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About

nextPYP is a comprehensive platform for single-particle cryo-EM/ET image analysis developed and maintained by the Bartesaghi Lab at Duke University.

Developers

Jeff Martin

Ye Zhou

Hsuan-Fu Liu

Xiaochen Du

Qinwen Huang

Alberto Bartesaghi

References

nextPYP implements algorithms reported in the following publications:

• 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.

• 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.

Funding

Development of nextPYP is supported by grants from NIGMS (R01-GM141223), NIAID (U54-AI170752), the Chan Zuckerberg Initiative (2021-234602), and Duke University.

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