Profil

SAUTER Thomas

University of Luxembourg > Faculty of Science, Technology and Medicine (FSTM) > Department of Life Sciences and Medicine (DLSM)

Main Referenced Co-authors
PACHECO, Maria  (30)
SINKKONEN, Lasse  (22)
Kulms, Dagmar (13)
Sawodny, Oliver (11)
DE LANDTSHEER, Sébastien  (10)
Main Referenced Keywords
Humans (10); Models, Biological (10); Animals (5); Computer Simulation (5); Metabolic Modelling (4);
Main Referenced Unit & Research Centers
ULHPC - University of Luxembourg: High Performance Computing (15)
Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) (4)
Luxembourg Centre for Systems Biomedicine (LCSB): Machine Learning (Vlassis Group) (2)
Institute for Systems Biology (ISB) (1)
Life Sciences Research Unit (1)
Main Referenced Disciplines
Life sciences: Multidisciplinary, general & others (71)
Biochemistry, biophysics & molecular biology (34)
Computer science (6)
Human health sciences: Multidisciplinary, general & others (3)
Geriatrics (2)

Publications (total 118)

The most downloaded
842 downloads
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 https://hdl.handle.net/10993/36511

The most cited

614 citations (Scopus®)

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 https://hdl.handle.net/10993/39264

Gomez Ramos, B., Ohnmacht, J., de Lange, N., VALCESCHINI, E., GINOLHAC, A., CATILLON, M., FERRANTE, D., Rakovic, A., HALDER, R., Massart, F., ARENA, G., ANTONY, P., BOLOGNIN, S., Klein, C., KRAUSE, R., Schulz, M. H., SAUTER, T., Krüger, R., & SINKKONEN, L. (2023). Multiomics analysis identifies novel facilitators of human dopaminergic neuron differentiation. EMBO Reports. doi:10.1038/s44319-023-00024-2
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GAVRIIL, M., PROIETTO, M., PACZIA, N., GINOLHAC, A., HALDER, R., VALCESCHINI, E., SAUTER, T., LINSTER, C., & SINKKONEN, L. (November 2023). 2-Hydroxyglutarate modulates histone methylation at specific loci and alters gene expression via Rph1 inhibition. Life Science Alliance, 7 (2), 202302333. doi:10.26508/lsa.202302333
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de Sande, A. H., Turunen, T., Bouvy-Liivrand, M., Örd, T., Palani, S., Tundidor-Centeno, C., Liljenbäck, H., Virta, J., Smålander, O.-P., SINKKONEN, L., SAUTER, T., Roivainen, A., Lönnberg, T., Kaikkonen, M. U., & Heinäniemi, M. (2023). Cell-type-specific characterization of miRNA gene dynamics in immune cell subpopulations during aging and atherosclerosis disease development at single-cell resolution. ORBilu-University of Luxembourg. https://orbilu.uni.lu/handle/10993/58864. doi:10.1101/2023.10.09.561173

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
Peer reviewed

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

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
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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
Peer reviewed

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.
Peer reviewed

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
Peer reviewed

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
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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
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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
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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
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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
Peer reviewed

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
Peer reviewed

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
Peer reviewed

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
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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
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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
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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
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Thomas, M., Gui, Y., Garcia, P., Karout, M., Gomez Ramos, B., JÄGER, 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
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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
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Pfau, T., Galhardo, M., Lin, J., & Sauter, T. (2021). IDARE2-Simultaneous Visualisation of Multiomics Data in Cytoscape. Metabolites, 11 (5). doi:10.3390/metabo11050300
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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
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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
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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
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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
Peer reviewed

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
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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.

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
Peer reviewed

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
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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
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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
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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
Peer reviewed

Badkas, A., De Landtsheer, S., & Sauter, T. (2020). Topological network measures for drug repositioning. Briefings in Bioinformatics. doi:10.1093/bib/bbaa357
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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
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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., GERARD, 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
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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
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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
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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
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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
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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
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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

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.
Peer reviewed

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
Peer Reviewed verified by ORBi

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
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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
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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
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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.
Peer reviewed

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
Peer Reviewed verified by ORBi

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
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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
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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
Peer reviewed

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
Peer reviewed

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
Peer Reviewed verified by ORBi

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
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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
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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
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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
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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
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* 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
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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
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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
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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
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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
Peer reviewed

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
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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
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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
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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
Peer reviewed

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
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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
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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
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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
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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
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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
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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
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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
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* 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
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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). Fast reconstruction of compact context-specific metabolic network models. ORBilu-University of Luxembourg. https://orbilu.uni.lu/handle/10993/11095.

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.
Peer reviewed

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.
Peer reviewed

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
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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
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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
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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.
Peer reviewed

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.
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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.
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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.
Peer reviewed

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
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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
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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
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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
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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
Peer reviewed

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
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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.
Peer reviewed

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.
Peer reviewed

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
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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
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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
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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.
Peer reviewed

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
Peer reviewed

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
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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
Peer reviewed

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
Peer reviewed

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.
Peer reviewed

Sauter, T., & Bullinger, E. (2004). Detailed Mathematical Modeling of Metabolic and Regulatory Networks. BIOforum Europe, 02, 62-64.

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
Peer reviewed

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.
Peer reviewed

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