Author

Jessica S. Yu

Allen Institute for Cell ScienceORCID 0000-0003-4464-904XUnclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Systems Biology· 2 Biophysics· 1

Signature Assays, Organisms & Methods

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Research Focus:benchmarking· 2 Approach:deep learning· 2 Organism:human· 2 Research Focus:cell type annotation· 1 Research Focus:clustering· 1 Research Focus:differential expression· 1 Assay:fluorescence / live-cell microscopy· 1 Assay:scRNA-seq· 1

Frequent Co-Authors

Julie A. TheriotiD· 2 shared Neda BagheriiD· 2 shared Susanne M. RafelskiiD· 2 shared Amber PhaniD· 1 shared Benjamin MorrisiD· 1 shared Blair M. LyonsiD· 1 shared Brock RobertsiD· 1 shared Caroline HookwayiD· 1 shared

Activity by Year

2024-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 33 mutual co-author links

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2 shared papersBiophysics

Julie A. TheriotORCID

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Author profile →

3 papers

Recent·Most cited

BiophysicsbioRxivPreprintJul 11, 2026

Dynamics of ML-based Morphological Features Indicate a Shear Stress-Dependent Bifurcation of hiPSC-Derived Endothelial Cell States

Erin Angelini, Chantelle L. Leveille, Serge E. Parent…·Matheus Palhares Viana

The paper uses ML to analyze morphological dynamics of hiPSC-derived endothelial cells under shear stress, identifying a bifurcation between two stable cell states.

DOI 10.64898/2026.07.07.736803

humanfluorescence / live-cell microscopy

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Systems BiologybioRxivPreprintAug 12, 2024

4D hybrid model interrogates agent-level rules and parameters driving hiPS cell colony dynamics

Jessica S. Yu, Blair M. Lyons, Susanne M. Rafelski…·Graham T. Johnson

The paper develops a hybrid agent-based model to simulate hiPS cell colony dynamics, identifies limitations of the CPM approach, and suggests improvements for accurate simulations.

DOI 10.1101/2024.08.12.607546

humanstatistical model

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Systems BiologyBioinformaticsPeer-reviewedMar 1, 2024

Incorporating temporal information during featureengineering bolsters emulation of spatio-temporalemergence

Jason Y. Cain, Jacob I. Evarts, Jessica S. Yu, Neda Bagheri

The paper improves machine learning emulation of a tumor microenvironment model by incorporating temporal information from intermediate simulation states, enhancing predictive performance.

DOI 10.1093/bioinformatics/btae131

scRNA-seqdeep learning

𝕏 PostBluesky