Methods papers for MD997 – 2020 edition

I run a Masters module called MD997. Over six weeks, students have to write a grant proposal and then assess their peers’ proposals at a mock grant panel. Each student bases their proposal on a paper. They present that paper to the class and then they write their proposal using the paper as a springboard.

I refreshed my paper list this year to consist of solely papers published (or posted on bioRxiv) in 2019. The previous list is here. The criteria for selection are:

  • papers must be methods-based or centred on a core methodology
  • must be in research topic from our faculty (cell bio/biophysics, immuno, microbiology, structure, neuro, stats/ML, chemistry…)

My task was made easier by a Rxivist and Alexis’s list.

The list of papers I selected is below. It’s not meant to be exhaustive, exclusive, or anything… but it may be useful for you to check out, maybe you missed so of these in 2019.

  • Abdelfattah AS, Kawashima T, Singh A, Novak O, Liu H, Shuai Y, Huang Y-C, Campagnola L, Seeman SC, Yu J, Zheng J, Grimm JB, Patel R, Friedrich J, Mensh BD, Paninski L, Macklin JJ, Murphy GJ, Podgorski K, Lin B-J, et al (2019) Bright and photostable chemigenetic indicators for extended in vivo voltage imaging. Science 365: 699–704
  • Anzalone AV, Randolph PB, Davis JR, Sousa AA, Koblan LW, Levy JM, Chen PJ, Wilson C, Newby GA, Raguram A & Liu DR (2019) Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 576: 149–157
  • Athey S, Tibshirani J & Wager S (2019) Generalized random forests. Ann. Stat. 47: 1148–1178
  • Cornell CE, Black RA, Xue M, Litz HE, Ramsay A, Gordon M, Mileant A, Cohen ZR, Williams JA, Lee KK, Drobny GP & Keller SL (2019) Prebiotic amino acids bind to and stabilize prebiotic fatty acid membranes. Proc. Natl. Acad. Sci. 116: 17239–17244
  • Dana H, Sun Y, Mohar B, Hulse BK, Kerlin AM, Hasseman JP, Tsegaye G, Tsang A, Wong A, Patel R, Macklin JJ, Chen Y, Konnerth A, Jayaraman V, Looger LL, Schreiter ER, Svoboda K & Kim DS (2019) High-performance calcium sensors for imaging activity in neuronal populations and microcompartments. Nat. Methods 16: 649–657
  • Fultz NE, Bonmassar G, Setsompop K, Stickgold RA, Rosen BR, Polimeni JR & Lewis LD (2019) Coupled electrophysiological, hemodynamic, and cerebrospinal fluid oscillations in human sleep. Science 366: 628–631
  • Gil AA, Zhao EM, Wilson MZ, Goglia AG, Carrasco-Lopez C, Avalos JL & Toettcher JE (2019) Optogenetic control of protein binding using light-switchable nanobodies Biochemistry Available at: http://biorxiv.org/lookup/doi/10.1101/739201 [Accessed December 23, 2019]
  • Gwosch KC, Pape JK, Balzarotti F, Hoess P, Ellenberg J, Ries J & Hell SW (2019) MINFLUX nanoscopy delivers multicolor nanometer 3D-resolution in (living) cells Biophysics Available at: http://biorxiv.org/lookup/doi/10.1101/734251 [Accessed December 23, 2019]
  • Hafemeister C & Satija R (2019) Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression Genomics Available at: http://biorxiv.org/lookup/doi/10.1101/576827 [Accessed December 23, 2019]
  • Hoffman DP, Shtengel G, Xu CS, Campbell KR, Freeman M, Wang L, Milkie DE, Pasolli HA, Iyer N, Bogovic JA, Stabley DR, Shirinifard A, Pang S, Peale D, Schaefer K, Pomp W, Chang C-L, Lippincott-Schwartz J, Kirchhausen T, Solecki DJ, et al (2019) Correlative three-dimensional super-resolution and block face electron microscopy of whole vitreously frozen cells Cell Biology Available at: http://biorxiv.org/lookup/doi/10.1101/773986 [Accessed December 23, 2019]
  • Homan KA, Gupta N, Kroll KT, Kolesky DB, Skylar-Scott M, Miyoshi T, Mau D, Valerius MT, Ferrante T, Bonventre JV, Lewis JA & Morizane R (2019) Flow-enhanced vascularization and maturation of kidney organoids in vitro. Nat. Methods 16: 255–262
  • Laverty D, Desai R, Uchański T, Masiulis S, Stec WJ, Malinauskas T, Zivanov J, Pardon E, Steyaert J, Miller KW & Aricescu AR (2019) Cryo-EM structure of the human α1β3γ2 GABAA receptor in a lipid bilayer. Nature565: 516–520
  • Lomakin AJ, Cattin CJ, Cuvelier D, Alraies Z, Molina M, Nader G, Srivastava N, Garcia-Arcos JM, Zhitnyak IY, Bhargava A, Driscoll MK, Welf ES, Fiolka R, Petrie RJ, Manel N, Lennon-Duménil AM, Müller DJ & Piel M (2019) The nucleus acts as a ruler tailoring cell responses to spatial constraints Cell Biology Available at: http://biorxiv.org/lookup/doi/10.1101/863514 [Accessed December 23, 2019]
  • Mitchell C, Caroff L, Vigilante A, Solis-Lemus JA, Reyes-Aldasoro CC, de Chaumont F, Dufour A, Dallongeville S, Olivo-Marin J-C & Knight R (2019) Cell Tracking Profiler: a user-driven analysis framework for evaluating 4D live cell imaging data Cell Biology Available at: http://biorxiv.org/lookup/doi/10.1101/859397 [Accessed December 23, 2019]
  • Paul DM, Mantell J, Borucu U, Coombs J, Surridge KJ, Squire J, Verkade P & Dodding MP (2019) In situ cryo-electron tomography reveals filamentous actin within the microtubule lumen Cell Biology Available at: http://biorxiv.org/lookup/doi/10.1101/844043 [Accessed December 23, 2019]
  • Rapisarda C, Cherrak Y, Kooger R, Schmidt V, Pellarin R, Logger L, Cascales E, Pilhofer M, Durand E & Fronzes R (2019) In situ and high‐resolution cryo‐ EM structure of a bacterial type VI secretion system membrane complex. EMBO J. 38: Available at: https://onlinelibrary.wiley.com/doi/abs/10.15252/embj.2018100886 [Accessed December 23, 2019]
  • Schmidli C, Albiez S, Rima L, Righetto R, Mohammed I, Oliva P, Kovacik L, Stahlberg H & Braun T (2019) Microfluidic protein isolation and sample preparation for high-resolution cryo-EM. Proc. Natl. Acad. Sci. 116:15007–15012
  • Silva D-A, Yu S, Ulge UY, Spangler JB, Jude KM, Labão-Almeida C, Ali LR, Quijano-Rubio A, Ruterbusch M, Leung I, Biary T, Crowley SJ, Marcos E, Walkey CD, Weitzner BD, Pardo-Avila F, Castellanos J, Carter L, Stewart L, Riddell SR, et al (2019) De novo design of potent and selective mimics of IL-2 and IL-15. Nature565: 186–191
  • Stephan T, Roesch A, Riedel D & Jakobs S (2019) Live-cell STED nanoscopy of mitochondrial cristae. Sci. Rep. 9: 12419
  • Triclin S, Inoue D, Gaillard J, Htet ZM, De Santis M, Portran D, Derivery E, Aumeier C, Schaedel L, John K, Leterrier C, Reck-Peterson S, Blanchoin L & Thery M (2018) Self-repair protects microtubules from their destruction by molecular motors: Cell Biology Available at: http://biorxiv.org/lookup/doi/10.1101/499020 [Accessed December 23, 2019]
  • Vassilopoulos S, Gibaud S, Jimenez A, Caillol G & Leterrier C (2019) Ultrastructure of the axonal periodic scaffold reveals a braid-like organization of actin rings. Nat. Commun. 10: 5803
  • Zakharov E, Shysheya A, Burkov E & Lempitsky V (2019) Few-Shot Adversarial Learning of Realistic Neural Talking Head Models. ArXiv190508233 Cs Available at: http://arxiv.org/abs/1905.08233 [Accessed December 23, 2019]
  • Zivanov J, Nakane T, Forsberg BO, Kimanius D, Hagen WJ, Lindahl E & Scheres SH (2018) New tools for automated high-resolution cryo-EM structure determination in RELION-3. eLife 7: e42166

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