Author

Elvira Mennillo

University of California, San FranciscoORCID 0000-0002-3210-1004Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

Click to filter author papers

Immunology· 2 Bioinformatics· 1

Signature Assays, Organisms & Methods

Click to filter · or open tag

Approach:benchmark study· 2 Research Focus:cell type annotation· 2 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1 Research Focus:cell signaling & trafficking· 1 Research Focus:cell-cell communication· 1 Approach:deep learning· 1 Research Focus:differential expression· 1

Frequent Co-Authors

Gyehyun LeeiD· 2 shared Michael G. KattahiD· 2 shared A.D. Choudhury· 1 shared Ahmad SalehiiD· 1 shared Alan Gi-Lun ChengiD· 1 shared Alexis J. CombesiD· 1 shared Ali Reza Rais Sadati· 1 shared Amber Casillas· 1 shared

Activity by Year

2025-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 31 mutual co-author links

Click any collaborator node to inspect or filter shared papers

Focal author (center)Selected co-authorORCID co-authorUnlinked name

Curved chords = mutual co-authorship

2 shared papersImmunology

Gyehyun LeeORCID

Mutual co-authors in cluster

Author profile →

3 papers

Recent·Most cited

Single-cell spatial transcriptomics of fixed, paraffin-embedded biopsies reveals colitis-associated cell networks

Elvira Mennillo, Madison L. Lotstein, Gyehyun Lee, Julian H. Hou, Vrinda Johri, Donna Leet, Christina A. Ekstrand, Jessica Tsui, Jun He, Uma Mahadevan, Walter L. Eckalbar, Ryan M. Gill, Christopher Bowman, David Yoonsuk Oh, Gabriela K. Fragiadakis, , Alexis J. Combes

This study develops an iSCST framework for FFPE biopsies, identifying colitis-associated cell networks and VDZ response signatures in IBD patients.

Journal of Clinical Investigation · Jun 9, 2026Peer-reviewedImmunology

Telocytes link epithelial nutrient sensing with amplification of the ILC2-tuft cell circuit

Chang Liao, Elvira Mennillo, Michael G. Kattah, Ming Ji, Zhi‐En Wang, Daniel J. Drucker, Hong-Erh Liang, Richard M. Locksley

The paper shows that telocytes relay signals from enteroendocrine cells to ILC2s, amplifying the tuft cell circuit in response to feeding.

Nature Immunology · Nov 12, 2025Peer-reviewedImmunology

Benchmarking Cell Type and Gene Set Annotation by Large Language Models with AnnDictionary

George Crowley, Robert C. Jones, Mark A. Krasnow, Angela Oliveira Pisco, Julia Salzman, Nir Yosef, Siyu He, Madhav Mantri, Jessie Aguirre, Ron Garner, Sal Guerrero, William Harper, Resham Irfan, Sophia Mahfouz, Ravi Ponnusamy, , David Seong

The paper benchmarks large language models for cell-type and gene set annotation using AnnDictionary, finding high accuracy in cell-type annotation and strong functional gene set recovery.

Nature Communications · Oct 28, 2025Peer-reviewedBioinformatics