Scientific Talks Session I

Using a Pathway/Genome Database for Plasmodium falciparum to Find Novel Drug Targets
Iwei Yeh, Theodor Hanekamp, Peter D. Karp and Russ B. Altman

Module Networks: Reconstruction of Molecular Modules and Their Regulation from Gene Expresssion
Eran Segal, Michael Shapira, Aviv Regev, Dana Pe'er, Daphne Koller and Nir Friedman

Interactive Simulation of the Human Hand
Leonard Sibille and Jean-Claude Latombe

Native-like Mean Structure in the Unfolded Ensemble of Small Proteins -- A Distributed Computing Study
Bojan Zagrovic, Siraj Khaliq, Michael R. Shirts, Christopher D. Snow and Vijay S. Pande

3D Differential Descriptors for Computer Aided Diagnosis of Colonic Polyps in CTC
Burak Acar, David S. Paik, Christopher F. Beaulieu, R.B. Jeffrey, Jr., Marta Davila and Sandy Napel

Multiple Genomic Sequence Alignment
Michael Brudno, Chuong Do, Michael Kim and Serafim Batzoglou

Scientific Talks Session II

Knowledge-Based Public Health Surveillance
David L. Buckeridge, Martin O'Connor, Justin Graham, Michael K. Choy, Zachary Pincus and Mark Musen

Enzyme Reaction Modeling of Hazardous Pollutant Transformation: Structural Basis of Biodegradability
Brett T. Kawakami, Sean Mooney, Charles B. Musgrave, Martin Reinhard and Paul V. Roberts

Using Scientific Literature Automatically to Understand Gene Expression Data
Soumya Raychaudhuri and Russ B. Altman

Comparison of Simulated and Experimental Protein Folding
Christopher D. Snow, Houbi Nguyen, Vijay S. Pande and Martin Gruebele

Targeted Clustering: A Method for Building Context-specific Clusters around Genes of Interest in DNA Microarray Data
Joshua M. Stuart, Kathy E. Mach, Stuart K. Kim and Art B. Owen

Automated Vessel Identification and Mobile Interactive Reporting for CT Angiography
Bhargav Raman, Raghav Raman, Sandy Napel and Geoffrey D. Rubin

Poster Session

P01 A Coupled Momentum Method for Modeling Blood Flow in Deformable Arteries
C. Alberto Figueroa Alvarez and Charles A. Taylor

P02 Decomposing Gene Expression into Cellular Processes
Alexis Battle, Eran Segal and Daphne Koller

P03 Collection and Transformation of Chromosomal Imbalances in Human Neoplasias for Data Mining Procedures
Michael Baudis

P04 Image Based Finite Element Modeling
Erik Bekkers and Charley Taylor

P05 Identification of Functional Regions in Proteins on the Basis of Evolutionary Sequence Analysis
Jonathan Binkley and Arend Sidow

P06 Creating an Online Dictionary of Abbreviations from MEDLINE
Jeffrey T. Chang, Hinrich Schutze and Russ B. Altman

P07 Direct Hydroxide Attack is a Plausible Mechanism for Amidase Antibody 43C9
Lillian T. Chong, Pradipta Bandyopadhyay, Thomas S. Scanlan, Irwin D. Kuntz and Peter A. Kollman

P08 The Draft Problem: Genomic Sequence Alignment Reconsidered
Chuong B. Do, Michael Brudno and Serafim Batzoglou

P09 Inferring Conformational Flexibility from Variations in Experimental Measurements
Irene S. Gabashvili, Michelle Whirl-Carrillo, Michael Bada, D. Rey Banatao and Russ B. Altman

P10 Establishing Standards in Medical Education: Use of Statistical Data Mining to Define Performance Characteristics
Kunal S. Girotra and Carla M. Pugh

P11 Large Multiple Sequence Alignments and Phylogenetic Analysis of the CFTR Locus
Gregory Cooper and Arend Sidow (collaborations: Eric Green, Serafim Batzoglou)

P12 Single Trial Classification of Independent Sources from MEG Task Related Recordings
Marcos Perreau Guimaraes, Dik Kin Wong, E. Timothy Uy and Patrick Suppes

P13 Predicting Growth-Generated Strains During Cranial Development
James H. Henderson and Dennis R. Carter

P14 Coherent Array Processing for Cost-effective Real-time Acoustic Imaging
Jeremy Johnson, Ömer Oralkan, Mustafa Karaman, A. Sanli Ergun and Butrus T. Khuri-Yakub

P15 Alternative Sensory Representations of the Visual World
Neel Joshi, Dan Morris and Kenneth Salisbury

P16 GeneXPress: Visualization and Analysis of Gene Expression and Sequence Data
Amit Kaushal, Roman Yelensky, Tuan Pham, Eran Segal, Nir Friedman and Daphne Koller

P17 Python Interface between PHYLIP and R
Martina Koeva and Susan Holmes

P18 Large-Scale Computational Protein Design: Sequence Space, Structure Prediction, and Protein Evolution
Stefan M. Larson, Jeremy L. England, Amit Garg, John R. Desjarlais and Vijay S. Pande

P19 CT Colonography Prone and Supine Data Registration
P. Li, S. Napel, B. Acar, D. Paik, R. B. Jeffrey and C. F. Beaulieu

P20 Applying Disclosure Control Methods to Biomedical Data
Zhen Lin, Micheal Hewett and Russ Altman

P21 Alternative Splicing: Data Storage and Analysis
Shuo Liu and Russ B. Altman

P22 Searching for Exons within Introns and Using Mutual Information to Help Find and Define DNA Regulatory Motifs
Brian T. Naughton and Douglas L. Brutlag

P23 Analysis of DNA Microarrays Using Knowledge-Based Algorithms
Kuang-Hung Pan, Chih-Jian Lih and Stanley N. Cohen

P24 Support for Guideline Development through Error Classification and Constraint Checking
Mor Peleg

P25 Modeling Mutations, Abnormal Processes, and Disease Phenotypes Using a Workflow/Petri Net Model
Mor Peleg, Irene S. Gabashvili and Russ B. Altman

P26 Teleoperable Dermatology: A Feasibility Study for Haptic Displays
Kirk Phelps and Ken Salisbury

P27 Like Standards but Better: Sharing Non-Traditional Health Data and Metadata
Zachary Pincus, David L. Buckeridge, Michael K. Choy, Justin V. Graham, Martin J. O'Connor, Mark Musen

P28 Automated Quantification of Arterial Calcification Using CT Angiography (CTA): Method and Evaluation
Raghav Raman, Bhargav Raman, Sandy Napel and Geoffrey D. Rubin

P29 Computational Modeling of T Cell Receptor Signal Integration
Tim Reddy, Peter Lee, Arancha Casal, Cenk Sumen and Mark Alber

P30 Protein Folding Simulation with Multiplexed Replica Exchange Molecular Dynamics Method
Young Min Rhee and Vijay S. Pande

P31 Fast DRRs Using Light Field Rendering
Daniel Russakoff, Torsten Rohlfing, Daniel Rueckert, Daniel Kim and Calvin Maurer, Jr.

P32 Structural Motif Discovery Using an Improved Structural Superposition Algorithm
Jessica Shapiro and Douglas Brutlag

P33 Interactive Segmentation and Visualization of Volumes
Anthony Sherbondy, Mike Houston, Pat Hanrahan and Sandy Napel

P34 SOURCE: The Stanford Online Universal Resource for Clones and ESTs
G. Sherlock, T. Hernandez-Boussard, M. Diehn, A. Alizadeh, J.C. Matese, G. Binkley, H. Jin, J. Gollub, J. Demeter, J. Hebert, C.A. Ball, P.O. Brown and D. Botstein

P35 An Elastic Model of the Malleus-incus Complex of the Human Middle Ear
Jae Hoon Sim and Afraaz R. Irani

P36 Identifying Structural Motifs in Proteins
Rohit Singh and Mitul Saha

P37 Characterizing Genomic Divergence between Two Urochordates, Ciona savignyi and Ciona intestinalis
Kerrin Small and Arend Sidow

P38 Distances Between Phylogenetic Trees -- An Algorithm Using Bipartite Graphs
Aaron Staple and Susan Holmes

P39 Weighting Data Related by Phylogeny
Eric A. Stone

P40 CT Colonography: Does Improved Z Resolution Aid Computer-Aided Polyp Detection?
Padmavathi Sundaram, Christopher F. Beaulieu, David S. Paik, Pamela K. Schraedley, R. Brooke Jeffrey and Sandy Napel

P41 Confidence Regions and Topology of Phylogenetic Trees
Henry Towsner and Susan Holmes

P42 Dry Electroencephalography
E. Timothy Uy, Dik Kin Wong, Marcos P. Guimaraes and Patrick Suppes

P43 A Coupled Multi-domain Method for Computational Modeling of Blood Flow
Irene Vignon, Brooke N. Steele and Charles A. Taylor

P44 Supervised Neural Network for Brainwave Recognition Using Individual Trials
Dik Kin Wong, Marcos Perreau Guimaraes, E. Timothy Uy and Patrick Suppes

P45 From Promoter Sequence to Expression: A Probabilistic Framework
Roman Yelensky, Eran Segal and Daphne Koller

P46 Differential Gene Expression in a Partial Trisomy 16 Mouse Model of Down Syndrome
Shuli Zhang, Farshid Oshidari, Ahmad Salehi and William C. Mobley

P47 Classification of Gene Microarrays by Penalized Logistic Regression
Ji Zhu and Trevor Hastie

P48 Endoscope Calibration and Accuracy Testing for 3D/2D Image Registration
Michael R Bax, Rasool Khadem, Jeremy A Johnson, Eric P Wilkinson, Ramin Shahidi