Publications of Sagar Khavnekar

Khavnekar, S.; Erdmann, P. S.; Wan, W.: TOMOMAN: A software package for large-scale cryo-electron tomography data preprocessing, community data sharing and collaborative computing. Journal of Applied Crystallography 57, pp. 2010 - 2016 (2024)

Rangan, R.; Feathers, R.; Khavnekar, S.; Lerer, A.; Johnston, J. D.; Kelley, R.; Obr, M.; Kotecha, A.; Zhong, E. D.: CryoDRGN-ET: deep reconstructing generative networks for visualizing dynamic biomolecules inside cells. Nature Methods 21 (8), pp. 1537 - 1545 (2024)

Wan, W.; Khavnekar, S.; Wagner, J.: STOPGAP: an open-source package for template matching, subtomogram alignment and classification. Acta Crystallographica Section D: Structural Biology 80 (5), pp. 336 - 349 (2024)

Khavnekar, S.; Wan, W.; Majumder, P.; Wietrzynski, W.; Erdmann, P. S.; Plitzko, J. M.: Multishot tomography for high-resolution in situ subtomogram averaging. Journal of Structural Biology 215 (1), 107911 (2023)

Hajarolasvadi, N.; Sunkara, V.; Khavnekar, S.; Beck, F.; Brandt, R.; Baum, D.: Volumetric macromolecule identification in cryo-electron tomograms using capsule networks. BMC Bioinformatics 23 (1), 360 (2022)

Koh, A.; Khavnekar, S.; Yang, W.; Karia, D.; Cats, D.; van der Ploeg, R.; Grollios, F.; Raschdorf, O.; Kotecha, A.; Nemecek, D.: Routine collection of high-resolution cryo-EM datasets using 200 KV transmission electron microscope. Journal of Visualized Experiments (181), e63519 (2022)

Khavnekar, S.; Vrbovská, V.; Zaoralová, M.; Kelley, R.; Beck, F.; Klumpe, S.; Kotecha, A.; Plitzko, J.; Erdmann, P. S.: Optimizing Cryo-FIB Lamellas for sub-5Å in situ Structural Biology. bioRxiv: the preprint server for biology (2022)

Erdmann, P. S.; Hou, Z.; Klumpe, S.; Khavnekar, S.; Beck, F.; Wilfling, F.; Plitzko, J. M.; Baumeister, W.: In situ cryo-electron tomography reveals gradient organization of ribosome biogenesis in intact nucleoli. Nature Communications 12 (1), 5364 (2021)

Karia, D.; Koh, A. F.; Yang, W.; Cushing, V. I.; Basanta, B.; Mihaylov, D. B.; Khavnekar, S.; Vyroubal, O.; Malínský, M.; Sháněl, O. et al.; Doležal, V.; Plitzko, J. M.; Yu, L.; Lander, G. C.; Aricescu, A. R.; Greber, B. J.; Kotecha, A.: Sub-3 Å resolution protein structure determination by single-particle cryo-EM at 100 keV. bioRxiv: the preprint server for biology (2024)