Papers for MD9A8 – 2026 edition

It’s 2026 and so it’s time for another edition of "the papers I selected for a module that I teach". Previous selections are here (2025, 2024, 2023, 2022).

The list serves as a snapshot of interesting papers published in the previous 12 months or so. I hope it’s useful to others who are looking for lists of papers to read, or for student selections, or for anything else.

For the module I teach (MD9A8), each student picks a paper from the list and then uses it to write a "grant application" for a research project. They also present the paper to the class and finally we do a grant panel where projects are scored.

I gear the selection towards papers that suit the students' backgrounds and their likely PhD topics. They are papers that caught my eye or were recommended to me. The papers should be recent (so there’s less chance of follow-up work that “scoops” their grant application) and should have the possibility for a Masters student to dream up an extension to the work. Most papers throw up new questions, but some are more fertile for new directions than others. It’s for these reasons that the students pick from a vetted list and don’t get a free choice of paper for the exercise.

Once again, huge thanks to the everyone who responded to my posts with suggestions.

The papers

1. Choi, S.R., Blum, T.B., Giono, M., Roy, B., Vakonakis, I., Schmid, D., Oelgarth, N., Ranganathan, A., Gossert, A.D., Shivashankar, G.V., et al. (2025). Structural basis of microtubule-mediated signal transduction. Cell, S0092867425013078. https://doi.org/10.1016/j.cell.2025.11.011.

2. Curantz, C., Krasovec, G., Horkan, H.R., Ryan, L., Varley, Á., and Frank, U. (2025). An unexpected mode of whole-body regeneration from reaggregated cell suspension in Hydractinia (Cnidaria, Hydrozoa). Preprint at Developmental Biology, https://doi.org/10.1101/2025.01.06.631080.

3. Faust, T.E., Lee, Y.-H., O'Connor, C.D., Boyle, M.A., Gunner, G., Durán-Laforet, V., Ferrari, L.L., Murphy, R.E., Badimon, A., Sakers, K., et al. (2025). Microglia-astrocyte crosstalk regulates synapse remodeling via Wnt signaling. Cell 188, 5212-5230.e21. https://doi.org/10.1016/j.cell.2025.08.023.

4. Foley, S.L., and Johnson, M.E. (2025). Membrane-Associated Self-Assembly for Cellular Decision Making. Preprint at arXiv, https://doi.org/10.48550/arXiv.2505.17290.

5. Gade, V.R., Heinrich, S., Paloni, M., Gómez-García, P.A., Dzanko, A., Oswald, A., Marchand, D., Khawaja, S., Barducci, A., and Weis, K. (2025). Polysomes and mRNA control the biophysical properties of the eukaryotic cytoplasm. Cell Reports 44, 116204. https://doi.org/10.1016/j.celrep.2025.116204.

6. Geißler, K., Kreysing, J.P., Wang, Y., Glushkova, D., Obarska-Kosinska, A., Hoffmann, P.C., Böhm, S., Schmidt, A., Meier-Credo, J., Langer, J.D., et al. (2025). The vault associates with membranes in situ. Preprint at Cell Biology, https://doi.org/10.64898/2025.12.12.693869.

7. Gopaulchan, D., Moore, C., Ali, N., Sukha, D., Florez González, S.L., Herrera Rocha, F.E., Yang, N., Lim, M., Dew, T.P., González Barrios, A.F., et al. (2025). A defined microbial community reproduces attributes of fine flavour chocolate fermentation. Nat Microbiol 10, 2130–2152. https://doi.org/10.1038/s41564-025-02077-6.

8. Guzelsoy, G., Elorza, S.D., Ros, M., Schachtner, L.T., Hayashi, M., Hobson-Gutierrez, S., Rundstrom, P., Brunner, J.S., Pillai, R., Walkowicz, W.E., et al. (2025). Cooperative nutrient scavenging is an evolutionary advantage in cancer. Nature 640, 534–542. https://doi.org/10.1038/s41586-025-08588-w.

9. Haubner, M., Williams, H.M., Hruby, J., Straub, M.S., Guskov, A., Kovalev, K., Drabbels, M., and Lorenz, U.J. (2025). Microsecond Time-Resolved Cryo-EM Based on Jet Vitrification. Preprint at Biophysics, https://doi.org/10.1101/2025.11.21.689681.

10. Hoffmann, D., Agranov, T., Kühl, L., Ermlich, L., Reichman-Fried, M., Simons, B.D., Gov, N.S., and Raz, E. (2025). Corrections in single-cell migration path in vivo are controlled by pulses in polar Rac1 activation. Current Biology 35, 4365-4382.e8. https://doi.org/10.1016/j.cub.2025.07.063.

11. Jame-Chenarboo, F., Reyes, J.N., Twells, N.M., Ng, H.H., Macdonald, D., Hernando, E., and Mahal, L.K. (2025). Screening the human miRNA interactome reveals coordinated up-regulation in melanoma, adding bidirectional regulation to miRNA networks. Sci. Adv. 11, eadr0277. https://doi.org/10.1126/sciadv.adr0277.

12. Jia, B.Z., Tang, X., Rossmann, M.P., Zon, L.I., Engert, F., and Cohen, A.E. (2025). Swimming motions evoke Piezo1-dependent Ca2+ events in vascular endothelial cells of larval zebrafish. Current Biology 35, 6137-6146.e5. https://doi.org/10.1016/j.cub.2025.10.053.

13. Lai, C., Tanaka, S., Harris, T.D., and Lee, A.K. (2023). Volitional activation of remote place representations with a hippocampal brain–machine interface. Science 382, 566–573. https://doi.org/10.1126/science.adh5206.

14. Lee, S., Chakraborty, S., Kim, S., Ali, A., Mitra, K., Zajac, M., Brown, A., Pincus, D., and Krishnan, Y. (2025). Organelles harbour pH gradients. Preprint at Cell Biology, https://doi.org/10.64898/2025.12.12.694065.

15. Liu, Y.-T., Fan, H., Jih, J., Tran, L., Zhang, X., and Zhou, Z.H. (2025). IsoNet2 determines cellular structures at submolecular resolution without averaging. Preprint at Cell Biology, https://doi.org/10.64898/2025.12.09.693325.

16. M'Saad, O., Cairns, A., Gulcicek, J., Kasula, R.K., Liao, J., Kondratiuk, I., Bewersdorf, E.H., Kidd, P., Falahati, H., Gentile, J.E., et al. (2025). All-optical visualization of specific molecules in the ultrastructural context of brain tissue. Nat Biotechnol. https://doi.org/10.1038/s41587-025-02905-4.

17. Mille-Fragoso, L.S., Wang, J.N., Driscoll, C.L., Dai, H., Widatalla, T., Zhang, X., Hie, B.L., and Gao, X.J. (2025). Efficient generation of epitope-targeted de novo antibodies with Germinal. Preprint at Synthetic Biology, https://doi.org/10.1101/2025.09.19.677421.

18. Moore, W.M., Brea, R.J., Knittel, C.H., Wrightsman, E., Hui, B., Lou, J., Ancajas, C.F., Best, M.D., Obara, C.J., Devaraj, N.K., et al. (2025). Leaflet-specific phospholipid imaging using genetically encoded proximity sensors. Nat Chem Biol. https://doi.org/10.1038/s41589-025-02021-z.

19. Mout, L., Moreno-Rodriguez, T., Grillo, G., Nand, A., Keshavarzian, T., Bahl, S., Kang, K., Bootsma, M., Minnee, E., Zhou, S., et al. (2025). Genetic and Epigenetic Reprogramming of Transposable Elements Drives ecDNA-Mediated Metastatic Prostate Cancer. Preprint at Cancer Biology, https://doi.org/10.1101/2025.08.08.668693.

20. Mur, M., Kavcic, A., Jagodic, U., Podlipec, R., and Humar, M. (2025). Two-photon 3D printing of functional microstructures inside living cells. Preprint at arXiv, https://doi.org/10.48550/arXiv.2506.13232.

21. Nordmann, G.C., Balay, S.D., Kapuruge, T.N., Numi, M., Leeb, C., Nimpf, S., Malkemper, E.P., Landler, L., and Keays, D.A. (2025). A global screen for magnetically induced neuronal activity in the pigeon brain. Science, eaea6425. https://doi.org/10.1126/science.aea6425.

22. Rappaport, H.B., Petek-Seoane, N.A., Tyml, T., Mikus, F., Labutti, K., Ani, G., Niblo, J.K., MacVicar, E., Shepherd, R.M., De La Higuera, I., et al. (2025). A geothermal amoeba sets a new upper temperature limit for eukaryotes. Preprint at Microbiology, https://doi.org/10.1101/2025.11.24.690213.

23. Rhoads, S.N., Dong, W., Hsu, C.-H., Mfulama, N.R., Yarlagadda, R., Ragusa, J.V., Ye, M., Henrie, A., Zanellati, M.C., Diering, G.H., et al. (2025). Neurons and astrocytes have distinct organelle signatures and responses to stress. Cell Reports 44, 116280. https://doi.org/10.1016/j.celrep.2025.116280.

24. Rossine, F., Sanchez, C., Eaton, D., Paulsson, J., and Baym, M. (2025). Intracellular competition shapes plasmid population dynamics. Science, eadx0665. https://doi.org/10.1126/science.adx0665.

25. Smith, J.W., Wilburn, D.B., and Belyy, V. (2025). Optogenetic Clustering of Human IRE1 Reveals Differential Regulation of Transcription and mRNA Splice Isoform Abundance by the UPR. Preprint at Cell Biology, https://doi.org/10.1101/2025.07.16.66521.

26. Tischbirek, C.H., Fang, L., Chadly, D.M., Lobbia, S., Aguirre, J.D., Takei, Y., Chen, C.-H., Sternberg, P.W., Lois, C., Elowitz, M.B., et al. (2025). Synaptic MEMOIR: mapping individual synapses of neurons with protein barcodes. Preprint at Neuroscience, https://doi.org/10.1101/2025.11.25.690442.

27. Yang, Z., Yorke, S.K., Knowles, T.P.J., and Buehler, M.J. (2024). Learning the rules of peptide self-assembly through data mining with large language models. Preprint at arXiv, https://doi.org/10.48550/arXiv.2411.05421.

28. Yin, S., Jarosz, D.F., and Ting, A.Y. (2025). Towards CRISPR-based editing of the mitochondrial genome in yeast. Preprint at Genetics, https://doi.org/10.64898/2025.12.09.693232.

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DOI: https://doi.org/10.59350/trqsp-19k22