SYS-Stomach

Publikationen

2018

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, 141–149. doi.org/10.1038/labinvest.2017.110

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, 159–166. doi.org/10.1002/rcm.8022

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, 441–462. doi.org/10.1002/1878-0261.12170

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, 705–707. doi.org/10.1093/bioinformatics/btx676

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. doi.org/10.1210/en.2018-00064

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, 51–60. doi.org/10.1016/j.bbagen.2017.10.005

2017

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. doi.org/10.1016/j.cmet.2017.04.012

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. doi.org/10.1186/s12918-017-0433-1

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. doi.org/10.1002/path.4987

Fröhlich, F., Kaltenbacher, B., Theis, F.J., Hasenauer, J., 2017a. Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks. PLoS Comput. Biol. 13, e1005331. doi.org/10.1371/journal.pcbi.1005331

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. doi.org/10.1093/bioinformatics/btw764

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. doi.org/10.1158/0008-5472.CAN-16-1621

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. doi.org/10.1016/j.cels.2016.12.002

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. doi.org/10.1186/s12885-017-3822-3

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. doi.org/10.1007/s00432-016-2308-z

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. doi.org/10.18632/oncotarget.19137

Maier, D., 2017. Applying Systems Medicine in the Clinic. Current Opinion in Systems Biology. doi.org/10.1016/j.coisb.2017.04.014

2016

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. doi.org/10.1038/srep22212

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. doi.org/10.3389/fcimb.2016.00060

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. doi.org/10.1021/acs.analchem.6b00460

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. doi.org/10.1186/s12918-016-0319-7

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. doi.org/10.1371/journal.pcbi.1005030

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. doi.org/10.1093/bioinformatics/btw190

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. doi.org/10.1038/srep32097

Hross, S., Hasenauer, J., 2016. Analysis of CFSE time-series data using division-, age- and label-structured population models. Bioinformatics 32, 2321–2329. doi.org/10.1093/bioinformatics/btw131

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. doi.org/10.1007/s00432-016-2308-z

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. doi.org/10.1038/nprot.2016.081

2015

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. doi.org/10.1002/path.4436

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. doi.org/10.1016/j.cpc.2015.01.001

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. doi.org/10.3390/v7102875

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. doi.org/10.1002/path.4560

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. doi.org/10.1007/s00418-014-1258-2

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. doi.org/10.1166/jcsmd.2015.1069

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. doi.org/10.1098/rsif.2015.0439

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. doi.org/10.1007/s11222-015-9550-0

Kempf, H., Bleicher, M., Meyer-Hermann, M., 2015. Spatio-Temporal Dynamics of Hypoxia during Radiotherapy. PLoS ONE 10, e0133357. doi.org/10.1371/journal.pone.0133357

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. doi.org/10.3389/fmicb.2015.00257

Sukhorukov, V.M., Meyer-Hermann, M., 2015. Structural Heterogeneity of Mitochondria Induced by the Microtubule Cytoskeleton. Sci Rep 5, 13924. http://doi.org/10.1038/srep13924

2014

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. doi.org/10.3748/wjg.v20.i38.13648

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. doi.org/10.18632/oncotarget.2268

Meyer-Hermann, M., 2014. Overcoming the dichotomy of quantity and quality in antibody responses. J. Immunol. 193, 5414–5419. doi.org/10.4049/jimmunol.1401828

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. doi.org/10.1371/journal.pcbi.1003798

 

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