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BIOCOMP'08: July 17, 2008 Schedule
Last modified
2008-06-20 18:57
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6:45am - 5:00pm: Registration (Second Floor, Conference Lobby: 1-5)
SESSION 21-BIOCOMP: APPLICATION OF ENGINEERING TECHNIQUES AND MATHEMATICS IN MEDICINE AND BIOLOGY
Chair: Lavanya Devi Golagani, Andhra University, India
July 17, 2008 (Thursday); 08:00am - 10:20am
(LOCATION: Ballroom 5)
08:00 - 08:20am: A Group Monitoring Wireless System for Health Care Monitoring
Alessandro Brawerman* and Mauricio Perreto
University of Positivo, Curitiba, Brazil
08:20 - 08:40am: Reverse Engineering Module Networks by PSO-RNN Hybrid Modeling
Yuji Zhang**, Jianhua Xuan**, Benildo G. de los Reyes***, Robert Clarke*,
and Habtom W. Ressom*
*Lombardi Comprehensive Cancer Center, Georgetown Univ., Washington, DC, USA
**Virginia Polytechnic Institute and State University, Virginia
***University of Maine, Orono, Maine, USA
08:40 - 09:00am: Stochastic Simulation Algorithms for Chemical Reactions
Tae-Hyuk Ahn*, Yang Cao, and Layne T. Watson
Virginia Polytechnic Institute and State University, USA
09:00 - 09:20am: A Full Dimensional Numerical Study of Pulsatile Human Blood Flow
in Aortic Arch
Renat A. Sultanov*, Dennis Guster, Brent Engelbrekt and
Richard Blankenbecler; St. Cloud State University, USA
09:20 - 09:40am: Long-Term HIV Dynamics: Mathematical Modeling and Optimal Control
M. M. Hadjiandreou*, R. Conejeros, V. S. Vassilidis, and D. I. Wilson
University of Cambridge, UK
09:40 - 10:00am: No Tale in The Tail
Dayananda Sagar Gangadharaiah** and Sridhar Ramachandran*
*Indiana University Southeast, New Albany, Indiana, USA
**Wright State University, Dayton, Ohio, USA
10:00 - 10:20am: FREE SLOT
10:20 - 10:40am: BREAK
SESSION 22-BIOCOMP: (CONCURRENT SESSION with 26-BIOCOMP)
MEDICAL DIAGNOSTIC TOOLS AND METHODS
Chair: Dr. Diana Magalhaes de Oliveira
Universidade Estadual do Ceara, Brazil
July 17, 2008 (Thursday); 10:40am - 12:20pm
(LOCATION: Ballroom 5)
10:40 - 11:00am: Observation and Reporting Experiments Undertaken in the Development
of an Image Description Language for the Reporting by Pathologists
of the Grading of Cancers
Jon Plumley*, Richard A. Gatward*, Alison G. Todman*,
Raouf N. G. Naguib*, and Mark K. Bennett**
*Coventry University, United Kingdom
**Newcastle upon Tyne Hospitals, United Kingdom
11:00 - 11:20am: MATCH: A Decision Support System for Integration of Biomedical Data
Jawed Siddiqi*, Babak Akhgar*, Sally Atkinson*, Alicia Grudz*,
Alexandra Ihatowicz*, Massimo** and Lorenzo**, and Peter Scriven***
*Sheffield Hallam University, Sheffield, United Kingdom
**Fondazione IOM, Italy
***Royal Hallamshire Hospital, Sheffield, United Kingdom
11:20 - 11:40am: Laryngeal Pathology Detection by LPC and LPC-Based Cepstral Analysis
Silvana Cunha Costa*, Benedito G. Aguiar Neto and Joseana M. Fechine
Federal University of Campina Grande, Brazil
11:40 - 12:00pm: Recirculation in Vascular Access for Hemodialysis Treatment by
Employ the On-Line Mesuring System of Urea in Blood
Gustavo Adolfo Martinez
Military Hospital Center, Mexico City
12:00 - 12:20pm: FREE SLOT
12:20 - 01:00pm: LUNCH (On Your Own)
SESSION 23-BIOCOMP: (CONCURRENT SESSION with 26-BIOCOMP)
STRUCTURE AND DYNAMICS OF MACRO MOLECULES + STRUCTURE ALIGNMENT I
Chair: TBA
July 17, 2008 (Thursday); 01:00pm - 03:00pm
(LOCATION: Ballroom 5)
01:00 - 01:20pm: Inverse Protein Folding in 3D Hexagonal Prism Lattice Under HP Model
Arvind Gupta, Alireza Hadj Khodabakhshi*, Jan Manuch, and Arash Rafiey
Simon Fraser University, BC, Canada
01:20 - 01:40pm: Noise Tolerance of Universal Similarity Metric Applied to Protein
Contact Map Comparison in Two Dimensions
Sara Rahmati* and Janice Glasgow; Queen's University, Canada
01:40 - 02:00pm: Protein Fold Family Recognition From Unassigned Residual
Dipolar Coupling Data
Rishi Mukhopadhyay, Paul Shealy, and Homayoun Valafar*
University of South Carolina, Columbia, South Carolina, USA
02:00 - 02:20pm: A New Algorithm for RNA Secondary Structure Prediction and Fast
Method for Prediction of Simple H-type Pseudoknots
Oyun-Erdene Namsrai* and Keun Ho Ryu
Chungbuk National University, Korea
02:20 - 02:40pm: Automated Assignment of Backbone Resonances Using Residual
Dipolar Couplings Acquired from a Protein with Known Structure
P. Shealy, R. Mukhopadhyay, S. Smith, and H. Valafar*
University of South Carolina, Columbia, South Carolina, USA
02:40 - 03:00pm: Bivariate Estimator for cDNA Microarray Images Using Complex Wavelets
Tamanna Howlader* and Yogendra P. Chaubey
Concordia University, Montreal, Quebec, Canada
03:00 - 03:40pm: DISCUSSION SESSION C-BIOCOMP (Refreshments will be available)
July 17, 2008 (Thursday)
(LOCATION: Hallways - Ballrooms 1-5)
O. Analysis of Microarray Titration Experiments
Ionut Bebu*, Francoise Seillier-Moiseiwitsch and Hongfang Liu
Georgetown University, USA
O. Platescale: The Birthday Problem Applied to Single Molecule PCR
Chris Stowers and Erik Boczko; Vanderbilt University, USA
O. A Strategy for High Throughput Microarray Oligo Probe Design Using
454 and Sanger Sequencing Data of Eisenia Fetida Expressed Sequence Tags
Ping Gong, Mehdi Pirooznia, Youping Deng, Xin Guan, Chaoyang Zhang,
Chun Liang, and Edward J. Perkins
SpecPro Inc., USA; University of Southern Mississippi, USA;
Miami University, USA
O. Constrained Competitive Learning Algorithm for DNA Microarray Gene
Expression Data Analysis
Shuanhu Wu, Hong Yan, Qingshang Zeng, Yanjie Zhang and Yibin Song
Yantai university, China; City University of Hong Kong, Hong Kong;
University of Sydney, Australia
O. Hybrid Approach Based on Principal Component and Multiple Discriminant
Analysis for Microarray Classification
Arwa Al-Sultan and M. Arif Wani; King Saud University, Saudi Arabia
O. BindN+ for Improved Prediction of DNA or RNA Binding Residues in
Protein Sequences Using Evolutionary Information
Liangjiang Wang; Clemson University, USA
O. Protein-Protein Interaction Detection from Primary Structure Using
Support Vector Machine
Taskeed Jabid, Mohammad Shoyaib, Syed Murtuza Baker, Firoz Anwar,
and Md. Mehedi Hasan; East West University, Bangladesh
O. Statistical Analysis on Detecting Signals of Adverse Drug Events
with Drug-Drug Interactions
Yu-Ting Huang, Shih-Fang Lin, and Von-Wun Soo
National Tsing Hua Univ., Taiwan; National Univ. of Kaohsiung, Taiwan
O. Development of a Human Arm-Liked Robotic Surgical System with
Force Measurement for Laparoscopic Surgery
Ki-Young Kim*, Ho-Seok Song and Jung-Ju Lee; KAIST, Korea
O. Dynamic Graph-based Relational Learning of Temporal Patterns in
Biological Networks Changing over Time
Chang Hun You, Lawrence B. Holder and Diane J. Cook
Washington State University, USA
O. A Stepwise Generalization Method for Extracting Minimum
Generalized Set of Mismatch Clusters
Hiroaki Kimura, Hajime Kitakami, Kotaro Araki and Keiichi Tamura
Hiroshima City University, Japan
O. A Robust Network Alignment Algorithm for Detecting Evolutionarily
Conserved Networks and Protein Complexes Across Species
Yu-Chun Lin, Hsiang-Yuan Yeh, Cheng-Yu Yeh and Von-Wun Soo
National Tsing Hua University, Taiwan
O. Identification of Gene Using Machine Learning Technique
Firoz Anwar, Syed Murtuza Baker, Mohammad Shoyaib, Taskeed Jabid,
and Mehedi Hasan; East West University, Bangladesh
O. A Case Study of Genetic influence via Principal Component
Analysis and Bayesian Factor Analysis
Gaolin Zheng, Tonny Sangutei and Yingjun Cao
North Carolina Central University, USA
O. Fuzzy Ontology Based Querying
Ana Aguilera, Leonid Tineo, and Harold Vasquez
Universidad de Carabobo, Venezuela
SESSION 24-BIOCOMP: (CONCURRENT SESSION with 27-BIOCOMP)
STRUCTURE AND DYNAMICS OF MACRO MOLECULES + STRUCTURE ALIGNMENT II
Chair: Dr. Qiang Cheng, Southern Illinois University, USA
July 17, 2008 (Thursday); 03:40pm - 05:40pm
(LOCATION: Ballroom 5)
03:40 - 04:00pm: Blueprint for an Algorithm for Conformational Transformation
Tolerant Search Through a Database of Protein Structures
I. Mihalek; Bioinformatics Institute, A*STAR, Singapore
04:00 - 04:20pm: Molecular Dynamics Simulations of Folding and Insertion of the
Ebola Virus Fusion Peptide into a Membrane Bilayer
Mark A. Olson, In-Chul Yeh, and Michael S. Lee
Institute of Infectious Diseases, USA
04:20 - 04:40pm: Analysis of Protein-Ligand Interactions Using Localized
Stereochemical Features
Reetal Pai, James C. Sacchettini, and Thomas R. Ioerger
Texas A&M University, USA
04:40 - 05:00pm: New Algorithm and Web Server for Finding Proteins with Similar
3D Structures
Zaixin Lu, Zhiyu Zhao, Sergio Garcia, and Bin Fu
University of Texas Pan American, USA
05:00 - 05:20pm: GIPSCo: A Method for Comparison of Protein Structures Based on
Geometric Invariants
Sandeep Deshmukh, Aniket Dalal, and Pramod P. Wangikar
Indian Institute of Technology, India
05:20 - 05:40pm: Protein Structure Searching Using Suffix Arrays
Tarek F. Gharib, A. Salah, I. M. El Henawy, and Abdel-Badeeh M. Salem
Ain Shams University, Cairo, Egypt; Zagazig University, Zagazig, Egypt
SESSION 25-BIOCOMP: (CONCURRENT SESSION with 27-BIOCOMP)
BIOMOLECULAR PATHWAYS AND SYSTEM BIOLOGY
Chair: TBA
July 17, 2008 (Thursday); 05:40pm - 07:00pm
(LOCATION: Ballroom 5)
05:40 - 06:00pm: Stochastic Stability Analysis of the Heat Shock Response in E. Coli
A. Meyer-Baese; Florida State University, USA
06:00 - 06:20pm: An Efficient Intelligent Binary Tree for Alternative Splice Site Detection
Minseo Park; University of Massachusetts, USA
06:20 - 06:40pm: Relating Microbial Community Structure to a Dominant Environmental
Variable in a Complex Environment: An Example from a Chromium
Contaminated Site
A. V. Palumbo, J. C. Schryver, S. M. Pfiffner, T. L. Marsh, and C. C. Brandt
Oak Ridge National Laboratory, USA; The University of Tennessee, USA;
Michigan State University, USA
06:40 - 07:00pm: Optimize Observational Time Points to Maximize the Inferability of
Gene Networks
Frank Emmert-Streib and Andre S. Ribeiro
Queen's University Belfast, UK
SESSION 26-BIOCOMP: (CONCURRENT SESSION with 22-BIOCOMP and 23-BIOCOMP)
PHYLOGENETIC RECONSTRUCTION AND MOLECULAR EVOLUTION
Chair: TBA
July 17, 2008 (Thursday); 11:40am - 03:00pm
(LOCATION: Ballroom 1)
11:40 - 12:00pm: Inferring Functional Linkage from Residue Level Co-Evolution Information
Roger A. Craig, Keyur Malaviya, Krishna Balasubramanian, and Li Liao
University of Delaware, Newark, Delaware, USA
12:00 - 12:20pm: Incomparability of Results Between Phylogenetic Search Programs
Kenneth Sundberg, Hyrum Carroll, Quinn Snell, and Mark Clement
Brigham Young University, Provo, Utah, USA
12:20 - 01:00pm: LUNCH (On Your Own)
01:00 - 01:20pm: An Integrative Approach to Phylogenetic Inference
P. Wang, B. B. Zhou, and A. Y. Zomaya
University of Sydney, NSW, Australia
01:20 - 01:40pm: Major Factors of Protein Evolution Revealed by Eigenvalue
Decomposition Analysis
Xin Liu*, Li-Mei Zhang**, Jun Yin*, and Ya-Pu Zhao*
*Chinese Academy of Sciences, Beijing, P. R. China
**Beijing Jiaotong University, Beijing, P. R. China
01:40 - 02:00pm: Computing the Mixture Distance Between Mixture Trees
Chen-Hui Lin and Justie Su-Tzu Juan
National Chi Nan University, Nantou, Taiwan
02:00 - 02:20pm: A Near ME ML Phylogenetic Reconstruction Method
P. Wang, B. B. Zhou, P. Pang, and A. Y. Zomaya
University of Sydney, NSW, Australia
02:20 - 02:40pm: Does Nucleotide Compositional Bias Explain Amino Acid
Usage in Viral Genomes?
Rishi Mukhopadhyay and John R. Rose
University of South Carolina, Columbia, South Carolina, USA
02:40 - 03:00pm: FREE SLOT
03:00 - 03:40pm: DISCUSSION SESSION C-BIOCOMP (Refreshments will be available)
July 17, 2008 (Thursday)
(LOCATION: Hallways - Ballrooms 1-5)
SESSION 27-BIOCOMP: (CONCURRENT SESSION with 24-BIOCOMP and 25-BIOCOMP)
GENE IDENTIFICATION AND CLUSTERING
Chair: Lavanya Devi Golagani, Andhra University, India
July 17, 2008 (Thursday); 03:40pm - 06:20pm
(LOCATION: Ballroom 1)
03:40 - 04:00pm: Exploring Transcriptional Modules by Integrative Gene Clustering
Guided by Transcription Factor Binding Information
Ting Gong, Jianhua Xuan, Rebecca B. Riggins, Yue Wang,
Eric P. Hoffman, and Robert Clarke
Virginia Polytechnic Institute and State University, Virginia, USA
Georgetown University School of Medicine, Washington, DC, USA
Children' National Medical Center, Washington, DC, USA
04:00 - 04:20pm: Algorithms for Designing the Minimal Set of Multiplexed Degenerate
Universal Tagged Primers for RNA Virus Detection
Jian Song, Jason Gans, Murray Wolinsky, Po-E Li, Emily Curd,
Chris Detter and Hong Cai
Biosecurity and Public Health (B-7), Los Alamos National Lab.,
New Mexico, USA; Genomics Science/Joint Genome Institute (B-6),
Los Alamos National Lab., New Mexico, USA; Center for Tropical Research,
University of California, Los Angeles, CA, USA
04:20 - 04:40pm: Mining Intronic Sequence Features of Splice Sites with
Depth-Breadth Fused Codon Analyses
Sing-Wu Liou* and Yin-Fu Huang
National Yunlin University of Science and Technology, Yunlin, Taiwan
04:40 - 05:00pm: Stochastic Context Free Grammar for RNA Modeling: An Overview
Muhammed Al-Mulhem
King Fahd University of Petroleum and Minerals, Dhahran, Saudi Arabia
05:00 - 05:20pm: Mutual Information Measure for Distinguishing Coding and
Non-Coding DNA Sequences
John R. Rose and Achraf El Allali
University of South Carolina, Columbia, South Carolina, USA
05:20 - 05:40pm: Data Mining Pathogen Genomes Using GeneOrder and CoreGenes:
Gene Order, Synteny, and Proteomes
Padmanabhan Mahadevan and Donald Seto
George Mason University, USA
05:40 - 06:00pm: Use of Nucleotide Genomic Signals in the Analysis of
Variability and Inserts in Prokaryote Genomes
Paul Dan Cristea and Rodica Aurora Tuduce
Politehnica University of Bucharest, Romania
06:00 - 06:20pm: TandemXP - A Computational Approach to Finding Approximate
Tandem Repeats in Genomic Sequences
Avinash Shankaranarayanan and Christine Amaldas
Auckland University of Technology, Auckland, New Zealand
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