Selected Publications

Bansal V, Mitjans M, Burik CAP, Karlsson Linner R, Okbay A, Rietveld CA,Begemann M, Bonn S, Ripke S, de Vlaming R, Nivard MG, Ehrenreich H, Koellinger PD (2018) Genome-wide association study results for educational attainment aid in identifying genetic heterogeneity of schizophrenia. bioRxiv doi: 10.1101/114405

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) Violent aggression predicted by multiple pre-adult environmental hits. Molecular Psychiatry doi.10.1038/s41380-018-0043-3

Rahman RU, Gautam A, Bethune J, Sattar A, Fiosins M, Magruder DS, Capece V, Shomroni O, Bonn S. (2018)
Oasis 2: improved online analysis of small RNA-seq data. BMC Bioinformatics. 2018 Feb 14;19(1):54

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)
Epigenetic alterations in longevity regulators, reduced life span, and exacerbated aging-related pathology in old father offspring mice. Proc Natl Acad Sci U S A. 2018 Mar 6;115(10)

Hatje K, Rahman RU, Vidal RO, Simm D, Hammesfahr B, Bansal V, Rajput A, Mickael ME, Sun T, Bonn S, Kollmar M. (2017) The landscape of human mutually exclusive splicing. Mol Syst Biol. 2017 Dec 14;13(12):959

Ehrenreich H, Mitjans M, Van der Auwera S, Centeno TP, Begemann M, Grabe HJ, Bonn S, Nave K-A, (2017) OTTO: a new strategy to extract mental disease-relevant combinations of GWAS hits from individuals. Mol Psychiatry. 2018 Feb;23(2):476-486.

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) DNA methylation changes in functional and structural plasticity genes regulate the formation and maintenance of memory. Nature Neuroscience 19:102-110.

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) Endophilin-A Deficiency Induces the Foxo3a-Fbxo32 Network in the Brain and Causes Dysregulation of Autophagy and the Ubiquitin-Proteasome System. Cell Rep. 17:1071-1086.

Capece V, Garcia Vizcaino JC, Vidal R, Rahman RU, Pena Centeno T, Shomroni O, Suberviola I, Fischer A, Bonn S (2015) Oasis: online analysis of small RNA deep sequencing data. Bioinformatics 31: 2205-2207.

Bonn S, Zinzen RP, Girardot C, Gustafson E, Perez-Gonzalez A, Delhomme N, Ghavi-Helm Y, Wilczynski B, Riddell A, Furlong EE (2012) Tissue specific analysis of chromatin state reveals predictive signatures of enhancer activity during embryonic development. 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).