Measuring quality of DNA sequence data via degradation.

We formulate and apply a novel paradigm for characterization of genome data quality, which quantifies the effects of intentional degradation of quality. The rationale is that the higher the initial quality, the more fragile the genome and the greater the effects of degradation. We demonstrate that this phenomenon is ubiquitous, and that quantified measures of degradation can be used for multiple purposes, illustrated by outlier detection.

Specified Certainty Classification, with Application to Read Classification for Reference-Guided Metagenomic Assembly.

Specified Certainty Classification (SCC) classifiers whose outputs carry uncertainties, typically in the form of Bayesian posterior probabilities. By allowing the classifier output to be less precise than one of a set of atomic decisions, SCC allows all decisions to achieve a specified level of certainty, as well as provides insights into classifier behavior by examining all decisions that are possible. Our primary illustration is read classification for reference-guided genome assembly, but we demonstrate the breadth of SCC by also analyzing COVID-19 vaccination data.

Ascorbate-Dependent Peroxidase (APX) from Leishmania amazonensis Is a Reactive Oxygen Species-Induced Essential Enzyme That Regulates Virulence.

The molecular mechanisms underlying biological differences between two species that cause cutaneous disease, and , are poorly understood. In , reactive oxygen species (ROS) signaling drives differentiation of nonvirulent promastigotes into forms capable of infecting host macrophages. Tight spatial and temporal regulation of HO is key to this signaling mechanism, suggesting a role for ascorbate-dependent peroxidase (APX), which degrades mitochondrial HO Earlier studies showed that -null parasites are viable, accumulate higher levels of HO, generate a greater yield of infective metacyclic promastigotes, and have increased virulence.