Spring 2004

The First Annual RECOMB Satellite Workshop on
Regulatory Genomics

March 26th-27th, 2004
University of California, San Diego

(immediately preceding RECOMB 2004)

Sponsored by:

The recent availability of the human and mouse genomes have shown that the vast majority of the genes are almost identical between human and mouse. The differences between human and mouse most likely stem from variations in the gene regulatory networks. However, much of this regulatory network is unknown. In fact, with the tremendous success of genome sequencing efforts and the numerous complete genome sequences available, much is unknown about the regulatory networks of any of these sequenced genomes. One of the main challenges facing researchers today is deciphering the regulatory mechanisms of genes. This challenge includes detecting the transcription factor binding sites involved in regulation as well as discovering the regulatory networks.

Automatic methods for helping decipher the regulatory mechanism are crucial for understanding the regulatory network. The core of these methods are the motif-finding algorithms that can help identify regulatory elements. However, many new challenges are presented when analyzing complete genomes. These challenges include scaling to very large samples, incorporating multiple genomes, detection of weak signals and incorporating different types of genomic data such as protein localization data and gene expression.

The RECOMB Regulatory Genomics workshp plans to build upon the success of previous RECOMB satellite workshops including workshops on sequencing, comparative genomics, and SNPs.

TOPICS

Original research papers (including significant work-in-progress) or state-of-the-art surveys are solicited in all aspects of regulation including modeling and recognition of regulatory elements, identification and modeling of cis-regulatory regions, modeling the structure and function of the regulatory region, and comparative genomics of regulation.

AGENDA AT A GLANCE

Friday, March 26, 2004
8:00am - 5:30pm	Registration
8:00am - 9:00am	Continental Breakfast
9:00am - 9:45am	Trey Ideker, University of California, San Diego PathBLAST: Finding conserved pathways via protein network alignment
9:45am - 10:00am	Biological Networks Involving Metabolic Pathways and Gene Regulation: Modeling and Inference Irit Gat-Viks, Amos Tanay, and Ron Shamir
10:00am - 10:30am	Martin Tompa, University of Washington An Assessment of Algorithms for the Discovery of Transcription Factor Binding Sites
10:30am - 11:15am	Break
11:15am - 12:00pm	Michael Eisen, Lawrence Berkeley National Lab
12:00pm - 12:45pm	Jim Kadonaga, University of California, San Diego The MTE, a New Core Promoter Element for Transcription by RNA Polymerase II
12:45pm - 2:00pm	Lunch
2:00pm - 2:45pm	Rotem Sorek, Compugen and Tel Aviv University The "promoters" of splicing: Intronic sequences that regulate alternative splicing
2:45pm - 3:00pm	Predicting Genetic Regulatory Response using Classification: Yeast Stress Response Manuel Middendorf, Anshul Kundaje, Chris Wiggins, Yoav Freund, and Christina Leslie
3:00pm - 3:45pm	Ron Shamir, Tel Aviv University Revealing selection patterns in the evolution of yeast transcription regulation
3:45pm - 4:30pm	Break
4:30pm - 5:15pm	Lee Newberg, Wadsworth Center How Much is Another Mammal Worth
5:15pm - 5:30pm	Detecting Functional Modules of Transcription Factor Binding Sites in the Human Genome Thomas Manke, Christoph Dieterich, and Martin Vingron
5:30pm - 5:45pm	Illustration of a Computational Gene Characterization Approach Based on the Identification of Orthologous Clusters of Transcription Factor Binding Sites in Human Genomic Sequence. William Krivan
5:45pm - 6:00pm	PhyloGibbs: A Gibbs sampler incorporating phylogenetic information Rahul Siddharthan, Erik van Nimwegen, and Eric D. Siggia
Saturday, March 27, 2004
8:00am - 5:30pm	Registration
8:00am - 9:00am	Continental Breakfast
9:00am - 9:45am	Bing Ren, University of California, San Diego Dissecting gene regulatory networks in cancer cells
9:45am - 10:00am	Application of kernel method to reveal subtypes of TF binding motifs. Causal analysis of gene expression data. Alexander Kel, Yury Tikunov, Nico Voss, Jurgen Borlak and Edgar Wingender E.
10:00am - 10:30am	William Hayes, Astrazeneca Pharmaceutical relevance of promoter analysis
10:30am - 11:15am	Break
11:15am - 12:00pm	Hao Li, University of California, San Francisco Genomic Reconstruction of Yeast Transcription Networks
12:00pm - 12:30pm	Eran Segal, Stanford Genome-wide discovery of transcriptional modules from DNA sequence and gene expression
12:30pm - 12:45pm	Learning Regulatory Network Models that Represent Regulator States and Roles. Keith Noto and Mark Craven
12:45pm - 2:00pm	Lunch
2:00pm - 2:45pm	Terry Hwa, University of California, San Diego Combinatorial control of gene expression from simple molecular interactions
2:45pm - 3:30pm	Yitzhak Pilpel, Weizman Institute Revealing the architecture of genetic backup circuits through inspection of transcription regulatory networks
3:30pm - 4:00pm	Industry Round Table: William Hayes, Astrazeneca; Rotem Sorek, Compugen and Tel Aviv University; William Krivan, ZymoGenetics; Zohar Yakhini, Agilent; Qicheng Ma, Novartis; Jeanette Schmidt, Incyte
4:00pm - 4:30pm	Break
4:30pm - 5:15pm	Zohar Yakhini, Agilent Variation in mRNA expression levels: the role of sequence motifs and of DNA copy number
5:15pm - 5:30pm	Using expression data to discover RNA and DNA regulatory sequence motifs Chaya Ben-Zaken Zilberstein, Eleazar Eskin, Zohar Yakhini
5:30pm - 5:45pm	Parameter Landscape Analysis for Common Motif Discovery Programs Natalia Poluliakh, Michiko Konno, Paul Horton, and Kenta Nakai
5:45pm - 6:00pm	Inferring Cis-region Hierarchies from Patterns in Time-Course Gene Expression Data Vladimir Filkov and Nameeta Shah
6:00pm - 8:00pm	RECOMB Opening Reception (Westin Hotel Downtown)
Ben...

Effective Monday, April 5, each presentation and roundtable discussion will be archived and viewable on demand. Bookmark this page, or go to http://www.calit2.net/multimedia/index.html .

Local Information

--------------------------------------------------------------

2004 RECOMB Satellite Workshop on Regulatory Genomics
Registration Form

Name:  

Affiliation:

Email:

URL (optional): 

Mailing Address:

Phone Number:

Fax Number:

Category:  [ ] Student [ ] Faculty [ ] Industry [ ] Government

Conference Fee:
Before March 1st:
[ ] $150 Regular
[ ] $75  Student/Post-Doc

After March 1st:
[ ] $175 Regular
[ ] $100  Student/Post-Doc


You will receive a confirmation email within 2 business days
containing payment information.

---------------------------------------------------------------

--------------------------------------------------------------

2004 RECOMB Satellite Workshop on Regulatory Genomics
Travel Support Form

Name:  

Affiliation:

Email:

URL (optional): 

Category:  [ ] Undergraduate Student [ ] Graduate Student [ ] Post-Doc

University of California Affiliate:  [   ] Yes  [   ]  No

Geographical Location:

Brief Budget:




Reasons for Applying for Travel Support:




Did you receive travel support for RECOMB 2004:  [  ] Yes  [  ] No

Are you attending RECOMB 2004:  [  ] Yes  [  ] No

If you are attending RECOMB 2004, describe what additional costs are
needed to attend the workshop:



---------------------------------------------------------------