Author Archive | dreamadmin

November 8, 2019

DREAM Challenges Announces Changes in its Leadership that Support a Rich Future in Open Benchmarking


SEATTLE – DREAM Challenges has announced changes to its governance and leadership to reflect its vision for future growth. DREAM is a volunteer organization of more than 30,000 solvers focused on crowd-sourced challenges to benchmark informatic algorithms in biomedicine. The peer-based governance process has been formalized by charter and will be led by a volunteer board of directors, with a rotating chair position. Dr. Justin Guinney, VP of Computational Oncology at Sage Bionetworks, is the new chair.

Sage Bionetworks has partnered with DREAM since 2013, providing the technology platform, governance protocols, and data science expertise that underpin DREAM Challenges. The DREAM methodology has already been adopted by other groups that host challenges. By assuming a key role in the charter, Sage is making a clear commitment to upholding and growing DREAM’s mission to enable collaborative science.

DREAM was founded in 2006 by Dr. Gustavo Stolovitzky, who announced this week at the 14th DREAM Challenges Conference in New York that he would be stepping back from actively leading the organization, though he will remain involved. Dr. Stolovitzky, the Director of the IBM Translational Systems Biology and Nanobiotechnology Program at IBM’s Thomas J. Watson Research Center, will continue to support the mission of DREAM as Chair Emeritus and DREAM Board Director.

“I’m proud of the community we’ve created with the DREAM Challenges,” said Dr. Stolovitzky. “Our approach has confirmed that data sharing and collaborative science is a powerful methodology not only for scientific research but also for the rigorous evaluation of algorithmic performance that is necessary for reproducible science. There is much to discover yet and it will be a pleasure to watch DREAM evolve under Justin Guinney’s creative leadership.”

Dr. Guinney, who has served on the DREAM board since in 2013, will work closely with Dr. Stolovitzky and the board to develop a vision for how to extend the reach of DREAM Challenges to untapped domains that are poised to benefit from crowd-sourced solutions. Dr. Guinney’s contributions to DREAM have focused on advanced predictive modeling in diagnostic mammography screening and drug combination therapy; prognostic modeling in breast and prostate cancer and multiple myeloma; and, recently, a benchmarking challenge using electronic healthcare records.

“The power of DREAM is the power to connect,” said Dr. Guinney, whose work at Sage Bionetworks focuses on integrative data analysis for prognostic and predictive modeling of cancer outcomes and response to therapy. “Building on the foundation of our past successes, DREAM will continue to serve its mission of connecting individuals and teams with data and algorithms to tackle complex biomedical questions.”

Under Dr. Stolovitzky’s leadership, DREAM evolved into a model of how to use crowdsourcing and open science in biomedicine, with first-of-its-kind Challenges that led to scientific insights in a wide range of research topics including biological network inference, cancer genomics and pharmacogenomics, predicting disease progression, and medical imaging among others. DREAM has launched more than 60 challenges that have engaged and touched the careers of thousands of scientists from dozens of institutions across the public and private sectors around the world.

“Having been involved with DREAM all these years, it’s an honor to help usher in the next generation of Challenges,” said Dr. Guinney.

In addition to Drs. Guinney and Stolovitzky, other board directors include: Dr. Laura Heiser, Oregon Health Sciences University; Dr. Paul Boutros, University of California, Los Angeles; Dr. James Costello, University of Colorado; Dr. Pablo Meyer, IBM; and Dr. Julio Saez-Rodriguez, Heidelberg University. More information about the DREAM leadership and governance can be found at www.dreamchallenges/people.


DREAM (Dialogue on Reverse Engineering and Assessment Methods) Challenges emerged in 2006 to leverage the wisdom of the multidisciplinary scientific community to solve fundamental and difficult questions in biomedical research. DREAM’s methodology is based on crowd-sourcing scientific Challenges, fostering open and collaborative research, and promoting data sharing. In 2013, DREAM partnered with Sage Bionetworks, which developed and administers the technology platform that underpins DREAM Challenges.


Sage Bionetworks is a nonprofit biomedical research and technology development organization that was founded in Seattle in 2009. Our focus is to develop and apply open practices to data-driven research for the advancement of human health. Our interdisciplinary team of scientists and engineers work together to provide researchers access to technology tools and scientific approaches to share data, benchmark methods, and explore collective insights, all backed by Sage’s gold-standard governance protocols and commitment to user-centered design. Sage is a 501c3 and is supported through a portfolio of competitive research grants, commercial partnerships, and philanthropic contributions.

Contact: Hsiao-Ching Chou

June 18, 2019

12th Annual RECOMB/ISCB Conference on Regulatory and Systems Genomics, with DREAM Challenges

November 4 – 6, 2019 New York, NY

This year’s RECOMB/ISCB Conference on Regulatory and Systems Genomics, with DREAM Challenges will be held at Memorial Sloan Kettering Cancer Center, in New York City, New York on November 4-6, 2019.

Now in its twelfth year, the RECOMB/ISCB Conference on Regulatory and Systems Genomics with DREAM Challenges, is one of the premier annual meetings in the fields of regulatory genomics, systems biology, and network visualization. This multidisciplinary conference brings together both computational and experimental researchers from across the world to discuss recent discoveries about genomic and molecular regulatory networks as well as innovative, integrative methods for developing a systems-level understanding of biological activity.

May 30, 2019

Idea Competition Winner Announced for the CTSA Program

The CD2H Idea Competition for the CTSA Program is pleased to announce the winner of the Idea Challenge Competition: University of Alabama, Birmingham “Automated Scoring of Radiographic Damage in Rheumatoid Arthritis” (PI S. Louis Bridges). This will be developed into an upcoming DREAM Challenge. (read more)

February 26, 2019

PrecisionFDA and NCI CPTAC Announce the Best Performers in Multi-omics Sample Mislabeling Big Data Challenge

PrecisionFDA and the National Cancer Institute’s (NCI) Clinical Proteomic Tumor Analysis Consortium (CPTAC) (in coordination with DREAM Challenges) are pleased to announce the Best Performers in the first-ever Crowdsourced Multi-omics Sample Mislabeling Big Data Challenge. This unique challenge utilized proteogenomic datasets generated by CPTAC and clinical annotation information. A total of 230 submissions from participants around the globe were received and evaluated. Subchallenge 1 focused on the development of next-gen computational models for detecting mislabeled samples using proteomic and clinical data generated by CPTAC, while Subchallenge 2 took a step further, aiming to identify and correct mismatched samples with one data type mislabeled among three data types (clinical, transcriptomic, and proteomic data). Visit us to learn more about this big data computational multi-omics challenge and its best performers and come here them their findings at  DREAM Challenges@RECOMB 2019. (learn more)

January 31, 2019

Announcing Agenda for DREAM Challenges@RECOMB 2019

Join us at this years DREAM Challenges@RECOMB workshop on May 4, 2019 in Washington, DC at George Washington University.  This years’ workshop has two main objectives. The first objective is to present the final results of two recent Challenges: the FDA/NCI-CPTAC Multi-omics Enabled Sample Mislabeling Correction Challenge and the ICGC-TCGA DREAM Somatic Mutation Calling – RNA Fusion Detection Challenge. The second objective is to foster an in-depth dialogue between various big-data initiatives being carried out by different agencies in the US Federal Government (such as NCI and NASA) and the scientific community, to explore the role that crowd-sourced Challenges can play in increasing the creative use of data in big-data projects. For this we have invited administrators and scientists leading big data projects to present talks focusing on what these initiatives are doing programmatically and scientifically. This will be followed by a panel discussing how each of these initiatives could benefit by crowd-sourcing their data through scientific challenges. After the panel we will break into groups and work on potential challenges of relevance to these programs. The day should provide an incentive for large-scale data initiatives to leverage crowdsourced challenges as a strategy for enhanced data use by the community and an overview on the process of challenge organization from inception to results. (Learn more)

January 31, 2019

DREAM Challenges@RECOMB 2019


The 2019 DREAM Challenges@RECOMB workshop was held on May 4, 2019 in Washington, DC at George Washington University.  This years’ DREAM Challenges@RECOMB workshop had two main objectives, first to present the final results of two recent Challenges; and second to foster an in-depth dialogue between big-data initiatives being carried out by different agencies in the US Federal Government and the scientific community and explore the role of crowd-sourced Challenges in increasing the use of their data.

January 14, 2019

2019 Publications

Ellrott, K, et al; Reproducible biomedical benchmarking in the cloud: lessons from crowd-sourced data challenges: Genome Biology: volume 20, Article number: 195 (2019): doi.org/10.1186/s13059-019-1794-0

Choobdar, S et al; Assessment of network module identification across complex diseases; Nature Methods; volume 16, pages 843–852; (2019) DOI:10.1038/s41592-019-0509-5

Menden, M, et al; Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen; Nature Communications; volume 10, Article number: 2674 (2019);  DOI: 10.1038/s41467-019-09799-2

Kueffner R et al, Stratification of amyotrophic lateral sclerosis patients: a crowdsourcing approach.; Sci Rep. 2019 Jan 24;9(1):690. doi: 10.1038/s41598-018-36873-4.

Keilwagen, J, Posch S and Grau J; Accurate prediction of cell type-specific transcription factor binding; Genome Biology; 2019; 20:9; DOI:10.1186/s13059-018-1614-y

Davis, S et al, Leveraging crowdsourcing to accelerate global health solutions; Nature Biotechnology (2019); DOI:10.1038/s41587-019-0180-5

Listing of DREAM publications on Google Scholar

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)