Chengran Fang, Zheyi Yang, Demian Wassermann, Jing-Rebecca Li
A simulation-driven supervised learning framework to estimate brain microstructure using diffusion MRI
Medical Image Analysis. 2023. Article.

Marwa Kchaou, Jing-Rebecca Li
A second order asymptotic model for diffusion MRI in permeable media
ESAIM: Mathematical Modelling and Numerical Analysis, 2023. Article.

Zheyi Yang, Chengran Fang, Jing-Rebecca Li
Incorporating interface permeability into the diffusion MRI signal representation using impermeable Laplace eigenfunctions
IOP Physics in Medicine & Biology, 2023. Article.

Mojtaba Lashgari, Nishant Ravikumar, Irvin Teh, Jing-Rebecca Li, David Buckley, Jurgen Schneider, Alejandro Frangi
Three-dimensional micro-structurally informed in silico myocardium—Towards virtual imaging trials in cardiac diffusion weighted MRI
Medical Image Analysis, 2022. Article.

Chengran Fang, Demian Wassermann, and Jing-Rebecca Li
Fourier representation of the diffusion MRI signal using layer potentials
SIAM Journal on Applied Mathematics, 2022. Article.

Zheyi Yang, Imen Mekkaoui, Jan Hesthaven, Jing-Rebecca Li
Asymptotic models of the diffusion MRI signal accounting for geometrical deformations.
MathematicS In Action, 2022. Article.

S. D. Agdestein, T. N. Tran, J.-R. Li
Practical computation of the diffusion MRI signal based on Laplace eigenfunctions: permeable interfaces.
NMR in Biomedicine, 2021. Article.

I. Mekkaoui, J. Pousin, J. Hesthaven, J.-R.Li
Apparent diffusion coefficient measured by diffusion MRI of moving and deforming domains
Journal of Magnetic Resonance. 2020. Article.

C. Fang, V.-D. Nguyen, D. Wassermann, J.-R. Li
Diffusion MRI simulation of realistic neurons with SpinDoctor and the Neuron Module.
Neuroimage. 2020. Article.

J.-R. Li, T. N. Tran, V.-D. Nguyen
Practical computation of the diffusion MRI signal of realistic neurons based on Laplace eigenfunctions.
NMR in Biomedicine. 2020. Article.

V. Menon, G. Gallardo, M. Pinsk, V.-D. Nguyen, J.-R. Li, W. Cai, D. Wassermann
Microstructural organization of human insula is linked to its macrofunctional circuitry and predicts cognitive control.
eLife. 2020. Article.

V.-D. Nguyen, M. Leoni, T. Dancheva, J. Jansson, J. Hoffman, D. Wassermann, J.-R. Li
Portable simulation framework for diffusion MRI.
Journal of Magnetic Resonance. 2019. Article.

J.-R. Li, V.-D. Nguyen, T. N. Tran, J. Valdman, C.-B. Trang, K. V. Nguyen, D. T. S. Vu, H. A. Tran, H. T. A. Tran, T. M. P. Nguyen
SpinDoctor: a Matlab toolbox for diffusion MRI simulation.
Neuroimage. 2019. Article.

K.-V. Nguyen, D. Le Bihan, L. Ciobanu, J.-R. Li
The time-dependent diffusivity in the abdominal ganglion of Aplysia californica, experiments and simulations.
Biomedical Physics & Engineering Express. 2019. Article.

D. V. Nguyen, J. Jansson, H. T. A. Tran, J. Hoffman, J.-R. Li.
Diffusion MRI simulation in thin-layer and thin-tube media using a discretization on manifolds.
Journal of Magnetic Resonance. 2019. Article.

D. V. Nguyen, J. Jansson, J. Hoffman, J.-R. Li.
A partition of unity finite element method for computational diffusion MRI.
Journal of Computational Physics. 2018. Article.

H. Haddar, J.-R. Li, S. Schiavi
Understanding the time-dependent diffusion tensor measured by diffusion MRI: the intra-cellular case.
SIAM Journal of Applied Mathematics. 2017. Article.

P. Svehla, K. V. Nguyen, J.-R. Li, L. Ciobanu.
Quantitative DLA-based Compressed Sensing for T1-weighted Acquisitions
Journal of Magnetic Resonance. 2017. Article.

G. Fournet, J.-R. Li, A. Cerjanic, B. Sutton, L. Ciobanu, D. Le Bihan
A two pool model to describe the IVIM cerebral perfusion.
Journal of Cerebral Blood Flow and Metabolism. 2016. Article.

F. Caubet, H. Haddar, J.-R. Li, D. V. Nguyen.
New transmission condition accounting for diffusion anisotropy in thin layers applied to diffusion MRI.
ESAIM: Mathematical Modelling and Numerical Analysis. 2016. Article.

H. Haddar, J.-R. Li, S. Schiavi.
Adapting the K�ärger model to account for finite diffusion-encoding pulses in diffusion MRI.
IMA Journal of Applied Mathematics. 2016. Article.

H. Haddar, J.-R. Li, S. Schiavi.
A macroscopic model for the diffusion MRI signal accounting for time-dependent diffusivity.
SIAM Journal of Applied Mathematics. 2016. Article.

K. V. Nguyen, J.-R. Li, G. Radecki, L. Ciobanu.
DLA based compressed sensing for high resolution MR microscopy of neuronal tissue.
Journal of Magnetic Resonance. 2015. Article.

H. T. Nguyen, D. Grebenkov, D. V. Nguyen, C. Poupon, D. Le Bihan, J.-R. Li.
Parameter estimation using macroscopic diffusion MRI signal models.
Physics in Medicine and Biology. 2015. Article.

D. V. Nguyen, D. Grebenkov, D. Le Bihan, J.-R. Li.
Numerical study of a cylinder model of the diffusion MRI signal for neuronal dendrite trees.
Journal of Magnetic Resonance. 2015. Article.

J.-R. Li, H. T. Nguyen, D. V. Nguyen, H. Haddar, J. Coatléven, D. Le Bihan.
Numerical study of a macroscopic finite pulse model of the diffusion MRI signal.
Journal of Magnetic Resonance. 2014. Article.

D. Grebenkov, D. V. Nguyen, J.-R. Li.
Exploring diffusion across permeable barriers at high gradients. I. Narrow pulse approximation.
Journal of Magnetic Resonance. 2014. Article.

D. Nguyen, J.-R. Li, D. Grebenkov, D. Le Bihan.
A finite elements method to solve the Bloch-Torrey equation applied to diffusion magnetic resonance imaging.
Journal of Computational Physics. 2014. Article.

J. Coatleven, H. Haddar, J.-R. Li.
A new macroscopic model including membrane exchange for diffusion MRI.
SIAM Journal of Applied Mathematics. 2014. Article.

M. Iima, O. Reynaud, T. Tsurugizawa, L. Ciobanu, J.-R. Li, F. Geffroy, B. Djemai, M. Umehana, D. Le Bihan.
Characterization of Glioma Microcirculation and Tissue Features Using Intravoxel Incoherent Motion Magnetic Resonance Imaging in a Rat Brain Model.
Investigative Radiology. 2014. Article.

J.-R. Li, D. Calhoun, C. Poupon, D. Le Bihan.
Numerical simulation of diffusion MRI signals using an adaptive time-stepping method.
Physics in Medicine and Biology. 12/2013; 59(2):441-454. Article.

C.-H. Yeh, B. Schmitt, D. Le Bihan, J.-R. Li, C.-P. Lin, C. Poupon.
Diffusion Microscopist Simulator: A General Monte Carlo Simulation System for Diffusion Magnetic Resonance Imaging.
PLOS ONE. 2013. Article.

D. Grebenkov, H.T. Nguyen, J.-R. Li.
A fast random walk algorithm for computing diffusion-weighted NMR signals in multiscale porous media: a feasibility study for a Menger sponge.
Microporous and Mesoporous Materials, 2013. Article.

J.-R. Li.
A fast time stepping method for evaluating fractional integrals.
SIAM Journal on Scientific Computing. Vol 31, 2010. pp. 4696-4714 (19 pages) Article.

H. Haddar, J.-R. Li, D. Matignon.
Efficient solution of a wave equation with fractional-order dissipative terms.
Volume 234, Issue 6, 15 July 2010, Pages 2003-2010
Journal of Computational and Applied Mathematics. Article.

J.-R. Li, L.Greengard.
High Order Accurate Methods for the Evaluation of Layer Heat Potentials.
SIAM Journal on Scientific Computing. Vol 31, 2009. pp. 3847-3860 (14 pages) Article.

J.-R. Li, D. Calhoun, L. Brush.
Efficient thermal field computation in phase field models.
Journal of Computational Physics. Volume 228, Issue 24, 20 December 2009, Pages 8945-8957. Article.

P. Benner, J.-R. Li, T. Penzl.
Numerical solution of large-scale Lyapunov equations, Riccati equations, and linear-quadratic optimal control problems.
Numerical Linear Algebra with Applications, Volume 15, 2008, Pages 755-777. Article.

J.-R. Li, L. Greengard.
On the numerical solution of the heat equation I: fast solvers in free space.
Journal of Computational Physics, Volume 226, Issue 2, 1 October 2007, Pages 1891-1901. Article.

P.Joly, J.-R. Li, S.Fliss.
Exact boundary conditions for periodic waveguides containing a local perturbation.
Communications in Computational Physics, 1 (2006), pp. 945-973. Article.

J. Li.
Low order approximation of the spherical nonreflecting boundary kernel for the wave equation.
Linear Algebra and its Applications, Special Issue on Order Reduction of Large-Scale Systems, Volume 415, Issues 2-3, June 2006, Pages 455-468. Article.

S. Gugercin, J.-R. Li.
Smith-Type methods for balanced truncation of large sparse systems.
Dimension Reduction of Large-Scale Systems Proceedings of a Workshop held in Oberwolfach, Germany, October 19-25, 2003. Series: Lecture Notes in Computational Science and Engineering , Vol. 45 Benner, Peter; Mehrmann, Volker; Sorensen, Danny C. (Eds.) 2005. Article.

J.-R. Li, J. White.
Low rank solution of Lyapunov equations.
SIAM Review, SIGEST selection, issue 46-4, December 2004. Article.

J.-R. Li, L. Greengard.
High order marching schemes for the wave equation in complex geometry.
Journal of Computational Physics, Volume 198, Issue 1, 20 July 2004, Pages 295-309. Article.

J.-R. Li, L. Greengard.
Strongly consistent marching schemes for the wave equation.
Journal of Computational Physics, Volume 188, Issue 1, 10 June 2003, Pages 194-208. Article.

J.-R. Li, J. White.
Low rank solution of {L}yapunov equations.
SIAM Journal on Matrix Analysis and Applications, {\bf 24} (2002), no.~1, 260 -- 280. Article.

J.-R. Li, J. White.
Reduction of large circuit models via low rank approximate {G}ramians.
International Journal of Applied Mathematics and Computer Science, {\bf 11} (2001), no.~5, 1151 -- 1171. Article.

J.-R. Li, J. White.
Efficient Model Reduction of Interconnect via Approximate System Grammians.
IEEE/ACM International Conference on Computer-Aided Design, 1999. Digest of Technical Papers. 7-11 Nov. 1999 Page(s):380 - 383. Article.

J.-R. Li, F. Wang, J. White.
An Efficient Lyapunov Equation-Based Approach for Generating Reduced Order Models of Interconnect.
Design Automation Conference, 1999. Proceedings. 36th, 21-25 June 1999, Page(s):1 - 6. Article.

J.-R. Li, J. White.
Improving the efficiency of multipole-accelerated method-of-moments solvers using dual grid multipole expansions.
IEEE 6th Topical Meeting on Electrical Performance of Electronic Packaging, 1997. 27-29 Oct. 1997 Page(s):236 - 239. Article.