indianapolis, IN 46202
Mathew Palakal , School of Informatics, Indiana University-Purdue University, Indianapolis, IN 46202
pp. 341-345

A new method for alignment of LC-MALDI-TOF data (PDF)

Zhiqun Tang , Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
Lihua Zhang , Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
K. Cheema Amrita , Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
W. Ressom Habtom , Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
pp. 346-351

Module-based biomarker discovery in breast cancer (PDF)

Yuji Zhang , Dept. of Electrical & Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA
J. Xuan Jason , Dept. of Electrical & Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA
Robert Clarke , Lombardi Comprehensive Cancer Center, Georgetown University medical Center, Washington, DC
W. Ressom Habtom , Lombardi Comprehensive Cancer Center, Georgetown University medical Center, Washington, DC
pp. 352-356

A graph-based elastic net for variable selection and module identification for genomic data analysis (PDF)

Zheng Xia , Department of Radiology, The Methodist Hospital Research Institute, Houston, TX 77030, USA, Weill Cornell Medical College, New York, NY 10065, USA
Xiaobo Zhou , Department of Radiology, The Methodist Hospital Research Institute, Houston, TX 77030, USA, Weill Cornell Medical College, New York, NY 10065, USA
Wei Chen , Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong, PR China
Chunqi Chang , Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong, PR China
pp. 357-362

Cis-regulatory module detection using constraint programming (PDF)

Tias Guns , Department of Computer Science, Katholieke Universiteit Leuven, Belgium
Hong Sun , Department of Microbial and Molecular systems, Katholieke Universiteit Leuven, Belgium
Kathleen Marchal , Department of Microbial and Molecular systems, Katholieke Universiteit Leuven, Belgium
Siegfried Nijssen , Department of Computer Science, Katholieke Universiteit Leuven, Belgium
pp. 363-368

A generalized sequence pattern matching algorithm using complementary dual-seeding (PDF)

Bing Ni , Computer Science and Engineering, The Chinese Univ. of Hong Kong, Hong Kong
Leung Yau Lo , Computer Science and Engineering, The Chinese Univ. of Hong Kong, Hong Kong
Kwong Sak Leung , Computer Science and Engineering, The Chinese Univ. of Hong Kong, Hong Kong
pp. 369-372

Integrated analysis of the various types of microarray data using linear-mixed effects models (PDF)

Sung Gon Yi , Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA
Taesung Park , Department of Statistics, Seoul National University, Seoul, South Korea
pp. 373-379

A dynamic qualitative probabilistic network approach for extracting gene regulatory network motifs (PDF)

Zina M. Ibrahim , School of Computer Science, University of Windsor, Windsor, Canada
Alioune Ngom , School of Computer Science, University of Windsor, Windsor, Canada
Ahmed Y. Tawfik , School of Computing and Engineering, The French University in Egypt, Egypt
pp. 380-385

A parameterless automatic spot detection method for cDNA microarray images (PDF)

Iman Rezaeian , School of Computer Science, University of Windsor, Windsor, Canada
Luis Rueda , School of Computer Science, University of Windsor, Windsor, Canada
pp. 388-392

An accurate, automatic method for markerless alignment of electron tomographic images (PDF)

Qi Chu , Advanced Computer Research Center, Institute of Computing Technology, CAS, Beijing, China
Fa Zhang , Advanced Computer Research Center, Institute of Computing Technology, CAS, Beijing, China
Kai Zhang , National Key Laboratory of Biomacromolecules, CAS, Beijing, China
Xiaohua Wan , Advanced Computer Research Center, Institute of Computing Technology, CAS, Beijing, China
Mingwei Chen , Advanced Computer Research Center, Institute of Computing Technology, CAS, Beijing, China
Zhiyong Liu , Advanced Computer Research Center, Institute of Computing Technology, CAS, Beijing, China
pp. 393-396

Spatially constrained fuzzy hyper-prototype clustering with application to brain tissue segmentation (PDF)

Jin Liu , School of Engineering and Information Technology, University of New South Wales, Canberra, ACT 2600, Australia
Tuan D. Pham , School of Engineering and Information Technology, University of New South Wales, Canberra, ACT 2600, Australia
Wei Wen , School of Psychiatry, University of New South Wales, Sydney, NSW 2052, Australia
Perminder S. Sachdev , School of Psychiatry, University of New South Wales, Sydney, NSW 2052, Australia
pp. 397-400

Exploring matrix factorization techniques for significant genes identification of microarray dataset (PDF)

Wei Kong , Information Engineering College, Shanghai Maritime University, Shanghai, P.R. China
Xiaoyang Mou , Department of Radiology, Brigham and Women's Hospital and Harvard Medical School Boston, MA 02115, USA
Xiaohua Hu , College of Information Science, and Technology, Drexel University, Philadelphia, PA 19104, USA
pp. 401-405

Hybrid SVM/CART classification of pathogenic species of bacterial meningitis with surface-enhanced Raman scattering (PDF)

Wen-Jie Lin , Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
Chung-Yueh Huang , Institute of Atomic and Molecular Sciences, Academic Sinica, Taipei, Taiwan
Bing-Cheng Wen , Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
Chia-Wen Chung , Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
Yung-Jui Li , Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
Ya-Ching Chuang , Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
Tsung-Heng Tsai , Institute of Information Science, Academic Sinica, Taipei, Taiwan
Li-Li Li , Institute of Atomic and Molecular Sciences, Academic Sinica, Taipei, Taiwan
Juen-Kai Wang , Institute of Atomic and Molecular Sciences, Academic Sinica, Taipei, Taiwan
Yuh-Lin Wang , Institute of Atomic and Molecular Sciences, Academic Sinica, Taipei, Taiwan
Chi-Hung Lin , Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
Da-Wei Wang , Institute of Information Science, Academic Sinica, Taipei, Taiwan
pp. 406-409

Improved mammographic mass retrieval performance using multi-view information (PDF)

Wei Liu , College of Life Information Science and Instrument, Engineering, Hangzhou Dianzi University, Hangzhou, China
Weidong Xu , College of Life Information Science and Instrument, Engineering, Hangzhou Dianzi University, Hangzhou, China
Lihua Li , College of Life Information Science and Instrument, Engineering, Hangzhou Dianzi University, Hangzhou, China
Shuang Li , College of Life Information Science and Instrument, Engineering, Hangzhou Dianzi University, Hangzhou, China
Huanping Zhao , College of Life Information Science and Instrument, Engineering, Hangzhou Dianzi University, Hangzhou, China
Juan Zhang , Medical Imaging Center, Zhejiang Cancer Hospital, Hangzhou, China
pp. 410-415

A fast and noise-adaptive rough-fuzzy hybrid algorithm for medical image segmentation (PDF)

Arpit Srivastava , Department of Electronics and Communication Mualana Azad National Institute of Technology Bhopal, India
Abhinav Asati , Department of Electronics and Communication Mualana Azad National Institute of Technology Bhopal, India
Mahua Bhattacharya , ABV Indian Institute of Information Technology and Management Gwalior, India
pp. 416-421

Sparse canonical correlation analysis applied to fMRI and genetic data fusion (PDF)

David Boutte , The Mind Research Network, Albuquerque, NM 87131
Jingyu Liu , The Mind Research Network, Albuquerque, NM 87131
pp. 422-426

A Naïve Bayes classifier for differential diagnosis of Long QT Syndrome in children (PDF)

Long Qu , Divisions of Oncology, Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, USA
Victoria L. Vetter , Cardiology, Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, USA
Geoffrey L. Bird , Cardiology, Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, USA
Haijun Qiu , Divisions of Oncology, Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, USA
Peter S. White , Divisions of Oncology, Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, USA
pp. 433-437

Non-negative matrix and tensor factorization based classification of clinical microarray gene expression data (PDF)

Yifeng Li , School of Computer Science, University of Windsor, Windsor, Ontario, Canada
Alioune Ngom , School of Computer Science, University of Windsor, Windsor, Ontario, Canada
pp. 438-443

Improving robustness of gene ranking by resampling and permutation based score correction and normalization (PDF)

Feng Yang , School of Electrical & Electronic Engineering, Nanyang Technological University, Singapore
K. Z. Mao , School of Electrical & Electronic Engineering, Nanyang Technological University, Singapore
pp. 444-449

Autoregressive modeling of DNA features for short exon recognition (PDF)

Nancy Y. Song , Department of Electronic Engineering, City University of Hong Kong, Kowloon, Hong Kong
Hong Yan , Department of Electronic Engineering, City University of Hong Kong, Kowloon, Hong Kong
pp. 450-455

Hierarchical decomposition of vessel skeletons for graph creation and feature extraction (PDF)

Klaus Drechsler , Cognitive Computing & Medical Imaging, Fraunhofer Institute for Computer Graphics Research IGD, Darmstadt, Germany
Cristina Oyarzun Laura , Cognitive Computing & Medical Imaging, Fraunhofer Institute for Computer Graphics Research IGD, Darmstadt, Germany
pp. 456-461

Semi-supervised feature learning from clinical text (PDF)

Zhuoran Wang , Department of Computer Science, University College London, London, United Kingdom
John Shawe-Taylor , Department of Computer Science, University College London, London, United Kingdom
Anoop Shah , Clinical Toxicology, Guy's and St Thomas NHS Foundation Trust, London, United Kingdom
pp. 462-466

Predicting human microRNA-disease associations based on support vector machine (PDF)

Qinghua Jiang , Bio-X Center, Academy of Fundamental and Interdisciplinary Sciences
Guohua Wang , School of Computer Science and Technology, Harbin Institute of Technology Harbin, Heilongjiang, 150001, China
Tianjiao Zhang , School of Computer Science and Technology, Harbin Institute of Technology Harbin, Heilongjiang, 150001, China
Yadong Wang , School of Computer Science and Technology, Harbin Institute of Technology Harbin, Heilongjiang, 150001, China
pp. 467-472

A sparse regulatory network of copy-number driven expression reveals putative breast cancer oncogenes (PDF)

Yinyin Yuan , Cancer Research UK, Cambridge Research Institute, UK, Department of Oncology, University of Cambridge, UK
Christina Curtis , Cancer Research UK, Cambridge Research Institute, UK, Department of Oncology, University of Cambridge, UK
Carlos Caldas , Cancer Research UK, Cambridge Research Institute, UK, Department of Oncology, University of Cambridge, UK
Florian Markowetz , Cancer Research UK, Cambridge Research Institute, UK, Department of Oncology, University of Cambridge, UK
pp. 473-478

Network-based identification of smoking-associated gene signature for lung cancer (PDF)

Ying-Wooi Wan , Mary Babb Randolph Cancer Center, West Virginia University, Morgantown, WV 26506-9300
Changchang Xiao , Mary Babb Randolph Cancer Center, West Virginia University, Morgantown, WV 26506-9300
Nancy Lan Guo , Mary Babb Randolph Cancer Center, West Virginia University, Morgantown, WV 26506-9300
pp. 479-484

Detection and application of CagA sequence markers for assessing risk factor of gastric cancer caused by Helicobacter pylori (PDF)

Chao Zhang , Department of Computer Science, University of Missouri, Columbia, MO, USA
Shunfu Xu , C.S. Bond Life Science Center, University of Missouri, Columbia, MO, USA
Dong Xu , Department of Computer Science, University of Missouri, Columbia, MO, USA
pp. 485-488

Discovering negative correlated gene sets from integrative gene expression data for cancer prognosis (PDF)

Tao Zeng , School of Computer, Wuhan University, Wuhan 430072, China
Xuan Guo , School of Computer, Wuhan University, Wuhan 430072, China
Juan Liu , School of Computer, Wuhan University, Wuhan 430072, China
pp. 489-492

A gene ranking method using text-mining for the identification of disease related genes (PDF)

Hyungmin Lee , Graduate School of EECS, Kyungpook National University, Daegu, Korea
Miyoung Shin , Graduate School of EECS, Kyungpook National University, Daegu, Korea
Munpyo Hong , College of Liberal Arts, Sungkyunkwan University, Seoul, Korea
pp. 493-498

A novel reinforcement learning framework for online adaptive seizure prediction (PDF)

Shouyi Wang , Department of Industrial and Systems Engineering, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
Wanpracha Art Chaovalitwongse , Department of Industrial and Systems Engineering, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
Stephen Wong , Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, New Brunswick, NJ, USA
pp. 499-504

Metabolomic profiling for biomarker discovery in pancreatic cancer (PDF)

Prabhjit Kaur , Department of Oncology, LCCC at Georgetown University Medical Center, Washington, D.C. 20057, USA
Kathryn Sheikh , Department of Oncology, LCCC at Georgetown University Medical Center, Washington, D.C. 20057, USA
Alexander Kirilyuk , Department of Oncology, LCCC at Georgetown University Medical Center, Washington, D.C. 20057, USA
Ksenia Kirilyuk , Department of Oncology, LCCC at Georgetown University Medical Center, Washington, D.C. 20057, USA
Habtom W. Ressom , Department of Oncology, LCCC at Georgetown University Medical Center, Washington, D.C. 20057, USA
Amrita K Cheema , Department of Oncology, LCCC at Georgetown University Medical Center, Washington, D.C. 20057, USA
Bhaskar Kallakury , Department of Pathology, LCCC at Georgetown University Medical Center, Washington, D.C. 20057, USA
pp. 505-509

Intracranial pressure level prediction in traumatic brain injury by extracting features from multiple sources and using machine learning methods (PDF)

Wenan Chen , Department of Computer Science and VCURES
Charles Cockrell , Department of Radiology
Kevin R. Ward , Department of Emergency Medicine and VCURES, Virginia Commonwealth University, Richmond, USA
Kayvan Najarian , Department of Computer Science and VCURES
pp. 510-515

Exploitation of 3D Stereotactic Surface Projection for automated classification of Alzheimer's disease according to dementia levels (PDF)

Murat Seckin Ayhan , Center for Advanced Computer Studies University of Louisiana at Lafayette Lafayette, LA, USA
Ryan G. Benton , Center for Advanced Computer Studies University of Louisiana at Lafayette Lafayette, LA, USA
Vijay V. Raghavan , Center for Advanced Computer Studies University of Louisiana at Lafayette Lafayette, LA, USA
Suresh Choubey , Applied Science Laboratory GE Healthcare Waukesha, WI, USA
pp. 516-519

Gene selection using 1-norm regularization for multi-class microarray data (PDF)

Xiaofei Nan , The University of Mississippi, USA
Nan Wang , The University of Southern Mississippi, USA
Ping Gong , SpecPro Inc., Environmental Services, USA
Chaoyang Zhang , The University of Southern Mississippi, USA
Yixin Chen , The University of Mississippi, USA
Dawn Wilkins , The University of Mississippi, USA
pp. 520-524

Eigenspectra, a robust regression method for multiplexed Raman spectra analysis (PDF)

Shuo Li , Computer Science and Engineering Department, University of Texas at Arlington, Arlington, USA
Jean Gao , Computer Science and Engineering Department, University of Texas at Arlington, Arlington, USA
James O Nyagilo , Bioengineering Department, University of Texas at Arlington, Arlington, USA
Digant P Dave , Bioengineering Department, University of Texas at Arlington, Arlington, USA
pp. 525-530

A new method for measuring the semantic similarity on gene ontology (PDF)

Ying Shen , Department of Computer Science, City University of Hong Kong, Hong Kong
Shaohong Zhang , Department of Computer Science, City University of Hong Kong, Hong Kong
Hau-San Wong , Department of Computer Science, City University of Hong Kong, Hong Kong
pp. 533-538

seGOsa: Software environment for gene ontology-driven similarity assessment (PDF)

Huiru Zheng , School of Computing and, Mathematics, Computer Science, Research Institute, University of Ulster, Co. Antrim, UK
Francisco Azuaje , Laboratory of Cardiovascular, Research, Public Research Centre for Health, (CRP-Santé), L-1150, Luxembourg
Haiying Wang , School of Computing and, Mathematics, Computer Science, Research Institute, University of Ulster, Co. Antrim, UK
pp. 539-542

Examining the sublineage structure of Mycobacterium tuberculosis complex strains with multiple-biomarker tensors (PDF)

Cagri Ozcaglar , Computer Science Department and (2) Mathematical Sciences Department, Rensselaer Polytechnic Institute
Amina Shabbeer , Computer Science Department and (2) Mathematical Sciences Department, Rensselaer Polytechnic Institute
Scott Vandenberg , Computer Science Department, Siena College
Buulent Yener , Computer Science Department and (2) Mathematical Sciences Department, Rensselaer Polytechnic Institute
Kristin P. Bennett , Computer Science Department and (2) Mathematical Sciences Department, Rensselaer Polytechnic Institute
pp. 543-548

Two-stage clustering based effective sample selection for classification of pre-miRNAs (PDF)

Ping Xuan , School of Computer Science and Technology, Harbin Institute of Technology, Harbin Heilongjiang 150001, P.R. China
Mao-zu Guo , School of Computer Science and Technology, Harbin Institute of Technology, Harbin Heilongjiang 150001, P.R. China
Lei-lei Shi , The Computing Laboratory, University of Kent, Canterbury, CT2 7NF, U.K.
Jun Wang , School of Computer Science and Technology, Harbin Institute of Technology, Harbin Heilongjiang 150001, P.R. China
Xiao-yan Liu , School of Computer Science and Technology, Harbin Institute of Technology, Harbin Heilongjiang 150001, P.R. China
Wen-bin Li , Soybean Research Institute, Northeast Agricultural University, Harbin Heilongjiang 150030 P.R. China
Ying-peng Han , Soybean Research Institute, Northeast Agricultural University, Harbin Heilongjiang 150030 P.R. China
pp. 549-552

Biomedical concept extraction using concept graphs and ontology-based mapping (PDF)

Said Bleik , Department of Information Systems New Jersey Institute of Technology
Wei Xiong , Department of Information Systems New Jersey Institute of Technology
Yiran Wang , Department of Information Systems New Jersey Institute of Technology
Min Song , Department of Information Systems New Jersey Institute of Technology
pp. 553-556

Identification of critical location on a microstructural bone network (PDF)

Taehyong Kim , Department of Computer Science, and Engineering, State University of, New York at Buffalo, USA
Jaehan Koh , Department of Computer Science, and Engineering, State University of, New York at Buffalo, USA
Kang Li , Department of Computer Science, and Engineering, State University of, New York at Buffalo, USA
Murali Ramanathan , Department of Pharmaceutical, Sciences, State University of New, York at Buffalo, USA
Aidong Zhang , Department of Computer Science, and Engineering, State University of, New York at Buffalo, USA
pp. 557-562

An automatic procedure to search highly repetitive sequences in genome as fluorescence in situ hybridization probes and its application on Brachypodium distachyon (PDF)

Qiwei Li , Department of Information Engineering, Institute of Plant Molecular Biology and Agricultural Biotechnology, State (China) Key Laboratory for Agrobiotechnology The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong
Tong Liang , Department of Information Engineering, Institute of Plant Molecular Biology and Agricultural Biotechnology, State (China) Key Laboratory for Agrobiotechnology The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong
Xiaodan Fan , Department of Statistics, Institute of Plant Molecular Biology and Agricultural Biotechnology, State (China) Key Laboratory for Agrobiotechnology The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong
Chunhui Xu , Department of Biology, Institute of Plant Molecular Biology and Agricultural Biotechnology, State (China) Key Laboratory for Agrobiotechnology The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong
Weichang Yu , Department of Biology, Institute of Plant Molecular Biology and Agricultural Biotechnology, State (China) Key Laboratory for Agrobiotechnology The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong
Shuo-Yen Robert Li , Department of Information Engineering, Institute of Plant Molecular Biology and Agricultural Biotechnology, State (China) Key Laboratory for Agrobiotechnology The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong
pp. 563-568

Exploratory analysis of the BioAssay Network with implications to therapeutic discovery (PDF)

Jintao Zhang , Center for Bioinformatics, University of Kansas, Lawrence, KS 66045
Gerald H. Lushington , Molecular Graphics & Modeling Lab, University of Kansas, Lawrence, KS 66045
Jun Huan , Department of Electrical Engineering, & Computer Science, University of Kansas, Lawrence, KS 66045
pp. 569-572

Link-based cluster ensembles for heterogeneous biological data analysis (PDF)

Natthakan Iam-On , Department of Computer Science, Aberystwyth University, Aberystwyth, Ceredigion, UK
Simon Garrett , Department of Computer Science, Aberystwyth University, Aberystwyth, Ceredigion, UK
Chris Price , Department of Computer Science, Aberystwyth University, Aberystwyth, Ceredigion, UK
Tossapon Boongoen , Department of Mathematics and Computer Science, Royal Thai Air Force Academy, Bangkok, Thailand
pp. 573-578

FluRF, an automated flu virus reassortment finder based on phylogenetic trees (PDF)

Alisa Yurovsky , Laboratory for Computational Biology and Bioinformatics, EPFL (Swiss Federal Institute of Technology), Lausanne, Switzerland
Bernard M.E. Moret , Laboratory for Computational Biology and Bioinformatics, EPFL (Swiss Federal Institute of Technology), Lausanne, Switzerland
pp. 579-584

Decomposing protein interactome networks by graph entropy (PDF)

Hao Lian , Department of Computer Science, Baylor University, Waco, TX, USA
Chengsen Song , Department of Computer Science, Baylor University, Waco, TX, USA
Young-Rae Cho , Department of Computer Science, Baylor University, Waco, TX, USA
pp. 585-589

NWE: Node-weighted expansion for protein complex prediction using random walk distances (PDF)

Osamu Maruyama , Faculty of Mathematics and Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
Ayaka Chihara , Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
pp. 590-594

Ranking SVM for multiple kernels output combination in protein-protein interaction extraction from biomedical literature (PDF)

Zhihao Yang , Department of Computer Science and Engineering, Dalian University of Technology, Dalian, China
Yuan Lin , Department of Computer Science and Engineering, Dalian University of Technology, Dalian, China
Jiajin Wu , Department of Computer Science and Engineering, Dalian University of Technology, Dalian, China
Nan Tang , Department of Computer Science and Engineering, Dalian University of Technology, Dalian, China
Hongfei Lin , Department of Computer Science and Engineering, Dalian University of Technology, Dalian, China
Yanpeng Li , Department of Computer Science and Engineering, Dalian University of Technology, Dalian, China
pp. 595-598

Concurrent analysis of copy number variation and gene expression: Application in paired non-smoking female lung cancer patients (PDF)

Jung-Chih Chang , Graduate Institute of Biomedical, Electronics and Bioinformatics, National, Taiwan University
Tzu-Pin Lu , Graduate Institute of Biomedical, Electronics and Bioinformatics, National, Taiwan University
Eric Y. Chuang , Graduate Institute of Biomedical, Electronics and Bioinformatics, National, Taiwan University
Liang-Chuan Lai , Institute of Biotechnology, National Taiwan, University
Mong-Hsun Tsai , Institute of Biotechnology, National Taiwan, University
Chuhsing Kate Hsiao , Department of Public Health, National, Taiwan University
Pei-Chun Chen , Department of Statistics and Informatics, Science, Providence University
pp. 599-602

Robust hidden semi-Markov modeling of array CGH data (PDF)

Jiarui Ding , Molecular Oncology, University of British Columbia, Vancouver BC Canada
Sohrab P. Shah , Molecular Oncology, University of British Columbia, Vancouver BC Canada
pp. 603-608

Computational modeling of phagocyte transmigration during biomaterial-mediated foreign body responses (PDF)

Mingon Kang , Department of Computer Science, University of Texas at Arlington, Arlington, Texas, 76019, USA
Jean X. Gao , Department of Computer Science, University of Texas at Arlington, Arlington, Texas, 76019, USA
Liping Tang , Department of Bioengineering, University of Texas at Arlington, Arlington, Texas, 76019, USA
pp. 609-612

Rex: A toolset for reproducing software experiments (PDF)

Somu Perianayagam , Department of Computer Science, The University of Arizona, Tucson, AZ, USA
Gregory R. Andrews , Department of Computer Science, The University of Arizona, Tucson, AZ, USA
John H. Hartman , Department of Computer Science, The University of Arizona, Tucson, AZ, USA
pp. 613-617

A comparative study of two matrix factorization methods applied to the classification of gene expression data (PDF)

Vladimir Nikulin , Department of Mathematics, University of Queensland, Brisbane, Australia
Tian-Hsiang Huang , Institute of Information Management, National Cheng Kung University, Tainan, Taiwan
Geoffrey J. McLachlan , Department of Mathematics, and Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
pp. 618-621

Time- and space-efficient maximal repeat finding using the burrows-wheeler transform and wavelet trees (PDF)

M. Oguzhan Kiilekci , National Research Institute of Electronics & Cryptology, Turkey
Jeffrey Scott Vitter , Information and Telecommunication Technology Center, University of Kansas, USA
Bojian Xu , Information and Telecommunication Technology Center, University of Kansas, USA
pp. 622-625

IsoKEGG: A logic based system for querying biological pathways in KEGG (PDF)

Kazi Zakia Sultana , Department of Computer Science, Wayne State University, USA
Anupam Bhattacharjee , Department of Computer Science, Wayne State University, USA
Hasan Jamil , Department of Computer Science, Wayne State University, USA
pp. 626-631

Feature selection for graph kernels (PDF)

Mehmet Tan , Dept. of Comp. Engineering, TOBB Univ. of Economics and Technology, Ankara, Turkey
Faruk Polat , Dept. of Comp. Engineering, Middle East Technical University, Ankara, Turkey
Reda Alhajj , Dept. of Comp. Science, University of Calgary, Calgary, AB, Canada
pp. 632-637

Toward automatically drawn metabolic pathway atlas with peripheral node abstraction algorithm (PDF)

Myungha Jang , Bioinformatics Laboratory, School of Engineering, Ewha Womans University, Seoul, Korea
Arang Rhie , Bioinformatics Laboratory, School of Engineering, Ewha Womans University, Seoul, Korea
Hyun-Seok Park , Bioinformatics Laboratory, School of Engineering, Ewha Womans University, Seoul, Korea
pp. 638-642

An Evolutionary Monte Carlo algorithm for identifying short adjacent repeats in multiple sequences (PDF)

Jin Xu , Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam, Hong Kong Island, Hong Kong
Qiwei Li , Department of Information Engineering, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong
Xiaodan Fan , Department of Statistics, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong
Victor O. K. Li , Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam, Hong Kong Island, Hong Kong
Shuo-Yen Robert Li , Department of Information Engineering, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong
pp. 643-648

Gene expression rule discovery with a multi-objective neural-genetic hybrid (PDF)

Ed Keedwell , School of Engineering, Computing and Mathematics, Harrison Building, North Park Road, University of Exeter, Exeter, EX4 4QF, UK
Ajit Narayanan , School of Computing and Mathematical Sciences, Auckland University of Technology, AUT Tower, 2-14 Wakefield St, Auckland 1142, New Zealand
pp. 649-656

Represented indicator measurement and corpus distillation on focus species detection (PDF)

Chih-Hsuan Wei , Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan, Taiwan, R.O.C.
Hung-Yu Kao , Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan, Taiwan, R.O.C.
pp. 657-662

PSI-RA: A parallel sparse index for read alignment on genomes (PDF)

M. Oguzhan Kulekci , National Research Institute of Electronics & Cryptology, Turkey
Wing-Kai Hon , Dept. of Computer Science, National Tsing Hua University, Taiwan
Rahul Shah , Dept. of Computer Science, Louisiana State University, USA
Jeffrey Scott Vitter , Information and Telecomunication Technology Center, University of Kansas, USA
Bojian Xu , Information and Telecomunication Technology Center, University of Kansas, USA
pp. 663-668

Exploring a multi-source fusion approach for genomics information retrieval (PDF)

Qinmin Vivian Hu , Information Retrieval and Knowledge Management Research Lab, York University, Toronto, Canada
Xiangji Jimmy Huang , Information Retrieval and Knowledge Management Research Lab, York University, Toronto, Canada
Jun Miao , Information Retrieval and Knowledge Management Research Lab, York University, Toronto, Canada
pp. 669-672

GPU-based triangulation of the van der Waals surface (PDF)

Sergio Dias , Universidade da Beim Interior, Departamento de Informática, 6201-001 Covilhä, Portugal
Abel Gomes , Universidade da Beira Interior, Departamento de Informa´tica, 6201-001 Covilhaä, Portugal
pp. 673-676

Selecting informative genes by Lasso and Dantzig selector for linear classifiers (PDF)

Songfeng Zheng , Department of Mathematics, Missouri State University, Springfield, MO 65897, USA
Weixiang Liu , Biomedical Engineering Lab, School of Medicine, Shenzhen University, Shenzhen, Guangdong 518060, China
pp. 677-680

Scalable, updatable predictive models for sequence data (PDF)

Neeraj Koul , Artificial Intelligence Research Laboratory, Dept. of Computer Science, Iowa State University, Ames, IA - 50014, USA
Ngot Bui , Artificial Intelligence Research Laboratory, Dept. of Computer Science, Iowa State University, Ames, IA - 50014, USA
Vasant Honavar , Artificial Intelligence Research Laboratory, Dept. of Computer Science, Iowa State University, Ames, IA - 50014, USA
pp. 681-685

Computational prediction of toxicity (PDF)

Meenakshi Mishra , Department of Electrical Engineering and Computer Science, University of Kansas
Hongliang Fei , Department of Electrical Engineering and Computer Science, University of Kansas
Jun Huan , Department of Electrical Engineering and Computer Science, University of Kansas
pp. 686-691

A relevance-novelty combined model for genomics search result diversification (PDF)

Xiaoshi Yin , College of Computer Science and Engineering, Beihang University, Beijing, China
Zhoujun Li , College of Computer Science and Engineering, Beihang University, Beijing, China
Jimmy Xiangji Huang , School of Information Technology, York University, Toronto, Canada
Xiaohua Hu , College of Information Science and Technology, Drexel University, Philadelphia, PA, USA
pp. 692-695

Gene clustering by structural prior based local factor analysis model under Bayesian Ying-Yang harmony learning (PDF)

Lei Shi , Dept. of Computer Sci. and Eng., The Chinese University of Hong Kong, Shatin, NT, Hong Kong
Shikui Tu , Dept. of Computer Sci. and Eng., The Chinese University of Hong Kong, Shatin, NT, Hong Kong
Lei Xu , Dept. of Computer Sci. and Eng., The Chinese University of Hong Kong, Shatin, NT, Hong Kong
pp. 696-699
91 ms
(Ver 3.3 (11022016))