You can find my publications on Google Scholar
Sagar Khavnekar, William Wan, "An approach for coherent periodogram averaging of tilt-series data for improved contrast transfer function estimation." FEBS Open Bio, 2025.
Florent Waltz, Ricardo Righetto, Lorenz Lamm, Thalia Salinas-Giegé, Ron Kelley, Xianjun Zhang, Martin Obr, Sagar Khavnekar, Abhay Kotecha, Benjamin Engel, "In-cell architecture of the mitochondrial respiratory chain." Science, 2025.
Ron Kelley*, Sagar Khavnekar*, Ricardo Righetto*, Jessica Heebner*, Martin Obr*, Xianjun Zhang*, Saikat Chakraborty*, Grigory Tagiltsev*, Alicia Michael*, Sofie Dorst*, Florent Waltz, Caitlyn McCafferty, Lorenz Lamm, Simon Zufferey, Philippe Stappen, Hugo Hoek, Wojciech Wietrzynski, Pavol Harar, William Wan, John Briggs, Jürgen Plitzko, Benjamin Engel, Abhay Kotecha, "Towards community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii." bioRxiv, 2024.
Sagar Khavnekar, Philipp Erdmann, William Wan, "TOMOMAN: a software package for large-scale cryo-electron tomography data preprocessing, community data sharing and collaborative computing." Journal of Applied Crystallography, 2024.
Dimple Karia, Adrian Koh, Wen Yang, Victoria Cushing, Benjamin Basanta, Daniel Mihaylov, Sagar Khavnekar, Ondřej Vyroubal, Miloš Malínský, Ondřej Sháněl, Vojtěch Doležal, Juergen Plitzko, Lingbo Yu, Gabriel Lander, A. Aricescu, Basil Greber, Abhay Kotecha, "Sub-3 Å resolution protein structure determination by single-particle cryo-EM at 100 keV." bioRxiv, 2024.
Ramya Rangan, Ryan Feathers, Sagar Khavnekar, Adam Lerer, Jake Johnston, Ron Kelley, Martin Obr, Abhay Kotecha, Ellen Zhong, "CryoDRGN-ET: deep reconstructing generative networks for visualizing dynamic biomolecules inside cells." Nature Methods, 2024.
William Wan, Sagar Khavnekar, Jonathan Wagner, "STOPGAP: an open-source package for template matching, subtomogram alignment and classification." Acta Crystallographica Section D: Structural Biology, 2024.
Sagar Khavnekar, William Wan, Parijat Majumder, Wojciech Wietrzynski, Philipp Erdmann, Juergen Plitzko, "Multishot tomography for high-resolution in situ subtomogram averaging." Journal of Structural Biology, 2023.
Noushin Hajarolasvadi, Vikram Sunkara, Sagar Khavnekar, Florian Beck, Robert Brandt, Daniel Baum, "Volumetric macromolecule identification in cryo-electron tomograms using capsule networks." BMC Bioinformatics, 2022.
Sagar Khavnekar, Veronika Vrbovská, Magda Zaoralová, Ron Kelley, Florian Beck, Sven Klumpe, Abhay Kotecha, Jürgen Plitzko, Philipp Erdmann, "Optimizing Cryo-FIB Lamellas for sub-5Å in situ Structural Biology." bioRxiv, 2022.
Adrian Koh*, Sagar Khavnekar*, Wen Yang, Dimple Karia, Dennis Cats, Rob Ploeg, Fanis Grollios, Oliver Raschdorf, Abhay Kotecha, Daniel Němeček, "Routine Collection of High-Resolution cryo-EM Datasets Using 200 KV Transmission Electron Microscope." JoVE (Journal of Visualized Experiments), 2022.
Philipp Erdmann, Zhen Hou*, Sven Klumpe*, Sagar Khavnekar*, Florian Beck, Florian Wilfling, Jürgen Plitzko, Wolfgang Baumeister, "In situ cryo-electron tomography reveals gradient organization of ribosome biogenesis in intact nucleoli." Nature Communications, 2021.
Sarath Dantu, Sagar Khavnekar, Avinash Kale, "Conformational dynamics of Peb4 exhibit “mother’s arms” chain model: a molecular dynamics study." Journal of Biomolecular Structure and Dynamics, 2017.
Sagar Khavnekar, Sarath Dantu, Svetlana Sedelnikova, Sylvia Ayora, John Rafferty, Avinash Kale, "Structural insights into dynamics of RecU–HJ complex formation elucidates key role of NTR and stalk region toward formation of reactive state." Nucleic Acids Research, 2017.
Tushar Raskar, Sagar Khavnekar, Madhusoodan Hosur, "Time-dependent X-ray diffraction studies on urea/hen egg white lysozyme complexes reveal structural changes that indicate onset of denaturation." Scientific Reports, 2016.
Poster at WE-Heraeus-Seminar: Cryo‐EM on the Move: New Applications and Challenges, Bad Honnef, Germany
Seminar at Integrated Structural Biology Department, IGBMC, Strasbourg, France
Seminar at Institute of Molecular Biology & Biophysics, ETH, Zurich, Switzerland
Seminar at 4D-STEM Steering Group, Thermo Fisher Scientific, Eindhoven, The Netherlands
Talk at PICO 2024, Eighth Conference on Frontiers of Aberration Corrected Electron Microscopy, The Netherlands
Talk at Inaugural Symposium of the Cryo-ET Platform, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
Seminar at CEITEC, Brno, Czech Republic
Seminar at Department of Bioengineering and Therapeutic Sciences, UCSF, San Francisco, USA
Talk at SPACET 2023, BIOCEV, Prague, Czech Republic
Talk at Bioimaging Methods Seminar Series, CSSB, Hamburg, Germany
Seminar at Interdisciplinary Center for Nanostructured Films, FAU Erlangen-Nürnberg, Erlangen, Germany
Seminar at Centre for Computational Biology, Flatiron Institute, New York City, USA
Seminar at New York Structural Biology Center, New York City, USA
Seminar at Research and Technology Seminar Series, Max Planck Institute of Biochemistry, Martinsried, Germany