An immune-focused supplemental alignment pipeline captures information missed from dominant single-cell RNA-seq analyses, including allele-specific MHC-I regulation
Combining nimble data with standard pipelines enhances the fidelity and accuracy of experiments, maximizing the value of expensive datasets, and identifying cellular subsets not possible with standard tools alone.
Authors
- William Goodwin
- Carla Boyle (ORCID: https://orcid.org/0000-0003-4800-0301)
- Daniel N. Streblow (ORCID: https://orcid.org/0000-0002-6828-2492)
- Caralyn S. Labriola
- Afam A. Okoye (ORCID: https://orcid.org/0000-0001-9671-550X)
- Aaron Barber-Axthelm
- Jonah B. Sacha (ORCID: https://orcid.org/0000-0002-7633-3122)
- Michael K. Axthelm (ORCID: https://orcid.org/0000-0002-1984-5906)
- S.A. Benjamin (ORCID: https://orcid.org/0000-0001-6064-042X)
- Nicole N. Haese (ORCID: https://orcid.org/0000-0003-4871-2763)
- Derick M. Duell
- GW McElfresh
- Scott G. Hansen (ORCID: https://orcid.org/0000-0002-9845-6481)
- Tyler James Bennett (ORCID: https://orcid.org/0000-0003-0110-965X)
- Courtney Waytashek
- Candice Nkoy
- Andrea N. Selseth (ORCID: https://orcid.org/0000-0001-9536-463X)
- Helen L. Wu (ORCID: https://orcid.org/0000-0001-7101-5160)
- Benjamin N. Bimber (ORCID: https://orcid.org/0000-0001-8092-3080)
- R. Keith Reeves (ORCID: https://orcid.org/0000-0003-3157-2557)
- Gregory J. Boggy (ORCID: https://orcid.org/0000-0002-8283-5620)
- Louis J. Picker (ORCID: https://orcid.org/0000-0003-0546-398X)
- Jeremy Smedley (ORCID: https://orcid.org/0000-0003-3369-4662)
- Sohita Ojha (ORCID: https://orcid.org/0009-0008-4473-7078)
- Benjamin D. Varco-Merth
- Shana Feltham (ORCID: https://orcid.org/0009-0004-5862-5860)
- Maanasa Kaza (ORCID: https://orcid.org/0009-0000-4278-9108)
Institutions
- Oregon National Primate Research Center (US)
- Oregon Health & Science University (US)
- Duke University (US)
- Children's Cancer Therapy Development Institute (US)
Publication Details
- Journal
- Frontiers in Immunology
- Published
- 2025-08-08
- DOI
- https://doi.org/10.3389/fimmu.2025.1596760
- Primary Topic
- Single-cell and spatial transcriptomics
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- Bill and Melinda Gates Foundation
- National Institutes of Health
- Oregon National Primate Research Center
- NIH Office of the Director
- National Institute of Allergy and Infectious Diseases