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Publications

50 latest publications

[1]
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).
[2]
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.
[3]
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).
[4]
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).
[5]
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.
[6]
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.
[7]
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).
[8]
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.
[9]
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.
[10]
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).
[11]
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.
[12]
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.
[13]
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.
[14]
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).
[15]
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.
[16]
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.
[17]
Hansen, J. N. (2024). Morphometric Analyses of Macrophages. In Tissue-Resident Macrophages: Methods and Protocols (pp. 519-541). Springer Nature.
[18]
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).
[19]
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.
[20]
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.
[21]
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.
[22]
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.
[23]
Kuodyte, K., Galea, G., Käller Lundberg, E. & Pepperkok, R. (2023). The Golgi complex serves as a platform for the DNA damage response pathways. Molecular Biology of the Cell, 34(2), 209-209.
[24]
Kuodyte, K., Galea, G., Käller Lundberg, E. & Pepperkok, R. (2023). The Golgi complex serves as a platform for the DNA damage response pathways. Molecular Biology of the Cell, 34(2), 63-63.
[25]
Jain, Y., Godwin, L. L., Joshi, S., Mandarapu, S., Le, T., Lindskog, C. ... Börner, K. (2023). Segmenting functional tissue units across human organs using community-driven development of generalizable machine learning algorithms. Nature Communications, 14(1).
[26]
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.
[27]
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).
[28]
Jain, S., Birgersson, M., Kipen, J., Jaldén, J., Stemme, G., Niklaus, F. ... Herland, A. (2023). Sensing of protein and DNA complexes using solid-state nanopores. Biophysical Journal, 122(3S1).
[29]
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).
[30]
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).
[31]
Thrikawala, S., Mesmar, F., Bhattacharya, B., Muhsen, M., Mukhopadhyay, S., Flores, S. ... Bondesson, M. (2023). Triazole fungicides induce adipogenesis and repress osteoblastogenesis in zebrafish. Toxicological Sciences, 193(2), 119-130.
[32]
Vivekanand, A. C., Atasoy, M., Williams, C. & Cetecioglu, Z. (2023). Statistical Analysis of SARS-CoV-2 Using Wastewater-Based Data of Stockholm, Sweden. International Journal of Environmental Research and Public Health, 20(5).
[33]
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.
[34]
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).
[35]
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).
[36]
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.
[37]
Giovannelli, P., Ramaraj, P. & Williams, C. (2022). Editorial : Role of Sex Steroids and Their Receptor in Cancers. Frontiers in Endocrinology, 13.
[38]
Hases, L., Archer, A. & Williams, C. (2022). ERβ and Inflammation. In Advances in Experimental Medicine and Biology (pp. 213-225). Springer Nature.
[39]
Andrews, B., Chang, J. -., Collinson, L., Li, D., Lundberg, E., Mahamid, J. ... Zaritsky, A. (2022). Imaging cell biology. Nature Cell Biology, 24(8), 1180-1185.
[40]
Mund, A., Coscia, F., Kriston, A., Hollandi, R., Kovács, F., Brunner, A. -. ... Mann, M. (2022). Deep Visual Proteomics defines single-cell identity and heterogeneity. Nature Biotechnology, 40(8), 1231-1240.
[41]
Kustatscher, G., Collins, T., Gingras, A. -., Guo, T., Hermjakob, H., Ideker, T. ... Rappsilber, J. (2022). An open invitation to the Understudied Proteins Initiative. Nature Biotechnology, 40(6), 815-817.
[42]
Hases, L., Birgersson, M., Indukuri, R., Archer, A. & Williams, C. (2022). Colitis Induces Sex-Specific Intestinal Transcriptomic Responses in Mice. International Journal of Molecular Sciences, 23(18), 10408.
[43]
Norreen-Thorsen, M., Struck, E. C., Oling, S., Zwahlen, M., von Feilitzen, K., Odeberg, J. ... Butler, L. M. (2022). A human adipose tissue cell-type transcriptome atlas. Cell Reports, 40(2).
[44]
Song, D., He, H., Indukuri, R., Huang, Z., Stepanauskaite, L., Sinha, I. ... Williams, C. (2022). ER alpha and ER beta Homodimers in the Same Cellular Context Regulate Distinct Transcriptomes and Functions. Frontiers in Endocrinology, 13.
[45]
Huang, D., Huang, Z., Indukuri, R., Revanna, C. B., Berglund, M., Guan, J. ... Okret, S. (2022). Estrogen Receptor beta (ESR2) Transcriptome and Chromatin Binding in a Mantle Cell Lymphoma Tumor Model Reveal the Tumor-Suppressing Mechanisms of Estrogens. Cancers, 14(13), 3098.
[46]
Imbert, A., Ouyang, W., Safieddine, A., Coleno, E., Zimmer, C., Bertrand, E. ... Mueller, F. (2022). FISH-quant v2 : a scalable and modular tool for smFISH image analysis. RNA : A publication of the RNA Society, 28(6), 786-795.
[47]
Archer, A., Kutter, C. & Williams, C. (2022). Expression Profiles of Estrogen-Regulated MicroRNAs in Cancer Cells. Methods in Molecular Biology, 2418, 313-343.
[48]
Birgersson, M., Katona, B., Lindskog, C., Pontén, F. & Williams, C. (2022). Antibody Validation for Estrogen Receptor Beta. Methods in Molecular Biology, 2418, 1-23.
[49]
Indukuri, R., Damdimopoulos, A. & Williams, C. (2022). An Optimized ChIP-Seq Protocol to Determine Chromatin Binding of Estrogen Receptor Beta. Methods in Molecular Biology, 2418, 203-221.
[50]
Bagheri, N., Carpenter, A. E., Lundberg, E., Plant, A. L. & Horwitz, R. (2022). Commentary The new era of quantitative cell imaging-challenges and opportunities. Molecular Cell, 82(2), 241-247.