Another year, another edition of “the papers I selected for a module that I teach”. 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 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.
Once again, huge thanks to the everyone who responded to my posts about this:
I got some great suggestions and really struggled to get the final number down to 25 papers.
The papers
Allier, C., M.C. Schneider, M. Innerberger, L. Heinrich, J.A. Bogovic, and S. Saalfeld. 2024. Decomposing heterogeneous dynamical systems with graph neural networks. doi:10.48550/ARXIV.2407.19160.
Barhoosh, H., A. Dixit, W.G. Cochrane, V. Cavett, R.N. Prince, B.O. Blair, F.R. Ward, K.F. McClure, P.A. Patten, M.G. Paulick, and B.M. Paegel. 2024. Activity-Based DNA-Encoded Library Screening for Selective Inhibitors of Eukaryotic Translation. ACS Cent. Sci. 10:1960–1968. doi:10.1021/acscentsci.4c01218.
Belliveau, N.M., M.J. Footer, A. Platenkamp, H. Kim, T.E. Eustis, and J.A. Theriot. 2024. Galvanin is an electric-field sensor for directed cell migration. doi:10.1101/2024.09.23.614580.
Benzinger, D., and J. Briscoe. 2024. Illuminating morphogen and patterning dynamics with optogenetic control of morphogen production. doi:10.1101/2024.06.11.598403.
Bertocchi, C., J.J. Alegría, S. Vásquez-Sepúlveda, R. Ibanez-Prat, A. Srinivasan, I. Arrano-Valenzuela, B. Castro-Pereira, C. Soto-Montandon, A. Trujillo-Espergel, G.I. Owen, P. Kanchanawong, M. Cerda, G. Motta, R. Zaidel-Bar, and A. Ravasio. 2024. AI-assisted imaging screening reveals mechano-molecular tissue organizers and network of signaling hubs. doi:10.1101/2024.11.14.623670.
Boukacem, N.E., A. Leary, R. Thériault, F. Gottlieb, M. Mani, and P. François. 2024. Waddington landscape for prototype learning in generalized Hopfield networks. Phys. Rev. Research. 6:033098. doi:10.1103/PhysRevResearch.6.033098.
Bracha, S., H.J. Johnson, N.A. Pranckevicius, F. Catto, A.E. Economides, S. Litvinov, K. Hassi, M.T. Rigoli, C. Cheroni, M. Bonfanti, A. Valenti, S. Stucchi, S. Attreya, P.D. Ross, D. Walsh, N. Malachi, H. Livne, R. Eshel, V. Krupalnik, D. Levin, S. Cobb, P. Koumoutsakos, N. Caporale, G. Testa, A. Aguzzi, A.A. Koshy, L. Sheiner, and O. Rechavi. 2024. Engineering Toxoplasma gondii secretion systems for intracellular delivery of multiple large therapeutic proteins to neurons. Nat Microbiol. 9:2051–2072. doi:10.1038/s41564-024-01750-6.
Follain, G., S. Ghimire, J.W. Pylvänäinen, M. Vaitkevičiūtė, D. Wurzinger, C. Guzmán, J.R. Conway, M. Dibus, S. Oikari, K. Rilla, M. Salmi, J. Ivaska, and G. Jacquemet. 2024. Fast label-free live imaging reveals key roles of flow dynamics and CD44-HA interaction in cancer cell arrest on endothelial monolayers. doi:10.1101/2024.09.30.615654.
Haimovich, G., S. Dasgupta, A.G. Ravi, and J.E. Gerst. 2024. Complementation of a human disease phenotype in vitro by intercellular mRNA transfer. doi:10.1101/2024.11.06.622258.
Ham, L., M.A. Coomer, K. Öcal, R. Grima, and M.P.H. Stumpf. 2024. A stochastic vs deterministic perspective on the timing of cellular events. Nat Commun. 15:5286. doi:10.1038/s41467-024-49624-z.
Huang, B., M. Abedi, G. Ahn, B. Coventry, I. Sappington, C. Tang, R. Wang, T. Schlichthaerle, J.Z. Zhang, Y. Wang, I. Goreshnik, C.W. Chiu, A. Chazin-Gray, S. Chan, S. Gerben, A. Murray, S. Wang, J. O’Neill, L. Yi, R. Yeh, A. Misquith, A. Wolf, L.M. Tomasovic, D.I. Piraner, M.J. Duran Gonzalez, N.R. Bennett, P. Venkatesh, M. Ahlrichs, C. Dobbins, W. Yang, X. Wang, D.D. Sahtoe, D. Vafeados, R. Mout, S. Shivaei, L. Cao, L. Carter, L. Stewart, J.B. Spangler, K.T. Roybal, P.J. Greisen, X. Li, G.J.L. Bernardes, C.R. Bertozzi, and D. Baker. 2024. Designed endocytosis-inducing proteins degrade targets and amplify signals. Nature. doi:10.1038/s41586-024-07948-2.
Kang, J., M.E. Schroeder, Y. Lee, C. Kapoor, E. Yu, T.B. Tarr, K. Titterton, M. Zeng, D. Park, E. Niederst, D. Wei, G. Feng, and E.S. Boyden. 2024. Multiplexed expansion revealing for imaging multiprotein nanostructures in healthy and diseased brain. Nat Commun. 15:9722. doi:10.1038/s41467-024-53729-w.
Lacoste, J., M. Haghighi, S. Haider, C. Reno, Z.-Y. Lin, D. Segal, W.W. Qian, X. Xiong, T. Teelucksingh, E. Miglietta, H. Shafqat-Abbasi, P.V. Ryder, R. Senft, B.A. Cimini, R.R. Murray, C. Nyirakanani, T. Hao, G.G. McClain, F.P. Roth, M.A. Calderwood, D.E. Hill, M. Vidal, S.S. Yi, N. Sahni, J. Peng, A.-C. Gingras, S. Singh, A.E. Carpenter, and M. Taipale. 2024. Pervasive mislocalization of pathogenic coding variants underlying human disorders. Cell. 187:6725-6741.e13. doi:10.1016/j.cell.2024.09.003.
Liu, Z., and B.H. Good. 2024. Dynamics of bacterial recombination in the human gut microbiome. PLoS Biol. 22:e3002472. doi:10.1371/journal.pbio.3002472.
Lo, J., K.F. Vaeth, G. Bhardwaj, N. Mukherjee, H.A. Russ, J.K. Moore, and J.M. Taliaferro. 2024. The RNA binding protein HNRNPA2B1 regulates RNA abundance and motor protein activity in neurites. doi:10.1101/2024.08.26.609768.
McNamara, H.M., S.C. Solley, B. Adamson, M.M. Chan, and J.E. Toettcher. 2024. Recording morphogen signals reveals mechanisms underlying gastruloid symmetry breaking. Nat Cell Biol. 26:1832–1844. doi:10.1038/s41556-024-01521-9.
O’Toole, Á., R.A. Neher, N. Ndodo, V. Borges, B. Gannon, J.P. Gomes, N. Groves, D.J. King, D. Maloney, P. Lemey, K. Lewandowski, N. Loman, R. Myers, I.F. Omah, M.A. Suchard, M. Worobey, M. Chand, C. Ihekweazu, D. Ulaeto, I. Adetifa, and A. Rambaut. 2023. APOBEC3 deaminase editing in mpox virus as evidence for sustained human transmission since at least 2016. Science. 382:595–600. doi:10.1126/science.adg8116.
Pacesa, M., L. Nickel, C. Schellhaas, J. Schmidt, E. Pyatova, L. Kissling, P. Barendse, J. Choudhury, S. Kapoor, A. Alcaraz-Serna, Y. Cho, K.H. Ghamary, L. Vinué, B.J. Yachnin, A.M. Wollacott, S. Buckley, A.H. Westphal, S. Lindhoud, S. Georgeon, C.A. Goverde, G.N. Hatzopoulos, P. Gönczy, Y.D. Muller, G. Schwank, D.C. Swarts, A.J. Vecchio, B.L. Schneider, S. Ovchinnikov, and B.E. Correia. 2024. BindCraft: one-shot design of functional protein binders. doi:10.1101/2024.09.30.615802.
Peukes, J., C. Lovatt, C. Leistner, J. Boulanger, D. Morado, M. Fuller, W. Kukulski, F. Zhu, N. Komiyama, J. Briggs, S. Grant, and R. Frank. 2024. The molecular infrastructure of glutamatergic synapses in the mammalian forebrain. doi:10.7554/eLife.100335.1.
Ryu, K.W., T.S. Fung, D.C. Baker, M. Saoi, J. Park, C.A. Febres-Aldana, R.G. Aly, R. Cui, A. Sharma, Y. Fu, O.L. Jones, X. Cai, H.A. Pasolli, J.R. Cross, C.M. Rudin, and C.B. Thompson. 2024. Cellular ATP demand creates metabolically distinct subpopulations of mitochondria. Nature. 635:746–754. doi:10.1038/s41586-024-08146-w.
Sahl, S.J., J. Matthias, K. Inamdar, M. Weber, T.A. Khan, C. Brüser, S. Jakobs, S. Becker, C. Griesinger, J. Broichhagen, and S.W. Hell. 2024. Direct optical measurement of intramolecular distances with angstrom precision. Science. 386:180–187. doi:10.1126/science.adj7368.
Siehler, J., S. Bilekova, P. Chapouton, A. Dema, P. Albanese, S. Tamara, C. Jain, M. Sterr, S.J. Enos, C. Chen, C. Malhotra, A. Villalba, L. Schomann, S. Bhattacharya, J. Feng, M. Akgün Canan, F. Ribaudo, Ansarullah, I. Burtscher, C. Ahlbrecht, O. Plettenburg, T. Kurth, R. Scharfmann, S. Speier, R.A. Scheltema, and H. Lickert. 2024. Inceptor binds to and directs insulin towards lysosomal degradation in β cells. Nat Metab. 6:2374–2390. doi:10.1038/s42255-024-01164-y.
Swanson, K., W. Wu, N.L. Bulaong, J.E. Pak, and J. Zou. 2024. The Virtual Lab: AI Agents Design New SARS-CoV-2 Nanobodies with Experimental Validation. doi:10.1101/2024.11.11.623004.
Thayer, R.C., E.S. Polston, J. Xu, and D.J. Begun. 2024. Regional specialization, polyploidy, and seminal fluid transcripts in the Drosophila female reproductive tract. Proc. Natl. Acad. Sci. U.S.A. 121:e2409850121. doi:10.1073/pnas.2409850121.
Tumminia, S., L. Mezache, T. Wiesner, B. Vianay, M. Théry, M.-J. Papandréou, and C. Leterrier. 2024. Deciphering the nanoscale architecture of presynaptic actin using a micropatterned presynapse-on-glass model. doi:10.1101/2024.09.05.611287.