Papers for MD9A8 – 2022 edition

It is an annual event on quantixed to post the papers I have selected for what is now called MD9A8 (the module formerly known as MD997 Frontier Techniques and Research Skills in Biomedicine). Previous selections are grouped 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.

The papers

  1. Aguilera-Castrejon, Alejandro, Bernardo Oldak, Tom Shani, Nadir Ghanem, Chen Itzkovich, Sharon Slomovich, Shadi Tarazi, et al. ‘Ex Utero Mouse Embryogenesis from Pre-Gastrulation to Late Organogenesis’. Nature 593, no. 7857 (6 May 2021): 119–24. https://doi.org/10.1038/s41586-021-03416-3.
  2. Alfaro, Javier Antonio, Peggy Bohländer, Mingjie Dai, Mike Filius, Cecil J. Howard, Xander F. van Kooten, Shilo Ohayon, et al. ‘The Emerging Landscape of Single-Molecule Protein Sequencing Technologies’. Nature Methods 18, no. 6 (June 2021): 604–17. https://doi.org/10.1038/s41592-021-01143-1.
  3. Ben-Sasson, Ariel J., Joseph L. Watson, William Sheffler, Matthew Camp Johnson, Alice Bittleston, Logeshwaran Somasundaram, Justin Decarreau, et al. ‘Design of Biologically Active Binary Protein 2D Materials’. Nature 589, no. 7842 (21 January 2021): 468–73. https://doi.org/10.1038/s41586-020-03120-8.
  4. Deo, Claire, Ahmed S. Abdelfattah, Hersh K. Bhargava, Adam J. Berro, Natalie Falco, Helen Farrants, Benjamien Moeyaert, Mariam Chupanova, Luke D. Lavis, and Eric R. Schreiter. ‘The HaloTag as a General Scaffold for Far-Red Tunable Chemigenetic Indicators’. Nature Chemical Biology 17, no. 6 (June 2021): 718–23. https://doi.org/10.1038/s41589-021-00775-w.
  5. Eelderink-Chen, Zheng, Jasper Bosman, Francesca Sartor, Antony N. Dodd, Ákos T. Kovács, and Martha Merrow. ‘A Circadian Clock in a Nonphotosynthetic Prokaryote’. Science Advances 7, no. 2 (6 January 2021): eabe2086. https://doi.org/10.1126/sciadv.abe2086.
  6. Funk, Luke, Kuan-Chung Su, David Feldman, Avtar Singh, Brittania Moodie, Paul C. Blainey, and Iain M. Cheeseman. ‘The Phenotypic Landscape of Essential Human Genes’. Preprint. Cell Biology, 28 November 2021. https://doi.org/10.1101/2021.11.28.470116.
  7. Garcia-Beltran, Wilfredo F., Kerri J. St. Denis, Angelique Hoelzemer, Evan C. Lam, Adam D. Nitido, Maegan L. Sheehan, Cristhian Berrios, et al. ‘MRNA-Based COVID-19 Vaccine Boosters Induce Neutralizing Immunity against SARS-CoV-2 Omicron Variant’. Preprint. Infectious Diseases (except HIV/AIDS), 14 December 2021. https://doi.org/10.1101/2021.12.14.21267755.
  8. Go, Christopher D., James D. R. Knight, Archita Rajasekharan, Bhavisha Rathod, Geoffrey G. Hesketh, Kento T. Abe, Ji-Young Youn, et al. ‘A Proximity-Dependent Biotinylation Map of a Human Cell’. Nature 595, no. 7865 (1 July 2021): 120–24. https://doi.org/10.1038/s41586-021-03592-2.
  9. González-Rodríguez, Patricia, Enrico Zampese, Kristen A. Stout, Jaime N. Guzman, Ema Ilijic, Ben Yang, Tatiana Tkatch, et al. ‘Disruption of Mitochondrial Complex I Induces Progressive Parkinsonism’. Nature 599, no. 7886 (25 November 2021): 650–56. https://doi.org/10.1038/s41586-021-04059-0.
  10. Le, Anh Hoang, Tamas Yelland, Nikki R. Paul, Loic Fort, Savvas Nikolaou, Shehab Ismail, and Laura M. Machesky. ‘CYRI-A Limits Invasive Migration through Macropinosome Formation and Integrin Uptake Regulation’. Journal of Cell Biology 220, no. 9 (6 September 2021): e202012114. https://doi.org/10.1083/jcb.202012114.
  11. Liu, Yun-Tao, Heng Zhang, Hui Wang, Chang-Lu Tao, Guo-Qiang Bi, and Z. Hong Zhou. ‘Isotropic Reconstruction of Electron Tomograms with Deep Learning’. Preprint. Cell Biology, 19 July 2021. https://doi.org/10.1101/2021.07.17.452128.
  12. Meiring, Joyce C. M., Ilya Grigoriev, Wilco Nijenhuis, Lukas C. Kapitein, and Anna Akhmanova. ‘Opto-Katanin: An Optogenetic Tool for Localized Microtubule Disassembly’. Preprint. Cell Biology, 23 December 2021. https://doi.org/10.1101/2021.12.22.473806.
  13. Melani, Riccardo, and Nicolas X. Tritsch. ‘Inhibitory Co-Transmission from Midbrain Dopamine Neurons Relies on Presynaptic GABA Uptake’. Preprint. Neuroscience, 26 November 2021. https://doi.org/10.1101/2021.11.26.470142.
  14. Moore, Andrew S., Stephen M. Coscia, Cory L. Simpson, Fabian E. Ortega, Eric C. Wait, John M. Heddleston, Jeffrey J. Nirschl, et al. ‘Actin Cables and Comet Tails Organize Mitochondrial Networks in Mitosis’. Nature 591, no. 7851 (25 March 2021): 659–64. https://doi.org/10.1038/s41586-021-03309-5.
  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. Oren, Yaara, Michael Tsabar, Michael S. Cuoco, Liat Amir-Zilberstein, Heidie F. Cabanos, Jan-Christian Hütter, Bomiao Hu, et al. ‘Cycling Cancer Persister Cells Arise from Lineages with Distinct Programs’. Nature 596, no. 7873 (26 August 2021): 576–82. https://doi.org/10.1038/s41586-021-03796-6.
  17. Özugur, Suzan, Myra N. Chávez, Rosario Sanchez-Gonzalez, Lars Kunz, Jörg Nickelsen, and Hans Straka. ‘Green Oxygen Power Plants in the Brain Rescue Neuronal Activity’. IScience 24, no. 10 (October 2021): 103158. https://doi.org/10.1016/j.isci.2021.103158.
  18. Pulido, Camila, and Timothy A. Ryan. ‘Synaptic Vesicle Pools Are a Major Hidden Resting Metabolic Burden of Nerve Terminals’. Science Advances 7, no. 49 (3 December 2021): eabi9027. https://doi.org/10.1126/sciadv.abi9027.
  19. Qiao, Chang, Di Li, Yuting Guo, Chong Liu, Tao Jiang, Qionghai Dai, and Dong Li. ‘Evaluation and Development of Deep Neural Networks for Image Super-Resolution in Optical Microscopy’. Nature Methods 18, no. 2 (February 2021): 194–202. https://doi.org/10.1038/s41592-020-01048-5.
  20. Rosenberg, Matthew, Tony Zhang, Pietro Perona, and Markus Meister. ‘Mice in a Labyrinth Show Rapid Learning, Sudden Insight, and Efficient Exploration’. ELife 10 (1 July 2021): e66175. https://doi.org/10.7554/eLife.66175.
  21. Specht, Harrison, Edward Emmott, Aleksandra A. Petelski, R. Gray Huffman, David H. Perlman, Marco Serra, Peter Kharchenko, Antonius Koller, and Nikolai Slavov. ‘Single-Cell Proteomic and Transcriptomic Analysis of Macrophage Heterogeneity Using SCoPE2’. Genome Biology 22, no. 1 (December 2021): 50. https://doi.org/10.1186/s13059-021-02267-5.
  22. Stapornwongkul, Kristina S., Marc de Gennes, Luca Cocconi, Guillaume Salbreux, and Jean-Paul Vincent. ‘Patterning and Growth Control in Vivo by an Engineered GFP Gradient’. Science 370, no. 6514 (16 October 2020): 321–27. https://doi.org/10.1126/science.abb8205.
  23. Szórádi, Tamás, Tong Shu, Gururaj R. Kidiyoor, Ying Xie, Nora L. Herzog, Andrew Bazley, Martina Bonucci, et al. ‘NucGEMs Probe the Biophysical Properties of the Nucleoplasm’. Preprint. Biophysics, 20 November 2021. https://doi.org/10.1101/2021.11.18.469159.
  24. Tunyasuvunakool, Kathryn, Jonas Adler, Zachary Wu, Tim Green, Michal Zielinski, Augustin Žídek, Alex Bridgland, et al. ‘Highly Accurate Protein Structure Prediction for the Human Proteome’. Nature 596, no. 7873 (26 August 2021): 590–96. https://doi.org/10.1038/s41586-021-03828-1.
  25. Wu, Zonghan, Shirui Pan, Fengwen Chen, Guodong Long, Chengqi Zhang, and Philip S. Yu. ‘A Comprehensive Survey on Graph Neural Networks’. IEEE Transactions on Neural Networks and Learning Systems 32, no. 1 (January 2021): 4–24. https://doi.org/10.1109/TNNLS.2020.2978386.
  26. Xu, C. Shan, Song Pang, Gleb Shtengel, Andreas Müller, Alex T. Ritter, Huxley K. Hoffman, Shin-ya Takemura, et al. ‘An Open-Access Volume Electron Microscopy Atlas of Whole Cells and Tissues’. Nature 599, no. 7883 (4 November 2021): 147–51. https://doi.org/10.1038/s41586-021-03992-4.
  27. Zheng, Pengli, Christopher J. Obara, Ewa Szczesna, Jonathon Nixon-Abell, Kishore K. Mahalingan, Antonina Roll-Mecak, Jennifer Lippincott-Schwartz, and Craig Blackstone. ‘ER Proteins Decipher the Tubulin Code to Regulate Organelle Distribution’. Nature, 15 December 2021. https://doi.org/10.1038/s41586-021-04204-9.

Student selections

The students selected papers 2,3,7,9,12,13,14,16,17,20,21,27

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