Author

Ksenia R. Safina

Broad InstituteORCID 0000-0002-5126-9953Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Cancer Biology· 1 Cell Biology· 1 Immunology· 1

Signature Assays, Organisms & Methods

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Research Focus:cell type annotation· 3 Organism:human· 3 Assay:scRNA-seq· 3 Approach:deep learning· 2 Research Focus:differential expression· 2 Approach:statistical model· 2 Assay:CITE-seq· 1 Research Focus:clustering· 1

Frequent Co-Authors

Peter van GaleniD· 2 shared Andrew A. LaneiD· 1 shared Antonia KresoiD· 1 shared Basit SalikiD· 1 shared Catherine J. WuiD· 1 shared Chen WengiD· 1 shared Corey S. CutleriD· 1 shared Dylan KotliariD· 1 shared

Activity by Year

2025-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 25 mutual co-author links

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2 shared papersCell Biology

Peter van GalenORCID

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3 papers

Recent·Most cited

An Inflammatory and Quiescent HSC Subpopulation Expands with Age in Humans

Ksenia R. Safina, Basit Salik, Dylan Kotliar, Michelle L. Curtis, Jonathan Good, Chen Weng, Shawn David, Soumya Raychaudhuri, Antonia Kreso, Jennifer J. Trowbridge, Vijay G. Sankaran, Peter van Galen

The paper identifies an age-related expansion of an inflammatory and quiescent HSC subpopulation using integrated single-cell data.

Genome biology · Jan 16, 2026Peer-reviewedCell Biology

Early persistence of recipient stem-cells and T-cell dysregulation are associated with relapse after transplant in AML/MDS

Nurefsan E. Sariipek, Ksenia R. Safina, Wesley S. Lu, Shuqiang Li, J. Thomas Janes, McKayla Van Orden, Kenneth J. Livak, Haynes Heaton, Vincent T. Ho, John Koreth, Marlise Rachael Luskin, Gabriel Kenneth Griffin, Jacqueline Suen Garcia, Robert Coleman Lindsley, Corey S. Cutler, , Peter van Galen

The paper identifies recipient stem-cell persistence and T-cell dysregulation as predictors of relapse after HSCT in AML/MDS by analyzing single-cell RNA and TCR sequencing data.

bioRxiv · Nov 13, 2025 · PreprintCancer Biology

scRepertoire 2: Enhanced and Efficient Toolkit for Single-Cell Immune Profiling

Qile Yang, Ksenia R. Safina, Kieu Diem Quynh Nguyen, Zewen Kelvin Tuong, Nicholas C. Borcherding

R package rebuild for single-cell T/B cell receptor analysis: Rcpp rewrites reportedly make clonal pairing and edit-distance clustering scale linearly; adds auto-detected multi-format import, AIRR-compatible export, CDR3 summaries.

PLoS Computational Biology · Jun 27, 2025Peer-reviewedImmunology✦ In-depth digest