CAGI3 Conference

The conference to discuss the outcome of the 2012-13 CAGI experiment was held at the Max Planck Institute for Molecular Genetics in Berlin, Germany on 17-18 July 2013 (the two days preceding the ISMB 2013 SIGs). 

As with the previous conferences, the aim of this CAGI Conference was to disseminate the results of the most recent CAGI experiment and assess our collective ability to make accurate and meaningful predictions of phenotypes from genomic information. CAGI assessors and selected predictors gave the majority of the talks at the conference, with significant time allocated for discussions.

Acknowledgements

We are most grateful to Professor Martin Vingron for agreeing to act as co-chair and to host the meeting at his home institute. Funding for this conference was made possible (in part) by R13 HG006650 from the National Human Genome Research Institute. The views expressed in written conference materials or publications and by speakers and moderators do not necessarily reflect the official policies of the Department of Health and Human Services; nor does mention by trade names, commercial practices, or organizations imply endorsement by the U.S. Government.

Logistics, Accommodation and Transportation

For detailed information see logistics, accommodation and transportation

Conference Program

Slides from the CAGI conference: registered users only, limited by CAGI Data Use Agreement

17 July 2013

9:00am: Registration and breakfast

10:00am: Welcome and Introduction to CAGI 

                 Steven E. Brenner, University of California, Berkeley

                 John Moult, University of Maryland

10:20am-11:10am: Splicing session

Session chair: Steve Mount, University of Maryland

10:20am: Introduction from the session chair

                 Steve Mount, University of Maryland

10:25am: Data provider talk & Assessment 

                 Jeremy Sanford, University of California, Santa Cruz

10:45am: Predictor talk 

                  Adam Frankish, Wellcome Trust Sanger Institute

10:55am: Predictor talk 

                  Sean Mooney, The Buck Institute

11:05am: Overall prediction comments and conclusions

11:10am: Coffee break

11:40am-1:00pm: p16 session

Session chair: Silvio Tosatto, University of Padua

11:40am: Data provider talk 

                  Maria Chiara Scaini, Immunology and Molecular Oncology Unit, IOV

11:55am: Assessment 

                  Silvio Tosatto, University of Padua

12:25pm: Predictor talk 

                  Panagiotis Katsonis, Baylor College of Medicine

12:35pm: Predictor talk 

                  Emidio Capriotti, University of Alabama, Birmingham

12:45pm: Overall prediction comments and conclusions

1:00pm: Lunch

2:00pm-3.00pm: MRN session

Session chair: Rachel Karchin, Johns Hopkins University

2:00pm: Introduction from the session chair

                Rachel Karchin, Johns Hopkins University

2:05pm: Data provider and Assessment

                Sean Tavtigian, University of Utah

2:30pm: Predictor talk 

                Ronald Dunbrack, Fox Chase Cancer Center

2:40pm: Overall prediction comments and conclusions

3:00pm-4:30pm: FCH & HA session

Session Chair: Tim Hubbard, Wellcome Trust Sanger Institute

3:00pm: Introduction from the session chair

                Tim Hubbard, Wellcome Trust Sanger Institute

3:05pm: Data provider talk 

                Angel Mak, University of California, San Francisco

3:15pm: Assessor talk 

                Shamil Sunyaev, Harvard University

3:40pm: Predictor talk 

                Lipika Ray, University of Maryland

3:50pm: Predictor talk 

                Emanuela Leonardi, University of Padua 

4:00pm: Predictor talk 

                Yanay Ofran, Bar-Ilan University 

4:10pm: Predictor talk 

                Nathaniel Pearson, Ingenuity Systems 

4:20pm: Overall prediction comments and conclusions

4:30pm-5:30pm: BRCA session

Session Chair: Roland Dunbrack, Fox Chase Cancer Center

4:30pm: Data provider talk (slides included in BRCA assessment slides)

                Robert Nussbaum, University of California, San Franc

4:50pm: Assessor talk 

                Roland Dunbrack, Fox Chase Cancer Center

5:10pm: Overall prediction comments and conclusions

5:30pm: Coffee break

6:00pm: Outlook and prospects for informatics in cancer genomics

                Discussion chair: Julian Gough, University of Bristol

6:30pm: Reception

8:00pm: Group dinner at Alter Krug

                Königin-Luise-Straße 52

                14195 Berlin, Germany

18 July 2013

9:00am: Breakfast

10:00am-1:20am: Crohn's Disease session

Session chair: Stephen Yee, University of California, Berkeley

10:00am: Introduction from the session chair

                  Stephen Yee, University of California, Berkeley

10:05am: Assessment 

                  Alexander Morgan, Stanford University

10:35am: Predictor talk 

                  Manuel Giollo, University of Padua

10:45am: Predictor talk 

                  Predrag Radivojac, University of Indiana, Bloomington 

10:55am: Predictor talk 

                  Pietro Di Lena, University of Bologna

11:05am: Overall prediction comments and conclusion

11:20am: Coffee break

11:55am-12:45pm: riskSNPs session

Session chair: John Moult, University of Maryland

11:55am: Data provider talk & Assessment 

                  John Moult, University of Maryland

12:15pm: Predictor talk (slides included in riskSNPs assessment slides)

                  Christopher Yates, Imperial College London

12:20pm: Predictor talk 

                  Steve Mount, University of Maryland 

12:30pm: Overall prediction comments and conclusions

12:45pm: Lunch

1:45pm: Keynote talk: The future of genomic medicine in the UK

                Tim Hubbard, Wellcome Trust Sanger Institute

2:20pm: Structure vs. evolution for variant interpretation

                Discussion chair: Yana Bromberg, Rutgers University

2:40pm: Poster session and refreshments

4:10pm-5:30pm: PGP session

Session chair: Sean Mooney, The Buck Institute

4:10pm: Data provider talk 

                Madeleine Price Ball, Harvard University & The Personal Genome Project

4:25pm: Assessment 

                Sean Mooney, The Buck Institute

4:50pm: Predictor talk 

                Rachel Karchin, Johns Hopkins University

5:00pm: Predictor talk 

                Mary Wahl, Harvard University

5:10pm: Overall prediction comments and conclusions

5:30pm: What did we learn?

                Discussion chairs: Steven Brenner and John Moult

6:00pm: The future of CAGI and publication plans

                Discussion chairs: Steven Brenner and John Moult