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BIOCOMP'06: June 27, 2006 Schedule
Last modified
2006-06-03 18:32
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6:30am - 5:00pm: Registration (Second Floor, Conference Lobby: 1-5)
6:30am - 5:00pm: Registration (Second Floor, Conference Lobby: 1-5)
SESSION 2-BIOCOMP: BIOMOLECULAR PATHWAYS AND SYSTEM BIOLOGY + PHYLOGENETIC
RECONSTRUCTION AND MOLECULAR EVOLUTION
Chairs: Dr. Hikmet Budak* and Dr. Jack Y. Yang**
*Sabanci University, Istanbul, Turkey
**Harvard University, Harvard Medical School, USA
June 27, 2006 (Tuesday); 8:00am - 10:20am
(LOCATION: Meeting Room 3)
08:00 - 08:20am: Using Neural Nets to Estimate Evolutionary Parameters
Chi-Chiang Lee and Paul Marjoram
University of Southern California, USA
08:20 - 08:40am: Inferring Ancestral Chloroplast Genomes with Inverted Repeat
Liying Cui**, Feng Yue*, and Jijun Tang*
*University of South Carolina, Columbia, South Carolina, USA
**Pennsylvania State University, University Park, PA, USA
08:40 - 09:00am: Evidence for Functional Protein Fragment Homology in Viral
Genome Types
John R. Rose, Rishi Mukhopadhyay
University of South Carolina, USA
09:00 - 09:20am: Dynamic Bayesian Network (DBN) with Structure Expectation
Maximization (SEM) for Modeling of Gene Network from Time
Series Gene Expression Data
Yu Zhang, Zhidong Deng, Hongshan Jiang, and Peifa Jia
Tsinghua University, Beijing, P. R. China
09:20 - 09:40am: Comparative Sequence Analysis of the p53 Response Elements
Associated with Apoptosis and Cell Cycle Arrest
Feng Cui, Michael Sirotin and Victor B. Zhurkin
National Institutes of Health, Bethesda, MD USA
09:40 - 10:00am: A Relational Genomics Search Engine
Jay Urbain and Nazli Goharian
Illinois Institute of Technology Research Institute, USA
10:00 - 10:20am: On a New Quartet-based Phylogeny Reconstruction Algorithm
B. B. Zhou, M. Tarawneh, D. Chu, P. Wang, C. Wang, A. Y. Zomaya,
and R. P. Brent
University of Sydney, Australia
Australian National University, Australia
10:20 - 10:40am: BREAK
10:40a - 12:20p: Note: There are a number of other sessions (not listed
here) that are of significant interest to BIOCOMP conference
participants (sessions belonging to other joint conferences in
this event.) Therefore, you are encouraged to also check the
schedules for other joint conferences. (In particular,
schedules for PDPTA'06, ICAI'06, MLMTA'06, IPCV'06, DMIN'06,
and IKE'06).
12:20 - 01:20pm: LUNCH (On Your Own)
SESSION 3-BIOCOMP: MICROARRAY DATA ANALYSIS AND GENE EXPRESSION
Chairs: Dr. Mary Qu Yang* and Dr. Hikmet Budak**
*National Institutes of Health (NIH), USA and Purdue University, USA
**Sabanci University, Istanbul, Turkey
June 27, 2006 (Tuesday); 1:20pm - 2:40pm
(LOCATION: Meeting Room 3)
01:20 - 01:40pm: Needs Assessment for Scientific Visualization of Multivariate,
High-dimensional Microarray Data
Vetria L. Byrd* and Tarynn M. Witten**
*University of Alabama at Birmingham, Alabama, USA
**Virginia Commonwealth University, Richmond, Virginia, USA
01:40 - 02:00pm: Reduced-Rank Multivariate Model for Time-Course Microarray Data
Rafal Kustra
University of Toronto, Toronto, ON, Canada
02:00 - 02:20pm: Data Mining of Ests for Genetic Improvement of Salt
Tolerance in Wheat
Ahu Altinkut, Aysen Yumurtaci, Yildiz Aydin, Ismail Cakmak,
Meral Unal, Emel Yesil, Sema Karanlik, and Hikmet Budak
Tubitak, Turkey; Marmara University, Turkey;
Sabanci University, Turkey; Mustafa Kemal University, Turkey
02:20 - 02:40pm: Abstracted Stochastic Analysis of Type 1 Pili Expression in E. coli
Hiroyuki Kuwahara, Chris Myers, and Michael Samoilov
University of Utah, Salt Lake City, Utah, USA
University of California, Berkeley, California, USA
02:40 - 03:20pm: DISCUSSION SESSION B-BIOCOMP (Refreshments will be available)
June 27 (Tuesday)
(LOCATION: Hallways - Meeting Rooms 1-5)
List of papers appears at the end of BIOCOMP's schedule.
SESSION 4-BIOCOMP: PREDICTION OF STRUCTURE AND DYNAMICS OF MACRO MOLECULES
Chairs: Dr. Jack Y. Yang* and Dr. Hikmet Budak**
*Harvard University, Harvard Medical School, USA
**Dr. Hikmet Budak, Sabanci University, Istanbul, Turkey
June 27, 2006 (Tuesday); 3:20pm - 6:00pm
(LOCATION: Meeting Room 3)
03:20 - 03:40pm: A Multi-Strategy Approach to Protein Structural Alphabet Design
Shih-Yen Ku and Yuh-Jyh Hu
National Chiao Tung University, Taiwan
03:40 - 04:00pm: Study on Properties of Protein Folding Conformation Network
Wang Nengchao** and Wang Zhongjun*/**
*Wuhan University of Technology, Wuhan, P. R. China
**Huazhong University of Science & Technology, Wuhan, P. R. China
04:00 - 04:20pm: Statistical Analysis of Long-range Interactions in Proteins
Jinmiao Chen and Narendra S. Chaudhari
Nanyang Technological University, Singapore
04:20 - 04:40pm: Identification of Intrinsically Unstructured Regions in
Proteins Using Primary Structure
Mary Qu Yang*/** and Jack Y. Yang
*National Human Genome Research Institute, National Institutes of Health (NIH), USA
**Purdue University, USA
***Harvard University, Harvard Medical School, USA
04:40 - 05:00pm: Membrane Remodeling and Diffusion of Cytochrome C from a
Geometrically Idealized Mitochondrial Crista
John C. Manor IV*, T. Frey, A. Baljon, J. Mahaffy J. Nulton, and
P. Salamon
San Diego State University, California, USA
05:00 - 05:20pm: Prediction of Structure of Potato Large Subunit ADP-Glucose
Pyrophosphatase
Aytug Tuncel, I Halil Kavakli, and Ozlem Keskin
Koc University, Istanbul, Turkey
05:20 - 05:40pm: Discrete Molecular Dynamics Study of Alzheimer Amyloid
B-protein (AB) Folding
Alfonso R. Lam, Brigita Urbanc, Jose M. Borreguero,
Noel D. Lazoy, David B. Teplowy, and H. Eugene Stanley
Boston University, Boston, MA, USA
Georgia Institute of Technology, Atlanta, GA, USA
University of California, Los Angeles, CA, USA
05:40 - 06:00pm: Melting Free Energies of DNA Duplexes with Oxidized Base
Residues and Abasic Sites: A Molecular Dynamics Characterization
Latifa Douali, Matt Ernst, John Miller, and Michel Dupuis
Pacific Northwest National Laboratory, Richland, Washington, USA
Washington State University, USA
06:00 - 9:00pm: TWO TUTORIALS (planned)
CONFERENCE TUTORIAL C
Heterogeneous Parallel and Distributed Computing: Model,
Resource Management, and Robustness
Prof. H. J. Siegel
Colorado State University, Fort Collins, Colorado, USA
June 27, 2006 (Tuesday)
(LOCATION: Meeting Room 1)
CONFERENCE TUTORIAL D
Security, Privacy, Computing, and Data Management
Kenneth W. Kousky* and Bon K. Sy**
*CEO, IP3, Inc., USA
**Queens College of the City of New York, New York, USA
June 27, 2006 (Tuesday)
(LOCATION: Meeting Room 3)
| DISCUSSION SESSION |
DISCUSSION SESSION B-BIOCOMP
June 27 (Tuesday), 2006
RRR/SRP/PST Papers
02:40 - 03:20pm
(LOCATION: Hallways/Lobby - Meeting Rooms 1-5)
LIST OF PAPERS IN DISCUSSION SESSION B-BIOCOMP:
O. WebDock: A Structure-Based Drug Discovery Web Service
Joseph Gill, Legand Burge, Zengjian Hu, and William Southerland
Howard University Washington, DC, USA
O. Performance of Sequence Alignment Bioinformatics Applications on
General Purpose Processors: A Case Study
Pradeep S. Nair and Eugene B. John
University of Texas at San Antonio, Texas, USA
O. An Approach to Selecting Putative RNA Motifs Using MDL Principle
Mohammad Anwar and Marcel Turcotte
University of Ottawa, Ontario, Canada
O. Methodology for Data Modeling of miRNA
Sarah Lopez and Z. Chen
University of Nebraska at Omaha, Nebraska, USA
O. Introducing Hippy: A Visualization Tool for Understanding the
alph-Helix Pair Interface
Robert Fraser and Janice Glasgow
Queen's University, Kingston, ON, Canada
O. Homology Modeling of Myoglobin using Adaptive Neurofuzzy Systems
Achuthsankar S. Nair** and Koshy P. Vaidyan*
**University of Kerala, India
*Tata Consultancy Services, India
O. Parameterized Computation of LCS for Two Sequences
Yuan Lin, Jeff Jenness, and Xiuzhen Huang
Arkansas State University, USA
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