  | 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. |
 | 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 |
 | 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 |
 | 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 |
 | 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 |
 | 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 |
 | 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 |
 | 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 |
 | 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. |
 | 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 |
 | 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 |
 | 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 |
 | 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 |
 | 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 |
 | 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 |
 | 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 |
 | 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 |
 | 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: |
 | 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 |
 | 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 |
 | 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 |
 | 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 |
 | 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 |
 | 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 |
 | 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 |
 | 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 |
 | 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 |
 | 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 |
 | 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 |
 | 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 |
 | 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 |
 | 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 |
 | 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 |
 | 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 |
 | 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 |
 | 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. |
 | 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 |
 | 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 |
 | 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 |
 | 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., & 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 |
 | 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 |
 | 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 |
