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Research Areas
Additional Information
Reasearchers
Venkat Balagursamy
Sungwook Nam
Hongbo Peng
Chao Wang
Deqiang Wang
Project Name
Functional Genomics & Systems Biology Group
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2012
Slowing and controlling the translocation of DNA in a solid-state nanopore
B. Luan, G Stolovitzky, G Martyna
Nanoscale 4(4), 1068-1077, The Royal Society of Chemistry, 2012
2011
Cardiac electromechanical models: from cell to organ
N A Trayanova, J J Rice
Frontiers in Physiology2, Frontiers Media SA, 2011
Orthogonal recursive bisection as data decomposition strategy for massively parallel cardiac simulations
M. Reumann, B.G. Fitch, A. Rayshubskiy, M.C. Pitman, J.J. Rice
Biomedizinische Technik/Biomedical Engineering 56(3), 129--145, Walter de Gruyter, 2011
Nanopore-Based DNA Sequencing and DNA Motion Control
H Peng, B Luan, G Stolovitzky
Nanopores: Sensing and Fundamental Biological Interactions; Iqbal, Samir M. and Bashir, Rashid (Eds.) , pp. 255, Springer Verlag, 2011
Characterizing and controlling the motion of ssDNA in a solid-state nanopore
B. Luan, G. Martyna, G. Stolovitzky
Biophysical journal 101(9), 2214--2222, Elsevier, 2011
Development of an electrical nanopore device towards the control of the translocation of DNA with single base resolution
H Peng, B Luan, S Polonsky, S Rossnagel, G Stolovitzky
Bulletin of the American Physical Society56, APS, 2011
2010
Characterize and Control the Motion of DNA in a Solid-State Nanopore
B Luan, G Stolovitzky, G Martyna
Bulletin of the American Physical Society55, APS, 2010
Base-by-base ratcheting of single stranded DNA through a solid-state nanopore
B Luan, H Peng, S Polonsky, S Rossnagel, G Stolovitzky, G Martyna
Physical Review Letters 104(23), 238103, APS, 2010
Electrochemical Characterization of Thin Film Electrodes Toward Developing a DNA Transistor
S. Harrer, S. Ahmed, A. Afzali-Ardakani, B. Luan, P. S. Waggoner, X. Shao, H. Peng, D. L. Goldfarb, G. J Martyna, S. M. Rossnagel, L. Deligianni, G. A. Stolovitzky
Langmuir 26(24), 153103--153103, ACS Publications, 2010
Towards a rigorous assessment of systems biology models: The DREAM3 challenges
R J Prill, D Marbach, J Saez-Rodriguez, P K Sorger, L G Alexopoulos, X Xue, N D Clarke, G Altan-Bonnet, G Stolovitzky
PLoS ONE 5(2), e9202, Public Library of Science, 2010
2009
Orthogonal recursive bisection data decomposition for high performance computing in cardiac model simulations: Dependence on anatomical geometry
M Reumann, BG Fitch, A Rayshubskiy, DUJ Keller, G Seemann, O Dossel, MC Pitman, JJ Rice
Engineering in Medicine and Biology Society, 2009, pp. 2799--2802
Towards run time visualization in cardiac modeling
M Reumann, C Morris, DUJ Keller, G Seemann, O Doessel, GD Abram, JJ Rice
World Congress on Medical Physics and Biomedical Engineering, Munich, Germany, pp. 999--1002, 2009
Strong scaling and speedup to 16,384 processors in cardiac electro—Mechanical simulations
M Reumann, BG Fitch, A Rayshubskiy, D Keller, G Seemann, O Dossel, MC Pitman, JJ Rice
Engineering in Medicine and Biology Society, 2009, pp. 2795--2798
Orthogonal Recursive Bisection as Data Decomposition Strategy for Cardiac Modeling in High Performance Computer Simulations on the IBM Blue Gene
M Reumann, BG Fitch, MC Pitman, JJ Rice
L supercomputer. BMC Systems Biology (submitted), 2009
Stick-Slip Motion of DNA in a Solid Nanopore
B Luan, G Martyna
Bulletin of the American Physical Society54, APS, 2009
Lessons from the DREAM2 Challenges
G Stolovitzky, R J Prill, A Califano
Annals of the New York Academy of Sciences 1158(1), 159--195, Wiley Online Library, 2009
2008
Spatially-compressed cardiac myofilament models generate hysteresis that is not found in real muscle
J J Rice, Y Tu, C Poggesi, P P De Tombe
Pac, pp. 366--377, 2008
Large scale cardiac modeling on the Blue Gene supercomputer
M Reumann, B G Fitch, A Rayshubskiy, D U Keller, D L Weiss, G Seemann, O Doessel, M C Pitman, J J Rice
Conf proc IEEE Eng Med Biol Soc, pp. 577--580, 2008
2007
Experimental test of specific predictions of a model for the oscillatory response of p53 to DNA damage.
G Stolovitzky, J Wagner, J J Rice, L Ma, W Hu, Z Feng, A Levine
Bulletin of the American Physical Society52, APS, 2007
A single nucleotide polymorphism in the MDM2 gene disrupts the oscillation of p53 and MDM2 levels in cells
W Hu, Z Feng, L Ma, J Wagner, J J Rice, G Stolovitzky, A J Levine
Cancer research 67(6), 2757, AACR, 2007
Nanopore in metal-dielectric sandwich for DNA position control
S Polonsky, S Rossnagel, G Stolovitzky
Applied Physics Letters91, 153103, 2007
2005
p53-Mdm2 loop controlled by a balance of its feedback strength and effective dampening using ATM and delayed feedback
J Wagner, L Ma, JJ Rice, W Hu, AJ Levine, GA Stolovitzky, others
Systems biology 152(3), 109, IEE, 2005
A plausible model for the digital response of p53 to DNA damage
L Ma, J Wagner, J J Rice, W Hu, A J Levine, G A Stolovitzky
Proc. Natl. Acad. Sci. U S A 102(40), 14266, National Acad Sciences, 2005
Others
DIMACS Workshop on Dialogue on Reverse Engineering Assessment and Methods (DREAM)
J S Bader
dimacs.rutgers.edu, 0