Wednesday, November 15
11:00 Registration
1:00 Welcome – Organizers: Kris Gunsalus, David Hill, Fritz Roth, Marian Walhout

1:15 Session I: Keynote I
Robert Waterston (University of Washington)
Automated gene expression analysis at the single cell level in C. elegans

2:00 Session I: Transcriptional Networks
Chair: David Hill (CCSB/DFCI)
Tim Hughes (University of Toronto) – Cracking the second genetic code
Susan Celniker (Berkeley University) – Functional genomics: Gene expression and transcription networks in Drosophila
Marian Walhout (UMass Med) – Transcription factor modularity in a gene-centered C. elegans protein-DNA interaction network

3:30 Coffee break

4:00 Session III: ORFeomes
Chair: Gary Temple (NIH/NHGRI)
Kourosh Salehi-Ashtiani (DFCI) – Update on the CCSB ORFeome initiatives
Kris Gunsalus (NYU) – Toward an encyclopedia of C. elegans 3'UTRs and their regulatory elements
Joseph Ecker (Salk Institute, San Diego) – Growing a parts list for plant systems biology studies

5:30 Reception

6:15 Session IV: Keynote II
Michael Snyder (Yale University)
Analyze this and that: Genomes and proteomes

7:15 Dinner and Poster Session (Dinner will be provided)

Thursday, November 16
8:30 Session I: Interactomes
Chair: Jean-François Rual (CCSB/DFCI)
Huda Zoghbi (Baylor College of Medicine) – Phenotype-based interactome to study inherited ataxias
Irma Lemmans (Ghent University) – The MAPPIT tooldbox: new strategies for the analysis of molecular interactions in mammalian cells
Xavier De Bolle (University of Namur (FUNDP)) – Interspecies interactomic approach for the identification of bacterial effectors

10:00 Coffee Break

10:30 Session II: Systems and Circuits
Chair: Marian Walhout (UMASS Med)
Peter Sorger (MIT) – Analyzing life-death decisions in human cells using a systems approach
Siobhan Brady (Duke University) – A high resolution spatiotemporal gene expression map of the Arabidopsis root
Alex Van Oudenaarden (MIT) – Identification of biological networks using periodic stimuli

12:00 Lunch and poster session (Lunch will be provided)

1:30 Session III: Cancer and Disease Networks
Chair: Michael Cusick (CCSB/DFCI)
Ed Harlow (HMS) – Functional screens in human tumor cells
Muhammed Yildirim (DFCI) – Drug target network
Bryan Miller (University of Toronto) – An integrated high-throughput approach to investigate the Wnt signaling pathway

3:00 Coffee Break

3:30 Session IV: Integration and Modeling
Chair: Troy Moore (Open Biosystems)
Rich Bonneau (NYU) – The human proteome folding project and the inferelator
Sue Rhee (Stanford University)–Generating benchmark datasets from the literature for facilitating the analyses of large-scale data in Arabidopsis
Mark Gerstein (Yale University) – Understanding protein function on a genome-scale using networks

5:00 Reception

5:45 Session V: Keynote III
Brenda Andrews (University of Toronto)
Systematic yeast genetics to explore biological pathways, gene toxicity and kinase targets

Friday, November 17
8:30 Session I: Emerging Technologies
Chair: Jim Hartley (SAIC/NCI)
David Weitz (Harvard University) – Microfluidics for high-throughput analysis of molecular and cellular bioassays
Job Dekker (UMASS, Worcester) – Mapping chromatin interaction networks
Steve Elledge (HMS) – Genome-wide shRNA libraries and recombination cloning methods

10:00 Coffee Break

10:30 Session II: Disrupting Nodes and Networks
Chair: Kris Gunsalus (NYU)
Guri Giaever (University of Toronto) – Chemogenomic profiling: resolving essential gene function and genetic pathways
Fritz Roth (HMS) – Systematic analysis of epistasis applied to DNA repair in S. cerevisiae
Andrew Fraser (Wellcome Trust Sanger Institute) – RNAi screens to examine genetic interactions in C. elegans development

12:00 Lunch Break (Lunch will not be provided)

2:00 Session III: Genetic Interaction Networks
Chair: Marc Vidal (CCSB/DFCI)
Jonathan Weissman (UCSF) – Biology without bias: functional insights from high-resolution genetic interaction maps
Anna Lee (McGill University) – Statistical models for predicting aggravating and buffering genetic interactions in C. elegans
Jef Boeke (Johns Hopkins Medical Institutions) – New tricks with microarrays

3:30 Coffee Break

4:00 Session IV: Regulatory Networks
Chair: Job Dekker (UMASS, Worcester)
Dana Pe'er (Columbia University) – Genetic variation and regulatory networks: Mechanisms and complexity
Frank Holstege (UMC Utrecht) – Understanding regulatory circuitry
Corey Nislow (University of Toronto) – A complete genome-wide map of nucleosome positions
Yoshihide Hayashizaki/Jun Kawai(Riken) – The RNA impact on the central dogma: The road to knowledge goes through the RNA continent

5:30 Posters and Reception

6:15 Dinner (Dinner will be provided)

Saturday, November 18
8:30 Session I: Network modeling
Chair: Fabio Piano (NYU)
Ed Marcotte (University of Texas) – Predicting disease outcomes and developmental defects in C. elegans
Serafim Batzoglou (Stanford University ) – Models and algorithms for genomic sequences, proteins, and networks of protein interactions
Harmen Bussemaker (Columbia University) – Data-driven biophysical modeling of gene expression regulation by DNA and RNA binding factors

10:30 Coffee Break

11:00 Session II: Systems II
Chair: Fritz Roth (HMS)
Olga Troyanskaya (Princeton University) – Understanding and modeling diverse biological data: from measurements to biology
Federico De Masi (BWH) – High throughput analysis of transcription factor complexes’ DNA specifities using protein binding microarrays
Marc Vidal (DFCI/HMS) – False false positives

1:00 Wrap-up

Thank you to our 2006 Sponsors

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