BIOCOMP'08: July 16, 2008 Schedule

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6:45am - 5:00pm:  Registration (Second Floor, Conference Lobby: 1-5)


SESSION 12-BIOCOMP: MULTISCALE MODELS FOR SYSTEMS AND SYNTHETIC BIOLOGY
                  Chair: Prof. Yiannis N. Kaznessis
                  University of Minnesota, Minneapolis, Minnesota, USA
                  July 16, 2008 (Wednesday); 08:00am - 09:20am
                  (LOCATION: Ballroom 5)

08:00 - 08:20am:  Multiscale Effects in Host-Pathogen Interactions
                  J. Peccoud
                  Virginia Polytechnic Institute and State University, Blacksburg, VA, USA

08:20 - 08:40am:  Development of a Multi-Scale Model for Biomembrane Deformations
                  Dmitry Kopelevich
                  University of Florida, Gainesville, Florida, USA

08:40 - 09:00am:  Multiscale Models for Synthetic Biology
                  Yiannis N. Kaznessis
                  University of Minnesota, Minneapolis, Minnesota, USA

09:00 - 09:20am:  Quantitative Systems Analysis of Multicellular Morphodynamics
                  Anand R. Asthagiri
                  California Institute of Technology, Pasadena, California, USA


SESSION 13-BIOCOMP: APPLICATION OF ENGINEERING TECHNIQUES AND MATHEMATICS IN MEDICINE AND BIOLOGY
                  Chairs: Dr. Getachew K. Befekadu* and Reetal Pai**
                  *Georgetown University, USA; **Texas A&M, USA
                  July 16, 2008 (Wednesday); 09:20am - 12:00noon
                  (LOCATION: Ballroom 5)

09:20 - 09:40am:  Analysis of Goldbeter-Koshland Switch Using the Chemical Master Equation
                  Jingwei Zhang*, Layne T. Watson, Masha Sosonkina, and Yang Cao
                  Virginia Polytechnic Institute and State University, USA

09:40 - 10:00am:  Classifying Proteins Related to Adverse Drug Reactions
                  from Drug Targets Using Support Vector Machines
                  Shih-Fang Lin*, Ke-Ting Xiao*, Chung-Cheng Chiu*, and Von-Wun Soo*/**
                  *National Tsing Hua University, HsinChu, Taiwan
                  **National University of Kaohsiung, Kaohsiung, Taiwan

10:00 - 10:20am:  Probabilistic-Based Mixture Regression Models for Multi-Class
                  Alignment of LC-MS Data
                  G. K. Befekadu and H. W. Ressom*
                  Georgetown University, Washington, DC, USA

10:20 - 10:40am:  BREAK

10:40 - 11:00am:  Identifying Factors that Improve the Predictive Quality of BMI
                  for Health Status
                  M. L. D. Ponce, J. Ding, and M. H. N. Tabrizi*
                  East Carolina University, Greenville, North Carolina, USA

11:00 - 11:20am:  Application of Framelet Transform to the MS-Based Proteomics
                  Data Preprocessing
                  Haihui Wang* and Yijun Chang; Beihang University, Beijing, P. R. China

11:20 - 11:40am:  Efficient Sparse Dynamic Programming for the Merged LCS Problem
                  Yung-Hsing Peng, Chang-Biau Yang*, Chiou-Ting Tseng, and Chiou-Yi Hor
                  National Sun Yat-Sen University, Taiwan

11:40 - 12:00pm:  Evaluation of the Deformity of Cleft Nose Based on Statistical
                  and Neural Network
                  Wang Xi*, D. W. Kim**, and Kil To Chong*
                  *Chonbuk National University, Jeonju, Korea
                  **Yonsei University College of Medicine, Seoul, Korea

12:00 - 12:40pm:  LUNCH (On Your Own)


SESSION 14-BIOCOMP: METABLOMICS, PROTEOMIC AND PROTEIN FUNCTION
                  Chairs: Dr. Harold J. Drabkin* and Prof. Omar Bagasra**
                  *The Jackson Laboratory, Bar Harbor Maine, USA
                  **Director, Dept. Biology, South Carolina Center for Biotechnology, USA
                  July 16, 2008 (Wednesday); 12:40pm - 01:40pm
                  (LOCATION: Ballroom 5)

12:40 - 01:00pm:  Prediction of Protein Function Using Graph Container and
                  Message Passing
                  Hongbo Zhou*, Qiang Cheng and Mehdi Zargham
                  Southern Illinois University, USA

01:00 - 01:20pm:  Simulation of FGF-2 Binding with Receptors on Cell Surface on
                  the Wall in a Bioreactor System
                  Changjiang Zhang, Wensheng Shen, Kimberly Forsten Williams,
                  Michael Fannon and Jun Zhang*
                  University of Kentucky, USA

01:20 - 01:40pm:  Proteins: From Structural Classification to Amino Acid
                  Interaction Networks
                  Stefan Balev and Omar Gaci*
                  LITIS, Universite du Havre, France


SESSION 15-BIOCOMP: GENETIC NETWORK MODELING AND INFERENCE
                  Chair: Dr. Chaoyang Zhang, University of Southern Mississippi, USA
                  July 16, 2008 (Wednesday); 01:40pm - 02:40pm
                  (LOCATION: Ballroom 5)

01:40 - 02:00pm:  Generating Robust Gene Interaction Network Using Bayesian Methods
                  Nan Wang*, Changhe Yuan, Bindu Nandurri, and Susan Bridge
                  Mississippi State, Mississippi, USA

02:00 - 02:20pm:  Inferring Gene Regulatory Network of Yeast Cell-Cycle
                  Using Dynamic Bayesian Network
                  Peng Li, Chaoyang Zhang*, Edward J. Perkins, Ping Gong, and Youping Deng
                  University of Southern Mississippi, Mississippi, USA

02:20 - 02:40pm:  Creating an Automation Expressed Sequence Tags Analysis Workflow
                  Mehdi Pirooznia*, Edward J. Perkins, Ping Gong, Chaoyang Zhang,
                  and Youping Deng
                  University of Southern Mississippi, Mississippi, USA


SESSION 16-BIOCOMP: BIOINFORMATICS AND MEDICAL INFORMATICS
                  Chairs: Dr. Frank Emmert-Streib and Dr. Nan Mei*
                  *National Center for Toxicological Research, USA
                  July 16, 2008 (Wednesday); 02:40pm - 04:20pm
                  (LOCATION: Ballroom 5)

02:40 - 03:00pm:  An Overview of the BioExtract Server - a Distributed, Web Based
                  Application for Bioinformatic Analysis
                  C. M. Lushbough
                  University of South Dakota, USA

03:00 - 03:40pm:  DISCUSSION SESSION B-BIOCOMP (Refreshments will be available)
                  July 16, 2008 (Wednesday)
                  (LOCATION: Hallways - Ballrooms 1-5)

                  O. Improving Automatic Inference of Biological Networks Governing C. Elegans
                     Vulval Induction by Incorporating Interaction Data
                     Xiaoyun Sun and Pengyu Hong
                     National Center of Behavioral Genomics, USA
                  O. An Efficient Algorithm for the Longest Pattern Subsequence Problem
                     Xiaodong Wang*, Lei Wang**, and Yingjie Wu*
                     *Fuzhou University, Fuzhou, P. R. China
                     **Georgia Institute of Technology, Atlanta, Georgia, USA
                  O. Genomic Scale Reconstruction of Gene Regulatory Networks from
                     Microarray Data
                     Kenneth Sundberg*, Daniel Ence, Daniel Wilcox, Quinn Snell, and
                     Mark Clement; Brigham Young University, Provo, Utah, USA
                  O. Validation of the Human Alu Phylogeny: a Whole-Genome Analysis
                     Sridhar Ramachandran* and Travis Doom**
                     *Indiana University Southeast, New Albany, Indiana, USA
                     **Wright State University, Dayton, Ohio, USA
                  O. Fuzzy C-Means Algorithm for Clustering Protein Sequences
                     G Lavanya Devi*, Allam Apparao, GRSridhar, A. Damodaram, and
                     G. Jaya Suma; Andhra University, India
                  O. E.Coli Promoter Recognition Through Wavelets
                     T. Sobha Rani* and Raju S. Bapi; Univeristy of Hyderabad, India
                  O. Two Dimensional Modeling and Computer Simulation of Tumor Growth
                     Loretta Ichim*, Radu Dobrescu, and Catalin Vasilescu
                     Politehnica University of Bucharest, Romania
                  O. Using Simple Computer Exercises to Assist in the Rehabilitation
                     of Stroke Patients: A Prototype
                     G. Jones, G. Pearce, and M. Smith
                     University of Wolverhampton, Wolverhampton, United Kingdom
                  O. An Algorithm for Estimation of Abdominal Pressure by Electromyography
                     K. S. Kim, Y. S. An, J. H. Seo, and C. G. Song*
                     Chonbuk National University, Korea
                  O. Analysis of Physiological Measures for Human Cognitive State Estimation
                     Rajesh Singla and Hari Singh*; NIT Jalandhar, India
                  O. Classification of Normal and Abnormal Knee Joint Using
                     Back-Propagation Neural Network
                     K. S. Kim, J. H. Seo, and C. G. Song*; Chonbuk National Univ., Korea
                  O. Comparison of Acoustical Parameters of Knee Sound According to
                     Pathological Condition For Pattern Extraction
                     C. G. Song*, K. S. Kim, and J. H. Seo; Chonbuk National Univ., Korea
                  O. Optimum Electrode Configuration to Estimate Abdominal Pressure
                     Using Regression Analysis of Bio-Impedance Signal
                     C. G. Song*, K. S. Kim, Y. S. An, and J. H. Seo
                     Chonbuk National University, Korea


SESSION 16-BIOCOMP: Continued: BIOINFORMATICS AND MEDICAL INFORMATICS
                  Chairs: Dr. Frank Emmert-Streib and Dr. Nan Mei*
                  *National Center for Toxicological Research, USA
                  July 16, 2008 (Wednesday); 02:40pm - 04:20pm
                  (LOCATION: Ballroom 5)

03:40 - 04:00pm:  Combinations of Context-Free Shifts and Shifts of Finite Type
                  Hiroshi Kamabe
                  Gifu University, Japan

04:00 - 04:20pm:  A Computational Framework for Performance Optimization of
                  Bioinformatics Applications
                  Avinash Shankaranarayanan and Christine Amaldas
                  Auckland University of Technology, Auckland, New Zealand


SESSION 17-BIOCOMP: (CONCURRENT SESSION with 18-BIOCOMP)
                  GENE EXPRESSION AND DATA ANALYSIS
                  Chairs: Dr. Nan Mei* and Jingwei Zhang**
                  *National Center for Toxicological Research, USA
                  **Virginia Polytechnic Institute and State University, USA
                  July 16, 2008 (Wednesday); 04:20pm - 05:20pm
                  (LOCATION: Ballroom 5)

04:20 - 04:40pm:  Mouse Liver Gene Expression Profile of Acrylamide Administered
                  in Drinking Water
                  Nan Mei*, Mugimane G. Manjanatha*, Jo Tseng**, Stacey L. Dial*,
                  Wayne Liao**, and Lei Guo*
                  *National Center for Toxicological Research, Jefferson, Arkansas, USA
                  **PhalanxBio, Inc., Palo Alto, California, USA

04:40 - 05:00pm:  Majority Logic Decoding for Probe-Level Microarray Data
                  Humberto Ortiz-Zuazaga*, Tim Tully**, and Oscar Moreno***
                  *University of Puerto Rico, San Juan, Puerto Rico
                  **Dart Neuroscience LLC, San Diego, California, USA
                  ***Gauss Research Laboratory, Inc., San Juan, Puerto Rico

05:00 - 05:20pm:  PC-Relief-F Feature Filtering Algorithm: Application and Utilization
                  in Selecting Informative Genes from Microarray Data
                  Sapna Kumari and Huann-Sheng Chen*
                  Michigan Technological University, Houghton, Michigan, USA


SESSION 18-BIOCOMP: (CONCURRENT SESSION with 17-BIOCOMP and 19-BIOCOMP)
                  BIOMOLECULAR PATHWAYS AND SYSTEM BIOLOGY
                  Chair: Dr. Jianhua Ruan, University of Texas at San Antonio, USA
                  July 16, 2008 (Wednesday); 04:40pm - 06:00pm
                  (LOCATION: Ballroom 1)

04:40 - 05:00pm:  A Modified Dirichlet Process Mixture Model for Clustering
                  Phosphopeptides Based on Their Response to Anti-Cancer Drug Peturbation
                  Babak Shahbaba*, Eva Prenosil**, Anjali Jain**, and Sylvia K. Plevritis*
                  *Stanford University, USA; **Cedars-Sinai Medical Center, USA

05:00 - 05:20pm:  Identification of Condition-Specific Regulatory Modules by
                  Multi-Level Motif and mRNA Expression Analysis
                  Li Chen, Jianhua Xuan, Rebecca B. Riggins, Yue Wang, Eric P. Hoffman,
                  and Robert Clarke
                  Virginia Polytechnic Institute and State University, USA;
                  Georgetown University School, USA; Children's National Medical Center, USA

05:20 - 05:40pm:  Word-Based Characterization of the Bidirectional Promoters from
                  the Human DNA-Repair Pathway 
                  Jens Lichtenberg, Edwin Jacox, Mary Q Yang, Laura Elnitski, and Lonnie Welch
                  Ohio University, USA

05:40 - 06:00pm:  Discovery of Regulatory Elements in Oomycete Orthologs
                  Jens Lichtenberg*, Paul Morris**, Klaus Ecker*, and Lonnie Welch*
                  *Ohio University, Athens, Ohio, USA
                  **Bowling Green State University, Bowling Green, Ohio, USA


SESSION 19-BIOCOMP: (CONCURRENT SESSION with 18-BIOCOMP)
                  MEDICAL DIAGNOSTIC TOOLS AND METHODS
                  Chair: Dr. Igor Szczyrba, University of Northern Colorado, USA
                  July 16, 2008 (Wednesday); 05:20pm - 06:20pm
                  (LOCATION: Ballroom 5)

05:20 - 05:40pm:  On the Role of a Nonlinear Stress-Strain Relation in Brain Trauma
                  Igor Szczyrba*, Martin Burtscher**, and Rafal Szczyrba***
                  *University of Northern Colorado, Greeley, Colorado, USA
                  **The University of Texas at Austin, Texas, USA
                  ***Funiosoft, LLC, Silverthorne, Colorado, USA

05:40 - 06:00pm:  A Federative Approach for a Virtual Community in Elderly Care:
                  a Different Way in eCare
                  Giovanni Rinaldi*, Mike Martin**, and Massimo Busuoli***
                  *CUP 2000 Spa, Bologna, Italy; **University of Newcastle, UK;
                  ***ENEA, Liaison Office, Bruxelles, Belgium

06:00 - 06:20pm:  Modified Detrended Fluctuation Analysis Method in Depth of
                  Anesthesia Assessment Application
                  T. Nguyen-Ky, Peng Wen, and Yan Li
                  University of Southern Queensland, Toowoomba, Australia


SESSION 20-BIOCOMP: BIOINFORMATICS AND APPLIED GENOMICS IN LATIN AMERICA
                  Chairs: Dr. Diana Magalhaes de Oliveira, Dr. Jeronimo C. Ruiz,
                  Dr. Goran Neshich, and Prof. Vasco Ariston C. Azevedo; Brazil
                  July 16, 2008 (Wednesday); 06:20pm - 07:00pm
                  (LOCATION: Ballroom 5)

06:20 - 06:40pm:  The Table of Interface Forming Residues as the Specificity
                  Indicator for Serine Proteases Bound to Different Inhibitors
                  R. C. Togawa, C. Ribeiro, I. Mazoni, T. Pelligrinelli,
                  J. G. Jardine, and G. Neshich
                  Embrapa Information Technologies - CNPTIA, Campinas, SP, Brazil

06:40 - 07:00pm:  HiperMUSCLE: An Intuitive Graphical User Interface for the
                  Multiple Sequence Alignment Program MUSCLE (Edgar, 2004)
                  G. A. C. Santos, I. M. C. Maia, F. F. Araujo, A. C. L. Pacheco,
                  S. R. Medeiros, C. R. F. Gadelha, S. C. Silva, R. Araujo-Filho,
                  and D. M. Oliveira*
                  Nucleo Tarcisio Pimenta de Pesquisa Genomica e Bioinformatica -
                  NUGEN; Universidade Estadual do Ceara, Itaperi, Brazil


06:00 - 09:30pm:  Tutorials (please see the list of tutorials)

To select a different schedule CLICK HERE