Wang, J., N. Sun, T. Kunzke, J. Shen, P. Zens, V. M. Prade, A. Feuchtinger, S. Berezowska, and A. Walch (2023). "Spatial metabolomics identifies distinct tumor-specific and stroma-specific subtypes in patients with lung squamous cell carcinoma." Npj Precision Oncology 7(1).


Ebert, K., I. Haffner, G. Zwingenberger, S. Keller, E. Raimúndez, R. Geffers, R. Wirtz, E. Barbaria, V. Hollerieth, R. Arnold, A. Walch, J. Hasenauer, D. Maier, F. Lordick, and B. Luber (2022). "Combining gene expression analysis of gastric cancer cell lines and tumor specimens to identify biomarkers for anti-HER therapies—the role of HAS2, SHB and HBEGF." BMC Cancer 22(1): 1–17.

Kolbe, K., I. Haffner, K. Schierle, D. Maier, B. Geier, B. Luber, H. Bläker, C. Wittekind, and F. Lordick (2022). "Deviating HER2 test results in gastric cancer: analysis from the prospective multicenter VARIANZ study." J Cancer Res Clin Oncol: 1–11.

Shen, J., N. Sun, P. Zens, T. Kunzke, A. Buck, V. M. Prade, J. Wang, Q. Wang, R. Hu, A. Feuchtinger, S. Berezowska, and A. Walch (2022). "Spatial metabolomics for evaluating response to neoadjuvant therapy in non-small cell lung cancer patients." Cancer Commun n/a(n/a).

Wang, J., T. Kunzke, V. M. Prade, J. Shen, A. Buck, A. Feuchtinger, I. Haffner, B. Luber, D. H. W. Liu, R. Langer, F. Lordick, N. Sun, and A. Walch (2022). "Spatial Metabolomics Identifies Distinct Tumor-Specific Subtypes in Gastric Cancer Patients." Clin Cancer Res 28(13): 2865–2877.


Haffner, I., K. Schierle, E. Raimúndez, B. Geier, D. Maier, J. Hasenauer, B. Luber, A. Walch, K. Kolbe, J. R. Knorrenschild, A. Kretzschmar, B. Rau, L. F. von Weikersthal, M. Ahlborn, G. Siegler, S. Fuxius, T. Decker, C. Wittekind, and F. Lordick (2021). "HER2 Expression, Test Deviations, and Their Impact on Survival in Metastatic Gastric Cancer: Results From the Prospective Multicenter VARIANZ Study." J Clin Oncol 39(13): 1468.

Kunzke, T., F. T. Hölzl, V. M. Prade, A. Buck, K. Huber, A. Feuchtinger, K. Ebert, G. Zwingenberger, R. Geffers, S. M. Hauck, I. Haffner, B. Luber, F. Lordick, and A. Walch (2021). "Metabolomic therapy response prediction in pretherapeutic tissue biopsies for trastuzumab in patients with HER2-positive advanced gastric cancer." Clin Transl Med 11(9): e547.

Kunzke, T., V. M. Prade, A. Buck, N. Sun, A. Feuchtinger, M. Matzka, I. E. Fernandez, W. Wuyts, M. Ackermann, D. Jonigk, M. Aichler, R. A. Schmid, O. Eickelberg, S. Berezowska, and A. Walch (2021). "Patterns of Carbon-Bound Exogenous Compounds in Patients with Lung Cancer and Association with Disease Pathophysiology." Cancer Res 81(23): 5862–5875.

Schmiester, L., Y. Schälte, F. T. Bergmann, T. Camba, E. Dudkin, J. Egert, F. Fröhlich, L. Fuhrmann, A. L. Hauber, S. Kemmer, P. Lakrisenko, C. Loos, S. Merkt, W. Müller, D. Pathirana, E. Raimúndez, L. Refisch, M. Rosenblatt, P. L. Stapor, P. Städter, D. Wang, F.-G. Wieland, J. R. Banga, J. Timmer, A. F. Villaverde, S. Sahle, C. Kreutz, J. Hasenauer, and D. Weindl (2021). "PEtab—Interoperable specification of parameter estimation problems in systems biology." PLoS Comput. Biol. 17(1).


Alfonso, J. C. L., L. A. Papaxenopoulou, P. Mascheroni, M. Meyer-Hermann, and H. Hatzikirou (2020). "On the Immunological Consequences of Conventionally Fractionated Radiotherapy." ISCIENCE 23(3).

Ebert, K., G. Zwingenberger, E. Barbaria, S. Keller, C. Heck, R. Arnold, V. Hollerieth, J. Mattes, R. Geffers, E. Raimúndez, J. Hasenauer, and B. Luber (2020). "Determining the effects of trastuzumab, cetuximab and afatinib by phosphoprotein, gene expression and phenotypic analysis in gastric cancer cell lines." BMC Cancer 20(1): 1–19.

Kunzke, T., A. Buck, V. M. Prade, A. Feuchtinger, O. Prokopchuk, M. E. Martignoni, S. Heisz, H. Hauner, K.-P. Janssen, A. Walch, and M. Aichler (2020). "Derangements of amino acids in cachectic skeletal muscle are caused by mitochondrial dysfunction." Journal of Cachexia, Sarcopenia and Muscle 11(1): 226-240.

Neef, S. K., S. Winter, U. Hofmann, T. E. Mürdter, E. Schaeffeler, H. Horn, A. Buck, A. Walch, J. Hennenlotter, G. Ott, F. Fend, J. Bedke, M. Schwab, and M. Haag (2020). "Optimized protocol for metabolomic and lipidomic profiling in formalin-fixed paraffin-embedded kidney tissue by LC-MS." Anal Chim Acta 1134: 125–135.

Prade, V. M., T. Kunzke, A. Feuchtinger, M. Rohm, B. Luber, F. Lordick, A. Buck, and A. Walch (2020). "De novo discovery of metabolic heterogeneity with immunophenotype-guided imaging mass spectrometry." Molecular Metabolism 36: 100953.

Raimundez, E., S. Keller, G. Zwingenberger, K. Ebert, S. Hug, F. J. Theis, D. Maier, B. Luber, and J. Hasenauer (2020). "Model-based analysis of response and resistance factors of cetuximab treatment in gastric cancer cell lines." PLoS Comput Biol 16(3).

Schmiester, L., Y. Schaelte, F. Froehlich, J. Hasenauer, and D. Weindl (2020). "Efficient parameterization of large-scale dynamic models based on relative measurements." Bioinformatics (Oxford, England) 36(2): 594–602.


Balluff, B., Buck, A., Martin-Lorenzo, M., Dewez, F., Langer, R., McDonnell, L. A., Walch, A. and Heeren, R. M. A. (2019). "Integrative Clustering in Mass Spectrometry Imaging for Enhanced Patient Stratification." Proteomics Clin Appl 13(1): e1800137.

Ebert, K., Mattes, J., Kunzke, T., Zwingenberger, G. and Luber, B. (2019). "MET as resistance factor for afatinib therapy and motility driver in gastric cancer cells." PLoS One 14(9): e0223225.

Fischer, D. S., Fiedler, A. K., Kernfeld, E. M., Genga, R. M. J., Bastidas-Ponce, A., Bakhti, M., Lickert, H., Hasenauer, J., Maehr, R. and Theis, F. J. (2019). "Inferring population dynamics from single-cell RNA-sequencing time series data." Nat Biotechnol 37(4): 461-468.

Huber, K., Kunzke, T., Buck, A., Langer, R., Luber, B., Feuchtinger, A. and Walch, A. (2019). "Multimodal analysis of formalin-fixed and paraffin-embedded tissue by MALDI imaging and fluorescence in situ hybridization for combined genetic and metabolic analysis." Lab Invest 99(10): 1535-1546.

Mascheroni, P., Lopez Alfonso, J. C., Kalli, M., Stylianopoulos, T., Meyer-Hermann, M. and Hatzikirou, H. (2019). "On the Impact of Chemo-Mechanically Induced Phenotypic Transitions in Gliomas." Cancers (Basel) 11(5).

Papathomas, T. G., Sun, N., Chortis, V., Taylor, A. E., Arlt, W., Richter, S., Eisenhofer, G., Ruiz-Babot, G., Guasti, L. and Walch, A. K. (2019). "Novel methods in adrenal research: a metabolomics approach." Histochem Cell Biol 151(3): 201-216.


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. and Meyer-Hermann, M. (2016). "Functional modules of sigma factor regulons guarantee adaptability and evolvability." Scientific Reports 6: 22212.

Boianelli, A., Sharma-Chawla, N., Bruder, D. and Hernandez-Vargas, E. A. (2016). "Oseltamivir PK/PD Modeling and Simulation to Evaluate Treatment Strategies against Influenza-Pneumococcus Coinfection." Frontiers in Cellular and Infection Microbiology 6: 60.

Buck, A., Balluff, B., Voss, A., Langer, R., Zitzelsberger, H., Aichler, M. and 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?" Analytical Chemistry 88(10): 5281-5289.

Fiedler, A., Raeth, S., Theis, F. J., Hausser, A. and Hasenauer, J. (2016). "Tailored parameter optimization methods for ordinary differential equation models with steady-state constraints." BMC systems biology 10(1): 80.

Fröhlich, F., Thomas, P., Kazeroonian, A., Theis, F. J., Grima, R. and Hasenauer, J. (2016). "Inference for Stochastic Chemical Kinetics Using Moment Equations and System Size Expansion." PLoS computational biology 12(7): e1005030.

Geissen, E.-M., Hasenauer, J., Heinrich, S., Hauf, S., Theis, F. J. and Radde, N. E. (2016). "MEMO: multi-experiment mixture model analysis of censored data." Bioinformatics (Oxford, England) 32(16): 2464-2472.

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

Hross, S. and Hasenauer, J. (2016). "Analysis of CFSE time-series data using division-, age- and label-structured population models." Bioinformatics (Oxford, England) 32(15): 2321-2329.

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. and Walch, A. (2016). "High-mass-resolution MALDI mass spectrometry imaging of metabolites from formalin-fixed paraffin-embedded tissue." Nature Protocols 11(8): 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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