Bonn, Stefan

[["dc.contributor.author","Fiosina, Jelena"],["dc.contributor.author","Fiosins, Maksims"],["dc.contributor.author","Bonn, Stefan"],["dc.date.accessioned","2022-08-26T07:22:02Z"],["dc.date.available","2022-08-26T07:22:02Z"],["dc.date.issued","2019"],["dc.identifier.arxiv","1909.11956"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/113246"],["dc.identifier.url","https://sfb1286.uni-goettingen.de/literature/publications/49"],["dc.relation","SFB 1286: Quantitative Synaptologie"],["dc.relation","SFB 1286 | Z02: Integrative Datenanalyse und -interpretation. Generierung einer synaptisch-integrativen Datenstrategie (SynIDs)"],["dc.relation.workinggroup","RG Bonn"],["dc.title","Explainable Deep Learning for Augmentation of sRNA Expression Profiles"],["dc.type","preprint"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","959"],["dc.bibliographiccitation.issue","12"],["dc.bibliographiccitation.journal","Molecular systems biology"],["dc.bibliographiccitation.volume","13"],["dc.contributor.author","Hatje, Klas"],["dc.contributor.author","Rahman, Raza-Ur"],["dc.contributor.author","Vidal, Ramon O."],["dc.contributor.author","Simm, Dominic"],["dc.contributor.author","Hammesfahr, Björn"],["dc.contributor.author","Bansal, Vikas"],["dc.contributor.author","Rajput, Ashish"],["dc.contributor.author","Mickael, Michel Edwar"],["dc.contributor.author","Sun, Ting"],["dc.contributor.author","Bonn, Stefan"],["dc.contributor.author","Kollmar, Martin"],["dc.date.accessioned","2019-07-30T10:25:25Z"],["dc.date.available","2019-07-30T10:25:25Z"],["dc.date.issued","2017"],["dc.description.abstract","Mutually exclusive splicing of exons is a mechanism of functional gene and protein diversification with pivotal roles in organismal development and diseases such as Timothy syndrome, cardiomyopathy and cancer in humans. In order to obtain a first genomewide estimate of the extent and biological role of mutually exclusive splicing in humans, we predicted and subsequently validated mutually exclusive exons (MXEs) using 515 publically available RNA-Seq datasets. Here, we provide evidence for the expression of over 855 MXEs, 42% of which represent novel exons, increasing the annotated human mutually exclusive exome more than fivefold. The data provide strong evidence for the existence of large and multi-cluster MXEs in higher vertebrates and offer new insights into MXE evolution. More than 82% of the MXE clusters are conserved in mammals, and five clusters have homologous clusters in Drosophila Finally, MXEs are significantly enriched in pathogenic mutations and their spatio-temporal expression might predict human disease pathology."],["dc.identifier.doi","10.15252/msb.20177728"],["dc.identifier.pmid","29242366"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/62194"],["dc.language.iso","en"],["dc.relation.eissn","1744-4292"],["dc.relation.issn","1744-4292"],["dc.relation.issn","1744-4292"],["dc.relation.issn","1744-4292"],["dc.title","The landscape of human mutually exclusive splicing"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","D204"],["dc.bibliographiccitation.issue","D1"],["dc.bibliographiccitation.journal","Nucleic Acids Research"],["dc.bibliographiccitation.lastpage","D219"],["dc.bibliographiccitation.volume","48"],["dc.contributor.author","Rahman, Raza-Ur"],["dc.contributor.author","Liebhoff, Anna-Maria"],["dc.contributor.author","Bansal, Vikas"],["dc.contributor.author","Fiosins, Maksims"],["dc.contributor.author","Rajput, Ashish"],["dc.contributor.author","Sattar, Abdul"],["dc.contributor.author","Magruder, Daniel S"],["dc.contributor.author","Madan, Sumit"],["dc.contributor.author","Sun, Ting"],["dc.contributor.author","Gautam, Abhivyakti"],["dc.contributor.author","Heins, Sven"],["dc.contributor.author","Liwinski, Timur"],["dc.contributor.author","Bethune, Jörn"],["dc.contributor.author","Trenkwalder, Claudia"],["dc.contributor.author","Fluck, Juliane"],["dc.contributor.author","Mollenhauer, Brit"],["dc.contributor.author","Bonn, Stefan"],["dc.date.accessioned","2020-12-10T18:19:36Z"],["dc.date.available","2020-12-10T18:19:36Z"],["dc.date.issued","2019"],["dc.identifier.doi","10.1093/nar/gkz869"],["dc.identifier.eissn","1362-4962"],["dc.identifier.issn","0305-1048"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/75307"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-354"],["dc.title","SEAweb: the small RNA Expression Atlas web application"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","109"],["dc.bibliographiccitation.journal","iScience"],["dc.bibliographiccitation.lastpage","126"],["dc.bibliographiccitation.volume","4"],["dc.contributor.author","Narayanan, Ramanathan"],["dc.contributor.author","Pham, Linh"],["dc.contributor.author","Kerimoglu, Cemil"],["dc.contributor.author","Watanabe, Takashi"],["dc.contributor.author","Castro Hernandez, Ricardo"],["dc.contributor.author","Sokpor, Godwin"],["dc.contributor.author","Ulmke, Pauline Antonie"],["dc.contributor.author","Kiszka, Kamila A."],["dc.contributor.author","Tonchev, Anton B."],["dc.contributor.author","Rosenbusch, Joachim"],["dc.contributor.author","Seong, Rho H."],["dc.contributor.author","Teichmann, Ulrike"],["dc.contributor.author","Frahm, Jens"],["dc.contributor.author","Fischer, Andre"],["dc.contributor.author","Bonn, Stefan"],["dc.contributor.author","Stoykova, Anastassia"],["dc.contributor.author","Staiger, Jochen F."],["dc.contributor.author","Tuoc, Tran"],["dc.date.accessioned","2020-12-10T14:24:42Z"],["dc.date.available","2020-12-10T14:24:42Z"],["dc.date.issued","2018"],["dc.identifier.doi","10.1016/j.isci.2018.05.014"],["dc.identifier.issn","2589-0042"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/72326"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-354"],["dc.title","Chromatin Remodeling BAF155 Subunit Regulates the Genesis of Basal Progenitors in Developing Cortex"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.journal","Der Internist"],["dc.bibliographiccitation.volume","57"],["dc.contributor.author","Khadjeh, Sara"],["dc.contributor.author","Vidal, Ramon"],["dc.contributor.author","Capece, V."],["dc.contributor.author","Lbik, D."],["dc.contributor.author","Mohamed, B."],["dc.contributor.author","Danner, Bernhard Christoph"],["dc.contributor.author","Sossalla, Samuel T."],["dc.contributor.author","Fischer, A."],["dc.contributor.author","Bonn, Stefan"],["dc.contributor.author","Hasenfuß, Gerd"],["dc.contributor.author","Toischer, Karl"],["dc.date.accessioned","2018-11-07T10:15:52Z"],["dc.date.available","2018-11-07T10:15:52Z"],["dc.date.issued","2016"],["dc.format.extent","S61"],["dc.identifier.isi","000375417500120"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/40903"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Springer"],["dc.publisher.place","New york"],["dc.relation.issn","1432-1289"],["dc.relation.issn","0020-9554"],["dc.title","Of mice and men - a direct comparison of signaling in pressure overload induced hypertrophy and failure"],["dc.type","conference_abstract"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","3572"],["dc.bibliographiccitation.issue","9"],["dc.bibliographiccitation.journal","Journal of Clinical Investigation"],["dc.bibliographiccitation.lastpage","3584"],["dc.bibliographiccitation.volume","125"],["dc.contributor.author","Benito-Garagorri, Eva"],["dc.contributor.author","Urbanke, Hendrik"],["dc.contributor.author","Ramachandran, Binu"],["dc.contributor.author","Barth, Jonas"],["dc.contributor.author","Haider, Rashi"],["dc.contributor.author","Awasthi, Ankit"],["dc.contributor.author","Jain, Gaurav"],["dc.contributor.author","Capece, Vincenzo"],["dc.contributor.author","Burkhardt, Susanne"],["dc.contributor.author","Navarro-Sala, Magdalena"],["dc.contributor.author","Nagarajan, Sankari"],["dc.contributor.author","Schuetz, Anna-Lena"],["dc.contributor.author","Johnsen, Steven A."],["dc.contributor.author","Bonn, Stefan"],["dc.contributor.author","Luehrmann, Reinhard"],["dc.contributor.author","Dean, Camin"],["dc.contributor.author","Fischer, Andre"],["dc.date.accessioned","2017-09-07T11:43:34Z"],["dc.date.available","2017-09-07T11:43:34Z"],["dc.date.issued","2015"],["dc.description.abstract","Aging and increased amyloid burden are major risk factors for cognitive diseases such as Alzheimer's disease (AD). Effective therapies for these diseases are lacking. Here, we evaluated mouse models of age-associated memory impairment and amyloid deposition to study transcriptome and cell type-specific epigenome plasticity in the brain and peripheral organs. We determined that aging and amyloid pathology are associated with inflammation and impaired synaptic function in the hippocampal CA1 region as the result of epigenetic-dependent alterations in gene expression. In both amyloid and aging models, inflammation was associated with increased gene expression linked to a subset of transcription factors, while plasticity gene deregulation was differentially mediated. Amyloid pathology impaired histone acetylation and decreased expression of plasticity genes, while aging altered H4K12 acetylation-linked differential splicing at the intron-exon junction in neurons, but not nonneuronal cells. Furthermore, oral administration of the clinically approved histone deacetylase inhibitor vorinostat not only restored spatial memory, but also exerted antiinflammatory action and reinstated epigenetic balance and transcriptional homeostasis at the level of gene expression and exon usage. This study provides a systems-level investigation of transcriptome plasticity in the hippocampal CA1 region in aging and AD models and suggests that histone deacetylase inhibitors should be further explored as a cost-effective therapeutic strategy against age-associated cognitive decline."],["dc.identifier.doi","10.1172/JCI79942"],["dc.identifier.gro","3141833"],["dc.identifier.isi","000362303600031"],["dc.identifier.pmid","26280576"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/1579"],["dc.language.iso","en"],["dc.notes.intern","WoS Import 2017-03-10"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.relation.eissn","1558-8238"],["dc.relation.issn","0021-9738"],["dc.title","HDAC inhibitor-dependent transcriptome and memory reinstatement in cognitive decline models"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dspace.entity.type","Publication"]]

[["dc.contributor.author","Hausmann, Fabian"],["dc.contributor.author","Ergen-Behr, Can"],["dc.contributor.author","Khatri, Robin"],["dc.contributor.author","Marouf, Mohamed"],["dc.contributor.author","Hänzelmann, Sonja"],["dc.contributor.author","Gagliani, Nicola"],["dc.contributor.author","Huber, Samuel"],["dc.contributor.author","Machart, Pierre"],["dc.contributor.author","Bonn, Stefan"],["dc.date.accessioned","2022-08-26T07:40:40Z"],["dc.date.available","2022-08-26T07:40:40Z"],["dc.date.issued","2022"],["dc.identifier.doi","10.1101/2022.03.09.483600"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/113249"],["dc.identifier.url","https://sfb1286.uni-goettingen.de/literature/publications/159"],["dc.relation","SFB 1286: Quantitative Synaptologie"],["dc.relation.workinggroup","RG Bonn"],["dc.title","DiSCERN - Deep Single Cell Expression ReconstructioN for improved cell clustering and cell subtype and state detection"],["dc.type","preprint"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","250"],["dc.bibliographiccitation.lastpage","253"],["dc.bibliographiccitation.seriesnr","8"],["dc.contributor.author","Hofmann, M."],["dc.contributor.author","Langholz, H."],["dc.contributor.author","Bonn, S."],["dc.contributor.author","Isselstein, J."],["dc.contributor.editor","Wrage, N."],["dc.contributor.editor","Isselstein, J."],["dc.date.accessioned","2017-09-07T11:51:52Z"],["dc.date.available","2017-09-07T11:51:52Z"],["dc.date.issued","2007"],["dc.identifier.gro","3148075"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/5420"],["dc.language.iso","de"],["dc.notes.status","fcwi"],["dc.notes.submitter","chake"],["dc.publisher","Arbeitsgemeinschaft Grünland und Futterbau der Gesellschaft für Pflanzenbauwissenschaften e. V."],["dc.relation.conference","51. Jahrestagung der AGGF"],["dc.relation.crisseries","Mitteilungen der Arbeitsgemeinschaft Grünland und Futterbau"],["dc.relation.eventend","2007-09-01"],["dc.relation.eventlocation","Göttingen"],["dc.relation.eventstart","2007-08-30"],["dc.relation.isbn","978-3-00-022335-8"],["dc.relation.ispartof","Neue Funktionen des Grünlands: Ökosystem, Energie, Erholung"],["dc.relation.ispartofseries","Mitteilungen der Arbeitsgemeinschaft für Grünland und Futterbau; 8"],["dc.title","Möglichkeiten der Diversifizierung von Grasland durch Endozoochorie"],["dc.type","conference_paper"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","no"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","112"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","RNA Biology"],["dc.bibliographiccitation.lastpage","124"],["dc.bibliographiccitation.volume","17"],["dc.contributor.author","Samir, Mohamed"],["dc.contributor.author","Vidal, Ramon O."],["dc.contributor.author","Abdallah, Fatma"],["dc.contributor.author","Capece, Vincenzo"],["dc.contributor.author","Seehusen, Frauke"],["dc.contributor.author","Geffers, Robert"],["dc.contributor.author","Hussein, Ashraf"],["dc.contributor.author","Ali, Ahmed A. H."],["dc.contributor.author","Bonn, Stefan"],["dc.contributor.author","Pessler, Frank"],["dc.date.accessioned","2021-06-01T10:51:12Z"],["dc.date.available","2021-06-01T10:51:12Z"],["dc.date.issued","2019"],["dc.identifier.doi","10.1080/15476286.2019.1669879"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/86930"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-425"],["dc.relation.eissn","1555-8584"],["dc.relation.issn","1547-6286"],["dc.title","Organ-specific small non-coding RNA responses in domestic (Sudani) ducks experimentally infected with highly pathogenic avian influenza virus (H5N1)"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.contributor.author","Menden, Kevin"],["dc.contributor.author","Marouf, Mohamed"],["dc.contributor.author","Oller, Sergio"],["dc.contributor.author","Dalmia, Anupriya"],["dc.contributor.author","Kloiber, Karin"],["dc.contributor.author","Heutink, Peter"],["dc.contributor.author","Bonn, Stefan"],["dc.date.accessioned","2022-08-26T07:11:08Z"],["dc.date.available","2022-08-26T07:11:08Z"],["dc.date.issued","2019"],["dc.identifier.doi","10.1101/659227"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/113243"],["dc.identifier.url","https://sfb1286.uni-goettingen.de/literature/publications/8"],["dc.relation","SFB 1286: Quantitative Synaptologie"],["dc.relation","SFB 1286 | Z02: Integrative Datenanalyse und -interpretation. Generierung einer synaptisch-integrativen Datenstrategie (SynIDs)"],["dc.relation.workinggroup","RG Bonn"],["dc.title","Deep-learning-based cell composition analysis from tissue expression profiles"],["dc.type","preprint"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]