Author

Daniel S. Whittaker

University of California San DiegoORCID 0000-0002-4293-5192Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Neuroscience· 2 Genomics· 1

Signature Assays, Organisms & Methods

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Organism:mouse· 3 Approach:statistical model· 2 Research Focus:benchmarking· 1 Research Focus:cell type annotation· 1 Research Focus:differential expression· 1 Approach:experimental assay· 1 Assay:metagenomics· 1 Research Focus:spatial domain detection· 1

Frequent Co-Authors

Paula DesplatsiD· 3 shared Haylie K. Romero· 2 shared Alexander Richter· 1 shared Alon GelberiD· 1 shared Amir ZarrinpariD· 1 shared Asako Tan· 1 shared Christopher Scott ColwelliD· 1 shared Daniel E. CarliniD· 1 shared

Activity by Year

2022-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 21 mutual co-author links

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3 shared papersNeuroscience

Paula DesplatsORCID

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3 papers

Recent·Most cited

Spatial transcriptomics reveals brain-wide circadian disruption in an Alzheimer's disease model

Alon Gelber, Haylie K. Romero, Dominic R. W. Burrows, Daniel S. Whittaker, Daniel E. Carlin, Eran A. Mukamel, Paula Desplats

This study uses spatial transcriptomics to show that Alzheimer's disease disrupts circadian rhythms in specific brain regions before amyloid plaques form in a mouse model.

bioRxiv · Jan 28, 2026 · PreprintNeuroscience

Optimizing mouse metatranscriptome profiling by selective removal of redundant nucleic acid sequences

Morgan Roos, Samuel Bunga, Asako Tan, Erica S. Maissy, Dylan Skola, Alexander Richter, Daniel S. Whittaker, Paula Desplats, Amir Zarrinpar, Rick Conrad, Scott Kuersten

The paper improves rRNA depletion for mouse cecal metatranscriptome analysis by designing probes based on sequence abundance rather than taxonomy, increasing mRNA reads and reducing bias.

mSystems · Jun 16, 2025Peer-reviewedGenomics

Circadian modulation by time-restricted feeding restores brain transcription and slows amyloid deposition in a mouse model of Alzheimer's disease.

Daniel S. Whittaker, Laila Akhmetova, Haylie K. Romero, David K. Welsh, Christopher Scott Colwell, Paula Desplats

Time-restricted feeding reduces amyloid deposition, improves behavior, and normalizes gene expression in a mouse model of Alzheimer's disease.

bioRxiv · Oct 7, 2022 · PreprintNeuroscience