RGASP |
- The RNAseq Genome
|
 |
Introduction
Following the successful
format of the EGASP
workshop in 2005, the RNAseq genome annotation assessment
project is being launched to assess the current progress of automatic
gene building using RNAseq as its primary dataset.
The main aim of the workshop is to assess the status of computational methods to map human RNAseq data, assemble them into transcripts and quantify the abundance of that transcript in particular datasets.
Transcript predictions will be evaluated against the GENCODE annotation produced as part of the ENCODE project. Special attention/assessment will be given to newly manually annotated chromosomes not previously publicly released before the workshop release.
Promising transcript predictions not covered by Gencode annotation will be validated by experimental methods
The project is open to all researchers, but places are limited.
We will also include modEncode drosophila data and would like to encourage participants working on model organisms to participate.
More details will be posted on this website.
The main aim of the workshop is to assess the status of computational methods to map human RNAseq data, assemble them into transcripts and quantify the abundance of that transcript in particular datasets.
Transcript predictions will be evaluated against the GENCODE annotation produced as part of the ENCODE project. Special attention/assessment will be given to newly manually annotated chromosomes not previously publicly released before the workshop release.
Promising transcript predictions not covered by Gencode annotation will be validated by experimental methods
The project is open to all researchers, but places are limited.
We will also include modEncode drosophila data and would like to encourage participants working on model organisms to participate.
More details will be posted on this website.
Dates
| Registration deadline: | 03.07.2009 | |
| Submission of predictions: | 21.09.2009 (Extended) | |
| Workshop days: | 10. & 11.11.2009 |
|
| Submission of predictions for second dataset: | 15.01.2010 |
Details
Data, rules and further details can be found here.
Agenda and other information for the meeting.
Workshop slides, results etc. (curr. for participants only)
Current list of participating groups (in no particular order)
- Lior Pachter, Cole Trapnell, Ali Mortazavi, Steven Salzberg, Geo Pertea, Barbara Wold (Berkeley & Caltech) USA
- Regina Bohnert, Georg Zeller, Sören Sonnenburg, Lisa Thalheim, Jonas Behr, Gunnar Rätsch (Max Planck Institut), Tübingen, Germany
- Tyler Alioto, Micha Sammeth, Paolo Ribeca, David Gonzalez, Julien Lagarde, Thomas Derrien, Roderic Guigo (CRG), Spain
- Alessandro Guffanti (Genomnia srl), Elena Brini (Genomnia srl), Armando Felsani (Genomnia srl), Giulia Maria Solda (University of Milano), Anand Santosh (DIBIT-San Raffaele), Dario Corrada (ITB-National Reseach Council), Italy
- Jeltje van Baren (WUSTL), Cole Trapnell (Berkeley), USA
- Christian Iseli, Philipp Bucher, Brian Stevenson, Armand Valsesia, Gregory Lefebvre, Heinz Stockinger, Naryttza Diaz, Giovanna Ambrosini, Jacques Rougemont (Ludwig Institute for Cancer Research and Swiss Institute of Bioinformatics) Switzerland
- Mark Gerstein lab (Yale) USA
- Mario Stanke (University of Goettingen) Germany
- Hugues Richard, Marcel H Schulz, David Weese (Max Planck Institute) Germany, Daniel R Zerbino (formerly EBI, now UCSC)
- Sean Grimmond (Institute For Molecular Bioscience), Nicole Cloonan (The University of Queensland) Australia
- Simon White, Steve Searle (Wellcome Trust Sanger Instritute) UK
- Jie Wu, Michael Zhang, Chenghai Xue (CSHL) USA
- Carrie A Davis, Alexander Dobin, Tom Gingeras (CSHL) USA
- Zefeng Zhang (BioinformaticsSolutions Inc.), Hao Lin (Univ. of Waterloo) Canada
- Victor Solovyev (University of London) UK
- Thomas Wu (Genentech) USA
Steering Committee
Jen Harrow, Wellcome Trust Sanger Institute
Tim Hubbard, Wellcome Trust Sanger Institute
Barbara Wold, CalTech
Tom Gingeras, CSHL
Roderic Guigo, CRG
Ali Mortazavi, CalTech
Mark Gerstein, Yale
Alex Reymond, Univ Lausanne
Sandrine Dudoit, Berkeley
Contact the committee.
(this is not a public mailing list)
Technical questions:
Felix Kokocinski, Wellcome Trust Sanger Institute
Analysis group:
Josep F. Abril, Genetics Dep, Universitat de Barcelona / IBUB
and many others
