Author

James Burgess

Stanford University

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Bioinformatics· 2

Signature Assays, Organisms & Methods

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Assay:imaging· 2 Research Focus:benchmarking· 1 Research Focus:clustering· 1 Approach:deep learning· 1 Approach:diffusion model· 1 Research Focus:dimensionality reduction· 1 Research Focus:software / tool· 1 Approach:variational autoencoder· 1

Frequent Co-Authors

Jeffrey NirschliD· 2 shared Serena Y. YeungiD· 2 shared Alejandro LozanoiD· 1 shared Chenyu WangiD· 1 shared Daisy Yi DingiD· 1 shared Emma K. LundbergiD· 1 shared He Li· 1 shared Linqi ZhouiD· 1 shared

Activity by Year

2022-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 33 mutual co-author links

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2 shared papersBioinformatics

Jeffrey NirschlORCID

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2 papers

Recent·Most cited

CellFluxV2: An Image Generative Foundation Model for Virtual Cell Modeling

Yuhui Zhang, Yuchang Su, Zoe Wefers, Shiye Su, He Li, Tianhong Li, Chenyu Wang, James Burgess, Alejandro Lozano, Linqi Zhou, Daisy Yi Ding, Jeffrey Nirschl, Emma K. Lundberg, Serena Y. Yeung

CellFluxV2 is an image-generative model that predicts cell morphology changes under perturbations, achieving higher image fidelity than baselines and enabling batch-effect correction and cell-state interpolation.

bioRxiv · Jan 20, 2026 · PreprintBioinformatics

Learning orientation-invariant representations enables accurate and robust morphologic profiling of cells and organelles

James Burgess, Jeffrey Nirschl, Maria Clara Zanellati, Sarah Cohen, Serena Y. Yeung

This paper introduces O2-VAE, an orientation-invariant representation learning method for morphologic profiling of cells and organelles, improving clustering and outlier detection.

bioRxiv · Dec 8, 2022 · PreprintBioinformatics