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TCR germline diversity reveals evidence of natural selection on variable and joining alpha chain genes.
Mantena, Sreekar, Ali Akbari, and Soumya Raychaudhuri. 2025. “TCR Germline Diversity Reveals Evidence of Natural Selection on Variable and Joining Alpha Chain Genes.”. BioRxiv : The Preprint Server for Biology.
Functional and dysfunctional T regulatory cell states in human tissues in RA and other autoimmune arthritic diseases.
Koh, Byunghee, Shani T Gal Oz, Ryota Sato, Hung N Nguyen, Garrett Dunlap, Chrisopher Mahony, Chrissy Bolton, et al. 2025. “Functional and Dysfunctional T Regulatory Cell States in Human Tissues in RA and Other Autoimmune Arthritic Diseases.”. BioRxiv : The Preprint Server for Biology.
Integration of large, complex single-cell datasets with Harmony2.
Patikas, Nikolaos, Hongcheng Yao, Roopa Madhu, Soumya Raychaudhuri, Martin Hemberg, and Ilya Korsunsky. 2026. “Integration of Large, Complex Single-Cell Datasets With Harmony2.”. BioRxiv : The Preprint Server for Biology.
Isabella Kruger
An Inflammatory and Quiescent HSC Subpopulation Expands with Age in Humans.
Safina, Ksenia R, Dylan A Kotliar, Michelle Curtis, Jonathan D Good, Chen Weng, Shawn David, Soumya Raychaudhuri, et al. 2025. “An Inflammatory and Quiescent HSC Subpopulation Expands With Age in Humans.”. BioRxiv : The Preprint Server for Biology.
Author Correction: Distinct fibroblast subsets drive inflammation and damage in arthritis.
Croft, Adam P, Joana Campos, Kathrin Jansen, Jason D Turner, Jennifer Marshall, Moustafa Attar, Loriane Savary, et al. 2025. “Author Correction: Distinct Fibroblast Subsets Drive Inflammation and Damage in Arthritis.”. Nature.
immunogenomics
Reproducible single-cell annotation of programs underlying T cell subsets, activation states and functions.
Kotliar, Dylan, Michelle Curtis, Ryan Agnew, Kathryn Weinand, Aparna Nathan, Yuriy Baglaenko, Kamil Slowikowski, et al. 2025. “Reproducible Single-Cell Annotation of Programs Underlying T Cell Subsets, Activation States and Functions.”. Nature Methods.
Modeling heterogeneity in single-cell perturbation states enhances detection of response eQTLs.
Valencia, Cristian, Aparna Nathan, Joyce B Kang, Laurie Rumker, Hyunsun Lee, and Soumya Raychaudhuri. 2025. “Modeling Heterogeneity in Single-Cell Perturbation States Enhances Detection of Response EQTLs.”. Nature Genetics.