Dr. Alexander Skupin
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| Faculté ou Centre | Luxembourg Centre for Systems Biomedicine | ||||
| Department | Integrative Cell Signalling | ||||
| Adresse postale |
Université du Luxembourg 6, avenue du Swing L-4367 Belvaux |
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| Bureau sur le campus | BioTech II, 2.15 | ||||
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| Téléphone | (+352) 46 66 44 5268 | ||||
| Video |
Associate Prof. Dr. Alexander Skupin (LCSB)
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Principal Investigator in Integrative Cell Signalling group (Skupin Lab)
Alexander Skupin studied physics at the Humboldt University in Berlin and graduated in 2004 under supervision of Lutz Schimansky-Geier with work on noise-induced effects in neuronal networks. In 2008, he obtained his PhD in theoretical biophysics at the Humboldt University for his interdisciplinary work on calcium signaling with Martin Falcke. After his first postdoc focusing on metabolism with Oliver Ebenhöh at the Max-Planck Institute for Molecular Plant Physiology in Potsdam, he spent 2 years at the Institute for Systems Biology in Seattle (USA) where he continued his interdisciplinary work with Aimee Dudley on Systems Genetics, with Sui Huang on cell fate dynamics and with David Galas on information flow in biological systems. In 2014, he started his interdisciplinary “Integrative Cell Signalling” research group at the Luxembourg Centre for Systems Biomedicine where his team combines microscopy and single cell analysis techniques with theoretical concepts from physics to investigate principles of living matter and their implications for health and disease.
He is also heading the LCSB imaging platform and is co-coordinator of the CriTICS DTU.
CV:
| 2020 - |
Associate Professor |
University of Luxembourg |
| 2016 - |
Project Scientist III |
University California San Diego, USA |
| 2014 - |
Principal Investigator |
Luxembourg Centre for Systems Biomedicine, University of Luxembourg |
| 2014 - 2015 |
Project Scientist I |
University California San Diego, USA |
| 2011 - 2014 |
Research Associate |
Luxembourg Centre for Systems Biomedicine, University of Luxembourg |
| 2011 - 2013 |
Visiting Scholar |
Institute for Systems Biology, Seattle, USA |
| 2009 - 2011 |
Postdoctoral Fellow |
Max Planck Institute for Molecular Plant Physiology, Potsdam, Germany |
| 2009 |
PhD in Biophysics |
Humboldt University Berlin, Germany |
| 2004 |
Diploma in Physics |
Humboldt University Berlin, Germany |
Last updated on: lundi 21 septembre 2020
2022
Single-cell transcriptional profiling and gene regulatory network modeling in Tg2576 mice reveal gender-dependent molecular features preceding Alzheimer-like pathologies; ; ; ; ; ; ; ; ;
in Molecular Neurobiology (2022), in press (doi:10.1007/s12035-022-02985-2)(in press),
Stress hormone signalling inhibits Th1 polarization in a CD4 T-cell-intrinsic manner via mTORC1 and the circadian gene PER1; ; ; ; ; ; ; ;
in Immunology (2022), 165(4), 428--444
Combinatorial analysis reveals highly coordinated early-stage immune reactions that predict later antiviral immunity in mild COVID-19 patients; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in Cell Reports Medicine (2022), 3(4), 100600
A CutFEM Method for a Mechanistic Modelling of Astrocytic Metabolism in 3D Physiological Morphologies; ; ; ;
Scientific Conference (2022, June 07)
3D Modelling of a Spatially Resolved Energy Metabolism in Physiological Astrocytic Morphology; ; ; ; ; ;
Scientific Conference (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; ; ; ; ; ; ; ; ; ;
in Acta Neuropathologica Communications (2022), 10(1), 36
Morphological principles of neuronal mitochondria; ; ; ; ; ; ; ; ; ; ; ; ; ;
in Journal of Comparative Neurology (2022), 530(6), 886--902
Single-cell transcriptomics of human iPSC differentiation dynamics reveal a core molecular network of Parkinson’s disease; ; ; ; ; ; ;
in Communications Biology (2022), 5(1), 1--19
Model-based assessment of COVID-19 epidemic dynamics by wastewater analysis; ; ; ; ; ; ;
in Science of the Total Environment (2022), 827
Buffering variability in cell regulation motifs close to criticality; ; ;
in Physical Review. E. (2022)
Midbrain organoids mimic early embryonic neurodevelopment and recapitulate LRRK2-p.Gly2019Ser-associated gene expression; ; ; ; ; ; ; ;
in American Journal of Human Genetics (2022)
2021
PRAQA: Protein Relative Abundance Quantification Algorithm for 3D Fluorescent Images.; ; ;
in BIOIMAGING (2021)
The Contribution of Microglia to Neuroinflammation in Parkinson's Disease.; ; ; ;
in International journal of molecular sciences (2021), 22(9),
A new brain organoid model to study Parkinson’s Disease; ; ; ; ; ; ; ;
in Biomedical Science and Engineering (2021)
COVID-19 Crisis Management in Luxembourg: Insights from an Epidemionomic Approach; ; ; ; ; ; ; ; ; ; ;
in Economics and Human Biology (2021), 43
The benefits, costs and feasibility of a low incidence COVID-19 strategy; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in The Lancet Regional Health - Europe (2021), 12(100193),
A cut finite element method for spatially resolved energy metabolism models in complex neuro-cell morphologies with minimal remeshing; ; ; ;
in Advanced Modeling and Simulation in Engineering Sciences (2021), 8
Single‑nuclei chromatin profiling of ventral midbrain reveals cell identity transcription factors and cell‑type‑specific gene regulatory variation; ; ; ; ; ; ; ;
in Epigenetics and Chromatin (2021)
Modelling COVID-19 dynamics and potential for herd immunity by vaccination in Austria, Luxembourg and Sweden; ; ; ; ; ; ; ; ;
in Journal of Theoretical Biology (2021)
Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in Nature Microbiology (2021), 6(1), 123--135
Dynamical SPQEIR model assesses the effectiveness of non-pharmaceutical interventions against COVID-19 epidemic outbreaks.; ; ; ; ; ; ; ; ;
in PloS one (2021), 16(5), 0252019
Single-Cell Transcriptomics and In Situ Morphological Analyses Reveal Microglia Heterogeneity Across the Nigrostriatal Pathway; ; ; ; ; ; ; ; ;
in Frontiers in Immunology (2021)
The Parkinson’s-disease-associated mutation LRRK2-G2019S alters dopaminergic differentiation dynamics via NR2F1; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in Cell Reports (2021)
SARS-CoV-2 transmission risk from asymptomatic carriers: Results from a mass screening programme in Luxembourg; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in The Lancet Regional Health. Europe (2021), 4
2020
Patient-derived organoids and orthotopic xenografts of primary and recurrent gliomas represent relevant patient avatars for precision oncology.; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in Acta Neuropathologica (2020)
Primary and recurrent glioma patient-derived orthotopic xenografts (PDOX) represent relevant patient avatars for precision medicine; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
E-print/Working paper (2020)
ROS networks: designs, aging, Parkinson's disease and precision therapies.; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in NPJ Systems Biology and Applications (2020)
Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in Nature Microbiology (2020)
A Statistical View on Calcium Oscillations.; ; ; ; ;
in Advances in experimental medicine and biology (2020), 1131
Assessing suppression strategies against epidemicoutbreaks like COVID-19: the SPQEIR model; ; ; ; ; ; ; ; ;
E-print/Working paper (2020)
Single-cell transcriptomics reveals multiple neuronal cell types in human midbrain-specific organoids; ; ; ; ; ; ; ; ; ;
in Cell and Tissue Research (2020)
L-Isoaspartyl methyltransferase deficiency in zebrafish leads to impaired calcium signaling in the brain; ; ; ; ; ; ; ; ;
in Frontiers in Genetics (2020)
New insights into the early mechanisms of epileptogenesis in a zebrafish model of Dravet syndrome; ; ; ; ; ; ; ; ; ; ;
in Epilepsia (2020)
2019
From Diagnosing Diseases to Predicting Diseases; ; ; ; ;
in Betz, Ulrich A.K. (Ed.) Curious2018 (2019)
Stem cell-associated heterogeneity in Glioblastoma results from intrinsic tumor plasticity shaped by the microenvironment; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in Nature communications (2019), 10(1), 1787
Mitochondrial morphology provides a mechanism for energy buffering at synapses; ; ; ; ; ; ;
E-print/Working paper (2019)
Mitochondrial morphology provides a mechanism for energy buffering at synapses.; ; ; ; ; ; ;
in Scientific reports (2019), 9
Mutations in RHOT1 disrupt ER-mitochondria contact sites interfering with calcium homeostasis and mitochondrial dynamics in Parkinson's disease.; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in Antioxidants & redox signaling (2019)
Data-driven multiscale modeling reveals the role of metabolic coupling for the spatio-temporal growth dynamics of yeast colonies.; ; ; ; ; ; ;
in BMC molecular and cell biology (2019), 20
Single-cell transcriptomics reveals multiple neuronal cell types in human midbrain-specific organoids; ; ; ; ; ; ;
E-print/Working paper (2019)
Neural Stem Cells of Parkinson's Disease Patients Exhibit Aberrant Mitochondrial Morphology and Functionality; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in Stem Cell Reports (2019)
2018
On the phase space structure of IP3 induced Ca2+ signalling and concepts for predictive modeling; ; ; ;
in Chaos (2018), 28(4), 045115
Loss of inter-cellular cooperation by complete epithelial-mesenchymal transition supports favorable outcomes in basal breast cancer patients; ; ; ; ; ; ; ;
in Oncotarget (2018), 9(28), 20018
Data-driven dynamical model indicates that the heat shock response in Chlamydomonas reinhardtii is tailored to handle natural temperature variation; ; ;
in Journal of the Royal Society, Interface (2018), 15(142), 20170965
Single-cell transcriptomics reveals distinct inflammation-induced microglia signatures; ; ; ; ; ; ; ; ; ; ; ;
in EMBO Reports (2018)
2017
Analysis of mitochondrial metabolism in situ: Combining stable isotope labeling with selective permeabilization; ; ; ; ; ; ; ;
in Metabolic Engineering (2017)
How to address cellular heterogeneity by distribution biology;
in Current Opinion in Systems Biology (2017), 3
Inhibition of the mitochondrial calcium uniporter rescues dopaminergic neurons in pink1-/- zebrafish; ; ; ; ; ; ; ; ;
in European Journal of Neuroscience (2017), 45(4), 528
2016
Loss of DJ-1 impairs antioxidant response by altered glutamine and serine metabolism; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
in Neurobiology of Disease (2016), 89
Cell Fate Decision as High-Dimensional Critical State Transition; ; ; ; ; ; ; ;
in PLoS Biology (2016), 14(12), 2000640
Neurological Diseases from a Systems Medicine Point of View.; ;
in Methods in Molecular Biology (2016), 1386
2015
Stemness of the hybrid Epithelial/Mesenchymal State in Breast Cancer and Its Association with Poor Survival.; ; ; ; ; ; ; ;
in PLoS ONE (2015), 10(5), 0126522
Protocols and programs for high-throughput growth and aging phenotyping in yeast.; ; ; ;
in PloS one (2015), 10(3), 0119807
Multiscale Modeling Indicates That Temperature Dependent [Ca2+]i Spiking in Astrocytes Is Quantitatively Consistent with Modulated SERCA Activity; ; ;
in Neural Plasticity (2015), Volume 2015
Pro-inflammatory macrophages sustain pyruvate oxidation through pyruvate dehydrogenase for the synthesis of itaconate and to enable cytokine expression; ; ; ; ; ; ;
in Journal of Biological Chemistry (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 (2015, October)
Critical transitions in chronic disease: transferring concepts from ecology to systems medicine; ; ; ;
in Current Opinion in Biotechnology (2015), 34
2014
Mesoscopic behavior from microscopic Markov dynamics and its application to calcium release channels.; ; ; ; ;
in Journal of Theoretical Biology (2014), 343
Describing the complexity of systems: multivariable "set complexity" and the information basis of systems biology.; ; ;
in Journal of Computational Biology (2014), 21(2), 118-40
Unidirectional P-body transport during the yeast cell cycle.; ; ; ; ; ; ; ; ;
in PloS one (2014), 9(6), 99428
Discovering pair-wise genetic interactions: an information theory-based approach.; ; ;
in PloS one (2014), 9(3), 92310
ROS homeostasis in a dynamic model: How to save PD neuron?; ; ; ; ; ; ; ; ; ; ; ;
Poster (2014, December)
Automated nuclei clump splitting by combining local concavity orientation and graph partitioning; ; ;
in International Conference on Biomedical and Health Informatics (2014)
Reliable encoding of stimulus intensities within random sequences of intracellular Ca2+ spikes.; ; ; ; ; ; ; ;
in Science Signaling (2014), 7(331), 59
2013
Aneuploidy underlies a multicellular phenotypic switch.; ; ; ; ; ; ; ;
in Proceedings of the National Academy of Sciences of the United States of America (2013), 110(30), 12367-72
2012
New methods for finding associations in large data sets: Generalizing the maximal information coefficient (MIC); ; ;
in Proceedings of the Ninth International Workshop on Computational Systems Biology (2012)
Calcium signaling: from single channels to pathways;
in Advances in Experimental Medicine and Biology (2012), 740
Fundamentalproperties of Ca2+ signals; ; ;
in Biochimica et Biophysica Acta - General Subjects (2012), 1820(8), 1185-94
2011
Thermodynamic Characterisation of Carbohydrate-Active Enzymes; ; ; ;
in Experimental Standard Conditions of Enzyme Characterisation, Ruedesheim 12-16 2011 (2011)
Carbohydrate-active enzymes exemplify entropic principles in metabolism; ; ;
in Molecular Systems Biology (2011), 7(542),
2010
Statistical Analysis of Calcium Oscillations;
in European Physical Journal. Special Topics (2010), 187
2009
From puffs to global Ca2+ signals: how molecular properties shape global signals.;
in Chaos (2009), 19(3), 037111
Clustering of InsP3 receptors by InsP3 retunes their regulation by InsP3 and Ca2+.; ; ;
in Nature (2009), 458(7238), 655-9
2008
Temperature and nitric oxide control spontaneous calcium transients in astrocytes.; ; ; ; ;
in Cell calcium (2008), 43(3), 285-95
The role of IP3R clustering in Ca2+ signaling.;
in Genome informatics. International Conference on Genome Informatics (2008), 20
How does intracellular Ca2+ oscillate: by chance or by the clock?; ; ; ; ; ; ;
in Biophysical journal (2008), 94(6), 2404-11
2007
Statistical properties and information content of calcium oscillations.;
in Genome informatics. International Conference on Genome Informatics (2007), 18
