Scientific Journals and Refereed Proceedings:

S. Gopalakrishnan, H. Montazeri, S. Menz, N. Beerenwinkel and W. Huisinga

Estimating HIV-1 Fitness Characteristics from Cross-sectional Genotype Data

PLoS Computational Biology, Vol. 10  (2014), e1003886, pp. 1-14.

Journal (open access), Suppl. Data (R and Matlab codes)

N. Makarava, S. Menz, M. Theves, C. Beta, W. Huisinga and M. Holschneider

Quantifying the degree of persistence in random amoeboid motion based on the Hurst exponent of fractional Brownian motion

Phys Rev E 90 (2014), 042703.

Journal

L. Fronton, S. Pilari and W. Huisinga

Monoclonal antibody disposition: a simplified PBPK model and its implications for the derivation and interpretation of classical compartment models

J. Pharmacokinet. Pharmacodyn. 41 (2014), pp 87-107.

Journal, Suppl. Data (Matlab code)

O. Kuß, A. Hoyer and A. Solms

Meta-analysis for diagnostic accuracy studies: A new statistical model using beta-binomial distributions and bivariate copulas.

Statistics in Medicine 33 (2014), pp. 17-30.

Journal

S. Menz, J.C. Latorre, C. Schütte and W. Huisinga

Hybrid stochastic-deterministic solution of the chemical master equation

SIAM Multiscale Modelling and Simulation, 10 (2012) pp. 1232-1262

Journal

W. Huisinga, A. Solms, L. Fronton and S. Pilari

Modeling inter-individual variability in physiologically-based pharmacokinetics and its link to mechanistic covariate modeling

CPT: Pharmacometrics & Systems Pharmacology, 1 (2012), e4.

Journal (open access), Suppl Material (Data & Matlab code)

B.-F. Krippendorff,  D. A. Oyarzún and W. Huisinga

Predicting the F(ab)-mediated effect of monoclonal antibodies in vivo by combining cell-level kinetic and pharmacokinetic modelling

J. Pharmacokinet. Pharmacodyn. 39 (2012), pp 125-139.

Journal (open access)

S. Unverzagt,  M.-T. Machemer, A. Solms, H. Thiele, D. Burkhoff, M. Seyfarth, A. de Waha et al.

Intra-aortic balloon pump counterpulsation (IABP) for myocardial infarction complicated by cardiogenic shock.

Cochrane Database of Systematic Reviews 6 (2011), CD007398.

Journal

M. von Kleist, S. Menz, H. Stocker, K. Arasteh, C. Schütte, W. Huisinga

HIV Quasispecies Dynamics during Pro-Active Treatment Switching: Impact on Multi-Drug Resistance and Resistance Archiving in Latent Reservoirs

PLoS ONE, Vol. 6 (2011), e18204.

Journal (open access)

A. Y. Weiße,  and W. Huisinga

Error-Controlled Global Sensitivity Analysis of Ordinary Differential Equations

J. Comput. Phys. 230 (2011), pp 6824-6842.

Journal (open access), Suppl Material (zip)

C. Böckmann, A. Kammanee, H.-A. Braunß

Logarithmic convergence rate of Levenberg_Marquardt method with application to an inverse potential problem.

Journal of Inverse and III-Posed Problems, Vol. 19 (2011), pp. 345-367.

Journal

S. Pilari,  C. Preusse and W. Huisinga

Gestational Influences on the Pharmacokinetics of Gestagenic Drugs: A Combined In Silico, In Vitro and In Vivo Analysis

Eur J Pharm Sci., 42 (2011), pp. 318-331.

Journal

W. Huisinga and B.-F. Krippendorff

Eine gute Dosis Mathematik - Modellbasierte Arzneimittelentwicklung am Beispiel therapeutischer Proteine.

Systembiologie.de, Ausg. 02, December 2010.

Journal

S. Pilari  and W. Huisinga

Lumping of Physiologically Based Pharmacokinetic Models and a Mechanistic Derivation of Classical Compartmental Models

J. Pharmacokinet. Pharmacodyn. 37 (2010), pp 365-405.

Journal

A. Y. Weiße,  R. Middleton and W. Huisinga

Quantifying uncertainty, variability and likelihood for ordinary differential equation models

BMC Systems Biology, 4 (2010).

Journal (open access)

M. von Kleist, S. Menz and W. Huisinga

Drug-Class Specific Impact of Antivirals on the Reproductive Capacity of HIV

PLoS Comput Biol 5 (2010): e1000720.

Journal (open access).

N. Véron, H. Bauer, A. Y. Weiße, G. Lüder, M. Werber, and B. G. Herrmann

Retention of gene products in syncytial spermatids promotes non-Mendelian inheritance as revealed by the t-complex-responder

Genes & Development Vol 23 (2009), pp 2705-10 .

Journal

B.-F. Krippendorff, D. Oyarzun  and W. Huisinga

Ligand accumulation counteracts therapeutic inhibition of receptor systems

Proceedings of Foundations of Systems Biology in Engeneering, FOSBE (2009), pp. 173-176.

PDF-Preprint

B.-F. Krippendorff, K. Küster, C. Kloft, W. Huisinga

Nonlinear Pharmacokinetics of Therapeutic Proteins Resulting from Receptor Mediated Endocytosis

J. Pharmacokinet. Pharmacodyn, 36 (2009), pp 239-260.

Journal (open access), Suppl Material (zip)

B.-F. Krippendorff, R. Neuhaus, P. Lienau, A. Reichel, W. Huisinga

Mechanism-based Inhibition: Deriving KI and kinact directly from Time-Dependent IC50 Values

J Biomol Screen. 14 (2009), pp. 913-923.

Journal PDF-Preprint Suppl Material  

M. von Kleist, and W. Huisinga

Pharmacokinetic-Pharmacodynamic relationship of NRTIs and its connection to viral escape: An example based on Zidovudine

Eur J Pharm Sci. 36 (2009), pp. 532-543.

Journal PDF-Preprint

P. Deuflhard, W. Huisinga, T. Jahnke, and M. Wulkow

Adaptive discrete Galerkin methods applied to the  chemical master equation

SIAM J. Sci. Comput. 30 (2008), pp. 2990-3011.

Journal PDF-Preprint

T. Jahnke, and W. Huisinga

A dynamical low-rank approach to the chemical master equation

Bull. Math. Biol. 70 (2008), pp. 2283-2302.

Journal PDF-Preprint

M. von Kleist and W. Huisinga

Physiologically based pharmacokinetic modelling: A sub-compartmentalized model of tissue distribution 

J. Pharmacokinet. Pharmacodyn. 34 (2007), pp 789-806.

Journal PDF-Preprint

S. Rüdiger, J.W. Shuai, W. Huisinga, Ch. Nagaiah, G. Warnecke, I. Parker, M. Falcke

Hybrid stochastic and deterministic simulations of calcium blips

Biophys. J. 93 (2007), pp. 1847-1857.

Journal PDF-Preprint

M. von Kleist, C. Kloft  and W. Huisinga

Combining Systems Biology with physiologically-based pharmacokinetics to support the understanding of drug effects

Proceedings of Foundations of Systems Biology in Engeneering FOSBE (2007), pp. 231-236.

PDF-Preprint

T. Jahnke, and W. Huisinga

Solving the chemical master equation for monomolecular reaction systems analytically

J. Math. Biol. 54 (2007) pp. 1-26.

Journal PDF-Preprint

B.-F. Krippendorff, P. Lienau, A. Reichel, W. Huisinga

Optimizing Classification of Drug-Drug Interaction Potential for CYP450 Isoenzyme Inhibition Assays in Early Drug Discovery

J Biomol Screen. Vol. 12 (2007), pp. 92-99.

Journal PDF-Preprint

R. Telgmann, M. von Kleist, and W. Huisinga

Software Supported Modelling in Pharmacokinetics

In 'Computational Life Sciences II', Lecture Notes in Computer Science 4216 (2006), M.R. Berthold, R. Glen, and I. Fischer (Eds.), Springer, pp. 216–225.

Journal PDF-Preprint

A. Weiße, I. Horenko, and W. Huisinga

Adaptive Approach for Modelling Variability in Pharmacokinetics

In 'Computational Life Sciences II’, Lecture Notes in Computer Science 4216 (2006), M.R. Berthold, R. Glen, and I. Fischer (Eds.), Springer, pp. 194-204

Journal PDF-Preprint

W. Huisinga, R. Telgmann, and M. Wulkow

The virtual lab approach to pharmacokinetic: Design principles and concepts

Drug Discov Today 11(2006) pp. 800-805

Journal PDF-Preprint

A. Alfonsi, E. Cances, G. Turinici, B. Di Ventura and W. Huisinga

Adaptive  simulation of hybrid stochastic and deterministic models for biochemical systems

ESAIM: Proc. 14 (2005), pp. 1-13.

Journal PDF-Preprint

W. Huisinga and B. Schmidt

Metastability and Dominant Eigenvalues of Transfer Operators

In 'Advances in Algorithms for Macromolecular Simulation', Lecture Notes in Computational Science and Engineering 49, C. Chipot, R. Elber, A. Laaksonen, B. Leimkuhler, A. Mark, T. Schlick, C. Schütte, and R. Skeel (Eds.) Springer (2005).

Book PDF-Preprint

I. Horenko, S. Lorenz, C. Schütte and W. Huisinga

Adaptive Approach for Non-Linear Sensitivity Analysis of Reaction Kinetics

 J. Comp. Chem. 26 (2005), pp. 941-948.

Journal   PDF-Preprint

K. Abraham, H. Mielke, W. Huisinga and U. Gundert-Remy

Elevated Internal Exposure of Children in Simulated Acute Inhalation of Volatile Organic Compounds: Dependency on Properties of the Chemical,

Basic & Clinical Pharmacology & Toxicology 96 (2005), pp. 242–243.

Journal PDF-Preprint

K. Abraham, H. Mielke, W. Huisinga and U. Gundert-Remy

Elevated Internal Exposure of Children in Simulated Acute Inhalation of Volatile Organic Compounds: Effects of Concentration and Duration

Arch Toxicol 79 (2005) pp. 63-73

Journal PDF-Preprint

Ch. Schütte, J. Walter, C. Hartmann and W. Huisinga

An Averaging Principle for Fast Degrees of Freedom Exhibiting Long-Term Correlations

SIAM Multiscale Modeling and Simulation 2 (2004) pp. 501-526

Journal  PDF-Preprint 

W. Huisinga, S. Meyn and Ch. Schütte

Phase Transitions & Metastability in Markovian and Molecular Systems

Ann. Appl. Probab. 14 (2004), 419-458.

Journal PDF-Preprint

Ch. Schütte, W. Huisinga and S. Meyn

Metastability of Diffusion Processes

Proceeding of the IUTAM Symposium on Nonlinear Stochastic Dynamics (August 26 - August 30, 2002, Illinois/USA), 2003

Book  PDF-Preprint

W. Huisinga, Ch. Schütte and A. M. Stuart

Extracting Macroscopic Stochastic Dynamics: Model Problems

Comm. Pure Appl. Math. 56 (2003),234-269

Journal PDF-Peprint

Ch. Schütte and W. Huisinga

Biomolecular Conformations can be Identified as Metastable Sets of Molecular Dynamics

in Handbook of Numerical Analysis edited by P. G. Ciarlet, Special Volume: Computational Chemistry (Vol X) , guest editor C. Le Bris (2003)

Book PDF-Preprint

Ch. Schütte, W. Huisinga and P. Deuflhard

Transfer Operator Approach to Conformational Dynamics in Biomolecular Systems

in "Ergodic Theory, Analysis, and Efficient Simulation of Dynamical Systems" edited by B. Fiedler (2001) pp.191-223

Book  PDF-Preprint

Ch. Schütte and W. Huisinga

Biomolecular Conformations as Metastable Sets of Markov Chains

Proceedings of the 38th. Annual Allerton Conference on Communication, Control, and Computing, Oct. 4-6, Allerton House, Monticello, Illinoins/USA (2000) pp.1106-1115

Journal  PDF-Preprint 

T. Galliat, Wilhelm Huisinga and P. Deuflhard

Self-Organizing Maps Combined with Eigenmode Analysis for Automated Cluster Identification

in "Neural Computation" edited by H. Bothe and R. Rojas, ICSC Academic Press (2000) pp.227-232.

PDF-Preprint

Ch. Schütte and W. Huisinga

On Conformational Dynamics induced by Langevin Processes

in "International Conference on Differential Equations (EquaDiff 99)", edited by B. Fiedler K. Gröger and J. Sprekels, Vol.2 (2000) pp.1247-1262

Book PDF-Preprint

P. Deuflhard, W. Huisinga, A. Fischer and Ch. Schütte

Identification of Almost Invariant Aggregates in Reversible Nearly Uncoupled Markov Chains

Lin. Alg. Appl. 315 (2000) pp. 39-59

Journal  PDF-Preprint 

W. Huisinga, Ch. Best, R. Roitzsch, Ch. Schütte and F. Cordes

From Simulation Data to Conformational Ensembles: Structure and Dynamics based Methods

J. Comp. Chem. , Vol.20 (1999) pp.1760-1774

Journal  PDF-Preprint

Ch. Schütte, A. Fischer, W. Huisinga and P. Deuflhard

A Direct Approach to Conformational Dynamics based on Hybrid Monte Carlo

J. Comp. Phys. 151 (1999) pp. 146-168

Journal PDF-Preprint

W. Huisinga, L. Pesce, R. Kosloff and P. Saalfrank

Faber and Newton Polynomial Integrators for Open-System Density Matrix Propagation

J. Chem. Phys., Vol.110 (1999) pp.5538-5547.

Journal  PDF-Preprint

 

Others:

W. Huisinga

Using math to optimize medication

NUI Maynooth Research Magazine, Vol. 1, January 2009.

Research Magazine

W. Huisinga

Computational Physiology

European Communications in Mathematical and Theoretical Biology, No. 8, January 2006, pp. 12-13

Journal

 

Preprints:

W. Huisinga; 2000

The Esssential Spectral Radius and Asymptotic Properties of Transfer Operators

PDF-Preprint 

Ch. Schütte, A. Fischer, W. Huisinga and P. Deuflhard

Hybrid Monte Carlo Method for Essential Molecular Dynamics

ZIB Preprint, 1998.

P. Nettesheim, W. Huisinga and Ch. Schütte

Chebyshev Approximation for Wavepacket Dynamics: better than expected

ZIB preprint, 1996

PDF-Preprint

 

Theses:

W. Huisinga

Metastability of Markovian systems: A transfer operator approach in application to molecular dynamics

PhD thesis in mathematics, Freie Universität Berlin, 2001

PDF Preprint

W. Huisinga

Faber-, Newton- und Krylov-Approximation zur Integration grosser Differentialgleichungssysteme aus der Quantenmechanik

Diploma thesis in mathematics at Free University Berlin, 1997
Awarded by the Deutsche Mathematiker Vereinigung (1998).

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