Assistant Professor, Biomedical Engineering, Johns Hopkins University
733 N. Broadway, BRB 573
Baltimore, MD 21205
Phone: (410) 502-3688
Fax: (410) 502-7544
Research Interest Statement
Computational identification of regulatory networks from microarray expression data and whole-genome DNA sequence, and experimental validation of regulatory pathways in C. elegans.
D. J. Katz, M. A. Beer , J. M. Levorse, and S. Tilghman , Functional characterization of a novel Ku70/80 pause site at the H19/Igf2 imprinting control region. Mol. Cell Biol. 25, 3855-63 (2005).
M. A. Beer and S. Tavazoie, Predicting gene expression from sequence. Cell 177 , 185-198 (2004), highlighted in Nature Reviews Genetics 6 , 410 (2004); and The Scientist 18 (12) , 28 (2004).
M. Pritsker, Y. C. Liu, M. A. Beer , and S. Tavazoie , Whole-genome discovery of transcription factor binding sites by network topology conservation. Genome Research 14 , 99-108 (2004).
D.W. Ross, R.V. Bravenec, W. Dorland, M. A. Beer , G. W. Hammett, G. R. McKee, R. J. Fonck, M. Murakami, K. H. Burrell, G. L. Jackson, and G. M. Staebler, Comparing Simulation of Plasma Turbulence with Experiment. Phys. Plasmas 9 , 177 (2002).
W. Dorland, B. N. Rogers, F. Jenko, M. Kotschenruther, G. W. Hammett, D. Mikkelsen, D. W. Ross, M. A. Beer , P. B. Snyder, R. Bravenec, M. Greenwald, D. Ernst, R. Budny, Gyrokinetic Simulations of Tokamak Microturbulence. In Fusion Energy 2000 , Proceedings of the 18th International Conference on Plasma Physics and Controlled Fusion, Sorrento (International Atomic Energy Agency, Vienna , 2000).
2005 15 th International C. Elegans Meeting, UCL A, "Systematic genome-wide identification of transcriptional cis -regulatory logic in C. elegans ."
2004 Short Course on Transcription, BioMAPS Institute for Quantitative Biology, Rutgers University, "Predictive Learning of Combinatorial Regulatory Logic."
1999 Autumn College on Plasma Physics, International Centre for Theoretical Physics, Trieste , Italy, "Fundamentals of Gyrofluid Turbulence Simulations," "Dynamics of Turbulence Driven Zonal ExB Flows", and "Turbulence Suppression with Reversed Magnetic Shear."
1998 Joint International Workshop on the Theory of Fusion Plasmas, Varenna , Italy , "The Dynamics of Small-scale Turbulence Driven Flows."
1997 Joint APS Meeting, Washington , DC , "Simulations of Plasma Turbulence Suppression and Transport Barriers in Tokamaks."
1996 APS-DPP Meeting, Denver, CO, "Gyrofluid Simulations of Turbulence Suppression in Reversed-shear Experiments on the Tokamak Fusion Test Reactor."
1996 Workshop on Transport & Transport Barriers, Austin , TX , "Nonlinear Gyrofluid Simulations of Improved Confinement with Reversed Magnetic Shear."
1995 Physics Computing Conference, Pittsburg , PA , "Simulations of Plasma Turbulence in the Long Mean Free Path Regime."
1995 International Sherwood Fusion Theory Conference, Incline Village , NV , "Bounce-Averaged Electron Fluid Equations: ITG and TEM Driven Transport."
1995 U.S.-European Transport Task Force Workshop, Marina Del Ray, CA, "Gyrofluid Models of Toroidal ITG & TEM Driven Transport."