Ellen D. Zhong, Ph.D.

Year of Graduation: 



Prof. Bonnie Berger & Prof. Joey Davis

Current Position: 

Assistant Professor of Computer Science at Princeton University

Zhong Lab Website

Doctoral Thesis Title:  Machine Learning for Reconstructing Dynamic Protein Structures from Cryo-EM Images


Publications while at MIT:

Conformational landscape of the yeast SAGA complex as revealed by cryo-EM.

Vasyliuk D, Felt J, Zhong EDBerger B, Davis JH, Yip CK.Sci Rep. 2022 Jul 19;12(1):12306. doi: 10.1038/s41598-022-16391-0.PMID: 35853968 Free PMC article.


Cryo-EM structure of the plant 26S proteasome.

Kandolf S, Grishkovskaya I, Belačić K, Bolhuis DL, Amann S, Foster B, Imre R, Mechtler K, Schleiffer A, Tagare HD, Zhong ED, Meinhart A, Brown NG, Haselbach D.Plant Commun. 2022 May 9;3(3):100310. doi: 10.1016/j.xplc.2022.100310. Epub 2022 Mar 11.PMID: 35576154 Free PMC article.


RNA timestamps identify the age of single molecules in RNA sequencing.

Rodriques SG, Chen LM, Liu S, Zhong ED, Scherrer JR, Boyden ES, Chen F.Nat Biotechnol. 2021 Mar;39(3):320-325. doi: 10.1038/s41587-020-0704-z. Epub 2020 Oct 19.PMID: 33077959 Free PMC article.


CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks.

Zhong ED, Bepler T, Berger B, Davis JH.Nat Methods. 2021 Feb;18(2):176-185. doi: 10.1038/s41592-020-01049-4. Epub 2021 Feb 4.PMID: 33542510 Free PMC article.


Learning the language of viral evolution and escape.

Hie B, Zhong EDBerger B, Bryson B.Science. 2021 Jan 15;371(6526):284-288. doi: 10.1126/science.abd7331.PMID: 33446556


Structures of radial spokes and associated complexes important for ciliary motility.

Gui M, Ma M, Sze-Tu E, Wang X, Koh F, Zhong EDBerger B, Davis JH, Dutcher SK, Zhang R, Brown A.Nat Struct Mol Biol. 2021 Jan;28(1):29-37. doi: 10.1038/s41594-020-00530-0. Epub 2020 Dec 14.PMID: 33318703 Free PMC article.