Author

Naomi Claffey

Salk Institute for Biological Studies

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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Neuroscience· 3 Genomics· 2

Signature Assays, Organisms & Methods

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Approach:statistical model· 5 Research Focus:cell type annotation· 4 Assay:DNA methylation· 4 Organism:human· 4 Research Focus:differential expression· 3 Research Focus:gene regulatory network inference· 3 Assay:Hi-C· 3 Research Focus:database / resource· 2

Frequent Co-Authors

Anna BartlettiD· 5 shared Carolyn O’ConnoriD· 5 shared Joseph R. EckeriD· 5 shared Joseph R. NeryiD· 5 shared Michelle LiemiD· 5 shared Rosa CastanoniD· 5 shared Cynthia ValadoniD· 4 shared Hanqing LiuiD· 4 shared

Activity by Year

2022-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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5 shared papersNeuroscience

Anna BartlettORCID

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Author profile →

5 papers

Recent·Most cited

Human Body Single-Cell Atlas of 3D Genome Organization and DNA Methylation

Jingtian Zhou, Yue Wu, Hanqing Liu, Wei Tian, Rosa Castanon, Anna Bartlett, Zuolong Zhang, Guocong Yao, Difang Shi, Ben Clock, Samantha Marcotte, Joseph R. Nery, Michelle Liem, Naomi Claffey, Lara Boggeman, , Joseph R. Ecker

The paper maps 3D genome organization and DNA methylation across 86,689 single nuclei from 16 human tissues, revealing cell-type-specific variations and discrepancies between methylation and chromatin structure.

Science · Jul 23, 2026Peer-reviewedGenomics

Cell type-specific effects of age and sex on human cortical neurons

Jo-fan Chien, Hanqing Liu, Bang-An Wang, Chongyuan Luo, Anna Bartlett, Rosa Castanon, Nicholas D. Johnson, Joseph R. Nery, Julia K. Osteen, Junhao Li, Jordan Altshul, Mia A. Kenworthy, Cynthia Valadon, Michelle Liem, Naomi Claffey, , Eran A. Mukamel

The paper examines age and sex effects on human cortical neurons using multiomic data, finding age-related changes in gene expression and DNA methylation, and sex differences in gene expression and X-inactivation escape.

Neuron · Jun 5, 2024Peer-reviewedNeuroscience

Epigenome erosion in Alzheimer's disease brain cells and induced neurons

Bang-An Wang, Jeffrey R. Jones, Jingtian Zhou, Wei Tian, Yue Wu, Wenliang Wang, Peter Berube, Anna Bartlett, Rosa Castanon, Joseph R. Nery, Huaming Chen, Mia A. Kenworthy, Jordan Altshul, Cynthia Valadon, Yichen Wang, , Joseph R. Ecker

This study identifies AD-specific DNA methylation signatures and chromosomal epigenome erosion in LOAD brain cells and shows their conservation in induced neurons.

bioRxiv · Oct 15, 2023 · PreprintGenomics

Brain-wide Correspondence Between Neuronal Epigenomics and Long-Distance Projections

Jingtian Zhou, Zhuzhu Zhang, May Wu, Hanqing Liu, Yan Pang, Anna Bartlett, Angeline C. Rivkin, Will N. Lagos, Elora Williams, Cheng-Ta Lee, Paula Assakura Miyazaki, Andrew I. Aldridge, Qiurui Zeng, J. L. Angelo Salinda, Naomi Claffey, , Edward M. Callaway

The paper links single-cell epigenomes and projection patterns of 33,034 mouse neurons to identify transcriptomic and epigenomic properties of projection cell types.

bioRxiv · May 1, 2023 · PreprintNeuroscience

Epigenomic complexity of the human brain revealed by single-cell DNA methylomes and 3D genome structures

Wei Tian, Jingtian Zhou, Anna Bartlett, Qiurui Zeng, Hanqing Liu, Rosa Castanon, Mia A. Kenworthy, Jordan Altshul, Cynthia Valadon, Andrew I. Aldridge, Joseph R. Nery, Huaming Chen, Jiaying Xu, Nicholas D. Johnson, Jacinta D. Lucero, , Joseph R. Ecker

The paper identifies 188 cell types in the human brain using single-cell DNA methylation and 3D genome data, and develops a tool to predict cell types based on methylation patterns.

bioRxiv · Nov 30, 2022 · PreprintNeuroscience