I'm David Silva Sánchez. A PhD student in Applied Mathematics at Yale University. This is a compilation of software development projects related to cryo-EM where I have collaborated or acted as the leading developer.
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cryo-EM Ensemble Optimization with cryoJAX (Main developer): A physics-guided ensemble optimization method for fitting ensembles of atomic structures to single-particle cryo-EM images. Built with cryoJAX and OpeMM. Preprint coming soon.
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Cryo-EM Heterogeneity Challenge (Main developer): Preprocessing and Analysis pipeline for the Cryo-EM Heterogeneity Challenge. Developed the preprocessing pipeline, and the PCA metric. A preprint describing the challenge and the results can be in bioarxiv.
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cryoJAX (Collaborator): A flexible and differentiable simulator for cryo-EM data from volumes or atomic structures. Generates data compatible with Relion / Cryosparc. Developed the interface for atom-based volume representations, and the interface for reading PDB files and Relion datasets.
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cryoSBI (Collaborator): A simulation-based inference pipeline for estimating the posterior probability of conformational structures given cryo-EM data. Set the basis for the initial design of the API, and collaborated in testing/developing the current API. Results available in our (PNAS article)[https://www.pnas.org/doi/10.1073/pnas.2420158122].
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AnaVox. Adapted the PCA pipeline from the Cryo-EM Challenge for the analysis of volume series obtained by different heterogeneity methods. See our [preprint] for results.
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Observation on Kmeans: Theoretical study on the behaviour of Lloyd K-Means in the high noise, high dimension regime for a simple k=2 GMM Model. A description of the theory and numerical experiments can be found in our manuscript in ArXiv.