R.O. Dror, D.H. Arlow, D.W. Borhani, M.Ø. Jensen, S. Piana, and D.E. Shaw. Identification of Two Distinct Inactive Conformations of the β2-Adrenergic Receptor Reconciles Structural and Biochemical Observations. Proceedings of the National Academy of Sciences of the USA 106:4689-4694, 2009.
Y. Shan, M.A. Seeliger, M.P. Eastwood, F. Frank, H. Xu, M.Ø. Jensen, R.O. Dror, J. Kuriyan, and D.E. Shaw. A Conserved Protonation-Dependent Switch Controls Drug Binding in the Abl Kinase. Proceedings of the National Academy of Sciences of the United States of America . 106:139-144, 2009.
C.R. Ho, M. Theobald, B. Batson, J.P. Grossman, S.C. Wang, J. Gagliardo, M.M. Deneroff, R.O. Dror, and D.E. Shaw. Post-Silicon Debug Using Formal Verification Waypoints. Proceedings of the Design and Verification Conference and Exhibition (DVCon '09), San Jose, California, 2009
J.L. Klepeis, K. Lindorff-Larsen, R.O. Dror, and D.E. Shaw. Long-Timescale Molecular Dynamics Simulations of Protein Structure and Function. Current Opinion in Structural Biology, 19:1-18, 2009.
M.Ø. Jensen, R.O. Dror, H. Xu, D.W. Borhani, I.T. Arkin, M.P. Eastwood, and D.E. Shaw. Dynamic Control of Slow Water Transport by Aquaporin 0: Implications for Hydration and Junction Stability in the Eye Lens. Proceedings of the National Academy of Sciences of the USA 105:14430-14435, 2008.
T. Tu, C.A. Rendleman, D.W. Borhani, R.O. Dror, J. Gullingsrud, M.Ø. Jensen, J.L. Klepeis, P. Maragakis, P. Miller, K.A. Stafford, and D.E. Shaw. A Scalable Parallel Framework for Analyzing Terascale Molecular Dynamics Simulation Trajectories. Proceedings of the ACM/IEEE Conference on Supercomputing (SC08), Austin, Texas, 2008.
J.P. Grossman, J.K. Salmon, C.R. Ho, D.J. Ierardi, B. Towles, B. Batson, J. Spengler, S.C. Wang, R. Mueller, M. Theobald, C. Young, J. Gagliardo, M.M. Deneroff, R.O. Dror, and D.E. Shaw. Hierarchical Simulation-Based Verification of Anton, a Special-Purpose Parallel Machine. Proceedings of the 26th IEEE International Conference on Computer Design (ICCD '08), Lake Tahoe, California, 2008.
J.P. Grossman, C. Young, J.A. Bank, K. Mackenzie, D.J. Ierardi, J.K. Salmon, R.O. Dror, and D.E. Shaw. Simulation and Embedded Software Development for Anton, a Parallel Machine with Heterogeneous Multicore ASICs. Proceedings of the 6th IEEE/ACM/IFIP International Conference on Hardware/Software Codesign and System Synthesis (CODES/ISSS '08), Atlanta, Georgia, 2008.
D.E. Shaw, M.M. Deneroff, R.O. Dror, J.S. Kuskin, R.H. Larson, J.K. Salmon, C. Young, B. Batson, K.J. Bowers, J.C. Chao, M.P. Eastwood, J. Gagliardo, J.P. Grossman, C.R. Ho, D.J. Ierardi, I. Kolossvary, J.L. Klepeis, T. Layman, C. McLeavey, M.A. Moraes, R. Mueller, E.C. Priest, Y. Shan, J. Spengler, M. Theobald, B. Towles, and S.C. Wang. Anton, A Special-Purpose Machine for Molecular Dynamics Simulation. Communications of the ACM 51:91-97, 2008.
C.R. Ho, M. Theobald, M.M. Deneroff, R.O. Dror, J. Gagliardo, and D.E. Shaw, Early Formal Verification of Conditional Coverage Points to Identify Intrinsically Hard-to-Verify Logic. Proceedings of the 45th Annual Design Automation Conference (DAC '08) , Anaheim, CA, 2008.
P. Maragakis, K. Lindorff-Larsen, M.P. Eastwood, R.O. Dror, J.L. Klepeis, I.T. Arkin, M.Ø. Jensen, H. Xu, N. Trbovic, R.A. Friesner, A.G. Palmer, and D.E. Shaw. Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins. Journal of Physical Chemistry B 112:6155-6158, 2008.
R.H. Larson, J.K. Salmon, R.O. Dror, M.M. Deneroff, R.C. Young, J.P. Grossman, Y. Shan, J.L. Klepeis, and D.E. Shaw. High-throughput pairwise point interactions in Anton, a specialized machine for molecular dynamics simulation. Proceedings of the 14th International Symposium on High-Performance Computer Architecture, Salt Lake City, Utah, 2008.
J.S. Kuskin, R.C. Young, J.P. Grossman, B. Batson, M.M. Deneroff, R.O. Dror, and D.E. Shaw. Incorporating flexibility in Anton, a specialized machine for molecular dynamics simulation. Proceedings of the 14th International Symposium on High-Performance Computer Architecture, Salt Lake City, Utah, 2008.
I.T. Arkin, H. Xu, M.Ø. Jensen, E. Arbely, E.R. Bennett, K.J. Bowers, E. Chow, R.O. Dror, M.P. Eastwood, R. Flitman-Tene, B.A. Gregersen, J.L. Klepeis, I. Kolossvary, Y. Shan, and D.E. Shaw. Mechanism of Na+/H+ Antiporting. Science 317:799-803, 2007.
[Abstract]
R.A. Lippert, K.J. Bowers, R.O. Dror, M.P. Eastwood, B.A. Gregersen, J.L. Klepeis, I. Kolossvary, and D.E. Shaw. A common, avoidable source of error in molecular dynamics integrators. Journal of Chemical Physics 126:046101, 2007.
[Abstract]
D.E. Shaw, M.M. Deneroff, R.O. Dror, J.S. Kuskin, R.H. Larson, J.K. Salmon, C. Young, B. Batson, K.J. Bowers, J.C. Chao, M.P. Eastwood, J. Gagliardo, J.P. Grossman, C.R. Ho, D.J. Ierardi, I. Kolossvary, J.L. Klepeis, T. Layman, C. McLeavey, M.A. Moraes, R. Mueller, E.C. Priest, Y. Shan, J. Spengler, M. Theobald, B. Towles, and S.C. Wang. Anton: A special-purpose machine for molecular dynamics simulation. Proceedings of the 34th Annual International Symposium on Computer Architecture, San Diego, California, 2007.
[Abstract]
K.J. Bowers, R.O. Dror and D.E. Shaw. Zonal methods for the parallel execution of range-limited N-body simulations. Journal of Computational Physics 221:303-329, 2007.
[Abstract]
K.J. Bowers, R.O. Dror and D.E. Shaw. The midpoint method for parallelization of particle simulations. Journal of Chemical Physics, 124:184109, 2006.
[Abstract]
K.J. Bowers, E.Chow, H. Xu, R.O. Dror, M.P. Eastwood, B.A. Gregersen, J.L. Klepeis, I. Kolossvary, M.A. Moraes, F.D. Sacerdoti, J.K. Salmon, Y. Shan, and D.E. Shaw. Scalable algorithms for molecular dynamics simulations on commodity clusters. Proceedings of the 2006 ACM/IEEE Conference on Supercomputing (SC06), Tampa, Florida, 2006.
[Abstract]
Y. Shan, J.L. Klepeis, M.P. Eastwood, R.O. Dror, and
D.E. Shaw. Gaussian split Ewald: A fast Ewald mesh method for
molecular simulation. Journal of Chemical Physics, 122:054101, 2005.
[Abstract]
K.J. Bowers, R.O. Dror and D.E. Shaw. Overview of neutral territory methods for the parallel evaluation of pairwise particle interactions. Journal of Physics Conference Series 16:300-304, 2005.
[Abstract]
R.O. Dror, J.G. Murnick, N.J. Rinaldi, V.D. Marinescu, R.M. Rifkin, and R.A.
Young. Bayesian estimation of transcript levels using a
general model of array measurement noise. Journal of
Computational Biology 10:433-452, 2003.
[Abstract] [Full text, PDF]
R.O. Dror, J.G. Murnick, N.J. Rinaldi, V.D. Marinescu, R.M. Rifkin, and R.A.
Young. A Bayesian approach to transcript estimation from gene array data: the
BEAM technique. Proceedings of the Sixth Annual International Conference on
Research in Computational Molecular Biology, Washington, DC, April 2002.
[Abstract] [Full text, PDF]
R.O. Dror, D.C. O'Carroll, and S.B. Laughlin. Accuracy of velocity
estimation by Reichardt correlators. Journal of the Optical Society of
America A 18:241-252, 2001.
[Abstract] [Full text, PDF]
R.O. Dror, D.C. O'Carroll, and S.B. Laughlin. The role of natural image
statistics in biological motion estimation. IEEE International Workshop
on Biologically Motivated Computer Vision. Springer Lecture Notes in Computer
Science 1811:492-501, 2000.
[Abstract] [Full text, PDF]
R.O. Dror, C.C. Canavier, R.J. Butera, J.W. Clark, and J.H. Byrne. A
mathematical criterion based on phase response curves for stability in a ring
of coupled oscillators. Biological Cybernetics 80:11-23, 1999.
[Abstract] [Full text, PDF]
C.C. Canavier, R.J. Butera, R.O. Dror, D.A. Baxter, J.W. Clark, and J.H. Byrne. Phase response characteristics of model neurons determine
which patterns are expressed in a ring circuit model of gait generation. Biological Cybernetics 77:367-380, 1997.
[Abstract] [Full text, PDF]
R.O. Dror, A.S. Willsky, and E.H. Adelson. Statistical characterization of real-World illumination. Journal of Vision 4:821-837, 2004. http://journalofvision.org/4/9/11.
[Abstract] [Full text, PDF]
R.O. Dror, T.K. Leung, E.H. Adelson, and A.S. Willsky. Statistics of
real-world illumination Proceedings of CVPR , Hawaii, December,
2001.
[Abstract] [Full text, PDF]
R.O. Dror, E.H. Adelson, and A.S. Willsky. Recognition of surface
reflectance properties from a single image under unknown real-world
illumination. Proceedings of the Workshop on Identifying Objects
Across Variations in Lighting at CVPR, Hawaii, December, 2001.
[Abstract] [Full text, PDF]
R.O. Dror, E.H. Adelson, and A.S. Willsky. Surface reflectance
estimation and natural illumination statistics. Proceedings of the
Second International Workshop on Statistical and Computational Theories of
Vision at ICCV, Vancouver, Canada, July 2001.
[Abstract] [Full text, PDF]
R.O. Dror, E.H. Adelson, and A.S. Willsky. Estimating surface reflectance
properties from images under unknown illumination. Proceedings of the
SPIE 4299: Human Vision and Electronic Imaging IV , 2001.
[Abstract]
[Full text, PDF] [Copyright notice]
R.W. Fleming, R.O. Dror, and E.H. Adelson. Real-world illumination and the perception of surface reflectance properties. Journal of Vision 3:347-368, 2003. http://journalofvision.org/3/5/3.
[Abstract] [Full text, PDF]
R.W. Fleming, R.O. Dror, and E.H. Adelson. How do humans determine
reflectance properties under unknown illumination? Proceedings of the
Workshop on Identifying Objects Across Variations in Lighting at CVPR,
Hawaii, December, 2001.
[Abstract] [Full text, PDF]
R.O. Dror, S. Ganguli, and R.S. Strichartz. A search for best constants in
the Hardy-Littlewood maximal theorem. Journal of Fourier Analysis and
Applications 2:473-86, 1996.
[Abstract] [Full text, PDF]
R.O. Dror. Surface reflectance recognition and real-world illumination statistics. PhD thesis, Massachusetts Institute of Technology, 2002.
[Abstract] [Full text, PDF]
R.O. Dror. Accuracy of visual velocity estimation by Reichardt correlators.
Master's thesis, University of Cambridge, 1998.
[Abstract] [Full text, PDF]
R.O. Dror. Noise models in gene array analysis. Area exam report, MIT
Department of Electrical Engineering and Computer Science, 2001.
[Abstract] [Full text, PDF]