J. Jeremy Rice  J. Jeremy Rice photo       

contact information

Research Staff Member
Thomas J. Watson Research Center, Yorktown Heights, NY USA
  +1dash914dash945dash3728

links



2015

A high-resolution computational model of the deforming human heart
V. Gurev, P. Pathmanathan, J. L. Fattebert, H. F. Wen, J. Magerlein, R. A. Gray, D. F. Richards, J. J. Rice
Biomech Model Mechanobiol 14(4), 829--849, 2015


2014

Understanding the limits of animal models as predictors of human biology: lessons learned from the sbv IMPROVER Species Translation Challenge
Rhrissorrakrai, Kahn and Belcastro, Vincenzo and Bilal, Erhan and Norel, Raquel and Poussin, Carine and Mathis, Carole and Dulize, R{'e}mi HJ and Ivanov, Nikolai V and Alexopoulos, Leonidas and Rice, J Jeremy and others
Bioinformatics, btu611, Oxford Univ Press, 2014


2013

sbv IMPROVER Diagnostic Signature Challenge: Scoring strategies
Norel, Raquel and Bilal, Erhan and Conrad-Chemineau, Nathalie and Bonneau, Richard and de la Fuente, Alberto and Jurisica, Igor and Marbach, Daniel and Meyer, Pablo and Rice, J Jeremy and Tuller, Tamir and others
Systems Biomedicine 1(4), 208--216, Taylor & Francis, 2013

sbv IMPROVER diagnostic signature challenge: design and results
Rhrissorrakrai, Kahn and Rice, J Jeremy and Boue, Stephanie and Talikka, Marja and Bilal, Erhan and Martin, Florian and Meyer, Pablo and Norel, Raquel and Xiang, Yang and Stolovitzky, Gustavo and others
Systems Biomedicine 1(4), 196--207, Taylor & Francis, 2013

Towards real-time simulation of cardiac electrophysiology in a human heart at high resolution
Richards, David F and Glosli, James N and Draeger, Erik W and Mirin, Arthur A and Chan, Bor and Fattebert, Jean-luc and Krauss, William D and Oppelstrup, Tomas and Butler, Chris J and Gunnels, John A and others
Computer methods in biomechanics and biomedical engineering 16(7), 802--805, Taylor & Francis, 2013

Strengths and limitations of microarray-based phenotype prediction: lessons learned from the IMPROVER Diagnostic Signature Challenge
Tarca, Adi L and Lauria, Mario and Unger, Michael and Bilal, Erhan and Boue, Stephanie and Dey, Kushal Kumar and Hoeng, Julia and Koeppl, Heinz and Martin, Florian and Meyer, Pablo and others
Bioinformatics 29(22), 2892--2899, Oxford Univ Press, 2013


2012

Toward real-time modeling of human heart ventricles at cellular resolution: simulation of drug-induced arrhythmias
Mirin, Arthur A and Richards, David F and Glosli, James N and Draeger, Erik W and Chan, Bor and Fattebert, Jean-luc and Krauss, William D and Oppelstrup, Tomas and Rice, John Jeremy and Gunnels, John A and others
Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis, pp. 2, 2012

In silico cardiac risk assessment in patients with long QT syndrome: type 1: clinical predictability of cardiac models
Hoefen, Ryan and Reumann, Matthias and Goldenberg, Ilan and Moss, Arthur J and Jin, O and Gu, Yiping and McNitt, Scott and Zareba, Wojciech and Jons, Christian and Kanters, Jorgen K and others
Journal of the American College of Cardiology 60(21), 2182--2191, Am Coll Cardio Found, 2012

Industrial methodology for process verification in research (IMPROVER): toward systems biology verification
Meyer, Pablo and Hoeng, Julia and Rice, J Jeremy and Norel, Raquel and Sprengel, J{"o}rg and Stolle, Katrin and Bonk, Thomas and Corthesy, Stephanie and Royyuru, Ajay and Peitsch, Manuel C and others
Bioinformatics 28(9), 1193--1201, Oxford Univ Press, 2012

In Silico Cardiac Risk Assessment in Patients With Long QT SyndromeType 1: Clinical Predictability of Cardiac Models
Ryan Hoefen, Matthias Reumann, Ilan Goldenberg, Arthur J Moss, O Jin, Yiping Gu, Scott McNitt, Wojciech Zareba, Christian Jons, Jorgen K Kanters, others
Journal of the American College of Cardiology 60(21), 2182--2191, Am Coll Cardio Found, 2012


2011

The self-assessment trap: can we all be better than average?
Norel, Raquel and Rice, John Jeremy and Stolovitzky, Gustavo
Molecular systems biology 7(1), 537, EMBO Press, 2011

Performance of hybrid programming models for multiscale cardiac simulations: Preparing for petascale computation
Pope, Bernard J and Fitch, Blake G and Pitman, Michael C and Rice, John Jeremy and Reumann, Matthias
Biomedical Engineering, IEEE Transactions on 58(10), 2965--2969, IEEE, 2011

Verification of systems biology research in the age of collaborative competition
Meyer, Pablo and Alexopoulos, Leonidas G and Bonk, Thomas and Califano, Andrea and Cho, Carolyn R and de la Fuente, Alberto and de Graaf, David and Hartemink, Alexander J and Hoeng, Julia and Ivanov, Nikolai V and others
Nature biotechnology 29(9), 811, 2011

Use of Mutant-Specific Ion Channel Characteristics for Risk Stratification of Long QT Syndrome Patients
C Jons, O Jin, A J Moss, M Reumann, J J Rice, I Goldenberg, W Zareba, A A M Wilde, W Shimizu, J K Kanters, others
Science Translational Medicine 3(76), 76ra28--76ra28, American Association for the Advancement of Science, 2011

The self-assessment trap: can we all be better than average?
R. Norel, J.J. Rice, G. Stolovitzky
Molecular Systems Biology 7(1), Nature Publishing Group, 2011

Petascale computation performance of lightweight multiscale cardiac models using hybrid programming models
B.J. Pope, B.G. Fitch, M.C. Pitman, J.J. Rice, M. Reumann
Engineering in Medicine and Biology Society, EMBC, 2011 Annual International Conference of the IEEE, pp. 433--436

Combination in vitro and in silico methodology for risk assessment of Long QT type 1 patients
J J Rice, M Reumman, C Lopes
Biophysical Journal 100(3), 574a--574a, Cell Press, 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
Biomed Tech (Berl) 56(3), 129--145, 2011

Cardiac electromechanical models: from cell to organ
N A Trayanova, J J Rice
Frontiers in Physiology2, Frontiers Media SA, 2011


2010

Scaling performance of low and high computational load cardiac models on the IBM Blue Gene supercomputer
M K Reumann, B G Fitch, A Rayshubskiy, M C Pitman, J J Rice
eResearch Australasia 2010

Distribution of electromechanical delay in the heart: insights from a three-dimensional electromechanical model
V Gurev, J Constantino, JJ Rice, NA Trayanova
Biophysical journal 99(3), 745--754, Elsevier, 2010


2009

Orthogonal recursive bisection data decomposition for high performance computing in cardiac model simulations: dependence on anatomical geometry
M. Reumann, B. G. Fitch, A. Rayshubskiy, D. U. Keller, G. Seemann, O. Dossel, M. C. Pitman, J. J. Rice
Conf Proc IEEE Eng Med Biol Soc2009, 2799--2802

Computational modeling of cardiac disease: potential for personalized medicine
M Reumann, V Gurev, J J Rice
Personalized Medicine 6(1), 45--66, Future Medicine, 2009

Glass microneedles for force measurements: a finite-element analysis model
P N Ayittey, J S Walker, J J Rice, P P De Tombe
Pfl{\"u}gers Archiv European Journal of Physiology 457(6), 1415--1422, Springer, 2009

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


2008

Spatially-compressed cardiac myofilament models generate hysteresis that is not found in real muscle.
Rice, John Jeremy and Tu, Yuhai and Poggesi, Corrado and Pieter P. deTombe
Pacific Symposium on Biocomputing, pp. 366--377, 2008

Approximate model of cooperative activation and crossbridge cycling in cardiac muscle using ordinary differential equations
J. J. Rice, F. Wang, D. M. Bers, P. P. de Tombe
Biophys. J. 95(5), 2368--2390, 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 Symp Biocomput, 366--377, 2008

Error estimates and communication overhead in the computation of the bidomain equations on the distributed memory parallel Blue Gene/L supercomputer
M Reumann, BG Fitch, A Rayshubskiy, DL Weiss, G Seemann, O Doessel, MC Pitman, JJ Rice
Computers in Cardiology, 2008, pp. 81--84

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. Dossel, M. C. Pitman, J. J. Rice
Conf Proc IEEE Eng Med Biol Soc2008, 577--580


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

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


2006

A spatially detailed myofilament model as a basis for large-scale biological simulations
Hussan, Jagir and De Tombe, PP and Rice, John Jeremy
IBM journal of research and development 50(6), 583--600, IBM, 2006

A spatially-detailed model of actin and myosin interaction in the cardiac myofilament including strain-based rates and cooperative mechanisms
J R Hussan, P P Tombe de, J J Rice
Proceedings of the 24th IASTED international conference on Biomedical engineering, pp. 124--132, IBM, 2006


2005

Lasting impressions: motifs in protein--protein maps may provide footprints of evolutionary events
Rice, J Jeremy and Kershenbaum, Aaron and Stolovitzky, Gustavo
Proceedings of the National Academy of Sciences of the United States of America 102(9), 3173--3174, National Acad Sciences, 2005

A plausible model for the digital response of p53 to DNA damage
Ma, Lan and Wagner, John and Rice, John Jeremy and Hu, Wenwei and Levine, Arnold J and Stolovitzky, Gustavo A
Proceedings of the National Academy of Sciences of the United States of America 102(40), 14266--14271, National Acad Sciences, 2005

p53-Mdm2 loop controlled by a balance of its feedback strength and effective dampening using ATM and delayed feedback
J. Wagner, L. Ma, J. J. Rice, W. Hu, A. J. Levine, G. A. Stolovitzky
Syst Biol (Stevenage) 152(3), 109--118, 2005

Analyzing and reconstructing gene regulatory networks
J.J. Rice, A. Kershenbaum and G. Stolovitzky
Specialist review to The Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, Jorde, Little, Dunn and Subramaniam, eds. John Wiley & Sons, Ltd:Chichester, 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--14271, 2005

Formation of regulatory patterns during signal propagation in a Mammalian cellular network
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
Science 309(5737), 1078-83, American Association for the Advancement of Science, 2005

Lasting impressions: Motifs in protein--protein maps may provide footprints of evolutionary events
J J Rice, A Kershenbaum, G Stolovitzky
Proc. Natl. Acad. Sci. U S A 102(9), 3173, National Acad Sciences, 2005

Reconstructing biological networks using conditional correlation analysis
J. J. Rice, Y. Tu, G. Stolovitzky
Bioinformatics 21(6), 765--773, 2005


2004


Approaches to modeling crossbridges and calcium-dependent activation in cardiac muscle
J J Rice, P P Tombe de
Progress in biophysics and molecular biology 85(2-3), 179--195, Elsevier, 2004



2003



2001

Influence of transmural repolarization gradients on the electrophysiology and pharmacology of ventricular myocardium. Cellular basis for the Brugada and long--QT syndromes
Antzelevitch, Charles and Nesterenko, Vladislav V and Muzikant, Adam L and Rice, J Jeremy and Chen, Gang and Colatsky, Thomas
Philosophical Transactions of the Royal Society of London A: Mathematical, Physical and Engineering Sciences 359(1783), 1201--1216, The Royal Society, 2001

Modelling calcium handling in cardiac cells
J J Rice, M S Jafri
Philosophical Transactions of the Royal Society of London. Series A: Mathematical, Physical and Engineering Sciences 359(1783), 1143, The Royal Society, 2001


2000

Modeling short-term interval-force relations in cardiac muscle
J J Rice, M S Jafri, R L Winslow
American Journal of Physiology-Heart and Circulatory Physiology 278(3), H913--H931, Am Physiological Soc, 2000

Comparison of putative cooperative mechanisms in
J J Rice, R L Winslow, W C Hunter
Am J Physiol Heart Circ Physiol 278(3), H913--931, 2000


1999

Modeling gain and gradedness of Ca 2+ release in the functional unit of the cardiac diadic space
Rice, John J and Jafri, M Saleet and Winslow, Raimond L
Biophysical journal 77(4), 1871--1884, Elsevier, 1999

Modeling Gain and Gradedness of Ca< sup> 2+ Release in the Functional Unit of the Cardiac Diadic Space
John J Rice, M Saleet Jafri, Raimond L Winslow
Biophysical journal 77(4), 1871--1884, Elsevier, 1999

Comparison of putative cooperative mechanisms in cardiac muscle: length dependence and dynamic responses
J Jeremy Rice, Raimond L Winslow, William C Hunter
American Journal of Physiology-Heart and Circulatory Physiology 276(5), H1734--H1754, Am Physiological Soc, 1999


1998

Modeling Short-Term Interval-Force Relations in Cardiac Muscle
Rice, Jeremy J and Jafri, M Saleet and Winslow, Raimond L
Annals of the New York Academy of Sciences 853(1), 345--349, Wiley Online Library, 1998

Cardiac Ca 2+ dynamics: the roles of ryanodine receptor adaptation and sarcoplasmic reticulum load
Jafri, M Saleet and Rice, J Jeremy and Winslow, Raimond L
Biophysical Journal 74(3), 1149--1168, Elsevier, 1998

Cardiac Ca2+ dynamics: the roles of ryanodine receptor adaptation and sarcoplasmic reticulum load
M S Jafri, J J Rice, R L Winslow
Biophysical journal 74(3), 1149--1168, Elsevier, 1998

Model studies of the role of mechano-sensitive currents in the generation of cardiac arrhythmias
J J Rice, R L Winslow, J Dekanski, E McVeigh
Journal of theoretical biology 190(4), 295--312, Elsevier, 1998


1997

Head-related transfer functions in cat: neural representation and the effects of pinna movement
Young, ED and Rice, JJ and Spirou, GA and Nelken, I and Conley, RA
Binaural and Spatial Hearing in Real and Virtual Environments, 475--498, New York: Erlbaum, 1997

Modeling calcium handling, force generation, and length effects in cardiac cells
J J Rice
Ph.D. Thesis, 1997


1996

Effects of pinna position on head-related transfer functions in the cat
E D Young, J J Rice, S C Tong
Journal of the Acoustical Society of America 99(5), 3064--3076, [New York: Acoustical Society of America], 1996


1995

Auditory-nerve encoding of pinna-based spectral cues: Rate representation of high-frequency stimuli
Rice, John J and Young, Eric D and Spirou, George A
The Journal of the Acoustical Society of America 97(3), 1764--1776, Acoustical Society of America, 1995

Auditory-nerve encoding of pinna-based spectral cues: Rate representation of high-frequency stimuli
John J Rice, Eric D Young, George A Spirou
The Journal of the Acoustical Society of America97, 1764, 1995


1992

Representation of pinna-produced spectral notches in dorsal cochlear nucleus (DCN)
Young, ED and Spirou, GA and Rice, JJ
Soc Neurosci Abstr, pp. 1037, 1992

Pinna-based spectral cues for sound localization in cat
J J Rice, B J May, G A Spirou, E D Young
Hearing research 58(2), 132--152, Elsevier, 1992

Interneurons of the dorsal cochlear nucleus shape the responses of principal cells to complex sounds
GA Spirou, JJ Rice, ED Young
Auditory Physiology and Perception, edited by Y. Cazals, K. Horner and L. Demany. Oxford: Pergamon, 389--396, 1992

Neural organization and responses to complex stimuli in the dorsal cochlear nucleus [and discussion]
E D Young, G A Spirou, J J Rice, H F Voigt, A Rees
Philosophical Transactions: Biological Sciences, 407--413, JSTOR, 1992


1989



Year Unknown