In February 2013, Sage Bionetworks merged efforts with the Dialogue on Reverse Engineering Assessment and Methods (DREAM) project to run Challenges that activate collaborative teams of scientists to work on biological and translational medicine discoveries. In June 2013, we launched three DREAM8 Challenges that completed in the fall, and in November 2013 we launched three DREAM8.5 Challenges that will complete in Summer 2014 (read more about the DREAM8 and DREAM8.5 Challenges). You can find much more information about DREAM available on the DREAM website.

The Dialogue on Reverse Engineering Assessment and Methods (DREAM) project, founded in 2006 by Andrea Califano (Columbia University) and Gustavo Stolovitzky (IBM), was originally conceived as an initiative to advance the nascent field of network biology through the organization of Challenges on network reconstruction and pathway inference. Since the first set of network inference challenges of 2007 (DREAM2) the concept of using collaborative-competitions as a vehicle to carry on a meaningful dialogue in the computational biology community has evolved significantly. In 2012, the last DREAM7 project featured four powerful challenges of which one was on network biology and the other three dealt with three important problems in translational medicine. With the experience gathered by the launching of 24 successful challenges over the past five years, the “Challenge” concept has reached a status of legitimacy and maturity. The DREAM Challenges have brought rigor in the process of verification of computational methods, have enabled the democratization of different kinds of biological data, and have facilitated the collaboration of dozens of research teams. This success has triggered considerable interest by different government institutions and private organizations in working with DREAM to engage distributed teams to solve tough computational problems in biomedical research.

GustaGustavovo Stolovitzky
Leader of DREAM Challenges
Dr. Stolovitzky currently leads IBM’s Functional Genomcis and Systems Biology Group and is the Director (and a co-Founder) of the DREAM Initiative.   Dr. Stolovitzky received his M.Sc. in Physics from the University of Buenos Aires (1987) and his Ph.D. in Mechanical Engineering from Yale University (1994), which awarded him the Henry Prentiss Becton Prize for Excellence in Engineering and Applied Sciences. In 1998 he joined the IBM Computational Biology Center where he is currently the manager of the IBM Functional Genomics & System Biology Group. He also holds a position as an Adjunct Associate Professor at Columbia Unversity. Dr. Stolovitzky is the co-founder and leader of the DREAM initiative, an international effort that nucleates thousands of participants to address important problems of validation of systems biology methods, and to foster scientific collaboration. He has co-authored over 100 scientific publications, 11 issued patents and 2 edited books. His work has been highlighted in The New York Times, The Economist, Technology Review and Scientific American (where his DNA transistor project was chosen as one of the 10 world changing ideas of 2010) among other media. He has been elected fellow of American Association for the Advancement of Science and the American Physical Society. His most recent scientific interests are in the field of high-throughput biological-data analysis, reverse engineering biological circuits, the mathematical modeling of biological processes and new generation technologies for DNA sequencing.

BilalErhan Bilal
Affiliate Member of Sage Bionetworks
Erhan Bilal is a post-doctoral researcher in the Functional Genomics and Systems Biology group at IBM’s Computational Biology Center, as well as an affiliate member of Sage Bionetworks. He received MSc and BS degrees in Automatic Control and Industrial Informatics from the Politehnica University of Bucharest in Romania, and a PhD degree in Computational Biology from Rutgers University. His research is focused on the application of big data analytics to the development of biomarkers and therapeutic strategies in cancer.

 

 

CokkelaerThomas Cokkelaer
Affiliate Member of Sage Bionetworks
Thomas Cokkelaer is a Staff Research Associate at the European Bioinformatics Institute (EBI-EMBL), Cambridge, U.K, and a member of the Saez-Rodriguez research group since August 2011. He is involved in the development of CellNOpt (software dedicated to  the optimisation of protein signalling networks trained to data) and DREAM project challenges since DREAM6. Dr Cokelaer studied Physics (Université du Littoral, France) and Astronomy (Université de Nice-Sophia-Antipolis, France). He received a PhD in Astronomy (Observatoire de Nice-Côte d’Azur, France, 2003) within the VIRGO project. Also involved in the Data Analysis Group of LIGO during a Research Associate position  in Wales, U.K., (Physics and Astronomy Department of Cardiff University).  He moved to Montpellier, France in 2008 to work in Plant Science at the French National Institute of Computer Science, INRIA and Agricultural Research for Development, CIRAD. In particular, He worked on OpenAlea, an open source project dedicated to plant modelisation.

 

CostelloJim Costello
Affiliate Member of Sage Bionetworks
Jim is an Associate Bioinformaticist at Brigham and Women’s Hosptial and an Instructor of Medicine at Harvard Medical School.  Jim’s research focuses on developing computational approaches to analyze and interpret genomics data.  He did his graduate work at Indiana University in Bloomington where his dissertation topic was integrating large-scale, independent genomic measurements in Drosophila to predict the function of uncharacterized genes.  Jim then moved to Boston to do his postdoctoral research in Prof. Jim Collin’s lab at Boston University where he focused on developing methods to identify novel therapeutic strategies. During his postdoctoral training, Jim became involved with the DREAM challenges and helped organize and run the DREAM5 network inference challenge and the NCI-DREAM drug sensitivity prediction challenge. Most recently, Jim made the short move to Brigham and Women’s Hospital to join the newly formed Men’s Health Unit, where he will continue developing computational approaches to understand the effects of testosterone on muscle diseases, prostate cancer, and aging.

 

Heiser_jpgLaura Heiser
Affiliate Member of Sage Bionetworks
Dr. Heiser is a Research Assistant Professor at Oregon Health and Science University. Dr. Heiser studied molecular biology at the University of California, Berkeley (1998), and earned her PhD in neuroscience from the University of Pittsburgh in 2007. She completed postdoctoral studies under the direction of Paul Spellman and Joe Gray at Lawrence Berkeley National Laboratory. Her research focuses on the genomic and epigenomic changes that drive oncogenic behavior in breast cancer, with the goal of identifying aberrations and pathways associated with therapeutic response and resistance.  She has been involved with DREAM since 2012.

 

 

KuffnerRobert Kuffner
Affiliate Member of Sage Bionetworks
Robert Küffner graduated in informatics in 2010 and is, since 2003, a group leader and lecturer for computer science and bioinformatics at the Ludwig-Maximilians Universität München, Germany. Between 2000 and 2003, he was head of software development at the National Center for Genome Resources (NCGR) in New Mexico, USA. He received his PhD in molecular biology in 1998 at the Heinrich-Heine Universität Düsseldorf, Germany. Küffner’s main interests include the investigation and reconstruction of biological networks via Petri Nets as well as research in the areas of text mining, expression analysis, gene regulation, and systems biology. Approaches and tools resulting from this research have been applied in many projects to provide systematic bioinformatics support; e.g. for the pre-processing, analysis and integration of large-scale transcriptomics and proteomics datasets. Recently, his team was recognized as best performer in two international community-wide challenges where comprehensive blinded assessments of network inference approaches have been conducted.

marbachDaniel Marbach
Affiliate Member of Sage Bionetworks
Dr. Marbach is currently a postdoctoral fellow at the MIT computational biology group directed by Prof. Manolis Kellis. Dr. Marbach’s research is centered on (1) developing computational methods to unravel molecular networks from large-scale data and (2) leveraging these networks to improve our understanding of disease mechanisms. With a strong interest in community-based, collaborative approaches to tackle these problems, Dr. Marbach has been actively involved in the DREAM systems biology challenges from the start. In the first edition of the DREAM challenges in 2007, he was a participant and best performer. Subsequently, he designed and led three editions of the DREAM network inference challenge (2008, 2009, 2010), pioneering community-based approaches in gene regulatory network inference. Dr. Marbach’s background is in computer science, he obtained his Ph.D at the Swiss Federal Institute of Technology in Lausanne (EPFL) in 2010.

 

mendenMichael Menden
Affiliate Member of Sage Bionetworks
Michael Menden is currently a PhD student in Molecular Biology at the University of Cambridge and is carrying out his research at the European Bioinformatics Institute (EBI) in the Saez-Rodriguez group since 2011. In his PhD he is analyzing the drug response of cancer cell lines depending on their genomic heterogeneity in collaboration with the Genomics of Drug Sensitivity in Cancer (GDSC) project at the Welcome Trust Sanger Institute. Previously, he studied Bioinformatics at the University of Applied Science Weihenstephan-Triesdorf in Germany (2006-2011), where he was also involved in research projects at the EBI (Proteomics Service Team) in cooperation with the University of Cambridge (FlyMine Group), and  at Harvard Medical School (Sorger Lab) in the Department for Systems Biology. He did his diploma thesis at the Technical University of Munich (Rost Lab).

 

MeyerPablo Meyer
Affiliate Member of Sage Bionetworks
Dr. Meyer received his Bachelor degree in Physics from the Universidad Nacional Autonoma de Mexico (2002), MS in Physics from the University of Paris (1999) and his PhD in Biology from Rockefeller University (2005) receiving a Burroughs Wellcome Fellowship for his work on live imaging of protein interactions in the Drosophila circadian clock. In 2007 he received a Helen Hay Whitney Fellowship to work at Columbia University on live-imaging of metabolism during in Bacillus Subtillis. In 2010 he joined the IBM Computational Biology center at IBM Research where he is a DREAM project organizer and finds himself in the intersection between modeling, data analysis and wet lab. His most recent interests are in enzyme distribution in the cell and their link to Metabolism/Cancer via high-throughput biological-data production/analysis.
NorelRaquel Norel
Affiliate Member of Sage Bionetworks
Dr. Norel holds a Ph.D. in computer science from Tel Aviv University on the topic of Algorithms for Protein Docking; an M.Sc. in computer science from Weizmann Institute and a B.Sc. in civil engineering from Universidad de Chile. Dr. Norel currently holds the position of Research Staff Member of the Computational Biology Center in IBM Research. Dr. Norel uses math and computing to bring insight to complex biological problems. For example she has worked on mathematical models for cell cycle progression, algorithms for structural protein representation, protein docking, and physico-chemical scoring of protein complexes among other topics. Dr. Norel has more than 30 publications, several of them with over 100 citations. Dr. Norel is currently working on collaboration-by-competition projects; since 2010 she has contributed to the DREAM project as an organizer and scorer, and as of 2013 she is an Affiliate Member at Sage Bionetworks. She regularly contributes literature reviews to the Faculty of 1000, another crowd-sourcing effort.

 

RodriguezJulio Saez Rodriguez
Affiliate Member of Sage Bionetworks
Julio is a group leader at EMBL-EBI since July 2010, with a joint appointment in the EMBL Genome Biology Unit in Heidelberg; he is also a senior fellow at Wolfson College (Cambridge).   He has been involved with DREAM since 2008, initially as a Challenge provider, and since 2010 as a co-organizer. He studied Chemical Engineering at the University of Oviedo in Spain and the University of Stuttgart in Germany (2001), and obtained his PhD at the University of Magdeburg (2007) based on his research at the Max-Planck-Institute with E. D. Gilles. After his graduate work he was a postdoctoral fellow at Harvard Medical School with Peter Sorger, in collaboration with Doug Lauffenburger at M.I.T., and a Scientific Coordinator of the NIH-NIGMS Cell Decision Process Center. His group develops and applies computational methods to acquire a functional understanding of signaling networks and their deregulation in disease, and to apply this knowledge to develop novel therapeutics. More information at www.ebi.ac.uk/saezrodriguez.