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Dr. Alexander Skupin

Alexander Skupin

Associate professor/Chief scientist 2 in Modelling of Biomedical Data

Faculté ou Centre Luxembourg Centre for Systems Biomedicine
Department Integrative Cell Signalling
Adresse postale Université du Luxembourg
6, avenue du Swing
L-4367 Belvaux
Bureau sur le campus BioTech II, 2.15
Téléphone (+352) 46 66 44 5268
Fax (+352) 46 66 44 35268
Video Associate Prof. Dr. Alexander Skupin (LCSB)
Associate Prof. Dr. Alexander Skupin (LCSB)
LCSB - Associate Prod. Dr. Alexander Skupin (LCSB)

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.


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


PhD in Biophysics

Humboldt University Berlin, Germany


Diploma in Physics

Humboldt University Berlin, Germany

Last updated on: lundi 21 septembre 2020

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See detailPrimary and recurrent glioma patient-derived orthotopic xenografts (PDOX) represent relevant patient avatars for precision medicine
Golebiewska, Anna; Hau, Ann-Christin; Oudin, Anais; Stieber, Daniel; Yabo, Yahaya A.; Baus, Virginie; Barthelemy, Vanessa; Klein, Eliane; Bougnaud, Sebastien; Keunen, Olivier; Wantz, May; Michelucci, Alessandro; Neirinckx, Virginie; Muller, Arnaud; Kaoma, Tony; Nazarov, Petr V.; Azuaje, Francisco; De Falco, Alfonso; Flies, Ben; Richart, Lorraine; Poovathingal, Suresh; Arns, Thais; Grzyb, Kamil; Mock, Andreas; Herold-Mende, Christel; Steino, Anne; Brown, Dennis; May, Patrick; Miletic, Hrvoje; Malta, Tathiane M.; Noushmehr, Houtan; Kwon, Yong-Jun; Jahn, Winnie; Klink, Barbara; Tanner, Georgette; Stead, Lucy F.; Mittelbronn, Michel; Skupin, Alexander; Hertel, Frank; Bjerkvig, Rolf; Niclou, Simone

E-print/Working paper (2020)

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See detailA Statistical View on Calcium Oscillations.
Powell, Jake; Falcke, Martin; Skupin, Alexander; Bellamy, Tomas C.; Kypraios, Theodore; Thul, Rüdiger

in Advances in experimental medicine and biology (2020), 1131

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See detailAssessing suppression strategies against epidemicoutbreaks like COVID-19: the SPQEIR model
Proverbio, Daniele; Kemp, Francoise; Magni, Stefano; Husch, Andreas; Aalto, Atte; Mombaerts, Laurent; Goncalves, Jorge; Skupin, Alexander; Ameijeiras-Alonso, Jose; Ley, Christophe

E-print/Working paper (2020)

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See detailSingle-cell transcriptomics reveals multiple neuronal cell types in human midbrain-specific organoids
Smits, Lisa; Magni, Stefano; Kinugawa, Kaoru; Grzyb, Kamil; Luginbühl, Joachim; Sabaté Soler, Sonia; Bolognin, Silvia; Shin, Jay; Mori, Eiichiro; Skupin, Alexander; Schwamborn, Jens Christian

in Cell and Tissue Research (2020)

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See detailNew insights into the early mechanisms of epileptogenesis in a zebrafish model of Dravet syndrome
Tiraboschi, Ettore; Martina, Silvia; van der Ent, Wietske; Grzyb, Kamil; Gawel, Kinga; Cordero-Maldonado, Maria Lorena; Poovathingal, Suresh Kumar; Heintz, Sarah; Satheesh, Somisetty Venkata; Brattespe, Jarle; Skupin, Alexander; Esguerra, Camila

in Epilepsia (2020)

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See detailFrom Diagnosing Diseases to Predicting Diseases
Balling, Rudi; Goncalves, Jorge; Magni, Stefano; Mombaerts, Laurent; Oldano, Alice; Skupin, Alexander

in Betz, Ulrich A.K. (Ed.) Curious2018 (2019)

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See detailStem cell-associated heterogeneity in Glioblastoma results from intrinsic tumor plasticity shaped by the microenvironment
Dirkse, Anne; Golebiewska, Anna; Buder, Thomas; Nazarov, Petr V.; Muller, Arnaud; Poovathingal, Suresh; Brons, Nicolaas H. C.; Leite, Sonia; Sauvageot, Nicolas; Sarkisjan, Dzjemma; Seyfrid, Mathieu; Fritah, Sabrina; Stieber, Daniel; Michelucci, Alessandro; Herold-Mende, Christel; Bjerkvig, Rolf; Azuaje, Francisco; Skupin, Alexander; Deutsch, Andreas; Voss-Böhme, Anja; Niclou, Simone

in Nature communications (2019), 10(1), 1787

See detailMitochondrial morphology provides a mechanism for energy buffering at synapses
Garcia, Guadalupe Clara; Bartol, Thomas M.; Phan, Sebastien A.; Bushong, Eric A.; Perkins, Guy; Sejnowski, Terrence J.; Ellisman, Mark H.; Skupin, Alexander

E-print/Working paper (2019)

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See detailMitochondrial morphology provides a mechanism for energy buffering at synapses.
Garcia, Guadalupe Clara; Bartol, Thomas M.; Phan, Sébastien; Bushong, Eric A.; Perkins, Guy; Sejnowski, Terrence J.; Ellisman, Mark H.; Skupin, Alexander

in Scientific reports (2019), 9

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See detailMutations in RHOT1 disrupt ER-mitochondria contact sites interfering with calcium homeostasis and mitochondrial dynamics in Parkinson's disease.
Grossmann, Dajana; Berenguer, Clara; Bellet, Marie Estelle; Scheibner, David; Bohler, Jill; Massart, François; Rapaport, Doron; Skupin, Alexander; Fouquier d'Hérouël, Aymeric; Sharma, Manu; Ghelfi, Jenny; Rakovic, Aleksandar; Lichtner, Peter; Antony, Paul; Glaab, Enrico; May, Patrick; Dimmer, Kai Stefan; Fitzgerald, Julia Catherine; Grünewald, Anne; Krüger, Rejko

in Antioxidants & redox signaling (2019)

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See detailData-driven multiscale modeling reveals the role of metabolic coupling for the spatio-temporal growth dynamics of yeast colonies.
Intosalmi, Jukka; Scott, Adrian C.; Hays, Michelle; Flann, Nicholas; Yli-Harja, Olli; Lähdesmäki, Harri; Dudley, Aimée M.; Skupin, Alexander

in BMC molecular and cell biology (2019), 20

See detailSingle-cell transcriptomics reveals multiple neuronal cell types in human midbrain-specific organoids
Smits, Lisa; Magni, Stefano; Grzyb, Kamil; Antony, Paul; Krüger, Rejko; Skupin, Alexander; Bolognin, Silvia; Schwamborn, Jens Christian

E-print/Working paper (2019)

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See detailNeural Stem Cells of Parkinson's Disease Patients Exhibit Aberrant Mitochondrial Morphology and Functionality
Walter, Jonas; Bolognin, Silvia; Antony, Paul; Nickels, Sarah; Poovathhingal, Suresh; Salamanca, Luis; Magni, Stefano; Perfeito, Rita; Hoel, Fredrik; Qing, Xiaobing; Jarazo, Javier; Arias-Fuenzalida, Jonathan; Ignac, Tomasz; Monzel, Anna Sophia; Gonzalez-Cano, Laura; Pereira de Almeida, Luis; Skupin, Alexander; Tronstad, Karl; Schwamborn, Jens Christian

in Stem Cell Reports (2019)

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See detailOn the phase space structure of IP3 induced Ca2+ signalling and concepts for predictive modeling
Falcke, Martin; Moein, Mahsa; Tilunaite; Thul, Rüdiger; Skupin, Alexander

in Chaos (2018), 28(4), 045115

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See detailLoss of inter-cellular cooperation by complete epithelial-mesenchymal transition supports favorable outcomes in basal breast cancer patients
Grosse-Wilde, Anne; Kuestner, Rolf E.; Skelton, Stephanie M.; MacIntosh, Ellie; Fouquier d'Hérouël, Aymeric; Ertaylan, Gökhan; del Sol, Antonio; Skupin, Alexander; Huang, Sui

in Oncotarget (2018), 9(28), 20018

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See detailData-driven dynamical model indicates that the heat shock response in Chlamydomonas reinhardtii is tailored to handle natural temperature variation
Magni, Stefano; Succurro, Antonella; Skupin, Alexander; Ebenhöh, Oliver

in Journal of the Royal Society, Interface (2018), 15(142), 20170965

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See detailCaSiAn: a Calcium Signaling Analyzer tool
Moein, Mahsa; Grzyb, Kamil; Gonçalves Martins, Teresa; Komoto, Shinya; Peri, Francesca; Crawford, Alexander Dettmar; Fouquier d’Herouel, Aymeric; Skupin, Alexander

in Bioinformatics (2018), 1

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See detailSingle-cell transcriptomics reveals distinct inflammation-induced microglia signatures
Sousa, Carole; Golebiewska, Anna; Poovathingal, Suresh K; Kaoma, Tony; Pires-Afonso, Yolanda; Martina, Silvia; Coowar, Djalil; Azuaje, Francisco; Skupin, Alexander; Balling, Rudi; Biber, Knut; Niclou, Simone P; Michelucci, Alessandro

in EMBO Reports (2018)

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See detailAnalysis of mitochondrial metabolism in situ: Combining stable isotope labeling with selective permeabilization
Nonnenmacher, Yannic; Palorini, Roberta; Fouquier d'Hérouël, Aymeric; Krämer, Lisa; Neumann-Schaal, Meina; Chiaradonna, Ferdinando; Skupin, Alexander; Wegner, Andre; Hiller, Karsten

in Metabolic Engineering (2017)

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See detailHow to address cellular heterogeneity by distribution biology
Skupin, Alexander; Komin, Niko

in Current Opinion in Systems Biology (2017), 3

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See detailInhibition of the mitochondrial calcium uniporter rescues dopaminergic neurons in pink1-/- zebrafish
Soman, Smijin; Keatinge, Marcus; Moein, Mahsa; Da Costa, Mark; Mortiboys, Meather; Skupin, Alexander; Sugunan, Sreedevi; Bazala, Michal; Kuznicki, Jacek; Bandmann, Oliver

in European Journal of Neuroscience (2017), 45(4), 528

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See detailLoss of DJ-1 impairs antioxidant response by altered glutamine and serine metabolism
Meiser, Johannes; Delcambre, Sylvie; Wegner, André; Jäger, Christian; Ghelfi, Jenny; Fouquier d'Hérouël, Aymeric; Dong, Xiangyi; Weindl, Daniel; Stautner, Constantin; Nonnenmacher, Yannic; Michelucci, Alessandro; Popp, Oliver; Giesert, Florian; Schildknecht, Stefan; Kraemer, Lisa; Schneider, Jochen G.; Woitalla, Dirk; Wurst, Wolfgang; Skupin, Alexander; Vogt Weisenhorn, Daniela M.; Krüger, Rejko; Leist, Marcel; Hiller, Karsten

in Neurobiology of disease (2016), 89

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See detailCell Fate Decision as High-Dimensional Critical State Transition
Mojtahedi, Mitra; Skupin, Alexander; Zhou, Joseph; Castaño, Ivan G.; Leong-Quong, Rebecca Y. Y.; Chang, Hannah; Trachana, Kalliopi; Giuliani, Alessandro; Huang, Sui

in PLOS Biology (2016), 14(12), 2000640

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See detailNeurological Diseases from a Systems Medicine Point of View.
Ostaszewski, Marek; Skupin, Alexander; Balling, Rudi

in Methods in molecular biology (Clifton, N.J.) (2016), 1386

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See detailStemness of the hybrid Epithelial/Mesenchymal State in Breast Cancer and Its Association with Poor Survival.
Grosse-Wilde, Anne; Fouquier d'Hérouël, Aymeric; McIntosh, Ellie; Ertaylan, Gökhan; Skupin, Alexander; Kuestner, Rolf E.; del Sol Mesa, Antonio; Walters, Kathie-Anne; Huang, Sui

in PLoS ONE (2015), 10(5), 0126522

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See detailProtocols and programs for high-throughput growth and aging phenotyping in yeast.
Jung, Paul; Christian, Nils; Kay, Daniel; Skupin, Alexander; Linster, Carole

in PloS one (2015), 10(3), 0119807

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See detailMultiscale Modeling Indicates That Temperature Dependent [Ca2+]i Spiking in Astrocytes Is Quantitatively Consistent with Modulated SERCA Activity
Komin, Niko; Moein, Mahsa; Ellisman, Mark; Skupin, Alexander

in Neural Plasticity (2015), Volume 2015

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See detailPro-inflammatory macrophages sustain pyruvate oxidation through pyruvate dehydrogenase for the synthesis of itaconate and to enable cytokine expression
Meiser, Johannes; Kraemer, Lisa; Sapcariu, Sean; Battello, Nadia; Ghelfi, Jenny; Fouquier d'Hérouël, Aymeric; Skupin, Alexander; Hiller, Karsten

in Journal of Biological Chemistry (2015)

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See detailImproved Parkinson’s disease classification from diffusion MRI data by Fisher vector descriptors
Salamanca Mino, Luis; Vlassis, Nikos; Diederich, Nico; Bernard, Florian; Skupin, Alexander

in Improved Parkinson’s disease classification from diffusion MRI data by Fisher vector descriptors (2015, October)

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See detailCritical transitions in chronic disease: transferring concepts from ecology to systems medicine
Trefois, Christophe; Antony, Paul; Goncalves, Jorge; Skupin, Alexander; Balling, Rudi

in Current Opinion in Biotechnology (2015), 34

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See detailMesoscopic behavior from microscopic Markov dynamics and its application to calcium release channels.
Christian, Nils; Skupin, Alexander; Morante, Silvia; Karl, Jansen; Rossi, Giancarlo; Ebenhöh, Oliver

in Journal of Theoretical Biology (2014), 343

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See detailDescribing the complexity of systems: multivariable "set complexity" and the information basis of systems biology.
Galas, David J.; Sakhanenko, Nikita A.; Skupin, Alexander; Ignac, Tomasz

in Journal of computational biology: a journal of computational molecular cell biology (2014), 21(2), 118-40

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See detailUnidirectional P-body transport during the yeast cell cycle.
Garmendia-Torres, Cecilia; Skupin, Alexander; Michael, Sean A.; Ruusuvuori, Pekka; Kuwada, Nathan J.; Falconnet, Didier; Cary, Gregory A.; Hansen, Carl; Wiggins, Paul A.; Dudley, Aimee M.

in PloS one (2014), 9(6), 99428

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See detailDiscovering pair-wise genetic interactions: an information theory-based approach.
Ignac, Tomasz; Skupin, Alexander; Sakhanenko, Nikita A.; Galas, David J.

in PloS one (2014), 9(3), 92310

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See detailROS homeostasis in a dynamic model: How to save PD neuron?
Kolodkin, Alexey; Ignatenko, Andrew; Sangar, Vineet; Simeonidis, Vangelis; Peters, Bernhard; Westerhoff, Hans; Skupin, Alexander; Yilmaz, Nilgun; Barberis, Matteo; Mondeel, Thierry; Price, Nathan; Brady, Nathan; Balling, Rudi

Poster (2014, December)

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See detailAutomated nuclei clump splitting by combining local concavity orientation and graph partitioning
Samsi, Siddharth; Trefois, Christophe; Antony, Paul; Skupin, Alexander

in International Conference on Biomedical and Health Informatics (2014)

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See detailReliable encoding of stimulus intensities within random sequences of intracellular Ca2+ spikes.
Thurley, Kevin; Tovey, Stephen C.; Moenke, Gregor; Prince, Victoria L.; Meena, Abha; Thomas, Andrew P.; Skupin, Alexander; Taylor, Colin W.; Falcke, Martin

in Science Signaling (2014), 7(331), 59

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See detailAneuploidy underlies a multicellular phenotypic switch.
Tan, Zhihao; Hays, Michelle; Cromie, Gareth A.; Jeffery, Eric W.; Scott, Adrian C.; Ahyong, Vida; Sirr, Amy; Skupin, Alexander; Dudley, Aimee M.

in Proceedings of the National Academy of Sciences of the United States of America (2013), 110(30), 12367-72

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See detailNew methods for finding associations in large data sets: Generalizing the maximal information coefficient (MIC)
Ignac, Tomasz; Sakhanenko, N. A.; Skupin, Alexander; Galas, David J.

in Proceedings of the Ninth International Workshop on Computational Systems Biology (2012)

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See detailCalcium signaling: from single channels to pathways
Skupin, Alexander; Thurley, K.

in Advances in Experimental Medicine and Biology (2012), 740

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See detailFundamentalproperties of Ca2+ signals
Thurley, K.; Skupin, Alexander; Thul, R.; Falcke, M.

in Biochimica et Biophysica Acta - General Subjects (2012), 1820(8), 1185-94

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See detailThermodynamic Characterisation of Carbohydrate-Active Enzymes
Ebenhoeh, Oliver; Skupin, Alexander; Kartal, Oender; Mahlow, Sebastian; Steup, Martin

in Experimental Standard Conditions of Enzyme Characterisation, Ruedesheim 12-16 2011 (2011)

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See detailCarbohydrate-active enzymes exemplify entropic principles in metabolism
Kartal, O.; Mahlow, S.; Skupin, Alexander; Ebenhöh, O.

in Molecular Systems Biology (2011), 7(542),

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See detailModeling the complex dynamics of enzyme-pathway coevolution.
Schutte, Moritz; Skupin, Alexander; Segre, Daniel; Ebenhoh, Oliver

in Chaos (2010), 20(4), 045115

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See detailStatistical Analysis of Calcium Oscillations
Skupin, Alexander; Falcke, Martin

in European Physical Journal. Special Topics (2010), 187

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See detailCalcium signals driven by single channel noise.
Skupin, Alexander; Kettenmann, Helmut; Falcke, Martin

in PLoS computational biology (2010), 6(8),

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See detailFrom puffs to global Ca2+ signals: how molecular properties shape global signals.
Skupin, Alexander; Falcke, Martin

in Chaos (2009), 19(3), 037111

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See detailClustering of InsP3 receptors by InsP3 retunes their regulation by InsP3 and Ca2+.
Taufiq-Ur-Rahman; Skupin, Alexander; Falcke, Martin; Taylor, Colin W.

in Nature (2009), 458(7238), 655-9

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See detailTemperature and nitric oxide control spontaneous calcium transients in astrocytes.
Schipke, Carola G.; Heidemann, Antje; Skupin, Alexander; Peters, Oliver; Falcke, Martin; Kettenmann, Helmut

in Cell calcium (2008), 43(3), 285-95

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See detailThe role of IP3R clustering in Ca2+ signaling.
Skupin, Alexander; Falcke, Martin

in Genome informatics. International Conference on Genome Informatics (2008), 20

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See detailHow does intracellular Ca2+ oscillate: by chance or by the clock?
Skupin, Alexander; Kettenmann, Helmut; Winkler, Ulrike; Wartenberg, Maria; Sauer, Heinrich; Tovey, Stephen C.; Taylor, Colin W.; Falcke, Martin

in Biophysical journal (2008), 94(6), 2404-11

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See detailStatistical properties and information content of calcium oscillations.
Skupin, Alexander; Falcke, Martin

in Genome informatics. International Conference on Genome Informatics (2007), 18

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