Core Facility Bioinformatics

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Abdelrazek, Ibrahim M.; Knaus, Alexej; Javanmardi, Behnam; Krawitz, Peter M.; Horn, Denise; Abdalla, Ebtesam M.; Kumar, Sheetal (2024): Acromesomelic Dysplasia With Homozygosity for a Likely Pathogenic BMPR1B Variant: Postaxial Polydactyly as a Novel Clinical Finding. In: Molecular genetics & genomic medicine 12 (10), e70023. DOI: 10.1002/mgg3.70023.
Al Zaidi, M.; Eschweiler, J.; Shakeri, F.; Sylvester, M.; Repges, E.; Nickenig, G. et al. (2024): Activation, regulation, and effects of the mitochondrial unfolded protein response in endothelial cells. In: European Heart Journal 45 (Supplement_1), Artikel ehae666.3842. DOI: 10.1093/eurheartj/ehae666.3842.
Arlt, Annabelle; Knaus, Alexej; Hsieh, Tzung-Chien; Klinkhammer, Hannah; Bhasin, Meghna Ahuja; Hustinx, Alexander et al. (2024): Next-generation phenotyping in Nigerian children with Cornelia de Lange syndrome. In: American journal of medical genetics. Part A 194 (9), e63641. DOI: 10.1002/ajmg.a.63641.
Bhasin, Meghna Ahuja; Knaus, Alexej; Incardona, Pietro; Schmid, Alexander; Holtgrewe, Manuel; Elbracht, Miriam et al. (2024): Enhancing Variant Prioritization in VarFish through On-Premise Computational Facial Analysis. In: Genes 15 (3). DOI: 10.3390/genes15030370.
Claus, I.; Sivalingam, S.; Koller, A. C.; Weiß, A.; Mathey, C. M.; Sindermann, L. et al. (2024): Contribution of Rare and Potentially Functionally Relevant Sequence Variants in Schizophrenia Risk-Locus Xq28,distal. In: American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics, e33011. DOI: 10.1002/ajmg.b.33011.
Goel, Manish; Campoy, José A.; Krause, Kristin; Baus, Lisa C.; Sahu, Anshupa; Sun, Hequan et al. (2024): The vast majority of somatic mutations in plants are layer-specific. In: Genome biology 25 (1), S. 194. DOI: 10.1186/s13059-024-03337-0.
Kaade, Edgar; Mausbach, Simone; Erps, Nina; Sylvester, Marc; Shakeri, Farhad; Jachimowicz, Ron D. et al. (2024): Starvation-induced metabolic rewiring affects mTORC1 composition in vivo. In: Sci Rep 14 (1), S. 28296. DOI: 10.1038/s41598-024-78873-7.
Kim, Hyuntae; Melliti, Nesrine; Breithausen, Eva; Michel, Katrin; Colomer, Sara Ferrando; Poguzhelskaya, Ekaterina et al. (2024): Paroxysmal dystonia results from the loss of RIM4 in Purkinje cells. In: Brain : a journal of neurology 147 (9), S. 3171–3188. DOI: 10.1093/brain/awae081.
Nourisa, Jalil; Passemiers, Antoine; Shakeri, Farhad; Omidi, Maryam; Helmholz, Heike; Raimondi, Daniele et al. (2024): Gene regulatory network analysis identifies MYL1, MDH2, GLS, and TRIM28 as the principal proteins in the response of mesenchymal stem cells to Mg2+ ions. In: Computational and structural biotechnology journal 23, S. 1773–1785. DOI: 10.1016/j.csbj.2024.04.033.
Schmidt, Axel; Danyel, Magdalena; Grundmann, Kathrin; Brunet, Theresa; Klinkhammer, Hannah; Hsieh, Tzung-Chien et al. (2024): Next-generation phenotyping integrated in a national framework for patients with ultrarare disorders improves genetic diagnostics and yields new molecular findings. In: Nature genetics 56 (8), S. 1644–1653. DOI: 10.1038/s41588-024-01836-1.
Sieckmann, Katharina; Winnerling, Nora; Silva Ribeiro, Dalila Juliana; Kardinal, Ronja; Steinheuer, Lisa Maria; Schermann, Geza et al. (2024): BBSome-dependent ciliary Hedgehog signaling governs cell fate in the white adipose tissue.
Theodorou, Maria Rafailia; Yu, Jiangyan; Nikolka, Fabian; Zurkovic, Jelena; Wientjens, Chantal; Weiss, Patricia et al.: Anabolic lipid metabolism regulates adipose type 2 innate lymphoid cell differentiation to maintain metabolic health: bioRxiv. Online verfügbar unter https://www.biorxiv.org/content/10.1101/2024.03.26.586766v1, zuletzt geprüft am 22.11.2024.
van Baarle, Lies; Simone, Veronica de; Schneider, Linda; Santhosh, Sneha; Abdurahiman, Saeed; Biscu, Francesca et al. (2024): IL-1R signaling drives enteric glia-macrophage interactions in colorectal cancer. In: Nat Commun 15 (1), S. 6079. DOI: 10.1038/s41467-024-50438-2.
Vosbeck, Karla; Förster, Sarah; Mayr, Thomas; Sahu, Anshupa; Haddouti, El-Mustapha; Al-Adilee, Osamah et al. (2024): Neuropilin2 in Mesenchymal Stromal Cells as a Potential Novel Therapeutic Target in Myelofibrosis. In: Cancers 16 (10). DOI: 10.3390/cancers16101924.
Weiss, Felix D.; Alvarez, Yubell; Shakeri, Farhad; Sahu, Anshupa; Leka, Petro; Dernst, Alesja et al. (2024): Retention of ES cell-derived 129S genome drives NLRP1 hypersensitivity and transcriptional deregulation in Nlrp3tm1Flv mice. In: Cell death and differentiation 31 (12), S. 1717–1729. DOI: 10.1038/s41418-024-01379-2.
Aldisi, Rana; Hassanin, Emadeldin; Sivalingam, Sugirthan; Buness, Andreas; Klinkhammer, Hannah; Mayr, Andreas et al. (2023): Gene-based burden scores identify rare variant associations for 28 blood biomarkers. In: BMC genomic data 24 (1), S. 50. DOI: 10.1186/s12863-023-01155-0.
Fabian, Julia; Dworschak, Gabriel C.; Waffenschmidt, Lea; Schierbaum, Luca; Bendixen, Charlotte; Heilmann-Heimbach, Stefanie et al. (2023): Genome-wide identification of disease-causing copy number variations in 450 individuals with anorectal malformations. In: European journal of human genetics : EJHG 31 (1), S. 105–111. DOI: 10.1038/s41431-022-01216-5.
Hanssen, Friederike; Gabernet, Gisela; Bäuerle, Famke; Stöcker, Bianca; Wiegand, Felix; Smith, Nicholas H. et al. (2023): NCBench: providing an open, reproducible, transparent, adaptable, and continuous benchmark approach for DNA-sequencing-based variant calling. In: F1000Res 12, S. 1125. DOI: 10.12688/f1000research.140344.1.
Hanssen, Friederike; Gabernet, Gisela; Bäuerle, Famke; Stöcker, Bianca; Wiegand, Felix; Smith, Nicholas H. et al. (2023): NCBench: providing an open, reproducible, transparent, adaptable, and continuous benchmark approach for DNA-sequencing-based variant calling. In: F1000Res 12, S. 1125. DOI: 10.12688/f1000research.140344.2.
Henn, Jonas; Hatterscheidt, Simon; Sahu, Anshupa; Buness, Andreas; Dohmen, Jonas; Arensmeyer, Jan et al. (2023): Maschinelles Lernen als Entscheidungshilfe bei akuten Bauchschmerzen – Proof-of-Concept und zentrale Überlegungen. In: Zentralblatt fur Chirurgie 148 (4), S. 376–383. DOI: 10.1055/a-2125-1559.
Henne, Sabrina Katrin; Aldisi, Rana; Sivalingam, Sugirthan; Hochfeld, Lara Maleen; Borisov, Oleg; Krawitz, Peter Michael et al. (2023): Analysis of 72,469 UK Biobank exomes links rare variants to male-pattern hair loss. In: Nat Commun 14 (1), S. 5492. DOI: 10.1038/s41467-023-41186-w.
Ishorst, Nina; Henschel, Leonie; Thieme, Frederic; Drichel, Dmitriy; Sivalingam, Sugirthan; Mehrem, Sarah L. et al. (2023): Identification of de novo variants in nonsyndromic cleft lip with/without cleft palate patients with low polygenic risk scores. In: Molecular genetics & genomic medicine 11 (3), e2109. DOI: 10.1002/mgg3.2109.
Kumar, Sheetal; Hausen, Jonas; Sivalingam, Sugirthan; Humbatova, Aytaj; Buness, Andreas; Frank, Jorge et al. (2023): Altered Notch signalling in Dowling-Degos disease: a transcriptomic insight into disease pathogenesis. In: The British journal of dermatology 189 (6), S. 772–774. DOI: 10.1093/bjd/ljad306.
Leven, Patrick; Schneider, Reiner; Schneider, Linda; Mallesh, Shilpashree; Vanden Berghe, Pieter; Sasse, Philipp et al. (2023): β-adrenergic signaling triggers enteric glial reactivity and acute enteric gliosis during surgery. In: Journal of neuroinflammation 20 (1), S. 255. DOI: 10.1186/s12974-023-02937-0.
Schumann, Tina; Ramon, Santiago Costas; Schubert, Nadja; Mayo, Mohamad Aref; Hega, Melanie; Maser, Katharina Isabell et al. (2023): Deficiency for SAMHD1 activates MDA5 in a cGAS/STING-dependent manner. In: The Journal of experimental medicine 220 (1). DOI: 10.1084/jem.20220829.
Tzaridis, Theophilos; Weller, Johannes; Bachurski, Daniel; Shakeri, Farhad; Schaub, Christina; Hau, Peter et al. (2023): A novel serum extracellular vesicle protein signature to monitor glioblastoma tumor progression. In: International journal of cancer 152 (2), S. 308–319. DOI: 10.1002/ijc.34261.
Venneti, Sriram; Kawakibi, Abed Rahman; Ji, Sunjong; Waszak, Sebastian M.; Sweha, Stefan R.; Mota, Mateus et al. (2023): Clinical Efficacy of ONC201 in H3K27M-Mutant Diffuse Midline Gliomas Is Driven by Disruption of Integrated Metabolic and Epigenetic Pathways. In: Cancer discovery 13 (11), S. 2370–2393. DOI: 10.1158/2159-8290.CD-23-0131.
Aldisi, Rana; Hassanin, Emadeldin; Sivalingam, Sugirthan; Buness, Andreas; Klinkhammer, Hannah; Mayr, Andreas et al. (2022): GenRisk: a tool for comprehensive genetic risk modeling. In: Bioinformatics (Oxford, England) 38 (9), S. 2651–2653. DOI: 10.1093/bioinformatics/btac152.
Braegelmann, C.; Niebel, D.; Ferring-Schmitt, S.; Fetter, T.; Landsberg, J.; Hölzel, M. et al. (2022): Epigallocatechin-3-gallate exhibits anti-inflammatory effects in a human interface dermatitis model-implications for therapy. In: Journal of the European Academy of Dermatology and Venereology : JEADV 36 (1), S. 144–153. DOI: 10.1111/jdv.17710.
Brand, Fabian; Vijayananth, Aswinkumar; Hsieh, Tzung-Chien; Schmidt, Axel; Peters, Sophia; Mangold, Elisabeth et al. (2022): Next-generation phenotyping contributing to the identification of a 4.7 kb deletion in KANSL1 causing Koolen-de Vries syndrome. In: Human mutation 43 (11), S. 1659–1665. DOI: 10.1002/humu.24467.
Esser, Laura Kristin; Branchi, Vittorio; Shakeri, Farhad; Simon, Adrian Georg; Stephan, Carsten; Kristiansen, Glen et al. (2022): Overexpression of Parkin in clear cell renal cell carcinoma decreases tumor aggressiveness by regulating CKS2 levels. In: International journal of oncology 60 (2). DOI: 10.3892/ijo.2022.5310.
Ferreira, Rafaela Furioso; Blees, Thomas; Shakeri, Farhad; Buness, Andreas; Sylvester, Marc; Savoini, Giovanni et al. (2022): Effects of different ratios of omega-6:omega-3 fatty acids in the diet of sows on the proteome of milk-derived extracellular vesicles. In: Journal of proteomics 264, S. 104632. DOI: 10.1016/j.jprot.2022.104632.
Henn, Jonas; Buness, Andreas; Schmid, Matthias; Kalff, Jörg C.; Matthaei, Hanno (2022): Machine learning to guide clinical decision-making in abdominal surgery-a systematic literature review. In: Langenbeck's archives of surgery 407 (1), S. 51–61. DOI: 10.1007/s00423-021-02348-w.
Hsieh, Tzung-Chien; Bar-Haim, Aviram; Moosa, Shahida; Ehmke, Nadja; Gripp, Karen W.; Pantel, Jean Tori et al. (2022): GestaltMatcher facilitates rare disease matching using facial phenotype descriptors. In: Nature genetics 54 (3), S. 349–357. DOI: 10.1038/s41588-021-01010-x.
Karagiannis, Fotios; Peukert, Konrad; Surace, Laura; Michla, Marcel; Nikolka, Fabian; Fox, Mario et al. (2022): Impaired ketogenesis ties metabolism to T cell dysfunction in COVID-19. In: Nature 609 (7928), S. 801–807. DOI: 10.1038/s41586-022-05128-8.
Korencak, Marek; Sivalingam, Sugirthan; Sahu, Anshupa; Dressen, Dietmar; Schmidt, Axel; Brand, Fabian et al. (2022): Reconstruction of the origin of the first major SARS-CoV-2 outbreak in Germany. In: Computational and structural biotechnology journal 20, S. 2292–2296. DOI: 10.1016/j.csbj.2022.05.011.
Leven, Patrick; Schneider, Reiner; Siemens, Kevin D.; Jackson, Walker S.; Wehner, Sven (2022): Application of a RiboTag-based approach to generate and analyze mRNA from enteric neural cells. In: Neurogastroenterology and motility 34 (7), e14309. DOI: 10.1111/nmo.14309.
Niemann, Birte; Haufs-Brusberg, Saskia; Puetz, Laura; Feickert, Martin; Jaeckstein, Michelle Y.; Hoffmann, Anne et al. (2022): Apoptotic brown adipocytes enhance energy expenditure via extracellular inosine. In: Nature 609 (7926), S. 361–368. DOI: 10.1038/s41586-022-05041-0.
Schwab, Lara S. U.; Londrigan, Sarah L.; Brooks, Andrew G.; Hurt, Aeron C.; Sahu, Anshupa; Deng, Yi-Mo et al. (2022): Induction of Interferon-Stimulated Genes Correlates with Reduced Growth of Influenza A Virus in Lungs after RIG-I Agonist Treatment of Ferrets. In: Journal of virology 96 (16), e0055922. DOI: 10.1128/jvi.00559-22.
Umer, Naila; Phadke, Sharang; Shakeri, Farhad; Arévalo, Lena; Lohanadan, Keerthika; Kirfel, Gregor et al. (2022): PFN4 is required for manchette development and acrosome biogenesis during mouse spermiogenesis. In: Development (Cambridge, England) 149 (16). DOI: 10.1242/dev.200499.
Zietzer, Andreas; Breitrück, Nils; Düsing, Philip; Böhle, Sabrina; Klussmann, Jens Peter; Al-Kassou, Baravan et al. (2022): The lncRNA MRPL20-AS1 is associated with severe OSAS and downregulated upon hypoxic injury of endothelial cells. In: International journal of cardiology 369, S. 65–68. DOI: 10.1016/j.ijcard.2022.08.035.
Andreas Buness
Building A11, 2G/616
Venusberg-Campus 1
53127 Bonn
Dr. rer. nat. Farhad Shakeri
Building A11, 2G/621
Venusberg-Campus 1
53127 Bonn
Svetozar Nesic PhD
Building A11, 2G/621
Venusberg-Campus 1
53127 Bonn
Yu-Yu Lin PhD
Building A11, 2G/621
Venusberg-Campus 1
53127 Bonn
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The Core Facilities thank the German Research Foundation for continuous support.
