Alkes L Price

Jan 2, 2025 | nature.com | Alkes L Price

AbstractComplex diseases often have distinct mechanisms spanning multiple tissues. We propose tissue–gene fine-mapping (TGFM), which infers the posterior inclusion probability (PIP) for each gene–tissue pair to mediate a disease locus by analyzing summary statistics and expression quantitative trait loci (eQTL) data; TGFM also assigns PIPs to non-mediated variants.

Apr 9, 2024 | nature.com | Saori Sakaue |Kushal Dey |Karthik A. Jagadeesh |Masahiro Kanai |Michael Brenner |Alkes L Price | +1 more

AbstractTranslating genome-wide association study (GWAS) loci into causal variants and genes requires accurate cell-type-specific enhancer–gene maps from disease-relevant tissues. Building enhancer–gene maps is essential but challenging with current experimental methods in primary human tissues.

Nov 30, 2023 | nature.com | Aparna Nathan |Saori Sakaue |Alkes L Price |Tiffany Amariuta

AbstractIn autoimmune diseases such as rheumatoid arthritis, the immune system attacks the body’s own cells. Developing a precise understanding of the cell states where noncoding autoimmune risk variants impart causal mechanisms is critical to developing curative therapies.

Oct 9, 2023 | nature.com | Xilin Jiang |Martin Zhang |Alkes L Price

AbstractThe analysis of longitudinal data from electronic health records (EHRs) has the potential to improve clinical diagnoses and enable personalized medicine, motivating efforts to identify disease subtypes from patient comorbidity information. Here we introduce an age-dependent topic modeling (ATM) method that provides a low-rank representation of longitudinal records of hundreds of distinct diseases in large EHR datasets.

Aug 14, 2023 | nature.com | Tiffany Amariuta |Alkes L Price

AbstractIntegrative analyses of genome-wide association studies and gene expression data have implicated many disease-critical tissues. However, co-regulation of genetic effects on gene expression across tissues impedes distinguishing biologically causal tissues from tagging tissues.