BIOCOMP'07: June 27, 2007 Schedule

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


SESSION 8-BIOCOMP: GENOMICS
                  Chair: Dr. Jianlin Cheng, University of Central Florida, Florida, USA
                  June 27, 2007 (Wednesday); 08:00am - 09:20am
                  (LOCATION: Ballroom 5)

08:00 - 08:20am:  HHMMVE: A Visual Editor for Profile Hidden Markov Model
                  Jianyong Dai and Jianlin Cheng
                  University of Central Florida, Florida, USA

08:20 - 08:40am:  Inter and Intra Combinatorial Regulation by Transcriptions
                  Factors and MicroRNAs
                  Yiming Zhou, John Ferguson, Joseph T. Chang, and Yuval Kluger
                  New York University, New York, USA;
                  Yale University, USA

08:40 - 09:00am:  uShuffle: a Useful Tool for Shuffling Biological Sequences
                  While Preserving the K-Let Counts
                  Minghui Jiang, James Anderson, Joel Gillespie, and Martin Mayne
                  Utah State University, USA

09:00 - 09:20am:  Estimating the Lower Bounds of Recombination with or Without
                  Recurrent Mutations
                  Xiaoming Liu and Yun-Xin Fu
                  University of Texas at Houston, Texas, USA


SESSION 9-BIOCOMP: GENOMICS
                  Chair: Dr. My T. Thai, University of Florida, Gainesville, FL, USA
                  June 27, 2007 (Wednesday); 09:20am - 10:20am
                  (LOCATION: Ballroom 5)

09:20 - 09:40am:  Quality-Based Similarity Search for Biological Sequence
                  Databases
                  Xuehui Li and Tamer Kahveci
                  University of Florida, Gainesville, Florida, USA

09:40 - 10:00am:  A Non-Unique Probes Selection Algorithm Using D-Disjunct Matrix
                  Ping Deng, My T. Thai, and Weili Wu
                  University of Texas at Dallas, Texas, USA

10:00 - 10:20am:  Detecting Categorical Discrimination Using Selective Support
                  Vector Machines
                  Onur Seref, Claudio Cifarelli, O. Erhun Kundakcioglu,
                  Panos M. Pardalos, and Mingzhou Ding
                  University of Florida, Gainesville, Florida, USA

10:20 - 10:40am:  BREAK


SESSION 10-BIOCOMP: SYSTEM MODELING AND GENOME ANALYSIS
                  Chair: Drs. Yufang Jin and Yufeng Wang
                  University of Texas at San Antonio, USA
                  June 27, 2007 (Wednesday); 10:40am - 12:20pm
                  (LOCATION: Ballroom 5)

10:40 - 11:00am:  A Novel Tool for Comprehensive Analysis of Protein
                  Interaction Networks
                  Xun Gu
                  Iowa State University, Ames, Iowa, USA

11:00 - 11:20am:  Metabolic Pathway Complements of Five Francisella Strains
                  Yufeng Wang
                  University of Texas at San Antonio, Texas, USA

11:20 - 11:40am:  Clustering of Gene Expression Data Based on Shape Similarity
                  Yufei Huang
                  University of Texas at San Antonio, Texas, USA

11:40 - 12:00pm:  Lineage Specific Expansion in Vibrio Species
                  Jianying Gu
                  The City University of New York, Staten Island, New York, USA

12:00 - 12:20pm:  Stability Analysis of Genetic Regulatory Network with
                  Time Delay
                  Yufang Jin
                  University of Texas at San Antonio, San Antonio, Texas, USA

12:20 - 01:00pm:  LUNCH (On Your Own)


SESSION 11-BIOCOMP: ALGORITHMS AND MODELS  + INTELLIGENT DRUG DESIGN
                  Chair: Prof. Allam Appa Rao, Dean, Andhra University College of
                  Engineering, India;
                  June 27, 2007 (Wednesday); 01:00pm - 02:00pm
                  (LOCATION: Ballroom 5)

01:00 - 01:20pm:  Calcium Alternans in Cardiac Cell Mathematical Models
                  R. Samade and B. Kogan
                  University of California Los Angeles, California, USA

01:20 - 01:40pm:  Interaction Models for Biochemical Reactions
                  Mila Majster-Cederbaum, Nils Semmelrock, and Verena Wolf
                  University of Mannheim, Germany

01:40 - 02:00pm:  A Logical Data Model for Genome Data
                  Gregory Vert and Radhika Radhakrishnan
                  University of Nevada, Reno, Nevada, USA


SESSION 12-BIOCOMP: PREDICTION OF STRUCTURE AND DYNAMICS OF MACRO MOLECULES
                  Chairs: Dr. Nicholas Tan*, Dr. Chengpeng Bi**, and Dr. Xiongwu Wu***
                  *Bioinformatics Institute, Singapore
                  **University of Missouri, Kansas City, Missouri, USA
                  ***National Institutes of Health, Bethesda, Maryland, USA
                  June 27, 2007 (Wednesday); 02:00pm - 05:40pm
                  (LOCATION: Ballroom 5)

02:00 - 02:20pm:  An Optimized Ribosome Binding Model Using Communication
                  Theory Concepts
                  Mohammad Al Bataineh, Maria Alonso, Siyun Wang, Wei Zhang,
                  and Guillermo Atkin
                  Illinois Institute of Technology, Chicago, Illinois, USA

02:20 - 02:40pm:  A New Algorithm for RNA Secondary Structure Prediction
                  Junilda Spirollari, Jason T. L. Wang, and Yongkyu Park
                  New Jersey Institute of Technology, Newark, New Jersey, USA;
                  University of Medicine and Dentistry of New Jersey, USA


02:40 - 03:20pm:  DISCUSSION SESSION B-BIOCOMP (Refreshments will be available)
                  June 27 (Wednesday)
                  (LOCATION: - Hallways - Ballrooms 1-5)
                  List of papers appears at the end of BIOCOMP's schedule.


SESSION 12-BIOCOMP: PREDICTION OF STRUCTURE AND DYNAMICS OF MACRO MOLECULES (Continued ...)
                  Chairs: Dr. Nicholas Tan*, Dr. Chengpeng Bi**, and Dr. Xiongwu Wu***
                  *Bioinformatics Institute, Singapore
                  **University of Missouri, Kansas City, Missouri, USA
                  ***National Institutes of Health, Bethesda, Maryland, USA
                  June 27, 2007 (Wednesday); 02:00pm - 05:00pm
                  (LOCATION: Ballroom 5)

03:20 - 03:40pm:  Blind Test is a Pragmatic Test for a New Protein Secondary
                  Structure Classifier
                  Saad Osman Abdalla Subair and Safaai Deris
                  Al Ghurair University, Dubai, UAE;
                  University of Technology Malaysia, UTM, Malaysia

03:40 - 04:00pm:  Design of Artificial Tubular Protein Structures in 3D Hexagonal
                  Prism Lattice Under HP Model
                  Arvind Gupta, Mehdi Karimi, Alireza Khodabakhsi, Jan Manuch,
                  and Arash Rafiey
                  Simon Fraser University, Burnaby, BC, Canada

04:00 - 04:20pm:  Protein Side-Chain Modeling Using a Combination of Knowledge and
                  Energy Based Approaches
                  Aleksandar Poleksic and Joseph F. Danzer
                  University of Northern Iowa, Cedar Falls, Iowa, USA;
                  Eidogen-Sertanty Inc., San Diego, California, USA

04:20 - 04:40pm:  Simulations of Protein Folding Process
                  Jing Zhang, Mao-zu Guo, and Yang Yu
                  Harbin Engineering University, Harbin, P. R. China

04:40 - 05:00pm:  Modeling of Macromolecular Assemblies with Map Objects
                  Xiongwu Wu and Bernard R. Brooks
                  NHLBI/NIH, USA


SESSION 13-BIOCOMP: GENOMICS
                  Chairs:  Dr. Mary Qu Yang* and Dr. Rattikorn Hewett**
                  *National Human Genome Research Institute, National Institutes of
                  Health, U.S. Department of Health and Human Services, Maryland, USA;
                  **Dr. Rattikorn Hewett, Texas Tech University, Abilene, Texas, USA;
                  June 27, 2007 (Wednesday); 05:00pm - 06:00pm
                  (LOCATION: Ballroom 5)

05:00 - 05:20pm:  Double Feature Selection and Cluster Selection Analyses in
                  Developing Cotton Fiber Microarray Data
                  Magdy S. Alabady, Eunseog Youn, and Thea Wilkins
                  Texas Tech University, Lubbock, Texas, USA

05:20 - 05:40pm:  Analysis of Gene Expression Profiling Data with a Boosting-Based
                  Ranking Algorithm
                  Rattikorn Hewett and Phongphun Kijsanayothin
                  Texas Tech University, Abilene, Texas, USA

05:40 - 06:00pm:  Orthology of Bidirectional Promoters Enables Use of a Multiple
                  Class Predictor for Discriminating Functional Elements in the
                  Human Genome
                  Mary Qu Yang and Laura L. Elnitski
                  National Human Genome Research Institute, USA


06:00 - 09:00pm:  FOUR TUTORIALS  (planned)

                  Factor Graphs for Advanced Algorithm Design in Wireless Communications
                  Dr. Henk Wymeersch
                  Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
                  Location: Ballroom 2

                  Data Mining in Time Series and Multimedia Databases
                  Dr. Eamonn Keogh
                  University of California - Riverside, California, USA
                  Location: Ballroom 1

                  Cryptographic Features and Applications in Java (and C++)
                  Prof. Ray Kresman
                  Bowling Green State University, USA
                  Location: Ballroom 4

                  Mobile Terminal Software Architecture - Present and Future
                  S. Vijay Anand
                  General Manager, SASKEN Communication Technologies Limited - CTO Team, India
                  Location: Ballroom 3

                   DISCUSSION SESSION B-BIOCOMP
                     June 27 (Wednesday), 2007
                       RRR/SRP/PST Papers
                        02:40pm - 03:20pm
         (LOCATION: Hallways/Lobby - Ballrooms 1-5)

LIST OF PAPERS IN DISCUSSION SESSION B-BIOCOMP:

O.  Computational Binding Study of Protein-Ligand Complexes
    Zengjian Hu, Guy Lingani, and William Southerland
    Howard University College of Medicine, USA
O.  Enhancing Biomedical Knowledge through Computational Methods: Howard
    University Center for Computational Biology and Bioinformatics
    Guy Lingani, Zengjian Hu, and William Southerland
    Howard University College of Medicine, USA
O.  Supervised-Learning Based Microarray Gene Selection and TagSNPs for
    Genome-wide Disease Classification
    Qingzhong Liu, Jack Y. Yang, Zhongxue Chen, and Andrew H. Sung
    Harvard University, USA
O.  Bioinformatic Study of Brain-Pancreas-Gut System
    Allam Appa Rao, G. R. Sridhar, Bolem Srinivas, K. M. Deepak, and
    R. Srihari
    AUCE, India
O.  Support Vector Regression with Feature Selection for the Multivariate
    Calibration of Spectrofluorimetric Determination of Aromatic Amino Acids
    Guo-Zheng Li, Hao-Hua Meng, Jack Y. Yang, and Mary Qu Yang
    Shanghai University, P. R. China; Harvard University, USA;
    National Institutes of Health (NIH), USA
O.  A Two-Stage Approach to Finding Common Structure Elements in Unaligned
    RNA Sequences
    Chiyang Huang and Yuh-Jyh Hu
    National Chiao Tung University, Taiwan
O.  Bayesian Biclustering of Microarray Data
    Jiajun Gu and Jun S. Liu
    Harvard University, Cambridge, MA, USA
O.  Bio Informatics for Disease Associated with Bone Marrow Depression
    G. Gunasekaran, Tapas Kumar Basak, and P. T. Kalaichelvan
    Jadavpur University, India; University of Madras, India
O.  MIAME-Compliant Microarray Data Integrated System
    Marie-Michele Cordonnier-Pratt, Virgil E. Johnson, Dmitri S. Kolychev,
    Chun Liang, Junfeng Qu, Feng Sun, Zheng Xia, and Lee H. Pratt
    Clayton State University, Georgia, USA; University of Georgia, Georgia, USA;
    Medical College of Georgia, Augusta, Georgia, USA; Nanosphere Inc., IL, USA
O.  Combining Gene Expression and Transcription Factor Regulation Data Using
    Simultaneous Nonnegative Matrix Factorization
    Liviu Badea
    AI Lab, National Institute for Research & Development in Informatics, Romania
O.  GO Based Inference of Gene Regulatory Networks from Gene Expression Data
    Kumar Abhishek and Harish Karnick
    Google Inc., Hyderabad, India;  Indian Institute of Technology, Kanpur, India
O.  Estimating Microbial Population Densities Based on Genomic Signatures
    Yijun Sun, Fanhong Yu, Li Liu, and William Farmerie
    University of Florida, Gainesville, Florida, USA
O.  An Approach for Analyzing DNA Copy Number Aberrations in Genome
    Using aCGH Profiles
    Amitava Karmaker and Stephen Kwek
    University of Texas at San Antonio, San Antonio, Texas, USA
O.  An Ontologically Driven Decision Support System for Colorectal Caner
    Treatment: Data Relevance and Model Integration
    Jawed Siddiqi, Babak Akhgar, Alicja Gruzdz, Aleksandra Ihnatowicz,
    and Ghasem Zaefarian
    Sheffield Hallam University, Sheffield, UK

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