Author

Nicole L. Fong

Calico Life Sciences

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· 1 Ecology· 1 Genetic & Genomic Medicine· 1 Immunology· 1 Neuroscience· 1

Signature Assays, Organisms & Methods

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Approach:experimental assay· 3 Organism:mouse· 3 Research Focus:cell type annotation· 2 Assay:spatial transcriptomics· 2 Assay:whole-genome sequencing· 2 Assay:bulk RNA-seq· 1 Research Focus:cell-cell communication· 1 Approach:deep learning· 1

Frequent Co-Authors

David G. HendricksoniD· 4 shared Irene Lam· 3 shared Jordan Brown· 2 shared Margaret A. RoyiD· 2 shared Po-Han TaiiD· 2 shared Wenjun KongiD· 2 shared Aaron W. StebbinsiD· 1 shared Agnieszka A. WendorffiD· 1 shared

Activity by Year

2019-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 23 mutual co-author links

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4 shared papersImmunology

David G. HendricksonORCID

Mutual co-authors in cluster

Author profile →

5 papers

Recent·Most cited

PTPN1/2 inhibits alveolar macrophage-mediated control of lung metastasis

Yue Liu, Im-Meng Sun, Marc Creixell, Jordan Brown, Samir Kharbanda, James J. Lee, Varahram Shahryari, Kayley Hake, Jacqueline O'Hara, Kenneth J. Finn, Nianxin Yang, Lolita Penland, Jiaxi Wang, Ka Man Li, John Balibalos, , Jonathan D. Powell

This study shows that inhibiting PTPN1/2 enhances alveolar macrophage anti-metastatic activity through IFN-gamma-STAT1 signaling, offering a therapeutic strategy for metastasis.

bioRxiv · Feb 26, 2026 · PreprintImmunology

Ribosomal DNA copy number variation shapes human physiology and disease risk

Anil Raj, Jordan Brown, Nathaniel H. Thayer, Manuel Hotz, Irene Lam, Nicole L. Fong, Elena P. Sorokin, Marjola Thanaj, Daphna Rothschild, Jonathan K. Pritchard, Maria Barna, David G. Hendrickson

The paper analyzes rDNA copy number variation in humans, finding distinct associations with metabolic diseases and growth traits.

medRxiv · Jan 13, 2026 · PreprintGenetic & Genomic Medicine

Geographic distribution of genetic diversity of Heterocephalus glaber analyzed using whole genome sequencing and a chromosome-scale genome assembly

Kevin M. Wright, Pranidhi Sood, Elena D. Zemlemerova, Danila S. Kostin, Nicole L. Fong, Nelda Yi, Andrea T. Ireland, Irene Lam, Kaitlyn N. Lewis Hardell, Megan Smith, Jackie Villalta, Calvin H. Jan, Margaret A. Roy, David Botstein, Leonid A. Lavrenchenko, , Rochelle Buffenstein

The paper analyzes genetic diversity in naked mole-rats from Kenya and Ethiopia using whole-genome sequencing and a chromosome-scale genome assembly, revealing unexpected genetic divergence patterns.

Frontiers in Ecology and Evolution · Nov 24, 2025Peer-reviewedEcology

Heterochronic myeloid cell replacement reveals the local brain environment as key driver of microglia aging

Claire Gizowski, Galina Popova, Heather Shin, Marius Marc-Daniel Mader, Wendy Craft, Wenjun Kong, Yohei Shibuya, Bernd J. Wranik, Yan Hong Huang Fu, Constanze Depp, Tzu‐Hua Lin, Baby Martin-McNulty, Yongjin Yoo, Po-Han Tai, Maximilian Hingerl, , Oliver Hahn

This study uses heterochronic myeloid cell replacement to show that the local brain environment, not intrinsic factors, drives microglia aging.

bioRxiv · Sep 2, 2025 · PreprintNeuroscience

Solo: doublet identification via semi-supervised deep learning

Nicholas Bernstein, Nicole L. Fong, Irene Lam, Margaret A. Roy, David G. Hendrickson, David R. Kelley

Solo identifies doublets in scRNA-seq data using semi-supervised deep learning, improving accuracy over existing methods.

bioRxiv · Nov 14, 2019 · PreprintBioinformatics