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Publications

  1. Rahimi, K., Perrimon, N., et al. (2025). AI-Driven Enhancements in Single-Cell Genomics: A Novel Foundational Model for Improved Data Interpretation, Cell Types Projection and In Vivo Validation in Drosophila.
    Manuscript in preparation.
     

  2. Ahmadi, S., Vali, A., Amiri, S., Rostami, D., Majidi, M., Rahimi, K. (2025). Alterations in Circular RNAs circOprm1 and circSerpini in the Striatum are Associated with Changes in Spatial Working Memory Performance after Morphine Dependence and Withdrawal in Rats.
    Neurochem Res. 50, 20-2025.
    https://doi.org/10.1007/s11064-024-04284-9
     

  3. Rashidi, A., Füchtbauer, E.-M., Vahabzadeh, Z., Soleimani, F., Rahimi, K., Nikkhoo, B., Fakhari, S., Erfan, M. B. K., Azarnezhad, A., Pooladi, A., Soheili, F. & Fathi, F. (2025). CRISPR/Cas9-mediated knockout of DYRK1B in triple-negative breast cancer cells: implications for cell proliferation, apoptosis, and therapeutic sensitivity.
    Biochemical Engineering Journal.
    https://doi.org/10.1016/j.bej.2024.109553
     

  4. Rybiczka-Tešulov, M., Garritsen, O., Venø, M. T., Wieg, L., van Dijk, R., Rahimi, K., Gomes-Duarte, A., de Wit, M., van de Haar, L. L., Michels, L., van Kronenburg, N. C. H., van der Meer, C., Kjems, J., Vangoor, V. R. & Pasterkamp, R. J. (2024). Circular RNAs regulate neuron size and migration of midbrain dopamine neurons during development.
    Nature Communications, 15, 6773.
    https://doi.org/10.1038/s41467-024-51041-1
     

  5. Rahimi, K. (2024). Revealing full-length structure of circRNAs with global and panel adjusted long-read nanopore sequencing. 
    Invitation from Nature Protocols,
    Manuscript in preparation.
     

  6. Sherifi E, Fathi F, Khadem Erfan M B, Soleimani F, Rahimi K, et al. Deletion of the Long Non-coding RNA ANRIL In Addition to the Protein-Coding Genes of the INK4-ARF Locus in the A549 Cell Line: An Existing Phenomenon or a Novel Genetic Alteration?.
    Int J Cancer Manag. 2024;17(1):e151972. 
    https://doi.org/10.5812/ijcm-151972
     

  7. 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
     

  8. 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
     

  9. Zhou, X., Rahimi, K., Kjems, J. & Lin, L. (2023). High-resolution RNA isoform variation analysis by combining the advantages of single-cell RNA and nanopore sequencing.
    Neuroscience Day Conference Abstract :
    Aarhus University, Denmark, June 13, 2023.
    Conference abstract
     

  10. 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
     

  11. 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
     

  12. 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, 2022.08.30.505797.
    https://doi.org/10.1101/2022.08.30.505797
     

  13. 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
     

  14. 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
     

  15. 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
     

  16. 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
     

  17. 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
     

  18. 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
     

  19. 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
     

  20. 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
     

  21. 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
     

  22. 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
     

  23. 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
     

  24. 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
     

  25. 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
     

  26. 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
     

  27. 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
     

  28. 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
     

  29. 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
     

  30. 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    ​

 

Contact Information

77 Avenue Louis Pasteur,
NRB 3rd Floor Perrimon's Lab,
Department of Genetics,

Harvard Medical School,

Harvard University, 

Boston, MA 02115

USA

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©2021 by Karim Rahimi

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