Author

Saskia Ilcisin

Allen Institute for ImmunologyORCID 0000-0002-1045-735XUnclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Immunology· 2 Developmental Biology· 1

Signature Assays, Organisms & Methods

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Research Focus:cell type annotation· 2 Research Focus:differential expression· 2 Approach:experimental assay· 2 Organism:human· 2 Assay:scRNA-seq· 2 Approach:statistical model· 2 Research Focus:cell-cell communication· 1 Research Focus:clustering· 1

Frequent Co-Authors

Matthew R. HartiD· 2 shared N KauliD· 2 shared Peter J. SkeneiD· 2 shared Alexander F. SchieriD· 1 shared Anastasia A. MinervinaiD· 1 shared Andrew J. Fiore-GartlandiD· 1 shared Anne Roshella GomesiD· 1 shared Beth MartiniD· 1 shared

Activity by Year

2024-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 19 mutual co-author links

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2 shared papersImmunology

Matthew R. HartORCID

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Author profile →

3 papers

Recent·Most cited

HIV-1 prime-boost vaccination shapes distinct clonal trajectories and memory precursor states of Env- and Gag-specific T cells

Guoyue Xu, Joshua X. Yee, Saskia Ilcisin, N Kaul, Koshlan Mayer-Blackwell, Ernest Moelhman, David Richard Glass, Anastasia A. Minervina, Shelly Karuna, Magdalena E. Sobieszczyk, Matthew R. Hart, Paul Glyndwr Thomas, Peter J. Skene, Stephen C. De Rosa, M. Juliana McElrath, , Evan William Newell

This study shows that HIV-1 DNA/rAd5 vaccination leads to distinct clonal expansion and memory precursor states in Env- and Gag-specific CD8 T cells.

bioRxiv · Sep 29, 2026 · PreprintImmunology

REFLEX, a Novel Immune Profiling Assay, Combining TCR Repertoire and Multiome at Massively Scalable Single-cell Resolution to Catapult Exploration of T-cell Derived Immunity

Matthew R. Hart, Zachary Thomson, N Kaul, Saskia Ilcisin, Matthieu Landreau, Tyanna J. Stuckey, Peter J. Wittig, Michael Daniel Keller, Chase D. McCann, Troy R. Torgerson, Peter J. Skene

REFLEX enables scalable, multiomic T cell profiling with TCR sequencing, identifying novel CMV-reactive clonotypes in over 1.4 million T cells.

bioRxiv · Oct 24, 2025 · PreprintImmunology

A single-cell transcriptional timelapse of mouse embryonic development, from gastrula to pup

Chengxiang Qiu, Beth Martin, Ian C. Welsh, Riza M. Daza, Truc-Mai Le, Xingfan Huang, Eva K. Nichols, Megan L. Taylor, Olivia Fulton, Diana R. O’Day, Anne Roshella Gomes, Saskia Ilcisin, Sanjay R Srivatsan, Xinxian Deng, Christine M. Distèche, , Jay Shendure

12.4 million single-nucleus transcriptomes from 83 staged mouse embryos (E8 to P0) yield 190 cell types, a zygote-to-pup cell-type tree, and rapid postnatal transcriptional shifts.

Nature · Feb 14, 2024Peer-reviewedDevelopmental Biology✦ In-depth digest