Workshop IV: Search and Knowledge Building for Biological Datasets - IPAM

Workshop IV: Search and Knowledge Building for Biological Datasets

Part of the Long Program Mathematics of Knowledge and Search Engines
November 26 - 30, 2007

Schedule

All times in this Schedule are Pacific Time (PT)

Monday, November 26, 2007

Morning Session

08:00-08:50
Check-In/Light Breakfast (Hosted by IPAM)
08:50-09:00
Welcome and Opening Remarks
09:00-10:00
Olga Troyanskaya (Princeton University)
Title not available
10:00-10:30
Break
10:30-11:30
Vipin Kumar (University of Minnesota, Twin Cities)
Association Analysis-based Extraction of Functional Information from Protein-Protein Interaction Data
11:30-13:00
Lunch (on your own)

Afternoon Session

13:00-14:00
Chris Wiggins (Columbia University)
Defining, Inferring, and Encoding modularity
14:00-14:30
Break
14:30-15:30
William Noble (University of Washington)
Consistent probabilistic outputs for gene function prediction
15:30-16:00
Coffee Break
16:00-17:00
Alexandre Morozov (Rutgers University)
A biophysical approach to predicting intrinsic and extrinsic nucleosome positioning signals
17:00-18:30
Reception (Location: IPAM Lobby)

Tuesday, November 27, 2007

Morning Session

08:00-08:30
Continental Breakfast
08:30-09:30
Srinivasan Parthasarathy (Ohio State University)
Integrated Mining of Protein Interaction Networks: A Case for Ensemble Clustering
09:30-10:30
Alexander Urban (Yale University)
Integrated approaches for the analysis of complex human genomic sequence variation and its correlation to complex phenotypes
10:30-11:00
Break
11:00-12:00
Christina Leslie (Memorial Sloan-Kettering Cancer Center)
Learning predictive models of gene regulation

Afternoon Session

12:00-13:30
Lunch (on your own)
13:30-14:30
Trey G. Ideker (University of California, San Diego (UCSD))
Protein Network Comparative Genomics
14:30-15:30
Jiawei Han (University of Illinois at Urbana-Champaign)
Mining, Indexing, and Searching Graphs in Biological Databases
15:30-16:00
Coffee Break
16:00-17:00
Andrey Rzhetsky (University of Chicago)
Computational analysis of complex traits: text- and network- and phenotype-mining

Wednesday, November 28, 2007

Morning Session

08:00-09:00
Continental Breakfast
09:00-10:00
Ronen Basri (Weizmann Institute of Science)
Multiscale Edge Detection and Segmentation Algorithms for Biomedical Image Analysis
10:00-10:30
Break
10:30-11:30
Yoav Freund (University of California, San Diego (UCSD))
From microscopy images to models of cellular processes
11:30-13:00
Lunch (on your own)

Afternoon Session

13:00-14:00
Amit Singer (Yale University)
Cryo-EM and NMR Structure Determination through Eigenvectors of Sparse Matrices
14:00-14:30
Break
14:30-15:30
Leon Glass (McGill University)
Using Logical Circuits to Analyze and Model Genetic Networks
15:30-16:00
Coffee Break
16:00-17:00
Richard Bonneau (New York University)
Learning global transcriptional dynamics with the Inferelator and cMonkey

Thursday, November 29, 2007

Morning Session

08:00-08:30
Continental Breakfast
08:30-09:30
Alexander Krasnitz (Cold Spring Harbor Laboratory)
Epicenter Analysis in Cancer
09:30-10:30
Gilad Lerman (University of Minnesota, Twin Cities)
Defining functional distance using manifold embeddings of gene ontology annotations
10:30-11:00
Break
11:00-12:00
John Storey (University of Washington)
Harnessing Naturally Randomized Transcription to Infer Causal Regulatory Relationships Among Genes

Afternoon Session

12:00-13:30
Lunch (on your own)
13:30-14:30
Petros Drineas (Rensselaer Polytechnic Institute)
Identifying Ancestry Informative Markers via Principal Components Analysis
14:30-15:30
Stephen Altschul (National Center for Biotechnology Information)
Protein Sequence Database Searches Using Compositionally Adjusted Amino Acid Substitution Matrices
15:30-16:00
Coffee Break
16:00-17:00
Weixiong Zhang (Washington University in St. Louis)
Integrative computational analysis of microRNA transcriptional regulation

Friday, November 30, 2007

Morning Session

08:00-09:00
Continental Breakfast
09:00-10:00
Laxmi Parida (IBM Research)
Combinatorics and Statistics of Gene Clusters
10:00-10:30
Break
10:30-11:30
John Doyle (California Institute of Technology)
Title not available
11:30-13:00
Lunch (on your own)

Afternoon Session

13:00-14:00
Avi Ma'ayan (Mount Sinai School of Medicine, CUNY)
Graph Theory Based Querying to Identify Novel Functions of Components and Pathways in Mammalian Cells
14:00-14:30
Break
14:30-15:30
Jeffrey Morris (University of Texas M. D. Anderson Cancer Center)
Applications of Wavelet-Based Functional Mixed Models to Proteomics and Genomics Data
15:30-16:00
Coffee Break
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