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Publications

50 latest publications

[1]
Pohjanen, E. (2026). Spatial proteome mapping of specialized subcellular structures in human cells (Doctoral thesis , KTH Royal Institute of Technology, TRITA-CBH-FOU 2026:2). Retrieved from https://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-375190.
[2]
Seifi, M., Dalle Nogare, D., Battagliotti, J. M., Galinova, V., Rao, A. K., Jouneau, P. H. ... Deschamps, J. (2025). FeatureForest : the power of foundation models, the usability of random forests. NPJ Imaging, 3(1).
[3]
Sigaeva, A., Gnann, C. & Käller Lundberg, E. (2025). What does oxidative stress look like? : Visualizing expression of redoxassociated proteins with imaging-based spatial proteomics. Free Radical Biology & Medicine, 233, S69-S69.
[4]
Lázár, E., Mauron, R., Andrusivova, Z., Foyer, J., He, M., Larsson, L. ... Lundeberg, J. (2025). Spatiotemporal gene expression and cellular dynamics of the developing human heart. Nature Genetics, 57(11), 2756-2771.
[5]
Schagerholm Stanev, C., Sifakis, E. G., Hases, L., Chen, X., Williams, C., Robertson, S. & Hartman, J. (2025). Transcriptomic profiles of endocrine-resistant breast cancer. BMC Cancer, 25(1), 1556.
[6]
Hansen, J. N., Sun, H., Kahnert, K., Westenius, E., Johannesson, A., Villegas, C. ... Käller Lundberg, E. (2025). Intrinsic heterogeneity of primary cilia revealed through spatial proteomics. Cell.
[7]
Burgess, J., Nirschl, J. J., Bravo-Sánchez, L., Lozano, A., Gupte, S. R., Galaz-Montoya, J. G., Zhang, Y., Su, Y., Bhowmik, D., Coman, Z., Hasan, S. M., Johannesson, A., Leineweber, W. D., Nair, M. G., Yarlagadda, R., Zuraski, C., Chiu, W., Cohen, S., Hansen, J. N., Leonetti, M. D., Liu, C., Käller Lundberg, E., Yeung-Levy, S. (2025). MicroVQA: A Multimodal Reasoning Benchmark for Microscopy-Based Scientific Research. In Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition. (pp. 19553-19564). Institute of Electrical and Electronics Engineers (IEEE).
[8]
Sun, H., Yu, S., Casals, A. M., Bäckström, A., Lu, Y., Lindskog, C. ... Murphy, R. F. (2025). Flexible and robust cell-type annotation for highly multiplexed tissue images. Cell Systems, 16(9).
[9]
Schroeder, K., Fernández-Rodríguez, J., Jenmalm-Jensen, A., Lundgren-Gawell, J., Sandin, S., Stadler, C. & Lindvall, J. M. (2025). From Recruitment to Retirement: Research Infrastructure Staff Views on the Diversification of Scientific Career Paths at Universities in Sweden in 2024. F1000 Research, 14.
[10]
Tampere, M., H. Le, T., Asp, E., Kalman, A., Mohanakrishnan Kaimal, J., Njenda, D. ... Stadler, C. (2025). Image based subcellular mapping of the protein landscape of SARS-CoV-2 infected cells for target-centric drug repurposing. Biomedicine and Pharmacotherapy, 191.
[11]
Munsch, G., Mohapatra, A. K., van Hylckama Vlieg, A., Kleber, M. E., Martinez-Perez, A., Le, N. Q. ... Morange, P. E. (2025). A multiomics approach reveals novel regulators of plasma factor V levels: highlight on CLEC4M as a clearance receptor. Blood, 146(5), 628-637.
[12]
Johansson, E., Iglesias, M. J., Odeberg, J. & Edfors, F. (2025). Shaping the future of precision medicine: plasma proteomics to uncover insights in thrombosis. Expert Review of Proteomics, 22(6), 237-254.
[13]
Monteiro, F. L., Voskuil, J. L.A. & Williams, C. (2025). YCharOS protocol for antibody validation : Antibody validation. Nature Protocols, 20(6), 1389-1390.
[14]
Schaffer, L. V., Huttlin, E. L., Käller Lundberg, E., Ideker, T. & et al., (2025). Multimodal cell maps as a foundation for structural and functional genomics. Nature.
[15]
Birgersson, M., Holm, M., Gallardo-Dodd, C. J., Chen, B., Stepanauskaitė, L., Hases, L. ... Williams, C. (2025). Intestinal estrogen receptor beta modulates the murine colon tumor immune microenvironment. Cancer Letters, 622.
[16]
Bajcsy, P., Bhattiprolu, S., Boerner, K., Cimini, B. A., Collinson, L., Ellenberg, J. ... Keppler, A. (2025). Enabling global image data sharing in the life sciences. Nature Methods, 22(4), 672-676.
[17]
Odeberg, J., Halling, A., Ringborn, M., Freitag, M., Persson, M. L., Vaara, I. ... Lindblad, U. (2025). Markers of inflammation predicts long-term mortality in patients with acute coronary syndrome – a cohort study. BMC Cardiovascular Disorders, 25(1).
[18]
Sommerauer, C., Gallardo-Dodd, C. J., Savva, C., Hases, L., Birgersson, M., Indukuri, R. ... Kutter, C. (2024). Estrogen receptor activation remodels TEAD1 gene expression to alleviate hepatic steatosis. Molecular Systems Biology, 20(4), 374-402.
[19]
Hidalgo-Cenalmor, I., Pylvänäinen, J. W., G. Ferreira, M., Russell, C. T., Saguy, A., Arganda-Carreras, I. ... Gómez-de-Mariscal, E. (2024). DL4MicEverywhere : deep learning for microscopy made flexible, shareable and reproducible. Nature Methods, 21(6), 925-927.
[20]
Deen, A. J., Thorsson, J., O’Roberts, E. M., Panshikar, P., Ullman, T., Krantz, D. ... Stadler, C. (2024). Making Multiplexed Imaging Flexible : Combining Essential Markers With Established Antibody Panels. Journal of Histochemistry and Cytochemistry, 72(8-9), 517-544.
[21]
Wernersson, E., Gelali, E., Girelli, G., Wang, S., Castillo, D., Mattsson Langseth, C. ... Bienko, M. (2024). Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images. Nature Methods, 21(7), 1245-1256.
[22]
Bunne, C., Gupta, A., Käller Lundberg, E., Quake, S. R. & et al., (2024). How to build the virtual cell with artificial intelligence : Priorities and opportunities. Cell, 187(25), 7045-7063.
[23]
Holm, M., Stepanauskaitė, L., Bäckström, A., Birgersson, M., Socciarelli, F., Archer, A. ... Williams, C. (2024). Spatial profiling of the mouse colonic immune landscape associated with colitis and sex. Communications Biology, 7(1).
[24]
Sariyar, S., Sountoulidis, A., Hansen, J. N., Marco Salas, S., Mardamshina, M., Martinez Casals, A. ... Ayoglu, B. (2024). High-parametric protein maps reveal the spatial organization in early-developing human lung. Nature Communications, 15(1).
[25]
Pacia, D. M., Ravitsky, V., Hansen, J. N., Käller Lundberg, E., Schulz, W. & Belisle-Pipon, J.-C. (2024). Early AI Lifecycle Co-Reasoning : Ethics Through Integrated and Diverse Team Science. American Journal of Bioethics, 24(9), 86-88.
[26]
Cesnik, A., Schaffer, L. V., Gaur, I., Jain, M., Ideker, T. & Käller Lundberg, E. (2024). Mapping the Multiscale Proteomic Organization of Cellular and Disease Phenotypes. Annual Review of Biomedical Data Science, 7(1), 369-389.
[27]
Lee, H., Langseth, C. M., Salas, S. M., Sariyar, S., Metousis, A., Rueda-Alana, E. ... Nilsson, M. (2024). Open-source, high-throughput targeted in situ transcriptomics for developmental and tissue biology. Development, 151(16).
[28]
Diaz, R. V., Munsch, G., Iglesias, M. J., Robles, A. P., Ibrahim-Kosta, M., Nourse, J. ... Goumidi, L. (2024). Plasma levels of complement components C5 and C9 are associated with thrombin generation. Journal of Thrombosis and Haemostasis, 22(9), 2531-2542.
[29]
Perez-Zabaleta, M., Williams, C. & Cetecioglu, Z. (2024). Development and implementation of assays to monitor human adenovirus F40/41 in wastewater : Trends preceding, during, and following the non-A-to-E hepatitis outbreak in Stockholm. Environment International, 190.
[30]
Chang, Y. C., Gnann, C., Steimbach, R. R., Bayer, F. P., Lechner, S., Sakhteman, A. ... Kuster, B. (2024). Decrypting lysine deacetylase inhibitor action and protein modifications by dose-resolved proteomics. Cell Reports, 43(6).
[31]
Monteiro, F. L., Stepanauskaite, L., Archer, A. & Williams, C. (2024). Estrogen receptor beta expression and role in cancers. Journal of Steroid Biochemistry and Molecular Biology, 242.
[32]
King, M. R., Ruff, K. M., Lin, A. Z., Pant, A., Farag, M., Lalmansingh, J. M. ... Pappu, R. V. (2024). Macromolecular condensation organizes nucleolar sub-phases to set up a pH gradient. Cell, 187(8), 24-1889.
[33]
Sariyar, S. (2024). Spatiotemporal Profiling of Human Development Using Multiplexed Imaging (Doctoral thesis , KTH Royal Institute of Technology, Sweden, TRITA-CBH-FOU 2024:14). Retrieved from https://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-345248.
[34]
Öling, S., Struck, E., Noreen-Thorsen, M., Zwahlen, M., von Feilitzen, K., Odeberg, J. ... Butler, L. M. (2024). A human stomach cell type transcriptome atlas. BMC Biology, 22(1).
[35]
Dou, D. R., Zhao, Y., Belk, J. A., Zhao, Y., Casey, K. M., Chen, D. C. ... Chang, H. Y. (2024). Xist ribonucleoproteins promote female sex-biased autoimmunity. Cell, 187(3), 16-733.
[36]
Struck, E. C., Belova, T., Hsieh, P. H., Odeberg, J., Kuijjer, M. L., Dusart, P. & Butler, L. M. (2024). Global Transcriptome Analysis Reveals Distinct Phases of the Endothelial Response to TNF. Journal of Immunology, 212(1), 117-129.
[37]
Hansen, J. N. (2024). Morphometric Analyses of Macrophages. In Tissue-Resident Macrophages: Methods and Protocols (pp. 519-541). Springer Nature.
[38]
Birgersson, M., Indukuri, R., Lindquist, L., Stepanauskaite, L., Luo, Q., Deng, Q. ... Williams, C. (2023). Ovarian ERβ cistrome and transcriptome reveal chromatin interaction with LRH-1. BMC Biology, 21(1).
[39]
Quardokus, E. M., Martinez Casals, A., Björklund, F., Käller Lundberg, E., Radtke, A. J. & et al., (2023). Organ Mapping Antibody Panels : a community resource for standardized multiplexed tissue imaging. Nature Methods, 20(8), 1174-1178.
[40]
Johnson, G. T., Agmon, E., Akamatsu, M., Käller Lundberg, E., Lyons, B., Ouyang, W. ... Horwitz, R. (2023). Building the next generation of virtual cells to understand cellular biology. Biophysical Journal, 122(18), 3560-3569.
[41]
Chemaly, M., Marlevi, D., Iglesias, M. J., Lengquist, M., Kronqvist, M., Bos, D. ... Hedin, U. (2023). Biliverdin Reductase B is a Plasma Biomarker for Intraplaque Hemorrhage and A Predictor of Ischemic Stroke in Symptomatic Carotid Stenosis. Atherosclerosis, 379, S180-S180.
[42]
Zhang, Y., Ripley, B., Ouyang, W., Coloma, R., Sturtz, M., Upton, E. ... Radoshevich, L. (2023). ISG15 modification of the Arp2/3 complex restricts pathogen spread. Molecular Biology of the Cell, 34(2), 818-818.
[43]
Cheng, Y., Lu, X., Li, F., Chen, Z., Zhang, Y., Han, Q. ... Xia, W. (2023). NDFIP1 limits cellular TAZ accumulation via exosomal sorting to inhibit NSCLC proliferation. Protein & Cell, 14(2), 123-136.
[44]
Birgersson, M., Indukuri, R., Antonson, P., Nalvarte, I., Archer, A. & Williams, C. (2023). ERβ in Granulosa Cell Tumors and Its Clinical Potential. Endocrinology, 164(6).
[45]
Chemaly, M., Marlevi, D., Iglesias, M. J., Lengquist, M., Kronqvist, M., Bos, D. ... Hedin, U. (2023). Biliverdin Reductase B Is a Plasma Biomarker for Intraplaque Hemorrhage and a Predictor of Ischemic Stroke in Patients with Symptomatic Carotid Atherosclerosis. Biomolecules, 13(6).
[46]
Iglesias, M. J., Sanchez-Rivera, L., Ibrahim-Kosta, M., Naudin, C., Munsch, G., Goumidi, L. ... Odeberg, J. (2023). Elevated plasma complement factor H related 5 protein is associated with venous thromboembolism. Nature Communications, 14(1).
[47]
Sountoulidis, A., Marco Salas, S., Braun, E., Avenel, C., Bergenstråhle, J., Theelke, J. ... Samakovlis, C. (2023). A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung. Nature Cell Biology, 25, 351-365.
[48]
Geroldinger-Simic, M., Bayati, S., Pohjanen, E., Sepp, N., Nilsson, P. & Pin, E. (2023). Autoantibodies against PIP4K2B and AKT3 Are Associated with Skin and Lung Fibrosis in Patients with Systemic Sclerosis. International Journal of Molecular Sciences, 24(6).
[49]
Hases, L., Stepanauskaite, L., Birgersson, M., Brusselaers, N., Schuppe-Koistinen, I., Archer, A. ... Williams, C. (2023). High-fat diet and estrogen modulate the gut microbiota in a sex-dependent manner in mice. Communications Biology, 6(1).
[50]
Perez-Zabaleta, M., Archer, A., Khatami, K., Jafferali, M. H., Nandy, P., Atasoy, M. ... Cetecioglu, Z. (2023). Long-term SARS-CoV-2 surveillance in the wastewater of Stockholm : What lessons can be learned from the Swedish perspective?. Science of the Total Environment, 858.