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2009-March Consortium Meeting

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The ENCODE and modENCODE Consortia will hold a joint meeting on March 25-27, 2009 in the Washington, DC/Bethesda, MD area. The meeting will begin around 8:30 AM on March 25 and end around 3:00 PM on March 27. This page will be updated with more information as it becomes available.

Relevant Documents
Final Agenda
List and Order of Presentations
ENCODE Production Summaries
modENCODE Production Summaries (1 of 2)
modENCODE Production Summaries (2 of 2)

Hot Topic Presentations
Masaomi Kato: Genome-scale analysis of RNA structures
Ryan McDaniell: Genome-wide identification of allele-specific and individual-specific open chromatin
Tim Reddy: Genomic variation and the interpretation of ENCODE data
Debasish Raha: Requirement of Pol II activity for transcription of Pol III genes
Pouya Kheradpour: Regulatory motifs associated with TF binding and chromatin dynamics in Drosophila and mammalian genomes
Michael Hoffman: Segway: a dynamic Bayesian network for genomic segmentation
Gary Karpen: Chromatin domain characterization in Drosophila melanogaster –a study in contrasts
John Stamatoyannopoulos: Genome-wide mapping of DNase I hypersensitive sites and cell-specific programming of gene expression
Job Dekker: A first long-range interaction map for the ENCODE regions

Integrative Analysis Presentations: modENCODE (Fly)
Jane Landolin: Integrative analysis to characterize promoters and transcripts
Manolis Kellis: Fly modENCODE data integration update
David MacAlpine: Molecular and chromosomal determinants of the Drosophila DNA replication program
Peter Kharchenko: modENCODE integration vignettes

Integrative Analysis Presentations: modENCODE (Worm)
Bob Waterston: Transplicing in C. elegans
Valerie Reinke: Multi-pronged approach to define the C. elegans transcriptome

Integrative Analysis Presentations: ENCODE
Roderic Guigo: Nucleosome positioning is a determinant of exon recognition
Ewan Birney: Small element integration
Anshul Kundaje: Integrating ENCODE tracks to predict in-vivo binding of transcription factors
Jason Ernst: Genome-wide discovery and characterization of chromatin states
Ross Hardison: ENCODE DNase hypersensitive sites cover most known erythroid regulatory regions
Alan Boyle: Fine-scale chromatin structure is revealed by genome-wide DNase-seq
Roderic Guigo: Nucleosome positioning is a determinant of exon recognition
Joel Rozowsky: Determining allele specific binding for GM12878/NA12878

Lightning Talk Presentations
Michael Lin: New and unusual protein-coding genes in 29 mammalian and 12 fly genomes
Eric Lai: Annotation of the Drosophila small RNAome
Timo Lassman: CAGE analysis
Adam Frankish: Conservation and consequences of alternative splicing in human and mouse
Brenton Graveley: modENCORE: ENCyclopedia Of drosophila RNA splicing regulatory Elements
Fabio Piano: C. elegans 3'UTRome project
Stuart Kim: Gene expression profiles at single cell resolution
Kevin Struhl: Epitope tagging of transcription factors
Qunhua Li: Evaluating the consistency of peak calling results for ChIP-seq data
Seth Frietze: A genome-wide test of the zinc finger DNA binding code
Stephen Henikoff: Genome-wide profiling of salt fractions maps physical properties of chromatin
Nick Negre: A comprehensive map of insulator elements for the Drosophila genome
Jason Leib: Exonic enrichment of H3K36me3, MES-4, and MRG-1 in C. elegans
Sara Powell: Ploidy analysis of three drosophila cell lines
John Stamatoyannopoulos: Genome-wide profiling of DNA replication time for ENCODE

Evaluating Next-Generation Sequencing Data Presentations
Ashish Agarwal: Transcriptome comparison between tiling arrays and next generation sequencing on matched worm samples towards making optimal use of arrays
Alex Dobin: Sequencing vs. arrays: fly and human transcriptomes
Roderic Guido: RGASP: RNAseq genome assesment project

NHGRI Staff Presentations
Welcome and introduction
ARRA funding opportunities
Goals of the meeting
Revamping the progress reports and milestones
Data production status update
Standards for data verification and validation
Meeting Summary

Breakout Session Reports
Chromatin and regulatory elements
Genes and transcripts
Project specific analysis discussion: ENCODE
Project specific analysis discussion: modENCODE
modENCODE DCC workshop

Other Presentations
Ewan Birney & Rick Myers: Overview of ENCODE analysis activities
Mark Gerstein & Lincoln Stein: Developing an ortholog resource
Brad Bernstein: Epigenomics roadmap activities
Edward Marcotte: Opportunities for cross-consortia interactions

Update 1-16-09
A request was sent to ENCODE PIs for a proposed list of attendees for the meeting. Responses are due to Laura Dillon by Friday, January 23.

Update 1-30-09
The meeting will be held at the Bethesda North Marriott Hotel & Conference Center. The logistics contractor for the meeting is in the process of setting up the registration website. Once the website is up, an invitation to the meeting (including the website link) will be sent to PIs for distribution to group members who will attend.

Update 2-11-09
Invitations to the meeting were sent to the ENCODE PIs to distribute to group members who will attend. The list of proposed attendees that was sent to NHGRI should be considered approved if the PI has not received a request for some group members to be placed on a waiting list.

Update 2-12-09
A solicitation for abstracts was sent to the ENCODE Consortium listserv. Abstracts are being solicitied for 3 sessions at the ENCODE-modENCODE meeting. These are a session to present new and exciting “hot topics” and findings (talk length TBD), a lightning talk session (5-minute short presentations), and a poster session. NHGRI will review the submitted abstracts to select topics for the hot topic and lightning talk sessions. Abstracts not selected for talks will be selected for the poster session. All abstracts will be e-mailed to meeting participants prior to the meeting and printed for inclusion in the meeting folders. Each abstract should include a title and a list of authors and affiliations with the name of the presenter underlined. The text of the abstract should not exceed 300 words. Abstracts are due to Julia Zhang ( by Monday, March 2.

Update 2-26-09
A request for 1-2 page production summaries from each ENCODE PI was sent to the ENCODE Consortium listserv. The purpose of the summaries is to provide an update on the output for each project, with an emphasis on the primary production activities, and to free up time at the meeting so presentations can focus on issues aside from production statistics. The summaries will be distributed to meeting participants in advance of the meeting and will be included in the meeting folders. Summaries are due to Julia Zhang ( by Monday, March 9.