Profil

TREFOIS Christophe

Main Referenced Co-authors
ANTONY, Paul  (14)
BALLING, Rudolf  (11)
SCHNEIDER, Reinhard  (11)
SATAGOPAM, Venkata Pardhasaradhi  (10)
OSTASZEWSKI, Marek  (7)
Main Referenced Keywords
Parkinson's disease (4); Bioinformatics (3); Knowledge repository (3); Microscopy (3); Molecular neuropathology (3);
Main Referenced Unit & Research Centers
Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) (11)
Luxembourg Centre for Systems Biomedicine (LCSB): Experimental Neurobiology (Balling Group) (8)
ULHPC - University of Luxembourg: High Performance Computing (4)
LCSB (3)
Luxembourg Centre for Systems Biomedicine (LCSB): Biomedical Data Science (Glaab Group) (2)
Main Referenced Disciplines
Life sciences: Multidisciplinary, general & others (16)
Genetics & genetic processes (5)
Computer science (4)
Biochemistry, biophysics & molecular biology (2)
Engineering, computing & technology: Multidisciplinary, general & others (1)

Publications (total 27)

The most downloaded
846 downloads
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 https://hdl.handle.net/10993/19379

The most cited

217 citations (OpenCitations)

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 https://hdl.handle.net/10993/4778

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

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.* , 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.

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.

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

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

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

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