University of Copenhagen

About: University of Copenhagen is a education organization based out in Copenhagen, Denmark. It is known for research contribution in the topics: Population & Medicine. The organization has 57645 authors who have published 149740 publications receiving 5903093 citations. The organization is also known as: Copenhagen University & Københavns Universitet.

mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters

Abstract: Motivation: Ancient DNA (aDNA) molecules in fossilized bones and teeth, coprolites, sediments, mummified specimens and museum collections represent fantastic sources of information for evolutionary biologists, revealing the agents of past epidemics and the dynamics of past populations. However, the analysis of aDNA generally faces two major issues. Firstly, sequences consist of a mixture of endogenous and various exogenous backgrounds, mostly microbial. Secondly, high nucleotide misincorporation rates can be observed as a result of severe post-mortem DNA damage. Such misincorporation patterns are instrumental to authenticate ancient sequences versus modern contaminants. We recently developed the user-friendly mapDamage package that identifies such patterns from next-generation sequencing (NGS) sequence datasets. The absence of formal statistical modeling of the DNA damage process however precluded rigorous quantitative comparisons across samples. Results: Here, we describe mapDamage 2.0 that extends the original features of mapDamage by incorporating a statistical model of DNA damage. Assuming that damage events depend only on sequencing position and post-mortem deamination, our Bayesian statistical framework provides estimates of four key features of aDNA molecules: the average length of overhangs (�), nick frequency (�), and cytosine deamination rates in both double stranded regions (�d) and overhangs (�s). Our model enables rescaling base quality scores according to their probability of being damaged. mapDamage 2.0 handles NGS datasets with ease and is compatible with a wide range of DNA library protocols. Availability: mapDamage 2.0 is available at XXXXX as a Python package and documentation is maintained at the Centre for GeoGenetics website (geogenetics.ku.dk/publications/mapdamage/).

Chiral quantum optics

Abstract: Spinorbit coupling in electrons leads to many fascinating phenomena and important applications, from topological insulators to spintronics. Researchers have recently been exploring whether effects analogous to spinorbit coupling can arise in photons and, if so, what sort of perspectives this provides. Optical spinorbit coupling can lead to direction-dependent emissions and so may allow quantum optics to be chiral. This Review looks at experiments in the realm of chiral quantum optics and discusses how these demonstrations could add a new dimension of control to quantum networks and quantum many-body physics.