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Publications

  1. Rahimi, K. (2023). “Revealing full-length structure of circRNAs with global and panel adjusted long-read nanopore sequencing” Invitation from “Nature Protocols”, In preparation.

  2. Rybiczka-Tešulov, M., Garritsen, O., Venø, M. T., Dijk, R. V., Rahimi, K., Duarte, A. G., Wit, M. D., Haar, L. V., Michels, L., Kronenburg, N. V., Meer, C. V., Kjems, J., Vangoor, V. R., Pasterkamp, R. J. (2023). Transcriptomic profiling of long non-coding RNAs identifies circRmst as a regulator of midbrain dopamine neuron migration. Nature Communications, (In Revision).

  3. Rahimi, K. (2023). The Future is Now: Artificial Intelligence is Transforming the Development of Biotech, Biomedicine, and Agriculture. Science and Modern Technology Journal, 1(1), 13-19. https://a4043e4a-88c2-4633-ac05.pdf

  4. Ghorbani, S., Füchtbauer, A. C., Møllebjerg, A., Martensen, P. M., Laursen, S. H., Kraft, D. C. E., Kjems, J., Meyer, R. L., Rahimi, K., Foss, M., Füchtbauer, E.-M. & Sutherland, D. S. (2023). Protein ligand and nanotopography separately drive the phenotype of mouse embryonic stem cells. Biomaterials, 301, 122244. https://doi.org/10.1016/j.biomaterials.2023.122244

  5. Rahbari, R., Rahimi, K., Rasmi, Y., Khadem-Ansari, M. H. & Abdi, M. (2022). miR-589-5p Inhibits Cell Proliferation by Targeting Histone Deacetylase 3 in Triple Negative Breast Cancer. Archives of Medical Research, 53(5), 483–491. https://doi.org/10.1016/j.arcmed.2022.06.006

  6. Barznegar, M., Rahimi, K., Mahdavi, P., Menbari, M., Darvishi, N., Vahabzadeh, Z., Hakhamaneshi, M., Andalibi, P. & Abdi, M. (2022). Relation between the circular and linear form of the Elongator Acetyltransferase Complex Subunit 3 in the progression of triple-negative breast cancer. Cell Biochemistry and Function, 40(6), 550–558. https://doi.org/10.1002/cbf.3724

  7. Rahimi, K., Andersen, M. S., Seeler, S., Hansen, T. B. & Kjems, J. (2022). Chemically synthesized guide RNAs can direct CRISPR-CasRx cleavage of circRNAs with high efficiency and specificity. bioRxiv (submitted – under revision), 2022.08.30.505797. https://doi.org/10.1101/2022.08.30.505797

  8. Shakeran, Z., Varshosaz, J., Keyhanfar, M., Mohammad-Beigi, H., Rahimi, K. & Sutherland, D. S. (2022). Co-delivery of STAT3 siRNA and methotrexate in breast cancer cells. Artificial Cells, Nanomedicine, and Biotechnology, 50(1), 29–39. https://doi.org/10.1080/21691401.2022.2030746

  9. Rahmani, G., Moloudi, M. R., Amini, R., Rahimi, K., Fathi, F., Abdi, M. & Najafi, R. (2022). Effect of histone deacetylase 8 gene deletion on breast cancer cellular mechanism in vitro and in vivo study. Life Sciences, 311(Pt A), 121156. https://doi.org/10.1016/j.lfs.2022.121156

  10. Seifi, T., Shafiei, M., Rahimi, K., Ghaedi, K. & Galehdari, H. (2022). Up-regulation of PDGF-D and NRP-1 in the Glioma Cell Line 1321N1 Attributed to Sialic Acid Treatment: Mini-review and Findings. Jentashapir Journal of Cellular and Molecular Biology, 13(2). https://doi.org/10.5812/jjcmb-130150

  11. Rahimi, K., Venø, M. T., Dupont, D. M. & Kjems, J. (2021). Nanopore sequencing of brain-derived full-length circRNAs reveals circRNA-specific exon usage, intron retention and microexons. Nature Communications, 12(1), 4825. https://doi.org/10.1038/s41467-021-24975-z

  12. Omid-Shafaat, R., Moayeri, H., Rahimi, K., Menbari, M., Vahabzadeh, Z., Hakhamaneshi, M., Nouri, B., Ghaderi, B. & Abdi, M. (2021). Serum Circ-FAF1/Circ-ELP3: A novel potential biomarker for breast cancer diagnosis. Journal of Clinical Laboratory Analysis, 35(11), e24008. https://doi.org/10.1002/jcla.24008

  13. Zarei, M., Rahimi, K., Hassanzadeh, K., Abdi, M., Hosseini, V., Fathi, A. & Kakaei, K. (2021). From the environment to the cells: An overview on pivotal factors which affect spreading and infection in COVID-19 pandemic. Environmental Research, 201, 111555. https://doi.org/10.1016/j.envres.2021.111555

  14. Rahimi, K., Füchtbauer, A. C., Fathi, F., Mowla, S. J. & Füchtbauer, E.-M. (2021). Expression of the miR-302/367 microRNA cluster is regulated by a conserved long non-coding host-gene. Scientific Reports, 11(1), 11115. https://doi.org/10.1038/s41598-021-89080-z

  15. Rahimi, K., Nielsen, A. F., Venø, M. T. & Kjems, J. (2021). Nanopore long-read sequencing of circRNAs. Methods, 196, 23–29. https://doi.org/10.1016/j.ymeth.2021.09.010

  16. Menbari, M., Rahimi, K., Ahmadi, A., Mohammadi-Yeganeh, S., Elyasi, A., Darvishi, N., Hosseini, V. & Abdi, M. (2020). miR-483-3p suppresses the proliferation and progression of human triple negative breast cancer cells by targeting the HDAC8 oncogene. Journal of Cellular Physiology, 235(3), 2631–2642. https://doi.org/10.1002/jcp.29167

  17. Darvishi, N., Rahimi, K., Mansouri, K., Fathi, F., Menbari, M.-N., Mohammadi, G. & Abdi, M. (2020). MiR-646 prevents proliferation and progression of human breast cancer cell lines by suppressing HDAC2 expression. Molecular and Cellular Probes, 53, 101649. https://doi.org/10.1016/j.mcp.2020.101649

  18. Rahimi, K., Parsa, S., Nikzaban, M., Khaledian, B., Mowla, S. J. & Fathi, F. (2020). Evaluation of miR-302 promoter activity in transgenic mice and pluripotent stem cell lines. In Vitro Cellular & Developmental Biology - Animal, 56(10), 896–905. https://doi.org/10.1007/s11626-020-00516-8

  19. Yoshimoto, R., Rahimi, K., Hansen, T. B., Kjems, J. & Mayeda, A. (2020). Biosynthesis of Circular RNA ciRS-7/CDR1as Is Mediated by Mammalian-wide Interspersed Repeats. iScience, 23(7), 101345. https://doi.org/10.1016/j.isci.2020.101345

  20. Menbari, M.-N., Rahimi, K., Ahmadi, A., Mohammadi-Yeganeh, S., Elyasi, A., Darvishi, N., Hosseini, V. & Abdi, M. (2020). Association of HDAC8 Expression with Pathological Findings in Triple Negative and Non-Triple Negative Breast Cancer: Implications for Diagnosis. Iranian Biomedical Journal, 24(5), 283–289. https://doi.org/10.29252/ibj.24.5.283  

  21. Menbari, M.-N., Rahimi, K., Ahmadi, A., Elyasi, A., Darvishi, N., Hosseini, V., Mohammadi-Yeganeh, S. & Abdi, M. (2019). MiR-216b-5p inhibits cell proliferation in human breast cancer by down-regulating HDAC8 expression. Life Sciences, 237, 116945. https://doi.org/10.1016/j.lfs.2019.116945

  22. Rahimi, K., Venø, M. T., Dupont, D. M. & Kjems, J. (2019). Nanopore sequencing of full-length circRNAs in human and mouse brains reveals circRNA-specific exon usage and intron retention. bioRxiv, 567164. https://doi.org/10.1101/567164

  23. Rahimi, K., Füchtbauer, A. C., Fathi, F., Mowla, S. J. & Füchtbauer, E.-M. (2019). Isolation of cancer stem cells by selection for miR-302 expressing cells. PeerJ, 7, e6635. https://doi.org/10.7717/peerj.6635

  24. Nasseri, S., Nikkho, B., Parsa, S., Ebadifar, A., Soleimani, F., Rahimi, K., Vahabzadeh, Z., Khadem-Erfan, M. B., Rostamzadeh, J., Baban, B., Banafshi, O., Assadollahi, V., Mirzaie, S. & Fathi, F. (2019). Generation of Fam83h knockout mice by CRISPR/Cas9-mediated gene engineering. Journal of Cellular Biochemistry, 120(7), 11033–11043. https://doi.org/10.1002/jcb.28381

  25. Knudsen, C. H., Ásgrímsdóttir, E. S., Rahimi, K., Gill, K. P., Frandsen, S., Buchholdt, S. H., Chen, M., Kjems, J., Febbraro, F. & Denham, M. (2018). A Modified Monomeric Red Fluorescent Protein Reporter for Assessing CRISPR Activity. Frontiers in Cell and Developmental Biology, 6, 54. https://doi.org/10.3389/fcell.2018.00054

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