Methods papers for MD997 – 2021 Edition

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It is an annual event on quantixed to post the papers I have selected for MD997 Frontier Techniques and Research Skills in Biomedicine. Previous selections are grouped here.

The deal is that 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!

This selection is biased towards recent methods-focussed papers that also suit the students’ backgrounds and their likely PhD topics.

This year’s selection

  1. Benedetti, Lorena, Jonathan S Marvin, Hanieh Falahati, Andres Guillén-Samander, Loren L Looger, and Pietro De Camilli. ‘Optimized Vivid-Derived Magnets Photodimerizers for Subcellular Optogenetics in Mammalian Cells’. ELife 9 (11 November 2020): e63230. https://doi.org/10.7554/eLife.63230.
  2. Bhave, Madhura, Rosa E. Mino, Xinxin Wang, Jeon Lee, Heather M. Grossman, Ashley M. Lakoduk, Gaudenz Danuser, Sandra L. Schmid, and Marcel Mettlen. ‘Functional Characterization of 67 Endocytic Accessory Proteins Using Multiparametric Quantitative Analysis of CCP Dynamics’. Proceedings of the National Academy of Sciences117, no. 50 (15 December 2020): 31591–602. https://doi.org/10.1073/pnas.2020346117.
  3. Chamier, Lucas von, Romain F. Laine, Johanna Jukkala, Christoph Spahn, Daniel Krentzel, Elias Nehme, Martina Lerche, et al. ‘ZeroCostDL4Mic: An Open Platform to Use Deep-Learning in Microscopy’. BioRxiv, 20 March 2020. https://doi.org/10.1101/2020.03.20.000133.
  4. Cho, Kelvin F., Tess C. Branon, Sanjana Rajeev, Tanya Svinkina, Namrata D. Udeshi, Themis Thoudam, Chulhwan Kwak, et al. ‘Split-TurboID Enables Contact-Dependent Proximity Labeling in Cells’. Proceedings of the National Academy of Sciences 117, no. 22 (2 June 2020): 12143–54. https://doi.org/10.1073/pnas.1919528117.
  5. Coté, Allison, Chris Coté, Sareh Bayatpour, Heather L. Drexler, Katherine A. Alexander, Fei Chen, Asmamaw T. Wassie, et al. ‘The Spatial Distributions of Pre-MRNAs Suggest Post-Transcriptional Splicing of Specific Introns within Endogenous Genes’. BioRxiv, 7 April 2020. https://doi.org/10.1101/2020.04.06.028092.
  6. Demichev, Vadim, Christoph B. Messner, Spyros I. Vernardis, Kathryn S. Lilley, and Markus Ralser. ‘DIA-NN: Neural Networks and Interference Correction Enable Deep Proteome Coverage in High Throughput’. Nature Methods 17, no. 1 (January 2020): 41–44. https://doi.org/10.1038/s41592-019-0638-x.
  7. Dunkelmann, Daniel L., Julian C. W. Willis, Adam T. Beattie, and Jason W. Chin. ‘Engineered Triply Orthogonal Pyrrolysyl–TRNA Synthetase/TRNA Pairs Enable the Genetic Encoding of Three Distinct Non-Canonical Amino Acids’. Nature Chemistry 12, no. 6 (June 2020): 535–44. https://doi.org/10.1038/s41557-020-0472-x.
  8. Fazal, Furqan M., Shuo Han, Kevin R. Parker, Pornchai Kaewsapsak, Jin Xu, Alistair N. Boettiger, Howard Y. Chang, and Alice Y. Ting. ‘Atlas of Subcellular RNA Localization Revealed by APEX-Seq’. Cell 178, no. 2 (July 2019): 473-490.e26. https://doi.org/10.1016/j.cell.2019.05.027.
  9. Geertsema, H. J., G. Aimola, V. Fabricius, J. P. Fuerste, B. B. Kaufer, and H. Ewers. ‘Left-Handed DNA-PAINT for Improved Super-Resolution Imaging in the Nucleus’. Nature Biotechnology, 4 January 2021. https://doi.org/10.1038/s41587-020-00753-y.
  10. Hoffman, David P., Gleb Shtengel, C. Shan Xu, Kirby R. Campbell, Melanie Freeman, Lei Wang, Daniel E. Milkie, et al. ‘Correlative Three-Dimensional Super-Resolution and Block-Face Electron Microscopy of Whole Vitreously Frozen Cells’. Science 367, no. 6475 (17 January 2020): eaaz5357. https://doi.org/10.1126/science.aaz5357.
  11. Imachi, Hiroyuki, Masaru K. Nobu, Nozomi Nakahara, Yuki Morono, Miyuki Ogawara, Yoshihiro Takaki, Yoshinori Takano, et al. ‘Isolation of an Archaeon at the Prokaryote–Eukaryote Interface’. Nature 577, no. 7791 (23 January 2020): 519–25. https://doi.org/10.1038/s41586-019-1916-6.
  12. Langan, Robert A., Scott E. Boyken, Andrew H. Ng, Jennifer A. Samson, Galen Dods, Alexandra M. Westbrook, Taylor H. Nguyen, et al. ‘De Novo Design of Bioactive Protein Switches’. Nature 572, no. 7768 (August 2019): 205–10. https://doi.org/10.1038/s41586-019-1432-8.
  13. Li, Jia Hui, Paula Santos-Otte, Braedyn Au, Jakob Rentsch, Stephan Block, and Helge Ewers. ‘Directed Manipulation of Membrane Proteins by Fluorescent Magnetic Nanoparticles’. Nature Communications 11, no. 1 (December 2020): 4259. https://doi.org/10.1038/s41467-020-18087-3.
  14. Li, Jiefu, Shuo Han, Hongjie Li, Namrata D. Udeshi, Tanya Svinkina, D.R. Mani, Chuanyun Xu, et al. ‘Cell-Surface Proteomic Profiling in the Fly Brain Uncovers Wiring Regulators’. Cell 180, no. 2 (January 2020): 373-386.e15. https://doi.org/10.1016/j.cell.2019.12.029.
  15. Müller, Andreas, Deborah Schmidt, C. Shan Xu, Song Pang, Joyson Verner D’Costa, Susanne Kretschmar, Carla Münster, et al. ‘3D FIB-SEM Reconstruction of Microtubule–Organelle Interaction in Whole Primary Mouse β Cells’. Journal of Cell Biology 220, no. 2 (1 February 2021): e202010039. https://doi.org/10.1083/jcb.202010039.
  16. Payne, Andrew C., Zachary D. Chiang, Paul L. Reginato, Sarah M. Mangiameli, Evan M. Murray, Chun-Chen Yao, Styliani Markoulaki, et al. ‘In Situ Genome Sequencing Resolves DNA Sequence and Structure in Intact Biological Samples’. Science (New York, N.Y.), 31 December 2020. https://doi.org/10.1126/science.aay3446.
  17. Senior, Andrew W., Richard Evans, John Jumper, James Kirkpatrick, Laurent Sifre, Tim Green, Chongli Qin, et al. ‘Improved Protein Structure Prediction Using Potentials from Deep Learning’. Nature 577, no. 7792 (30 January 2020): 706–10. https://doi.org/10.1038/s41586-019-1923-7.
  18. Stringer, Carsen, Tim Wang, Michalis Michaelos, and Marius Pachitariu. ‘Cellpose: A Generalist Algorithm for Cellular Segmentation’. Nature Methods, 14 December 2020. https://doi.org/10.1038/s41592-020-01018-x.
  19. Sun, De-en, Xinqi Fan, Yujie Shi, Hao Zhang, Zhimin Huang, Bo Cheng, Qi Tang, et al. ‘Click-ExM Enables Expansion Microscopy for All Biomolecules’. Nature Methods, 7 December 2020. https://doi.org/10.1038/s41592-020-01005-2.
  20. Vakirlis, Nikolaos, Anne-Ruxandra Carvunis, and Aoife McLysaght. ‘Synteny-Based Analyses Indicate That Sequence Divergence Is Not the Main Source of Orphan Genes’. ELife 9 (18 February 2020): e53500. https://doi.org/10.7554/eLife.53500.

This year I am posting the list after the students made their picks. There are more papers than students and the following papers were picked: 1, 4, 5, 9, 12, 13, 14, 18, 19, 20.

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