*co-first, +co-corresponding


  1. cryodrgn_et_SI2.gif
    Deep reconstructing generative networks for visualizing dynamic biomolecules inside cells
    Ramya Rangan, Sagar Khavnekar, Adam Lerer, Jake Johnston, Ron Kelley, Martin Obr, Abhay Kotecha, and Ellen D. Zhong
    bioRxiv, 2023
  2. 2023_tang.jpeg
    Conformational heterogeneity and probability distributions from single-particle cryo-electron microscopy
    Wai Shing Tang, Ellen D. Zhong, Sonya M. Hanson, Erik H. Thiede, and Pilar Cossio
    Current Opinion in Structural Biology, 2023


  1. cryofire.gif
    Amortized Inference for Heterogeneous Reconstruction in Cryo-EM
    Axel Levy, Gordon Wetzstein, Julien Martel, Frederic Poitevin, and Ellen D Zhong
    In Neural Information Processing Systems (NeurIPS), 2022
  2. covid_spike_short_small.gif
    Latent Space Diffusion Models of Cryo-EM Structures
    Karsten Kreis*, Tim Dockhorn*, Zihao Li, and Ellen D Zhong
    In NeurIPS Workshop on Machine Learning for Structural Biology (MLSB), 2022
    Oral presentation
  3. cryo_dgm_review.jpg
    Deep generative modeling for volume reconstruction in cryo-electron microscopy
    Claire Donnat, Axel Levy, Frederic Poitevin, Ellen D Zhong, and Nina Miolane
    Journal of Structural Biology, 2022
  4. thesis.png
    Machine Learning for Reconstructing Dynamic Protein Structures from Cryo-EM Images
    Massachusetts Institute of Technology, 2022
  5. plant_26S.png
    Cryo-EM structure of the plant 26S proteasome
    Susanne Kandolf, Irina Grishkovskaya, Katarina Belačić, Derek L Bolhuis, Sascha Amann, Brent Foster, Richard Imre, Karl Mechtler, Alexander Schleiffer, Hemant D Tagare, Ellen D Zhong, Anton Meinhard, Nicholas G Brown, and David Haselbach
    Plant Communications, 2022
  6. saga.gif
    Conformational landscape of the yeast SAGA complex as revealed by cryo-EM
    Diana Vasyliuk, Joeseph Felt, Ellen D Zhong, Bonnie Berger, Joseph H Davis, and Calvin K Yip
    Scientific Reports, 2022
  7. cryodrgn_protocols.png
    Uncovering structural ensembles from single-particle cryo-EM data using cryoDRGN
    Laurel F Kinman*, Barrett M Powell*, Ellen D Zhong*+, Bonnie Berger+, and Joseph H Davis+
    Nature Protocols, 2022


  1. cryodrgn2.png
    CryoDRGN2: Ab Initio Neural Reconstruction of 3D Protein Structures From Real Cryo-EM Images
    Ellen D Zhong, Adam Lerer, Joseph H Davis, and Bonnie Berger
    In International Conference on Computer Vision (ICCV), 2021
  2. spliceosome.gif
    CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks
    Ellen D Zhong, Tristan Bepler, Bonnie Berger+, and Joseph H Davis+
    Nature Methods, 2021
  3. radial_spoke.gif
    Structures of radial spokes and associated complexes important for ciliary motility
    Miao Gui, Meisheng Ma, Erica Sze-Tu, Xiangli Wang, Fujiet Koh, Ellen D Zhong, Bonnie Berger, Joseph H Davis, Susan K Dutcher, Rui Zhang+, and Alan Brown+
    Nature Structural & Molecular Biology, 2021
  4. cscs.png
    Learning the language of viral evolution and escape
    Brian Hie, Ellen D Zhong, Bonnie Berger+, and Bryan Bryson+
    Science, 2021


  1. cscs_neurips.png
    Learning mutational semantics
    Brian Hie, Ellen D Zhong, Bryan Bryson, and Bonnie Berger
    In Neural Information Processing Systems (NeurIPS), 2020
  2. cryofold.png
    Exploring generative atomic models in cryo-EM reconstruction
    Ellen D Zhong, Adam Lerer, Joseph H Davis, and Bonnie Berger
    In NeurIPS Workshop on Machine Learning for Structural Biology (MLSB), 2020
  3. tickertape.png
    RNA timestamps identify the age of single molecules in RNA sequencing
    Samuel G Rodriques, Linlin M Chen, Sophia Liu, Ellen D Zhong, Joseph R Scherrer, Edward S Boyden+, and Fei Chen+
    Nature Biotechnology, 2020
  4. cryodrgn_iclr.png
    Reconstructing continuous distributions of 3D protein structure from cryo-EM images.
    Ellen D Zhong, Tristan Bepler, Joseph H Davis, and Bonnie Berger
    In International Conference on Learning Representations (ICLR), 2020
    Spotlight presentation


  1. spatial_vae.png
    Explicitly disentangling image content from translation and rotation with spatial-VAE
    Tristan Bepler, Ellen D Zhong, Kotaro Kelley, Edward Brignole, and Bonnie Berger
    In Neural Information Processing Systems (NeurIPS), 2019


  1. sampl5_lessons.png
    Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset
    Michael R Shirts, Christoph Klein, Jason M Swails, Jian Yin, Michael K Gilson, David L Mobley, David A Case, and Ellen D Zhong
    Journal of Computer-Aided Molecular Design, 2017


  1. HMC.jpeg
    Thermodynamics of coupled protein adsorption and stability using hybrid Monte Carlo simulations
    Ellen D Zhong, and Michael R Shirts
    Langmuir, 2014


  1. messenger.png
    Areas of permanent shadow in Mercury’s south polar region ascertained by MESSENGER orbital imaging
    Nancy L Chabot, Carolyn M Ernst, Brett W Denevi, John K Harmon, Scott L Murchie, David T Blewett, Sean C Solomon, and Ellen D Zhong
    Geophysical Research Letters, 2012