Author

D. Thad Whitaker

National Institutes of HealthORCID 0000-0002-7697-2776Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Genomics· 2 Neuroscience· 2 Molecular Biology· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 4 Research Focus:differential expression· 3 Organism:human· 3 Assay:ATAC-seq· 1 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1 Assay:DNA methylation· 1 Approach:experimental assay· 1

Frequent Co-Authors

Jesse Raphael GibbsiD· 3 shared Jinhui DingiD· 3 shared Mark CooksoniD· 3 shared Sonja W. ScholziD· 3 shared Xylena ReediD· 3 shared Alexandra G. BeilinaiD· 2 shared Cory A. WelleriD· 2 shared Dominic J. AcriiD· 2 shared

Activity by Year

2019-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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3 shared papersGenomics

Jesse Raphael GibbsORCID

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Author profile →

5 papers

Recent·Most cited

Integration of cell-specific gene expression and chromatin accessibility facilitates localization of neurodegenerative risk in microglia

Xylena Reed, Dominic J. Acri, Alexandra G. Beilina, Jinhui Ding, Sara Sáez-Atiénzar, Mary Kaileh, Sarah Bromberek, Fangle Hu, Grigory Lerner, Daniel M. Ramos, Sultana Solaiman, Makayla Portley, Cory A. Weller, D. Thad Whitaker, Debra J. Ehrlich, , Mark Cookson

The paper integrates cell-specific gene expression and chromatin accessibility to identify neurodegenerative disease risk loci specific to microglia.

bioRxiv · Sep 17, 2026 · PreprintGenomics

Region-Specific Transcriptional Signatures of Brain Aging in the Absence of Neuropathology at the Single-cell Level

Monica E. Mesecar, Megan F. Duffy, Dominic J. Acri, Jinhui Ding, Rebekah G. Langston, Syed I. Shah, Mike A. Nalls, Xylena Reed, Sonja W. Scholz, D. Thad Whitaker, Pavan Kumar Auluck, Stefano Marenco, Alex R. DeCasien, Jesse Raphael Gibbs, Mark Cookson

This study uses snRNA-seq to analyze age-related transcriptional changes in four brain regions across young and aged individuals, identifying region-specific age-associated genes and biological processes.

npj Aging · May 13, 2026Peer-reviewedNeuroscience

Characterization of DNA methylation in PBMCs and donor-matched iPSCs shows methylation is reset during stem cell reprogramming

Xylena Reed, Cory A. Weller, Sara Sáez-Atiénzar, Alexandra G. Beilina, Sultana Solaiman, Makayla K. Portley, Mary Kaileh, Roshni Roy, Jinhui Ding, Ann Zenobia Moore, D. Thad Whitaker, Bryan J. Traynor, Jesse Raphael Gibbs, Sonja W. Scholz, Mark Cookson

The paper shows that DNA methylation is reset in iPSCs compared to donor PBMCs, with unique methylation sites influenced by genetics in each cell type.

bioRxiv · Dec 13, 2024 · PreprintMolecular Biology

Best practices for analyzing imputed genotypes from low-pass sequencing in dogs

Reuben M. Buckley, Alex C. Harris, Guodong Wang, D. Thad Whitaker, Ya‐Ping Zhang, Elaine A. Ostrander

The paper evaluates low-pass whole genome sequencing and imputation in dogs, optimizing variant filtering to reduce imputation error and provides guidelines for GWAS using imputed genotypes.

Mammalian Genome · Sep 8, 2021Peer-reviewedGenomics

NRL- and CRX-guided gene network modulates photoreceptor presynapse size and positioning during retinal development

D. Thad Whitaker, Anupam Kumar Mondal, Hannah Fann, Passley Jordan Hargrove, Matthew J. Brooks, Vijender Chaitankar, Wenhan Yu, Zhijian Wu, Soo‐Young Kim, Anand Swaroop

The paper identifies genes regulated by NRL and CRX that control rod photoreceptor presynapse morphology and validates their function through knockdown and CRISPR/Cas9 approaches.

bioRxiv · Aug 30, 2019 · PreprintNeuroscience

D. Thad Whitaker · henhao