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9th Annual International Workshop on

Bioinformatics and Systems Biology

July 27-29, 2009

Boston, MA

Sunday, July 26, 2009

7-8:30p.m.: Reception

Life Science and Engineering Building (LSEB)

24 Cummington Street

Monday, July 27, 2009

8:00 Breakfast

LSEB 103

SESSION I

Chair: Professor Charles DeLisi

9:10 a.m. Matsuyuki Shirota – Development of a Meta-score to Assess the Quality of a Protein Model

9:45 a.m. Florian Krull – Scoring Geometries of Protein-protein Complexes

10:20 a.m. Aysam Gürler – Detection of Non-sequential Structural Analogs

10:55 Break

11:15 Daichi Shigemizu – Analysis of Chemical Modification Patterns Extracted from KEGG Drug Structure Maps

11:50 Michihiro Tanaka – Analysis of Lipid Biosynthesis Protein Families and Phospholipid Structural Variations

12:25 p.m. Lunch

SESSION II

Chair: Professor Tom Tullius

1:30 p.m. Eric Franzosa — Structural Determinants of Protein Evolution Are Multi-Dimensional and Context-Sensitive at the Residue Level

2:05 p.m. Raphael Bauer (La Jolla) – n-Gram-based Detection of Structural
RNA Features

3:00 p.m. Ilka Axmann – Evolution and function of circadian clock proteins: lessons from bacteria

3:35 p.m. Nils Christian — Network-based Function Discrimination

4:15 p.m. Kaname Kojima – A State-Space Representation of VAR Models with Sparse Learning for Dynamic Gene Networks

5:30 Pizza dinner

6:45: Duck Boat Tour

Meet in front of 24 Cummington; bring a sweater!

Tuesday, July 28, 2009

8:00: Breakast

LSEB 103

SESSION III

Chair: Professor Daniel Segre

9:00 a.m.  Timothy Hancock – Active Pathway Identification and Classification with Probabilistic Ensembles

9:35 a.m. Hsuan-Chao Chiu – Exploring Evolutionary Landscapes with a Kinetic Model of Metabolism

10:10 a.m. Niels Klitgord – Assessing the Importance of Compartmentation in Metabolic Flux Models

10:45 Break

11:05 Christian Waltermann – Crosstalk in Signaling Pathways in Budding Yeast

11:40 Jonas Maaskola – Composition and Dynamics of Small RNA in C. elegans Embryogenesis and Development

12:15 p.m. Lunch

SESSION IV

Chair: Professor Brandon Xia

1:20 p.m. Yuehien Lee – Promoter Analysis of Genes Involved in T-helper Cell Fate Decisions and Lineage Maintenance

1:55 p.m. Robert Lehmann – Computational Modeling and Simulation of the Human Apoptosis Signal Transduction Network

2:30 p.m. Poster Session

6:15: Boston Harbor Cruise

Leave from 24 Cummington Street

Wednesday, July 29, 2009

8:00: Breakfast

LSEB 103

SESSION V

Chair: Professor Gary Benson

9:00 a.m. Ritsuko Onuki – New Kernel Methods for Phenotype Prediction from Genotype Data

9:35 a.m. Yoshiaki Tanaka — An Assessment of Prediction Algorithms for Nucleosome Positioning

10:10 a.m. Thomas Spießer – Is DNA Replication Rate Independent of Sequence Composition or Length in Budding Yeast?

10:45 Break

11:05 Clemens Kühn – Investigation of Osmoadaptation in Yeast

11:40 Juliane Zimmermann – Modelling Actin-based Cellular Motility

12:15 Lunch

SESSION VI

Chair: Professor Scott Mohr

1:20 p.m. Thomas Schendel – Modelling the Cardiac Myocyte

1:55 p.m. Anupama Reddy – A Predictor for Survival in Intermediate Grade ccRCC

2:30 p.m. Atsushi Niida – Expression Module Networks in Various Types of Cancers

3:05 Break

3:20 p.m. Masataka Takarabe – Characterization and Classification of Adverse Drug Interactions

3:55 p.m. Motoki Shiga – Annotating Gene Functions with Integrative Spectral Clustering on Microarray Expressions and Sequences

4:30 p.m. David Du Verle – CaMPDB: A Resource for Calpain and Modulatory Proteolysis

5:30: Farewell Barbeque

Warren Alpert Mall (behind Marsh Chapel at 735 Commonwealth Avenue)