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Science Studies Examine Ancient Smallpox, Cell Deconvolution Approach

An analysis of viral DNA isolated from ancient human remains reveals that smallpox was widespread in Northern Europe in the 7th century, nearly 1,000 years earlier than previously known. A team led by scientists from the University of Cambridge and the University of Copenhagen recovered viral sequences from 13 northern European individuals, including 11 from the Viking Age, and reconstructed near-complete smallpox virus genomes for four of them. The sequences reveal a now-extinct sister clade of the modern smallpox viruses that was in circulation before the eradication of the disease, with the most recent common ancestor dated to around 1,700 years ago. "Distinct patterns of gene inactivation in the four near-complete sequences show that different evolutionary paths of genotypic host adaptation resulted in variola viruses that circulated widely among humans," the study's authors write. GenomeWeb has more on this here.

A computational method for cell deconvolution based on gene expression is presented in Science Advances this week. Called Scaden, the deep neural network was trained on single-cell RNA sequencing data to predict cell type proportions for input expression samples of cell mixtures. According to its developers at the German Center for Neurodegenerative Diseases and University Medical Center Hamburg-Eppendorf, a single trained network reliably deconvolves bulk RNA-seq and microarray data, as well as human and mouse tissue expression data, and leverages the combined information of multiple datasets. Scaden outperforms existing deconvolution algorithms in both precision and robustness, suggesting that deep neural network-based architectures "will become an algorithmic mainstay of cell type deconvolution," the researchers write.