THE IntiQuan TEAM

All IntiQuan team members are highly committed towards supporting our clients in the efficient development of innovative medicines from tomorrow. Team members have an excellent technical, mathematical, statistical, modeling, and analytical capability. At the same time IntiQuan team members combine many years of experience in the model based support of drug development projects, and do have the communication skills that are needed to enable non-technical teams a detailed understanding of provided results.

Henning Schmidt, PhD

Managing Director and Senior Consultant

Tel: +41 76 603 28 06
Email: henning.schmidt@intiquan.com

Short CV

Henning Schmidt is an expert for Model Based Drug Development with over thirteen years of industry experience. His experience ranges from target validation in the early phases of drug discovery to study design for post marketing commitments.

During the last years, he has provided decision-making support to drug discovery and development teams in various therapeutic areas, including oncology, dermatology, immunology, respiratory, bone and muscle wasting diseases. This has led to several go/no-go decisions on the progression of novel drugs through their development cycle and successful registrations.

Henning Schmidt greatly enjoys working in all stages of drug discovery and development, supporting project teams through integrative quantitative analyses, targeting informed decision making. He also focuses on development and implementation of novel and creative quantitative pharmacology and pharmacometric approaches.

Henning Schmidt received undergraduate education at Darmstadt University and SUPELEC in Paris. He obtained his PhD in Control Theory and Systems Biology at the Royal Institute of Technology in Stockholm, Sweden.

Publications

Journal Articles

Schmidt, H., Radivojevic, A. (2014) Enhancing population pharmacokinetic (popPK) modeling efficiency using an integrated workflow, Journal of Pharmacokinetics and Pharmacodynamics, invited paper, 41(4)

Hallow, K.M., et al. (2014) A model-based approach to investigating the pathophysiological mechanisms of hypertension and response to antihypertensive therapies: Extending the Guyton model, American Journal of Physiology, DOI: 10.1152/ajpregu.00039.2013

Sunnaker, M., Schmidt, H., Jirstrand, M., Cedersund, G. (2010) Zooming of states and parameters using a lumping approach including back-translation, BMC Systems Biology, 4(28)

Dell’Orco, D., Schmidt, H., Mariani, S, Fanelli, F. (2009) Network-level analysis of light adaptation in rod cells under normal and altered conditions, Molecular BioSystems, DOI: 10.1039/b908123b

Schmidt, H., Madsen, M., Danø, S., Cedersund, G. (2008) Complexity Reduction of Biochemical Rate Expressions, Bioinformatics, doi: 10.1093/bioinformatics/btn035

Dell’Orco, D., Schmidt, H. (2008) Mesoscopic Monte Carlo simulations of stochastic encounters between photoactivated rhodopsin and transducin in the ROS-disc membrane, Journal of Physical Chemistry, doi: 10.1021/jp709963f

Nedbal, L., Červený, J., Rascher, U., Schmidt, H. (2007) A modeling approach to understand chlorophyll fluorescence transients and complex dynamic features of photosynthesis in fluctuating light, Photosynthesis Research, 93, 223-234

Schmidt, H., Drews, G., Vera, J., Wolkenhauer, O. (2007) SBML Export Interface for the Systems Biology Toolbox for MATLAB, Bioinformatics, 23, 1297-1298

Schmidt, H. (2007) SBaddon: High Performance Simulation for the Systems Biology Toolbox for MATLAB, Bioinformatics, 23, 646-647

Danø, S., Madsen, M., Schmidt, H., Cedersund, G. (2006) Reduction of a biochemical model with preservation of its basic dynamic properties, FEBS Journal, 273, 4862-4877

Schmidt, H., Jirstrand, M., Wolkenhauer, O. (2006) Information Technology in Systems Biology, invited article for it–Information Technology, 48(3), 133-139

Schmidt, H., Jirstrand, M. (2006) Systems Biology Toolbox for MATLAB: A computational platform for research in Systems Biology, Bioinformatics, 22(4), 514-515

Ullah, M., Schmidt, H., Cho, K.-H., Wolkenhauer, O. (2006) Deterministic Modelling and Stochastic Simulation of Pathways using MATLAB, IEE Proceedings – Systems Biology, 153(2), 53-60

Schmidt, H., Jacobsen, E.W., Cho, K.-H. (2005) Identification of Small Scale Biochemical Networks Based on General Type System Perturbations, FEBS Journal, 272(9), 2141-2151

Schmidt, H., Jacobsen, E.W. (2004) Linear systems approach to analysis of complex dynamic behaviours in biochemical networks, IEE Systems Biology, 1, 149-158

Schmidt, H., Jacobsen, E.W. (2004) Identifying feedback mechanisms behind complex cell behaviour, IEEE Control Systems Magazine, 24(4), 91-102

Book Chapters

Nedbal, N., Červený, J., Schmidt, H. (2009) Scaling and Integration of Kinetic Models of C3 Photosynthesis: Towards Comprehensive E-Photosynthesis, book chapter, Photosynthesis in silico, Springer

Ericsson, A., Mojzita, D., Schmidt, H., Hohmann, S. (2008) Case study in systematic modelling: Thiamine uptake in Yeast S. cerevisiae, book chapter, Essays in Biochemistry – Systems Biology, Portland Press

Conference posters

Johnson, M., Schmidt, H., Sunnaker, M., Hamren, B., AlHuniti, N., Nayak, S., Tomkinson, H., Vishwanathan, K. (2017) Exposure response relationship of interstitial lung disease (ILD) events following Osimertinib treatment, Population Approach Group (PAGE) meeting 2017, Budapest, Hungary

Johnson, M., Schmidt, H., Sunnaker, M., Nash, T., Nayak, S., Tomkinson, H., Vishwanathan, K. (2017) Population pharmacokinetic and pharmacodynamic analysis of osimertinib, American Society of Clinical Oncology – 53rd Annual Meeting (ASCO2017), Chicago, USA

Sunnåker, M., Schmidt, H. (2016) IQM Tools: Efficient State of the Art Modeling across Pharmacometrics and Systems Pharmacology (ACoP7), Seattle, USA

Radivojevic, A., Schmidt, H. (2015) Datasets for pharmacometric analyses: internal review and standardization efforts, Sixth American Conference on Pharmacometrics (ACoP6), Arlington, VA, USA

Schmidt, H. (2015) SBPOP/mPD: Informing dose-concentration-response relationships – Application to study design and information generation based on competitor data, Population Approach Group (PAGE) meeting 2015, Hersonissos, Greece

Weber, F. Schmidt, H., Pfister, M., J v.d. Anker (2015) Pharmacometric approach to characterize key metabolites of acetaminophen in preterm and term neonates, Population Approach Group (PAGE) meeting 2015, Hersonissos, Greece

Goldhahn, J., Radivojevic, A., Tanko, L., 3, Papanicolaou, DA., Schmidt, H. (2013) Modeling rehabilitation after hip fracture, 2nd Fragility Fracture Network Congress, Berlin, Germany

Schmidt, H. (2013) The “SBPOP Package”: Efficient Support for Model Based Drug Development – From Mechanistic Models to Complex Trial Simulation, Population Approach Group (PAGE) meeting 2013, Glasgow, Scotland

Radivojevic, A., Fink, M., Steimer, J.-L., Schmidt, H. (2013) Enhancing Population PK modeling efficiency using an integrated workflow, Population Approach Group (PAGE) meeting 2013, Glasgow, Scotland

Zhudenkov, K., Helmlinger, G., Schmidt, H. (2012) Application of the SBTOOLBOX2 in drug discovery and development, Population Approach Group (PAGE) meeting 2012, Venice, Italy

Frey, S., Schmidt, H., Rateitschak, K., Beltran, G., Garcia-Salcedo, R., Elbing, K., Bosch, D., Ye, T., Hohmann, S., Wolkenhauer, O. (2009) Modelling Snf1 regulation in Saccharomyces cerevisiae, 9th International Conference on Systems Biology, Gothenburg, Sweden

Egea, J.A., Schmidt, H., Banga, J.R. (2008) A new tool for parameter estimation in nonlinear dynamic biological systems using global optimization, 9th International Conference on Systems Biology, Gothenburg, Sweden

Liebal, U.W., Schmidt, H. (2008) Sensitivity Analysis based Adaptive Search-Space Reduction for Parameter Estimation Applications, 9th International Conference on Systems Biology, Gothenburg, Sweden

Bittig, A.T., Schmidt,H. (2008) Format Overflow? Handling of Modeling Projects in Systems Biology, 9th International Conference on Systems Biology, Gothenburg, Sweden

Dell’Orco, D., Fanelli, F., Schmidt, H. (2008) Dynamic modeling of phototransduction biochemistry in vertebrate rods: from dark/light adaptation to disease, 9th International Conference on Systems Biology, Gothenburg, Sweden

Almquist, J., Schmidt, H., Lang, P., Prätzel-Wolters, D., Deitmer, J.W., Jirstrand, M., Becker, H.M. (2008) A model reduction approach to the kinetics of the monocarboxylate transporter MCT1 and carbonic anhydrase II, 9th International Conference on Systems Biology, Gothenburg, Sweden

Schmidt, H. (2008) Hierarchical Modelling of Metabolism: From Methodology to Application, ISGSB 2008, Elsinor, Denmark

Schmidt, H., Jirstrand, M., Cedersund, G. (2006) A Systematic Modelling Framework for Biochemical and Biological Systems, 7th International Conference on Systems Biology, Yokohama, Japan

Cedersund, G., Jirstrand, M., Schmidt, H. (2006) Model reduction for various levels of model development, 7th International Conference on Systems Biology, Yokohama, Japan

Jirstrand, M., Schmidt, H., Cedersund, G. (2006) Parameter Estimation Using Alternative Cost Functions, 7th International Conference on Systems Biology, Yokohama, Japan

Mojzita, D., Nahmany, A., Schmidt, H., Homann, S. (2006) Dynamic modelling of thiamine regulation in Saccharomyces cerevisiae based on High Performance Liquid Chromatography (HPLC) measurements, International Specialised Symposium on Yeasts, Helsinki, Finland

Schmidt, H., Jirstrand, M. (2005) Systems Biology Toolbox for MATLAB: A computational platform for research in Systems Biology, 6th International Conference on Systems Biology, Boston, USA

Schmidt, H., Jacobsen, E.W. (2004) On the Decomposition of Biochemical Networks, H. Schmidt and E. Jacobsen, 5th International Conference on Systems Biology, Heidelberg, Germany

Schmidt, H., Jacobsen, E.W. (2004) Identification of the dynamic structure of biochemical networks based on least squares estimation of the Jacobian, 5th International Conference on Systems Biology, Heidelberg, Germany

Schmidt, H., Jacobsen, E.W. (2003) A linear systems approach to the analysis of complex behaviours within biochemical reaction networks – application to the cell cycle, 4th International Conference on Systems Biology, Saint Louis, USA

Mikael Sunnåker, PhD

Consultant

Tel: +41 78 888 07 58
Email: mikael.sunnaker@intiquan.com

Short CV

Mikael Sunnåker is a an expert in quantitative analysis and modeling with over 10 years of experience in the domains of Systems Biology, Pharmacometrics, and Health Sciences. He has a strong interest in computational methods and practical applications of mathematical modeling, simulation, optimization, and statistical inference of dynamical systems.

Mikael received his BSc and MSc in engineering physics from Chalmers University of Technology in Sweden, with one year spent at HKUST in Hong Kong. His MSc was focused on complex adaptive systems, which drew his attention to the emerging field of computation biology.

After his studies he worked for two years as an applied scientist in the computational systems biology and bioimaging group at the Fraunhofer-Chalmers Center, where he developed tools for NLME modeling with applications in PK/PD and drug development. This was followed by a PhD and PostDoc in computational biology at ETH in Zurich, and a PostDoc at Swiss Paraplegic Research in Luzern with the focus on large amounts of patient data from hospitals and rehabilitation centers.

Publications

Journal articles

Bossuyt, F., Arnet U., Brinkhof, M.W.G., Eriks-Hoogland I., Lay V., Müller R., Sunnåker M., Hinrichs T., 2017, Shoulder pain in the Swiss spinal cord injury community: prevalence and associated factors, Disability and Rehabilitation, Accepted

Schillings, C., Sunnåker, M., Stelling, J. and Schwab, C., 2015. Efficient Characterization of Parametric Uncertainty of Complex (Bio) chemical Networks. PLoS Comput Biol11(8), p.e1004457.

Sunnåker, M., Zamora-Sillero, E., de Lomana, A.L.G., Rudroff, F., Sauer, U., Stelling, J. and Wagner, A., 2014. Topological augmentation to infer hidden processes in biological systems. Bioinformatics30(2), pp.221-227.

Sunnåker, M., Busetto, A.G., Numminen, E., Corander, J., Foll, M. and Dessimoz, C., 2013. Approximate bayesian computation. PLoS Comput Biol9(1), p.e1002803

Sunnåker, M., Zamora-Sillero, E., Dechant, R., Ludwig, C., Busetto, A.G., Wagner, A. and Stelling, J., 2013. Automatic generation of predictive dynamic models reveals nuclear phosphorylation as the key Msn2 control mechanism. Sci. Signal.6(277), pp.ra41-ra41.

Busetto, A.G., Hauser, A., Krummenacher, G., Sunnåker, M., Dimopoulos, S., Ong, C.S., Stelling, J. and Buhmann, J.M., 2013. Near-optimal experimental design for model selection in systems biology. Bioinformatics29(20), pp.2625-2632.

Berglund, M., Sunnåker, M., Adiels, M., Jirstrand, M. and Wennberg, B., 2012. Investigations of a compartmental model for leucine kinetics using non-linear mixed effects models with ordinary and stochastic differential equations. Mathematical Medicine and Biology29(4), pp.361-384.

Sunnåker, M., Cedersund, G. and Jirstrand, M., 2011. A method for zooming of nonlinear models of biochemical systems. BMC systems biology5(1), p.140.

Sunnåker, M., Schmidt, H., Jirstrand, M. and Cedersund, G., 2010. Zooming of states and parameters using a lumping approach including back-translation. BMC systems biology4(1), p.1.

Book chapters

Sunnåker, M. and Stelling, J., 2016. Model extension and model selection. In Uncertainty in Biology (pp. 213-241). Springer International Publishing.

Busetto, A.G., Sunnåker, M. and Buhmann, J.M., 2014. Computational Design of Informative Experiments in Systems Biology. In A Systems Theoretic Approach to Systems and Synthetic Biology I: Models and System Characterizations (pp. 281-305). Springer Netherlands.

Selection of conference posters

Johnson, M., Schmidt, H., Sunnaker, M., Hamren, B., AlHuniti, N., Nayak, S., Tomkinson, H., Vishwanathan, K. (2017) Exposure response relationship of interstitial lung disease (ILD) events following Osimertinib treatment, Population Approach Group (PAGE) meeting 2017, Budapest, Hungary

Johnson, M., Schmidt, H., Sunnaker, M., Nash, T., Nayak, S., Tomkinson, H., Vishwanathan, K. (2017) Population pharmacokinetic and pharmacodynamic analysis of osimertinib, American Society of Clinical Oncology – 53rd Annual Meeting (ASCO2017), Chicago, USA

Sunnåker, M., Schmidt, H., 2016, IQM Tools: Efficient State of the Art Modeling across Pharmacometrics and Systems Pharmacology (ACoP7), Seattle, USA

Sunnåker, M., Berglund, M., Wennberg, B., Adiels, M. and Jirstrand, M., 2008. A Matlab Toolbox for Nonlinear Mixed Effects Modeling–Illustrated with a Model for Lipoprotein Kinetics. In 9th International Conference on Systems Biology, Gothenburg, Sweden

Anne Kümmel, PhD

Senior Consultant

Tel: +41 76 345 1807
Email: anne.kuemmel@intiquan.com

Short CV

Anne Kümmel is an experienced professional in supporting pharmaceutical research with quantitative analyses and modeling. In the last six years she contributed to projects at different stages of drug development ranging from preclinical assessments of candidates, translational modeling, and PK/PD modeling in Phase 1 to Phase 3 to pediatric dose selection.

With a solution-oriented mindset Anne enjoys creatively applying most suitable modeling and simulation approaches. She is proficient in mechanistic as well as NLME modeling and has a sound knowledge in PBPK. She has a strong interest in graphical visualization to facilitate modeling results to biologist and clinicians.

After her graduation from the RWTH Aachen as biochemical engineer, Anne obtained her PhD at ETH Zurich at the Bioprocess Laboratory and the Institute of Molecular Systems Biology. With a post-doctoral project at the Novartis Institutes of Biomedical Research she entered pharmaceutical research.

Publications

Selected peer-reviewed Articles

Kümmel A., Selzer P., Siebert D., Schmidt I., Reinhard J., Götte M, Ibig-Rehm Y., Parker C. N., Gabriel D. Differentiation and visualization of diverse cellular phenotypic responses in primary high-content screening Journal of Biomolecular Screening 16(3): 338-347 2012

Kümmel A., Ewald J. C., Fendt S.-M., Jol S., Picotti P., Aebersold R., Sauer U., Zamboni N., Heinemann M. Differential glucose repression in common yeast strains in response to a HXK2 deletion. FEMS Yeast Research 10(3): 322-32, 2010

Kümmel A., Beibel M., Gehin P., Gubler H., Gabriel D., Parker C. N. Integration of multiple readouts into the Z’ factor for assay quality control Journal of Biomolecular Screening 15(1): 95-101, 2010.

Kümmel A., Panke S., Heinemann M. Systematic assignment of thermodynamic constraints in metabolic network models BMC Bioinformatics 7:512, 2006

Kümmel A., Panke S., Heinemann M. Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data Molecular Systems Biology 2, 2006, doi:10.1038/msb4100074

Book chapters

Lowe P. J., Kümmel A., Vasalou C., Matsushima S., Skerjanec A. Integrated quantitation of drug-target binding, biomarkers and clinical response to support rational dose regimen selection. in ADME and translational pharmacokinetics/pharmacodynamics of therapeutic proteins: Applications in drug discovery and development. Zhou, H., Theil F.-P. Eds., John Wiley & Sons Inc.: Hoboken, New Jersey, 2015

Kümmel A., Parker C. N. The interweaving of cheminformatics and high-throughput screening in Cheminformatics and Computational Chemical Biology, Bajorath J. Ed., Humana Press/Springer: Totowa, N. J., 2010

Selected Poster and Oral Presentations at Conferences

Kümmel A., Abuhelwa A., Krause A. Try yourself! Making clinical teams explore dose response relationships in R Shiny Oral presentation @ 12th Basel M&S seminar, Basel, Switzerland, 19-20/09/2016

Kümmel A., Abuhelwa A., Krause A. PECAN, a Shiny application for calculating confidence intervals and prediction intervals for pharmacokinetic and pharmacodynamic models Poster presentation @ 25th PAGE meeting, Lisboa, Portugal, 07-10/06/2016

Kümmel A., Lowe P. Mechanism-based population PK modeling describing pharmacological effects from dose to clinical response enables mechanistics insights and projections beyond the studied treatment Poster presentation @ 7th Noordwijkerhout Symposium on Pharmacokinetics, Pharmacodynamics and Systems Pharmacology, Noordwijk, Netherlands, 23-25/04/2014

Daniel Kaschek, PhD

Consultant

Email: daniel.kaschek@intiquan.com

Short CV

Daniel Kaschek is an experienced modeler working in the field of Systems Biology and Computational Biology since 2008. Over the past years, he has actively worked on the developed of novel mathematical and statistical approaches to data analysis and parameter estimation in ordinary differential equations with applications in Systems Biology and Systems Pharmacology. He is an enthusiast R package developer, authoring several packages on Data Preprocessing and Dynamic Modeling.

Daniel has a background in Physics and specialized on Mathematical Physics at the University of Freiburg, Germany. For his PhD he changed field and started his research in Systems Biology and Data Analysis at the Physics department in Freiburg. During his PhD he covered a broad range of biological applications, e.g., in Immunology, Cancer Research or Drug-Induced Liver Injury, developing and applying diverse mathematical methods related to statistical inference, optimal control and identifiability analysis.

After his PhD, he became leader of the subgroup “Physical Methods in Systems Biology” where he worked with his team on the translation of concepts from theoretical physics to applications in Systems Biology. He joined our IntiQuan team in October 2017.

Publications

Selected publications:

Kaschek, D.; Sharanek, A.; Guillouzo, A.; Timmer, J. & Weaver, R. J., A dynamic mathematical model of bile acid clearance in HepaRG cells, Toxicological Sciences, Oxford University Press, 2017

Rosenblatt, M.; Timmer, J. & Kaschek, D, Customized steady-state constraints for parameter estimation in non-linear ordinary differential equation models, Frontiers in Cell and Developmental Biology, Frontiers Media SA, 2016

Maiwald, T.; Hass, H.; Steiert, B.; Vanlier, J.; Engesser, R.; Raue, A.; Kipkeew, F.; Bock, H. H.; Kaschek, D.; Kreutz, C. & Timmer, J., Driving the model to its limit: profile likelihood based model reduction PloS ONE, Public Library of Science, 2016

Kaschek, D.; Mader, W.; Fehling-Kaschek, M.; Rosenblatt, M. & Timmer, J., Dynamic Modeling, Parameter Estimation and Uncertainty Analysis in R, bioRxiv, Cold Spring Harbor Labs Journals, 2016

Hass, H.; Kreutz, C.; Timmer, J. & Kaschek, D., Fast integration-based prediction bands for ordinary differential equation models, Bioinformatics, Oxford Univ Press, 2016

Kaschek, D.; Henjes, F.; Hasmann, M.; Korf, U. & Timmer, J., Testing the pattern of AKT activation by variational parameter estimation, IEEE Life Science Letters, 2016

Kaschek, D. & Timmer, J., A unified approach to integration and optimization of parametric ordinary differential equations, Springer, 2015

Merkt, B.; Timmer, J. & Kaschek, D., Higher-order Lie symmetries in identifiability and predictability analysis of dynamic models, Physical Review E, APS, 2015

Raue, A.; Schilling, M.; Bachmann, J.; Matteson, A.; Schelke, M.; Kaschek, D.; Hug, S.; Kreutz, C.; Harms, B. D.; Theis, F. J. & others, Lessons learned from quantitative dynamical modeling in systems biology, PloS One, Public Library of Science, 2013

Fiala, G. J.; Kaschek, D.; Blumenthal, B.; Reth, M.; Timmer, J. & Schamel, W. W., Pre-clustering of the B cell antigen receptor demonstrated by mathematically extended electron microscopy, Frontiers in Immunology, Frontiers Media SA, 2013

Kreutz, C.; Raue, A.; Kaschek, D. & Timmer, J., Profile likelihood in systems biology, FEBS Journal, Wiley Online Library, 2013

Kaschek, D. & Timmer, J., A variational approach to parameter estimation in ordinary differential equations, BMC Systems Biology, BioMed Central Ltd, 2012

Pfeifer, A. C.; Kaschek, D.; Bachmann, J.; Klingmüller, U. & Timmer, J., Model-based extension of high-throughput to high-content data, BMC Systems Biology, BioMed Central Ltd, 2010

Willi Weber, MD, PhD, Privatdozent

Senior Medical Advisor