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![]() ![]() | Bintener, T., Pires Pacheco, M. I., Philippidou, D., Margue, C., Kishk, A., Del Mistro, G., Di Leo, L., Moscardo Garcia, M., Halder, R., Sinkkonen, L., De Zio, D., Kreis, S., Kulms, D., & Sauter, T. (26 July 2023). Metabolic modelling-based in silico drug target prediction identifies six novel repurposable drugs for melanoma. Cell Death and Disease, 14 (468). doi:10.1038/s41419-023-05955-1 ![]() |
![]() ![]() | Frias, A., Di Leo, L., Antoranz, A., Nazerai, L., Carretta, M., Bodemeyer, V., Pagliuca, C., Dahl, C., Claps, G., Mandelli, G. E., Andhari, M. D., Pires Pacheco, M. I., Sauter, T., Robert, C., Guldberg, P., Madsen, D. H., Cecconi, F., Bosisio, F. M., & De Zio, D. (2023). Ambra1 modulates the tumor immune microenvironment and response to PD-1 blockade in melanoma. Journal for ImmunoTherapy of Cancer, 11 (3). doi:10.1136/jitc-2022-006389 ![]() |
![]() ![]() | Sauter, T., & Albrecht, M. (2023). Introduction to Systems Biology - Workbook for Flipped-classroom Teaching. Cambridge, United Kingdom: OpenBookPublishers. doi:10.11647/obp.0291 |
![]() ![]() | Gergei, I., Pfau, T., Krämer, B. K., Schneider, J., Nguyen, T.-P., März, W., & Sauter, T. (2023). Cardiovascular risk prediction - a systems medicine approach. ORBilu-University of Luxembourg. https://orbilu.uni.lu/handle/10993/54719. doi:10.1101/2023.03.16.23287363 |
![]() ![]() | Badkas, A., de Landtsheer, S., & Sauter, T. (2023). Expanding the Disease Network of Glioblastoma Multiforme via Topological Analysis. International Journal of Molecular Sciences, 24 (4). doi:10.3390/ijms24043075 ![]() |
![]() ![]() | Pires Pacheco, M. I., Ji, J., Prohaska, T., Moscardo Garcia, M., & Sauter, T. (2022). scFASTCORMICS: A Contextualization Algorithm to Reconstruct Metabolic Multi-Cell Population Models from Single-Cell RNAseq Data. Metabolites. ![]() |
![]() ![]() | Didier, J., de Landtsheer, S., Pires Pacheco, M. I., Kishk, A., Schneider, J., Demuth, I., & Sauter, T. (26 October 2022). Improving Machine Learning-based Prediction of Frailty in Elderly People with Digital Wearables : Data from the Berlin Aging Study II (BASE-II) [Poster presentation]. European Digital Medicine Conference Luxembourg 2022, Belval, Luxembourg. |
![]() ![]() | Didier, J., de Landtsheer, S., Pires Pacheco, M. I., Kishk, A., Schneider, J., Demuth, I., & Sauter, T. (09 October 2022). Machine learning-based prediction of frailty in elderly people : Data from the Berlin Aging Study II (BASE-II) [Poster presentation]. 21st International Conference on Systems Biology, Berlin, Germany. |
![]() ![]() | Moscardo Garcia, M., Pires Pacheco, M. I., & Sauter, T. (2022). Integration of external biomass reactions into existing metabolic models. ORBilu-University of Luxembourg. https://orbilu.uni.lu/handle/10993/52225. |
![]() ![]() | Ternes, D., Tsenkova, M., Pozdeev, V., Meyers, M., Koncina, E., Atatri, S., Schmitz, M., Karta, J., Schmoetten, M., Heinken, A., Rodriguez, F., Delbrouck, C., Gaigneaux, A., Ginolhac, A., Dan Nguyen, T. T., Grandmougin, L., Frachet-Bour, A., Martin-Gallausiaux, C., Pires Pacheco, M. I., ... Letellier, E. (2022). The gut microbial metabolite formate exacerbates colorectal cancer progression. Nature Metabolism. doi:10.1038/s42255-022-00558-0 ![]() |
![]() ![]() | Del Mistro, G., Riemann, S., Schindler, S., Beissert, S., Kontermann, R. E., Ginolhac, A., Halder, R., Presta, L., Sinkkonen, L., Sauter, T., & Kulms, D. (2022). Focal adhesion kinase plays a dual role in TRAIL resistance and metastatic outgrowth of malignant melanoma. Cell Death and Disease. doi:10.1038/s41419-022-04502-8 ![]() |
![]() ![]() | Albrecht, M., Kogan, Y., Kulms, D., & Sauter, T. (2022). Mechanistically Coupled PK (MCPK) Model to Describe Enzyme Induction and Occupancy Dependent DDI of Dabrafenib Metabolism. Pharmaceutics, 14 (2). doi:10.3390/pharmaceutics14020310 ![]() |
![]() ![]() | Sauter, T., Bintener, T., Kishk, A., Presta, L., Prohaska, T., Guignard, D., Zeng, N., Cipriani, C., Arshad, S., Pfau, T., Martins Conde, P., & Pires Pacheco, M. I. (2022). Project-based learning course on metabolic network modelling in computational systems biology. PLoS Computational Biology, 18 (1), 1009711. doi:10.1371/journal.pcbi.1009711 ![]() |
![]() ![]() | Cipriani, C., Pires Pacheco, M. I., Kishk, A., Wachich, M., Abankwa, D., Schaffner-Reckinger, E., & Sauter, T. (2022). Bruceine D Identified as a Drug Candidate against Breast Cancer by a Novel Drug Selection Pipeline and Cell Viability Assay. Pharmaceuticals (Basel, Switzerland), 15 (2). doi:10.3390/ph15020179 ![]() |
![]() ![]() | Badkas, A., de Landtsheer, S., & Sauter, T. (2022). Construction and contextualization approaches for protein-protein interaction networks. Computational and Structural Biotechnology Journal, 20, 3280-3290. doi:10.1016/j.csbj.2022.06.040 ![]() |
![]() ![]() | Bintener, T., Pires Pacheco, M. I., Kishk, A., Didier, J., & Sauter, T. (2022). Drug Target Prediction Using Context-Specific Metabolic Models Reconstructed from rFASTCORMICS. In Methods in Molecular Biology (pp. 221-240). Clifton, N.J., United States: Springer. doi:10.1007/978-1-0716-2513-2_17 ![]() |
![]() ![]() | Kishk, A., Pires Pacheco, M. I., Heurtaux, T., Sinkkonen, L., Pang, J., Fritah, S., Niclou, S., & Sauter, T. (2022). Review of Current Human Genome-Scale Metabolic Models for Brain Cancer and Neurodegenerative Diseases. Cells, 11 (16). doi:10.3390/cells11162486 ![]() |
![]() ![]() | Nantajit, D., Presta, L., Sauter, T., & Tavassoli, M. (2022). EGFR-induced suppression of HPV E6/E7 is mediated by microRNA-9-5p silencing of BRD4 protein in HPV-positive head and neck squamous cell carcinoma. Cell death & disease, 13 (11), 921. doi:10.1038/s41419-022-05269-8 ![]() |
![]() ![]() | Gui, Y., Grzyb, K., Thomas, M., Ohnmacht, J., Garcia, P., Buttini, M., Skupin, A., Sauter, T., & Sinkkonen, L. (2021). Single‑nuclei chromatin profiling of ventral midbrain reveals cell identity transcription factors and cell‑type‑specific gene regulatory variation. Epigenetics and Chromatin. doi:10.1186/s13072-021-00418-3 ![]() |
![]() ![]() | Rufo, N., Korovesis, D., Van Eygen, S., Derua, R., Garg, A. D., Finotello, F., Vara-Perez, M., Rožanc, J., Dewaele, M., de Witte, P. A., Alexopoulos, L. G., Janssens, S., Sinkkonen, L., Sauter, T., Verhelst, S. H. L., & Agostinis, P. (2021). Stress-induced inflammation evoked by immunogenic cell death is blunted by the IRE1α kinase inhibitor KIRA6 through HSP60 targeting. Cell Death and Differentiation. doi:10.1038/s41418-021-00853-5 ![]() |
![]() ![]() | Frangez, Z., Gerard, D., He, Z., Gavriil, M., Fernández-Marrero, Y., Seyed Jafari, M., Hunger, R., Lucarelli, P., Yousefi, S., Sauter, T., Sinkkonen, L., & Simon, H.-U. (2021). ATG5 and ATG7 Expression Levels Are Reduced in Cutaneous Melanoma and Regulated by NRF1. Frontiers in Oncology. doi:10.3389/fonc.2021.721624 ![]() |
![]() ![]() | Thomas, M., Gui, Y., Garcia, P., Karout, M., Gomez Ramos, B., Jaeger, C., Michelucci, A., Gaigneaux, A., Kollmus, H., Centeno, A., Schughart, K., Balling, R., Mittelbronn, M., Nadeau, J. H., Sauter, T., Williams, R. W., Sinkkonen, L., & Buttini, M. (2021). Quantitative trait locus mapping identifies a locus linked to striatal dopamine and points to collagen IV alpha-6 chain as a novel regulator of striatal axonal branching in mice. Genes, Brain, and Behavior. doi:10.1111/gbb.12769 ![]() |
![]() ![]() | Machado, R. A. C., Stojevski, D., de Landtsheer, S., Lucarelli, P., Baron, A., Sauter, T., & Schaffner-Reckinger, E. (22 February 2021). L-plastin Ser5 phosphorylation is modulated by the PI3K/SGK pathway and promotes breast cancer cell invasiveness. Cell Communication and Signaling, 19 (22), 1-22. doi:10.21203/rs.3.rs-276404/v1 ![]() |
![]() ![]() | Di Leo, L., Bodemeyer, V., Bosisio, F. M., Claps, G., Carretta, M., Rizza, S., Faienza, F., Frias, A., Khan, S., Bordi, M., Pires Pacheco, M. I., Di Martino, J., Bravo-Cordero, J. J., Daniel, C. J., Sears, R. C., Donia, M., Madsen, D. H., Guldberg, P., Filomeni, G., ... Cecconi, F. (2021). Loss of Ambra1 promotes melanoma growth and invasion. Nature Communications, 12 (1), 2550. doi:10.1038/s41467-021-22772-2 ![]() |
![]() ![]() | Pfau, T., Galhardo, M., Lin, J., & Sauter, T. (2021). IDARE2-Simultaneous Visualisation of Multiomics Data in Cytoscape. Metabolites, 11 (5). doi:10.3390/metabo11050300 ![]() |
![]() ![]() | Martins Conde, P., Pfau, T., Pires Pacheco, M. I., & Sauter, T. (2021). A dynamic multi-tissue model to study human metabolism. NPJ Systems Biology and Applications, 7 (1), 5. doi:10.1038/s41540-020-00159-1 ![]() |
![]() ![]() | Moscardo Garcia, M., Pires Pacheco, M. I., Bintener, T. J. R., Presta, L., & Sauter, T. (2021). Importance of the biomass formulation for cancer metabolic modeling and drug prediction. iScience, 24 (10), 103110. doi:10.1016/j.isci.2021.103110 ![]() |
![]() ![]() | Walter, J., Bolognin, S., Poovathingal, S., Magni, S., Gerard, D., Antony, P., Nickels, S. L., Salamanca, L., Berger, E., Smits, L., Grzyb, K., Perfeito, R., Hoel, F., Qing, X., Ohnmacht, J., Bertacchi, M., Jarazo, J., Ignac, T., Monzel, A., ... Schwamborn, J. C. (2021). The Parkinson’s-disease-associated mutation LRRK2-G2019S alters dopaminergic differentiation dynamics via NR2F1. Cell Reports. doi:10.1016/j.celrep.2021.109864 ![]() |
![]() ![]() | Schommer, C., Sauter, T., Pang, J., Satagopam, V., Despotovic, V., & Goncalves, J. (2021). Proceedings of the AI4Health Lecture Series (2021) [Paper presentation]. AI4Health Lectures Series (2021), Campus Belval, University of Luxembourg, Luxembourg. |
![]() ![]() | Kishk, A., Pires Pacheco, M. I., & Sauter, T. (2021). DCcov: Repositioning of drugs and drug combinations for SARS-CoV-2 infected lung through constraint-based modeling. iScience, 24 (11), 103331. doi:10.1016/j.isci.2021.103331 ![]() |
![]() ![]() | Badkas, A., Nguyen, T.-P., Caberlotto, L., Schneider, J., de Landtsheer, S., & Sauter, T. (2021). Degree Adjusted Large-Scale Network Analysis Reveals Novel Putative Metabolic Disease Genes. Biology, 10 (2). doi:10.3390/biology10020107 ![]() |
![]() ![]() | Gui, Y., Thomas, M. H., Garcia, P., Karout, M., Halder, R., Michelucci, A., Kollmus, H., Zhou, C., Melmed, S., Schughart, K., Balling, R., Mittelbronn, M., Nadeau, J. H., Williams, R. W., Sauter, T., Buttini, M., & Sinkkonen, L. (2020). Pituitary Tumor Transforming Gene 1 Orchestrates Gene Regulatory Variation in Mouse Ventral Midbrain During Aging. Frontiers in Genetics. doi:10.3389/fgene.2020.566734 ![]() |
![]() ![]() | Sauter, T., & Pires Pacheco, M. I. (2020). Testing informed SIR based epidemiological model for COVID-19 in Luxembourg. ORBilu-University of Luxembourg. https://orbilu.uni.lu/handle/10993/43970. doi:10.1101/2020.07.21.20159046 |
![]() ![]() | Bintener, T. J. R., Pires Pacheco, M. I., & Sauter, T. (2020). Towards the routine use of in silico screenings for drug discovery using metabolic modelling. Biochemical Society Transactions. doi:10.1042/BST20190867 ![]() |
![]() ![]() | Muller, I., Strozyk, E., Schindler, S., Beissert, S., Oo, H. Z., Sauter, T., Lucarelli, P., Raeth, S., Hausser, A., Al Nakouzi, N., Fazli, L., Gleave, M. E., Liu, H., Simon, H.-U., Walczak, H., Green, D. R., Bartek, J., Daugaard, M., & Kulms, D. (2020). Cancer Cells Employ Nuclear Caspase-8 to Overcome the p53-Dependent G2/M Checkpoint through Cleavage of USP28. Molecular Cell. doi:10.1016/j.molcel.2019.12.023 ![]() |
![]() ![]() | Albrecht, M., Lucarelli, P., Kulms, D., & Sauter, T. (2020). Computational models of melanoma. Theoretical biology & medical modelling, 17 (1), 8. doi:10.1186/s12976-020-00126-7 ![]() |
![]() ![]() | Badkas, A., De Landtsheer, S., & Sauter, T. (2020). Topological network measures for drug repositioning. Briefings in Bioinformatics. doi:10.1093/bib/bbaa357 ![]() |
![]() ![]() | Martins Conde, P., Sauter, T., & Nguyen, T.-P. (2020). An efficient machine learning-based approach for screening individuals at risk of hereditary haemochromatosis. Scientific Reports, 10 (1), 20613. doi:10.1038/s41598-020-77367-6 ![]() |
![]() ![]() | Schommer, C., Sauter, T., Pang, J., & Abankwa, D. (2020). Proceedings of the AI4Health Lecture Series (2020) [Paper presentation]. AI4Health Lectures Series (2020), Campus Belval, University of Luxembourg, Luxembourg. |
![]() ![]() | Klaus, C., Hansen, J. N., Ginolhac, A., Gérard, D., Gnanapragassam, V. S., Horstkorte, R., Rossdam, C., Buettner, F. F. R., Sauter, T., Sinkkonen, L., Neumann, H., & Linnartz-Gerlach, B. (2020). Reduced sialylation triggers homeostatic synapse and neuronal loss in middle-aged mice. Neurobiology of Aging. doi:10.1016/j.neurobiolaging.2020.01.008 ![]() |
Pacheco, M., Bintener, T. J. R., & Sauter, T. (2019). Towards the Integration of Metabolic Network Modelling and Machine Learning for the Routine Analysis of High-Throughput Patient Data. In Automated Reasoning for Systems Biology and Medicine. Springer. doi:10.1007/978-3-030-17297-8_15 |
![]() ![]() | Becker, J. C., Gerard, D., Ginolhac, A., Sauter, T., & Sinkkonen, L. (2019). Identification of genes under dynamic post-transcriptional regulation from time-series epigenomic data. Epigenomics. doi:10.2217/epi-2018-0084 ![]() |
![]() ![]() | Pacheco, M., Bintener, T. J. R., Ternes, D., Kulms, D., Haan, S., Letellier, E., & Sauter, T. (May 2019). Identifying and targeting cancer-specific metabolism with network-based drug target prediction. EBioMedicine, 43 (May 2019), 98-106. doi:10.1016/j.ebiom.2019.04.046 ![]() |
![]() ![]() | Greenhalgh, K., Ramiro Garcia, J., Heinken, Ullmann, P., Bintener, T. J. R., Pacheco, M., Baginska, J., Shah, P., Frachet Bour, A., Halder, R., Fritz, J., Sauter, T., Thiele, I., Haan, S., Letellier, E., & Wilmes, P. (30 April 2019). Integrated In Vitro and In Silico Modeling Delineates the Molecular Effects of a Synbiotic Regimen on Colorectal-Cancer-Derived Cells. Cell Reports, 27, 1621–1632. doi:10.1016/j.celrep.2019.04.001 ![]() |
![]() ![]() | Nickels, S., Walter, J., Bolognin, S., Gerard, D., Jäger, C., Qing, X., Tisserand, J., Jarazo, J., Hemmer, K., Harms, A., Halder, R., Lucarelli, P., Berger, E., Antony, P., Glaab, E., Hankemeier, T., Klein, C., Sauter, T., Sinkkonen, L., & Schwamborn, J. C. (2019). Impaired serine metabolism complements LRRK2-G2019S pathogenicity in PD patients. Parkinsonism and Related Disorders. doi:10.1016/j.parkreldis.2019.09.018 ![]() |
![]() ![]() | Pacheco, M., Bintener, T. J. R., & Sauter, T. (2019). Towards the network-based prediction of repurposed drugs using patient-specific metabolic models. EBioMedicine. doi:10.1016/j.ebiom.2019.04.017 |
![]() ![]() | Heirendt, L., Arreckx, S., Pfau, T., Mendoza, S. N., Richelle, A., Heinken, A. K., Haraldsdottir, H. S., Wachowiak, J., Keating, S. M., Vlasov, V., Magnusdottir, S., Ng, C. Y., Preciat, G., Zagare, A., Chan, S. H. J., Aurich, M. K., Clancy, C. M., Modamio, J., Sauls, J. T., ... Fleming, R. M. T. (2019). Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0. Nature Protocols, 14 (3), 639-702. doi:10.1038/s41596-018-0098-2 ![]() |
![]() ![]() | Cecchini, V. F., Nguyen, T.-P., Pfau, T., De Landtsheer, S., & Sauter, T. (2019). An Efficient Machine Learning Method to Solve Imbalanced Data in Metabolic Disease Prediction. In V. F. Cecchini, An Efficient Machine Learning Method to Solve Imbalanced Data in Metabolic Disease Prediction (1st ed, pp. 5). Da Nang, Vietnam: DA NANG PUBLISHING HOUSE. ![]() |
![]() ![]() | Alsahafi, E., Begg, K., Amelio, I., Raulf, N., Lucarelli, P., Sauter, T., & Tavassoli, M. (2019). Clinical update on head and neck cancer: molecular biology and ongoing challenges. Cell Death and Disease, 10 (8), 540. doi:10.1038/s41419-019-1769-9 ![]() |
![]() ![]() | Gerard, D., Schmidt, F., Ginolhac, A., Schmitz, M., Halder, R., Ebert, P., Schulz, M., Sauter, T., & Sinkkonen, L. (2018). Temporal enhancer profiling of parallel lineages identifies AHR and GLIS1 as regulators of mesenchymal multipotency. Nucleic Acids Research. doi:10.1093/nar/gky1240 ![]() |
![]() ![]() | Del Mistro, G., Lucarelli, P., Muller, I., De Landtsheer, S., Zinoveva, A., Hutt, M., Siegemund, M., Kontermann, R. E., Beissert, S., Sauter, T., & Kulms, D. (November 2018). Systemic network analysis identifies XIAP and IkappaBalpha as potential drug targets in TRAIL resistant BRAF mutated melanoma. NPJ Systems Biology and Applications, 4, 39. doi:10.1038/s41540-018-0075-y ![]() |
![]() ![]() | Rozanc, J., Sakellaropoulos, T., Antoranz, A., Gutta, C., Podder, B., Vetma, V., Rufo, N., Agostinis, P., Pliaka, V., Sauter, T., Kulms, D., Rehm, M., & Alexopoulos, L. G. (2018). Phosphoprotein patterns predict trametinib responsiveness and optimal trametinib sensitisation strategies in melanoma. Cell Death and Differentiation. doi:10.1038/s41418-018-0210-8 ![]() |
![]() ![]() | De Landtsheer, S., Lucarelli, P., & Sauter, T. (2018). Using Regularization to Infer Cell Line Specificity in Logical Network Models of Signaling Pathways. Frontiers in Physiology, 9, 550. doi:10.3389/fphys.2018.00550 ![]() |
![]() ![]() | Seip, K., Jorgensen, K., Haselager, M. V., Albrecht, M., Haugen, M. H., Egeland, E. V., Lucarelli, P., Engebraaten, O., Sauter, T., Maelandsmo, G. M., & Prasmickaite, L. (2018). "Stroma-induced phenotypic plasticity offers phenotype-specific targeting to improve melanoma treatment". Cancer Letters. doi:10.1016/j.canlet.2018.09.023 ![]() |
![]() ![]() | Pacheco, M., & Sauter, T. (2018). The FASTCORE Family: For the Fast Reconstruction of Compact Context-Specific Metabolic Networks Models. In M. Fondi, Metabolic Network Reconstruction and Modeling. Springer. ![]() |
![]() ![]() | Raulf, N., Lucarelli, P., Thavaraj, S., Brown, S., Vicencio, J. M., Sauter, T., & Tavassoli, M. (2018). Annexin A1 regulates EGFR activity and alters EGFR-containing tumour-derived exosomes in head and neck cancers. European Journal of Cancer, 102, 52-68. doi:10.1016/j.ejca.2018.07.123 ![]() |
![]() ![]() | Pacheco, M., & Sauter, T. (2018). The FASTCORE Family: For the Fast Reconstruction of Compact Context-Specific Metabolic Networks Models. Methods in Molecular Biology, (1716), 101-110. doi:10.1007/978-1-4939-7528-0_4 ![]() |
![]() ![]() | Lucarelli, P., De Landtsheer, S., & Sauter, T. (2017). Systembasierte Analyse von Wirkstoffresistenzen bei Melanom. ORBilu-University of Luxembourg. https://orbilu.uni.lu/handle/10993/33864. |
![]() ![]() | De Landtsheer, S., Trairatphisan, P., Lucarelli, P., & Sauter, T. (2017). FALCON: A Toolbox for the Fast Contextualisation of Logical Networks. Bioinformatics. doi:10.1093/bioinformatics/btx380 ![]() |
![]() ![]() | Albrecht, M., Sciumè, G., Lucarelli, P., & Sauter, T. (12 October 2016). Thermodynamically constrained averaging theory for cancer growth modelling. IFAC-PapersOnLine, 49 (26), 289-294. doi:10.1016/j.ifacol.2016.12.141 ![]() |
![]() ![]() | Pacheco, M., Pfau, T., & Sauter, T. (2016). Benchmarking procedures for high-throughput context specific reconstruction algorithms. Frontiers in Physiology. doi:10.3389/fphys.2015.00410 ![]() |
![]() ![]() | Lommel, M., Trairatphisan, P., Gäbler, K., Laurini, C., Muller, A., Kaoma, T., Vallar, L., Sauter, T., & Schaffner, E. (2016). L-plastin Ser5 phosphorylation in breast cancer cells and in vitro is mediated by RSK downstream of the ERK/MAPK pathway. FASEB Journal. doi:10.1096/fj.15-276311 ![]() |
![]() ![]() | Martins Conde, P., Sauter, T., & Pfau, T. (2016). Constraint based modelling going multicellular. Frontiers in Molecular Biosciences, 3 (3). doi:10.3389/fmolb.2016.00003 ![]() |
![]() ![]() | Trairatphisan, P., Wiesinger, M., Bahlawane, C., Haan, S., & Sauter, T. (2016). A Probabilistic Boolean Network Approach for the Analysis of Cancer-Specific Signalling: A Case Study of Deregulated PDGF Signalling in GIST. PLoS ONE, 11 (5), 0156223. doi:10.1371/journal.pone.0156223 ![]() |
![]() ![]() | Pacheco, M., John, E.* , Kaoma, T., Heinäniemi, M., Nicot, N., Vallar, L., Bueb, J.-L., Sinkkonen, L., & Sauter, T. (19 October 2015). Integrated metabolic modelling reveals cell-type specific epigenetic control points of the macrophage metabolic network. BMC Genomics, 16 (809). doi:10.1186/s12864-015-1984-4 ![]() * These authors have contributed equally to this work. |
![]() ![]() | Galhardo, M. S., Berninger, P., Nguyen, T.-P., Sauter, T., & Sinkkonen, L. (03 September 2015). Cell type-selective disease-association of genes under high regulatory load. Nucleic Acids Research, 43 (18), 8839-8855. doi:10.1093/nar/gkv863 ![]() |
![]() ![]() | Makadia, H. K., Anderson, W. D., Fey, D., Sauter, T., Schwaber, J. S., & Vadigepalli, R. (2015). Multiscale model of dynamic neuromodulation integrating neuropeptide-induced signaling pathway activity with membrane electrophysiology. Biophysical Journal, 108 (1), 211-23. doi:10.1016/j.bpj.2014.11.1851 ![]() |
![]() ![]() | Dorosz, S. A., Ginolhac, A., Kähne, T., Naumann, M., Sauter, T., Salsmann, A., & Bueb, J.-L. (2015). Role of Calprotectin as a Modulator of the IL27-Mediated Proinflammatory Effect on Endothelial Cells. Mediators of Inflammation, 2015, 1-16. doi:10.1155/2015/737310 ![]() |
![]() ![]() | Roume, H., Buschart, A., Muller, E., May, P., Satagopam, V., Laczny, C. C., Narayanasamy, S., Lebrun, L., Hoopmann, M., Schupp, J., Gillece, J., Hicks, N., Engelthaler, D., Sauter, T., Keim, P., Moritz, R., & Wilmes, P. (2015). Comparative integrated omics: identification of key functionalities in microbial community-wide metabolic networks. Biofilms and Microbiomes, 1 (15007). doi:10.1038/npjbiofilms.2015.7 ![]() |
![]() ![]() | Pfau, T., Pacheco, M., & Sauter, T. (2015). Towards improved genome-scale metabolic network reconstructions: unification, transcript specificity and beyond. Briefings in Bioinformatics. doi:10.1093/bib/bbv100 ![]() |
![]() ![]() | Hillje, A.-L., Beckmann, E., Pavlou, M. A., Jäger, C., Pacheco, M., Sauter, T., Schwamborn, J. C., & Lewejohann, L. (2015). The neural stem cell fate determinant TRIM32 regulates complex behavioral traits. Frontiers in Cellular Neuroscience. doi:10.3389/fncel.2015.00075 ![]() |
![]() ![]() | Bahlawane, C., Eulenfeld, R., Wiesinger, M., Wang, J., Muller, A., Girod, A., Nazarov, P. V., Felsch, K., Vallar, L., Sauter, T., Satagopam, V., & Haan, S. (2015). Constitutive activation of oncogenic PDGFRalpha-mutant proteins occurring in GIST patients induces receptor mislocalisation and alters PDGFRalpha signalling characteristics. Cell Communication and Signaling, 13, 21. doi:10.1186/s12964-015-0096-8 ![]() |
![]() ![]() | Haan, S., Bahlawane, C., Wang, J., Nazarov, P. V., Muller, A., Eulenfeld, R., Haan, C., Rolvering, C., Vallar, L., Satagopam, V., Sauter, T., & Wiesinger, M. (2015). The oncogenic FIP1L1-PDGFRalpha fusion protein displays skewed signaling properties compared to its wild-type PDGFRalpha counterpart. JAK-STAT, 4 (1), 1062596. doi:10.1080/21623996.2015.1062596 ![]() |
![]() ![]() | Galhardo, M. S., Sinkkonen, L., Berninger, P., Lin, J., Sauter, T., & Heinäniemi, M. (December 2014). ChIP-seq profiling of the active chromatin marker H3K4me3 and PPARγ, CEBPα and LXR target genes in human SGBS adipocytes. Genomics Data, 2, 230-236. doi:10.1016/j.gdata.2014.07.002 ![]() |
![]() ![]() | Galhardo, M. S., Sinkkonen, L., Berninger, P., Lin, J., Sauter, T., & Heinäniemi, M. (December 2014). Transcriptomics profiling of human SGBS adipogenesis. Genomics Data, 2, 246-248. doi:10.1016/j.gdata.2014.07.004 ![]() |
![]() ![]() | Trairatphisan, P., Mizera, A., Pang, J., Tantar, A.-A., & Sauter, T. (01 July 2014). optPBN: An Optimisation Toolbox for Probabilistic Boolean Networks. PLoS ONE, 9 (7), 98001 (1-15. doi:10.1371/journal.pone.0098001 ![]() |
![]() ![]() | Liivrand, M., Heinäniemi, M., John, E., Schneider, J., Sauter, T., & Sinkkonen, L. (16 January 2014). Combinatorial regulation of lipoprotein lipase by microRNAs during mouse adipogenesis. RNA Biology, 11 (1), 76-91. doi:10.4161/rna.27655 ![]() |
![]() ![]() | Konrath, F., Witt, J., Sauter, T., & Kulms, D. (2014). Identification of New IkappaBalpha Complexes by an Iterative Experimental and Mathematical Modeling Approach. PLoS Computational Biology, 10 (3), 1003528. doi:10.1371/journal.pcbi.1003528 ![]() |
![]() ![]() | Ederer, M., Steinsiek, S., Stagge, S., Rolfe, M., Ter Beek, A., Knies, D., Teixeira de Mattos, M., Sauter, T., Green, J., Poole, R., Bettenbrock, K., & Sawodny, O. (2014). A mathematical model of metabolism and regulation provides a systems-level view of how Escherichia coli responds to oxygen. Frontiers in Microbiology, 5 (124). doi:10.3389/fmicb.2014.00124 ![]() |
![]() ![]() | Henkel, S. G., Beek, A. T., Steinsiek, S., Stagge, S., Bettenbrock, K., de Mattos, M. J. T., Sauter, T., Sawodny, O., & Ederer, M. (2014). Basic Regulatory Principles of Escherichia coli's Electron Transport Chain for Varying Oxygen Conditions. PLoS ONE, 9 (9), 107640. doi:10.1371/journal.pone.0107640 ![]() |
![]() ![]() | Vlassis, N., Pacheco, M., & Sauter, T. (January 2014). Fast reconstruction of compact context-specific metabolic network models. PLoS Computational Biology, 10 (1), 1003424. doi:10.1371/journal.pcbi.1003424 ![]() |
![]() ![]() | Galhardo, M. S.* , Sinkkonen, L.* , Berninger, P., Lin, J., Sauter, T., & Heinäniemi, M. (2013). Integrated analysis of transcript-level regulation of metabolism reveals disease-relevant nodes of the human metabolic network. Nucleic Acids Research. doi:10.1093/nar/gkt989 ![]() * These authors have contributed equally to this work. |
![]() ![]() | Trairatphisan, P., Mizera, A., Pang, J., Tantar, A.-A., Schneider, J., & Sauter, T. (01 July 2013). Recent development and biomedical applications of probabilistic Boolean networks. Cell Communication and Signaling, 11 (46). doi:10.1186/1478-811X-11-46 ![]() |
![]() ![]() | Mizera, A., Pang, J., Sauter, T., & Trairatphisan, P. (2013). A balancing act: Parameter estimation for biological models with steady-state measurements. In Proceedings of 11th Conference on Computational Methods in Systems Biology (CMSB'13) (pp. 253-254). Springer. ![]() |
![]() ![]() | Baumuratova, T., Dobre, S., Bastogne, T., & Sauter, T. (2013). Switch of Sensitivity Dynamics Revealed with DyGloSA Toolbox for Dynamical Global Sensitivity Analysis as an Early Warning for System's Critical Transition. PLoS ONE, 8 (12), 82973. doi:10.1371/journal.pone.0082973 ![]() |
![]() ![]() | Mizera, A., Pang, J., Sauter, T., & Trairatphisan, P. (2013). Mathematical modelling of the Platelet-Derived Growth Factor (PDGF) signalling pathway. In Proceedings of 4th Workshop on Computational Models for Cell Processes (CompMod'13) (pp. 35). |
![]() ![]() | Vlassis, N., Pacheco, M., & Sauter, T. (2013). Fastcore: An algorithm for fast reconstruction of context-specific metabolic network models. In Proc. 8th BeNeLux Bioinformatics Conference. ![]() |
Vlassis, N., Pacheco, M., & Sauter, T. (2013). Fast reconstruction of compact context-specific metabolic network models. ORBilu-University of Luxembourg. https://orbilu.uni.lu/handle/10993/11095. doi:10.1371/journal.pcbi.1003424 |
![]() ![]() | Rolfe, M., Ocone, A., Stapleton, M., Hall, S., Trotter, E., Poole, R., Sanguinetti, G., Green, J., SysMO-SUMO consortium, & Sauter, T. (Other coll.). (July 2012). Systems analysis of transcription factor activities in environments with stable and dynamic oxygen concentrations. Open Biology, 2 (7), 120091. doi:10.1098/rsob.120091 ![]() |
![]() ![]() | Witt, J., Konrath, F., Sawodny, O., Ederer, M., Kulms, D., & Sauter, T. (2012). Analysing the role of UVB-induced translational inhibition and PP2Ac deactivation in NF-kappaB signalling using a minimal mathematical model. PLoS ONE, 7 (7), 40274. doi:10.1371/journal.pone.0040274 ![]() |
![]() ![]() | Yuan, Q., Trairatphisan, P., Pang, J., Mauw, S., Wiesinger, M., & Sauter, T. (2012). Probabilistic model checking of the PDGF signaling pathway. Transactions on Computational Systems Biology, XIV, 151-180. ![]() |
![]() ![]() | Yuan, Q., Pang, J., Mauw, S., Trairatphisan, P., Wiesinger, M., & Sauter, T. (2011). A study of the PDGF signaling pathway with PRISM. Proceedings of the 3rd Workshop on Computational Models for Cell Processes, EPTCS 67, 65-81. ![]() |
![]() ![]() | Henkel, S., Nagele, T., Hormiller, I., Sauter, T., Sawodny, O., Ederer, M., & Heyer, A. G. (2011). A systems biology approach to analyse leaf carbohydrate metabolism in Arabidopsis thaliana. EURASIP Journal on Bioinformatics and Systems Biology, 2011 (1), 2. ![]() |
![]() ![]() | Witt, J., Barisic, S., Sawodny, O., Ederer, M., Kulms, D., & Sauter, T. (2011). Modeling time delay in the NFkappaB signaling pathway following low dose IL-1 stimulation. EURASIP Journal on Bioinformatics and Systems Biology, 2011 (1), 3. ![]() |
![]() ![]() | Nagele, T., Henkel, S., Hormiller, I., Sauter, T., Sawodny, O., Ederer, M., & Heyer, A. G. (2010). Mathematical modeling of the central carbohydrate metabolism in Arabidopsis reveals a substantial regulatory influence of vacuolar invertase on whole plant carbon metabolism. Plant Physiology, 153 (1), 260-72. doi:10.1104/pp.110.154443 ![]() |
![]() ![]() | Schlatter, R., Conzelmann, H., Gilles, E. D., Sawodny, O., & Sauter, T. (2009). Analysis of an apoptotic core model focused on experimental design using artificial data. IET Systems Biology, 3 (4), 255-65. doi:10.1049/iet-syb.2008.0138 ![]() |
![]() ![]() | Witt, J., Barisic, S., Schumann, E., Allgower, F., Sawodny, O., Sauter, T., & Kulms, D. (2009). Mechanism of PP2A-mediated IKK beta dephosphorylation: a systems biological approach. BMC Systems Biology, 3, 71. doi:10.1186/1752-0509-3-71 ![]() |
![]() ![]() | Schlatter, R., Schmich, K., Avalos Vizcarra, I., Scheurich, P., Sauter, T., Borner, C., Ederer, M., Merfort, I., & Sawodny, O. (2009). ON/OFF and beyond--a boolean model of apoptosis. PLoS Computational Biology, 5 (12), 1000595. doi:10.1371/journal.pcbi.1000595 ![]() |
![]() ![]() | Feuer, R., Ederer, M., Gilles, E. D., Sprenger, G., Sawodny, O., & Sauter, T. (2008). Analyse der evolutiven Adaptation am Beispiel einer pyruvat-auxotrophen Escherichia coli-Mutante. Automatisierungstechnik, 56, 257-268. doi:10.1524/auto.2008.0704 ![]() |
Witt, J., Husser, S., Kulms, D., Barisic, S., Sawodny, O., & Sauter, T. (2007). Modeling and Analysis of UVB Influence on IL-1 induced NF-kappaB Signaling. In Proceedings of the FOSBE, September 9-12, Stuttgart, Germany. ![]() |
Feuer, R., Ederer, M., Trachtmann, N., Sauter, T., Gilles, E. D., Sprenger, G., & Sawodny, O. (2007). Methods for analysis of evolutive adaptation of E. coli. In Proceedings of the SICE Annual Conference, September 17-20, 2007 Kagawa University, Takamatsu City, Japan. ![]() |
Bettenbrock, K., Sauter, T., Jahreis, K., Kremling, A., Lengeler, J. W., & Gilles, E.-D. (2007). Correlation between growth rates, EIIACrr phosphorylation, and intracellular cyclic AMP levels in Escherichia coli K-12. Journal of Bacteriology, 189 (19), 6891-900. doi:10.1128/JB.00819-07 ![]() |
Eissing, T., Bullinger, E., Waldherr, S., Gondro, C., Sawodny, O., Allgöwer, F., Scheurich, P., & Sauter, T. (2006). Sensitivity analysis of programmed cell death and implications for crosstalk phenomena during Tumor Necrosis Factor stimulation. In Proceedings of IEEE International Conference on Control Applications (CCA), October 4-6, 2006, Technische Universität München, Germany. ![]() |
Hao, H., Zak, D. E., Sauter, T., Schwaber, J., & Ogunnaike, B. A. (2006). Modeling the VPAC2-activated cAMP/PKA signaling pathway: from receptor to circadian clock gene induction. Biophysical Journal, 90 (5), 1560-71. doi:10.1529/biophysj.105.065250 ![]() |
Conzelmann, H., Saez-Rodriguez, J., Sauter, T., Kholodenko, B. N., & Gilles, E. D. (2006). A domain-oriented approach to the reduction of combinatorial complexity in signal transduction networks. BMC Bioinformatics, 7, 34. doi:10.1186/1471-2105-7-34 ![]() |
Bettenbrock, K., Fischer, S., Kremling, A., Jahreis, K., Sauter, T., & Gilles, E.-D. (2006). A quantitative approach to catabolite repression in Escherichia coli. Journal of Biological Chemistry, 281 (5), 2578-84. doi:10.1074/jbc.M508090200 ![]() |
Conzelmann, H., Saez-Rodriguez, J., Sauter, T., Bullinger, E., Allgower, F., & Gilles, E. D. (2004). Reduction of mathematical models of signal transduction networks: simulation-based approach applied to EGF receptor signalling. Systems biology, 1 (1), 159-69. doi:10.1049/sb:20045011 ![]() |
Kremling, A., Fischer, S., Sauter, T., Bettenbrock, K., & Gilles, E. D. (2004). Time hierarchies in the Escherichia coli carbohydrate uptake and metabolism. Bio Systems, 73 (1), 57-71. doi:10.1016/j.biosystems.2003.09.001 ![]() |
Kremling, A., Bettenbrock, K., Fischer, S., Ginkel, M., Sauter, T., & Gilles, E. D. (2004). Towards whole cell "in silico" models for cellular systems: model set-up and model validation. In Lecture Notes in Control and Information Sciences: Proceedings of the first multidisciplinary international symposium on Positive Systems (pp. 95-102). Springer. ![]() |
Sauter, T., & Bullinger, E. (2004). Detailed Mathematical Modeling of Metabolic and Regulatory Networks. BIOforum Europe, 02, 62-64. |
Sauter, T., & Gilles, E. D. (2004). Modeling and experimental validation of the signal transduction via the Escherichia coli sucrose phospho transferase system. Journal of Biotechnology, 110 (2), 181-99. doi:10.1016/j.jbiotec.2004.02.002 ![]() |
Kremling, A., Fischer, S., Gadkar, K., Doyle, F. J., Sauter, T., Bullinger, E., Allgower, F., & Gilles, E. D. (2004). A benchmark for methods in reverse engineering and model discrimination: problem formulation and solutions. Genome Research, 14 (9), 1773-85. doi:10.1101/gr.1226004 ![]() |
![]() ![]() | Sauter, T. (2003). Die bakterielle Signalverarbeitung am Beispiel des Sucrose Phosphotransferasesystems in Escherichia coli : Modellierung und experimentelle Überprüfung [Doctoral thesis, Universität Stuttgart]. ORBilu-University of Luxembourg. https://orbilu.uni.lu/handle/10993/2093 |
Ederer, M., Sauter, T., Bullinger, E., Gilles, E. D., & Allgöwer, F. (2003). An approach for dividing models of biological reaction networks into functional units. Simulation, 79, 703-716. doi:10.1177/0037549703040940 ![]() |
Kremling, A., Sauter, T., Bullinger, E., Ederer, M., Allgöwer, F., & Gilles, E. D. (2001). Biosystems Engineering: Applying methods from systems theory to biological systems. In Proceedings of the 2nd International Conference on Systems Biology 4.-7.11.2001, Pasadena. ![]() |