Publications by authors named "Ellen D Zhong"

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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, Fei Chen

Nat Biotechnol· March 2021

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The Inaugural Flatiron Institute Cryo-EM Conformational Heterogeneity Challenge.
Miro A Astore, Geoffrey Woollard, David Silva-Sánchez, Wenda Zhou, Mykhailo Kopylov, Ellen D Zhong

bioRxiv· November 2025

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CryoDRGN-AI: neural ab initio reconstruction of challenging cryo-EM and cryo-ET datasets.
Axel Levy, Rishwanth Raghu, J Ryan Feathers, Michal Grzadkowski, Frédéric Poitevin, Ellen D Zhong

Nat Methods· July 2025

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CryoDRGN-AI: Neural reconstruction of challenging cryo-EM and cryo-ET datasets.
Axel Levy, Rishwanth Raghu, J Ryan Feathers, Michal Grzadkowski, Frédéric Poitevin, Ellen D Zhong

bioRxiv· April 2025

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Cryo-ET reveals the in situ architecture of the polar tube invasion apparatus from microsporidian parasites.
Mahrukh Usmani, Nicolas Coudray, Margot Riggi, Rishwanth Raghu, Harshita Ramchandani, Ellen D Zhong

Proc Natl Acad Sci U S A· March 2025

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Addendum: Accurate structure prediction of biomolecular interactions with AlphaFold 3.
Josh Abramson, Jonas Adler, Jack Dunger, Richard Evans, Tim Green, Ellen D Zhong

Nature· December 2024

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CryoDRGN-ET: deep reconstructing generative networks for visualizing dynamic biomolecules inside cells.
Ramya Rangan, Ryan Feathers, Sagar Khavnekar, Adam Lerer, Jake D Johnston, Ellen D Zhong

Nat Methods· August 2024

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Cryo-ET reveals the architecture of the polar tube invasion apparatus from microsporidian parasites.
Mahrukh Usmani, Nicolas Coudray, Margot Riggi, Rishwanth Raghu, Harshita Ramchandani, Ellen D Zhong

bioRxiv· July 2024

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Accurate structure prediction of biomolecular interactions with AlphaFold 3.
Josh Abramson, Jonas Adler, Jack Dunger, Richard Evans, Tim Green, Ellen D Zhong

Nature· June 2024

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Conformational states of the microtubule nucleator, the γ-tubulin ring complex.
Brianna Romer, Sophie M Travis, Brian P Mahon, Collin T McManus, Philip D Jeffrey, Ellen D Zhong

bioRxiv· December 2023

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Time-resolved cryo-EM (TR-EM) analysis of substrate polyubiquitination by the RING E3 anaphase-promoting complex/cyclosome (APC/C).
Tatyana Bodrug, Kaeli A Welsh, Derek L Bolhuis, Ethan Paulаkonis, Raquel C Martinez-Chacin, Ellen D Zhong

Nat Struct Mol Biol· November 2023

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Conformational heterogeneity and probability distributions from single-particle cryo-electron microscopy.
Wai Shing Tang, Ellen D Zhong, Sonya M Hanson, Erik H Thiede, Pilar Cossio

Curr Opin Struct Biol· August 2023

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Uncovering structural ensembles from single-particle cryo-EM data using cryoDRGN.
Laurel F Kinman, Barrett M Powell, Ellen D Zhong, Bonnie Berger, Joseph H Davis

Nat Protoc· February 2023

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Deep generative modeling for volume reconstruction in cryo-electron microscopy.
Claire Donnat, Axel Levy, Frédéric Poitevin, Ellen D Zhong, Nina Miolane

J Struct Biol· December 2022

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Amortized Inference for Heterogeneous Reconstruction in Cryo-EM.
Axel Levy, Gordon Wetzstein, Julien Martel, Frédéric Poitevin, Ellen D Zhong

Adv Neural Inf Process Syst· December 2022

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Conformational landscape of the yeast SAGA complex as revealed by cryo-EM.
Diana Vasyliuk, Joeseph Felt, Ellen D Zhong, Bonnie Berger, Joseph H Davis

Sci Rep· July 2022

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Cryo-EM structure of the plant 26S proteasome.
Susanne Kandolf, Irina Grishkovskaya, Katarina Belačić, Derek L Bolhuis, Sascha Amann, Ellen D Zhong

Plant Commun· May 2022

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CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks.
Ellen D Zhong, Tristan Bepler, Bonnie Berger, Joseph H Davis

Nat Methods· February 2021

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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

Nat Struct Mol Biol· January 2021

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Learning the language of viral evolution and escape.
Brian Hie, Ellen D Zhong, Bonnie Berger, Bryan Bryson

Science· January 2021

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Erratum to: Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset.
Michael R Shirts, Christoph Klein, Jason M Swails, Jian Yin, Michael K Gilson, Ellen D Zhong

J Comput Aided Mol Des· August 2017

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Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset.
Michael R Shirts, Christoph Klein, Jason M Swails, Jian Yin, Michael K Gilson, Ellen D Zhong

J Comput Aided Mol Des· January 2017

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

Langmuir· May 2014

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