Our group investigates integrative approaches to combine functional and systems level knowledge with more traditional omics data and annotation information. We apply a wide range of tools including network inference, machine learning, topological analysis and multi-scale simulation. Simulation studies have included models at the level of molecules, subcellular pathways, cells, tissues and organisms. Recent work has focused on next generation sequencing techniques based on nanopores and on methods to better verify systems biology research.
- The PLoS Collection of DREAM papers
- R.J. Prill, J. Saez-rodriguez, L.G. Alexopoulos, P.K. Sorger, G. Stolovitzky Crowdsourcing network inference: the DREAM predictive signaling network challenge. Science signaling, 4(189),mr7,2011.
- R.J. Prill, D. Marbach, J. Saez-rodriguez, P.K. Sorger, L.G. Alexopoulos, X. Xue, N.D. Clarke, G. Altan-bonnet, G. Stolovitzky Towards a rigorous assessment of systems biology models: the DREAM3 challenges. PloS one, 5(2),e9202,2010.
- G. Stolovitzky, R.J. Prill, A. Califano Lessons from the DREAM2 ChallengesAnnals Of The New York Academy Of Sciences,1158(1),159--195,2009.
In the News:
- DREAM6 Breaks New Ground August 2, 2011.
- Q&A: IBM's Gustavo Stolovitzky on DREAM 5 Challenges and the Evolution of Reverse Engineering July 23, 2010.
- Math Lens Sharpens Biological Picture:Scientific Challenge Supports Competing Views of Complex Living Systems January 8, 2010
- DREAM Project Vision Expands April 16, 2009.
- More news on DREAM.
Upcoming DREAM 7:
- DREAM7 Conference:Nov 12-16, 2012: 5th RECOMB Conference on Regulatory and Systems Genomics and DREAM Challenges
- DREAM7 Challenges: This year we will have 4 DREAM challenges. We will post the nature of the challenges in the mid to late June time frame (details will be communicated at a later time).
- Challenge submission deadline: October 1st, 2012
In the News:
- See the latest challenge: Diagnostics Signature Challenge
- P. Meyer, L.G. Alexopoulos, T. Bonk, A. Califano, C.R. Cho, A. de la Fuente, D. de Graaf, A.J. Hartemink, J. Hoeng, N.V Ivanov, H. Koeppl, R. Linding, D. Marbach, R. Norel, M.C. Peitsch, J.J. Rice, A. Royyuru, F. Schacherer, J. Sprengel, K. Stolle, D. Vitkup, G. Stolovitzky Verification of systems biology research in the age of collaborative competition. Nature Biotechnology 29, 811-815. (2011).
- P. Meyer, J. Hoeng, R. Norel, J. Sprengel, K. Stolle, T. Bonk, S. Corthesy, A. Royyuru, M.C. Peitsch, , J.J. Rice and G. Stolovitzky Industrial Methodology for Process Verification in Research (IMPROVER): Towards Systems Biology Verification. Bioinformatics (2012).
- B.J. Pope, B.G. Fitch, M.C. Pitman, J.J. Rice, M. Reumann Performance of hybrid programming models for multiscale cardiac simulations: preparing for petascale computation.IEEE Trans Biomed Eng. 2011 Oct;58(10):2965-9
- M. Reumann, B.G. Fitch, A. Rayshubskiy, M.C. Pitman, J.J. Rice Orthogonal recursive bisection as data decomposition strategy for massively parallel cardiac simulations.Biomed Tech (Berl). Jun;56(3):129-45 (2011).
- C. Jons, J. O-Uchi, A.J. Moss, M. Reumann, J.J. Rice, I. Goldenberg, W. Zareba, A.A. Wilde, W. Shimizu, J.K. Kanters, S. McNitt, N. Hofman, J.L. Robinson, C.M. Lopes Use of mutant-specific ion channel characteristics for risk stratification of long QT syndrome patients.Sci Transl Med. 2011.
- B. Luan, G. Stolovitzky, G. Martyna Slowing and controlling the translocation of DNA in a solid-state nanopore. Nanoscale, The Royal Society of Chemistry, 2012.
- B. Luan, G. Martyna, G. Stolovitzky Characterizing and Controlling the Motion of ssDNA in a Solid-State Nanopore. Biophysical Journal, Elsevier, 2011
- H. Peng, B. Luan, S. Plonsky, S. Rossnagel, G. Stolovitzky Development of an electrical nanopore device towards the control of the translocation of DNA with single base resolution. Bulletin of the American Physical Society, APS, 2011.
In the News:
- IBM's Killer Idea: The $100 DNA-Sequencing Machine November 16, 2011.
- IBM's 'DNA transistor' January 7, 2010.
- 'DNA Transistor' Could Revolutionize Genetic Testing October 6, 2009.