DREAM News

Author Archive | dreamadmin

July 30, 2018

Call for Papers for DREAM Conference in December 2018!

This year we are inviting posters and oral presentations about past DREAM Challenges. We encourage participants to submit abstracts about their published or unpublished work on DREAM Challenges, such as the SMC Challenges, ENCODE challenge, the AZ synergy Challenge, etc. Abstracts may be either original unpublished work related to challenges or work that was published or accepted for publication in a journal previously. (Submit here)

July 30, 2018

11th Annual RECOMB/ISCB Conference on Regulatory and Systems Genomics, with DREAM Challenges

Now in its eleventh year, the RECOMB/ISCB Conference on Regulatory and Systems Genomics, with DREAM Challenges is excited to announce that it will be held again in NYC! This year we will be at NYU Langone Health December 8-10, 2018.

Call for Papers!

This year we are inviting posters and oral presentations about past Challenges. We encourage participants to submit abstracts about their published or unpublished work on past Challenges, such as the SMC Challenges, ENCODE challenge, the AZ synergy Challenge, etc.

Key Dates:

Abstract Submission for Oral Presentation & Poster deadline: Monday, September 24, 2018
Author notifications will occur on or around Monday, October 15, 2018

Late Breaking Poster deadline: Monday, October 15, 2018
Author notifications will occur on or around Monday October 29, 2018

Submit here

May 17, 2018

2018 Publications

Guinney J, Saez-Rodriguez J.; Alternative models for sharing confidential biomedical data.; Nat Biotechnol. 2018 May 9;36(5):391-392. doi: 10.1038/nbt.4128.

AY Lee, et al,; Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection.; Genome Biol. 2018 Nov 6;19(1):188. doi: 10.1186/s13059-018-1539-5.

CI Cooper Valection: design optimization for validation and verification studies.
BMC Bioinformatics. 2018 Sep 25;19(1):339. doi: 10.1186/s12859-018-2391-z.

Listing of DREAM publications on Google Scholar
https://scholar.google.com/citations?user=uGmMpmoAAAAJ&hl=en

 

March 19, 2018

Register NOW for DREAM Challenges and EPIDEMIUM@RECOMB in Paris 2018

Registration is open for DREAM Challenges and EPIDEMIUM@RECOMB April 19-20.   The meeting will focus on proteogenomics, single cell systems biology and cancer epidemiology, and how crowdsourced science, data sharing and a culture of collaboration can help advance research in these fields. We will highlight the solutions of the top performing strategies in the Epidemium program in cancer epidemiology and the recent NCI-CPTAC Proteogenomics DREAM Challenge. We will also brainstorm as a community on the possibility of organizing a DREAM challenge on Single Cell Systems Biology, and have a RAMP Challenge Hands on Session.  The RAMP challenge will be divided into an initial individual phase followed by a collaborative phase of discussion. Solutions will be shown instantly in a leaderboard. Ensemble predictions will also be performed during the RAMP workshop.  Pre-Sign up for RAMP Session.  (30 participants needed to preregister to reserve the session.)  (Learn more)

January 17, 2018

Winners in the DREAM Parkinson’s Disease Digital Biomarker Challenge Announced

Sage Bionetworks in Collaboration with The Michael J. Fox Foundation Announce Winners in the DREAM Parkinson’s Disease Digital Biomarker Challenge. Sage Bionetworks announced today the results of the Parkinson’s Disease Digital Biomarker (PDDM) DREAM challenge, an open crowd-sourced research project designed to benchmark the use of remote sensors to diagnose and track Parkinson’s disease (PD). The winners of this Challenge developed methods that are 38% better than previous models at detecting Parkinson’s disease from a simple walk and balance test (read more)

November 13, 2017

New DREAM Video

Calling all DREAMers…  The DREAM team is developing a video project about DREAM and our community, and needs your help.  We need Selfies of you holding signs that say either  “DREAM Challenges”  or “DREAM” or “Wisdom of the Crowd” .  Take a sheet of white unlined copier paper and write as big as you can with a marker (so it is legible).  You can take one selfie with one message or three.   Then we will include them in the video of our community of DREAMers adding to the Wisdom of the Crowd.  (12/6/17 – Thanks for your help.. this is done.. Please see video on the DREAM home page or on Youtube – https://youtu.be/PrAA-DnTQ7w)

October 17, 2017

DREAM Challenges and EPIDEMIUM@RECOMB in Paris 2018

DREAM Challenges and EPIDEMIUM@RECOMB in Paris
 – April 19-20, 2018

The meeting will focus on proteogenomics, single cell systems biology and cancer epidemiology, and how crowdsourced science, data sharing and a culture of collaboration can help advance research in these fields. We will highlight the solutions of the top performing strategies in the Epidemium program in cancer epidemiology and the recent NCI-CPTAC Proteogenomics DREAM Challenge. We will also brainstorm as a community on the possibility of organizing a DREAM challenge on Single Cell Systems Biology.

December 6, 2016

DREAM 11- 2016 All-Stars

AstraZeneca-Sanger Drug Combination Prediction DREAM Challenge

Sub-Challenge 1A

Best Performer:
Team Guan Lab – Yuanfang Guan, University of Michigan (USA)

Tied 2nd Place:
Team: North Atlantic
az-northatlantic

Russ Wolfinger, SAS Institute Inc. (USA); Tin Nguyen & Sorin Draghici, Advaita Corporation and Wayne State University (USA); and Bence Szalai, Gábor Turu, Miklós Cserző, & László Hunyady: Semmelweis University, and MTA-SE Laboratory of Molecular Physiology (Hungary)

Team: Mikhail Zaslavskiy
Mikhail Zaslavskiy

Sub-challenge 1B

Best Performer:
Team Guan Lab – Yuanfang Guan, University of Michigan (USA)

Tied 2nd Place:
Team: DMIS
az-teamdimsjpg

Jaewoo Kang, Minji Jeon, Sunkyu Kim, Sungjoon Park, Heewon Lee, Hyeokyoon Chang, Minhwan Yu, and Kwanghun Choi, Korea University, (Korea)

Team: North Atlantic
Russ Wolfinger, SAS Institute Inc. (USA); Tin Nguyen & Sorin Draghici, Advaita Corporation and Wayne State University (USA); and Bence Szalai, Gábor Turu, Miklós Cserző, & László Hunyady: Semmelweis University, and MTA-SE Laboratory of Molecular Physiology (Hungary)

Team Puruguraming
Amin Allam, KAUST (Saudi Arabia)

Sub-challenge 2

Best Performer:
Team Guan Lab – Yuanfang Guan, University of Michigan (USA)

Team: North Atlantic
Russ Wolfinger, SAS Institute Inc. (USA); Tin Nguyen & Sorin Draghici, Advaita Corporation and Wayne State University (USA); and Bence Szalai, Gábor Turu, Miklós Cserző, & László Hunyady: Semmelweis University, and MTA-SE Laboratory of Molecular Physiology (Hungary)

 Disease Module Identification DREAM Challenge –

Sub-Challenge 1

Best Performer:
Team Tusk:
disease_module-tusk

Jake Crawford, Junyuan Lin, Xiaozhe Hu, Benjamin Hescott, Donna Slonim, & Lenore Cowen; Tufts University (USA)

Honorable Mentions:

Team Aleph:
disease_module-aleph
Sergio Gómez, Manlio De Domenico, Alex Arenas.

Team: Causality:
Weijia Zhang, Thuc Le, Taosheng Xu, Junpeng Zhang, Lin Liu, Jiuyong Li.

Team: PureMichigan:
Minjun Kim, Yuanfang Guan, University of Michigan (USA).

Team: ShanHeLab:
Dong Li, Benjapun Kaveelerdpotjana, Jiarui Zhou, Ning Shi, Weiqi Chen, Shan He.

Team: TeamDMIS:
Sungjoon Park, Wonho Shin, Minji Jeon, Sunwon Lee, Jaewoo Kang, Korea University, (Korea)

Team: Tianle Ma:
Tianle Ma.

Team: TripleAHC:
Hatem Hamza, Anton Heijs, Antonis Loizou, Andra Waagmeester, Christine Chichester.

Sub-Challenge 2

Team Tsurumi-Ono:
disease_module-tsunami
Artem Lysenko, Piotr J. Kamola, Keith A. Boroevich, & Tatsuhiko Tsunoda; RIKEN Center for Integrative Medical Sciences (Japan)

ENCODE-DREAM in vivo Transcription Factor Binding Site Prediction Challenge

Conference Round

Team: autosome.ru
encode_autosome
Vsevolod Makeev, Andrey Lando, Grigory Sapunov, Ilya Vorontsov, Ivan Kulakovskiy, Valentina Boeva, & Irina Eliseeva; Russian Academy of Sciences; Moscow Institute of Physics and Technology; and Intento, (Russia) and Institut Cochin (France)

Team: J-Team
encode-j-team
Jens Keilwagen, Stefan Posch, & Jan Grau; Federal Research Centre for Cultivated Plants; and Martin Luther University Halle-Wittenberg  (Germany)

Team HINT
encode-hintjpg
Eduardo G. Gusmao, Zhijian Li, and  Ivan G. Costa; Aachen University Medical School  and RWTH Aachen University(Germany) Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health (USA)

ICGC-TCGA-DREAM Somatic Mutation Calling Challenge- Tumor Heterogeneity and Evolution (SMC-HET)

Team: GISL
smchet_gisl
Kaiyi Zhu, Tai-Hsien Ou Yang and Dimitris Anastassiou; Columbia University (USA)

Team: GuanLab
smchet_guan-lab-pg
Hongjiu Zhang and Yuanfang Guan; University of Michigan, (USA)