Schedule

 

Thursday

 

8:30 am Breakfast

 

9:00 Welcome [Raj Reddy]

 

9:10 – 10:30 Biology Tutorial:

·       20 minutes Techniques in Protein Science [Judith Klein-Seetharaman]

·       20 minutes X-ray crystallography [Michele Loewen]

·       20 minutes NMR spectroscopy [Chien Ho]

·       20 minutes Mass spectrometry [Catherine E. Costello]

 

10:30 – 11 Break

 

11 – 12:30 Computer Science Tutorial:

·       45 minutes language modeling [Roni Rosenfeld]

·       45 minutes classification [Yiming Yang]

 

12:30 take lunch from buffet

 

1 – 2:30 Session I* Protein (mis)folding and drug discovery [Chairperson Jonathan King]

Presenters: [Alain Rappaport], [Cathy Costello], [Hagai Meirovitch]

 

2:30 – 3 Break

 

3 – 4:30 Session II* Pushing the structure-dynamics-function paradigm to its limits in model systems such as hemoglobin and relating it back to amino acid sequence [Chairperson Raj Reddy]

Presenters: [Chien Ho], [Ivet Bahar], [Jaime Carbonell]

 

4:30 – 5 Break

 

5 – 5:45  Special Guest Lecture

Invited Speaker: Bud Mishra, Professor of Computer Science & Mathematics (Courant Institute, NYU), Professor (Watson School of Biological Sciences, CSHL)

New York University, 251 Mercer Street, New York, N.Y.10012

Title: Cell Talk

Abstract: Freeman Dyson, in his 1985 Tarner Lectures, asked: "Is Life one thing

or two things? Is there a logical connection between metabolism and replication?". As the study of the genomes and proteomes have become amenable to computational analysis to decipher "part-lists" of life (e.g. genes, mRNA's, proteins, promoters, etc.), it may now be possible to address Dyson's questions with algorithmic tools based on dynamical systems,

control theory and computational logic to study complex metabolic pathways.

This talk introduces the concept of algebraic differential automata (ADA) systems to model biological processes, and how we plan to use them to interpret experimental data modulated by regulatory, metabolic and intercellular signaling processes.

 

5:45 – 7 Session III* Classification of structure-sequence elements in overall genomes and roles for specific proteins [Chairperson Ivet Bahar]

Presenters: [Jonathan King], [Michele Loewen], [John Vries], [Yiming Yang]

 

7:15 pm Dinner and Welcome Address [Mark Kamlet, Provost Carnegie Mellon University]

 

Friday

 

7:30 am Breakfast

 

8 – 9:30 Session IV* n-grams and immune system recognition. [Chairperson Cathy Costello]

Presenters: [Jennifer Cochran], [Shlomo Ta’asan], [Roni Rosenfeld]

 

9:30 – 10 Break

 

10 – 11:30 Session V* Sequence segmentation (word and topic boundaries) and generality of structural features in G-protein coupled receptors. [Chairperson Roni Rosenfeld]

Presenters: [Judith Klein-Seetharaman], [Deborah Weisser], [John Lafferty]

 

11:30 take lunch from buffet

 

12 – 2 General discussion, summary, plans and milestones until next meeting [Raj Reddy], [Judith Klein-Seetharaman]

 

1. Summary of expected milestones
2. List of specific experiments to be carried out over the next months
3. List of tools required to achieve the milestones

Relation to current status of biological tool suite in Matlab and goals for the collaboration [Rob Henson]

4. Planning of monthly video conferences and next meeting

 

3 - 4 Guest Lecture: Center for Computational Biology and Bioinformatics, University of Pittsburgh Seminar Speaker

Speaker: Gary Stormo, Dept. of Genetics, School of Med., Washington University in St. Louis

            Title: Transcription Regulation and Methods for Identification of Binding Sites

            Location: S123 Biomedical Science Tower South (University of Pittsburgh Campus)

 

 

* General format of sessions:

Each presenter will be given ~5 minutes to present their research, and another ~5 minutes to present challenges and open questions. The rest of the time is for discussions.