References¶

Primary¶

• Liu, HF., Zhou, Y., Huang, Q., Piland, J., Jin, W., Mandel, J., Du, X., Martin, J., Bartesaghi, A. (2023), nextPYP: a comprehensive and scalable platform for characterizing protein variability in-situ using single-particle cryo-electron tomography, Nature Methods, 20:1909–1919.

Method-specific¶

• He, L., Bartesaghi, A. (2026), In situ structure determination of conformationally flexible targets using nextPYP, Structure, in press.

• Liu, HF., Zhou, Y., Huang, Q., Martin, J., Bartesaghi, A. (2025), In situ structure determination of conformationally flexible targets using nextPYP, Nature Protocols, 21:851–871.

• Huang, Q., Zhou, Y., Bartesaghi, A. (2024), MiLoPYP: self-supervised molecular pattern mining and particle localization in situ, Nature Methods, 21:1863–1872.

• Jin, W., Zhou, Y., Bartesaghi, A. (2024), Accurate size-based protein localization from cryo-ET tomograms, Journal of Structural Biology: X, 10:100104.

• Huang, Q., Zhou, Y., Liu, HF., Bartesaghi, A. (2023) Joint micrograph denoising and protein localization in cryo-electron microscopy, Biological Imaging, 2024;4:e4.

• Huang, Q., Zhou, Y., Liu, HF., Bartesaghi, A. (2022) Weakly Supervised Learning for Joint Image Denoising and Protein Localization in Cryo-Electron Microscopy, IEEE/CVF Winter Conference on Applications of Computer Vision (WACV), pp. 3246-3255.

• Huang, Q., Zhou, Y., Liu, HF., Bartesaghi, A. (2022) Accurate Detection of Proteins in Cryo-Electron Tomograms from Sparse Labels, European Conference on Computer Vision (ECCV) 13681, pp. 644-660.

• Liu, HF., Zhou, Y., Bartesaghi, A. (2022) High-resolution structure determination using high-throughput electron cryo-tomography, Acta Crystallographica Section D: Structural Biology 78 (7), pp. 817-824.

• Bouvette, J., Liu, HF., Du, X., Zhou, Y., Sikkema, AP., da Fonseca Rezende e Mello, J., Klemm, BP., Huang, R., Schaaper, RM., Borgnia, MJ., Bartesaghi. A., (2021) Beam image-shift accelerated data acquisition for near-atomic resolution single-particle cryo-electron tomography, Nature Communications 12, 1957.

• Zhou, Y., Moscovich, A., Bendory, T., Bartesaghi, A., (2019) Unsupervised particle sorting for high-resolution single-particle cryo-EM, Inverse Problems 36, 044002.

• Bartesaghi, A., Aguerrebere, C., Falconieri, V., Banerjee, S., Earl, L. A., Zhu, X., … & Subramaniam, S. (2018). Atomic resolution cryo-EM structure of β-galactosidase. Structure, 26(6), pp. 848-856.

• Bartesaghi, A., Lecumberry, F., Sapiro, G., Subramaniam, S., (2012). Protein secondary structure determination by constrained single-particle cryo-electron tomography, Structure, 20(12), pp. 2003-13.