Profil

SKUPIN Alexander

University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > Integrative Cell Signalling

ORCID
0000-0002-8955-8304
Main Referenced Co-authors
GRZYB, Kamil  (21)
MAGNI, Stefano  (13)
Falcke, Martin (11)
GONCALVES, Jorge  (9)
ANTONY, Paul  (7)
Main Referenced Keywords
Animals (10); Humans (8); COVID-19 (5); Calcium Signaling (4); Calcium/metabolism (4);
Main Referenced Unit & Research Centers
Luxembourg Centre for Systems Biomedicine (LCSB): Integrative Cell Signalling (Skupin Group) (15)
Luxembourg Centre for Systems Biomedicine (LCSB): Experimental Neurobiology (Balling Group) (13)
Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) (8)
Luxembourg Centre for Systems Biomedicine (LCSB) (2)
Luxembourg Centre for Systems Biomedicine (LCSB): Biomedical Data Science (Glaab Group) (2)
Main Referenced Disciplines
Life sciences: Multidisciplinary, general & others (47)
Biochemistry, biophysics & molecular biology (15)
Neurology (9)
Genetics & genetic processes (9)
Immunology & infectious disease (6)

Publications (total 97)

The most downloaded
498 downloads
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 https://hdl.handle.net/10993/19440

The most cited

304 citations (Scopus®)

Dirkse, A., Golebiewska, A., Buder, T., Nazarov, P. V., Muller, A., Poovathingal, S., Brons, N. H. C., Leite, S., Sauvageot, N., Sarkisjan, D., Seyfrid, M., Fritah, S., Stieber, D., Michelucci, A., Herold-Mende, C., Bjerkvig, R., Azuaje, F., Skupin, A., Deutsch, A., ... Hertel, F. (2019). Stem cell-associated heterogeneity in Glioblastoma results from intrinsic tumor plasticity shaped by the microenvironment. Nature communications, 10 (1), 1787. doi:10.1038/s41467-019-09853-z https://hdl.handle.net/10993/39391

VOORSLUIJS, V., AVANZINI, F., FALASCO, G., ESPOSITO, M., & SKUPIN, A. (15 March 2024). Calcium oscillations optimize the energetic efficiency of mitochondrial metabolism. iScience, 27 (3), 109078. doi:10.1016/j.isci.2024.109078
Peer Reviewed verified by ORBi

GHADERI, S., AHOOKHOSH, M., Arany, A., SKUPIN, A., Patrinos, P., & Moreau, Y. (March 2024). Smoothing unadjusted Langevin algorithms for nonsmooth composite potential functions. Applied Mathematics and Computation, 464, 128377. doi:10.1016/j.amc.2023.128377
Peer Reviewed verified by ORBi

Yabo, Y. A., Moreno-Sanchez, P. M., Pires-Afonso, Y., Kaoma, T., Nosirov, B., Scafidi, A., Ermini, L., Lipsa, A., Oudin, A., KYRIAKIS, D., GRZYB, K., POOVATHINGAL, S. K., Poli, A., Muller, A., TOTH, R., KLINK, B., BERCHEM, G. J. M. J., Berthold, C., HERTEL, F., ... GOLEBIEWSKA, A. (2023). Glioblastoma-instructed microglia transition to heterogeneous phenotypic states with phagocytic and dendritic cell-like features in patient tumors and patient-derived orthotopic xenografts. ORBilu-University of Luxembourg. https://orbilu.uni.lu/handle/10993/60199. doi:10.1101/2023.03.05.531162

ARNS, T., Fouquier d’Hérouël, A., MAY, P., TKATCHENKO, A., & SKUPIN, A. (2023). Mechanism-based classification of SARS-CoV-2 Variants by Molecular Dynamics Resembles Phylogenetic Tree. (v1). ORBilu-University of Luxembourg. https://orbilu.uni.lu/handle/10993/58649. doi:10.1101/2023.11.28.568639

Capelle, C. M., Ciré, S., Hedin, F., HANSEN, M., PAVELKA, L., GRZYB, K., KYRIAKIS, D., Hunewald, O., Konstantinou, M., Revets, D., TSLAF, V., Marques, T. M., GOMES, C., BARON, A., Domingues, O., Gomez, M., Zeng, N., BETSOU, F., MAY, P., ... Hefeng, F. Q. (20 November 2023). Early-to-mid stage idiopathic Parkinson's disease shows enhanced cytotoxicity and differentiation in CD8 T-cells in females. Nature Communications, 14 (1), 7461. doi:10.1038/s41467-023-43053-0
Peer Reviewed verified by ORBi

FARINA, S., VOORSLUIJS, V., FIXEMER, S., BOUVIER, D., Claus, S., Ellisman, M. H., BORDAS, S., & SKUPIN, A. (20 September 2023). Mechanistic multiscale modelling of energy metabolism in human astrocytes reveals the impact of morphology changes in Alzheimer's Disease. PLoS Computational Biology, 19 (9), 1011464. doi:10.1371/journal.pcbi.1011464
Peer Reviewed verified by ORBi

MARTINS, T., SOLIMAN, R., Cordero-Maldonado, M. L., DONATO, C., AMELI, C., MOMBAERTS, L., SKUPIN, A., Peri, F., & CRAWFORD, A. (September 2023). Seizure-induced increase in microglial cell population in the developing zebrafish brain. Epilepsy Research, 195, 107203. doi:10.1016/j.eplepsyres.2023.107203
Peer Reviewed verified by ORBi

RANDIC, T., MAGNI, S., PHILIPPIDOU, D., Margue, C., GRZYB, K., PREIS, J. R., WROBLEWSKA, J. P., NAZAROV, P., MITTELBRONN, M., FRAUENKNECHT, K., SKUPIN, A., & KREIS, S. (25 July 2023). Single-cell transcriptomics of NRAS-mutated melanoma transitioning to drug resistance reveals P2RX7 as an indicator of early drug response. Cell Reports, 42 (7), 112696. doi:10.1016/j.celrep.2023.112696
Peer Reviewed verified by ORBi

PROVERBIO, D., SKUPIN, A., & GONCALVES, J. (21 July 2023). Systematic analysis and optimization of early warning signals for critical transitions using distribution data. iScience, 26 (7), 107156. doi:10.1016/j.isci.2023.107156
Peer Reviewed verified by ORBi

KONCINA, E., NURMIK, M., POZDEEV, V., GILSON, C., TSENKOVA, M., BEGAJ, R., Stang, S., GAIGNEAUX, A., Weindorfer, C., RODRIGUEZ, F., SCHMOETTEN, M., KLEIN, E., KARTA, J., Atanasova, V. S., GRZYB, K., ULLMANN, P., HALDER, R., Hengstschläger, M., Graas, J., ... LETELLIER, E. (17 July 2023). IL1R1+ cancer-associated fibroblasts drive tumor development and immunosuppression in colorectal cancer. Nature Communications, 14 (1), 4251. doi:10.1038/s41467-023-39953-w
Peer Reviewed verified by ORBi

ALI, M.* , GARCIA, P.* , Laetitia P. Lunkes, SCIORTINO, A., THOMAS, M., HEURTAUX, T., GRZYB, K., HALDER, R., SKUPIN, A., MITTELBRONN, M., BUTTINI, M., & GLAAB, E. (12 May 2023). Gene Regulatory Network Analysis of Single-Cell Transcriptomes from THY-Tau22 Mice Reveals Sex-Dependent Immune Dysregulation associated with Alzheimer-like pathology [Poster presentation]. The 7th Venusberg Meeting on Neuroinflammation, Belval, Luxembourg.
* These authors have contributed equally to this work.

Pires-Afonso, Y., Muller, A., GRZYB, K., Oudin, A., Yabo, Y. A., SOUSA, C., Scafidi, A., Poli, A., COSMA, A., HALDER, R., COOWAR, D., GOLEBIEWSKA, A., SKUPIN, A., NICLOU, S. P., & MICHELUCCI, A. (September 2022). Elucidating tumour-associated microglia/macrophage diversity along glioblastoma progression and under ACOD1 deficiency. Molecular Oncology, 16 (17), 3167 - 3191. doi:10.1002/1878-0261.13287
Peer Reviewed verified by ORBi

Farina, S., Voorsluijs, V., Claus, S., Skupin, A., & Bordas, S. (07 June 2022). A CutFEM Method for a Mechanistic Modelling of Astrocytic Metabolism in 3D Physiological Morphologies [Paper presentation]. ECCOMAS Congress 2022, Oslo, Norway.

Farina, S., Voorsluijs, V., Fixemer, S., Bouvier, D., Claus, S., Bordas, S., & Skupin, A. (2022). 3D Modelling of a Spatially Resolved Energy Metabolism in Physiological Astrocytic Morphology [Paper presentation]. ECMTB 2022.

Proverbio, D., Noronha Montanari, A., Skupin, A., & Goncalves, J. (2022). Buffering variability in cell regulation motifs close to criticality. Physical Review. E. doi:10.1103/PhysRevE.106.L032402
Peer Reviewed verified by ORBi

Novak, G., Kyriakis, D., Grzyb, K., Bernini, M., Rodius, S., Dittmar, G., Finkbeiner, S., & Skupin, A. (2022). Single-cell transcriptomics of human iPSC differentiation dynamics reveal a core molecular network of Parkinson’s disease. Communications Biology, 5 (1), 1--19. doi:10.1038/s42003-021-02973-7
Peer reviewed

Proverbio, D., Kemp, F., Magni, S., Ogorzaly, L., Cauchie, H.-M., Goncalves, J., Skupin, A., & Aalto, A. (2022). Model-based assessment of COVID-19 epidemic dynamics by wastewater analysis. Science of the Total Environment, 827, 154235. doi:10.1016/j.scitotenv.2022.154235
Peer Reviewed verified by ORBi

Zagare, A., Barmpa, K., Smajic, S., Smits, L., Grzyb, K., Grünewald, A., Skupin, A., Nickels, S. L., & Schwamborn, J. C. (2022). Midbrain organoids mimic early embryonic neurodevelopment and recapitulate LRRK2-p.Gly2019Ser-associated gene expression. American Journal of Human Genetics. doi:10.1016/j.ajhg.2021.12.009
Peer Reviewed verified by ORBi

Fixemer, S., Ameli, C., Hammer, G., Salamanca, L., Uriarte Huarte, O., Schwartz, C., Gerardy, J.-J., Mechawar, N., Skupin, A., Mittelbronn, M., & Bouvier, D. (2022). Microglia phenotypes are associated with subregional patterns of concomitant tau, amyloid-β and α-synuclein pathologies in the hippocampus of patients with Alzheimer’s disease and dementia with Lewy bodies. Acta Neuropathologica Communications, 10 (1), 36. doi:10.1186/s40478-022-01342-7
Peer Reviewed verified by ORBi

Capelle, C. M., Ciré, S., Domingues, O., Ernens, I., Hedin, F., Fischer, A., Snoeck, C. J., Ammerlaan, W., Konstantinou, M., Grzyb, K., Skupin, A., Carty, C. L., Hilger, C., Gilson, G., Celebic, A., Wilmes, P., Del Sol, A., Kaplan, I. M., Betsou, F., ... He, F. (2022). Combinatorial analysis reveals highly coordinated early-stage immune reactions that predict later antiviral immunity in mild COVID-19 patients. Cell Reports Medicine, 3 (4), 100600. doi:10.1016/j.xcrm.2022.100600
Peer reviewed

Mendelsohn, R., Garcia, G. C., Bartol, T. M., Lee, C. T., Khandelwal, P., Liu, E., Spencer, D. J., Husar, A., Bushong, E. A., Phan, S., Perkins, G., Ellisman, M. H., Skupin, A., Sejnowski, T. J., & Rangamani, P. (2022). Morphological principles of neuronal mitochondria. Journal of Comparative Neurology, 530 (6), 886--902. doi:10.1002/cne.25254
Peer Reviewed verified by ORBi

Capelle, C. M., Chen, A., Zeng, N., Baron, A., Grzyb, K., Arns, T., Skupin, A., Ollert, M., & He, F. (2022). Stress hormone signalling inhibits Th1 polarization in a CD4 T-cell-intrinsic manner via mTORC1 and the circadian gene PER1. Immunology, 165 (4), 428--444. doi:10.1111/imm.13448
Peer Reviewed verified by ORBi

Ali, M., Huarte, O., Heurtaux, T., Garcia, P., Rodriguez, B. P., Grzyb, K., Halder, R., Skupin, A., Buttini, M., & Glaab, E. (2022). Single-cell transcriptional profiling and gene regulatory network modeling in Tg2576 mice reveal gender-dependent molecular features preceding Alzheimer-like pathologies. Molecular Neurobiology, in press (doi:10.1007/s12035-022-02985-2) (in press). doi:10.1007/s12035-022-02985-2
Peer Reviewed verified by ORBi

Novak, G., Finkbeiner, S., Skibinski, G., Bernini, M., Donato, C., & Skupin, A. (2022). Generation of two human induced pluripotent stem cell lines from fibroblasts of Parkinson’s disease patients carrying the ILE368ASN mutation in PINK1 (LCSBi002) and the R275W mutation in Parkin (LCSBI004). Stem Cell Research, 61, 102765. doi:10.1016/j.scr.2022.102765
Peer reviewed

Burzynski, Machado, J., Aalto, A., Beine, M., Haas, T., Kemp, F., Magni, S., Mombaerts, L., Picard, P. M., Proverbio, D., Skupin, A., & Docquier, F. (December 2021). COVID-19 Crisis Management in Luxembourg: Insights from an Epidemionomic Approach. Economics and Human Biology, 43, 101051. doi:10.1016/j.ehb.2021.101051
Peer Reviewed verified by ORBi

Bolognin, S., Smits, L., Nickels, S. L., Magni, S., Antony, P., Grzyb, K., Krüger, R., Skupin, A., & Schwamborn, J. C. (2021). A new brain organoid model to study Parkinson’s Disease. Biomedical Science and Engineering.

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
Peer Reviewed verified by ORBi

Kemp, F., Proverbio, D., Aalto, A., Mombaerts, L., Fouquier d'herouël, A., Husch, A., Ley, C., Goncalves, J., Skupin, A., & Magni, S. (2021). Modelling COVID-19 dynamics and potential for herd immunity by vaccination in Austria, Luxembourg and Sweden. Journal of Theoretical Biology. doi:10.1016/J.JTBI.2021.110874
Peer reviewed

Farina, S., Claus, S., Hale, J., Voorsluijs, V., Skupin, A., & Bordas, S. (May 2021). Mechanistic modelling of astrocytic metabolism in physiological geometries reveals spatiotemporal effects potentially driving neurodegeneration [Paper presentation]. DTU DRIVEN Colloquium.

Uriarte Huarte, O., Kyriakis, D., Heurtaux, T., Pires-Afonso, Y., Grzyb, K., Halder, R., Buttini, M., Skupin, A., Mittelbronn, M., & Michelucci, A. (2021). Single-Cell Transcriptomics and In Situ Morphological Analyses Reveal Microglia Heterogeneity Across the Nigrostriatal Pathway. Frontiers in Immunology. doi:10.3389/fimmu.2021.639613
Peer Reviewed verified by ORBi

Farina, S., Claus, S., Hale, J., Skupin, A., & Bordas, S. (22 March 2021). A cut finite element method for spatially resolved energy metabolism models in complex neuro-cell morphologies with minimal remeshing. Advanced Modeling and Simulation in Engineering Sciences, 8, 5. doi:10.1186/s40323-021-00191-8
Peer Reviewed verified by ORBi

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
Peer Reviewed verified by ORBi

Proverbio, D., Kemp, F., Magni, S., Husch, A., Aalto, A., Mombaerts, L., Skupin, A., Goncalves, J., Ameijeiras-Alonso, J., & Ley, C. (2021). Dynamical SPQEIR model assesses the effectiveness of non-pharmaceutical interventions against COVID-19 epidemic outbreaks. PLoS ONE, 16 (5), 0252019. doi:10.1371/journal.pone.0252019
Peer Reviewed verified by ORBi

Novak, G., Finkbeiner, S., Skibinski, G., & Skupin, A. (2021). Generation of two human induced pluripotent stem cell lines (iPSCs) with mutations of the α-synuclein (SNCA) gene associated with Parkinson’s disease; the A53T mutation (LCSBi003) and a triplication of the SNCA gene (LCSBi007). Stem Cell Research, 57, 102600. doi:10.1016/j.scr.2021.102600
Peer reviewed

Badanjak, K., Fixemer, S., Smajic, S., Skupin, A., & Grünewald, A. (2021). The Contribution of Microglia to Neuroinflammation in Parkinson's Disease. International Journal of Molecular Sciences, 22 (9). doi:10.3390/ijms22094676
Peer Reviewed verified by ORBi

Czypionka, T., Iftekhar, E., Prainsack, B., Priesemann, V., Bauer, S., Valdez, A. C., Cuschieri, S., Glaab, E., Grill, E., Krutzinna, J., Lionis, C., Machado, H., Martins, C., Pavlakis, G., Perc, M., Petelos, E., Pickersgill, M., Skupin, A., Schernhammer, E., ... Wilmes, P. (2021). The benefits, costs and feasibility of a low incidence COVID-19 strategy. The Lancet Regional Health - Europe, 12 (100193). doi:10.1016/j.lanepe.2021.100294
Peer reviewed

Martinez Arbas, S., Narayanasamy, S., Herold, M., Lebrun, L., Hoopmann, M. R., Li, S., Lam, T. J., Kunath, B. J., Hicks, N. D., Liu, C. M., Price, L. B., Laczny, C. C., Gillece, J. D., Schupp, J. M., Keim, P. S., Moritz, R. L., Faust, K., Tang, H., Ye, Y., ... Wilmes, P. (2021). Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics. Nature Microbiology, 6 (1), 123--135. doi:10.1038/s41564-020-00794-8
Peer Reviewed verified by ORBi

Ameli, C., Fixemer, S., Bouvier, D., & Skupin, A. (2021). PRAQA: Protein Relative Abundance Quantification Algorithm for 3D Fluorescent Images. In BIOIMAGING (pp. 21--30). doi:10.5220/0010187400210030
Peer reviewed

Novak, G., Finkbeiner, S., Skibinski, G., & Skupin, A. (2021). Generation of two human induced pluripotent stem cell lines from fibroblasts of unrelated Parkinson’s patients carrying the G2019S mutation in the LRRK2 gene (LCSBi005, LCSBi006). Stem Cell Research, 57, 102569. doi:10.1016/j.scr.2021.102569
Peer reviewed

Wilmes, P., Zimmer, J., Schulz, J., Glod, F., Veiber, L., Mombaerts, L., Rodrigues, B., Aalto, A., Pastore, J., Snoeck, C. J., Ollert, M., Fagherazzi, G., Mossong, J., Goncalves, J., Skupin, A., & Nehrbass, U. (2021). SARS-CoV-2 transmission risk from asymptomatic carriers: Results from a mass screening programme in Luxembourg. The Lancet Regional Health. Europe, 4, 100056. doi:10.1016/j.lanepe.2021.100056
Peer Reviewed verified by ORBi

Soliman, R., Cordero Maldonado, M. L., Martins, T., Moein, M., Conrotte, J.-F., Warmack, R., Skupin, A., Crawford, A., Clarke, S., & Linster, C. (2020). L-Isoaspartyl methyltransferase deficiency in zebrafish leads to impaired calcium signaling in the brain. Frontiers in Genetics. doi:10.3389/fgene.2020.612343
Peer Reviewed verified by ORBi

Martinez Arbas, S.* , Narayanasamy, S.* , Herold, M., Lebrun, L., Hoopmann, M. R., Li, S., Lam, T. J., Kunath, B., Hicks, N. D., Liu, C. M., Price, L. B., Laczny, C. C., Gillece, J. D., Schupp, J. M., Keim, P. S., Moritz, R. L., Faust, K., Tang, H., Ye, Y., ... Wilmes, P. (2020). Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics. Nature Microbiology.
Peer Reviewed verified by ORBi
* These authors have contributed equally to this work.

Kolodkin, A., Colangelo, A., Ignatenko, A., Martorana, F., Jennen, D., Briedé, J., Brady, N., Barberis, M., Mondeel, T., Papa, M., Kumar, V., Peters, B., Skupin, A., Alberghina, L., Balling, R., & Westerhoff, H. (2020). ROS networks: designs, aging, Parkinson's disease and precision therapies. NPJ Systems Biology and Applications. doi:10.1038/s41540-020-00150-w
Peer Reviewed verified by ORBi

Golebiewska, A., Hau, A.-C., Oudin, A., Stieber, D., Yabo, Y. A., Baus, V., Barthelemy, V., Klein, E., Bougnaud, S., Keunen, O., Wantz, M., Michelucci, A., Neirinckx, V., Muller, A., Kaoma, T., Nazarov, P. V., Azuaje, F., De Falco, A., Flies, B., ... Niclou, S. (2020). Patient-derived organoids and orthotopic xenografts of primary and recurrent gliomas represent relevant patient avatars for precision oncology. Acta Neuropathologica. doi:10.1007/s00401-020-02226-7
Peer Reviewed verified by ORBi

Golebiewska, A., Hau, A.-C., Oudin, A., Stieber, D., Yabo, Y. A., Baus, V., Barthelemy, V., Klein, E., Bougnaud, S., Keunen, O., Wantz, M., Michelucci, A., Neirinckx, V., Muller, A., Kaoma, T., Nazarov, P. V., Azuaje, F., De Falco, A., Flies, B., ... Niclou, S. (2020). Primary and recurrent glioma patient-derived orthotopic xenografts (PDOX) represent relevant patient avatars for precision medicine. ORBilu-University of Luxembourg. https://orbilu.uni.lu/handle/10993/43022. doi:10.1101/2020.04.24.057802

Smits, L., Magni, S., Kinugawa, K., Grzyb, K., Luginbühl, J., Sabaté Soler, S., Bolognin, S., Shin, J., Mori, E., Skupin, A., & Schwamborn, J. C. (2020). Single-cell transcriptomics reveals multiple neuronal cell types in human midbrain-specific organoids. Cell and Tissue Research. doi:10.1007/s00441-020-03249-y
Peer Reviewed verified by ORBi

Powell, J., Falcke, M., Skupin, A., Bellamy, T. C., Kypraios, T., & Thul, R. (2020). A Statistical View on Calcium Oscillations. Advances in experimental medicine and biology, 1131, 799--826. doi:10.1007/978-3-030-12457-1_32
Peer reviewed

Proverbio, D., Kemp, F., Magni, S., Husch, A., Aalto, A., Mombaerts, L., Goncalves, J., Skupin, A., Ameijeiras-Alonso, J., & Ley, C. (2020). Assessing suppression strategies against epidemicoutbreaks like COVID-19: the SPQEIR model. ORBilu-University of Luxembourg. https://orbilu.uni.lu/handle/10993/44206. doi:10.1101/2020.04.22.20075804doi:

Tiraboschi, E., Martina, S., van der Ent, W., Grzyb, K., Gawel, K., Cordero-Maldonado, M. L., Poovathingal, S. K., Heintz, S., Satheesh, S. V., Brattespe, J., Skupin, A., & Esguerra, C. (2020). New insights into the early mechanisms of epileptogenesis in a zebrafish model of Dravet syndrome. Epilepsia. doi:10.1111/epi.16456
Peer reviewed

Balling, R., Goncalves, J., Magni, S., Mombaerts, L., Oldano, A., & Skupin, A. (2019). From Diagnosing Diseases to Predicting Diseases. In U. A. K. Betz (Ed.), Curious2018 (pp. 95-103). Springer, Cham. doi:10.1007/978-3-030-16061-6_11

Grossmann, D., Berenguer, C., Bellet, M. E., Scheibner, D., Bohler, J., Massart, F., Rapaport, D., Skupin, A., Fouquier d'Hérouël, A., Sharma, M., Ghelfi, J., Rakovic, A., Lichtner, P., Antony, P., Glaab, E., May, P., Dimmer, K. S., Fitzgerald, J. C., Grünewald, A., & Krüger, R. (2019). Mutations in RHOT1 disrupt ER-mitochondria contact sites interfering with calcium homeostasis and mitochondrial dynamics in Parkinson's disease. Antioxidants & redox signaling. doi:10.1089/ars.2018.7718
Peer reviewed

Garcia, G. C., Bartol, T. M., Phan, S. A., Bushong, E. A., Perkins, G., Sejnowski, T. J., Ellisman, M. H., & Skupin, A. (2019). Mitochondrial morphology provides a mechanism for energy buffering at synapses. ORBilu-University of Luxembourg. https://orbilu.uni.lu/handle/10993/39715. doi:10.1101/643551

Salamanca, L., Mechawar, N., Murai, K. K., Balling, R., Bouvier, D., & Skupin, A. (2019). MIC-MAC: An automated pipeline for high-throughput characterization and classification of three-dimensional microglia morphologies in mouse and human postmortem brain samples. Glia. doi:10.1002/glia.23623
Peer reviewed

Smits, L., Magni, S., Grzyb, K., Antony, P., Krüger, R., Skupin, A., Bolognin, S., & Schwamborn, J. C. (2019). Single-cell transcriptomics reveals multiple neuronal cell types in human midbrain-specific organoids. ORBilu-University of Luxembourg. https://orbilu.uni.lu/handle/10993/39342. doi:10.1101/589598

Walter, J., Bolognin, S., Antony, P., Nickels, S., Poovathhingal, S., Salamanca, L., Magni, S., Perfeito, R., Hoel, F., Qing, X., Jarazo, J., Arias-Fuenzalida, J., Ignac, T., Monzel, A. S., Gonzalez-Cano, L., Pereira de Almeida, L., Skupin, A., Tronstad, K., & Schwamborn, J. C. (2019). Neural Stem Cells of Parkinson's Disease Patients Exhibit Aberrant Mitochondrial Morphology and Functionality. Stem Cell Reports. doi:10.1016/j.stemcr.2019.03.004
Peer Reviewed verified by ORBi

Intosalmi, J., Scott, A. C., Hays, M., Flann, N., Yli-Harja, O., Lähdesmäki, H., Dudley, A. M., & Skupin, A. (2019). Data-driven multiscale modeling reveals the role of metabolic coupling for the spatio-temporal growth dynamics of yeast colonies. BMC Molecular and Cell Biology, 20, 59. doi:10.1186/s12860-019-0234-z
Peer Reviewed verified by ORBi

Garcia, G. C., Bartol, T. M., Phan, S., Bushong, E. A., Perkins, G., Sejnowski, T. J., Ellisman, M. H., & Skupin, A. (2019). Mitochondrial morphology provides a mechanism for energy buffering at synapses. Scientific Reports, 9, 18306. doi:10.1038/s41598-019-54159-1
Peer Reviewed verified by ORBi

Dirkse, A., Golebiewska, A., Buder, T., Nazarov, P. V., Muller, A., Poovathingal, S., Brons, N. H. C., Leite, S., Sauvageot, N., Sarkisjan, D., Seyfrid, M., Fritah, S., Stieber, D., Michelucci, A., Herold-Mende, C., Bjerkvig, R., Azuaje, F., Skupin, A., Deutsch, A., ... Hertel, F. (2019). Stem cell-associated heterogeneity in Glioblastoma results from intrinsic tumor plasticity shaped by the microenvironment. Nature communications, 10 (1), 1787. doi:10.1038/s41467-019-09853-z
Peer reviewed

Sousa, C., Golebiewska, A., Poovathingal, S. K., Kaoma, T., Pires-Afonso, Y., Martina, S., Coowar, D., Azuaje, F., Skupin, A., Balling, R., Biber, K., Niclou, S., & Michelucci, A. (2018). Single-cell transcriptomics reveals distinct inflammation-induced microglia signatures. EMBO Reports. doi:10.15252/embr.201846171
Peer Reviewed verified by ORBi

Grosse-Wilde, A., Kuestner, R. E., Skelton, S. M., MacIntosh, E., Fouquier d'Hérouël, A., Ertaylan, G., del Sol, A., Skupin, A., & Huang, S. (2018). Loss of inter-cellular cooperation by complete epithelial-mesenchymal transition supports favorable outcomes in basal breast cancer patients. Oncotarget, 9 (28), 20018.
Peer reviewed

Moein, M., Grzyb, K., Gonçalves Martins, T., Komoto, S., Peri, F., Crawford, A. D., Fouquier d’Herouel, A., & Skupin, A. (2018). CaSiAn: a Calcium Signaling Analyzer tool. Bioinformatics, 1, 3. doi:10.1093/bioinformatics/bty281
Peer reviewed

Falcke, M., Moein, M., Tilunaite, Thul, R., & Skupin, A. (2018). On the phase space structure of IP3 induced Ca2+ signalling and concepts for predictive modeling. Chaos, 28 (4), 045115. doi:10.1063/1.5021073
Peer Reviewed verified by ORBi

Magni, S., Succurro, A., Skupin, A., & Ebenhöh, O. (2018). Data-driven dynamical model indicates that the heat shock response in Chlamydomonas reinhardtii is tailored to handle natural temperature variation. Journal of the Royal Society, Interface, 15 (142), 20170965. doi:10.1098/rsif.2017.0965
Peer Reviewed verified by ORBi

Skupin, A., & Komin, N. (May 2017). How to address cellular heterogeneity by distribution biology. Current Opinion in Systems Biology, 3, 154-160. doi:10.1016/j.coisb.2017.05.010
Peer reviewed

Soman, S., Keatinge, M., Moein, M., Da Costa, M., Mortiboys, M., Skupin, A., Sugunan, S., Bazala, M., Kuznicki, J., & Bandmann, O. (2017). Inhibition of the mitochondrial calcium uniporter rescues dopaminergic neurons in pink1-/- zebrafish. European Journal of Neuroscience, 45 (4), 528. doi:10.1111/ejn.13473
Peer Reviewed verified by ORBi

Nonnenmacher, Y., Palorini, R., Fouquier d'Hérouël, A., Krämer, L., Neumann-Schaal, M., Chiaradonna, F., Skupin, A., Wegner, A., & Hiller, K. (2017). Analysis of mitochondrial metabolism in situ: Combining stable isotope labeling with selective permeabilization. Metabolic Engineering. doi:10.1016/j.ymben.2016.12.005
Peer reviewed

Meiser, J., Delcambre, S., Wegner, A., Jäger, C., Ghelfi, J., Fouquier d'Hérouël, A., Dong, X., Weindl, D., Stautner, C., Nonnenmacher, Y., Michelucci, A., Popp, O., Giesert, F., Schildknecht, S., Kraemer, L., Schneider, J. G., Woitalla, D., Wurst, W., Skupin, A., ... Hiller, K. (2016). Loss of DJ-1 impairs antioxidant response by altered glutamine and serine metabolism. Neurobiology of Disease, 89, 112-125. doi:10.1016/j.nbd.2016.01.019
Peer Reviewed verified by ORBi

Ostaszewski, M., Skupin, A., & Balling, R. (2016). Neurological Diseases from a Systems Medicine Point of View. Methods in Molecular Biology, 1386, 221-50. doi:10.1007/978-1-4939-3283-2_11
Peer Reviewed verified by ORBi

Mojtahedi, M., Skupin, A., Zhou, J., Castaño, I. G., Leong-Quong, R. Y. Y., Chang, H., Trachana, K., Giuliani, A., & Huang, S. (2016). Cell Fate Decision as High-Dimensional Critical State Transition. PLoS Biology, 14 (12), 2000640. doi:10.1371/journal.pbio.2000640
Peer Reviewed verified by ORBi

Salamanca Mino, L., Vlassis, N., Diederich, N., Bernard, F., & Skupin, A. (2015). Improved Parkinson’s disease classification from diffusion MRI data by Fisher vector descriptors. In Improved Parkinson’s disease classification from diffusion MRI data by Fisher vector descriptors (pp. 119-126).
Peer reviewed

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

Grosse-Wilde, A., Fouquier d'Hérouël, A., McIntosh, E., Ertaylan, G., Skupin, A., Kuestner, R. E., del Sol Mesa, A., Walters, K.-A., & Huang, S. (28 May 2015). Stemness of the hybrid Epithelial/Mesenchymal State in Breast Cancer and Its Association with Poor Survival. PLoS ONE, 10 (5), 0126522. doi:10.1371/journal.pone.0126522
Peer Reviewed verified by ORBi

Jung, P., Christian, N., Kay, D., Skupin, A., & Linster, C. (30 March 2015). Protocols and programs for high-throughput growth and aging phenotyping in yeast. PLoS ONE, 10 (3), 0119807. doi:10.1371/journal.pone.0119807
Peer Reviewed verified by ORBi

Komin, N., Moein, M., Ellisman, M., & Skupin, A. (2015). Multiscale Modeling Indicates That Temperature Dependent [Ca2+]i Spiking in Astrocytes Is Quantitatively Consistent with Modulated SERCA Activity. Neural Plasticity, Volume 2015. doi:10.1155/2015/683490
Peer reviewed

Meiser, J., Kraemer, L., Sapcariu, S., Battello, N., Ghelfi, J., Fouquier d'Hérouël, A., Skupin, A., & Hiller, K. (2015). Pro-inflammatory macrophages sustain pyruvate oxidation through pyruvate dehydrogenase for the synthesis of itaconate and to enable cytokine expression. Journal of Biological Chemistry. doi:10.1074/jbc.M115.676817
Peer reviewed

Kolodkin, A., Ignatenko, A., Sangar, V., Simeonidis, V., Peters, B., Westerhoff, H., Skupin, A., Yilmaz, N., Barberis, M., Mondeel, T., Price, N., Brady, N., & Balling, R. (December 2014). ROS homeostasis in a dynamic model: How to save PD neuron? [Poster presentation]. Benelux Bioinformatics conference, Luxembourg, Luxembourg.

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

Garmendia-Torres, C., Skupin, A., Michael, S. A., Ruusuvuori, P., Kuwada, N. J., Falconnet, D., Cary, G. A., Hansen, C., Wiggins, P. A., & Dudley, A. M. (2014). Unidirectional P-body transport during the yeast cell cycle. PLoS ONE, 9 (6), 99428. doi:10.1371/journal.pone.0099428
Peer Reviewed verified by ORBi

Ignac, T., Skupin, A., Sakhanenko, N. A., & Galas, D. J. (2014). Discovering pair-wise genetic interactions: an information theory-based approach. PLoS ONE, 9 (3), 92310. doi:10.1371/journal.pone.0092310
Peer Reviewed verified by ORBi

Christian, N., Skupin, A., Morante, S., Karl, J., Rossi, G., & Ebenhöh, O. (2014). Mesoscopic behavior from microscopic Markov dynamics and its application to calcium release channels. Journal of Theoretical Biology, 343, 102--112. doi:10.1016/j.jtbi.2013.11.010
Peer Reviewed verified by ORBi

Thurley, K., Tovey, S. C., Moenke, G., Prince, V. L., Meena, A., Thomas, A. P., Skupin, A., Taylor, C. W., & Falcke, M. (2014). Reliable encoding of stimulus intensities within random sequences of intracellular Ca2+ spikes. Science Signaling, 7 (331), 59. doi:10.1126/scisignal.2005237
Peer Reviewed verified by ORBi

Galas, D. J., Sakhanenko, N. A., Skupin, A., & Ignac, T. (2014). Describing the complexity of systems: multivariable "set complexity" and the information basis of systems biology. Journal of Computational Biology, 21 (2), 118-40. doi:10.1089/cmb.2013.0039
Peer Reviewed verified by ORBi

Tan, Z., Hays, M., Cromie, G. A., Jeffery, E. W., Scott, A. C., Ahyong, V., Sirr, A., Skupin, A., & Dudley, A. M. (2013). Aneuploidy underlies a multicellular phenotypic switch. Proceedings of the National Academy of Sciences of the United States of America, 110 (30), 12367-72. doi:10.1073/pnas.1301047110
Peer Reviewed verified by ORBi

Skupin, A., & Thurley, K. (2012). Calcium signaling: from single channels to pathways. Advances in Experimental Medicine and Biology, 740, 531-51. doi:10.1007/978-94-007-2888-2_24
Peer reviewed

Ignac, T., Sakhanenko, N. A., Skupin, A., & Galas, D. J. (2012). New methods for finding associations in large data sets: Generalizing the maximal information coefficient (MIC). Proceedings of the Ninth International Workshop on Computational Systems Biology, 39-42.
Peer reviewed

Thurley, K., Skupin, A., Thul, R., & Falcke, M. (2012). Fundamentalproperties of Ca2+ signals. Biochimica et Biophysica Acta - General Subjects, 1820 (8), 1185-94. doi:10.1016/J.BBAGEN.2011.10.007
Peer Reviewed verified by ORBi

Ebenhoeh, O., Skupin, A., Kartal, O., Mahlow, S., & Steup, M. (2011). Thermodynamic Characterisation of Carbohydrate-Active Enzymes. In Experimental Standard Conditions of Enzyme Characterisation, Ruedesheim 12-16 2011.
Peer reviewed

Kartal, O., Mahlow, S., Skupin, A., & Ebenhöh, O. (2011). Carbohydrate-active enzymes exemplify entropic principles in metabolism. Molecular Systems Biology, 7 (542). doi:10.1038/msb.2011.76
Peer Reviewed verified by ORBi

Skupin, A., Kettenmann, H., & Falcke, M. (2010). Calcium signals driven by single channel noise. PLoS Computational Biology, 6 (8). doi:10.1371/journal.pcbi.1000870
Peer Reviewed verified by ORBi

Skupin, A., & Falcke, M. (2010). Statistical Analysis of Calcium Oscillations. European Physical Journal. Special Topics, 187, 231-240. doi:10.1140/epjst/e2010-01288-9
Peer reviewed

Schutte, M., Skupin, A., Segre, D., & Ebenhoh, O. (2010). Modeling the complex dynamics of enzyme-pathway coevolution. Chaos, 20 (4), 045115. doi:10.1063/1.3530440
Peer Reviewed verified by ORBi

Taufiq-Ur-Rahman, Skupin, A., Falcke, M., & Taylor, C. W. (2009). Clustering of InsP3 receptors by InsP3 retunes their regulation by InsP3 and Ca2+. Nature, 458 (7238), 655-9. doi:10.1038/nature07763
Peer Reviewed verified by ORBi

Skupin, A., & Falcke, M. (2009). From puffs to global Ca2+ signals: how molecular properties shape global signals. Chaos, 19 (3), 037111. doi:10.1063/1.3184537
Peer Reviewed verified by ORBi

Schipke, C. G., Heidemann, A., Skupin, A., Peters, O., Falcke, M., & Kettenmann, H. (2008). Temperature and nitric oxide control spontaneous calcium transients in astrocytes. Cell Calcium, 43 (3), 285-95. doi:10.1016/j.ceca.2007.06.002
Peer Reviewed verified by ORBi

Skupin, A., Kettenmann, H., Winkler, U., Wartenberg, M., Sauer, H., Tovey, S. C., Taylor, C. W., & Falcke, M. (2008). How does intracellular Ca2+ oscillate: by chance or by the clock? Biophysical Journal, 94 (6), 2404-11. doi:10.1529/biophysj.107.119495
Peer Reviewed verified by ORBi

Skupin, A., & Falcke, M. (2008). The role of IP3R clustering in Ca2+ signaling. Genome informatics. International Conference on Genome Informatics, 20, 15-24. doi:10.1142/9781848163003_0002
Peer reviewed

Skupin, A., & Falcke, M. (2007). Statistical properties and information content of calcium oscillations. Genome informatics. International Conference on Genome Informatics, 18, 44-53. doi:10.1142/9781860949920_0005
Peer reviewed

Contact ORBilu