Selected Publications

  • Realistic in silico generation and augmentation of single cell RNA-seq data using Generative Adversarial Neural Networks.
    S Bonn, P Machart, M Marouf, DS Magruder, V Bansal, C Kilian, CF Krebs.(2018) bioRxiv, 390153
  • Regional and subtype-dependent miRNA signatures in sporadic Creutzfeldt-Jakob disease are accompanied by alterations in miRNA silencing machinery and biogenesis.
    Llorens F, Thüne K, Martí E, Kanata E, Dafou D, Díaz-Lucena D, Vivancos A, Shomroni O, Zafar S, Schmitz M, Michel U, Fernández-Borges N, Andréoletti O Del Río JA, Díez J, Fischer A, Bonn S, Sklaviadis T, Torres JM, Ferrer I, Zerr I.(2018) PLoS Pathog. 2018 Jan 22;14(1):e1006802.
  • Upregulation of miR-370 and miR-543 is associated with reduced expression of heat shock
    protein40 in spinocerebellar ataxia type 3.
    Evert BO, Nalavade R, Jungverdorben J, Matthes F, Weber S, Rajput A, Bonn S, Brüstle O, Peitz M, Krauß S. (2018) PLoS One. 2018 Aug 7;13(8):e0201794.
  • Precisely measured protein lifetimes in the mouse brain reveal differences across tissues and
    subcellular fractions.
    Fornasiero EF, Mandad S, Wildhagen H, Alevra M, Rammner B, Keihani S, Opazo F, Urban I, Ischebeck T, Sakib MS, Fard MK, Kirli K, Centeno TP, Vidal RO, Rahman RU, Benito E, Fischer A, Dennerlein S, Rehling P, Feussner I, Bonn S, Simons M, Urlaub H, Rizzoli SO. Nat Commun. 2018 Oct 12;9(1):4230.
  • Genome-wide association study results for educational attainment aid in identifying genetic heterogeneity of schizophrenia.
    Bansal V, Mitjans M, Burik CAP, Linnér RK, Okbay A, Begemann M, Bonn S, Ripke S, de Vlaming R, Nivard MG, Ehrenreich H, Koellinger D. Nat Commun. 2018 , DOI: 10.1038/s41467-018-05510-z
  • Targeting myelin lipid metabolism as a potential therapeutic strategy in a model of CMT1A neuropathy. (2018) Fledrich R, Abdelaal T, Rasch L, Bansal V, Schütza V, Brügger B, Lüchtenborg C, Prukop T, Stenzel J, Rahman RU, Hermes D, Ewers D, Möbius W, Ruhwedel T, Katona I, Weis J, Klein D, Martini R, Brück W, Müller WC, Bonn S, Bechmann I, Nave KA, Stassart RM, Sereda MW. Nat Commun. 2018 Aug 2;9(1):3025.

  • Chromatin Remodeling BAF155 Subunit Regulates the Genesis of Basal Progenitors in Developing Cortex.
    Narayanan R, Pham L, Kerimoglu C, Watanabe T, Castro Hernandez R, Sokpor G, Ulmke PA, Kiszka KA, Tonchev AB, Rosenbusch J, Seong RH, Teichmann U, Frahm J, Fischer A, Bonn S, Stoykova A, Staiger JF, Tuoc T. iScience. 2018 Jun 29;4:109-126.
  • Violent aggression predicted by multiple pre-adult environmental hits.
    Mitjans M, Seidel J, Begemann M, Bockhop F, Moya-Higueras J, Bansal V, Wesolowski-J, Seelbach A, Ibáñez MI, Kovacevic F, Duvar O,Fañanás L, Wolf H-U, Ortet G,Zwanzger P, Klein V, Lange I, Tänzer A, Dudeck M, Penke L, Tebartz van Elst L, Bittner RA, Schmidmeier R, Freese R, Müller-Isberner R, Wiltfang J, Bliesener T, Bonn S, Poustka L, Müller JL, Arias B, Ehrenreich H (2018) Molecular Psychiatry doi.10.1038/s41380-018-0043-3
  • Oasis 2: improved online analysis of small RNA-seq data.
    Rahman RU, Gautam A, Bethune J, Sattar A, Fiosins M, Magruder DS, Capece V, Shomroni O, Bonn (2018) S.BMC Bioinformatics. 2018 Feb 14;19(1):54
  • Epigenetic alterations in longevity regulators, reduced life span, and exacerbated aging-related pathology in old father offspring mice.
    Xie K, Ryan DP, Pearson BL, Henzel KS, Neff F, Vidal RO, Hennion M, Lehmann I, Schleif M, Schröder S, Adler T, Rathkolb B, Rozman J, Schütz AL, Prehn C, Mickael ME, Weiergräber M, Adamski J, Busch DH, Ehninger G, Matynia A, Jackson WS, Wolf E, Fuchs H, Gailus-Durner V, Bonn S, Hrabě de Angelis M, Ehninger D. (2018)
    Proc Natl Acad Sci U S A. 2018 Mar 6;115(10)
  • The landscape of human mutually exclusive splicing.
    Hatje K, Rahman RU, Vidal RO, Simm D, Hammesfahr B, Bansal V, Rajput A, Mickael ME, Sun T, Bonn S, Kollmar M. (2017) Mol Syst Biol. 2017 Dec 14;13(12):959
  • OTTO: a new strategy to extract mental disease-relevant combinations of GWAS hits from individuals.Ehrenreich H, Mitjans M, Van der Auwera S, Centeno TP, Begemann M, Grabe HJ, Bonn S, Nave K-A, (2017) Mol Psychiatry. 2018 Feb;23(2):476-486.
  • DNA methylation changes in functional and structural plasticity genes regulate the formation and maintenance of memory.Halder R, Hennion M, Vidal R, Shomroni O, Rahman R, Rajput A, Pena Centeno T, van Bebber F, Capece V, Garcia Vizcaino J, Schuetz A-L, Burkhardt S, Benito E, Navarro Sala M, Bahari Javan S, Haass C, Schmid B, Fischer A, Bonn S (2016) Nature Neuroscience 19:102-110.
  • Endophilin-A Deficiency Induces the Foxo3a-Fbxo32 Network in the Brain and Causes Dysregulation of Autophagy and the Ubiquitin-Proteasome System.
    Murdoch JD, Rostosky CM, Gowrisankaran S, Arora AS, Soukup SF, Vidal R, Capece V, Freytag S, Fischer A, Verstrecken P, Bonn S, Raimundo N, Milosevic I (2016) Cell Rep. 17:1071-1086.
  • Oasis: online analysis of small RNA deep sequencing data.
    Capece V, Garcia Vizcaino JC, Vidal R, Rahman RU, Pena Centeno T, Shomroni O, Suberviola I, Fischer A, Bonn S (2015) Bioinformatics 31: 2205-2207.
  • Tissue specific analysis of chromatin state reveals predictive signatures of enhancer activity during embryonic development.
    Bonn S, Zinzen RP, Girardot C, Gustafson E, Perez-Gonzalez A, Delhomme N, Ghavi-Helm Y, Wilczynski B, Riddell A, Furlong EE (2012) Nature Genetics 44: 148-156.

Software

SEA ( https://sea.dzne.de ): SEA, the small RNA expression atlas, is a web application that allows querying, visualization, and analysis of small RNA expression information for over 30.000 small RNAs, over 2000 samples, hundreds of diseases, over 7 organisms, and plenty of tissues and cell types. SEA is fully interactive and lightning fast and a perfect showcase for the 'knowledge-bases' we build.

Oasis & Oasis 2 ( https://oasis.dzne.de ): Oasis, the online analysis of small RNAs, is a web application that allows for the detection, differential expression, and classification analysis of small RNAs. It is interactive, fast, and heavily used in the research community.

Memory Epigenome Browser ( https://memory-epigenome-browser.dzne.de ): The memory epigenome browser allows to select, visualize, and download over 200 cell type-specific epigenetic and transcriptomic datasets before and after learning. It is part of our manuscript on the epigenetic basis of learning and memory (Halder et al. Nature Neuroscience 2016).

GRAND: Graphs as nested dictionaries is a framework that allows for fast and memory efficient graph operations and interactive visualization. It is a free python package that can read many standard graph formats and supports many standard graph operations (e.g. search, shortest path).