Computational Microscopist

Computational Microscopist

@RNAcartography

Posts by Collection

datasets

EMPIAR-11830

Large scale (~1800 tilt-series) in situ cryo-ET dataset of Chlamydomonas reinhardtii prepared using cryo-plasmaFIB milling Read more

initiatives

portfolio

publications

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

Published in Nucleic Acids Research, 2017

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Recommended citation: 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.
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Routine Collection of High-Resolution cryo-EM Datasets Using 200 KV Transmission Electron Microscope

Published in JoVE (Journal of Visualized Experiments), 2022

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

Published in bioRxiv, 2024

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Recommended citation: 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.
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Towards community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii

Published in bioRxiv, 2024

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Recommended citation: 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.
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In-cell architecture of the mitochondrial respiratory chain

Published in Science, 2025

One of the very first visualisation of the respiratory chain in its native context. Read more

Recommended citation: 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.
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talks

teaching

Cryo-ET Workflow Training at MPIB

Internal training program, Department of Molecular Structural Biology, MPI of Biochemistry, 2018

Organized and led biweekly and annual workshops on Cryo-ET data acquisition and processing for members of the Baumeister Department, including Master’s students, PhD researchers, postdocs, and project group leaders (2018–2023). Read more

Cryo-ET and Subtomogram Averaging

EMBO practical course, EMBO Course: Advances in Cryo-EM and 3D Image Processing, EMBL Heidelberg, 2022

Instructor at the EMBO Practical Course on Advances in Cryo-Electron Microscopy and 3D Image Processing, teaching theory and practical aspects of Cryo-ET workflows, including alignment, reconstruction, and subtomogram analysis. Read more

Fundamentals of Cryo-ET and Subtomogram Averaging

Graduate course, Human Technopole Graduate School, SEMM course, 2023

Lecture on Fundamentals of Cryo-Electron Tomography and Subtomogram Averaging for the Human Technopole PhD Program, focusing on fundamentals and practical aspects of cellular cryo-ET. Read more

Cryo-ET and Subtomogram Averaging

International course, SPACET 2023 Cryo-EM Practical Course, BIOCEV, 2023

Instructor for hands-on sessions and lectures at the SPACET 2023 Cryo-EM Practical Course, focusing on tilt-series alignment, tomogram reconstruction, and subtomogram averaging. Read more

Image Processing of CryoEM Data – Applications and Future Perspectives

Graduate course, Universidade Federal do Rio de Janeiro, Graduate Program in Microscopy, 2023

Invited lecture for the Graduate Course on Advanced Topics in Light and Electron Microscopy, covering current and future trends in image processing of Cryo-EM data with a focus on integrative workflows and in situ structure determination. Read more

1st Rio School of CryoET and Subtomogram Averaging

International course (in preparation), To be held at Rio School of CryoET, 2025

In preparation: Organisation, coordination, and course design for the inaugural Rio School of CryoET and Subtomogram Averaging, scheduled for Autumn/Winter 2025. The program will introduce practical and theoretical concepts in Cryo-ET and subtomogram averaging to early career researchers across Latin America. Read more

tools

TOMOMAN

TOMOMAN (Tomogram Manager) is an extensible MATLAB-based package developed to reduce the complexity of combining different packages in order to streamline cryo-ET preprocessing and subtomogram averaging workflows. Read more

STOPGAP

STOPGAP is a subtomogram averaging workflow written in MATLAB for performing a number of subtomogram averaging tasks including template matching, high-resolution alignment and averaging, and classification. Read more