Organizer DREAM Challenge Stories – Our “Wall of DREAMers“
I am the CSO for Prize4Life. I first got involved with DREAM challenge in 2011, when we started the planning together the 2012 DREAM Phil Bowen ALS Prediction Prize4Life Challenge. The prize have attracted over 1000 of solvers from all over the world (63 countries) , almost all of them with no prior involvement in ALS research, and generated solutions that can substantially improve the development of novel treatments for ALS. It was truly inspiring- We felt as if for a rare disease like ALS, we really opened the door for a new type of research, that it the first intersection between state of the art computational research and ALS research, the first time such computational tools were widely used for accelerating the development of ALS treatments.
Now we want to create even more exciting solutions, with even more data for the DREAM 10 ALS Stratification Prize4Life Challenge launched on June 23, 2015!.
In 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.
Lara Mangravite, PhD is Director of the Systems Biology research group at Sage Bionetworks. This team focuses on application of systems biology approaches to advance understanding of disease biology and treatment outcomes with the overriding goal of improving clinical care. As part of these efforts, the team is working in parallel to pilot new approaches to scientific process that use open systems to enable community-based collaborative research efforts to solve complex problems in a collective manner that is more efficient and effective than standard research approaches. Lara’s previous research experience has focused on the identification of prognostic biomarkers through the analysis of genomic and molecular profiles derived from both clinical trials and experimental model systems. Lara obtained a BS in Physics from the Pennsylvania State University and a PhD in Pharmaceutical Chemistry from the University of California, San Francisco. She completed a postdoctoral fellowship in cardiovascular pharmacogenomics at the Children’s Hospital Oakland Research Institute.
Lara has been the scientific leads for the NIEHS-NCATS-UNC DREAM Toxicogenetics Challenge and Rheumatoid Arthritis Responder Challenge.
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. 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.
Dr. Heiser most recently served as the scientific lead for the HPN-DREAM breast cancer network inference challenge.
Pablo Meyer received studied Physics from the Universidad Nacional Autonoma de Mexico and his PhD in Biology from Rockefeller University (2005) studying with live imaging the protein interactions in the Drosophila circadian clock. He studied at Columbia University the live-imaging of metabolism during sporulation 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 modelling, data analysis and wet lab. His most recent interests are in enzyme distribution in the cell in and their link to Metabolism/Cancer via high-throughput biological-data analysis.
Pablo has been a member of the DREAM team since 2010 and most recently was the scientific lead for the Whole-cell parameter estimation DREAM challenge.
Federica is a postdoctoral fellow (EIPOD fellow – Marie Curie Fellow) at the European Bioinformatics Institute (EMBL-EBI) in Cambridge, UK. She joined Saez-Rodriguez group in February 2013 and is working in collaboration with Merten group in EMBL-Heidelberg, on a project aimed at the development of a droplet-based microfluidic platform with a setup designed to characterise signalling pathways, by combining high-throughput measurements with network modeling. Federica received my PhD in Bioengineering in 2013 from the University of Padova where she working in the field of Systems Biology using quantitative and qualitative computational modelling approaches to study transcriptional and post-transcriptional regulatory networks.
Federica was a scientific co-lead for the recently completed NIEHS-NCATS-UNC DREAM Toxicogenetics Challenge.