Author

Daniel Ji

University of California San DiegoORCID 0009-0003-2008-9583Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Biophysics· 2 Bioinformatics· 1

Signature Assays, Organisms & Methods

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Research Focus:clustering· 2 Assay:cryo-EM· 2 Research Focus:benchmarking· 1 Research Focus:cell type annotation· 1 Research Focus:cell-cell communication· 1 Approach:deep learning· 1 Research Focus:differential expression· 1 Research Focus:drug response / drug discovery· 1

Frequent Co-Authors

B. CookiD· 2 shared Mark A. HerzikiD· 2 shared Maxwell J. BachochiniD· 2 shared Andrew BrowniD· 1 shared Armin Foroughi· 1 shared Danielle Ann GrotjahniD· 1 shared Hamidreza RahmaniiD· 1 shared Hannah VerdonkiD· 1 shared

Activity by Year

2024-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 21 mutual co-author links

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2 shared papersBiophysics

B. CookORCID

Mutual co-authors in cluster

Author profile →

3 papers

Recent·Most cited

A Surfactant Cocktail Overcomes Air-Water Interface Artifacts in Single-Particle CryoEM

Suzanne E. Enos, B. Cook, Hamidreza Rahmani, Sarah M. Narehood, Yizhou Li, Inga Christine Kuschnerus, Trevor H Redford, Peter Dukakis, Daniel Ji, Maxwell J. Bachochin, Danielle Ann Grotjahn, Mark A. Herzik

The paper introduces SurfACT, a surfactant cocktail that reduces air-water interface artifacts in cryoEM, improving particle distribution and map completeness for four proteins.

bioRxiv · Mar 18, 2026 · PreprintBiophysics

ANTIDOTE: A Metadata-Driven Neural Network for Improving CryoEM 3-D Particle Sorting

Raymond F. Berkeley, B. Cook, Daniel Ji, Armin Foroughi, Yifei He, Maxwell J. Bachochin, Mark A. Herzik

ANTIDOTE improves cryoEM particle sorting by using metadata-driven neural networks, enhancing reconstruction quality and reducing manual curation efforts.

bioRxiv · Oct 6, 2025 · PreprintBiophysics

AUTO-TUNE: SELECTING THE DISTANCE THRESHOLD FOR INFERRING HIV TRANSMISSION CLUSTERS

Steven Weaver, Vanessa Dávila‐Conn, Daniel Ji, Hannah Verdonk, Santiago Ávila‐Ríos, Andrew Brown, Joel O. Wertheim, Sergei L. Kosakovsky Pond

The paper introduces a heuristic method to adaptively select a genetic distance threshold for HIV transmission network inference, demonstrating its utility in identifying clusters with different risk factors.

Frontiers in Bioinformatics · Jul 10, 2024Peer-reviewedBioinformatics