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John Jeremy Rice
- Current Position:
- Research Staff Member
Functional Genomics and Systems Biology Group
IBM Research, T.J. Watson Research Center
Yorktown Heights, NY 10598
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- Adjunct Faculty, Department of Biomedical Engineering
- The Johns Hopkins University, 2001-2005
- Contact Information:
- (914) 945-3728
(914) 945-4104 (fax)
e-mail: johnrice@us.ibm.com
- Education:
- Post Doctoral Fellowship, Center for Computational Medicine & Biology, The Johns Hopkins University School of Medicine, 1998
Ph. D., Department of Biomedical Engineering, The Johns Hopkins University, 1997
M.E.S., Department of Biomedical Engineering, The Johns Hopkins University, 1989
B.E.S., Department of Biomedical Engineering, The Johns Hopkins University, 1987
- Research Interests:
- Modeling, Simulations, Cardiac Physiology, Muscle Physiology, Biological
Applications for High-Performance Computing, Cellular Signaling and Pathway
Models, Cellular Calcium Dynamics, Neurophysiology, Auditory System
- Work Experience:
- Instrument Designer, Department of Otolaryngology - Head and Neck Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD, 1989-1990
Biomedical Engineer, Neural Encoding Laboratory, Department of Biomedical Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD, 1990-1991
Computational Modeler, Research Scientist, Physiome Sciences, Inc., Princeton, NJ, 1998-2000
Functional Genomics and Systems Biology Group, IBM T.J. Watson Research Center, 2000-present
- Other Professional Activities:
- Invited Speaker, IUPS Meeting Satellite Session on Cardiac Modeling, Aukland, New Zealand, 2001
Adjunct Faculty, Department of Biomedical Engineering, The Johns Hopkins University, 2001-2003
Invited Speaeker, Gordon Conference Cardiac Regulatory Mechanisms, Connecticut College, New London, CT, July 28 - Aug. 2, 2002
Gordon Conference Cardiac Regulatory Mechanisms, Colby-Sawyer College, New London, NH, July 23-28, 2000
Member of the Biophysical Society (since 1999)
Investigator in Integrated Human Function, a grant funded by the National Space Biomedical Research Institute, NASA, 2001
Grant review panel member for Advanced Modeling and Simulation of Biological Systems, Offices of Advanced Scientific Computing Research (ASCR) and Biological and Environmental Research (OBER) of the Office of Science (SC), USDOE, 2001
- Selected Publications:
- J.J. Rice, A. Kershenbaum and G. Stolovitzky, Lasting impressions: Motifs
in protein-protein maps may provide footprints of evolutionary events,
Proc. Natl. Acad. Sci. USA, in press (2005).
L. Ma, J. Wagner, J.J. Rice, W. Hu, A. Levine and G. Stolovitzky, A plausible
model for the digital response of p53 to DNA damage, submitted (2005).
A. Ma’ayan, S. L. Jenkins, S. Neves, A. Hasseldine, E. Grace, B. Dubin-Thaler,
N. J. Eungdamrong, G. Weng, P. Ram, J. J. Rice, A. Kershenbaum, G. Stolovitzky,
R. D. Blitzer and R. Iyengar, Emergence of regulatory patterns during propagation
of signal induced connectivity in a mammalian neuronal cellular network,
submitted (2005).
Rice, J.J., Tu, Y., and Stolovitzky, G. Reconstructing biological networks using conditional correlation analysis. Bioinformatics (2005, in press). (Pubmed) (pdf)(suppl. materials)
Rice, J.J., Kershenbaum, A.
and Stolovitzky, G. Analyzing and reconstructing gene regulatory
networks. “Specialist review” to The Encyclopedia of Genetics,
Genomics, Proteomics and Bioinformatics. Jorde, Little, Dunn
and Subramaniam, eds. John Wiley & Sons, Ltd:Chichester (2005,
in press).
Rice, J.J. and Bers, D.M. The response of cardiac muscle to stretch: The
role of calcium. In Cardiac Mechano-electric Feedback and Arrythmias: From
Pippette to Patient. Kohl, Franz, and Sachs, eds. Elsevier: Philadelphia
(2005, in press).
Rice, J.J. and Stolovitzky, G. Making the most of it: Pathway reconstruction and integrative simulation using the data at hand. Biosilico 2(2):70-7 (2004). (pdf)
Rice, J.J. and de Tombe, P.P. Approaches to modeling crossbridges and calcium-dependent activation in cardiac muscle. Prog Biophys Mol Biol. Jun-Jul;85(2-3):179-95 (2004). (Pubmed)
Lepre, J., Rice, J.J., , Tu, Y., and Stolovitzky, G. Genes@Work: an efficient
algorithm for pattern discovery and multivariate feature selection in gene
expression data. Bioinformatics. May 1;20(7):1033-44 (2004). (Pubmed)
Rice, J.J., Stolovitzky, G., Tu, Y., and de Tombe, P.P. Ising model of
cardiac thin filament with nearest-neighbor cooperative interactions. Biophysical
Journal Feb;84(2 Pt 1):897-909. (2003). (Pubmed)
Rice, J.J. and Jafri, M.S. Modeling calcium handling in cardiac cells. Philisophical Transactions of the Royal Society London, 359: 1143-1157 (2001).
- Rice, J.J., M. S. Jafri, and Winslow, R. L. Modeling gain and gradedness
of Ca2+ release in functional unit of the cardiac diadic space. Biophysical
Journal 77: 1871-1871 (1999).
Rice, J.J., Winslow, R.L., and Hunter, W.C. Comparison of putative cooperative
mechanisms in cardiac muscle: Modeling length-dependence and dynamic responses.
American Journal of Physiology 276:H1734-H1754 (1999).
Winslow, R.L., Rice, J.J., Jafri, S., Marban, E., and O'Rourke, B. Mechanisms of altered excitation-contraction coupling in canine tachycardia-induced heart failure, II: model studies. Circ Res. Mar 19;84(5):571-86 (1999).
- Winslow, R. L., Rice, J.J., and Jafri, M.S. Modeling the cellular basis of altered excitation-contraction coupling in heart failure. Progress in Biophysics & Molecular Biology 69:497-514 (1998).
- Jafri, M.S., Rice, J.J., and Winslow, R.L. Cardiac Ca2+ dynamics: The roles of ryanodine receptor adaptation and sarcoplasmic reticulum load. Biophysical Journal 74:1149-1168 (1998).
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Rice, J.J., Jafri, M.S., and Winslow, R.L. SR function plays a critical role in interval-force relations: A modeling study. In Cardiac Sarcoplasmic Reticulum Function and Regulation of Contractility. R.G. Johnson, Jr. and E.G. Kranias, Eds. The New York Academy of Sciences: New York 345-349 (1998).
Rice, J.J., Winslow, R.L., Dekanski, J., and McVeigh, E. Model studies of the role of mechano-sensitive currents in the generation of cardiac arrhythmias. Journal of Theoretical Biology 190(4):295-312 (1998).
Modeling Calcium Handling, Force Generation, and Length Effects in Cardiac Cells. Ph.D. Thesis. Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, MD (1998).
Young, E.D., Rice, J.J., and Tong, S.C. Effects of pinna position on head-related transfer functions in cat. Journal of the Acoustical Society of America 99:3064-3076 (1996).
Rice, J.J., Winslow, R.L., and Kohl, P. Conduction velocity in a model strand of cardiomyocytes is linearly related to intracellular sodium concentration. The Physiological Society, University of Oxford, July 11-14 (1995).
- Free Field to Eardrum Pressure Transformations in Cat. Masters Thesis. Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, MD (1989).
Rice, J.J., Young, E.D., and Spirou, G.A. Auditory nerve encoding of pinna-based
spectral cues: Rate representation of high-frequency stimuli. Journal of
the Acoustical Society of America. 97:1764-1776 (1995).
Rice, J.J., May, B., Spirou, G.A., and Young, E.D. Pinna-based spectral cues for sound localization in cat. Hearing Research: 58:132-152 (1992).
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