Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset. - Michael R. Shirts; Christoph Klein 003; Jason M. Swails; Jian Yin 005; Michael K. Gilson; David L. Mobley; David A. Case; Ellen D. Zhong (J. Comput. Aided Mol. Des., 2017)

Erratum to: Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset. - Michael R. Shirts; Christoph Klein 003; Jason M. Swails; Jian Yin 005; Michael K. Gilson; David L. Mobley; David A. Case; Ellen D. Zhong (J. Comput. Aided Mol. Des., 2017)

Explicitly disentangling image content from translation and rotation with spatial-VAE. - Tristan Bepler; Ellen D. Zhong; Kotaro Kelley; Edward Brignole; Bonnie Berger (NeurIPS, 2019)

Reconstructing continuously heterogeneous structures from single particle cryo-EM with deep generative models. - Ellen D. Zhong; Tristan Bepler; Joseph H. Davis; Bonnie Berger (CoRR, 2019)

Reconstructing continuous distributions of 3D protein structure from cryo-EM images. - Ellen D. Zhong; Tristan Bepler; Joseph H. Davis; Bonnie Berger (ICLR, 2020)

Learning Mutational Semantics. - Brian Hie; Ellen D. Zhong; Bryan Bryson; Bonnie Berger (NeurIPS, 2020)

CryoDRGN2: Ab initio neural reconstruction of 3D protein structures from real cryo-EM images. - Ellen D. Zhong; Adam Lerer; Joseph H. Davis; Bonnie Berger (ICCV, 2021)

Amortized Inference for Heterogeneous Reconstruction in Cryo-EM. - Axel Levy; Gordon Wetzstein; Julien N. P. Martel; Frédéric Poitevin; Ellen D. Zhong (NeurIPS, 2022)

CryoBench: Diverse and challenging datasets for the heterogeneity problem in cryo-EM. - Minkyu Jeon; Rishwanth Raghu; Miro Astore; Geoffrey Woollard; Ryan Feathers; Alkin Kaz; Sonya M. Hanson; Pilar Cossio; Ellen D. Zhong (NeurIPS, 2024)

Mixture of neural fields for heterogeneous reconstruction in cryo-EM. - Axel Levy; Rishwanth Raghu; David Shustin; Adele Rui-Yang Peng; Huan Li; Oliver Biggs Clarke; Gordon Wetzstein; Ellen D. Zhong (NeurIPS, 2024)

Solving Inverse Problems in Protein Space Using Diffusion-Based Priors. - Axel Levy; Eric R. Chan; Sara Fridovich-Keil; Frédéric Poitevin; Ellen D. Zhong; Gordon Wetzstein (CoRR, 2024)

Multiscale guidance of AlphaFold3 with heterogeneous cryo-EM data. - Rishwanth Raghu; Axel Levy; Gordon Wetzstein; Ellen D. Zhong (CoRR, 2025)