tbepler

@tbepler1

Scientist and Group Leader of the Simons Machine Learning Center . Opinions are my own.

Joined October 2018
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  1. Retweeted
    6 Dec 2021

    Here, led by , , & , we present Ptolemy, open-source software for automated cryoEM collection. Squares and holes are automatically identified and ranked based on machine learning and computer vision algorithms that generalizes well to new data.

    9 replies 43 retweets 151 likes
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  2. 29 Sep 2021

    We've got two new positions open in SMLC ! We're looking for a ML engineer () to help build ML software libraries for cryoEM and a postdoc () who wants to develop new cryoEM/ET ML methods!

    5 retweets 13 likes
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  3. Retweeted
    29 Jun 2021

    Proteins are not static bricks! Feasibility study to infer a continuous distribution of all states using an end-to-end model from Cryo-EM images to atom coordinates: . , , , , , ,

    9 replies 184 retweets 681 likes
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  4. Retweeted
    16 Jun 2021

    Bepler & Berger consider how protein language models can be enriched with prior biological knowledge & introduce an approach for encoding structural knowledge into the learned representations, improving downstream function prediction.

    10 retweets 18 likes
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  5. 16 Jun 2021

    Code and links to download the pre-trained models are at

    1 like
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  6. 16 Jun 2021

    Happy to announce a new synthesis paper out with on protein language modeling and sequence embedding!

    1 reply 2 likes
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  7. Retweeted
    20 Apr 2021

    A profile of our ❄️🐉 collaboration between Solve is a little strong 😅 but proud to contribute to a truly interdisciplinary problem with and

    Protein structures on the left and a woman smiling on the right
    Grad student reached across departmental lines to solve a long-standing problem in electron microscopy. Co-advised by and , she helped devise software to reconstruct molecules in motion. Article by :
    2 replies 13 retweets 102 likes
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  8. Retweeted
    11 Mar 2021
    Replying to

    Speaking of documentation, after I asked about it opened the GitHub repo's wiki for contributions. I started creating a page for each command, but dropped the ball (too busy these days). My idea is to gather all doc in one place. See for details.

    1 retweet 4 likes
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  9. Retweeted
    8 Feb 2021

    We are working on scheduling over 60 (!!) Topaz workshops now around the world. Thank you all for the incredible amount of interest! We truly believe that Topaz will optimize your single particle cryoEM workflows, leading to more accurate and complete biological insights.

    We are offering a 2-hour hands-on remote Topaz workshop for your institution to show best particle picking practices. Topaz picks more particles resulting in higher resolution, better classification, and more complete Euler angle distributions. Email us to schedule a workshop!
    3 replies 4 retweets 44 likes
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  10. 4 Feb 2021

    Amazing work by ! It was great working with Ellen, , and on this project!

    CryoDRGN: a deep neural network based approach for heterogeneous single particle cryo-EM reconstruction
    5 likes
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  11. Retweeted
    4 Feb 2021

    CryoDRGN: a deep neural network based approach for heterogeneous single particle cryo-EM reconstruction

    2 replies 41 retweets 156 likes
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  12. Retweeted
    4 Feb 2021

    Our cryoDRGN ❄️🐉 paper is out! A deep generative model for reconstruction and analysis of protein structures from cryo-EM images, including discovery of new conformations and visualizing continuous dynamics. 1/

    CryoDRGN: a deep neural network based approach for heterogeneous single particle cryo-EM reconstruction
    6 replies 87 retweets 387 likes
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  13. Retweeted
    4 Feb 2021

    O so excited our paper is out today. Amazing work in collaboration with , , and allows us to visualize proteins as they assemble and function. One step closer to understanding how Nature builds the incredible protein machines that enable life!

    CryoDRGN: a deep neural network based approach for heterogeneous single particle cryo-EM reconstruction
    4 replies 11 retweets 45 likes
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  14. Retweeted
    4 Feb 2021

    We are offering a 2-hour hands-on remote Topaz workshop for your institution to show best particle picking practices. Topaz picks more particles resulting in higher resolution, better classification, and more complete Euler angle distributions. Email us to schedule a workshop!

    5 replies 41 retweets 135 likes
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  15. Retweeted
    27 Jan 2021

    Very nice work and very nice Topaz picking optimization. Looks like the authors found 2x more particles with Topaz than before Topaz. 💪💪

    SARS-CoV-2 3a preprint update, 2.1Å! map with , processed by me and . We now have new PL uptake assays and RuR as an inhibitor from (Bautista Lab) and new 3a mutants patched by Ben Sorum. Led by
    1 retweet 13 likes
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  16. Retweeted
    14 Jan 2021

    Kevin Murphy's new edition of Probabilistic Machine Learning is out. It's substantial - 900 pages. Thanks for writing this!

    3 replies 141 retweets 622 likes
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  17. Retweeted
    6 Jan 2021

    We're pleased to announce the Simons Machine Learning Center (SMLC) at NYSBC: SMLC is a ML group for advancing structural biology, with continued focus on cryo-EM/ET. We are recruiting several Research Scientists & Postdocs. Please spread the word & apply!

    1 reply 18 retweets 37 likes
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