As spatial molecular data grow in scope, there is a pressing need to identify disease-associated spatial structures. Current approaches typically make restrictive assumptions such as representing tissue regions by abundances of discrete cell types and samples by abundances of discrete niches; this risks overlooking imp...
Yakir A. Reshef, Lakshay Sood, Michelle Curtis et al.· Nature Methods· 0 citations
Dynema (Dynamic eQTL mapping in single cells) is proposed for fast and accurate genome-wide mapping of context-dependent and independent eQTL effects at true single-cell resolution and shows that TSPAN32 and other autoimmune loci colocalize with cell-state-dependent eQTLs.
José Alquicira-Hernández, E. Dorans, Yoshihiro Tomofuji et al.· bioRxiv· 0 citations
Thousands of genetic variants are associated with autoimmune diseases, but causal variants, their mechanisms, and the pathogenic context in which they act are elusive. Knowledge of pathogenic contexts may enable effective targeted therapies, instead of broad immunosuppressive approaches. First, to focus on the genetics...
Yoshihiro Tomofuji, Ze-Peng Mu, Hafsa M Mire et al.· bioRxiv· 0 citations
Single-cell technologies enable linking disease-risk variants to gene regulatory effects in specific cell-state contexts. However, most so called “single-cell eQTL” studies use a “pseudobulking” strategy to identify expression Quantitative Trait Loci (eQTLs), obscuring subtle dynamic regulatory effects of disease allel...
José Alquicira-Hernández, E. Dorans, Yoshihiro Tomofuji et al.· bioRxiv· 0 citations
A near-complete map of human TCR germline diversity is generated, capturing over 94% of common alleles, and pervasive evidence of pathogen-driven natural selection on TCR genes is found, including diversifying selection across CDR and framework codons.
S. Mantena, Ali Akbari, S. Raychaudhuri· Journal of Immunology· 0 citations
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