For citations and H index, see this scholar profile.


Pu L et al. 2023. Dissecting the genetic landscape of GPCR signaling through phenotypic profiling in C. elegans. Nat.comm. Joint with Changchun Chen.

Pu L et al. 2023. Acute avoidance of hydrogen sulfide is modulated by external and internal states in C. elegans. Joint with Changchun Chen. Preprint

Hildebrandt F et al. 2023. scDual-Seq of Toxoplasma gondii-infected mouse BMDCs reveals heterogeneity and differential infection dynamics. Frontiers in immunology. Link

Chotiwan N et al. 2023. Type I interferon shapes brain distribution and tropism of tick-borne flavivirus. Nature comm. Link.

Mohammed M et al. 2023. Single-Cell Transcriptomics To Define Plasmodium falciparum Stage Transition in the Mosquito Midgut. Microbiology spectrum. Link.

Mihai IS, Chafle S, Henriksson J. 2023. Review: Representing and extracting knowledge from single cell data. Link

Mihai IS et al 2023. Telomemore enables single-cell analysis of cell cycle and chromatin condensation. Preprint.


Ebba Rosendal et al  2022. Serine protease inhibitors restrict host susceptibility to SARS-CoV-2 infections. mBio. Joint with Annasara Lenman and Anna Överby. Link.


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 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 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


Filcek K et al, 2019. Insertional mutagenesis in the zoonotic pathogen Chlamydia caviae. PLOS ONE. Joint 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


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.

Hagai, T. et al., 2018. Gene expression variability across cells and species shapes innate immunity. Nature, 563(7730), pp.197–202.

Miragaia, R.J. et al., 2018. Single-cell RNA-sequencing resolves self-antigen expression during mTEC development. Scientific reports, 8(1), p.685.

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.

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.

Vento-Tormo, R. et al., 2018. Single-cell reconstruction of the early maternal–fetal interface in humans. Nature, 563(7731), pp.347–353.


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.

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.


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.

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.


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.

Henriksson, J., Piasecki, B.P., et al., 2013. Finding ciliary genes: a computational approach. Methods in enzymology, 525, pp.327–350.

Henriksson, J., Hench, J., et al., 2013. Endrov: an integrated platform for image analysis. Nature methods, 10(6), pp.454–456.

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.


Henriksson, J., Lundh, T. & Wennberg, B., 2010. A model of sympatric speciation through reinforcement. Kinetic and Related Models, 3(1), pp.143–163.

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.


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.

Hench, J. et al., 2009. Spatio-temporal reference model of Caenorhabditis elegans embryogenesis with cell contact maps. Developmental biology, 333(1), pp.1–13.