Selected publications

    • Bhattacharya D, Theodoropoulos J, Nurmi K, Juutilainen T, Eklund KK, Koivuniemi R, Kelkka T, Mustjoki S & Lönnberg T: Single-cell characterisation of tissue homing CD4 + and CD8 + T cell clones in immune-mediated refractory arthritis.
      Molecular Medicine 2024 30(1):48. PMID: 38594612
    • Örd T, Lönnberg T, Nurminen V, Ravindran A, Niskanen H, Kiema M, Öunap K, Maria M, Moreau PR, Mishra PP, Palani S, Virta J, Liljenbäck H, Aavik E, Roivainen A, Ylä-Herttuala S, Laakkonen JP, Lehtimäki T & Kaikkonen MU: Dissecting the polygenic basis of atherosclerosis via disease-associated cell state signatures.
      The American Journal of Human Genetics 2023 110:1-19. PMID: 37060905
    • Huuhtanen J, Kasanen H, Peltola K, Lönnberg T, Glumoff V, Brück O, Dufva O, Peltonen K, Vikkula J, Jokinen E, Ilander M, Lee MH, Mäkelä S, Nyakas M, Li B, Hernberg M, Bono P, Lähdesmäki H, Kreutzman A & Mustjoki S: Single-cell characterization of anti-LAG3+anti-PD1 treatment in melanoma patients.
      Journal of Clinical Investigation 2023 e164809. PMID: 36719749
    • Vandamme C, Rytkönen-Nissinen M, Lönnberg T, Randell J, Harvima RJ, Kinnunen T & Virtanen T:
      Single-cell characterization of dog allergen-specific T cells reveals T H 2 heterogeneity in allergic individuals.
      J Allergy Clin Immunol. 2022 149(5):1732-1743. PMID: 34863852 
    • Huuhtanen J, Bhattacharya D, Lönnberg T, Kankainen M, Kerr C, Theodoropoulos J, Rajala H, Gurnari C, Kasanen T, Braun T, Teramo A, Zambello R, Herling M, Ishida F, Kawakami T, Salmi M, Loughran T, Maciejewski JP, Lähdesmäki H, Kelkka T, Mustjoki S: Single-cell characterization of leukemic and non-leukemic immune repertoires in CD8 + T-cell large granular lymphocytic leukemia
      Nature Communications 2022 13(1):1981. PMID: 35411050
    • Örd T, Õunap K, Stolze LK, Aherrahrou R, Nurminen V, Toropainen A, Selvarajan I, Lönnberg T, Aavik E, Ylä-Herttuala S, Civelek M, Romanoski CE, Kaikkonen MU: Single-Cell Epigenomics and Functional Fine-Mapping of Atherosclerosis GWAS Loci.
      Circulation Research 2021 129(2):240-258. PMID: 34024118
    • Oliva-Olivera W, Castellano-Castillo D, von Meyenn F, Cardona F, Lönnberg T *& Tinahones FJ*:
      Human adipose tissue-derived stem cell paracrine networks vary according metabolic risk and after TNFα-induced death: an analysis at the single-cell level.
      Metabolism 2021; 116:154466. PMID: 33333081
      *) Equal contribution
    • Soon M, Lee HJ, Engel J, Straube J, Thomas B, Pernold C, Clarke L, Haldar R, Williams C, Lansink L, Kazakoff S, Koufariotis L, Wood S, Chen X, James K, Lönnberg T, Lane S, Belz G, Engwerda C, Khoury D, Davenport MP, Svensson V, Teichmann SA & Haque A: Transcriptome Dynamics of CD4+ T cells during Malaria Maps Progressive Transition from Effector to Memory.
      Nature Immunology 2020; 21(12):1597-1610. PMID: 33046889
    • Miragaia RJ, Zhang X, Gomes T, Svensson V, Ilicic T, Henriksson J, Kar G & Lönnberg T: Single-cell RNA-sequencing resolves self-antigen expression during mTEC development.
      Scientific Reports 2018; 8(1):685. PMID: 29330484
    • Haque A, Engel J, Teichmann SA & Lönnberg T: A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications.
      Genome Medicine 2017; 9(1):75. Review. PMID:28821273
    • Kolodziejczyk AA* & Lönnberg T*: Global and targeted approaches to single-cell transcriptome characterization.
      Briefings in Functional Genomics 2017; Review. PMID:29028866
      *) Equal contribution
    • Lönnberg T*, Svensson V*, James KR*, Fernandez-Ruiz D, Sebina I, Montandon R, Soon MSF, Fogg LG, Nair AS, Liligeto UN, Stubbington MJT, Ly LH, Bagger FO, Zwiessele M, Lawrence ND, Souza-Fonseca-Guimaraes F, Bunn PT, Engwerda CR, Heath WR, Billker O, Stegle O, Haque A, & Teichmann SA: Single-cell RNA-seq and computational analysis using temporal mixture modelling resolves TH1/TFH fate bifurcation in malaria.
      Science Immunology 2017; 2:1-11. PMID 28345074
      *) Equal contribution
    • Proserpio V & Lönnberg T: Single-cell technologies are revolutionizing the approach to rare cells.
      Immunology and Cell Biology 2016; 94(3):225-9. Review. PMID: 26620630
    • Stubbington MJT*, Lönnberg T*, Proserpio V, Clare S, Speak AO, Dougan G & Teichmann SA:
      T cell fate and clonality inference from single-cell transcriptomes.
      Nature Methods 2016; 13(4):329-32. PMID: 26950746
      *) Equal contribution
    • Lönnberg T, Chen Z & Lahesmaa R: From a gene-centric to whole-proteome view of differentiation of T helper cell subsets.
      Briefings in Functional Genomics 2013; 12(6):471-82. Review. PMID: 24106101