Scientific Program
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Scientific Talks Session I

  1. A First Look at the tRNA and snoRNA Genes Sets in the Human & Arabidopsis Genomes
    Todd M. Lowe

  2. Relational Data Mining: Using Probabilistic Relational Models to Discover Patterns in Epidemiological Data
    Lise Carol Getoor, Benjamin Taskar, Jeanne Rhee, Peter Small, and Daphne Koller

  3. Blind Prediction of Protein Structure: What Have We Learnt and Where Do We Go?
    Ram Samudrala, Yu Xia, and Michael Levitt

  4. A Fluoroscopic X-Ray Registration Process for Three-Dimensional Surgical Navigation
    Hamid Reza Abbasi, Sanaz Hariri, Shao Chin, Robert Grzeszczuk, Daniel Kim, Gary Steinberg, and Ramin Shahidi

  5. Evaluation of Musculoskeletal Models Derived from Magnetic Resonance Images
    Silvia S. Blemker, Allison S. Arnold, Deanna S. Asakawa, and Scott L. Delp

  6. Mathematical Analysis of Ensemble Dynamics: Making Simulations of Protein Folding Feasible
    Michael Randall Shirts, and Vijay S. Pande


Scientific Talks Session II

  1. Discovering DNA Motifs in Upstream Regulatory Regions of Co-expressed Genes
    Xiaole Liu, Jun Liu, and Doug Brutlag

  2. Developing and Evaluating Assessment Measures From a Simulation Tool: Tinkering Towards Utopia?
    Carla Marie Pugh

  3. A One-Dimensional Finite Element Method For Simulation-Based Medical Planning For Cardiovascular Disease
    Jing Wan, Brooke Steele, Thomas J.R. Hughes, and Charles A. Taylor

  4. Finding Distinctive Expression Patterns in Microarray Data with Independent Components Analysis
    Joshua Michael Stuart, Soumya Raychaudhuri, Xiaole Liu, and Russ Altman

  5. Automated Quantification of 4D Ultrasound for Carotid Artery Disease
    Haobo Xu, David S. Paik, Barbara Ross, Thilaka Sumanaweera, John Hossack, R. Brooke Jeffrey, and Sandy Napel

  6. Designing a Knowledge Base for Pharmacogenomics: an Ontology for Genetic Information
    Daniel Rubin, and Russ Altman


Poster Session / Software Demonstration

    Posters:

  1. Project Mothra: Designing a System for Video-based, Markerless, Human Motion Analysis in an Arbitrary Environment
    Ajit M Chaudhari, Richard W Bragg, Eugene J Alexander, and Thomas P Andriacchi

  2. Using Metacomputing Tools To Facilitate Large-Scale Analyses of Biological Databases
    Allison Roberts Waugh, Glenn A. Williams, and Russ B. Altman

  3. Cluster Comparisons
    Alok Saldanha

  4. Prediction of Novel Functional Domains Using Rates of Evolution
    Alexander Simon

  5. Recognizing Polyps From 3D CT Colon Data
    Salih Burak Gokturk, Burak Acar, David Paik, Carlo Tomasi, Christopher Beaulieu, and Sandy Napel

  6. Folding of a Coarse-grained Model of the Tetrahymena Ribozyme
    Bradley J. Nakatani, and Vijay S. Pande

  7. Use of Multiple Clustering Algorithms for Analysis of Human Lung Cancer Gene Expression Data
    Jessica Ross, and Glenn Rosen

  8. In Vivo Validation of Cardiovascular Blood Flow Simulations
    Joy Ku, Gregory Wai Mong Chan, Mary Draney, Frank Arko, Chris Zarins, and Charles Taylor

  9. Computational Analyses of the Differences between Daily and Intermittent Alendronate Treatment
    Christopher J. Hernandez, Gary S. Beaupre, Robert Marcus, and Dennis R. Carter

  10. Mechanical Influences on Oblique Pseudarthrosis Formation
    Elizabeth G. Loboa Polefka, Gary S. Beaupre, and Dennis R. Carter

  11. Internal and Relative Structural Conservation of Discrete Protein Sequence Motifs
    Steven Paul Bennett, and Douglas Brutlag

  12. Constrained Global Optimization for Estimating Molecular Structure from Atomic Distances
    Glenn A. Williams, Jonathan M. Dugan, and Russ B. Altman

  13. Automated Individualized Decision Support
    George Christopher Scott, Ross Shachter, and Leslie Lenert

  14. A Comparative Statistical Error Analysis of Neuronavigation Systems in a Clinical Setting
    Hamid Reza Abbasi, Sanaz Hariri, David Martin; Daniel Kim, John Adler, Gary Steinberg, and Ramin Shahidi

  15. Neuronavigational Epilepsy Focus Mapping
    Hamid Reza Abbasi, Sanaz Hariri, David Martin, Michael Risinger, and Gary Heit

  16. Comparative Tracking Error Analysis of Five Different Optical Tracking Systems
    Jeremy Johnson, Rasool Khadem, Clement C Yeh, Mohammad Sadeghi-Tehrani, Michael R Bax, Jacqueline Nerney Welch, Eric P Wilkinson, and Ramin Shahidi

  17. Use of XML/RDF to Create Structured Metadata for Medical Images
    John Joseph Michon

  18. A Real-Time Freehand 3D Ultrasound System for Image Guided Surgery
    Jacqueline Nerney Welch, Jeremy A. Johnson, Michael R. Bax, and Ramin Shahidi

  19. Bridging the Gap: Simulated Dynamics of Lipid Bilayers at Boundaries
    Peter M. Kasson, Steven G. Boxer, and Vijay S. Pande

  20. KB-Driven Model Building: Challenges and Approaches
    Mike Cantor, Peter Karp, and Masaru Tomita

  21. MOTIFFEATURE: Automated Construction of 3D Models from Sequence Motifs
    Mike Hsin-Ping Liang, and Russ Altman

  22. Guideline Interchange Format: A Representation for Sharable, Computer-interpretable Guidelines
    Mor Peleg

  23. A Finite Element Model of the Human Cornea
    Assad Anshuman Oberai, Peter M. Pinsky, and Thomas A. Silvestrini

  24. Mechanical Regulation of Growth Plate Morphology
    Sandra Shefelbine, and Dennis R. Carter

  25. The Importance of Swing Phase Initial Conditions in Stiff-knee Gait: A Case Study
    Saryn Goldberg, Steven Piazza, and Scott Delp

  26. A New Twist on the Helix-Coil Transition: A Non-biological Helix with Protein-like Intermediates
    Sidney P. Elmer, and Vijay S. Pande

  27. Sequence Analysis and Structure Comparison of the SH3 Domain Family
    Stefan M. Larson, and Alan R. Davidson

  28. Representing Contextually Changing Decision Making Behavior in Medical Organizations
    Carol HF Cheng, and Raymond E Levitt

  29. Medline Query-by-Example
    Elmer Bernstam, Olga Troyanskaya, and Jeff Chang

  30. Offline Testing of a Computerized Decision Support System for Management of Hypertension
    Susana Martins, MK Goldstein, BB Hoffman, RW Coleman, SW Tu, R Shankar, M O'Connor, MA Musen, SB Martins, N Hastings

  31. Comparison of Ribosomal Models to Experimental Data with the RiboWeb System
    Michelle Whirl Carrillo, and Russ B. Altman

  32. The Mouse SNP Database: Mapping QTLs in silico
    Jonathan Usuka

  33. A New Method for Determining Protein Function Similarity based on Keywords and Gene Ontology
    Yueyi Liu, and Russ Altman

  34. Optimizing Knowledge-based Energy Functions. From Lattice Study to Real Proteins
    Yu Xia, and Michael Levitt

  35. Monte Carlo Simulations of Folding of Simple Alpha Helices
    Bojan Zagrovic, Jessica Shapiro, and Vijay Pande

  36. Automatic Detection and Quantification of Abdominal Aortic Thrombus in CT Angiograms Based on Clustering and Global Geometric Information
    Feng Zhuge, Sandy Napel, David Paik, and Geoffrey D. Rubin

  37. Quantification of the Hydrophobic Interaction by Simulations of the Aggregation of Small, Hydrophobic Solutes in Water
    Tanya M. Raschke, Jerry Tsai and Michael Levitt

  38. ViewFeature: Integrated Feature Analysis and Visualization
    D. Rey Banatao, Conrad C. Huang, Patricia C. Babbitt, Russ B. Altman, and Teri E. Klein

  39. Using Human Language Ability to Learn and Recognize Protein Folds
    Neil F. Abernethy

  40. Structure and Stability of Collagen
    Sean Mooney, Teri Klein

  41. Combining Kinetic Inference to Extract Parameters and Predictor-Corrector Method to Develop Genetic Regulatory Circuits that are Consistent with Heterogeneous Experimental Data
    Nizar Batada, Mike Laub, Harley McAdams

  42. Software Demonstrations:

  43. An Interactive Biomechanical Model of the Human Hand
    Robert Pao-Feng Cheng, Jean Heegaard, Parvati Dev, Sakti Srivastava, Leroy Heinrichs, and Tonia Sengelin

  44. Implementation of a Radio-Frequency Intravascular Ultrasound System for Quantitative Tissue Characterization in Coronary Arteries
    Brian Courtney, Abel L. Robertson, Paul G. Yock, and Peter J. Fitzgerald

  45. Two Sided Clustering for Yeast Gene Expression Using Probabilistic Relational Models
    Eran Segal, Ben Taskar, and Daphne Koller

  46. Web Applications for Microarray Data Analysis and Presentation
    Christian A. Rees, Charles M. Perou, Douglas T. Ross, Jonathan R. Pollack, J. Michael Cherry, Patrick O. Brown, and David Botstein

  47. IRaCS: A Literature Mining Tool for Fast Interpretation of Microarray Data
    Sep Kamvar, Eldar Giladi, Jeanne Loring, and Mike Walker


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