Scientific Talks Session I
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A First Look at the tRNA and snoRNA Genes Sets in the Human & Arabidopsis Genomes
Todd M. Lowe
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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
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Blind Prediction of Protein Structure: What Have We Learnt and Where Do We Go?
Ram Samudrala, Yu Xia, and Michael Levitt
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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
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Evaluation of Musculoskeletal Models Derived from Magnetic Resonance Images
Silvia S. Blemker, Allison S. Arnold, Deanna S. Asakawa, and Scott L. Delp
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Mathematical Analysis of Ensemble Dynamics: Making Simulations of Protein Folding Feasible
Michael Randall Shirts, and Vijay S. Pande
Scientific Talks Session II
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Discovering DNA Motifs in Upstream Regulatory Regions of Co-expressed Genes
Xiaole Liu, Jun Liu, and Doug Brutlag
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Developing and Evaluating Assessment Measures From a Simulation Tool: Tinkering Towards Utopia?
Carla Marie Pugh
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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
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Finding Distinctive Expression Patterns in Microarray Data with Independent Components Analysis
Joshua Michael Stuart, Soumya Raychaudhuri, Xiaole Liu, and Russ Altman
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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
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Designing a Knowledge Base for Pharmacogenomics: an Ontology for Genetic Information
Daniel Rubin, and Russ Altman
Poster Session / Software Demonstration
Posters:
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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
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Using Metacomputing Tools To Facilitate Large-Scale Analyses of Biological Databases
Allison Roberts Waugh, Glenn A. Williams, and Russ B. Altman
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Cluster Comparisons
Alok Saldanha
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Prediction of Novel Functional Domains Using Rates of Evolution
Alexander Simon
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Recognizing Polyps From 3D CT Colon Data
Salih Burak Gokturk, Burak Acar, David Paik, Carlo Tomasi, Christopher Beaulieu, and Sandy Napel
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Folding of a Coarse-grained Model of the Tetrahymena Ribozyme
Bradley J. Nakatani, and Vijay S. Pande
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Use of Multiple Clustering Algorithms for Analysis of Human Lung Cancer Gene Expression Data
Jessica Ross, and Glenn Rosen
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In Vivo Validation of Cardiovascular Blood Flow Simulations
Joy Ku, Gregory Wai Mong Chan, Mary Draney, Frank Arko, Chris Zarins, and Charles Taylor
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Computational Analyses of the Differences between Daily and Intermittent Alendronate Treatment
Christopher J. Hernandez, Gary S. Beaupre, Robert Marcus, and Dennis R. Carter
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Mechanical Influences on Oblique Pseudarthrosis Formation
Elizabeth G. Loboa Polefka, Gary S. Beaupre, and Dennis R. Carter
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Internal and Relative Structural Conservation of Discrete Protein Sequence Motifs
Steven Paul Bennett, and Douglas Brutlag
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Constrained Global Optimization for Estimating Molecular Structure from Atomic Distances
Glenn A. Williams, Jonathan M. Dugan, and Russ B. Altman
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Automated Individualized Decision Support
George Christopher Scott, Ross Shachter, and Leslie Lenert
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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
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Neuronavigational Epilepsy Focus Mapping
Hamid Reza Abbasi, Sanaz Hariri, David Martin, Michael Risinger, and Gary Heit
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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
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Use of XML/RDF to Create Structured Metadata for Medical Images
John Joseph Michon
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A Real-Time Freehand 3D Ultrasound System for Image Guided Surgery
Jacqueline Nerney Welch, Jeremy A. Johnson, Michael R. Bax, and Ramin Shahidi
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Bridging the Gap: Simulated Dynamics of Lipid Bilayers at Boundaries
Peter M. Kasson, Steven G. Boxer, and Vijay S. Pande
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KB-Driven Model Building: Challenges and Approaches
Mike Cantor, Peter Karp, and Masaru Tomita
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MOTIFFEATURE: Automated Construction of 3D Models from Sequence Motifs
Mike Hsin-Ping Liang, and Russ Altman
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Guideline Interchange Format: A Representation for Sharable, Computer-interpretable Guidelines
Mor Peleg
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A Finite Element Model of the Human Cornea
Assad Anshuman Oberai, Peter M. Pinsky, and Thomas A. Silvestrini
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Mechanical Regulation of Growth Plate Morphology
Sandra Shefelbine, and Dennis R. Carter
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The Importance of Swing Phase Initial Conditions in Stiff-knee Gait: A Case Study
Saryn Goldberg, Steven Piazza, and Scott Delp
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A New Twist on the Helix-Coil Transition: A Non-biological Helix with Protein-like Intermediates
Sidney P. Elmer, and Vijay S. Pande
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Sequence Analysis and Structure Comparison of the SH3 Domain Family
Stefan M. Larson, and Alan R. Davidson
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Representing Contextually Changing Decision Making Behavior in Medical Organizations
Carol HF Cheng, and Raymond E Levitt
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Medline Query-by-Example
Elmer Bernstam, Olga Troyanskaya, and Jeff Chang
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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
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Comparison of Ribosomal Models to Experimental Data with the RiboWeb System
Michelle Whirl Carrillo, and Russ B. Altman
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The Mouse SNP Database: Mapping QTLs in silico
Jonathan Usuka
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A New Method for Determining Protein Function Similarity based on Keywords and Gene Ontology
Yueyi Liu, and Russ Altman
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Optimizing Knowledge-based Energy Functions. From Lattice Study to Real Proteins
Yu Xia, and Michael Levitt
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Monte Carlo Simulations of Folding of Simple Alpha Helices
Bojan Zagrovic, Jessica Shapiro, and Vijay Pande
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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
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Quantification of the Hydrophobic Interaction by Simulations of the Aggregation of Small, Hydrophobic Solutes in Water
Tanya M. Raschke, Jerry Tsai and Michael Levitt
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ViewFeature: Integrated Feature Analysis and Visualization
D. Rey Banatao, Conrad C. Huang, Patricia C. Babbitt, Russ B. Altman, and Teri E. Klein
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Using Human Language Ability to Learn and Recognize Protein Folds
Neil F. Abernethy
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Structure and Stability of Collagen
Sean Mooney, Teri Klein
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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
Software Demonstrations:
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An Interactive Biomechanical Model of the Human Hand
Robert Pao-Feng Cheng, Jean Heegaard, Parvati Dev, Sakti Srivastava, Leroy Heinrichs, and Tonia Sengelin
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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
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Two Sided Clustering for Yeast Gene Expression Using Probabilistic Relational Models
Eran Segal, Ben Taskar, and Daphne Koller
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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
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IRaCS: A Literature Mining Tool for Fast Interpretation of Microarray Data
Sep Kamvar, Eldar Giladi, Jeanne Loring, and Mike Walker
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