2010 IEEE International

Conference on Bioinformatics

and Biomedicine Workshops

(BIBMW 2010)

Hong Kong, China

18 - 21 December 2010

IEEE IEEE Catalog Number: CFP1026D-PRT

ISBN: 978-1-4244-8303-7

2010 IEEE International Conference on

Bioinformatics and Biomedicine Workshops

BIBM 2010 WorkshopsTable of Contents

Keynotes:

Progress and Prospect of Objectivity Study on Four Diagnostic Methods in Traditional Chinese

Medicine 3

Yiqin Wang

Medical Biometrics-Computerized TCM Diagnosis 4

DavidZhang

Workshop 1: Graph Theoretic Analysis of Biological Networks

Predicting Metabolic Pathways from Metabolic Networks with Limited Biological Knowledge7

S.Y.Leung, Henry CM. Leung, LuXiang, S.M. Yiu, and Francis Y.L. Chin

PBSK Browser: navigate biological pathways ofPSI-MI, BioPAX, SBML and KGML formats

13

Donglin Huang, Yiling Huang, Christian Klukas, RalfHofestaedt, and Ming Chen

Using Graph Modularity Analysis to Identify Transcription Factor Binding Sites

19

Alexandre Francisco, Sophie Schbath, AnaFreitas, andArlindo Oliveira

Workshop 2: Computational Proteomics

Identification of core-attachment complexes based on maximal frequent patterns in protein-protein

interaction networks 29

Liang Yu, Lin Gao, and Chuiliang Kong

Association Network Modeling from Microarray Data around fermentation stress response gene NSF1

(YPL230W) using Significantly Co-expressed Gene Set 35

Kyrylo Bessonov, DavidK.Y. Chiu, and George van der Merwe

Eighth-Sphere Exposure: A Three-Dimensional Solvent Exposure Measure 41

Peipei Li, Ho Sun Shon, GoucholPok, and Keun Ho Ryu

i

Fuzzy Soft Subspace Clustering Method for Gene Co-expression Network Analysis

47

Qiang Wang, Yunming Ye, Joshua Zhexue Huang, and Shengzhong Feng

An efficient hybrid of hill-climbing and genetic algorithm for 2D triangular protein structure

prediction 51

Shih-Chieh Su, Cheng-Jian Lin, and Chuan-Kang Ting

Sparse Representation based feature selection for Mass Spectrometry Data 57

Jiqing Ke, Lei Zhu, Bin Han, Qi Dai, Yaojia Wang, Lihua Li, Shenhua Xu, Hanzhou Mou, and

Zhiguo Zheng

Structural Analysis of (TCR-)HLA/peptide Complexes: An Initial Study 63

Stephanus Daniel Handoko, Tran To Chinh Su, Chee KeongKwoh, and Yew Soon Ong

Using a Spike-InExperiment to Evaluate Analysis ofLC-MS Data 67

Leepika Tuli, Tsung-Heng Tsai, Rency Varghese, Amrita Cheema, and Habtom Ressom

FISH: Finding of Identical Spectra Set for Homogenous Peptide using Two-Stage Clustering

Algorithm 73

Seungmook Lee, Min-Seok Kwon, Hyoung-Joo Lee, Young-Ki Paik, Jae K Lee,

and TaesungPark

On the solution ofmolecular distance geometry problems with interval data 77

Carlile Lavor, Leo Liberti, and Antonio Mucherino

Speed Improvements ofPeptide-Spectrum Matching Using SIMD Instructions 83

Jian Zhang, Ian McQuillan, and FangXiang Wu

An adaptive approach to denoising tandem mass spectra 89

WenJun Lin, FangXiang Wu, Jinhong Shi, Jiarui Ding, and Wenjun Zhang

SyncPro: A Synchronized Visualization Tool for Differential Analysis of Proteomics Data Sets

, 95

Ling Sing Yung, Chao Yang, MohammedDakna, HaraldMischak, and Weichuan Yu

Prediction of Protein Structural Class Using a Combined Representation of Protein-sequence

Information and Support Vector Machine 101

Li Wu, Qi Dai, Bin Han, Lei Zhu, and Lihua Li

Computing the Connectivity Indices ofalpha- and beta-Cyclodextrins 107

Wu Jiang and Shenggui Zhang

ii

A Binary Matrix FactorizationAlgorithm for Protein Complex Prediction 113

Shikui Tu, Runsheng Chen, andLeiXu

Network-based Modeling forAnalyzing the Human Skin Microbiome 119

Yingzhuo Wei, Shaowu Zhang, Chunhui Zhao, Feng Yang, and Quan Pan

SProt - From Local to Global Protein Structure Similarity 124

Jakub Galgonek and DavidHoksza

SimpleTrPPI: A simple method for transferring knowledge between interaction networks for PPI

prediction 130

Qian Xu, Hao Hu, HongXue, and Qiang Yang

Workshop 3: Mining and Management of Biological and Health Data

The Apriori Property of Sequence Pattern Mining with Wildcard Gaps 138

Fan Min, Youxi Wu, andXindong Wu

Selective Estimation of Least Squares Based Predictor and Efficient Overhead Management

Algorithm for Lossless Compression of Digital Mammograms 144

Vinit Jakhetiya, Nitish Kumar Boyal and AnilKumar Thvari

A Hybridization Model for TilingArray Analysis 148

Quan Wang, Linbo Wang, Minping Qian, and Minghua Deng

Temporal Logics for Phylogenetic Analysis via Model Checking 152

Roberto Blanco, Gregorio De Miguel Casado, Jose Ignacio Requeno, andJose Manuel Colom

Segmentation of CE Videos by Finding Convex Skin 158

Balathasan Giritharan, Sandeep Panchakarala, andXiaohui Yuan

Biological Data Classifications with LDAand SPRT 164

Brittany Nkounkou, Colin Brown, Chih Lee, and Chun-Hsi Huang

EVOL Optimer - Tool for Gene Expression Analysis 169

Sairam G.L, Asha Vijayan, GeraldH.Lushington andMahesh Visvanathan

Temporal Clustering of Gene Expression Patterns Using Short-Time Segments 173

Nguyen Nguyen, Yufei Huang, Shou-Jiang Gao, Yidong Chen, Merry Lindsey, Yufang Jin,

and YingAnn Chiao

Adaptive Set-Membership Normalized Least Mean Squares: An Adaptive Filter for the Systems with

Bounded Noise 179

iii

Sardar Ansari, Kevin Ward, andKayvan Najarian

Cluster-based Query Expansion Using Language Modeling in the Biomedical Domain

185

Xuheng Xu andXiaoh.ua Hu

Using Topic-Concept Based Clustering for Genomic Information Retrieval in TREC 189

TengFei Jiang, TingTing He and Fang Li

Workshop 4: Integrative Data Analysis in Systems Biology

Quantitative Visualization of ChlP-chip Data by Using LinkedViews 195

Min-Yu Huang, Gunther Weber, Xiao-long Li, Mark Biggin, and Bernd Hamann

Performance ofDNAData Embedding Algorithms under Substitution Mutations 201

David Haughton and Filix Balado

Extending boolean regulatory network models with Answer Set Programming 207

Timur Fayruzov, Jeroen Janssen, Chris Cornells, Dirk Vermeir, and Martine De Cock

A Weighted Structural Model Clustering Approach for Identifying and Analyzing Core Genetic

Regulatory Modules 213

Binhua Tang and Su-Shing Chen

Process Calculi for Systems Biology and Applications in Severe Asthma 217

Caroline Baroukh, AnthonyRowe, and Yike Guo

CORAL-M: Heuristic COding RegionALignment Method for Multiple Genome Sequences

223

Che-Lun Hung, Chun-Yuan Lin, Yeh-Ching Chung, Shu Ju Hsieh, Chuan Yi Tang,

Shih-Cheng Chang, and Yaw-Ling Lin

Integrated Cellular and Gene Interaction Model for Cell Migration in Embryonic Development229

Hien Nguyen and Joe Song

Cellular Neural Networks, Navier-Stokes Equation and Microarray Image Reconstruction 234

Bachar Zineddin, Zidong Wang, and Xiaohui Liu

Analyzing Genetic Factors Involved in Recombinant Protein Expression Enhancement

240

Daniel Johnson, Keat Teoh, CodyAshby, Elizabeth Hood, andXiuzhen Huang

iv

Geometric Biclustering Analysis ofDNA Microarray Data based on Hypergraph Partitioning246

Zhiguan Wang and Hong Yan

Clustering-based Methodology with Minimal User Supervision for Displaying Cell-phenotype

Signatures in Image-based Screening 252

William-Chandra Tjhi, Kee Khoon Lee, Terence Hung, Yew Soon Ong, Ivor Wai Hung Tsang,

Victor Racine, andFrederic Bard

Investigating microRNA-transcrption factor mediated regulatory network in glioblastoma 258

Xue Gong, Peilin Jia, and Zhongming Zhao

Relational Database Index Choices for Genome Annotation Data 264

Oleksiy Karpenko and YangDai

Gene co-expression network analysis oftwo ovarian cancer datasets 269

Shengjun Hong andHua Dong

Workshop 5: Data Mining for High Throughput Data from Genome-wide

Association Studies

Mining Online Full-text Literature for Novel Protein Interaction Discovery 277

Jarvie Samuel, Xiaohui Yuan, Xiaojing Yuan, and Brian Walton

TOPPER: An algorithm for mining top k patterns in biological sequences based on regularity

measurement 283

Yun Xiong, Junhua He, and Yangyong Zhu

Bioinformatics Approaches in Tuberculosis Vaccination Strategies by Whole Genome Sequence

289

Ai Ling Ong and Chee Keong Kwoh

Protein-Protein Interaction Network Comparison Based On Wavelet and Principal Component

Analysis 294

YongLuo, Yan Zhao, Lei Cheng, Ping Jiang, andJianxin Wang

Testing the Genomic Control Parameter 299

Fang Liang andJurg Ott

Multilocus Association Analysis Under Polygenic Models 302

Dandan Sun and Jurg Ott

P-value Distribution in Case-Control Association Studies 306

v

Zhe Liu, Yuanyuan Shen, and Jurg Ott

Detecting Gene-Gene Interactions Using Support Vector Machines with LI penalty

309

Yuanyuan Shen, Zhe Liu, andJurg Ott

Selecting SNPs for Pharmacogenomic Association Study 312

TaeJin Ahn, Kynghee Park, Dae-Soon Song, Nam Huh, KyusangLee, Taejung Bae,

Jung-Sun Park, So-Hee Oh, Ji-HyunLee, KyoohyungRho, SungKim, and Tae Sung Park

A Scalable Method for Detecting Multiple Loci Associated with Traits using TF-IDF Weighting and

Association Rule Mining 318

Sunwon Lee, Jaewoo Kang, and Junho Oh

Discovery of Multivariate Phenotypes using Association Rule Mining and their Application to

Genome-wide Association Studies 324

SungHee Park and Sangsoo Kim

A Block-Based Evolutionary Optimization Strategy to Investigate Gene-Gene Interactions in Genetic

Association Studies 330

Joel Fontanarosa and Yang Dai

cuGWAM : Genome-wide Association Multifactor Dimensionality Reduction using CUDA-enabled

High-performance Graphics Processing Unit 336

Min-Seok Kwon, Kyunga Kim, Sungyoung Lee, and Taesung Park

A strategy for identifying multiple genetic factors for the multiple traits in genome wide association

studies: An application ofhyperlipidemia in Korean population 341

Ik-Soo Huh, Sohee Oh, Eunjin Lee, and Taesung Park

Unbalanced sample size effect on the genome-wide population differentiation studies

347

Kyunghee Han, Kyeezu Kim, and TaesungPark

Two-way interaction analysis of Obesity Trait from Korean population Using Generalized

MDR 353

SungyoungLee, Sohee Oh, Min-Seok Kwon, Seungyeoun Lee, and Taesung Park

KAREBrowser: SNP database ofKorea Association REsource Project 359

Young Jin Kim, Chang Bum Hon, Sanghoon Moon, Young-Ah Shin, Yoon Shin Cho,

and Jong-Young Lee

BioSMACK: a Linux Live CD for Analysis ofGenome-Wide association 362

vi

Chang Bum Hong, Young Jin Kim, Sanghoon Moon, Young-Ah Shin, Min Jin Go,

Jong-Young Lee, and Yoon Shin Cho

Workshop 6: Bioinformatics for MicroRNA and Disease

Mathematical Analysis of HIV Dynamics: A New Learning Algorithm For Genetic Signal

Representation 368

Amitabh Chaturvedi andArchana Tiwari

A Computational Framework for Predicting Drug Mode-of-Action 374

Chifeng Ma, Hung-I "Harry" Chen, Yufei Huang, and Yidong Chen

Incorporating miRNA target sites in protein-coding RNA 380

Dimitris Papamichail and Georgios Papamichail

Computational Prediction of microRNA Regulatory Pathways 386

Dong Yue, Yidong Chen, Shou-Jiang Gao, and Yufei Huang

A Composite Three-stage Normalization Method for cDNA Microarray Data 392

MingJie Ma andJinsoon Hwang

Workshop 7: Knowledge Engineering, Discovery and Dissemination in Health

Machine Science in Biomedicine: Practicalities, Pitfalls and Potential 399

Tom Kelsey and Hamish Wallace

Monitoring andAnalysis of Sleep Pattern for People with Early Dementia 405

Haiying Wang, Huiru Zheng, Juan Augusto, Suzanne Martin, Maurice Mulvenna,

William Carswell, Johnathson Wallace, Paul Jeffers, Barbara Taylor, andKevin McSorley

Evaluation ofDrowsiness during Driving based on Heart Rate Analysis - a driving simulation study

411

Masaru Tasaki, WangHui, Motoaki Sakai, QunJin, and Darning Wei

u-Healthcare System Protecting Privacy based on Cloaker 417

Seungjin Son, Kwangwoo Lee, Dongho Won, and Seungjoo Kim

Ontology-Based Knowledge Acquisition for Neuromotor Functional Recovery in Stroke

424

Christopher Townsend, Jingshan Huang, Dejing Dou, Haishan Liu, Lei He,

Patrick Hayes, Robert Rudnick, HardikShah, Dennis Fell, and Wei Liu

Predicting Pelvic Trauma Severity Using Features Extracted from Records and X-Ray and CT Images

Simina Vasilache, Rebecca Smith, Jie Wu, Pavani Davuluri, Kayvan Najarian,

Kevin Ward, and Charles Cockrell

430

Semantic Characterization of Hypertrophic Cardiomyopathy Disease 432

Catia M. Machado, Francisco Couto, Alexandra R Fernandes, Susana Santos,

Nuno Cardim, andAna Freitas

A Time-Series Approach for Shock Outcome Prediction Using Machine Learning440

Sharad Shandilya, Kayvan Najarian, and Kevin Ward

Identifying Inconsistencies in Multiple Clinical Practice Guidelines for a Patient with Co-morbidity447

Marisela Mainegra Hing, Martin Michalowski, Szymon Wilk, WojtekMichalowski,

andKen Farion

A Unified Signal Processing and Machine Learning Method for Detection of Abnormal Heart Beats

Using Electrocardiogram 453

AbedAIRaoofBsoul, Soo-YeonJi, Kevin Ward, andKayvan Najarian

Representing clinical documents to support automatic retrieval of evidence from The Cochrane

Library 461

Dympna O'Sullivan, Wojtek Michalowski, Martin Michalowski, Szymon Wilk, andKen Farion

Machine Learning of Patient Similarity: A Case Study on Predicting Survival in Cancer Patient after

Locoregional Chemotherapy 467

LWC Chan, TChan, LF Cheng, and WSMak

Impedance Plethysmography on the Arms: Respiration Monitoring 471

SardarAnsari, Ashwin Belle, Kevin Ward, andKayvan Najarian

TissueWikiMobile: an Integrative Workbench for Pathology Knowledge Retrieval and Sharing

Annotations ofHistological Images on a Mobile Device 473

Chihwen Cheng, ToddStokes, SovandyHang, and May D. Wang

A Multi-Agent Resource Allocation Framework for Patient Journey Shortening 481

Chung-ho Choi and William K, Cheung

Workshop 8: Data Mining for Biomarker Discovery

Comparison ofTriple Negative Breast Cancer betweenAsian and Western Data Sets

489

Vlll

Lee Chen, Liang-Chuan Lai, Chuhsing Hsiao, Pei-Chun Chen, Mong-Hsun Tsai,

Wen-Hung Kuo, King-Jen Chang, andEric Y. Chuang

Identification of Co-occurring Insertions in Cancer Genomes Using Association Analysis

494

Michael Steinbach, Haoyu Yu, and Vipin Kumar

A Model-driven Classification and Recursive Segmentation Method for Automatic Panel Extraction

from Biological and Medical Papers 500

Xiaohui Yuan and Dongyu Ang

Projecting Partial Least Square and Principle Component Regression Across Microarray Studies

506

Chi-Cheng Huang, Shin-Hsin Tu, Heng-Hui Lien, Ching-Shui Huang, Eric Y. Chuang,

andLiang-Chuan Lai

Position-specific Deformation Pattern of the Nucleosome DNA Revealed by Principal Component

Analysis and Sequence Alignment-based Statistics 512

Xi Yang and Hong Yan

Develop Integration Modeling Approach for Discovery Neuraminidase Inhibitors in Silico Based on

Pharmacophore and CoMSIA Models 518

Kuei-Chung Shih, Chun-Yuan Lin, Jiayi Zhou, Shih-Han Huang, and Chuan-Yi Tang

ANovel Peak Alignment Method for LC-MS DataAnalysis Using Cluster-based Techniques525

Yu-ChengLiu, Lien-Chin Chen, Hui-Ym Chang, Hsin-Yi Wu, Pao-Chi Liao,

and Vincent S. Tseng

Feature Relation Network That Can Identify Underlying Data Structure for Effective Pattern

Classification 531

Hai Long Zhu andHong Qiang Wang

Imputing Missing Values in Microarray Data with Ontology Information 535

Andy C. Yang, Hui-Huang Hsu, and Ming-Da Lu

Workshop 9: Data-mining of Next-Generation Sequencing Data

On Accelerating Iterative Algorithms with CUDA: A Case Study on Conditional Random Fields

Training Algorithm for Biological Sequence Alignment 543

ZhihuiDu, ZhaomingYm, Wenjie Liu, andDavidBader

A Re-sequencing Tool for High Mismatch-tolerant Short Read Alignment Based on Burrows-Wheeler

ix

Transform

Chen-HuaLu, Chun-Yuan Lin, and Chuan Ti Tang

,549

Peak detection on ChlP-Seq data using wavelet transformation 555

Heng-Yi Wu, Jie Zhang, and Kun Huang

In Search ofTrue Reads: A Classification Approach to Next Generation Sequencing Data

561

Edward Wijaya, Jean-Francois Pessiot, Martin C. Frith, Wataru Fujibuchi, KiyoshiAsai,

and Paul Horton

Sorting Next Generation Sequencing Data Improves Compression Effectiveness

567

Raymond Wan and KiyoshiAsai

bindSDb: A Binding-information Spatial Database 573

Damian Roqueiro, Jonna Frasor, and Yang Dai

A Distributed System for Fast Alignment ofNext-Generation Sequencing Data

579

Jaydeep K. Srimani, Po-Yen Wu, John H. Phan, and May D. Wang

Methy-Pipe: An Integrated Bioinformatics Data Analysis Pipeline for Whole Genome Methylome

Analysis 585

Peiyong Jiang, XiaoxiSu, Zhang Chen, Kun Sun, Rossa W.K Chiu, Y.M. Dennis Lo,

andHao Sun

Workshop 10: Information Technology for Chinese Medicine

Extracting Clinical Information from Free-text ofPathology and Operation Notes via Chinese Natural

Language Processing 593

QiangZeng, ZuofengLi, Weide Zhang, Xiaoyan Zhang, and Lei Liu

Syndrome differentiation offatty liver based on the whole network analysis theory

598

Shouyi Yin, Guang Ji, Tao Liu, and Huafeng Wei

Goal Based Bisimulation for Testing Therapies in Traditional Chinese Medicine 603

Guang Zheng, Xiaojuan He, Miao Jiang, andAipingLu

Getting started in MeSH text mining to find the biological network shared with rheumatoid arthritis,

coronary heart disease and diabetes mellitus 609

XiaorongDing, QinglinZha, andAipingLu

x

TCM Health Management System 613

BingZhou, Yang DongLu, GuangqinHu, JinghuaTian, QiangLiu, Li Jin, Yang Dong Lu,

and Min Zhu

Empirical Study on Treatment of Coronary Heart Disease with Famous Doctors' Method of

Regulating Spleen and Stomach based on Simplified Point-wise Mutual Information

617

PingLi, Xuezhong Zhou, Ronglin Gao, andSa Wu

Analysis of Synergistic and Antagonistic Effects ofTCM: Cases on Diabetes and Insomnia

620

Martin McGrane, Simon Poon, Josiah Poon, Xuezhong Zhou, Runshun Zhang,

Baoyan Liu, Clement Loy, Kwan Paul, Chan Kelvin, Daniel Sze, andJunbin Gao

Gene Selection by Using an Improved Fast Correlation-Based Filter 625

Xue-Qiang Zeng, Guo-Zheng Li, and Su-Fen Chen

Statistical Truths in Traditional Chinese Medicine Theories 631

Nevin L. Zhang and Shihong Yuan

Disciplines of Medicinal Formulas for Insomnia by Data Mining 635

Yuehan Song, FengLi, Changhai Wang, Jiamei Ma, Qing Han, and Jing Guan

An Ontology based Knowledge Management System Architecture for Traditional Chinese Medicine

640

Bai Yu, Cai Dongfeng, andDong Yanju

Multi-Class Feature Selection by Using Pair-class and All-class Techniques 644

Bo Chen, Guo-Zheng Li, andMingyu You

Traditional Chinese Medicine Data Mining: Associating Clinical Cancer Case Studies with Traditional

Chinese Medicine Therapies 648

Su-Shing Chen, Bairong Shen, and Yuan Li

Application ofRandom Forest Data Mining Method to Feature Select the Sub-health State in Female

651

Li-min Wang, Jia-Xu Chen, Min Fan, Xin Zhao, Hua-ting Cui, Mei-jing Qou, Shao-xian Wang,

Xiao-hong Li, You-mingJiang, Li-qian Zhou, andXin Peng

Education and training of acupuncture providers affect the results of systematic reviews and

meta-analyses 655

En-Hua Zhou, Yun Yang, Huan-gan Wu, Guang-Hong Ding, and Hui-Rong Liu

xi

Immunomodulatory activity of herb-partition moxibustion on Stat3 and Stat4 in the mucosa of

ulcerative colitis rats 660

En-Hua Zhou, Hui-Rong Liu, Xiao-Mei Wang, Lin-Ymg Tan, Huan-gan Wu, Yin Shi,

Shi-fenXu, Xiu-Di Qin, and Wen-Yan Huang

Application ofPCA and LDA methods on gloss recognition research in TCM complexion inspection

666

RuiZhou, Rui-WeiZhao, FufengLi, Guo-ZhengLi, YiQin Wang, andXiaoYan Zheng

Study on the Correlation between Tongue Diagnosis ofTraditional Chinese Medical and Assay Result

ofHealth Check 670

Fei Tian, Guangqin Hu, Bing Zhou, Xiaozuo Lu, Hongwu Wang, Chunquan Yu,

Hongmei Cao, Zhihao Jiang, and Shizhen Guo

Consulting Study of Experts' Opinions on Lung System Disease Location Characteristics

674

Zheng Xu

Deduction Research on Syndromes Diagnosis ofTCM Inquiry for Cardiovascular Diseases Based on

RBF Nerve Network 678

Xu Zhao-Xia, Wang Yi-Qin, Yan Jian-Jun, Xia Chun-Ming, Liu Guo-Ping, Xu Jin,

Guo Rui, Yan Hai-Xia, Li Fu-Feng, and HongYu-Jian

Research and Application of Non-negative Matrix Factorization with Sparseness Constraint in

Recognition of Traditional Chinese Medicine Pulse Condition 682

Rui Guo, Yiqin Wang, Haixia Yan, Jianjun Yan, FufengLi, and ZhaoxiaXu

The study of photoelectric facial blood flow volume Characteristic of heart blood stasis syndrome in

premature coronary heart disease and the relations between it and TXB2> 6-K-PGF1 a

686

Zhixi Hu, Jinghui Zheng, Yi Zou, Jie Chen, and Juan Chen

Procedure Recording and Telediagnosis ofPulse Diagnosis in Traditional Chinese Medicine

690

BingyiHu, LuXu, Ao Tong, Yan Zhao, andXu Zhang

Application of Bayesian Network in Information Fusion Analysis of Four Diagnostic Methods of

Traditional Chinese Medicine 694

WenjieXu, Yiqin Wang, Xiaojuan Zou, ZhaoxiaXu, and ChunfengChen

Study on Intelligent Syndrome Differentiation in Traditional Chinese Medicine Based on Information

Fusion Technology 698

xii

Yiqin Wang, Rui Guo, Haixia Yan, FufengLi, Chunming Xia, ZhaoxiaXu, and Jin Xu

The Construction of the Traditional Chinese Medicine Four Seasons Five Viscera System Calculation

Model 703

Xiaoxiang Guan, Zhijin Guan, Yonghua Zhao, and Shanli Chen

Analysis of Sound Signal of Five Internal Organs Based on Wavelet Packet 707

Jianjun Yan, Siyuan Mao, Yiqin Wang, FufengLi, Rui Guo, Chunfeng Chen, Haixia Yan,

Chunming Xia, and Chao Wang

On Classification Compatibility Laws ofZhongjing Prescriptions 712

Xuemei Yang, XinmeiLai, and CandongLi

Research on Proteins in Tongue Coating in Patients with Chronic Renal Failure and Chronic Gastritis

Based on SELDI-TOF-MS Technique 717

Yiming Hao, Yawei Cheng, Lei He, Peng Qian, Wenjing Wang, Fufeng Li, and Yiqin Wang

Studying Herb-Herb Interaction for Insomnia through the theory ofComplementarities 722

Josiah Poon, Simon Poon, Xuezhong Zhou, Runshun Zhang, Dawei Yin, Baoyan Liu,

Kelvin Chan, Paul Rwan, Clement Loy, Daniel Sze, andJunbin Gao

Study about the feature of some parts of the Traditional Chinese Medicine(TCM) physical

examination correlate with the indexes ofthe renal function 727

Hu Guangqin, LuXiaozuo, ZhouBing, Luo Yufu, Lu Yangdong, Zhu Min, and Liu Xiaomin

Research of Features in the Pulse Waves of Women during Pregnancy 730

Nanyue Wang, Youhua Yu, Dawei Huang, Zengyu Shan, Yan Chen, Tongda Li, Xiaoou Xue,

Yan Gao, Wanfeng Fu, and Yanping Chen

Attribute Weighting with Probability Estimation Trees for Improving Probability-based Ranking in

Liver Diagnosis 733

Na Chu, LizhuangMa, Min Zhou, YiyangHu, Ping Liu, and Zhiying Che

Relation between arterial elastic characteristic and time-domain parameters of pulse waveform in

Traditional Chinese Medicine 740

Haixia Yan, Yiqin Wang, Rui Guo, FufengLi, Yujian Hong, FengyingRun, Yuci Yang,

Yiming Hao, and Jianjun Yan

Analysis of 903 Voice Signals ofPatients with Five Organs Illness and Normal Persons in Traditional

Chinese Medicine Auscultation 745

Chunfeng Chen, Yiqin Wang, Jianjun Yan, Siyuan Mao, Rui Guo, Yong Shen, Xiaojing Shen,

and Wenjie Xu

xiii

Strategies to Enhance Computer Assisted Differential Diagnosis in Traditional Chinese Medicine for

Coronary Heart Disease: Validity and Standardisation of a Diagnostic Instrument 749

Laura Duck, Xiaoshu Zhu, Stefania Penkala, andAnthony Maeder

Correlation between TCM Inspection ofFacial Color and Pulmonary Function ofBronchial Asthma

754

Connie YukKin Hung, ZhaoxiaXu, Yiqin Wang, FufengLi, Haixia Yan, and Yuci Yang

Study on the Principle of Treatment, Medicine and Formula of Chinese Medicine in Congestive Heart

Failure Based on Literature Review and Data Mining Technology 758

Ruijing Luo and JianchengHe

Metabonomics Studies on Urine Specimens from Patients with Chronic Renal Failure 763

Qian Peng, Bai Guanfeng, Zhao Jie, and Wang Yiqin

Design ofthe Workstation for Hand Rehabilitation Based on Data Glove 769

Chen Hao, Cao Lixing, And Wang Qingxiang

Application ofthe Support Vector Machine to the Identification of Human Pulse Signals 772

Kunbao Cai, Xiaoming Wen, Yunzi Duan, AndKunbao Cai

The Ideas and Methods in studying Pulse Width ofTraditional Chinese Medicine 777

CongyingLiu

Research on the Three-region Multipath Pulse Detecting System 781

Weichang Tang

Symptom selection of inquiry diagnosis data for coronary heart disease in traditional Chinese

medicine by using social network techniques 785

Ya-Lei Wang, Guo-ZhengLi, Guo-PingLiu, andYi-Qin Wang

Association Analysis and Distribution of Chronic Gastritis Syndromes Based on Associated

Density 790

Guo-PingLiu, Yi-Qin Wang, Fu-FengLi, Hai-Xia Yan, Jing-JingFu, Jie Zhao, Rui-Wen Zhen,

Shi-Xing Yan, and Guo-ZhengLi

The Application of Statall.O in Clinical Evaluation ofTraditional Chinese Medicine 795

YmgDong, Pin-XianHuang, Guo-PingLiu, andYi-Qin Wang

Posters:

Fine-scale stratification analysis ofHong Kong Chinese population 802

Yu-Qing Qiu, Ting-Fan Leung, Ronald C. W. Ma, Brian Tomlinson, Juliana C.N. Chan,

xiv

Larry Baum, andNelson L.S. Tang

Transduced Tat-DJ-1 protein protects against oxidative stress-induced SH-SY5Y cells death and

Parkinson disease mouse model 805

Min Jea Shin

Positional preferences by 20 amino acids in beta sheets 806

Hossein Fallahi and Reza Yarani

Enhances the transdcution efficiency of Tat-catalase protein attenuate neuronal cell damage

808

Eun Jeong Sohn and Eun Hee Ahn

PEP-l-Peroxiredoxin protein efficiently protects Raw 264.7 cells from lipopolysaccharide

(LPS)-induced inflammation 809

Mi Jin Kim andHye Won Kang

Infinite Latent Process Decomposition 810

Tomonari Masada, Yuichiro Shibata, and Kiyoshi Oguri

Modeling and formal verification of biological regulatory networks: an integrative approach812

Pedro Tiago Monteiro, Ana Freitas, Delphine Ropers, Radu Mateescu, and Hidde de Jong

Identification of relevant subpathways from molecular pathways in gene expression data by a

probabilistic approach 814

SeungyoonNam

Network Modeling ofRNA Secondary Structures based on Integrative Randomized Clustering

815

Shang Gao, RedaAlhajj, andJon Rokne

A New Evaluation Measure Of Diagnostic Tests Based on Modified Area Under the Receiver

Operating Characteristic Curve 817

Wenbao Yu

Maximum Likelihood and Polynomial System Solving 819

Kim Batselier and Bart De Moor

NeuMORE: Ontology in Stroke Recovery 821

Christopher Townsend, Jingshan Huang, DejingDou, HaishanLiu, Lei He, PatrickHayes,

Robert Rudnick, HardikShah, Dennis Fell, and Wei Liu

XV

Genome-wide linkage and association analyses for the fasting glucose level in Korean population

including monozygotic twins 823

Young Ju Suh, Sung Hwan Kim, Hangseok Choi, MoonsukNam, So Hun Kim, andJoohon Sung

NWE: Node-Weighted Expansion for Protein Complex Prediction Using Random Walk Distances

825

Osamu Maruyama andAyaka Chihara

Correction of Copy Number Variation Data Using Principal Component Analysis

827

Jiayu Chen, Jingyu Liu, and Yince Calhoun

The decision to live or die in response to DNA damage controlled by differential p53 pathway

dynamics 829

Xi Chen and Jue Shi

Using Computational Method to Identify the Binding Site of 8R-Lipoxygenase for Arachidonic Acid

831

Tianchuan Du, Neelima Rama, Shuju Bai, and Ebrahim Khosravi

Modeling Glucose Transport in Skeletal Muscle 833

Dayu Lv and Bill Goodwine

Structural analysis ofheme proteins: implications for design and prediction 834

Ting Li, Herbert Bonkovsky, and Jun-tao Guo

Network Profiling Analysis for Generating Modulator-Dependent Gene Networks 836

Teppei Shimamura, Seiya Imoto, Atsushi Niida, Masao Nagasaki, Rui Yamaguchi,and Satoru Miyano

Development of a Pathway Comparison tool for analysis of bacteria genomes ,837

Haizhou Liu

MiRPara: a SVM-based Software tool for Prediction ofMature MiRNAs 839

Bo Wei and Bo Wei

Early Stage Evolution in Metabolic Related Protein Interaction Network 841

Jea woon Ryu and Hak Yong Kim

Transcriptional Regulation ofDrug Target Proteins from Cancer Related Disease Network

843

Byeolna Park, Yoon Kyeong Lee, and Hak YongKim

xvi

Similarity Search and Posttranslational Modifications in Tandem Mass Spectra 845

JiriNovak and David Hoksza

Computational Model ofVEGF, Thrombin, and Histamine signalling network 847

Xiaona Wei and Yuzong Chen

GPU acceleration of simulation tool for lipid-bilayers 849

Ardita Shkurti, Andrea Acquaviva, Elisa Ficarra, Mario Orsi, Martino Ruggiero,

and Enrico Macii

Algorithm for DNA Sequence Compression Based on Prediction of Mismatch Bases and Repeat

Location ,....851

Kalyan Kumar Kaipa, Ajit S Bopardikar, Srikantha Abhilash, Parthasarathy Venkataraman,

Kyusang Lee, TaeJin Ahn, and Rangavittal Narayanan

System for Random Access DNA Sequence Compression 853

Kalyan Kumar Kaipa, Kyusang Lee, TaeJin Ahn, andRangavittal Narayanan

Genome-wide DNA methylation analysis in tumor and normal tissues from lung squamous cell

carcinoma and serous cystadenocarcinoma 855

Hidenori Inaoka, Yutaka Fukuoka, andMakoto Noshiro

Effects of cyclic stretch on early response gene expressions in normal human pulmonary artery

endothelial cells in vitro 857

Kozue Kobayashi, Masumi Tanaka, Hidenori Inaoka, Satoru Nebuya, Yutaka Fukuoka,

Kenichi Kokubo, Hirosuke Kobayashi, andMakoto Noshiro

A Smart-Walk System for Various Kinds ofHandicapped 859

Joong-Yeub Lee, Kyung-Hee Lee, Yu-Jin Kang, Wan-Sup Cho, and Hwa-Shin Ryoo

Sequence Composition Analysis on Arsenic-binding Proteins in Human Cells 861

Yi-An Tung, Yu-Ying Chang, Rong-Nan Huang, and Chien-Yu Chen

Trace of Evolutionary Evidence by Analyzing Clustering Information of Metabolic Pathways in

Eukaryotes 862

ArangRhie, Myungha Jang, and Hyun-SeokPark

Mining Molecular Interactions from Scientific Literature Using Cloud Computing 864

Franco Nazareno, Kyung-Hee Lee, and Wan-Sup Cho

Multi-Resolution Tile-Based Follicle Detection using Color and Textural Information of Follicular

Lymphoma IHC Slides 866

JingHan, Dmitriy Shin, GeraldArthur, and Chi-Ren Shyu

xvii

A Genomic Data Warehouse Model forFast Manipulation Using Repeat Region,

Arang Rhie, Kyung-Eun Lee, and Hyun-Seok Park

868

Mitochondrial Protein Cleavage Site Predictor 870

Yoshinori Fukasawa, Raymond Wan, Szu-Chin Fu, Junko Tsuji, Noriyuki Sakiyama,Kenichiro Imai, and Paul Horton

microDoR for HUMAN:Aweb server to predict mode of miRNA-Mediated Gene Silencing

872

Lei Cheng, Tao Zhou, Xuejiang Guo, Xiaofeng Song, Xiaobai Zhang, Ping Han,

Yi-ping Phoebe Chen, andJiahao Sha

ANew PDS PORTAL for Clinical TeleGaming Rehabilitation and Intervention 874

Carl Taswell

Spectral Analysis ofNumerical Exon and Intron Sequences 876

Jennifer Yin Yee Kwan, Benjamin Yin MingKwan and Hon Keung Kwan

Author Index 878

xviii