Publications
For citations and H index, see this scholar profile.
2026
Gwon Y et al. 2026. “Dissecting placental host-pathogen interactions: Rift Valley fever virus infection in early human trophoblast stem cells”. iScience. Link. Joint work with Magnus Evander
Guerreiro DN, Henriksson J, Johansson J, et al. 2026. A rapid method to simultaneously separate bacterial and eukaryotic RNA during infections reveals increased intracellular expression of Staphylococcus aureus and Shigella flexneri virulence factors. Microbiology Spectrum 14(5). Link. Joint work with Jörgen Johansson
2025
Sara Vikberg et al. 2025. Placental intervillous blood harbors NK cells with distinct tissue-resident characteristics. Mucosal Immunology. Link. Joint work with Helen Kaipe
Gourlé H*, Yakovenko I*, Verma J*, Dicken J*, et al. 2025. Scalable single-cell metagenomic analysis with Bascet and Zorn. Preprint. Software
Yakovenko I*, Mihai IS*, Selinger M*, et al 2025. Telomemore enables single-cell analysis of cell cycle and chromatin condensation. Nucleic Acids Research. Link
Jonsdottir TK, Paoletta MS et al. 2025. A scalable CRISPR-Cas9 gene editing system facilitates CRISPR screens in the malaria parasite Plasmodium berghei. Nucleic Acids Research. Link. Joint work with Ellen Bushell
Khan M et al. 2025. Single-cell profiling uncovers regulatory programs of pathogenic Th2 cells in allergic asthma. Nature Communications. Link. Joint work with Nicole Boucheron
Pu L et al. 2025. Shaker/Kv1 potassium channel SHK-1 protects against pathogen infection and oxidative stress in C. elegans. PLOS Genetics. Link. Joint work with Changchun Chen.
2024
Hellman U et al. 2024. SARS-CoV-2 infection induces hyaluronan production in vitro and hyaluronan levels in COVID-19 patients relate to morbidity and long COVID. mBio 15(10). Link. Joint work with Anna Överby
Lazzaro N et al. 2024. Generative Models Validation via Manifold Recapitulation Analysis. Preprint
Rosendal E et al. 2024. Transcriptional response to flavivirus infection in neurons, astrocytes and microglia in vivo and in vitro. Viruses 16(8), 1327; https://doi.org/10.3390/v16081327. Link. Joint work with Anna Överby
Mubasher M et al. 2024. Single-cell transcriptomics reveal transcriptional programs underlying male and female cell fate during Plasmodium falciparum gametocytogenesis. Nature Communications. Link. Joint work with Johan Ankarklev
Westerlund A et al. 2024. Personalized oral care (Precaries): an intervention study customized according to genetic cause and risk. Preprint Joint work with Nicklas Strömberg
Mihai IS et al. 2024 The CD4 T cell epigenetic JUNB+ state is associated with proliferation and exhaustion Preprint
Selinger M et al. 2024. CRISPR-MIP replaces PCR and reveals GC and oversampling bias in pooled CRISPR screens Preprint
2023
Schoutrop E et al. 2023. Tuned activation of MSLN-CAR T cells induces superior antitumor responses in ovarian cancer models. Journal for Immunotherapy of Cancer. Link
Saudi A et al. 2023. Immune-activated B cells are dominant in prostate cancer. Cancers 15(3). Link
Lu Q et al. 2023. IL-17 undermines longevity and stress tolerance by inhibiting a protective transcriptional network. Preprint. Joint work with Changchun Chen.
Ramnath V et al. 2023 A community-curated, global atlas of Bacillus cereus sensu lato genomes for epidemiological surveillance. Preprint. Joint work with Laura Carroll
Pu L et al. 2023. Dissecting the genetic landscape of GPCR signaling through phenotypic profiling in C. elegans. Nature Communications Link. Joint work with Changchun Chen.
Pu L et al. 2023. Acute avoidance of hydrogen sulfide is modulated by external and internal states in C. elegans. eLife Link. Joint work with Changchun Chen.
Hildebrandt F et al. 2023. scDual-Seq of Toxoplasma gondii-infected mouse BMDCs reveals heterogeneity and differential infection dynamics. Frontiers in Immunology. Link. Joint work with Johan Ankarklev
Chotiwan N et al. 2023. Type I interferon shapes brain distribution and tropism of tick-borne flavivirus. Nature Communications. Link.
Mohammed M et al. 2023. Single-Cell Transcriptomics To Define Plasmodium falciparum Stage Transition in the Mosquito Midgut. Microbiology Spectrum. Link. Joint work with Johan Ankarklev
Mihai IS, Chafle S, Henriksson J. 2023. Review: Representing and extracting knowledge from single cell data. Biophysical Reviews. Link
2022
Ebba Rosendal et al 2022. Serine protease inhibitors restrict host susceptibility to SARS-CoV-2 infections. mBio. Joint work with Annasara Lenman and Anna Överby. Link.
2021
Haim-Vilmovsky, Henriksson et al, 2021. Mapping RORa expression in resting and activated CD4+ T cells. PLOS ONE. Link
Jafari et al, 2021. Stress and neuronal activity during a critical period regulate odorant receptor expression in Drosophila Melanogaster. PLOS biology. Joint work with the Alenius lab. Link
Dernstedt A, 2021, Regulation of Decay Accelerating Factor primes human germinal center B cells for phagocytosis. Frontiers in Immunology. Joint work with the Forsell lab. Link
Mihai IS et al, 2021. Meta-analysis on gene popularity; less than half gene citations stem from gene regulatory networks. MDPI Genes. Link ; see also the Resource-pages in the menus of this page
2019
Filcek K et al, 2019. Insertional mutagenesis in the zoonotic pathogen Chlamydia caviae. PLOS ONE. Joint work with the Sixt lab at MIMS. Link
Henriksson, J. et al., 2019. Genome-wide CRISPR screens in T helper cells reveal pervasive cross-talk between activation and differentiation. Cell. Link ; see also the Resource-pages in the menus of this page
Henriksson J. 2019. CRISPR screening in single cells. Methods in Molecular Biology (Single Cell Methods), 1979, pp.267–284. Link
2018
Arvidsson, G., Henriksson, J. & Sander, B., 2018. Mixed-species RNAseq analysis of human lymphoma cells adhering to mouse stromal cells identifies a core gene set that is also differentially expressed in the lymph node microenvironment of mantle cell lymphoma and chronic lymphocytic leukemia patients. Haematologica. Link
Hagai, T. et al., 2018. Gene expression variability across cells and species shapes innate immunity. Nature, 563(7730), pp.197–202. Link
Miragaia, R.J. et al., 2018. Single-cell RNA-sequencing resolves self-antigen expression during mTEC development. Scientific Reports, 8(1), p.685. Link
Pramanik, J. et al., 2018. Genome-wide analyses reveal the IRE1a-XBP1 pathway promotes T helper cell differentiation by resolving secretory stress and accelerating proliferation. Genome Medicine, 10(1), p.76. Link
Severo, M.S. et al., 2018. Unbiased classification of mosquito blood cells by single-cell genomics and high-content imaging. Proceedings of the National Academy of Sciences of the United States of America, 115(32), pp.E7568–E7577. Link
Vento-Tormo, R. et al., 2018. Single-cell reconstruction of the early maternal–fetal interface in humans. Nature, 563(7731), pp.347–353. Link
2017
Bürglin TR, Henriksson J. 2017. FACSanadu: Graphical user interface for rapid visualization and quantification of flow cytometry data. Preprint
2015
Kolodziejczyk, A.A. et al., 2015. Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation. Cell Stem Cell, 17(4), pp.471–485. Link
Dahlman, I. et al., 2015. The fat cell epigenetic signature in post-obese women is characterized by global hypomethylation and differential DNA methylation of adipogenesis genes. International Journal of Obesity, 39(6), pp.910–919. Link
Hench, J. et al., 2015. The Homeobox Genes of Caenorhabditis elegans and Insights into Their Spatio-Temporal Expression Dynamics during Embryogenesis. PLOS ONE, 10(5), p.e0126947. Link
2013
Mahani, A., Henriksson, J. & Wright, A.P.H., 2013. Origins of Myc proteins–using intrinsic protein disorder to trace distant relatives. PLOS ONE, 8(9), p.e75057. Link
Arczewska, K.D. et al., 2013. Active transcriptomic and proteomic reprogramming in the C. elegans nucleotide excision repair mutant xpa-1. Nucleic Acids Research, 41(10), pp.5368–5381. Link
Henriksson, J., Piasecki, B.P., et al., 2013. Finding ciliary genes: a computational approach. Methods in Enzymology, 525, pp.327–350. Link
Henriksson, J., Hench, J., et al., 2013. Endrov: an integrated platform for image analysis. Nature Methods, 10(6), pp.454–456. Link
Xue-Franzén, Y. et al., 2013. Distinct roles of the Gcn5 histone acetyltransferase revealed during transient stress-induced reprogramming of the genome. BMC Genomics, 14, p.479. Link
2010
Henriksson, J., Lundh, T. & Wennberg, B., 2010. A model of sympatric speciation through reinforcement. Kinetic and Related Models, 3(1), pp.143–163. Link
Xue-Franzén, Y. et al., 2010. Genome-wide characterisation of the Gcn5 histone acetyltransferase in budding yeast during stress adaptation reveals evolutionarily conserved and diverged roles. BMC Genomics, 11(1), p.200. Link
2009
Bratic, I. et al., 2009. Mitochondrial DNA level, but not active replicase, is essential for Caenorhabditis elegans development. Nucleic Acids Research, 37(6), pp.1817–1828. Link
Hench, J. et al., 2009. Spatio-temporal reference model of Caenorhabditis elegans embryogenesis with cell contact maps. Developmental Biology, 333(1), pp.1–13. Link