Workshop I: High Throughput Technologies and Methods of Analysis - IPAM

Workshop I: High Throughput Technologies and Methods of Analysis

Part of the Long Program Proteomics: Sequence, Structure, Function
March 22 - 26, 2004

Schedule

All times in this Schedule are Pacific Time (PT)

Monday, March 22, 2004

Morning Session

08:00-08:45
Check-In/Light Breakfast (Hosted by IPAM)
08:45-09:00
Welcome and Opening Remarks
09:00-10:00
Vicki H. Wysocki (University of Arizona)
Data-mining a Set of Truth Spectra to Determine Peptide Fragmentation Chemistry
10:00-10:30
Break
10:30-11:30
Peter Harrington (Ohio University)
Chemometric Considerations in Proteomic Analyses by Mass Spectrometry
11:30-13:30
Lunch (on your own)

Afternoon Session

13:30-14:30
Shankar Subramaniam (University of California at San Diego)
Contextual Analysis of Biochemical Networks in Mammalian Cells
14:30-15:00
Break
15:00-16:00
Joseph Loo (UCLA)
Strategies for Characterizing Proteins in Proteomics Research
16:00-17:00
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Title not available

Tuesday, March 23, 2004

Morning Session

08:00-09:00
Check-In/Light Breakfast (Hosted by IPAM)
09:00-10:00
Tim Veenstra (National Cancer Institute)
Analysis of the Human Serum Proteome
10:00-10:30
Break
10:30-11:30
Tim Ting Chen (University of Southern California)
Reliability of protein interaction data sets and prediction of protein domain interactions
11:30-13:30
Lunch (on your own)

Afternoon Session

13:30-14:30
Austin Yang (University of Southern California)
Title not available
14:30-15:00
Break
15:00-16:00
Christoph Borchers (University of North Carolina)
Novel Comprehensive Proteomic Approaches to Address Biological Problems
16:00-17:00
Nouri Neamati (University of Southern California)
Proteomics and the new frontiers
17:00-18:30
Wine/Cheese Reception (Hosted by IPAM)
18:30-19:30
Ruedi Aebersold (Institute for Systems Biology)
Data Collection and Analysis for High Throughput Quantitative Proteomics: Current Status And Challenges

Wednesday, March 24, 2004

Morning Session

08:00-09:00
Check-In/Light Breakfast (Hosted by IPAM)
09:00-10:00
Terry Speed (University of California, Berkeley (UC Berkeley))
Deriving statistical models for predicting peptide tandem MS product ion intensities
10:00-10:30
Break
10:30-11:30
Hongyu Zhao (Yale University)
Statistical Issues in the Analysis of Mass Spectrometry Data
11:30-13:30
Lunch (on your own)

Afternoon Session

13:30-14:30
Benno Schwikowski (Institute for Systems Biology)
Algorithms for the Multidimensional Analysis of Multidimensional LC-Mass Spectrometry Data
14:30-15:00
Break
15:00-16:00
Fernando Pineda (Johns Hopkins University)
Algorithms and Databases for rapid microorganism identification, Statistical model of proteolytic digestion for improved protein identification
16:00-17:00
Michael Snyder (Yale University)
Global analysis of Genomes and Proteomes

Thursday, March 25, 2004

Morning Session

08:00-09:00
Check-In/Light Breakfast (Hosted by IPAM)
09:00-10:00
Pavel Pevzner (University of California, San Diego (UCSD))
Title not available
10:00-10:30
Break
10:30-11:30
Weixiong Zhang (Washington University in St. Louis)
Discovering Temporal Gene Regulatory Networks
11:30-13:30
Lunch (Hosted by IPAM)

Afternoon Session

13:30-14:30
Vineet Bafna (University of California at San Diego)
De novo interpretation of tandem mass spectra
14:30-15:00
Break
15:00-16:00
Nathan Edwards (Applied Biosystems)
Generating Peptide Candidates from Protein Sequence Databases for Protein Identification via Mass Spectrometry
16:00-17:00
Alexander Hartemink (Duke University)
Classification in high-dimensional spaces: joint classification and feature selection

Friday, March 26, 2004

Morning Session

08:00-09:00
Check-In/Light Breakfast (Hosted by IPAM)
09:00-10:00
Edward Marcotte (University of Texas, Austin)
The structure and dynamics of genome-wide protein networks
10:00-10:30
Break
10:30-11:30
Fengzhu Sun (University of Southern California (USC))
An Integrated Approach for Protein Function Prediction
11:30-13:30
Lunch (on your own)

Afternoon Session

13:30-14:30
William Noble (University of Washington)
A kernel framework for genomic data fusion
14:30-15:00
Break
15:00-16:00
Golan Yona (Cornell University)
BIOZON: a unified knowledge resource on DNA sequences, proteins, complexes and cellular pathways
16:00-17:00
Bin Ma (University of West Ontario)
PEAKS: Accurate de novo sequencing using MS/MS
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