Author

Sydney K. Caldwell

Broad Institute

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 Immunology· 1 Neuroscience· 1

Signature Assays, Organisms & Methods

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Research Focus:cell type annotation· 3 Assay:bulk RNA-seq· 2 Research Focus:gene regulatory network inference· 2 Organism:mouse· 2 Approach:statistical model· 2 Research Focus:benchmarking· 1 Research Focus:cell signaling & trafficking· 1 Research Focus:development & morphogenesis· 1

Frequent Co-Authors

Alec J. WalkeriD· 2 shared Anushree S. Gupte· 2 shared Beth StevensiD· 2 shared Helena J. BarriD· 2 shared Justin M. ReimertziD· 2 shared Samuel E. MarshiD· 2 shared Toby Black LanseriD· 2 shared Alicia C. Walker· 1 shared

Activity by Year

2025-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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2 shared papersNeuroscience

Alec J. WalkerORCID

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Author profile →

3 papers

Recent·Most cited

Biological foundation models illuminate annotation blind spots in evolutionarily divergent genomes

Toby B. Lanser, Sydney K. Caldwell, Gaspar A. Pacheco, Jessica W. Chen, Shahab Saghaei, Mariah Hassan, Meydan Kronrod, Duane R. Wesemann, Hildreth Robert Frost

The paper introduces a hybrid annotation framework that improves cross-species protein similarity assignment and gene annotation in evolutionarily divergent genomes, expanding structural catalogs and improving single-cell immune cell state annotation in sea lamprey.

bioRxiv · May 16, 2026 · PreprintBioinformatics

The circadian clock regulates scavenging of fluid-borne substrates by brain border-associated macrophages

Helena J. Barr, Sydney K. Caldwell, Justin M. Reimertz, Constanze Depp, Alec J. Walker, Samuel E. Marsh, Anushree S. Gupte, Maximilian Hingerl, Jasmin Patel, Sang-O Park, Sarah Ferraro, Jonathan Lipton, Beth Stevens

This study identifies brain border-associated macrophages (BAMs) as rhythmic cells regulated by the circadian clock, showing that their endocytic activity and amyloid-beta uptake are disrupted with age and in a mouse model of Alzheimer's disease.

bioRxiv · Dec 11, 2025 · PreprintNeuroscience

Early-life stromal niches orchestrate B lymphopoiesis at the brain's borders

Alec J. Walker, Theodore M. Fisher, Sydney K. Caldwell, Anushree S. Gupte, Justin M. Reimertz, Bristy Sabikunnahar, Samuel E. Marsh, Yvanka de Soysa, Vahid Gazestani, Alicia C. Walker, Youtong Huang, Ananya Mavinkurve, Helena J. Barr, Toby Black Lanser, Sarah R. Murphy, , Beth Stevens

This study identifies the murine dura mater as a transient niche for early-postnatal B lymphopoiesis, highlighting the role of CXCL12-expressing fibroblasts in supporting B cell development.

bioRxiv · Nov 27, 2025 · PreprintImmunology