BIOCOMP'06: June 29, 2006 Schedule

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6:30a - 12:01p:    Registration (Second Floor, Conference Lobby: 1-5)


SESSION 8-BIOCOMP: INTELLIGENT DRUG DESIGN
                   Chair:  Xiaohua Douglas Zhang* and Dr. Homayoun Valafar**
                   *Merck Research Laboratories, West Point, PA, USA
                   **University of South Carolina, USA
                   June 29, 2006 (Thursday);  8:00am - 9:20am
                   (LOCATION: Meeting Room 3)

08:00 - 08:20am:   Toward In Vivo Disease Diagnosis and Treatment Using DNA
                   Yuriy Brun and Manoj Gopalkrishnan
                   University of Southern California, USA

08:20 - 08:40am:   Fusion Genes as Putative Microbial Drug Targets in H. Pylori
                   Kishore R. Sakharkar, Meena Kishore Sakharkar, and
                   Vincent T.K. Chow
                   National Universtiy of Singapore,  Singapore
                   Nanyang Technological University, Singapore

08:40 - 09:00am:   Structure Based Design and Analysis of Cytochrome p450
                   Inhibitors for the Treatment of Prostate Cancer
                   M Emre Ozdemir, Halil Kavkali, and Metin Turkay
                   Koc University, Istanbul, Turkey

09:00 - 09:20am:   Evaluation of a Novel Metric for Quality Control in an RNA
                   Interference High Throughput Screening Assay
                   Xiaohua Douglas Zhang*, Amy S. Espeseth**, Namjin Chung***
                   and Marc Ferrer
                   *Merck Research Laboratories, USA
                   **Molecular and Cellular Technology, MRL, West Point, PA, USA
                   ***Automated Biotechnology, MRL, North Wales, PA, USA


SESSION 9-BIOCOMP: ALGORITHMS AND MODELS + APPLICATION OF ENGINEERING TECHNIQUES
                   AND MATHEMATICS IN MEDICINE
                   Chair: Dr. Dawei Hong, Rutgers University, USA
                   June 29, 2006 (Thursday);  9:20am - 10:20am
                   (LOCATION: Meeting Room 3)

09:20 - 09:40am:   Implementation of a 2d Computed Tomography Backprojection
                   Algorithm on the Cell Broadband Engine Processor
                   Olivier Bockenbach, Sebastian Schuberth, and Hauke Bartsch
                   Mercury Computer Systems GmbH, Germany

09:40 - 10:00am:   Development of Maximized Total Capillary Surface: the Quarter
                   Power Scaling Law from Developmental Biology Perspective
                   Dawei Hong, Daniel Shain, Shushuang Man, Joseph V. Martin
                   Rutgers University, USA
                   Southwest Minnesota State University, USA

10:00 - 10:20am:   Surgeon's Magic Wand: A Screen Pointing Interactive Method
                   Naren Vira and Shaleen Vira
                   Howard University, Washington, D.C.  USA
                   New York University, USA

10:20 - 10:40am:   BREAK


SESSION 10-BIOCOMP (or 6-CDES/CNAN):
                   BIO-INSPIRED AND NANO-SCALE INTEGRATED COMPUTING
                   Chair: Prof. Mary M. Eshaghian-Wilner, UCLA, USA
                   June 29, 2006 (Thursday);  10:40am - 12:40pm
                   (LOCATION: Meeting Room 3)

10:40 - 11:00am:   Opening Remarks
                   Prof. Mary M. Eshaghian-Wilner, UCLA, USA

11:00 - 11:20am:   Hierarchical Multi-Scale Architectures with Spin Waves1
                   M. M. Eshaghian-Wilner, A. Khitun, S. Navab, and K. Wang
                   University of California, Los Angeles, California, USA

11:20 - 11:40am:   CMOL FPGA Circuits
                   Dmitri B. Strukov and Konstantin K. Likharev
                   Stony Brook University, New York, USA

11:40 - 12:00pm:   Integrity and Integration Issues for Nanotube Based Systems
                   Tulin Mangir and Chuhee Kwon
                   California State University Long Beach, California, USA

12:00 - 12:20pm:   Towards a Nanoscale Artificial Cortex
                   Alice C. Parker, Aaron K. Friesz, and Afshaneh Pakdaman
                   University of Southern California, Los Angeles, California, USA

12:20 - 12:40pm:   Graph Formations of Partial-Order Multiple-Sequence Alignments
                   Using Nano- and Micro-Scale Reconfigurable Meshes
                   M. M. Eshaghian-Wilner, J. Lau, D. Shin and S. Navab
                   University of California, Los Angeles, California, USA


12:40 - 01:40pm:   LUNCH (On Your Own)


01:40 - 02:40pm:   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).


02:40 - 03:20pm:   DISCUSSION SESSION D-BIOCOMP (Refreshments will be available)
                   June 29 (Thursday)
                   (LOCATION: Hallways - Meeting Rooms 1-5)
                   List of papers appears at the end of BIOCOMP's schedule.


SESSION 11-BIOCOMP: SOFTWARE TOOLS AND SYSTEMS
                   Chairs: Dr. Dawei Hong* and Yijie Han**
                   *Rutgers University, USA
                   **University of Missouri at Kansas City, USA
                   June 29, 2006 (Thursday);  3:20pm - 5:40pm
                   (LOCATION: Meeting Room 3)

03:20 - 03:40pm:   Fast Dictionary Lookup in Genomic Information Retrieval   
                   Simon M.C. Yuen, Fu-lai Chung* and Robert W.P. Luk
                   The Hong Kong Polytechnic University, Hong Kong

03:40 - 04:00pm:   SpA: Web-Accessible Spectratype Analysis: Application to
                   Investigate the Development of TCR Diversity in a Patient
                   with Complete DiGeorge Syndrome
                   Min He, Blythe H. Devlin, M. Louise Markert, Marcella Sarzotti,
                   and Thomas B. Kepler
                   Duke University Medical Center, USA

04:00 - 04:20pm:   Sensitivity of the Maximum Parsimony Algorithm to Missing Data
                   Jack K. Horner
                   Science Applications International Corporation (SAIC), New Mexico, USA

04:20 - 04:40pm:   Improving the Efficiency of Sorting by Reversals
                   Yijie Han
                   University of Missouri at Kansas City, Missouri, USA

04:40 - 05:00pm:   Automated Blood Volume Quantification from Color Doppler
                   Images while Tracking the Conduit Motion
                   Beomjin Kim
                   Indiana University-Purdue University, Fort Wayne, IN, USA

05:00 - 05:20pm:   AminoTrack: Automating the Entry and Analysis of Mutations
                   in Multiple Protein Sequences Using a Spreadsheet Format
                   Madhumita Mahalanabis, Jason Blue, and Nancy L. Haigwood
                   University of Washington, Seattle, Washington, USA
                   Seattle Biomedical Research Institute, USA

05:20 - 05:40pm:   Comparative Genomics Using Web-Based GeneOrder to Determine
                   Synteny and to Function as an Annotation Tool
                   Padmanabhan Mahadevan and Donald Seto
                   George Mason University, Manassas, Virginia, USA

05:40 - 06:00pm:   FREE SLOT

                   DISCUSSION SESSION D-BIOCOMP
                     June 29 (Thursday), 2006
                       RRR/SRP/PST Papers
                        02:40 - 03:20pm
         (LOCATION: Hallways/Lobby - Meeting Rooms 1-5)

LIST OF PAPERS IN DISCUSSION SESSION D-BIOCOMP:

O.  SPiC-MAS: a Multiagent Simulation of Stochastic pi-Calculus Models
    Mikael Bourhis and Vincent Rodin
    CERV (European Center of Virtual Reality), France
O.  Bioinformatics Web Services Provided by VBI
    Boyu Yang, Tian Xue, Jing Zhao, Chaitonya Kommidi, Jeetendra Soneja,
    Jian Li, Rebecca Will, Bruce Sharp, Ronald Kenyon, Oswald Crasta,
    Bruno W. Sobral
    Virginia Bioinformatics Institute, Virginia Tech, USA
O.  Finding Molecular Signature of Prostate Cancer: An Algorithmic Approach
    Patrick O. Bobbie*, Sandra Suther**, Renee Reams**, Clyde Perry-Brown**
    *Southern Polytechnic State University, USA
    **Florida A&M University, USA
O.  Support Vector Machines for Predicting MicroRNA Hairpins
    Karol Szafranski, Molly Megraw, Martin Reczko, and Artemis G. Hatzigeorgiou
    University of Pennsylvania, USA
    Foundation of Research and Technology, Greece
O.  A Design for Software to Assist in the Rehabilitation of Stroke Patients
    Gillian Pearce, Peter Wilson, David Smith, and Gill Jones
    University of Wolverhampton, UK
O.  The Use of Context-Sensitive Grammar For Modeling RNA Pseudoknots
    Keum-Young Sung
    Handong University, South Korea
O.  A New Algorithm to Predict the Location of Protein-Protein Binding
    Sites Using Amino Acid Vectors and Aromatic Features of Surface Patches
    Sunshin Kim, Shimei Jin, Chung-Sei Rhee, Keun Ho Ryu
    Chungbuk National University, The Republic of Korea
O.  Combined QM/MM Studies of Binding Effect of Cytochrome P450cam
    to Putidaredoxin
    Marek Freindorf, Yihan Shao, Jing Kong, and Thomas R. Furlani
    State University of New York at Buffalo, USA
    Q-Chem Inc., USA
O.  Analytical Solution of a Spatial Sir Epidemic Model with Memory Inside
    a Circular Habitat with Endemic Memory Using Cas
    Nicolas Guarin Z. and Juan Ospina G.
    EAFIT University, Colombia
O.  An Artificial Neural Network Based Model to Analyze Malarial Data and
    Predict Organ Failure
    Dinesh Mital and Radhika Uppalapati
    Univ. of Medicine and Dentistry of New Jersey, Newark, NJ, USA
O.  Directional Folding: Could Blast be Wrong?
    Faramarz Valafar
    San Diego State University, San Diego, California, USA
O.  Reducing Harmful Effects Of Road Excitations On Human Health By Designing
    Car Active Suspension Systems
    Sara Sharifi Sedeh**, Reza Sharifi Sedeh*, **Keivan Navi
    **Shahid Beheshti University, Tehran, Iran
    *Sharif University of Technology, Tehran , Iran
O.  Using Car Semi-Active Suspension Systems To Decrease Undesirable
    Effects Of Road Excitations On Human Health
    Sara Sharifi Sedeh**, Reza Sharifi Sedeh*, **Keivan Navi
    **Shahid Beheshti University, Tehran, Iran
    *Sharif University of Technology, Tehran , Iran
O.  Computer-Aided Cytogenetic Method of Breast Cancer Diagnosis PART I -
    Decision Rule
    R. I. Andrushkiw, Yu. I. Petunin, L. I. Ostapchenko, N. V. Boroday,
    Y. V. Lozovskaya
    New Jersey Institute of Technology, Newark, NJ, USA
    Kyiv National Taras Shevchenko University, Kyiv, Ukraine
    R.E.Kavetsky Institute of Oncology and Radiobiology of the
    National Academy of Sciences of Ukraine, Ukraine
    Institute of Oncology of the Academy of Medical Sciences of Ukraine
O.  Computer-Aided Cytogenetic Method of Breast Cancer Diagnosis Part II -
    Test Criteria
    R. I. Andrushkiw, D. A. Klyushin, K. N. Golubeva, M. Pokoyovy, A. V. Romanov
    New Jersey Institute of Technology, Newark, NJ, USA
    Kyiv National Taras Shevchenko University, Kyiv, Ukraine

 

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