 S.M: Krylov subspace methods for simultaneous primal-dual solutions and superconvergent functional estimates (2002) |
 .pdf |
|
Ph.D: An a posteriori error control framework for adaptive precision optimization using discontinuous Galerkin finite element method (2005) |
.pdf |
James Lu and David L. Darmofal: A quasi-minimal residual method for simultaneous primal-dual solutions and superconvergent functional estimates. |
SIAM Journal on
Scientific Computing, vol. 24 num. 5 (2003), pp 1693-1709. |
.pdf |
James Lu and David L. Darmofal: Higher-dimensional integration with Gaussian weight for applications in probabilistic design. |
SIAM Journal on
Scientific Computing, vol. 26 num. 2 (2004), pp. 613-624. |
.pdf |
| Eric J. Nielsen, James
Lu, Michael A. Park and David L. Darmofal: An implicit, exact dual adjoint solution
method for turbulent flows on unstructured grids. |
Computers
& Fluids, vol. 33 issue 9 (2004), pp. 1131-1155. |
.pdf |
| Krzysztof J. Fidkowski,
Todd A. Oliver, James Lu and David L. Darmofal: p-Multigrid solution of high-order
discontinuous Galerkin discretizations of the compressible
Navier-Stokes equations. |
Journal
of Computational Physics, vol. 207 issue 1 (2005), pp. 92-113. |
.pdf |
| Rainer Machne, Andrew
Finney, Stefan Mueller, James Lu, Stefanie Widder and Christoph Flamm:
The SBML ODE Solver
Library: a
native API for symbolic and fast numerical analysis of reaction
networks. |
Bioinformatics,
vol. 22
(2006), pp. 1405-1407. |
.pdf |
| James Lu, Heinz W. Engl
and Peter Schuster: Inverse
bifurcation analysis: applications to simple gene systems. |
Algorithms
for Molecular Biology, vol. 1:11 (2006) |
.pdf |
|
James Lu: Inverse eigenvalue problems for exploring the dynamics of systems biology models. |
Advances in Applied Mathematics and Mechanics, vol. 1:6 (2009): Special Issue for SCPDE08 | .pdf |
| Heinz W. Engl, Christoph Flamm, Philipp Kügler, James Lu, Stefan Müller, Peter Schuster: Inverse problems in systems biology. |
Inverse Problems, vol. 25:12 (2009): 25th Year Special Issue of Reviews |
.pdf |
| James Lu and David L.
Darmofal: Adaptive precision
methodology for flow optimization via discretization and iteration
error control. |
AIAA
Paper 2004-1096 |
.pdf |
| James Lu, Heinz W.
Engl, Rainer Machne, Peter Schuster: Inverse bifurcation analysis for a model
of the mammalian G1/S regulatory module. |
Bioinformatics Research and
Development '07 , pp. 168-184, Lecture
Notes in Bioinformatics 4414, Springer Verlag, March 2007. |
.pdf
|
| James Lu, Stefan Müller, Rainer Machne, Christoph Flamm: SBML ODE Solver Library: Extensions for
Inverse Analysis. |
Proceedings of the Fifth International Workshop on
Computational and Systems Biology (WCSB '08), TICSP Series #41,
Tampere, Finnland. |
.pdf |
| Stefan Mueller, James
Lu, Philipp Kuegler, Heinz W. Engl: Parameter identification in systems
biology: solving ill-posed inverse problems using regularization. |
RICAM
report 08-25 |
.pdf |
 James Lu, Heinz W. Engl and Peter Schuster: Modelling the dynamics of cell networks using inverse methods. IPAM Workshop on Systems Biology and Molecular Modeling, June 2006, Los Angeles, USA. |
.pdf
|
 James Lu, Heinz W. Engl, Rainer Machne and Peter Schuster: Inverse bifurcation analysis for reverse engineering of cell cycle and circadian rhythm models. 7th International Conference on Systems Biology (ICSB), Oct 2006, Yokohama, Japan. |
.pdf |
 James Lu, Heinz W. Engl, Rainer Machne and Peter Schuster: Inverse dynamical analysis. IMA Workshop on Optimization and Control, January 2007, Minneapolis, USA. |
.pdf |
 Bruce E. Shapiro, James Lu, Michael Hucka, Eric D. Mjolsness: Mathematica platforms for modeling in systems biology. ISMB/ECCB, July 2007, Vienna, Austria. |
.pdf |
| IPAM Inverse Problems
Reunion Conference II (Lake Arrowhead, California, June 2006). Inverse bifurcation analysis for reverse engineering of gene systems. |
.pdf
|
| Applied
Dynamical
Systems Workshop (Ghent, Belgium, June 2006). Inverse bifurcation analysis for reverse engineering of gene systems. |
.pdf |
| 11th SBML Forum
(with
Rainer Machne: Tokyo, Japan, October 2006). The SBML ODE Solver Library: capabilities, limitations and outlook . |
.pdf |
| Session
on Genes,
Dynamics Days 07
(Boston, USA, January 2007). Inverse dynamical analysis: from probing possible qualitative dynamical behaviors to inferring mechanisms underlying gene regulation. |
|
| Bioinformatics Research and
Development (BIRD07) (with
Rainer Machne: Berlin, Germany, March 2007). Inverse dynamical analysis: a methodology for probing dynamics in gene regulation and metabolism. |
.pdf |
| Radon Seminar at the RICAM
Scientific Boarding Meeting (with Philipp Kuegler,
Ronny Ramlau: Linz, April 2007). Regularization of Inverse Problems using sparsity constraints – Analysis and Applications. |
|
| 6th
International Congress on Industrial and Applied Mathematics
(Zurich,
Switzerland, July 2007). Mini-Symposium on Impact of Biology on Mathematical Modelling: Inverse dynamical analysis: application to gene networks. |
|
| 6th
International Congress on Industrial and Applied Mathematics (Zurich, Switzerland, July 2007). Mini-Symposium on Computational and Statistical Methods in Cell Biology: Inverse eigenvalue analysis: methodology and application to Eukarotic GATA transcription factor system |
 .nb |
| 8th
International Conference on Systems Biology (Long Beach, USA,
October 2007) Tutorial on Inverse Methodologies for Systems Biology: SOSLib, MathSBML and Matlab Extension |
.nb |
| RICAM Special
Semester on Quantitative Biology analyzed by Mathematical Methods (Linz, Austria, November
2007) Workshop on Systems Biology: Inverse Analysis for Qualitative Aspects of Gene Networks |
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