TE-Seq: A Transposable Element Annotation and RNA-Seq Pipeline.

Motivation: The recognition that transposable elements (TEs) play important roles in many biological processes has elicited growing interest in analyzing sequencing data derived from this 'dark genome'. This is however complicated by the highly repetitive nature of these sequences in genomes, requiring the deployment of several problem-specific tools as well as the curation of appropriate genome annotations. This pipeline aims to make the analysis of TE sequences and their expression more generally accessible.

cGAS deficient mice display premature aging associated with de-repression of LINE1 elements and inflammation.

Aging-associated inflammation, or 'inflammaging" is a driver of multiple age-associated diseases. Cyclic GMP-AMP Synthase (cGAS) is a cytosolic DNA sensor that functions to activate interferon response upon detecting viral DNA in the cytoplasm. cGAS contributes to inflammaging by responding to endogenous signals such as damaged DNA or LINE1 (L1) cDNA which forms in aged cells.

Associations between Minority Health Social Vulnerability Index Scores, Rurality, and Histoplasmosis Incidence, 8 US States.

To explore associations between histoplasmosis and race and ethnicity, socioeconomic status, and rurality, we conducted an in-depth analysis of social determinants of health and histoplasmosis in 8 US states. Using the Minority Health Social Vulnerability Index (MH SVI), we analyzed county-level histoplasmosis incidence (cases/100,000 population) from the 8 states by applying generalized linear mixed hurdle models. We found that histoplasmosis incidence was higher in counties with limited healthcare infrastructure and access as measured by the MH SVI and in more rural counties.