Author

Erik H. Thiede

Cornell UniversityORCID 0000-0002-5666-1372Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Assay:cryo-EM· 3 Approach:deep learning· 3 Research Focus:protein structure prediction· 2 Approach:Bayesian inference· 1 Approach:experimental assay· 1 Research Focus:protein design· 1 Assay:protein sequence· 1 Research Focus:software / tool· 1

Frequent Co-Authors

Pilar CossioiD· 3 shared David Silva-SáncheziD· 2 shared Alison BerezukiD· 1 shared Andrew Ahn· 1 shared Daniel J. NeedlemaniD· 1 shared Geoffrey WoollardiD· 1 shared Joshua AlmonteiD· 1 shared Kwanghwi JeiD· 1 shared

Activity by Year

2025-2026 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 16 mutual co-author links

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3 shared papersBiophysics

Pilar CossioORCID

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4 papers

Recent·Most cited

Multi-Peptide Prompting Enables In-Context Learning in Protein Language

Joshua Almonte, Minh Triet Vu, Andrew Ahn, Erik H. Thiede

This paper introduces multi-peptide example prompts (MPEPs) to enable in-context learning in protein language models for peptide classification without training.

bioRxiv · Oct 24, 2026 · PreprintBiochemistry

Cryo-electron microscopy ensemble optimization using individual particles and physical constraints

David Silva-Sánchez, Alison Berezuk, Xing Zhu, Erik H. Thiede, Roy R. Lederman, Pilar Cossio

This paper introduces a Bayesian optimization method for cryo-EM ensemble optimization, directly inferring structures and population weights from particle images and physical constraints.

Journal of Chemical Theory and Computation · May 11, 2026Peer-reviewedBiophysics

CryoJAX - A Cryo-Electron Microscopy Image Simulation Library in JAX

Michael O’Brien, David Silva-Sánchez, Geoffrey Woollard, Kwanghwi Je, Sonya M. Hanson, Daniel J. Needleman, Pilar Cossio, Erik H. Thiede, Miro A. Astore

The paper introduces cryoJAX, a cryo-EM image simulation library built on JAX for developing data analysis techniques in cryo-EM.

Acta Crystallographica Section D Structural Biology · Jan 26, 2026Peer-reviewedBiophysics

Counting particles could give wrong probabilities in Cryo-Electron Microscopy

Luke Evans, Lars Dingeldein, Roberto Covino, Marc Aurèle Gilles, Erik H. Thiede, Pilar Cossio

The paper warns that counting particle images in cryo-EM can lead to biased estimates of conformational state populations due to noise and orientation uncertainty, and suggests using full image datasets for more accurate modeling.

bioRxiv · Mar 27, 2025 · PreprintBiophysics