Schedule of Events

Day 1: Monday July 9, 2007

10:00 a.m. – 5:00 p.m.

Registration
Shriver Center Lobby

10:30 a.m. – 12:00 p.m.

Tutorial I: Statistical Microarray Analysis
Mario Medvedovic, Ph.D., Assistant Professor, Cincinnati Children's Research Hospital
Shriver Center

Tutorial II: SQL and Databases
Chun Liang, Ph.D., Assistant Professor, Miami University
Shriver Center

Tutorial III: The Fundamentals of Bioinformatics
Michael Raymer, Ph.D., Wright State University
Shriver Center

Tutorial IV: The Promise of FPGA-Acceleration Processors to Bioinformatics Research
Anthony Johnson, Ph.D., University of Toledo
Shriver Center

1:30 p.m. – 3:00 p.m.

Tutorial V: High Throughput Approaches for Network Biology
David E. Hill, Ph.D., Senior Research Scientist, Associate Director of Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Harvard University
Shriver Center

Tutorial VI: RNA Structure Prediction and Comparison
Neocles Leontis, Ph.D., Professor, Bowling Green State University
Shriver Center

Tutorial VII: Mass Spectrometry, Proteomics and Bioinformatics
Michael A. Freitas, Ph.D., Ohio State University
Location: Shriver Center

Tutorial VIII: Perl for Bioinformatics
Pete Carswell, Systems Developer/Engineer, Ohio Supercomputer Center
Location: Shriver Center

3:00 p.m. – 5:00 p.m.

Reception and Poster Session I
Multi-purpose Room A, Shriver Center

6:00 p.m. – 7:00 p.m.

Keynote Speaker
Multi-purpose Room, Shriver Center

Scott Cain, PhD
Coordinator, Generic Model Organisms Database
Cold Spring Harbor Laboratory, New York
Title: The GMOD infrastructure project

7:00 p.m. – 8:30 p.m.

Dinner
Heritage Room, Shriver Center

8:30 p.m. – 9:30 p.m.

Keynote Speaker
Heritage Room, Shriver Center

Ming Li, Ph.D.
Professor, Canada Research Chair in Bioinformatics
Fellow, Royal Society of Canada
School of Computer Science
University of Waterloo
Title: Modern Homology Search

Day 2: Tuesday July 10, 2007

7:00 a.m. – 7:50 a.m.

Buffet Breakfast
Heritage Room, Shriver Center

Session 1:
Multi-purpose Rooms B and C, Shriver Center
Session Chair: Jarek Meller Ph.D., Associate Professor, Cincinnati Children Research Hospital, Presiding

8:00 a.m. – 8:20 a.m.

“Genome-wide analysis of alternative promoters using a custom promoter tiling array platform”, Greg Singer

8:20 a.m. – 8:40 a.m.

“Predicting Protein Functions Using Decision Trees”, Venkata Yedida

8:40 a.m. – 9:30 a.m.

Keynote Speaker
Multi-purpose rooms B and C, Shriver Center

Ron Elber, Ph.D.
Professor, Department of Computer Science
Director, Computational Biology Service Unit
Cornell University
Title: The network of sequence flow between protein structures

9:30 a.m. – 9:50 a.m.

“Exploring Structural Implications of Positional Dependencies in Protein Sequence Alignments”, Hatice Gulcin Ozer

9:50 a.m. – 10:10 a.m.

“Lipid Accessibility Prediction in Membrane Proteins Using Low Complexity Regression Models”, Mukta Phatak

10:10 a.m. -- 10:30 a.m.

"Word Seeker: Discovering Genome-wide Patterns", Lonnie Welch

10:30 a.m. -- 10:50 a.m.

Break

Session II
Multi-purpose Rooms B and C, Shriver Center
Session Chair: Bruce Aronow, Ph.D., Professor, Cincinnati Children Research Hospital, Presiding

10:50 a.m. – 11:10 a.m.

“Predicting the functional impact of microRNAs on developmental processes”, Vivek Kaimal

11:10 a.m. – 11:30 a.m.

“Inferring function in non-coding DNA”, Sudhindra Gadagkar

11:30 a.m. – 11:50 a.m.

“Microregulation of a Master Regulatory Network”, Amit U. Sinha

11:50 a.m. – 12:10 p.m.

“Annotation of MicroRNA Gene Promoters in Human and Mouse by Integrative Bioinformatics Analysis”, Hao Sun

12:10 p.m. – 12:30 p.m.

“The GAIT System Defines an Auto-regulatory, Post-transcriptional Operon that Sequentially Restricts and Re- permits Inflammatory Gene Expression”, Paul Fox

12:30 p.m. – 1:10 p.m.

Lunch
Heritage Room, Shriver Center

1:10 p.m. -- 2:00 p.m.

Keynote Speaker
Heritage Room Shriver Center

Sudhir Kumar, Ph.D.
Professor, School of Life Sciences
Director, Center for Evolutionary Functional Genomics
Arizona State University
Title: Evolutionary anatomies of disease mutations in proteins

Session III
Multi-purpose Room B and C, Shriver Center
Session Chair: Michael Wagner, Ph.D., Assistant Professor, Cincinnati Children Research Hospital Presiding

2:10 p.m. – 2:30 p.m.

“Querying with the Gene Ontology and Its Annotations”, Valerie V. Cross

2:30 p.m. – 2:50 p.m.

“Bayesian hierarchical model for transcriptional module discovery by jointly modeling gene expression and ChIP-chip data”, Xiangdong Liu

2:50 p.m. – 3:10 p.m.

“Kolmogorov- Smirnov Based Scores for Protein Identification Using Peptide Mass Fingerprinting”, Rachana Jain

3:10 p.m. – 3:30 p.m.

“Comparison of Statistical Techniques for the Analysis of Metabolic Toxicological Data Derived from NMR Spectroscopy”, Paul Edward Anderson

3:30 p.m. – 3:50 p.m.

“A novel approach in identifying spurious and chimeric sequences in dbEST”, Alex Kloft, Chun Liang

3:50 p.m. – 5:00 p.m.

Poster Session II
Multi-purpose Room A, Shriver Center

Session IV
Multi-purpose Room B and C, Shriver Center
Session Chair: Jens Lichtenberg, Ohio University

5:00 p.m. – 5:20 p.m.

“Improved human disease candidate gene prioritization using mouse phenotype”, Jing Chen

5:20 p.m. – 5:40 p.m.

“Comparison of modeling methodologies in systems biology”, Carla Purdy

5:40 p.m. – 6:00 p.m.

“Mining and Ranking Disease Associated Entities on Biomedical Semantic Web”, Ranga Chandra Gudivada

6:00 p.m. – 6:20 p.m.

“A Hybrid Computational Model of Neural Pruning as a Cause of Schizophrenia”, Jason Shifflet

6:30 p.m.-- 7:30 p.m.

Poster Session III and Reception (Continued)
Multi-purpose Room A Shriver Center

7:30 p.m. – 8:30 p.m.

Dinner
Heritage Room, Shriver Center

Keynote Speaker
Room: 123 Shriver Center

David States, Ph.D., M.D.
Professor, Department of Human Genetics
Director, Bioinformatics Program
University of Michigan
Title: Integrating Genomics and Proteomics: Using Mass Spectrometry to Annotate the Genome

Day 3: Wednesday July 11, 2007

7:00 a.m. – 7:50 a.m.

Buffet Breakfast
Heritage Room, Shriver Center

8:00 a.m. – 10:45 a.m.

Specialty Technical sessions (Concurrent sessions)

Evolutionary Biology and Diseases
Session Chair: Daniel Janies, Ph.D., Assistant Professor, Ohio State University

• “Towards phylogenomic reconstruction”, Vinh Sy Le
• “Faster Local Searches under the Generalized Tree Alignment Problem”, Andres Varon
• “Novel Optimality Criteria for Phylogenetics”, Ward Wheeler
• “Genomic and geographic surveillance of infectious disease”, Daniel Janies
• Break
• “A Quantitative Genotype Algorithm Reflecting H5N1 Avian Influenza Niches”, Xiu-Feng Wan
• “Re-assortment Networks for Modeling the Evolution of Segmented Viruses”, Shahid Bokhari
• “Personal Phylogenomics: First Human Lineage Trees Based on Large HapMap Datasets”, Andrew D. Johnson & Daniel Janies
• “Patterns of sequence changes at epitopes and adaptive evolution of host-pathogen interactions”, Helen Piontkivska

Biomedical Informatics
Session Chair: Anil Jegga, DVM, MS, Assistant Professor, Cincinnati Children Research Hospital

• “Large scale genotype-phenotype correlation for continuous phenotypes”, Farhat Habib
• “High-Throughput Analysis of Human Phenome to Investigate Modular “Nature of Complex Disorders”, Ranga Chandra Gudivada
• “Frequent deletion of a 76-kb genomic DNA fragment with complement factor H-like genes CFHR3 and CFHR1 is protective against systemic lupus erythematosus (SLE) in European Americans”, Chack Yung Yu
• “Transcriptional Genomics of Heart Development”, Sivakumar Gowrisankar
• Break
• “Organization of Clusters to Reveal Deeper Domain Knowledge”, Raj Bhatnagar, PhD
• “Graph Clustering: Problems and Algorithms”, Yizhong Cheng
• “A Local Likelihood-based Active Contour Model for Medical Image Segmentation”, Jundong Liu

Genomic Features and Algorithms
Session Chairs: Robert Blumenthal, Ph.D., Professor, University of Toledo and Quinn Li, Ph.D., Associate Professor, Miami University

• “The exponential decay of GC-content in mammalian genomic regions subject to strand-symmetric substitution rates”, Dr. John E. Karro
• “Toward a Methodology for Discovery of Regulatory Motifs in Plants”, Dazhang Gu
• “Evolving Fractal Visualizations for Protein Secondary Structure Sequences”,
  Deborah Stoffer
• “Emergence Pathways of the Gs/Gd/96-like H5N1 Avian Influenza Virus”,
  Ziming Zhao
• “Using Fuzzy Measures for Protein Structure Alignment”, Suchitha Subramanian & Carla Purdy
• “Integrated functional genomics to study the modulation of aboveground insect herbivores and phytopathogens by belowground microbiota”, P. Larry Phelan
• “On the Use of Genome Rearrangement Measures for Assessing Evolutionary Relatedness”, Amit U Sinha

11:00 a.m. – 12:30 p.m.

Panel Discussion
Heritage Room, Shriver Center
“Accelerating Progress in Bioinformatics: Education, Technology, Infrastructure and Applications"

Panel Moderators:
Eric Stahlberg, Ohio Supercomputer Center and Wittenberg University
Lonnie Welch, Ohio University

Panelists:

• Anthony R. Arment, Ph.D., Associate Professor of Biology, Central State University (Keeping Pace with the Bioinformatics Revolution in Undergraduate Education)
• Ty Bryant, Founder, Future Path Medical, (An Entrepreneurial Perspective)
• Kelly Hall, Ph.D., Director of Planning, Research, and Grants Clark State Community College (Questions Educators Ask When Developing New Programs Such As Bioinformatics)
• Dr. Anthony D. Johnson, Associate Professor of Electrical Engineering and Computer Science, The University of Toledo (Hardware Accelerators For Bioinformatics)
• Maha Nagarajan, Ph.D, Associate Professor of Biology, Wilberforce University (Science and Technology: A Nation's Future)
• Dennis M. Sullivan, MD, MA (Ethics), Professor of Biology, Director, Center for Bioethics, Cedarville University (Overcoming Bottlenecks to Learning: Bioethics, Blogging, and the New Educational Technologies)
• Major Leamon Viveros, USAF ARFL/HEPB, (Bioinformatics Opportunities and Challenges at the Air Force Research Lab)
• Dean L. Zeller, Vice President, Association for Computing Machinery, Kent State University (Nifty Bioinformatics Assignments)
• GQ Zhang, Associate Chair, Department of EECS, Case Western Reserve University (Bench to Book: Vertically Integrated Infrastructure for Proteomics Cores)

12:40 p.m. – 1:20 p.m.

Lunch
Heritage Room, Shriver Center

1:20 p.m. -- 2:00 p.m.

Keynote Speaker
Heritage Room, Shriver Center

David E. Hill, Ph.D.
Senior Research Scientist, Associate Director of Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Harvard University
Title: Interactomics: experimental and theoretical basis of biological interactions networks

2:00 p.m.

Prizes and Conference closing