DREAM Challenges
July 27, 2015

Participant Stories

Participant DREAM Challenge Stories – Our “Wall of DREAMers

We asked DREAM Challenge Community – Participants and Organizer –  to share with us their experiences with the DREAM Challenges over the years.  This “Wall of DREAMers” has pretty cool examples of our DREAM Challenges’ community at work using DREAM Challenges for education and research.

Daniel Marbach

Daniel MarbachIn the first edition of the DREAM challenges in 2007, I was a participant and best performer. Subsequently, I designed and led three editions of the DREAM network inference challenge (2008, 2009, 2010). Currently, I’m co-leading the DREAM gene essentiality prediction challenge. My involvement with DREAM has been a central part of my PhD thesis and postdoctoral work. I will continue my engagement with DREAM in the future to help promote open and collaborative science through crowdsourced challenges. Through my involvement with DREAM I changed my research focus from trying to show that my own methods work best, towards unbiased method assessment and creation of useful resources for the community. This work led to several highly cited papers that helped advance my academic career.

Prostate Cancer Challenge Team Stories

The Prostate Cancer DREAM Challenge has been highlighting the top performing teams at the end of each leaderboard rounds. To learn more about these teams we asked a few questions about their experiences with the DREAM Challenge. These profiles bring names and faces of this part of the DREAM Community to life. (Read more)

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Teams – Brainstrom, UNC BIAS, TYTDreamChallenge

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Teams- Niels Hansen, Clinical Persona, Jeevomics

jayhawks_group_pic2ABavarianDreamteam-Simon

Teams- Jayhawks, A Bavarian dream, Team Simon

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Teams – Jing Lu and Yuting Ma

Keep up to date with the latest leaderboard progress here

Kevin Yip

When I participated in the DREAM3 in silico network reconstruction challenge, I had very little experience in reconstructing TF-regulatory networks (I was focusing on protein-protein interaction networks at that time). Given the many sophisticated methods existing at that time, I just hoped to participate and get some experience in this topic. However, perhaps because I was new to this topic, my method was apparently quite different from the other methods, and it seemed to put more emphasis on a new type of features (expression change due to perturbation) than the other methods, which turned out to be very useful. It has helped me to always ask if there are better features to use or better ways to use the existing features before drilling deep into improving subtle details of existing methods. I think this experience has guided my way to dealing with new problems.

DREAM Participant 2008 / 2009 / 2010 / 2013

The DREAM challenges have provided a platform to understand network inference algorithm behaviors and experimental data characteristics, unlikely to be as productive if done by individual researchers or labs. This provides an opportunity to evaluate ones work more objectively, in addition to the peer-review system.

DREAM Challenges have greatly influenced the research activities in our lab. We studied the performance of our algorithms in DREAM3,4,5 for their inherent limitations. This led to the design of a novel algorithm in 2010 now called FunChisq that claimed a best performer in DREAM8 network inference challenge. Without DREAM challenges, it would have been unlikely for us to invent the algorithm and even more unlikely to appreciate its power on diverse experimental data.

DREAM Participant 2010 & 2011

Thanks to the DREAM challenge on PBM data I got acquainted to the data, and more than half of my PhD thesis was on this technology and the field of high-throughput. Through the DREAM challenge I got familiar with protein binding microarrays. Analyzing the data of this technology was more than half of my PhD thesis.

Alex Williams

alex-williamsAlex is a research technician in Eve Marder’s lab at Brandeis University. His research interests are in computational neuroscience. Alex’s work examines how neurons maintain stable activity patterns over long time periods in spite of comparatively rapid protein turnover.

Alex Williams is a member of Team Whole-Sale Modelers – winners of the Whole Cell Parameter Estimation Challenge. Professor Markus Covert from Stanford, who co-sponsored this challenge, was so impressed with Team Whole-Sale Modelers’ solutions to the challenge that he has written Alex a recommendation for graduate school in the fall of 2014.

Wei-Yi Cheng

wei-yi-chengWei-Yi Cheng (right) along with Professor Dimitris Anastassiou (left) and Tai-Hsien Ou Yang (middle) won the DREAM7 Breast Cancer Prognosis Challenge (BCC). Wei-Yi and Professor Anastassiou have gone on to work as part of the TCGA Pan Cancer group exploring their Attractor Metagenes in these cohorts of patients. They have shown that these sets of strongly co-expressed genes are present with very little variation across many cancer types and appear to be associated with specific attributes of cancer.

Since winning the BCC Challenge as part of the Anastassiou lab, Wei-Yi has since been recruited to join Eric Schadt at the Mount Sinai School of Medicine (MSSM) Institute for Genomics and Multiscale Biology as a research scientist.

Andre O. Falcao

andre-falcaoProfessor Andre Falcao was a participant in the recently completed NIEHS-NCATS-UNC DREAM Toxicogenetics Challenge, along with his teammate Ana Teixeira. Professor Falcao was an active participant throughout the challenge both through submission to the real time leaderboards as well as by providing feedback on the community forum. He and others brought up valid criticisms regarding the scoring metrics that were being used for a portion of the challenge.

Professor Falcao now has taken a leadership role in the planning of the The Rheumatoid Arthritis Responder Challenge, showing how DREAMers can transition from participants to organizers.