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Klughammer Lab - Systems Immunology

klughammer_mainResearch Topics

  • Systems immunology
  • Computational (epi-) genomics and transcriptomics
  • Spatio-molecular tissue organization





Prof. Johanna Klughammer

Johanna will start her lab at the Gene Center in September 2021. Applications are welcome!

In multicellular organisms it is essential that cells work together in concerted ways while fulfilling dedicated functions. We want to understand how and why cells do what they do in health and disease, with a special focus on the immune system which is involved in virtually all aspects of multicellular life.
Conveniently, a cell’s functionality is largely defined by its molecular setup in the form of DNA, RNA, and Protein – information bearing sequences that we can efficiently read using high-throughput methods. Measured in bulk, at single-cell resolution or spatially resolved, the resulting high-dimensional data allow us to characterize and model cellular types, states, programs, and interactions in diverse biomedical contexts ranging from host-pathogen interactions, over malignant diseases, to evolutionary questions. Our research is primarily data-driven while combining wet-lab and computational methods. To efficiently leverage large amounts of high-dimensional data, we use and develop computational approaches including data-processing and integration frameworks, machine learning, and visualizations in a high-performance computing environment.

Selected Publications

Vickovic S, Eraslan G*, Salmén F*, Klughammer J*, Stenbeck L*, Schapiro D, Äijö T, Bonneau R, Bergenstråhle L, Navarro JF, Gould J, Griffin GK, Borg Å, Ronaghi M, Frisén J, Lundeberg J, Regev A, Ståhl PL. High-definition spatial transcriptomics for in situ tissue profiling. Nat Methods. 2019 Oct;16(10):987-990. doi: 10.1038/s41592-019-0548-y. PubMed

Klughammer J*, Kiesel B*, Roetzer T, Fortelny N, Nemc A, Nenning KH, Furtner J, Sheffield NC, Datlinger P, Peter N, Nowosielski M, Augustin M, Mischkulnig M, Ströbel T, Alpar D, Ergüner B, Senekowitsch M, Moser P, Freyschlag CF, Kerschbaumer J, Thomé C, Grams AE, Stockhammer G, Kitzwoegerer M, Oberndorfer S, Marhold F, Weis S, Trenkler J, Buchroithner J, Pichler J, Haybaeck J, Krassnig S, Mahdy Ali K, von Campe G, Payer F, Sherif C, Preiser J, Hauser T, Winkler PA, Kleindienst W, Würtz F, Brandner-Kokalj T, Stultschnig M, Schweiger S, Dieckmann K, Preusser M, Langs G, Baumann B, Knosp E, Widhalm G, Marosi C, Hainfellner JA, Woehrer A, Bock C. The DNA methylation landscape of glioblastoma disease progression shows extensive heterogeneity in time and space. Nat Med. 2018 Oct;24(10):1611-1624. doi: 10.1038/s41591-018-0156-x. PubMed

Li J*, Klughammer J*, Farlik M*, Penz T*, Spittler A, Barbieux C, Berishvili E, Bock C, Kubicek S. Single-cell transcriptomes reveal characteristic features of human pancreatic islet cell types. EMBO Rep. 2016 Feb;17(2):178-87. doi: 10.15252/embr.201540946. PubMed

Klughammer J, Datlinger P, Printz D, Sheffield NC, Farlik M, Hadler J, Fritsch G, Bock C. Differential DNA Methylation Analysis without a Reference Genome. Cell Rep. 2015 Dec 22;13(11):2621-2633. doi: 10.1016/j.celrep.2015.11.024. PubMed