Core Facility Bioinformatics

The Core Unit for Bioinformatics Data Analysis (CUBA) provides quantitative and computational analyses, training and consultancy.ction and presentation of the Core Facility. The unit is primarily focused on the research at the Medical Faculty of the University of Bonn. It aims to establish a platform for computational biology, to facilitate quantitative approaches and to share and offer validated methods, expertise and resources. It is continuously evolving according to the needs of its collaborators and the progress in science.

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Services include bioinformatics data processing and analyses of e.g. transcriptomics, proteomics, single cell and spatial data.

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Contact us to get more information, to schedule an appointment, to request services like bioinformatics data analysis or consultancy.

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Cost calculations for bioinformatics data analyses are based on the required resources. Consultancy is free of charge.

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News from the Core Facilities & Science News

New way to prevent duodenal cancer

People with the hereditary disease familial adenomatous polyposis (FAP) have a greatly increased risk of developing a malignant tumor of the duodenum. Researchers at the University Hospital Bonn (UKB) and the Cluster of Excellence ImmunoSensation2 at the University of Bonn have now discovered a mechanism in the local immune system that can drive the development of cancer. They see this as a promising new approach to preventing duodenal carcinoma in people with FAP. The results have now been published in the journal "Nature Communications".

New findings on hair loss in men

A receding hairline, a total loss of hair from the crown, and ultimately, the classical horseshoe-shaped pattern of baldness: Previous research into male pattern hair loss, also termed androgenetic alopecia, has implicated multiple common genetic variants. Human geneticists from the University Hospital of Bonn (UKB) and by the Transdisciplinary Research Unit “Life & Health” of the University of Bonn have now performed a systematic investigation of the extent to which rare genetic variants may also contribute to this disorder. For this purpose, they analyzed the genetic sequences of 72,469 male participants from the UK Biobank project. The analyses identified five significantly associated genes, and further corroborated genes implicated in previous research. The results have now been published in the prestigious scientific journal Nature Communications.

Publications

2024

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.

2023

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.

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.

2022

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.