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Items: 49


Data-driven multiscale modeling reveals the role of metabolic coupling for the spatio-temporal growth dynamics of yeast colonies.

Intosalmi J, Scott AC, Hays M, Flann N, Yli-Harja O, Lähdesmäki H, Dudley AM, Skupin A.

BMC Mol Cell Biol. 2019 Dec 19;20(1):59. doi: 10.1186/s12860-019-0234-z.


Mitochondrial morphology provides a mechanism for energy buffering at synapses.

Garcia GC, Bartol TM, Phan S, Bushong EA, Perkins G, Sejnowski TJ, Ellisman MH, Skupin A.

Sci Rep. 2019 Dec 4;9(1):18306. doi: 10.1038/s41598-019-54159-1.


A Statistical View on Calcium Oscillations.

Powell J, Falcke M, Skupin A, Bellamy TC, Kypraios T, Thul R.

Adv Exp Med Biol. 2020;1131:799-826. doi: 10.1007/978-3-030-12457-1_32. Review.


Mutations in RHOT1 Disrupt Endoplasmic Reticulum-Mitochondria Contact Sites Interfering with Calcium Homeostasis and Mitochondrial Dynamics in Parkinson's Disease.

Grossmann D, Berenguer-Escuder C, Bellet ME, Scheibner D, Bohler J, Massart F, Rapaport D, Skupin A, Fouquier d'Hérouël A, Sharma M, Ghelfi J, Raković A, Lichtner P, Antony P, Glaab E, May P, Dimmer KS, Fitzgerald JC, Grünewald A, Krüger R.

Antioxid Redox Signal. 2019 Dec 1;31(16):1213-1234. doi: 10.1089/ars.2018.7718. Epub 2019 Aug 21.


Stem cell-associated heterogeneity in Glioblastoma results from intrinsic tumor plasticity shaped by the microenvironment.

Dirkse A, Golebiewska A, Buder T, Nazarov PV, Muller A, Poovathingal S, Brons NHC, Leite S, Sauvageot N, Sarkisjan D, Seyfrid M, Fritah S, Stieber D, Michelucci A, Hertel F, Herold-Mende C, Azuaje F, Skupin A, Bjerkvig R, Deutsch A, Voss-Böhme A, Niclou SP.

Nat Commun. 2019 Apr 16;10(1):1787. doi: 10.1038/s41467-019-09853-z.


MIC-MAC: An automated pipeline for high-throughput characterization and classification of three-dimensional microglia morphologies in mouse and human postmortem brain samples.

Salamanca L, Mechawar N, Murai KK, Balling R, Bouvier DS, Skupin A.

Glia. 2019 Aug;67(8):1496-1509. doi: 10.1002/glia.23623. Epub 2019 Apr 14.


Neural Stem Cells of Parkinson's Disease Patients Exhibit Aberrant Mitochondrial Morphology and Functionality.

Walter J, Bolognin S, Antony PMA, Nickels SL, Poovathingal SK, Salamanca L, Magni S, Perfeito R, Hoel F, Qing X, Jarazo J, Arias-Fuenzalida J, Ignac T, Monzel AS, Gonzalez-Cano L, Pereira de Almeida L, Skupin A, Tronstad KJ, Schwamborn JC.

Stem Cell Reports. 2019 May 14;12(5):878-889. doi: 10.1016/j.stemcr.2019.03.004. Epub 2019 Apr 11.


Single-cell transcriptomics reveals distinct inflammation-induced microglia signatures.

Sousa C, Golebiewska A, Poovathingal SK, Kaoma T, Pires-Afonso Y, Martina S, Coowar D, Azuaje F, Skupin A, Balling R, Biber K, Niclou SP, Michelucci A.

EMBO Rep. 2018 Nov;19(11). pii: e46171. doi: 10.15252/embr.201846171. Epub 2018 Sep 11.


Loss of inter-cellular cooperation by complete epithelial-mesenchymal transition supports favorable outcomes in basal breast cancer patients.

Grosse-Wilde A, Kuestner RE, Skelton SM, MacIntosh E, d'Hérouël AF, Ertaylan G, Del Sol A, Skupin A, Huang S.

Oncotarget. 2018 Apr 13;9(28):20018-20033. doi: 10.18632/oncotarget.25034. eCollection 2018 Apr 13.


Data-driven dynamical model indicates that the heat shock response in Chlamydomonas reinhardtii is tailored to handle natural temperature variation.

Magni S, Succurro A, Skupin A, Ebenhöh O.

J R Soc Interface. 2018 May;15(142). pii: 20170965. doi: 10.1098/rsif.2017.0965.


CaSiAn: a Calcium Signaling Analyzer tool.

Moein M, Grzyb K, Gonçalves Martins T, Komoto S, Peri F, Crawford AD, Fouquier d'Herouel A, Skupin A.

Bioinformatics. 2018 Sep 1;34(17):3052-3054. doi: 10.1093/bioinformatics/bty281.


On the phase space structure of IP3 induced Ca2+ signalling and concepts for predictive modeling.

Falcke M, Moein M, Tilūnaitė A, Thul R, Skupin A.

Chaos. 2018 Apr;28(4):045115. doi: 10.1063/1.5021073.


Cell Fate Decision as High-Dimensional Critical State Transition.

Mojtahedi M, Skupin A, Zhou J, Castaño IG, Leong-Quong RY, Chang H, Trachana K, Giuliani A, Huang S.

PLoS Biol. 2016 Dec 27;14(12):e2000640. doi: 10.1371/journal.pbio.2000640. eCollection 2016 Dec.


Analysis of mitochondrial metabolism in situ: Combining stable isotope labeling with selective permeabilization.

Nonnenmacher Y, Palorini R, d'Herouël AF, Krämer L, Neumann-Schaal M, Chiaradonna F, Skupin A, Wegner A, Hiller K.

Metab Eng. 2017 Sep;43(Pt B):147-155. doi: 10.1016/j.ymben.2016.12.005. Epub 2016 Dec 15.


Inhibition of the mitochondrial calcium uniporter rescues dopaminergic neurons in pink1-/- zebrafish.

Soman S, Keatinge M, Moein M, Da Costa M, Mortiboys H, Skupin A, Sugunan S, Bazala M, Kuznicki J, Bandmann O.

Eur J Neurosci. 2017 Feb;45(4):528-535. doi: 10.1111/ejn.13473. Epub 2016 Dec 28.


Loss of DJ-1 impairs antioxidant response by altered glutamine and serine metabolism.

Meiser J, Delcambre S, Wegner A, Jäger C, Ghelfi J, d'Herouel AF, Dong X, Weindl D, Stautner C, Nonnenmacher Y, Michelucci A, Popp O, Giesert F, Schildknecht S, Krämer L, Schneider JG, Woitalla D, Wurst W, Skupin A, Weisenhorn DM, Krüger R, Leist M, Hiller K.

Neurobiol Dis. 2016 May;89:112-25. doi: 10.1016/j.nbd.2016.01.019. Epub 2016 Feb 1.


The penetration of acoustic cavitation bubbles into micrometer-scale cavities.

Vaidya HA, Ertunç Ö, Lichtenegger T, Delgado A, Skupin A.

Ultrasonics. 2016 Apr;67:190-198. doi: 10.1016/j.ultras.2015.12.009. Epub 2015 Dec 21.


Pro-inflammatory Macrophages Sustain Pyruvate Oxidation through Pyruvate Dehydrogenase for the Synthesis of Itaconate and to Enable Cytokine Expression.

Meiser J, Krämer L, Sapcariu SC, Battello N, Ghelfi J, D'Herouel AF, Skupin A, Hiller K.

J Biol Chem. 2016 Feb 19;291(8):3932-46. doi: 10.1074/jbc.M115.676817. Epub 2015 Dec 17.


Neurological Diseases from a Systems Medicine Point of View.

Ostaszewski M, Skupin A, Balling R.

Methods Mol Biol. 2016;1386:221-50. doi: 10.1007/978-1-4939-3283-2_11. Review.


Multiscale Modeling Indicates That Temperature Dependent [Ca2+]i Spiking in Astrocytes Is Quantitatively Consistent with Modulated SERCA Activity.

Komin N, Moein M, Ellisman MH, Skupin A.

Neural Plast. 2015;2015:683490. doi: 10.1155/2015/683490. Epub 2015 Aug 4.


Stemness of the hybrid Epithelial/Mesenchymal State in Breast Cancer and Its Association with Poor Survival.

Grosse-Wilde A, Fouquier d'Hérouël A, McIntosh E, Ertaylan G, Skupin A, Kuestner RE, del Sol A, Walters KA, Huang S.

PLoS One. 2015 May 28;10(5):e0126522. doi: 10.1371/journal.pone.0126522. eCollection 2015.


Protocols and programs for high-throughput growth and aging phenotyping in yeast.

Jung PP, Christian N, Kay DP, Skupin A, Linster CL.

PLoS One. 2015 Mar 30;10(3):e0119807. doi: 10.1371/journal.pone.0119807. eCollection 2015.


Critical transitions in chronic disease: transferring concepts from ecology to systems medicine.

Trefois C, Antony PM, Goncalves J, Skupin A, Balling R.

Curr Opin Biotechnol. 2015 Aug;34:48-55. doi: 10.1016/j.copbio.2014.11.020. Epub 2014 Dec 10. Review.


Reliable encoding of stimulus intensities within random sequences of intracellular Ca2+ spikes.

Thurley K, Tovey SC, Moenke G, Prince VL, Meena A, Thomas AP, Skupin A, Taylor CW, Falcke M.

Sci Signal. 2014 Jun 24;7(331):ra59. doi: 10.1126/scisignal.2005237.


Unidirectional P-body transport during the yeast cell cycle.

Garmendia-Torres C, Skupin A, Michael SA, Ruusuvuori P, Kuwada NJ, Falconnet D, Cary GA, Hansen C, Wiggins PA, Dudley AM.

PLoS One. 2014 Jun 11;9(6):e99428. doi: 10.1371/journal.pone.0099428. eCollection 2014.


Discovering pair-wise genetic interactions: an information theory-based approach.

Ignac TM, Skupin A, Sakhanenko NA, Galas DJ.

PLoS One. 2014 Mar 26;9(3):e92310. doi: 10.1371/journal.pone.0092310. eCollection 2014.


Describing the complexity of systems: multivariable "set complexity" and the information basis of systems biology.

Galas DJ, Sakhanenko NA, Skupin A, Ignac T.

J Comput Biol. 2014 Feb;21(2):118-40. doi: 10.1089/cmb.2013.0039. Epub 2013 Dec 30.


Mesoscopic behavior from microscopic Markov dynamics and its application to calcium release channels.

Christian N, Skupin A, Morante S, Jansen K, Rossi G, Ebenhöh O.

J Theor Biol. 2014 Feb 21;343:102-12. doi: 10.1016/j.jtbi.2013.11.010. Epub 2013 Nov 21.


Aneuploidy underlies a multicellular phenotypic switch.

Tan Z, Hays M, Cromie GA, Jeffery EW, Scott AC, Ahyong V, Sirr A, Skupin A, Dudley AM.

Proc Natl Acad Sci U S A. 2013 Jul 23;110(30):12367-72. doi: 10.1073/pnas.1301047110. Epub 2013 Jun 28.


Visualizing the topical structure of the medical sciences: a self-organizing map approach.

Skupin A, Biberstine JR, Börner K.

PLoS One. 2013;8(3):e58779. doi: 10.1371/journal.pone.0058779. Epub 2013 Mar 12.


Calcium signaling: from single channels to pathways.

Skupin A, Thurley K.

Adv Exp Med Biol. 2012;740:531-51. doi: 10.1007/978-94-007-2888-2_24. Review.


Fundamental properties of Ca2+ signals.

Thurley K, Skupin A, Thul R, Falcke M.

Biochim Biophys Acta. 2012 Aug;1820(8):1185-94. doi: 10.1016/j.bbagen.2011.10.007. Epub 2011 Oct 25. Review.


Carbohydrate-active enzymes exemplify entropic principles in metabolism.

Kartal O, Mahlow S, Skupin A, Ebenhöh O.

Mol Syst Biol. 2011 Oct 25;7:542. doi: 10.1038/msb.2011.76.


Clustering more than two million biomedical publications: comparing the accuracies of nine text-based similarity approaches.

Boyack KW, Newman D, Duhon RJ, Klavans R, Patek M, Biberstine JR, Schijvenaars B, Skupin A, Ma N, Börner K.

PLoS One. 2011 Mar 17;6(3):e18029. doi: 10.1371/journal.pone.0018029.


Modeling the complex dynamics of enzyme-pathway coevolution.

Schütte M, Skupin A, Segrè D, Ebenhöh O.

Chaos. 2010 Dec;20(4):045115. doi: 10.1063/1.3530440.


Calcium signals driven by single channel noise.

Skupin A, Kettenmann H, Falcke M.

PLoS Comput Biol. 2010 Aug 5;6(8). pii: e1000870. doi: 10.1371/journal.pcbi.1000870.


Multi-perspective analysis and spatiotemporal mapping of air pollution monitoring data.

Kolovos A, Skupin A, Jerrett M, Christakos G.

Environ Sci Technol. 2010 Sep 1;44(17):6738-44. doi: 10.1021/es1013328.


From puffs to global Ca2+ signals: how molecular properties shape global signals.

Skupin A, Falcke M.

Chaos. 2009 Sep;19(3):037111. doi: 10.1063/1.3184537.


Clustering of InsP3 receptors by InsP3 retunes their regulation by InsP3 and Ca2+.

Taufiq-Ur-Rahman, Skupin A, Falcke M, Taylor CW.

Nature. 2009 Apr 2;458(7238):655-9. doi: 10.1038/nature07763.


Statistical properties and information content of calcium oscillations.

Skupin A, Falcke M.

Genome Inform. 2007;18:44-53.


The role of IP3R clustering in Ca2+ signalinG.

Skupin A, Falcke M.

Genome Inform. 2008;20:15-24.


How does intracellular Ca2+ oscillate: by chance or by the clock?

Skupin A, Kettenmann H, Winkler U, Wartenberg M, Sauer H, Tovey SC, Taylor CW, Falcke M.

Biophys J. 2008 Mar 15;94(6):2404-11. Epub 2007 Dec 7.


Temperature and nitric oxide control spontaneous calcium transients in astrocytes.

Schipke CG, Heidemann A, Skupin A, Peters O, Falcke M, Kettenmann H.

Cell Calcium. 2008 Mar;43(3):285-95. Epub 2007 Aug 14.


The world of geography: visualizing a knowledge domain with cartographic means.

Skupin A.

Proc Natl Acad Sci U S A. 2004 Apr 6;101 Suppl 1:5274-8. Epub 2004 Feb 5.


Local production of interleukin-4 during radiation-induced pneumonitis and pulmonary fibrosis in rats: macrophages as a prominent source of interleukin-4.

Büttner C, Skupin A, Reimann T, Rieber EP, Unteregger G, Geyer P, Frank KH.

Am J Respir Cell Mol Biol. 1997 Sep;17(3):315-25.


Use of a double-lumen endotracheal tube with independent lung ventilation for treatment of refractory atelectasis.

Bochenek KJ, Brown M, Skupin A.

Anesth Analg. 1987 Oct;66(10):1014-7. No abstract available.


Complications of transthoracic needle biopsy decreased with isobutyl 2-cyanoacrylate: a pilot study.

Skupin A, Gomez F, Husain M, Skupin C, Bigman O.

Ann Thorac Surg. 1987 Apr;43(4):406-8.


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