Alexander Skupin

Title(s)Comp Data Sci Res Spec, Neurosciences
SchoolVc-health Sciences-schools
Address9500 Gilman Drive #
La Jolla CA 92093
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. The Contribution of Microglia to Neuroinflammation in Parkinson's Disease. Int J Mol Sci. 2021 Apr 28; 22(9). PMID: 33925154.
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    2. Single-Cell Transcriptomics and In Situ Morphological Analyses Reveal Microglia Heterogeneity Across the Nigrostriatal Pathway. Front Immunol. 2021; 12:639613. PMID: 33854507.
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    3. l-Isoaspartyl Methyltransferase Deficiency in Zebrafish Leads to Impaired Calcium Signaling in the Brain. Front Genet. 2020; 11:612343. Soliman R, Cordero-Maldonado ML, Martins TG, Moein M, Conrotte JF, Warmack RA, Skupin A, Crawford AD, Clarke SG, Linster CL. PMID: 33552132.
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    4. Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics. Nat Microbiol. 2020 Nov 02. Martínez Arbas S, Narayanasamy S, Herold M, Lebrun LA, Hoopmann MR, Li S, Lam TJ, Kunath BJ, Hicks ND, Liu CM, Price LB, Laczny CC, Gillece JD, Schupp JM, Keim PS, Moritz RL, Faust K, Tang H, Ye Y, Skupin A, May P, Muller EEL, Wilmes P. PMID: 33139880.
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    5. ROS networks: designs, aging, Parkinson's disease and precision therapies. NPJ Syst Biol Appl. 2020 10 26; 6(1):34. N Kolodkin A, Sharma RP, Colangelo AM, Ignatenko A, Martorana F, Jennen D, Briedé JJ, Brady N, Barberis M, Mondeel TDGA, Papa M, Kumar V, Peters B, Skupin A, Alberghina L, Balling R, Westerhoff HV. PMID: 33106503.
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    6. Patient-derived organoids and orthotopic xenografts of primary and recurrent gliomas represent relevant patient avatars for precision oncology. Acta Neuropathol. 2020 12; 140(6):919-949. Golebiewska A, Hau AC, Oudin A, Stieber D, Yabo YA, Baus V, Barthelemy V, Klein E, Bougnaud S, Keunen O, Wantz M, Michelucci A, Neirinckx V, Muller A, Kaoma T, Nazarov PV, Azuaje F, De Falco A, Flies B, Richart L, Poovathingal S, Arns T, Grzyb K, Mock A, Herold-Mende C, Steino A, Brown D, May P, Miletic H, Malta TM, Noushmehr H, Kwon YJ, Jahn W, Klink B, Tanner G, Stead LF, Mittelbronn M, Skupin A, Hertel F, Bjerkvig R, Niclou SP. PMID: 33009951.
      View in: PubMed   Mentions: 1     Fields:    
    7. Single-cell transcriptomics reveals multiple neuronal cell types in human midbrain-specific organoids. Cell Tissue Res. 2020 Dec; 382(3):463-476. Smits LM, Magni S, Kinugawa K, Grzyb K, Luginbühl J, Sabate-Soler S, Bolognin S, Shin JW, Mori E, Skupin A, Schwamborn JC. PMID: 32737576.
      View in: PubMed   Mentions: 1     Fields:    
    8. New insights into the early mechanisms of epileptogenesis in a zebrafish model of Dravet syndrome. Epilepsia. 2020 03; 61(3):549-560. Tiraboschi E, Martina S, van der Ent W, Grzyb K, Gawel K, Cordero-Maldonado ML, Poovathingal SK, Heintz S, Satheesh SV, Brattespe J, Xu J, Suster M, Skupin A, Esguerra CV. PMID: 32096222.
      View in: PubMed   Mentions: 3     Fields:    Translation:AnimalsCells
    9. A Statistical View on Calcium Oscillations. Adv Exp Med Biol. 2020; 1131:799-826. Powell J, Falcke M, Skupin A, Bellamy TC, Kypraios T, Thul R. PMID: 31646535.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    10. Data-driven multiscale modeling reveals the role of metabolic coupling for the spatio-temporal growth dynamics of yeast colonies. BMC Mol Cell Biol. 2019 Dec 19; 20(1):59. Intosalmi J, Scott AC, Hays M, Flann N, Yli-Harja O, Lähdesmäki H, Dudley AM, Skupin A. PMID: 31856706.
      View in: PubMed   Mentions:    Fields:    Translation:Animals
    11. Mitochondrial morphology provides a mechanism for energy buffering at synapses. Sci Rep. 2019 12 04; 9(1):18306. Garcia GC, Bartol TM, Phan S, Bushong EA, Perkins G, Sejnowski TJ, Ellisman MH, Skupin A. PMID: 31797946.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    12. Mutations in RHOT1 Disrupt Endoplasmic Reticulum-Mitochondria Contact Sites Interfering with Calcium Homeostasis and Mitochondrial Dynamics in Parkinson's Disease. Antioxid Redox Signal. 2019 12 01; 31(16):1213-1234. 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, Rakovic A, Lichtner P, Antony P, Glaab E, May P, Dimmer KS, Fitzgerald JC, Grünewald A, Krüger R. PMID: 31303019.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCells
    13. Stem cell-associated heterogeneity in Glioblastoma results from intrinsic tumor plasticity shaped by the microenvironment. Nat Commun. 2019 04 16; 10(1):1787. 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. PMID: 30992437.
      View in: PubMed   Mentions: 40     Fields:    Translation:HumansAnimalsCells
    14. MIC-MAC: An automated pipeline for high-throughput characterization and classification of three-dimensional microglia morphologies in mouse and human postmortem brain samples. Glia. 2019 08; 67(8):1496-1509. Salamanca L, Mechawar N, Murai KK, Balling R, Bouvier DS, Skupin A. PMID: 30983036.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansAnimalsCells
    15. Neural Stem Cells of Parkinson's Disease Patients Exhibit Aberrant Mitochondrial Morphology and Functionality. Stem Cell Reports. 2019 05 14; 12(5):878-889. 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. PMID: 30982740.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansCells
    16. Single-cell transcriptomics reveals distinct inflammation-induced microglia signatures. . 2018 11; 19(11). 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. PMID: 30206190.
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    17. CaSiAn: a Calcium Signaling Analyzer tool. Bioinformatics. 2018 09 01; 34(17):3052-3054. Moein M, Grzyb K, Gonçalves Martins T, Komoto S, Peri F, Crawford AD, Fouquier d'Herouel A, Skupin A. PMID: 29668830.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    18. Data-driven dynamical model indicates that the heat shock response in Chlamydomonas reinhardtii is tailored to handle natural temperature variation. J R Soc Interface. 2018 05; 15(142). Magni S, Succurro A, Skupin A, Ebenhöh O. PMID: 29720454.
      View in: PubMed   Mentions:    Fields:    Translation:Animals
    19. Loss of inter-cellular cooperation by complete epithelial-mesenchymal transition supports favorable outcomes in basal breast cancer patients. Oncotarget. 2018 Apr 13; 9(28):20018-20033. Grosse-Wilde A, Kuestner RE, Skelton SM, MacIntosh E, d'Hérouël AF, Ertaylan G, Del Sol A, Skupin A, Huang S. PMID: 29732000.
      View in: PubMed   Mentions: 7     Fields:    
    20. On the phase space structure of IP3 induced Ca2+ signalling and concepts for predictive modeling. Chaos. 2018 Apr; 28(4):045115. Falcke M, Moein M, Tilunaite A, Thul R, Skupin A. PMID: 31906671.
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    21. Inhibition of the mitochondrial calcium uniporter rescues dopaminergic neurons in pink1-/- zebrafish. Eur J Neurosci. 2017 02; 45(4):528-535. Soman S, Keatinge M, Moein M, Da Costa M, Mortiboys H, Skupin A, Sugunan S, Bazala M, Kuznicki J, Bandmann O. PMID: 27859782.
      View in: PubMed   Mentions: 17     Fields:    Translation:AnimalsCells
    22. Cell Fate Decision as High-Dimensional Critical State Transition. PLoS Biol. 2016 Dec; 14(12):e2000640. Mojtahedi M, Skupin A, Zhou J, Castaño IG, Leong-Quong RY, Chang H, Trachana K, Giuliani A, Huang S. PMID: 28027308.
      View in: PubMed   Mentions: 63     Fields:    Translation:Animals
    23. Analysis of mitochondrial metabolism in situ: Combining stable isotope labeling with selective permeabilization. . 2017 09; 43(Pt B):147-155. Nonnenmacher Y, Palorini R, d'Herouël AF, Krämer L, Neumann-Schaal M, Chiaradonna F, Skupin A, Wegner A, Hiller K. PMID: 27988388.
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    24. Neurological Diseases from a Systems Medicine Point of View. Methods Mol Biol. 2016; 1386:221-50. Ostaszewski M, Skupin A, Balling R. PMID: 26677186.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    25. Pro-inflammatory Macrophages Sustain Pyruvate Oxidation through Pyruvate Dehydrogenase for the Synthesis of Itaconate and to Enable Cytokine Expression. J Biol Chem. 2016 Feb 19; 291(8):3932-46. Meiser J, Krämer L, Sapcariu SC, Battello N, Ghelfi J, D'Herouel AF, Skupin A, Hiller K. PMID: 26679997.
      View in: PubMed   Mentions: 50     Fields:    Translation:AnimalsCells
    26. Multiscale Modeling Indicates That Temperature Dependent [Ca2+]i Spiking in Astrocytes Is Quantitatively Consistent with Modulated SERCA Activity. Neural Plast. 2015; 2015:683490. Komin N, Moein M, Ellisman MH, Skupin A. PMID: 26347125.
      View in: PubMed   Mentions: 6     Fields:    Translation:AnimalsCells
    27. Stemness of the hybrid Epithelial/Mesenchymal State in Breast Cancer and Its Association with Poor Survival. PLoS One. 2015; 10(5):e0126522. Grosse-Wilde A, Fouquier d'Hérouël A, McIntosh E, Ertaylan G, Skupin A, Kuestner RE, del Sol A, Walters KA, Huang S. PMID: 26020648.
      View in: PubMed   Mentions: 95     Fields:    Translation:HumansAnimalsCells
    28. Protocols and programs for high-throughput growth and aging phenotyping in yeast. PLoS One. 2015; 10(3):e0119807. Jung PP, Christian N, Kay DP, Skupin A, Linster CL. PMID: 25822370.
      View in: PubMed   Mentions: 21     Fields:    Translation:Animals
    29. Critical transitions in chronic disease: transferring concepts from ecology to systems medicine. Curr Opin Biotechnol. 2015 Aug; 34:48-55. Trefois C, Antony PM, Goncalves J, Skupin A, Balling R. PMID: 25498477.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansAnimals
    30. Reliable encoding of stimulus intensities within random sequences of intracellular Ca2+ spikes. Sci Signal. 2014 Jun 24; 7(331):ra59. Thurley K, Tovey SC, Moenke G, Prince VL, Meena A, Thomas AP, Skupin A, Taylor CW, Falcke M. PMID: 24962706.
      View in: PubMed   Mentions: 30     Fields:    Translation:HumansAnimalsCells
    31. Unidirectional P-body transport during the yeast cell cycle. PLoS One. 2014; 9(6):e99428. Garmendia-Torres C, Skupin A, Michael SA, Ruusuvuori P, Kuwada NJ, Falconnet D, Cary GA, Hansen C, Wiggins PA, Dudley AM. PMID: 24918601.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCells
    32. Discovering pair-wise genetic interactions: an information theory-based approach. PLoS One. 2014; 9(3):e92310. Ignac TM, Skupin A, Sakhanenko NA, Galas DJ. PMID: 24670935.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansAnimals
    33. Describing the complexity of systems: multivariable "set complexity" and the information basis of systems biology. J Comput Biol. 2014 Feb; 21(2):118-40. Galas DJ, Sakhanenko NA, Skupin A, Ignac T. PMID: 24377753.
      View in: PubMed   Mentions: 7     Fields:    
    34. Mesoscopic behavior from microscopic Markov dynamics and its application to calcium release channels. J Theor Biol. 2014 Feb 21; 343:102-12. Christian N, Skupin A, Morante S, Jansen K, Rossi G, Ebenhöh O. PMID: 24270093.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCells
    35. Aneuploidy underlies a multicellular phenotypic switch. Proc Natl Acad Sci U S A. 2013 Jul 23; 110(30):12367-72. Tan Z, Hays M, Cromie GA, Jeffery EW, Scott AC, Ahyong V, Sirr A, Skupin A, Dudley AM. PMID: 23812752.
      View in: PubMed   Mentions: 35     Fields:    Translation:AnimalsCells
    36. Calcium signaling: from single channels to pathways. Adv Exp Med Biol. 2012; 740:531-51. Skupin A, Thurley K. PMID: 22453959.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimalsCells
    37. Carbohydrate-active enzymes exemplify entropic principles in metabolism. Mol Syst Biol. 2011 Oct 25; 7:542. Kartal O, Mahlow S, Skupin A, Ebenhöh O. PMID: 22027553.
      View in: PubMed   Mentions: 14     Fields:    Translation:AnimalsCells
    38. Fundamental properties of Ca2+ signals. Biochim Biophys Acta. 2012 Aug; 1820(8):1185-94. Thurley K, Skupin A, Thul R, Falcke M. PMID: 22040723.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansAnimalsCells
    39. Modeling the complex dynamics of enzyme-pathway coevolution. Chaos. 2010 Dec; 20(4):045115. Schütte M, Skupin A, Segrè D, Ebenhöh O. PMID: 21198127.
      View in: PubMed   Mentions: 3     Fields:    Translation:AnimalsCells
    40. Calcium signals driven by single channel noise. PLoS Comput Biol. 2010 Aug 05; 6(8). Skupin A, Kettenmann H, Falcke M. PMID: 20700497.
      View in: PubMed   Mentions: 32     Fields:    Translation:AnimalsCells
    41. From puffs to global Ca2+ signals: how molecular properties shape global signals. Chaos. 2009 Sep; 19(3):037111. Skupin A, Falcke M. PMID: 19792036.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansAnimalsCells
    42. Clustering of InsP3 receptors by InsP3 retunes their regulation by InsP3 and Ca2+. Nature. 2009 Apr 02; 458(7238):655-9. Skupin A, Falcke M, Taylor CW. PMID: 19348050.
      View in: PubMed   Mentions: 66     Fields:    Translation:AnimalsCells
    43. The role of IP3R clustering in Ca2+ signalinG. Genome Inform. 2008; 20:15-24. Skupin A, Falcke M. PMID: 19425119.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    44. How does intracellular Ca2+ oscillate: by chance or by the clock? Biophys J. 2008 Mar 15; 94(6):2404-11. Skupin A, Kettenmann H, Winkler U, Wartenberg M, Sauer H, Tovey SC, Taylor CW, Falcke M. PMID: 18065468.
      View in: PubMed   Mentions: 57     Fields:    Translation:HumansAnimalsCells
    45. Temperature and nitric oxide control spontaneous calcium transients in astrocytes. Cell Calcium. 2008 Mar; 43(3):285-95. Schipke CG, Heidemann A, Skupin A, Peters O, Falcke M, Kettenmann H. PMID: 17698190.
      View in: PubMed   Mentions: 18     Fields:    Translation:AnimalsCells
    46. Statistical properties and information content of calcium oscillations. Genome Inform. 2007; 18:44-53. Skupin A, Falcke M. PMID: 18546473.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
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