Author

C. Dirk Keene

University of Washington

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

Click to filter author papers

Neuroscience· 4 Genomics· 1

Signature Assays, Organisms & Methods

Click to filter · or open tag

Organism:human· 5 Research Focus:cell type annotation· 3 Approach:statistical model· 3 Assay:scRNA-seq· 2 Assay:spatial transcriptomics· 2 Research Focus:trajectory inference· 2 Approach:Bayesian inference· 1 Assay:bulk RNA-seq· 1

Frequent Co-Authors

Ed S. LeiniD· 2 shared Aleksandra Bikkina· 1 shared Alexander MonelliD· 1 shared Alexandra CochoitiD· 1 shared Amanda KirklandiD· 1 shared Amber NolaniD· 1 shared Amit KleiniD· 1 shared Anamika AgrawaliD· 1 shared

Activity by Year

2023-2026 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 8 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 papersNeuroscience

Ed S. LeinORCID

Mutual co-authors in cluster

Author profile →

5 papers

Recent·Most cited

Single nucleus RNA sequencing and spatial transcriptomics reveal unique functionalities of gray matter versus white matter oligodendrocytes in aging and Alzheimer's Disease

Joseph P. Voth, Javier A. Ramos Benitez, Angela M. Wilson, Scott R. Kennedy, Mamatha Damodarasamy, Amanda Kirkland, Jeremy A. Miller, Caitlin S. Latimer, Emily Ragaglia, Amber Nolan, Daniel D. Child, Lisa M. Keene, Cindy Reichel, Brendan F. Kohrn, Larry S. Sherman, , C. Dirk Keene

The paper uses single-nucleus RNA sequencing and spatial transcriptomics to compare oligodendrocyte functions in gray and white matter across aging and Alzheimer's Disease.

bioRxiv · Sep 3, 2026 · PreprintNeuroscience

B-BIND: Biophysical Bayesian Inference forNeurodegenerative Dynamics

Anamika Agrawal, Victoria M. Rachleff, Kyle J. Travaglini, Shubhabrata Mukherjee, Paul K. Crane, Michael Hawrylycz, C. Dirk Keene, Ed S. Lein, Gonzalo E. Mena, Mariano I. Gabitto

This paper introduces a Bayesian framework to infer continuous disease states from discrete pathological protein measurements in Alzheimer's Disease, using pseudotime to model progression.

The Annals of Applied Statistics · Mar 1, 2026Peer-reviewedNeuroscience

Single-Cell Atlas of Transcription and Chromatin States Reveals Regulatory Programs in the Human Brain

Yang Xie, Lei Chang, Guojie Zhong, Jonathan A. Rink, Tatiana Baez-Becerra, Ethan J. Armand, Wubin Ding, Kai Li, Éric Bonne, Anita Lie, Hannah S. Indralingam, Keyi Dong, Timothy H. Loe, Bohan Huang, Zhaoning Wang, , Bing Ren

The paper creates a single-cell atlas of transcription and chromatin states in the human brain, identifying regulatory programs and linking them to neuropsychiatric disorders.

bioRxiv · Feb 3, 2026 · PreprintGenomics

Genetic risk implicating endolysosomal network genes correlates with endolysosomal dysfunction across neural cell types in Alzheimer's disease

Shannon E. Rose, Katherine E. Prater, Sainath Mamde, Isabelle Smith, Yu Fan Lin, Alexandra Cochoit, Aquene N. Reid, Corbin S.C. Johnson, Wei Qiu, Samuel D. Strohbehn, Catilin S. Latimer, C. Dirk Keene, Su‐In Lee, Kevin Z. Lin, Bradley A. Rolf, , Suman Jayadev

This study shows that genetic risk variants in endolysosomal network genes correlate with endolysosomal dysfunction in neural cells in Alzheimer's disease.

bioRxiv · Mar 16, 2025 · PreprintNeuroscience

Target cell-specific synaptic dynamics of excitatory to inhibitory neuron connections in supragranular layers of human neocortex

Mean-Hwan Kim, Cristina Radaelli, Elliot R. Thomsen, Deja Monet, Thomas Chartrand, Nikolas L. Jorstad, Joseph T. Mahoney, Michael J. Taormina, Brian Long, Katherine S. Baker, Luke Campagnola, Tamara Casper, Michael Clark, Nick Dee, Florence D. D’Orazi, , Ed S. Lein

The paper investigates target cell-specific synaptic dynamics between excitatory and inhibitory neurons in human neocortex, finding similarities to rodent studies.

eLife · May 30, 2023Peer-reviewedNeuroscience