  | KLEE, M., AHO, V., MAY, P., Heintz-Buschart, A., LANDOULSI, Z., JONSDOTTIR, S., PAULY, C., PAVELKA, L., DELACOUR, L., KAYSEN, A., Krüger, R., WILMES, P., LEIST, A., Acharya, G., Aguayo, G., Alexandre, M., ALI, M., Ammerlann, W., ARENA, G., ... ZELIMKHANOV, G. (2024). Education as Risk Factor of Mild Cognitive Impairment: The Link to the Gut Microbiome. Journal of Prevention of Alzheimer's Disease. doi:10.14283/jpad.2024.19  Peer reviewed |
  | Wilken, S. E., Besançon, M., Kratochvil, M., Kuate, C. A. F., Trefois, C., Gu, W., & Ebenhöh, O. (2022). Interrogating the effect of enzyme kinetics on metabolism using differentiable constraint-based models. Metabolic Engineering. doi:10.1016/j.ymben.2022.09.002 Peer reviewed |
 | Bernhofer, M., Dallago, C., Karl, T., Satagopam, V., Heinzinger, M., Littmann, M., Olenyi, T., Qiu, J., Schütze, K., Yachdav, G., Ashkenazy, H., Ben-Tal, N., Bromberg, Y., Goldberg, T., Kajan, L., O’Donoghue, S., Sander, C., Schafferhans, A., Schlessinger, A., ... Rost, B. (2021). PredictProtein - Predicting Protein Structure and Function for 29 Years. Nucleic Acids Research. doi:10.1093/nar/gkab354 Peer reviewed |
 | Kratochvil, M.* , Heirendt, L.* , Wilken, S. E., Pusa, T., Arreckx, S., Noronha, A., van Aalst, M., Satagopam, V., Ebenhöh, O., Schneider, R., Trefois, C., & Gu, W. (2021). COBREXA.jl: constraint-based reconstruction and exascale analysis. Bioinformatics. doi:10.1093/bioinformatics/btab782 Peer reviewed* These authors have contributed equally to this work. |
 | Richelle, A., Kellman, B. P., Wenzel, A. T., Chiang, A. W. T., Reagan, T., Gutierrez, J. M., Joshi, C., Li, S., Liu, J. K., Masson, H., Lee, J., Li, Z., Heirendt, L., Trefois, C., Juarez, E. F., Bath, T., Borland, D., Mesirov, J. P., Robasky, K., & Lewis, N. E. (2021). Model-based assessment of mammalian cell metabolic functionalities using omics data. Cell reports methods, 1 (3). doi:10.1016/j.crmeth.2021.100040 Peer reviewed |
 | Kratochvil, M.* , Hunewald, O.* , Heirendt, L., Verissimo, V., Vondrášek, J., Satagopam, V., Schneider, R., Trefois, C., & Ollert, M. (18 November 2020). GigaSOM.jl: High-performance clustering and visualization of huge cytometry datasets. GigaScience, 9 (11). doi:10.1093/gigascience/giaa127 Peer Reviewed verified by ORBi* These authors have contributed equally to this work. |
 | Hollmann, S., Kremer, A., Baebler, Š., Trefois, C., Gruden, K., Rudnicki, W. R., Tong, W., Gruca, A., Bongcam-Rudloff, E., Evolo, C. T., Nechyporenko, A., Frohme, M., Šafránek, D., Regierer, B., & D'Elia, D. (2020). The need for standardisation in life science research - an approach to excellence and trust. F1000Research, 9 (1398). doi:10.12688/f1000research.27500.1 Peer reviewed |
 | Becker, R.* , Alper, P.* , Groues, V., Munoz, S., Jarosz, Y., Lebioda, J., Rege, K., Trefois, C., Satagopam, V., & Schneider, R. (04 December 2019). DAISY: A Data Information System for accountability under the General Data Protection Regulation. GigaScience, 8 (12). doi:10.1093/gigascience/giz140 Peer Reviewed verified by ORBi* These authors have contributed equally to this work. |
 | Herzinger, S., Groues, V., Gu, W., Satagopam, V., Banda, P., Trefois, C., & Schneider, R. (2018). Fractalis: A scalable open-source service for platform-independent interactive visual analysis of biomedical data. GigaScience. doi:10.1093/gigascience/giy109 Peer reviewed |
 | Antony, P., Forster, J., Köglsberger, S., Trefois, C., Boyd, O., Baumuratov, A., Balling, R., & Buck, L. (2016). Characterization of Differentiated SH-SY5Y as Neuronal Screening Model Reveals Increased Oxidative Vulnerability. Journal of Biomolecular Screening. doi:10.1177/1087057115625190 Peer Reviewed verified by ORBi |
 | Trefois, C., Antony, P., Goncalves, J., Skupin, A., & Balling, R. (August 2015). Critical transitions in chronic disease: transferring concepts from ecology to systems medicine. Current Opinion in Biotechnology, 34, 48-55. doi:10.1016/j.copbio.2014.11.020 Peer Reviewed verified by ORBi |
 | Biryukov, M., Antony, P., Krishna, A., May, P., & Trefois, C. (2015). Evaluation of Cell Line Suitability for Disease Specific Perturbation Experiments. In B. Lausen, S. Krolak-Schwerdt, ... M. Böhmer (Eds.), Data Science, Learning by Latent Structures, and Knowledge Discovery. Luxembourg, Luxembourg: Springer. doi:10.1007/978-3-662-44983-7_26 Peer reviewed |
 | Antony, P., Boyd, O., Trefois, C., Ammerlaan, W., Ostaszewski, M., Baumuratov, A. S., Longhino, L., Antunes, L., Koopman, W., Balling, R., & Diederich, N. J. (2015). Platelet mitochondrial membrane potential in Parkinson's disease. Annals of Clinical and Translational Neurology, 2 (1), 67-73. doi:10.1002/acn3.151 Peer Reviewed verified by ORBi |
 | Krishna, A., Biryukov, M., Trefois, C., Antony, P., Hussong, R., Lin, J., Heinäniemi, M., Glusman, G., Köglsberger, S., Boyd, O., van den Berg, B. H. J., Linke, D., Huang, D., Wang, K., Hood, L., Tholey, A., Schneider, R., Galas, D. J., Balling, R., & May, P. (20 December 2014). Systems genomics evaluation of the SH-SY5Y neuroblastoma cell line as a model for Parkinson’s disease. BMC Genomics, 15 (1154). doi:10.1186/1471-2164-15-1154 Peer Reviewed verified by ORBi |
 | Trefois, C., Jarosz, Y., Gu, W., Satagopam, V., Coronado, S., & Schneider, R. (December 2014). Reproducible Research Results R3 [Poster presentation]. 9th Benelux Bioinformatics Conference, Luxembourg, Luxembourg. |
 | Trefois, C. (2014). Detection and characterization of critical transitions in mitochondrial activity via high content screening [Doctoral thesis, Unilu - University of Luxembourg]. ORBilu-University of Luxembourg. https://orbilu.uni.lu/handle/10993/17706 |
Antony, P., Boyd, O., Trefois, C., Ostaszewski, M., Baumuratov, A., Balling, R., & Diederich, N. (12 June 2014). Analysis of mitochondrial membrane potential in idiopathic Parkinson's disease: A case-control study [Paper presentation]. 18th International Congress of Parkinson's Disease and Movement. |
Antony, P., Ostaszewski, M., Gawron, P., Trefois, C., Fujita, K. A., Mosch, S., & Balling, R. (12 June 2014). Curation of complex molecular pathways of Parkinson's disease as a collaborative scientific community effort [Paper presentation]. 18th International Congress of Parkinson's Disease and Movement. |
 | Fujita, K. A., Ostaszewski, M., Matsuoka, Y., Ghosh, S., Glaab, E., Trefois, C., Crespo, I., Perumal, T. M., Jurkowski, W., Antony, P., Diederich, N., Buttini, M., Kodama, A., Satagopam, V., Eifes, S., del Sol Mesa, A., Schneider, R., Kitano, H., & Balling, R. (2014). Integrating Pathways of Parkinson's Disease in a Molecular Interaction Map. Molecular Neurobiology. doi:10.1007/s12035-013-8489-4 Peer Reviewed verified by ORBi |
 | Samsi, S., Trefois, C., Antony, P., & Skupin, A. (2014). Automated nuclei clump splitting by combining local concavity orientation and graph partitioning. In International Conference on Biomedical and Health Informatics (pp. 412-415). IEEE. doi:10.1109/BHI.2014.6864390 Peer reviewed |
Trefois, C. (12 April 2013). The Parkinson’s Disease Map: a framework for integration, curation and exploration of disease related pathways [Paper presentation]. RedOx Biology Symposium, Kaiserslautern, Germany. |
 | Antony, P., Trefois, C., Stojanovic, A., Baumuratov, A., & Kozak, K. (11 April 2013). Light microscopy applications in systems biology: opportunities and challenges. Cell Communication and Signaling, 11 (1), 1-19. doi:10.1186/1478-811X-11-24 Peer Reviewed verified by ORBi |
 | Ostaszewski, M., Fujita, K., Matsuoka, Y., Ghosh, S., Glaab, E., Trefois, C., Crespo, I., Perumal, T. M., Jurkowski, W., Antony, P., Diederich, N., Buttini, M., Kolodkin, A., Kodama, A., Satagopam, V., Biryukov, M., Eifes, S., del Sol Mesa, A., Schneider, R., ... Balling, R. (09 March 2013). The Parkinson's Disease Map: A Framework for Integration, Curation and Exploration of Disease-related Pathways [Poster presentation]. The 11th International Conference on Alzheimer's & Parkinson's Diseases, Florence, Italy. |
Antony, P., Krishna, A., May, P., Trefois, C., Boyd, O., Köglsberger, S., Baumuratov, A., Galas, D. J., & Balling, R. (2013). Differentiated SH-SY5Y Cells as PD Model for Mitochondrial Dysfunction: From Whole Genome Sequencing to an Educated Design of High-Throughput Experiments [Poster presentation]. The 11th International Conference on Alzheimer's & Parkinson's Diseases, Florence, Italy. |
Trefois, C., Fujita, A. K., Ostaszewski, M., Matsuoka, Y., Ghosh, S., Glaab, E., Crespo, I., Perumal, T. M., Jurkowski, W., Antony, P., Diederich, N., Buttini, M., Kodama, A., Satagopam, V., Eifes, S., del Sol Mesa, A., Schneider, R., Kitano, H., & Balling, R. (August 2012). Constructing a comprehensive map of Parkinson’s disease to elucidate underlying mechanisms of its multifaceted molecular pathology [Poster presentation]. The 13th International Conference on Systems Biology. |
Trefois, C., Antony, P., Baumuratov, A., Boyd, O., Köglsberger, S., & Balling, R. (12 December 2011). Analysis of critical transitions in Parkinson's disease [Poster presentation]. BeNeLux Bioinformatics Conference, Luxembourg, Luxembourg. |
 | Sorniotti, A., Molva, R., Gomez, L., Trefois, C., Laube, A., & Scaglioso, P. (2009). Efficient Access Control for Wireless Sensor Data. International Journal of Wireless Information Networks, 6 (3), 165--174. doi:10.1007/s10776-009-0102-4 Peer Reviewed verified by ORBi |