Papers for MD9A8 – 2024 edition

It is time for my annual post of the papers I selected for a module that I teach (MD9A8, the module formerly known as MD997). Previous selections are grouped here or here.

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

For this module, 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!

The selection is biased towards papers that suit the students’ interdisciplinary backgrounds and their likely PhD topics. They are papers that caught my eye or were recommended to me. Thanks to the people who responded to my post about this:

I got some great recommendations. I have to check that they are suitable for the students on the course, but most of the ones people suggested made the final cut. 

Here is this year’s list:

1. K. H. Kjær et al., ‘A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA’, Nature, vol. 612, no. 7939, pp. 283–291, Dec. 2022, doi: 10.1038/s41586-022-05453-y.
2. S. Bottone et al., ‘A fluorogenic chemically induced dimerization technology for controlling, imaging and sensing protein proximity’, Nat Methods, vol. 20, no. 10, pp. 1553–1562, Oct. 2023, doi: 10.1038/s41592-023-01988-8.
3. I. Justice and J. P. Saenz, ‘A tuneable minimal cell membrane reveals that two lipids suffice for life’, bioRxiv, Oct. 2023, doi: 10.1101/2023.10.24.563757.
4. A. Sciortino et al., ‘Active membrane deformations of a minimal synthetic cell’, bioRxiv, Dec. 2023, doi: 10.1101/2023.12.18.571643.
5. S. C. M. Reinhardt et al., ‘Ångström-resolution fluorescence microscopy’, Nature, vol. 617, no. 7962, pp. 711–716, May 2023, doi: 10.1038/s41586-023-05925-9.
6. D. Sun et al., ‘Assembly of tight junction belts by surface condensation and actin elongation’, bioRxiv, Jun. 2023, doi: 10.1101/2023.06.24.546380.
7. E. A. Francis and P. Rangamani, ‘Computational modeling establishes mechanotransduction as a potent entrainment cue for the mammalian circadian clock’, bioRxiv, Oct. 2023, doi: 10.1101/2023.10.09.561563.
8. S. V. Torres et al., ‘De novo design of high-affinity binders of bioactive helical peptides’, Nature, Dec. 2023, doi: 10.1038/s41586-023-06953-1.
9. J. P. Schessner, V. Albrecht, A. K. Davies, P. Sinitcyn, and G. H. H. Borner, ‘Deep and fast label-free Dynamic Organellar Mapping’, Nat Commun, vol. 14, no. 1, p. 5252, Aug. 2023, doi: 10.1038/s41467-023-41000-7.
10. S. Lövestam et al., ‘Disease-specific tau filaments assemble via polymorphic intermediates’, Nature, Nov. 2023, doi: 10.1038/s41586-023-06788-w.
11. W. Qin et al., ‘Dynamic mapping of proteome trafficking within and between living cells by TransitID’, Cell, vol. 186, no. 15, pp. 3307-3324.e30, Jul. 2023, doi: 10.1016/j.cell.2023.05.044.
12. G. Ahn et al., ‘Elucidating the cellular determinants of targeted membrane protein degradation by lysosome-targeting chimeras’, Science, vol. 382, no. 6668, p. eadf6249, Oct. 2023, doi: 10.1126/science.adf6249.
13. Á. Rodríguez Del Río et al., ‘Functional and evolutionary significance of unknown genes from uncultivated taxa’, Nature, Dec. 2023, doi: 10.1038/s41586-023-06955-z.
14. L. Piot et al., ‘GluD1 binds GABA and controls inhibitory plasticity’, Science, vol. 382, no. 6677, pp. 1389–1394, Dec. 2023, doi: 10.1126/science.adf3406.
15. M. El Maï et al., ‘Gut-specific telomerase expression counteracts systemic aging in telomerase-deficient zebrafish’, Nat Aging, vol. 3, no. 5, pp. 567–584, May 2023, doi: 10.1038/s43587-023-00401-5.
16. R. F. Laine et al., ‘High-fidelity 3D live-cell nanoscopy through data-driven enhanced super-resolution radial fluctuation’, Nat Methods, vol. 20, no. 12, pp. 1949–1956, Dec. 2023, doi: 10.1038/s41592-023-02057-w.
17. A. Madani et al., ‘Large language models generate functional protein sequences across diverse families’, Nat Biotechnol, vol. 41, no. 8, pp. 1099–1106, Aug. 2023, doi: 10.1038/s41587-022-01618-2.
18. B. Meadowcroft, I. Palaia, A.-K. Pfitzner, A. Roux, B. Baum, and A. Šarić, ‘Mechanochemical Rules for Shape-Shifting Filaments that Remodel Membranes’, Phys. Rev. Lett., vol. 129, no. 26, p. 268101, Dec. 2022, doi: 10.1103/PhysRevLett.129.268101.
19. L. Otsuki, S. Plattner, Y. Taniguchi-Sugiura, and E. Tanaka, ‘Molecular basis for positional memory and its reprogrammability in limb regeneration’, bioRxiv, Oct. 2023, doi: 10.1101/2023.10.27.564423.
20. V. Girish et al., ‘Oncogene-like addiction to aneuploidy in human cancers’, Science, vol. 381, no. 6660, p. eadg4521, Aug. 2023, doi: 10.1126/science.adg4521.
21. T. Lebek, M. Malaguti, A. Elfick, and S. Lowell, ‘PUFFFIN: A novel, ultra-bright, customisable, single-plasmid system for labelling cell neighbourhoods’, bioRxiv, Sep. 2023, doi: 10.1101/2023.09.06.556381.
22. E. M. Unterauer et al., ‘Spatial proteomics in neurons at single-protein resolution’, bioRxiv, May 2023, doi: 10.1101/2023.05.17.541210.
23. D. D. Nguyen et al., ‘The Interplay between Mutagenesis and Extrachromosomal DNA Shapes Urothelial Cancer Evolution’, bioRxiv, May 2023, doi: 10.1101/2023.05.07.538753.
24. D. Kirschenbaum et al., ‘Time-resolved single-cell transcriptomics defines immune trajectories in glioblastoma’, Cell, p. S009286742301317X, Dec. 2023, doi: 10.1016/j.cell.2023.11.032.
25. J. O. Wirth, E.-M. Schentarra, L. Scheiderer, V. Macarrón-Palacios, M. Tarnawski, and S. W. Hell, ‘Uncovering kinesin dynamics in neurites with MINFLUX’, bioRxiv, Dec. 2023, doi: 10.1101/2023.12.15.571866.
26. F. Schueder et al., ‘Unraveling cellular complexity with unlimited multiplexed super-resolution imaging’, bioRxiv, May 2023, doi: 10.1101/2023.05.17.541061.
27. A. Patel et al., ‘Using CombiCells, a platform for titration and combinatorial display of cell surface ligands, to study T-cell antigen sensitivity modulation by accessory receptors’, EMBO J, Dec. 2023, doi: 10.1038/s44318-023-00012-1.