BIOCOMP'07: June 28, 2007 Schedule

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


SESSION 14-BIOCOMP: GENOMICS
                  Chair: Dr. Mengxia Zhu, Southern Illinois University, Carbondale, Illinois, USA
                  June 28, 2007 (Thursday); 08:00am - 10:40am
                  (LOCATION: Ballroom 5)

08:00 - 08:20am:  Semantically Linking PubMed to the Gene Ontology for
                  Ontology-based Browsing
                  B. Vanteru, J. Shaik and M. Yeasin
                  University of Memphis, Tennessee, USA

08:20 - 08:40am:  Stability of RNA Structural Motifs and its Influence on
                  Editing Efficiency by ADARS
                  Vinhthuy Phan and Allen Thomas
                  University of Memphis, Tennessee, USA

08:40 - 09:00am:  Microarray Data Analysis and Mining Strategy to Reduce Type 1
                  and Type 2 Errors
                  Jian Wu, Nataliya I. Lenchik, and Ivan C. Gerling
                  University of Tennessee Health Science Center, & Research Service,
                  Veterans Affairs Medical Center, Memphis, Tennessee, USA

09:00 - 09:20am:  Characterizing Disease-Specific Pathways and their Coordination
                  by Integrative Microarray Analysis with Application to Cancer
                  Min Xu, Ming-Chih J. Kao, Juan Nunez-Iglesias, Joseph R. Nevins,
                  Mike West, and Xianghong Jasmine Zhou
                  University of Southern California, Los Angeles, California, USA;
                  University of Michigan, Ann Arbor, Michigan, USA;
                  Duke University, Durham, North Carolina, USA

09:20 - 09:40am:  A Parallel Computing Approach to Decipher Transcription Network
                  for Large-Scale Microarray Datasets
                  Mengxia Zhu and Qishi Wu
                  Southern Illinois University Carbondale, Illinois, USA;
                  University of Memphis, Memphis, Tennessee, USA

09:40 - 10:00am:  Supervised 3D Star Co-ordinate Projection for the Validation of
                  Differentially Expressed Genes from Microarrays
                  J. Shaik and M. Yeasin
                  University of Memphis, Memphis, Tennessee, USA

10:00 - 10:20am:  Reannotation of the Physical Map of Glycine Max for Ploidy by
                  BAC End Sequence Driven Whole Genome Shotgun Read Assembly
                  David A. Lightfoot, Jeffry Shultz and Navinder Saini
                  Southern Illinois University, Carbondale, Illinois, USA;
                  USDA-ARS, Crop Genetics and Production Research Unit, MS, USA;
                  Jawaharlal Nehru Krishi Vishwavidyalaya Adhartal, India

10:20 - 10:40am:  Physiological and Transcriptomic Analyses to Characterize the
                  Function of Fur and Iron Response in Shewanella Oneidensis
                  Yunfeng Yang, Daniel P. Harris, Feng Luo, Liyou Wu,
                  Andrea B. Parsons, Anthony V. Palumbo, and Jizhong Zhou
                  Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA;
                  Clemson University, Clemson, South Carolina, USA;
                  University of Oklahoma, Norman, Oklahoma, USA

10:40 - 11:00am:  BREAK


SESSION 15-BIOCOMP: GENOMICS
                  Chair: Dr. Yunlong Liu
                  Indiana University School of Medicine, Indianapolis, Indiana, USA
                  June 28, 2007 (Thursday); 11:00am - 02:40pm
                  (LOCATION: Ballroom 5)

11:00 - 11:20am:  xMAN: Extreme Mapping of OligoNucleotides
                  Wei Li, Jason S. Carroll, Myles Brown, and X. Shirley Liu
                  Harvard School of Public Health, Boston, MA, USA;
                  Harvard Medical School, Boston, MA, USA

11:20 - 11:40am:  Improving the Specificity of Exon Prediction Using Genomic Homology
                  Jing Wu
                  Purdue University, West Lafayette, Indiana, USA

11:40 - 12:00pm:  Discriminant Analysis Using Multigene Expression Profiles in
                  Molecular Classification of Breast Cancer
                  Xin Yan and Tian Zheng
                  Russell Investment Group, Tacoma, Washington, USA;
                  Columbia University, New York, USA

12:00 - 12:20pm:  Selection of Thermodynamic Models for Combinatorial Control
                  of Multiple Transcription Factors in Early Differentiation of
                  Embryonic Stem Cells
                  Chieh-Chun Chen, Xinguang Zhu, and Sheng Zhong
                  University of Illinois at Urbana Champaign, Illinois, USA

12:20 - 01:20pm:  LUNCH (On Your Own)

01:20 - 01:40pm:  Identification of Transcription Factor and microRNA Binding
                  Sites from Array-Derived Gene Expression Data
                  Guohua Wang, Xin Wang, Lang Li, Howard J. Edenberg,
                  Feng C. Zhou, and Yunlong Liu
                  Indiana University, Indianapolis, Indiana, USA;
                  Harbin Institute of Technology, Harbin, P. R. China;
                  Harbin Engineering University, Harbin, P. R. China

01:40 - 02:00pm:  Refining Detection of Protein Binding Regions Using
                  Pyrosequencing-Derived RNA Fragments
                  Xin Wang, Guohua Wang, Changyu Shen, Lang Li, Sean D. Mooney,
                  Howard J. Edenberg, Jeremy R. Sanford, and Yunlong Liu
                  Indiana University, Indianapolis, Indiana, USA;
                  Harbin Institute of Technology, Harbin, P. R. China;
                  Harbin Engineering University, Harbin, P. R. China

02:00 - 02:20pm:  Compressed Synteny Plots: a Tool for Visualizing Repeated
                  Genomic Sequences
                  Mitrick A. Johns
                  Northern Illinois University, Illinois, USA

02:20 - 02:40pm:  Comparative Genomics Using Coregenes to Analyze Small Bacterial
                  Genomes, with an Application for the Annotation of Hypothetical
                  Proteins
                  Padmanabhan Mahadevan and Donald Seto
                  George Mason University, Manassas, Virginia, USA


02:40 - 03:20pm:  DISCUSSION SESSION C-BIOCOMP (Refreshments will be available)
                  June 28 (Thursday)
                  (LOCATION: - Hallways - Ballrooms 1-5)
                  List of papers appears at the end of BIOCOMP's schedule.


SESSION 16-BIOCOMP: (CONCURRENT SESSION with 18-BIOCOMP)
                  BIOINFORMATICS AND MEDICAL INFORMATICS SOFTWARE TOOLS
                  Chair: Mehrdad S. Sharbaf* and Dr. Jack K. Horner**
                  *Founder/Principal, Senior Consultant, Sharbaf & Associates,
                  Los Angeles, California, USA;
                  **SAIC, Santa Fe, New Mexico
                  June 28, 2007 (Thursday); 03:20pm - 04:00pm
                  (LOCATION: Ballroom 5)

03:20 - 03:40pm:  Extracting Specific Medical Data Across Multiple Languages
                  Kerstin Denecke and Jochen Bernauer
                  Technical University of Braunschweig, Germany;
                  University of Hannover, Germany;
                  University of Applied Science, Germany

03:40 - 04:00pm:  Creating Bioinformatic Workflows within the BioExtract Server
                  Carol Lushbough, Michael K. Bergman, Carolyn J. Lawrence,
                  Doug Jennewein, and Volker Brendel
                  University of South Dakota, USA; Visual Metrics Corporation, USA;
                  Iowa State University, USA


SESSION 17-BIOCOMP: (CONCURRENT SESSION with 18-BIOCOMP and 19-BIOCOMP)
                  METABLOMICS, PROTEOMIC AND PROTEIN FUNCTION PREDICTION
                  Chair: Prof. Vladimir A. Kuznetsov* and Dr. Jack K. Horner**
                  *Genome Institute of Singapore, Singapore;
                  **SAIC, Santa Fe, New Mexico;
                  June 28, 2007 (Thursday); 04:00pm - 06:00pm
                  (LOCATION: Ballroom 5)

04:00 - 04:20pm:  A Semi-Supervised Learning Approach for Prediction of
                  DNA-Binding Residues in Protein Sequences
                  Liangjiang Wang
                  Clemson University, Clemson, South Carolina, USA

04:20 - 04:40pm:  Prediction of Polyanion Binding Potential in Proteins Using
                  Random Forest
                  Jianwen Fang, Nazila Salamat-miller, Yinghua Dong, and
                  C. Russell Middaugh
                  University of Kansas, Lawrence, Kansas, USA

04:40 - 05:00pm:  Graph-Based Protein Functional Classification
                  Hyunjung Shin, Andreas Martin Lisewski, and Olivier Lichtarge
                  Ajou University, Korea; Baylor College of Medicine, USA

05:00 - 05:20pm:  Primary-Structure/Oseltamivir-Inhibition Correlations in
                  Influenza-H5N1-Related Neuraminidases
                  Jack K. Horner
                  Science Applications International Corp., Santa Fe, New Mexico, USA

05:20 - 05:40pm:  Biases in Lipid Accessibility Prediction Can Be Used for the
                  Recognition of Protein Interaction Interfaces in Soluble Proteins
                  Aleksey Porollo, Baoqiang Cao, and Jaroslaw Meller
                  University of Cincinnati, Cincinnati, Ohio, USA;
                  University of Nebraska-Lincoln, Lincoln, Nebraska, USA;
                  Childrens Hospital Research Foundation, Cincinnati, Ohio, USA;
                  Nicholas Copernicus University, Poland

05:40 - 06:00pm:  A Bernoulli Process Approximation for the Reverse Translation of
                  Protein to DNA/mRNA
                  Kazim Ali, Arshad Ali, Abad Ali Shah, and Hafiz Farooq Ahmad
                  NUST Institute of Information Technology, Pakistan;
                  University of Engineering and Technology, Pakistan;
                  Communication Technologies, Japan


SESSION 18-BIOCOMP: (CONCURRENT SESSION with 16-BIOCOMP and 17-BIOCOMP)
                  GENE IDENTIFICATION AND CLUSTERING
                  Chairs: Dr. Cliff S. Han* and Dr. May D. Wang**
                  *Los Alamos National Laboratory, U.S. DOE, Los Alamos, New Mexico, USA;
                  **Georgia Institute of Technology - Emory University School of
                  Medicine Center of Cancer Nanotechnology Excellence, Georgia, USA;
                  June 28, 2007 (Thursday); 03:20pm - 05:00pm
                  (LOCATION: Ballroom 1)

03:20 - 03:40pm:  A Novel Approach to High Throughput Microbial Genome Finishing:
                  Incorporation of 454 Sequence Data for Gap Closure in Low Quality
                  Sanger Data
                  Avinash Kewalramani, Riley Arnaudville, Cliff Han, Olga Chertkov,
                  and Thomas Brettin
                  Los Alamos National Laboratory, Los Alamos, New Mexico, USA

03:40 - 04:00pm:  PRAP: An Automated De Novo Repeat Finder Pipeline for
                  Prokaryotic Genomes
                  Gwo-liang Chen
                  Oak Ridge National Laboratory, Oak Ridge, TN, USA

04:00 - 04:20pm:  Targetability and Orthology of Human Disease Genes
                  Meena K. Sakharkar and Kishore R. Sakharkar
                  National University of Singapore, Singapore;
                  Nanyang Technological University, Singapore

04:20 - 04:40pm:  Analysis Software for High-Density Pooled Genotyping Data
                  Waibhav D. Tembe, Nils Homer, Sotiris Mitropanopoulos,
                  Mitchell Storey, Szabolcs Szelinger, Marcel Brun,
                  Matt Huentelman, Ed Suh, Dietrich A. Stephan, James Lowey,
                  John V. Pearson, and David W. Craig
                  The Translational Genomics Research Institute, Phoenix, AZ, USA

04:40 - 05:00pm:  A Workflow to Discover Regulatory Motifs with Positional Bias
                  in Human Promoters
                  Yunkai Liu, Sujuan Ye, and Asai Asaithambi
                  University of South Dakota, Vermillion, South Dakota, USA


SESSION 19-BIOCOMP: (CONCURRENT SESSION with 17-BIOCOMP)
                  MEDICAL DIAGNOSTIC AND SOFTWARE TOOLS AND DEVICES
                  Chair: Dr. Mengxia (Michelle) Zhu
                  Southern Illinois University, Carbondale, Illinois, USA
                  June 28, 2007 (Thursday); 05:00pm - 07:00pm
                  (LOCATION: Ballroom 1)

05:00 - 05:20pm:  Predicting Breast Cancer Metastasis by Integrating Both
                  Clinical and Genetic Markers
                  Yijun Sun and Steve Goodison
                  University of Florida, Gainesville, Florida, USA

05:20 - 05:40pm:  An Interval Tree Based Feature Reduction Method for Cancer
                  Classification Using High-throughput DNA Copy Number Data
                  Siling Wang, Yuhang Wang, Luc Girard, and John D. Minna
                  Southern Methodist University, Dallas, Texas, USA;
                  UT Southwestern Medical Center at Dallas, Texas, USA

05:40 - 06:00pm:  Requirements and System Architecture for a Decision Support
                  System for the Treatment of Colorectal Cancer
                  Jawed Siddiqi, Babak Akhgar, Ghasem Zaefarian, Alicja Gruzdz,
                  and Aleksandra Ihnatowicz
                  Sheffield Hallam University, Sheffield, UK

06:00 - 06:20pm:  Developing Assays for the Detection of Influenza in Human
                  Samples
                  Chen Feng, Catherine Putonti, Michael Quance, Stephen Huff,
                  Andrey Belokrylov, Lennart Johnsson, Krishna Jayaraman,
                  Michael Hogan, and Yuriy Fofanov
                  University of Houston, Houston, Texas, USA;
                  Genomics USA, Tucson, Arizona, USA

06:20 - 06:40pm:  Analysis of Headache Disease Data By Neural Networks
                  Alper Kursat Uysal, Ali Gunes, and Ahmet Babanli
                  Anadolu University, Eskisehir, Turkey

06:40 - 07:00pm:  Intelligent Assistive Feeding Device for Physically Handicapped
                  Sumit Khurana and Rahul Pandhi
                  Netaji Subhash Institute of Technology, New Delhi, India;
                  Delhi College of Engineering, New Delhi, India

                   DISCUSSION SESSION C-BIOCOMP
                     June 28 (Thursday), 2007
                       RRR/SRP/PST Papers
                        02:40pm - 03:20pm
         (LOCATION: Hallways/Lobby - Ballrooms 1-5)

LIST OF PAPERS IN DISCUSSION SESSION C-BIOCOMP:

O.  A Comparison of Federated Databases with Web Services for the
    Integration of Bioinformatics Data
    Zhiming Wang, Xin Gao, Congzhou He, John A. Miller, Jessica C. Kissinger,
    Mark Heiges, Cristina Aurrecoechea, Eileen T. Kraemer And Cary Pennington
    University of Georgia, USA; University of Pennsylvania, USA
O.  Biometric Authentication: A Pragmatic Model To Measure Effectiveness of
    Biometric System In Information Systems Security
    Mehrdad S. Sharbaf
    Nova Southeastern University, Fort Lauderdale, Florida, USA
O.  Methods and Simulations for the Protein Folding
    Jing Zhang, Mao-zu Guo, and Yang Yu
    Harbin Engineering University, Harbin, P. R. China
O.  Neural Networks for Predicting Structural Classification of Protein
    from Primary Structure
    Navita Srivastava, Arti Saxena, and Rajeev Prithiani
    APS University, Rewa (MP), India
O.  Characterizing Pseudobase and Predicting RNA Secondary Structure with
    Simple H-Type Pseudoknots
    Oyun-Erdene Namsrai, Kwang Su Jung, Sunshin Kim, and Keun Ho Ryu
    Chungbuk National University, Korea
O.  Searching for Drug Targets in Salmonella Genomes
    Kishore R. Sakharkar and Meena K. Sakharkar
    National University of Singapore, Singapore;
    Nanyang Technological University, Singapore
O.  On an ODE Model for Development to AIDS
    B. D. Aggarwala
    University of Calgary, Alberta, Canada
O.  Classification of Brain Glioma by Using Neural Networks Ensemble
    with Multi-Task Learning
    Jack Y. Yang, Mary Q. Yang, Li-xin Liu and Guo-zheng Li
    Shanghai University, China; Harvard University, USA;
    National Institutes of Health (NIH), USA
O.  Improving a Protein Structure Similarity Measure Using Inter-Residue
    Distance Matrices
    Eunseog Youn
    Texas Tech University, Lubbock, Texas, USA
O.  Analysis of Distribution of Protein Functional Sites on Gene Structure
    Medvedeva I. V., Demenkov P. S., Ivanisenko V. A., and Kolchanov N. A.
    Institute of Cytology and Genetics, Russia
O.  Epidemic Spread Modeling: Alignment of Agent-Based Simulation with a
    Simple Mathematical Model
    Alexei Skvortsov, Russell Connell, Peter Dawson, and Ralph Gailis
    HPP Division, Defence Science and Technology Organization, Australia
O.  Prediction of Trans-Antisense Transcripts in Arabidopsis Thaliana
    Huan Wang, Nam-Hai Chua, and Xiu-Jie Wang
    Chinese Academy of Sciences, Beijing, P. R. China
O.  Identification of Essential Genes and Gene Pairs Associated with Survival
    Time of Cancer Patients
    Efthimios Motakis, Anna V. Ivshina, and Vladimir A. Kuznetsov
    Genome Institute of Singapore, Singapore
O.  Statistical Properties of Short N-mers Located in One Mismatch Area
    of Microbial Genomes
    Aaron Skewes, Michael Quance, Catherine Putonti, Viacheslav Fofanov,
    and Yuriy Fofanov
    University of Houston, USA; Rice University, USA
O.  Variant Combination of Multiple Classifiers Methods for Classifying The
    EEG Signals in Brain-Computer Interface
    Zahra Shoaie Shirehjini and Saeed Bagheri Shouraki
    Sharif University of Technology, Iran
O.  Potential Use of Graph Theoretical Properties of Protein Structures
    in Structural Alignment
    Alper Kucukural and O. Ugur Sezerman
    Sabanci University, Istanbul, Turkey
O.  Aldose Reductase and Nitric Oxide Synthase Role in Diabetic Retinopathy:
    A Bioinformatics Study
    Hanuman Thota, Nageswara Rao K., Suresh Babu Changalasetty, Appa Rao Allam,
    Ramachandra Sridhar Gumpeny, Undurti N. Das, R. Kiran Kumar, and
    TK. Rama Krishna Rao
    Acharya Nagarjuna University, India; Andhra University, India
O.  A Parallel Algorithm to Cluster Orthologous Proteins Across Phylogenetic
    Genomes
    Sunshin Kim, Chung Sei Rhee, and Jung-do Choi
    Chungbuk National University, Korea
O.  Using Bioinformatics and Machine Learning to Predict Potential Malignancies
    Jack Yang and Mary Q. Yang
    Harvard University, USA; NIH, USA
O.  A Genetic Programming Approach for Classification of the Spontaneous
    Termination of Atrial Fibrillation
    O. Valenzuela, Fernando Rojas Ruiz, M. Cepero, and F. J. Rojas
    Universidad de Granada, Granada
O.  A Data Warehouse for Prostate Cancer Biomarker Discovery
    Bernhard Pfeifer, Christian Baumgartner, Claudia Plant, Stefan Dreiseitl,
    Robert Modre, Gunter Schreier, and Bernhard Tilg
    University for Health Sciences, Austria

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