| Year |
Citation |
Score |
| 2024 |
Pacheco MP, Gerard D, Mangan RJ, Chapman AR, Hecker D, Kellis M, Schulz MH, Sinkkonen L, Sauter T. Epigenetic control of metabolic identity across cell types. Biorxiv : the Preprint Server For Biology. PMID 39091778 DOI: 10.1101/2024.07.24.604914 |
0.747 |
|
| 2024 |
Di Leo L, Pagliuca C, Kishk A, Rizza S, Tsiavou C, Pecorari C, Dahl C, Pacheco MP, Tholstrup R, Brewer JR, Berico P, Hernando E, Cecconi F, Ballotti R, Bertolotto C, ... ... Sauter T, et al. AMBRA1 levels predict resistance to MAPK inhibitors in melanoma. Proceedings of the National Academy of Sciences of the United States of America. 121: e2400566121. PMID 38870061 DOI: 10.1073/pnas.2400566121 |
0.691 |
|
| 2023 |
Bintener T, Pacheco MP, Philippidou D, Margue C, Kishk A, Del Mistro G, Di Leo L, Moscardó Garcia M, Halder R, Sinkkonen L, De Zio D, Kreis S, Kulms D, Sauter T. Metabolic modelling-based in silico drug target prediction identifies six novel repurposable drugs for melanoma. Cell Death & Disease. 14: 468. PMID 37495601 DOI: 10.1038/s41419-023-05955-1 |
0.795 |
|
| 2023 |
Frias A, Di Leo L, Antoranz A, Nazerai L, Carretta M, Bodemeyer V, Pagliuca C, Dahl C, Claps G, Mandelli GE, Andhari MD, Pacheco MP, Sauter T, Robert C, Guldberg P, et al. Ambra1 modulates the tumor immune microenvironment and response to PD-1 blockade in melanoma. Journal For Immunotherapy of Cancer. 11. PMID 36868570 DOI: 10.1136/jitc-2022-006389 |
0.674 |
|
| 2022 |
Pacheco MP, Ji J, Prohaska T, García MM, Sauter T. scFASTCORMICS: A Contextualization Algorithm to Reconstruct Metabolic Multi-Cell Population Models from Single-Cell RNAseq Data. Metabolites. 12. PMID 36557249 DOI: 10.3390/metabo12121211 |
0.755 |
|
| 2022 |
Kishk A, Pacheco MP, Heurtaux T, Sinkkonen L, Pang J, Fritah S, Niclou SP, Sauter T. Review of Current Human Genome-Scale Metabolic Models for Brain Cancer and Neurodegenerative Diseases. Cells. 11. PMID 36010563 DOI: 10.3390/cells11162486 |
0.749 |
|
| 2022 |
Bintener T, Pacheco MP, Kishk A, Didier J, Sauter T. Drug Target Prediction Using Context-Specific Metabolic Models Reconstructed from rFASTCORMICS. Methods in Molecular Biology (Clifton, N.J.). 2535: 221-240. PMID 35867234 DOI: 10.1007/978-1-0716-2513-2_17 |
0.799 |
|
| 2022 |
Cipriani C, Pacheco MP, Kishk A, Wachich M, Abankwa D, Schaffner-Reckinger E, Sauter T. Bruceine D Identified as a Drug Candidate against Breast Cancer by a Novel Drug Selection Pipeline and Cell Viability Assay. Pharmaceuticals (Basel, Switzerland). 15. PMID 35215292 DOI: 10.3390/ph15020179 |
0.756 |
|
| 2022 |
Albrecht M, Kogan Y, Kulms D, Sauter T. Mechanistically Coupled PK (MCPK) Model to Describe Enzyme Induction and Occupancy Dependent DDI of Dabrafenib Metabolism. Pharmaceutics. 14. PMID 35214043 DOI: 10.3390/pharmaceutics14020310 |
0.773 |
|
| 2022 |
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. Project-based learning course on metabolic network modelling in computational systems biology. Plos Computational Biology. 18: e1009711. PMID 35085230 DOI: 10.1371/journal.pcbi.1009711 |
0.765 |
|
| 2021 |
Kishk A, Pacheco MP, Sauter T. DCcov: Repositioning of drugs and drug combinations for SARS-CoV-2 infected lung through constraint-based modeling. Iscience. 24: 103331. PMID 34723158 DOI: 10.1016/j.isci.2021.103331 |
0.734 |
|
| 2021 |
Moscardó García M, Pacheco M, Bintener T, Presta L, Sauter T. Importance of the biomass formulation for cancer metabolic modeling and drug prediction. Iscience. 24: 103110. PMID 34622163 DOI: 10.1016/j.isci.2021.103110 |
0.814 |
|
| 2021 |
Di Leo L, Bodemeyer V, Bosisio FM, Claps G, Carretta M, Rizza S, Faienza F, Frias A, Khan S, Bordi M, Pacheco MP, Di Martino J, Bravo-Cordero JJ, Daniel CJ, Sears RC, ... ... Sauter T, et al. Loss of Ambra1 promotes melanoma growth and invasion. Nature Communications. 12: 2550. PMID 33953176 DOI: 10.1038/s41467-021-22772-2 |
0.699 |
|
| 2021 |
Martins Conde P, Pfau T, Pires Pacheco M, Sauter T. A dynamic multi-tissue model to study human metabolism. Npj Systems Biology and Applications. 7: 5. PMID 33483512 DOI: 10.1038/s41540-020-00159-1 |
0.315 |
|
| 2020 |
Albrecht M, Lucarelli P, Kulms D, Sauter T. Computational models of melanoma. Theoretical Biology & Medical Modelling. 17: 8. PMID 32410672 DOI: 10.1186/S12976-020-00126-7 |
0.77 |
|
| 2020 |
Bintener T, Pacheco MP, Sauter T. Towards the routine use of in silico screenings for drug discovery using metabolic modelling. Biochemical Society Transactions. PMID 32369553 DOI: 10.1042/Bst20190867 |
0.793 |
|
| 2019 |
Alsahafi E, Begg K, Amelio I, Raulf N, Lucarelli P, Sauter T, Tavassoli M. Clinical update on head and neck cancer: molecular biology and ongoing challenges. Cell Death & Disease. 10: 540. PMID 31308358 DOI: 10.1038/S41419-019-1769-9 |
0.307 |
|
| 2019 |
Pacheco MP, Bintener T, Ternes D, Kulms D, Haan S, Letellier E, Sauter T. Identifying and targeting cancer-specific metabolism with network-based drug target prediction. Ebiomedicine. 43: 98-106. PMID 31126892 DOI: 10.1016/J.Ebiom.2019.04.046 |
0.79 |
|
| 2019 |
Greenhalgh K, Ramiro-Garcia J, Heinken A, Ullmann P, Bintener T, Pacheco MP, Baginska J, Shah P, Frachet A, Halder R, Fritz JV, Sauter T, Thiele I, Haan S, Letellier E, et al. 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.e9. PMID 31042485 DOI: 10.1016/J.Celrep.2019.04.001 |
0.784 |
|
| 2019 |
Pacheco MP, Bintener T, Sauter T. Towards the network-based prediction of repurposed drugs using patient-specific metabolic models. Ebiomedicine. PMID 30979684 DOI: 10.1016/J.Ebiom.2019.04.017 |
0.794 |
|
| 2019 |
Heirendt L, Arreckx S, Pfau T, Mendoza SN, Richelle A, Heinken A, Haraldsdóttir HS, Wachowiak J, Keating SM, Vlasov V, Magnusdóttir S, Ng CY, Preciat G, Žagare A, Chan SHJ, ... ... Sauter T, et al. Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0. Nature Protocols. PMID 30787451 DOI: 10.1038/S41596-018-0098-2 |
0.378 |
|
| 2018 |
Gérard D, Schmidt F, Ginolhac A, Schmitz M, Halder R, Ebert P, Schulz MH, Sauter T, Sinkkonen L. Temporal enhancer profiling of parallel lineages identifies AHR and GLIS1 as regulators of mesenchymal multipotency. Nucleic Acids Research. PMID 30544251 DOI: 10.1093/Nar/Gky1240 |
0.317 |
|
| 2018 |
Rožanc J, Sakellaropoulos T, Antoranz A, Guttà C, Podder B, Vetma V, Rufo N, Agostinis P, Pliaka V, Sauter T, Kulms D, Rehm M, Alexopoulos LG. Phosphoprotein patterns predict trametinib responsiveness and optimal trametinib sensitisation strategies in melanoma. Cell Death and Differentiation. PMID 30323272 DOI: 10.1038/S41418-018-0210-8 |
0.355 |
|
| 2018 |
Seip K, Jørgensen K, Haselager MV, Albrecht M, Haugen MH, Egeland EV, Lucarelli P, Engebraaten O, Sauter T, Mælandsmo GM, Prasmickaite L. Stroma-induced phenotypic plasticity offers phenotype-specific targeting to improve melanoma treatment. Cancer Letters. 439: 1-13. PMID 30240588 DOI: 10.1016/J.Canlet.2018.09.023 |
0.773 |
|
| 2018 |
De Landtsheer S, Lucarelli P, Sauter T. Using Regularization to Infer Cell Line Specificity in Logical Network Models of Signaling Pathways. Frontiers in Physiology. 9: 550. PMID 29872402 DOI: 10.3389/Fphys.2018.00550 |
0.416 |
|
| 2018 |
Pacheco MP, Sauter T. The FASTCORE Family: For the Fast Reconstruction of Compact Context-Specific Metabolic Networks Models. Methods in Molecular Biology (Clifton, N.J.). 1716: 101-110. PMID 29222750 DOI: 10.1007/978-1-4939-7528-0_4 |
0.727 |
|
| 2017 |
De Landtsheer S, Trairatphisan P, Lucarelli P, Sauter T. FALCON: A Toolbox for the Fast Contextualisation of Logical Networks. Bioinformatics (Oxford, England). PMID 28673016 DOI: 10.1093/Bioinformatics/Btx380 |
0.377 |
|
| 2017 |
Seip K, Haselager MV, Jørgensen K, Albrecht M, Haugen MH, Egeland EV, Lucarelli P, Sauter T, Engebraaten O, Mælandsmo GM, Prasmickaite L. Abstract 4329: Targetable nodes in fibroblast-supported melanoma cells that show resistance to BRAF inhibitors Cancer Research. 77: 4329-4329. DOI: 10.1158/1538-7445.Am2017-4329 |
0.745 |
|
| 2016 |
Trairatphisan P, Wiesinger M, Bahlawane C, Haan S, Sauter T. A Probabilistic Boolean Network Approach for the Analysis of Cancer-Specific Signalling: A Case Study of Deregulated PDGF Signalling in GIST. Plos One. 11: e0156223. PMID 27232499 DOI: 10.1371/Journal.Pone.0156223 |
0.336 |
|
| 2016 |
Martins Conde Pdo R, Sauter T, Pfau T. Constraint Based Modeling Going Multicellular. Frontiers in Molecular Biosciences. 3: 3. PMID 26904548 DOI: 10.3389/Fmolb.2016.00003 |
0.367 |
|
| 2016 |
Nguyen T, Sauter T, Caberlotto L, Lammert F, Schneider J. Prioritizing drug targets for non-alcoholic fatty liver disease based on comorbidity network analysis Zeitschrift Fur Gastroenterologie. 54. DOI: 10.1055/S-0036-1586961 |
0.302 |
|
| 2016 |
Albrecht M, Sciumè G, Lucarelli P, Sauter T. Thermodynamically constrained averaging theory for cancer growth modelling * *Horizon 2020 MSCA grant agreement No 642295 www.melplex.eu Ifac-Papersonline. 49: 289-294. DOI: 10.1016/J.Ifacol.2016.12.141 |
0.777 |
|
| 2015 |
Pacheco MP, Pfau T, Sauter T. Benchmarking Procedures for High-Throughput Context Specific Reconstruction Algorithms. Frontiers in Physiology. 6: 410. PMID 26834640 DOI: 10.3389/Fphys.2015.00410 |
0.731 |
|
| 2015 |
Pfau T, Pacheco MP, Sauter T. Towards improved genome-scale metabolic network reconstructions: unification, transcript specificity and beyond. Briefings in Bioinformatics. PMID 26615025 DOI: 10.1093/Bib/Bbv100 |
0.756 |
|
| 2015 |
Pacheco MP, John E, Kaoma T, Heinäniemi M, Nicot N, Vallar L, Bueb JL, Sinkkonen L, Sauter T. Integrated metabolic modelling reveals cell-type specific epigenetic control points of the macrophage metabolic network. Bmc Genomics. 16: 809. PMID 26480823 DOI: 10.1186/S12864-015-1984-4 |
0.764 |
|
| 2015 |
Hillje AL, Beckmann E, Pavlou MA, Jaeger C, Pacheco MP, Sauter T, Schwamborn JC, Lewejohann L. The neural stem cell fate determinant TRIM32 regulates complex behavioral traits. Frontiers in Cellular Neuroscience. 9: 75. PMID 25852471 DOI: 10.3389/Fncel.2015.00075 |
0.705 |
|
| 2014 |
Galhardo M, Sinkkonen L, Berninger P, Lin J, Sauter T, Heinäniemi M. Transcriptomics profiling of human SGBS adipogenesis. Genomics Data. 2: 246-8. PMID 26484102 DOI: 10.1016/J.Gdata.2014.07.004 |
0.341 |
|
| 2014 |
Henkel SG, Ter Beek A, Steinsiek S, Stagge S, Bettenbrock K, de Mattos MJ, Sauter T, Sawodny O, Ederer M. Basic regulatory principles of Escherichia coli's electron transport chain for varying oxygen conditions. Plos One. 9: e107640. PMID 25268772 DOI: 10.1371/Journal.Pone.0107640 |
0.351 |
|
| 2014 |
Trairatphisan P, Mizera A, Pang J, Tantar AA, Sauter T. optPBN: an optimisation toolbox for probabilistic Boolean networks. Plos One. 9: e98001. PMID 24983623 DOI: 10.1371/Journal.Pone.0098001 |
0.306 |
|
| 2014 |
Ederer M, Steinsiek S, Stagge S, Rolfe MD, Ter Beek A, Knies D, Teixeira de Mattos MJ, Sauter T, Green J, Poole RK, Bettenbrock K, Sawodny O. A mathematical model of metabolism and regulation provides a systems-level view of how Escherichia coli responds to oxygen. Frontiers in Microbiology. 5: 124. PMID 24723921 DOI: 10.3389/Fmicb.2014.00124 |
0.398 |
|
| 2014 |
Konrath F, Witt J, Sauter T, Kulms D. Identification of new IκBα complexes by an iterative experimental and mathematical modeling approach. Plos Computational Biology. 10: e1003528. PMID 24675998 DOI: 10.1371/Journal.Pcbi.1003528 |
0.756 |
|
| 2014 |
Bouvy-Liivrand M, Heinäniemi M, John E, Schneider JG, Sauter T, Sinkkonen L. Combinatorial regulation of lipoprotein lipase by microRNAs during mouse adipogenesis. Rna Biology. 11: 76-91. PMID 24457907 DOI: 10.4161/Rna.27655 |
0.307 |
|
| 2014 |
Vlassis N, Pacheco MP, Sauter T. Fast reconstruction of compact context-specific metabolic network models. Plos Computational Biology. 10: e1003424. PMID 24453953 DOI: 10.1371/Journal.Pcbi.1003424 |
0.795 |
|
| 2014 |
Galhardo M, Sinkkonen L, Berninger P, Lin J, Sauter T, Heinäniemi M. Integrated analysis of transcript-level regulation of metabolism reveals disease-relevant nodes of the human metabolic network. Nucleic Acids Research. 42: 1474-96. PMID 24198249 DOI: 10.1093/Nar/Gkt989 |
0.404 |
|
| 2013 |
Baumuratova T, Dobre S, Bastogne T, Sauter T. 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: e82973. PMID 24367574 DOI: 10.1371/Journal.Pone.0082973 |
0.302 |
|
| 2013 |
Trairatphisan P, Mizera A, Pang J, Tantar AA, Schneider J, Sauter T. Recent development and biomedical applications of probabilistic Boolean networks. Cell Communication and Signaling : Ccs. 11: 46. PMID 23815817 DOI: 10.1186/1478-811X-11-46 |
0.396 |
|
| 2012 |
Witt J, Konrath F, Sawodny O, Ederer M, Kulms D, Sauter T. Analysing the role of UVB-induced translational inhibition and PP2Ac deactivation in NF-κB signalling using a minimal mathematical model. Plos One. 7: e40274. PMID 22815735 DOI: 10.1371/Journal.Pone.0040274 |
0.731 |
|
| 2012 |
Yuan Q, Trairatphisan P, Pang J, Mauw S, Wiesinger M, Sauter T. Probabilistic model checking of the PDGF signaling pathway Transactions On Computational Systems Biology. 14: 151-180. DOI: 10.1007/978-3-642-35524-0_7 |
0.352 |
|
| 2011 |
Witt J, Barisic S, Sawodny O, Ederer M, Kulms D, Sauter T. Modeling time delay in the NFκB signaling pathway following low dose IL-1 stimulation. Eurasip Journal On Bioinformatics & Systems Biology. 2011: 3. PMID 21910922 DOI: 10.1186/1687-4153-2011-3 |
0.733 |
|
| 2011 |
Henkel S, Nägele T, Hörmiller I, Sauter T, Sawodny O, Ederer M, Heyer AG. A systems biology approach to analyse leaf carbohydrate metabolism in Arabidopsis thaliana. Eurasip Journal On Bioinformatics & Systems Biology. 2011: 2. PMID 21910921 DOI: 10.1186/1687-4153-2011-2 |
0.377 |
|
| 2010 |
Nägele T, Henkel S, Hörmiller I, Sauter T, Sawodny O, Ederer M, Heyer AG. 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: 260-272. PMID 20207708 DOI: 10.1104/Pp.110.154443 |
0.402 |
|
| 2009 |
Schlatter R, Schmich K, Avalos Vizcarra I, Scheurich P, Sauter T, Borner C, Ederer M, Merfort I, Sawodny O. ON/OFF and beyond--a boolean model of apoptosis. Plos Computational Biology. 5: e1000595. PMID 20011108 DOI: 10.1371/Journal.Pcbi.1000595 |
0.788 |
|
| 2009 |
Schlatter R, Conzelmann H, Gilles ED, Sawodny O, Sauter T. Analysis of an apoptotic core model focused on experimental design using artificial data. Iet Systems Biology. 3: 255-65. PMID 19640164 DOI: 10.1049/Iet-Syb.2008.0138 |
0.771 |
|
| 2009 |
Witt J, Barisic S, Schumann E, Allgöwer F, Sawodny O, Sauter T, Kulms D. Mechanism of PP2A-mediated IKK beta dephosphorylation: a systems biological approach. Bmc Systems Biology. 3: 71. PMID 19607706 DOI: 10.1186/1752-0509-3-71 |
0.704 |
|
| 2008 |
Feuer R, Ederer M, Gilles ED, Sprenger GA, Sawodny O, Sauter T. Analyse der evolutiven Adaptation am Beispiel einer pyruvat-auxotrophen Escherichia coli-Mutante At-Automatisierungstechnik. 56: 257-268. DOI: 10.1524/Auto.2008.0704 |
0.576 |
|
| 2007 |
Bettenbrock K, Sauter T, Jahreis K, Kremling A, Lengeler JW, Gilles ED. Correlation between growth rates, EIIACrr phosphorylation, and intracellular cyclic AMP levels in Escherichia coli K-12. Journal of Bacteriology. 189: 6891-900. PMID 17675376 DOI: 10.1128/Jb.00819-07 |
0.711 |
|
| 2006 |
Conzelmann H, Saez-Rodriguez J, Sauter T, Kholodenko BN, Gilles ED. A domain-oriented approach to the reduction of combinatorial complexity in signal transduction networks. Bmc Bioinformatics. 7: 34. PMID 16430778 DOI: 10.1186/1471-2105-7-34 |
0.663 |
|
| 2006 |
Hao H, Zak DE, Sauter T, Schwaber J, Ogunnaike BA. Modeling the VPAC2-activated cAMP/PKA signaling pathway: from receptor to circadian clock gene induction. Biophysical Journal. 90: 1560-71. PMID 16339878 DOI: 10.1529/Biophysj.105.065250 |
0.334 |
|
| 2006 |
Bettenbrock K, Fischer S, Kremling A, Jahreis K, Sauter T, Gilles ED. A quantitative approach to catabolite repression in Escherichia coli. The Journal of Biological Chemistry. 281: 2578-84. PMID 16263707 DOI: 10.1074/Jbc.M508090200 |
0.746 |
|
| 2006 |
Schliemann M, Sauter T, Bullinger E, Eißing T, Allgöwer F, Sawodny O, Scheurich P. Mathematical Modelling of TNF Induced Apoptotic and Anti-apoptotic Crosstalk in Mammalian Cells Chemie Ingenieur Technik. 78: 1429-1430. DOI: 10.1002/Cite.200650407 |
0.306 |
|
| 2004 |
Conzelmann H, Saez-Rodriguez J, Sauter T, Bullinger E, Allgöwer F, Gilles ED. Reduction of mathematical models of signal transduction networks: simulation-based approach applied to EGF receptor signalling. Systems Biology. 1: 159-69. PMID 17052126 DOI: 10.1049/Sb:20045011 |
0.694 |
|
| 2004 |
Kremling A, Fischer S, Gadkar K, Doyle FJ, Sauter T, Bullinger E, Allgöwer F, Gilles ED. A benchmark for methods in reverse engineering and model discrimination: problem formulation and solutions. Genome Research. 14: 1773-85. PMID 15342560 DOI: 10.1101/Gr.1226004 |
0.735 |
|
| 2004 |
Sauter T, Gilles ED. Modeling and experimental validation of the signal transduction via the Escherichia coli sucrose phospho transferase system. Journal of Biotechnology. 110: 181-99. PMID 15121337 DOI: 10.1016/J.Jbiotec.2004.02.002 |
0.58 |
|
| 2004 |
Kremling A, Fischer S, Sauter T, Bettenbrock K, Gilles ED. Time hierarchies in the Escherichia coli carbohydrate uptake and metabolism. Bio Systems. 73: 57-71. PMID 14729282 DOI: 10.1016/J.Biosystems.2003.09.001 |
0.75 |
|
| 2002 |
Bullinger E, Sauter T, Allgöwer F, Gilles E. On Deriving a Hybrid Model for Carbohydrate Uptake in Escherichia Coli Ifac Proceedings Volumes. 35: 19-24. DOI: 10.3182/20020721-6-Es-1901.01312 |
0.638 |
|
| 2002 |
Sauter T. New trends in applied microbiology Trends in Biotechnology. 20: 43. DOI: 10.1016/S0167-7799(01)01870-4 |
0.353 |
|
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