Publications

2020

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See detailPatient-derived organoids and orthotopic xenografts of primary and recurrent gliomas represent relevant patient avatars for precision oncology.
Golebiewska, Anna; Hau, Ann-Christin; Oudin, Anaïs; Stieber, Daniel; Yabo, Yahaya A.; Baus, Virginie; Barthelemy, Vanessa; Klein, Eliane; Bougnaud, Sébastien; 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

in Acta neuropathologica (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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2019

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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2018

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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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2017

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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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2016

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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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2015

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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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2014

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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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2013

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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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2012

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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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2011

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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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2010

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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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2009

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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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2008

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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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2007

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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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