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About
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`nextPYP <https://nextpyp.app/>`_ is a comprehensive platform for single-particle cryo-EM/ET image analysis developed and maintained by the `Bartesaghi Lab <http://cryoem.cs.duke.edu>`_ at `Duke University <http://www.duke.edu>`_.

Developers
==========

   | Jeff Martin |jwm| |0000-0002-9773-3256| 

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   | Ye Zhou |yez| |0000-0002-0489-3614| 

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   | Hsuan-Fu Liu |hfl| |0000-0001-9302-7648|

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   | Xiaochen Du |dux| |0000-0001-6228-0907| 

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   | Qinwen Huang |qwh| |0000-0002-7082-5257| 

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   | Alberto Bartesaghi |alberto| |0000-0002-7360-1523|

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      :alt: ORCID profile for 0000-0002-7360-1523

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 <https://www.nature.com/articles/s41592-023-02045-0>`_, 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 <https://openaccess.thecvf.com/content/WACV2022/html/Huang_Weakly_Supervised_Learning_for_Joint_Image_Denoising_and_Protein_Localization_WACV_2022_paper.html>`_, 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 <https://doi.org/10.1007/978-3-031-19803-8_38>`_, 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 <https://doi.org/10.1107/S2059798322005010>`_, 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 <https://doi.org/10.1038/s41467-021-22251-8>`_, Nature Communications 12, 1957.

   - Zhou, Y., Moscovich, A., Bendory, T., Bartesaghi, A., (2019) `Unsupervised particle sorting for high-resolution single-particle cryo-EM <https://doi.org/10.1088/1361-6420/ab5ec8>`_, 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 <https://doi.org/10.1016/j.str.2018.04.004>`_. 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 <https://doi.org/10.1016/j.str.2012.10.016>`_, 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.