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Aichler, M., Kunzke, T., Buck, A., Sun, N., Ackermann, M., Jonigk, D., Gaumann, A.Walch, A., 2018. Molecular similarities and differences from human pulmonary fibrosis and corresponding mouse model: MALDI imaging mass spectrometry in comparative medicine. Lab. Invest., 98(1), 141-149.

Desbenoit, N., Walch, A., Spengler, B., Brunelle, A.Römpp, A., 2018. Correlative mass spectrometry imaging, applying time-of-flight secondary ion mass spectrometry and atmospheric pressure matrix-assisted laser desorption/ionization to a single tissue section. Rapid Commun. Mass Spectrom., 32(2), 159-166.

Fröhlich, F., Kessler, T., Weindl, D., Shadrin, A., Schmiester, L., Hache, H., Muradyan, A., Schütte, M., Lim, J.-H., Heinig, M., Theis, F. J., Lehrach, H., Wierling, C., Lange, B.Hasenauer, J., 2018. Efficient Parameter Estimation Enables the Prediction of Drug Response Using a Mechanistic Pan-Cancer Pathway Model. Cell Syst, 7(6), 567-579.e6.

Keller, S., Zwingenberger, G., Ebert, K., Hasenauer, J., Wasmuth, J., Maier, D., Haffner, I., Schierle, K., Weirich, G.Luber, B., 2018. Effects of trastuzumab and afatinib on kinase activity in gastric cancer cell lines. Mol Oncol, 12(4), 441-462.

Klinger, E., Rickert, D.Hasenauer, J., 2018. pyABC: distributed, likelihood-free inference. Bioinformatics, 34(20), 3591-3593.

Stapor, P., Weindl, D., Ballnus, B., Hug, S., Loos, C., Fiedler, A., Krause, S., Hroß, S., Fröhlich, F., Hasenauer, J.Wren, J., 2018. PESTO: Parameter EStimation TOolbox. Bioinformatics, 34(4), 705-707.

Sun, N., Fernandez, I. E., Wei, M., Witting, M., Aichler, M., Feuchtinger, A., Burgstaller, G., Verleden, S. E., Schmitt-Kopplin, P., Eickelberg, O.Walch, A., 2018. Pharmacometabolic response to pirfenidone in pulmonary fibrosis detected by MALDI-FTICR-MSI. Eur. Respir. J., 52(3).

Sun, N., Wu, Y., Nanba, K., Sbiera, S., Kircher, S., Kunzke, T., Aichler, M., Berezowska, S., Reibetanz, J., Rainey, W. E., Fassnacht, M., Walch, A.Kroiss, M., 2018. High-Resolution Tissue Mass Spectrometry Imaging Reveals a Refined Functional Anatomy of the Human Adult Adrenal Gland. Endocrinology, 159(3), 1511-1524.

Urban, C., Buck, A., Siveke, J. T., Lordick, F., Luber, B., Walch, A.Aichler, M., 2018. PAXgene fixation enables comprehensive metabolomic and proteomic analyses of tissue specimens by MALDI MSI. Biochim. Biophys. Acta, 1862(1), 51-60.


Aichler, M., Borgmann, D., Krumsiek, J., Buck, A., MacDonald, P.E., Fox, J.E.M., Lyon, J., Light, P.E., Keipert, S., Jastroch, M., Feuchtinger, A., Mueller, N.S., Sun, N., Palmer, A., Alexandrov, T., Hrabe de Angelis, M., Neschen, S., Tschöp, M.H., Walch, A., 2017. N-acyl Taurines and Acylcarnitines Cause an Imbalance in Insulin Synthesis and Secretion Provoking β Cell Dysfunction in Type 2 Diabetes. Cell Metab. 25, 1334–1347.e4.

Ballnus, B., Hug, S., Hatz, K., Görlitz, L., Hasenauer, J., Theis, F.J., 2017. Comprehensive benchmarking of Markov chain Monte Carlo methods for dynamical systems. BMC Syst Biol 11, 63.

Fichter, C.D., Przypadlo, C.M., Buck, A., Herbener, N., Riedel, B., Schäfer, L., Nakagawa, H., Walch, A., Reinheckel, T., Werner, M., Lassmann, S., 2017. A new model system identifies epidermal growth factor receptor-human epidermal growth factor receptor 2 (HER2) and HER2-human epidermal growth factor receptor 3 heterodimers as potent inducers of oesophageal epithelial cell invasion. J. Pathol. 243, 481–495.

Fröhlich, F., Kaltenbacher, B., Theis, F.J., Hasenauer, J., 2017a. Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks. PLoS Comput. Biol. 13, e1005331.

Fröhlich, F., Theis, F.J., Rädler, J.O., Hasenauer, J., 2017b. Parameter estimation for dynamical systems with discrete events and logical operations. Bioinformatics 33, 1049–1056.

Hatzikirou, H., López Alfonso, J.C., Leschner, S., Weiss, S., Meyer-Hermann, M., 2017. Therapeutic Potential of Bacteria against Solid Tumors. Cancer Res. 77, 1553–1563.

Jagiella, N., Rickert, D., Theis, F.J., Hasenauer, J., 2017. Parallelization and High-Performance Computing Enables Automated Statistical Inference of Multi-scale Models. Cell Syst 4, 194–206.e9.

Keller, S., Kneissl, J., Grabher-Meier, V., Heindl, S., Hasenauer, J., Maier, D., Mattes, J., Winter, P., Luber, B., 2017. Evaluation of epidermal growth factor receptor signaling effects in gastric cancer cell lines by detailed motility-focused phenotypic characterization linked with molecular analysis. BMC Cancer 17, 845.

Kneissl, J., Hartmann, A., Pfarr, N., Erlmeier, F., Lorber, T., Keller, S., Zwingenberger, G., Weichert, W., Luber, B., 2017. Influence of the HER receptor ligand system on sensitivity to cetuximab and trastuzumab in gastric cancer cell lines. J. Cancer Res. Clin. Oncol. 143, 573–600.

Kunzke, T., Balluff, B., Feuchtinger, A., Buck, A., Langer, R., Luber, B., Lordick, F., Zitzelsberger, H., Aichler, M., Walch, A., Kunzke, T., Balluff, B., Feuchtinger, A., Buck, A., Langer, R., Luber, B., Lordick, F., Zitzelsberger, H., Aichler, M., Walch, A., 2017. Native glycan fragments detected by MALDI-FT-ICR mass spectrometry imaging impact gastric cancer biology and patient outcome. Oncotarget 8, 68012–68025.

Maier, D., 2017. Applying Systems Medicine in the Clinic. Current Opinion in Systems Biology.


Binder, S.C., Eckweiler, D., Schulz, S., Bielecka, A., Nicolai, T., Franke, R., Häussler, S., Meyer-Hermann, M., 2016. Functional modules of sigma factor regulons guarantee adaptability and evolvability. Sci Rep 6, 22212.

Boianelli, A., Sharma-Chawla, N., Bruder, D., Hernandez-Vargas, E.A., 2016. Oseltamivir PK/PD Modeling and Simulation to Evaluate Treatment Strategies against Influenza-Pneumococcus Coinfection. Front Cell Infect Microbiol 6, 60.

Buck, A., Balluff, B., Voss, A., Langer, R., Zitzelsberger, H., Aichler, M., Walch, A., 2016. How Suitable is Matrix-Assisted Laser Desorption/Ionization-Time-of-Flight for Metabolite Imaging from Clinical Formalin-Fixed and Paraffin-Embedded Tissue Samples in Comparison to Matrix-Assisted Laser Desorption/Ionization-Fourier Transform Ion Cyclotron Resonance Mass Spectrometry? Anal. Chem. 88, 5281–5289.

Fiedler, A., Raeth, S., Theis, F.J., Hausser, A., Hasenauer, J., 2016. Tailored parameter optimization methods for ordinary differential equation models with steady-state constraints. BMC Syst Biol 10, 80.

Fröhlich, F., Thomas, P., Kazeroonian, A., Theis, F.J., Grima, R., Hasenauer, J., 2016b. Inference for Stochastic Chemical Kinetics Using Moment Equations and System Size Expansion. PLoS Comput. Biol. 12, e1005030.

Geissen, E.-M., Hasenauer, J., Heinrich, S., Hauf, S., Theis, F.J., Radde, N.E., 2016. MEMO: multi-experiment mixture model analysis of censored data. Bioinformatics 32, 2464–2472.

Ghanbari, A., Dehghany, J., Schwebs, T., Müsken, M., Häussler, S., Meyer-Hermann, M., 2016. Inoculation density and nutrient level determine the formation of mushroom-shaped structures in Pseudomonas aeruginosa biofilms. Sci Rep 6, 32097.

Hross, S., Hasenauer, J., 2016. Analysis of CFSE time-series data using division-, age- and label-structured population models. Bioinformatics 32, 2321–2329.

Kneissl, J., Hartmann, A., Pfarr, N., Erlmeier, F., Lorber, T., Keller, S., Zwingenberger, G., Weichert, W., Luber, B., 2016. Influence of the HER receptor ligand system on sensitivity to cetuximab and trastuzumab in gastric cancer cell lines. J. Cancer Res. Clin. Oncol.

Ly, A., Buck, A., Balluff, B., Sun, N., Gorzolka, K., Feuchtinger, A., Janssen, K.-P., Kuppen, P.J.K., van de Velde, C.J.H., Weirich, G., Erlmeier, F., Langer, R., Aubele, M., Zitzelsberger, H., McDonnell, L., Aichler, M., Walch, A., 2016. High-mass-resolution MALDI mass spectrometry imaging of metabolites from formalin-fixed paraffin-embedded tissue. Nat Protoc 11, 1428–1443.


Balluff, B., Frese, C.K., Maier, S.K., Schöne, C., Kuster, B., Schmitt, M., Aubele, M., Höfler, H., Deelder, A.M., Heck, A., Hogendoorn, P.C.W., Morreau, J., Maarten Altelaar, A.F., Walch, A., McDonnell, L.A., 2015. De novo discovery of phenotypic intratumour heterogeneity using imaging mass spectrometry. J. Pathol. 235, 3–13.

Binder, S.C., Hernandez-Vargas, E.A., Meyer-Hermann, M., 2015. Reducing complexity: An iterative strategy for parameter determination in biological networks. Computer Physics Communications 190, 15–22.

Boianelli, A., Nguyen, V.K., Ebensen, T., Schulze, K., Wilk, E., Sharma, N., Stegemann-Koniszewski, S., Bruder, D., Toapanta, F.R., Guzmán, C.A., Meyer-Hermann, M., Hernandez-Vargas, E.A., 2015. Modeling Influenza Virus Infection: A Roadmap for Influenza Research. Viruses 7, 5274–5304.

Buck, A., Ly, A., Balluff, B., Sun, N., Gorzolka, K., Feuchtinger, A., Janssen, K.-P., Kuppen, P.J.K., van de Velde, C.J.H., Weirich, G., Erlmeier, F., Langer, R., Aubele, M., Zitzelsberger, H., Aichler, M., Walch, A., 2015. High-resolution MALDI-FT-ICR MS imaging for the analysis of metabolites from formalin-fixed, paraffin-embedded clinical tissue samples. J. Pathol. 237, 123–132.

Feuchtinger, A., Stiehler, T., Jütting, U., Marjanovic, G., Luber, B., Langer, R., Walch, A., 2015. Image analysis of immunohistochemistry is superior to visual scoring as shown for patient outcome of esophageal adenocarcinoma. Histochem. Cell Biol. 143, 1–9.

Hasenauer, J., Jagiella, N., Hross, S., Theis, F.J., 2015. Data-Driven Modelling of Biological Multi-Scale Processes. Journal of Coupled Systems and Multiscale Dynamics 3, 101–121.

Hatzikirou, H., Alfonso, J.C.L., Mühle, S., Stern, C., Weiss, S., Meyer-Hermann, M., 2015. Cancer therapeutic potential of combinatorial immuno- and vasomodulatory interventions. J R Soc Interface 12.

Hug, S., Schwarzfischer, M., Hasenauer, J., Marr, C., Theis, F.J., 2015. An adaptive scheduling scheme for calculating Bayes factors with thermodynamic integration using Simpson’s rule. Stat Comput 26, 663–677.

Kempf, H., Bleicher, M., Meyer-Hermann, M., 2015. Spatio-Temporal Dynamics of Hypoxia during Radiotherapy. PLoS ONE 10, e0133357.

Nguyen, V.K., Binder, S.C., Boianelli, A., Meyer-Hermann, M., Hernandez-Vargas, E.A., 2015. Ebola virus infection modeling and identifiability problems. Front Microbiol 6, 257.

Sukhorukov, V.M., Meyer-Hermann, M., 2015. Structural Heterogeneity of Mitochondria Induced by the Microtubule Cytoskeleton. Sci Rep 5, 13924.


Aichler, M., Luber, B., Lordick, F., Walch, A., 2014a. Proteomic and metabolic prediction of response to therapy in gastric cancer. World J. Gastroenterol. 20, 13648–13657.

Aichler, M., Motschmann, M., Jütting, U., Luber, B., Becker, K., Ott, K., Lordick, F., Langer, R., Feith, M., Siewert, J.R., Walch, A., 2014b. Epidermal growth factor receptor (EGFR) is an independent adverse prognostic factor in esophageal adenocarcinoma patients treated with cisplatin-based neoadjuvant chemotherapy. Oncotarget 5, 6620–6632.

Meyer-Hermann, M., 2014. Overcoming the dichotomy of quantity and quality in antibody responses. J. Immunol. 193, 5414–5419.

Zhao, G., Dharmadhikari, G., Maedler, K., Meyer-Hermann, M., 2014. Possible role of interleukin-1β in type 2 diabetes onset and implications for anti-inflammatory therapy strategies. PLoS Comput. Biol. 10, e1003798.


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