CV

Research experience

Scientist, Cryo-Electron Tomography, 4D-STEM, and cryo-FIB-SEM, Thermo Fisher Scientific, Eindhoven, The Netherlands, 2023–present
Research Assistant, Department of Molecular Structural Biology & Cryo-EM Technology Group, Max Planck Institute of Biochemistry, Martinsried, Germany, 2018–2023
Research Assistant, Department of Molecular Biology, University of Geneva, Switzerland, 2016–2018
Supported by Swiss Government Excellence Fellowship.
Research Assistant, UM-DAE Centre for Excellence in Basic Sciences, Mumbai, India, 2014–2016
Research Intern, ACTREC, Navi Mumbai, India, 2013–2014

Service and leadership

Reviewer, Springer Nature
Editor, IMPRS-LS Newsletter, Max Planck Institute of Biochemistry, 2018–2020
Start-up Training, Commission for Technology and Innovation (CTI, Switzerland), 2018 (grade 5/6)
Organizer, PhD Retreat, University of Geneva Life Sciences Program, 2018
Organizer, Annual Meeting of Indian Biophysical Society & National Symposium on Frontiers of Biophysics, 2013
Outreach & Engagement: Science outreach for Astronomy (2009–2016);

Publications

You can find complete list of my publications on Google Scholar

Towards community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii

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.

Sub-3 Å resolution protein structure determination by single-particle cryo-EM at 100 keV

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.

An approach for coherent periodogram averaging of tilt-series data for improved contrast transfer function estimation

Sagar Khavnekar, William Wan, "An approach for coherent periodogram averaging of tilt-series data for improved contrast transfer function estimation." FEBS Open Bio, 2025.

In-cell architecture of the mitochondrial respiratory chain

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.

TOMOMAN: a software package for large-scale cryo-electron tomography data preprocessing, community data sharing and collaborative computing

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.

CryoDRGN-ET: deep reconstructing generative networks for visualizing dynamic biomolecules inside cells

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.

STOPGAP: an open-source package for template matching, subtomogram alignment and classification

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.

Multishot tomography for high-resolution in situ subtomogram averaging

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.

Volumetric macromolecule identification in cryo-electron tomograms using capsule networks

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.

Optimizing Cryo-FIB Lamellas for sub-5Å in situ Structural Biology

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.

Routine Collection of High-Resolution cryo-EM Datasets Using 200 KV Transmission Electron Microscope

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.

In situ cryo-electron tomography reveals gradient organization of ribosome biogenesis in intact nucleoli

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.

Conformational dynamics of Peb4 exhibit “mother’s arms” chain model: a molecular dynamics study

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.

Structural insights into dynamics of RecU–HJ complex formation elucidates key role of NTR and stalk region toward formation of reactive state

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.

Time-dependent X-ray diffraction studies on urea/hen egg white lysozyme complexes reveal structural changes that indicate onset of denaturation

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.

Talks

Towards Understanding RNA Biology with Cryo-Electron Tomography: Moving from Breathtaking Renderings to Quantitative, Context-Aware RNA Cartography

October 10, 2025

Seminar at Hubrecht Institute, Utrecht, The Netherlands

Towards Understanding RNA Biology with Cryo-Electron Tomography: Moving from Breathtaking Renderings to Quantitative, Context-Aware RNA Cartography

September 14, 2025

Poster at WE-Heraeus-Seminar: Cryo‐EM on the Move: New Applications and Challenges, Bad Honnef, Germany

What Will It Take to Understand Biology with Cryo-Electron Tomography and Subtomogram Averaging? Moving from Breathtaking Renderings to Quantitative, Context-Aware Visual Proteomics

May 14, 2025

Seminar at Integrated Structural Biology Department, IGBMC, Strasbourg, France

Education

Ph.D. Candidate, Natural Sciences, International Max Planck Research School Life Sciences, Max Planck Institute of Biochemistry & Technical University of Munich (TUM), Germany, 2018–present
M.Sc., Biophysics, University of Mumbai, India, 2012–2014
Master’s thesis with Dr. Madhusoodan Hosur.
B.Sc., Physics, University of Mumbai, India, 2009–2012

Sagar Khavnekar

CV

Research experience

Service and leadership

Publications

Talks

Teaching

Education