Utrecht University

About: Utrecht University is a education organization based out in Utrecht, Utrecht, Netherlands. It is known for research contribution in the topics: Population & Poison control. The organization has 58176 authors who have published 139351 publications receiving 6214282 citations. The organization is also known as: UU & Universiteit Utrecht.

Content-Based Music Information Retrieval: Current Directions and Future Challenges

Abstract: The steep rise in music downloading over CD sales has created a major shift in the music industry away from physical media formats and towards online products and services. Music is one of the most popular types of online information and there are now hundreds of music streaming and download services operating on the World-Wide Web. Some of the music collections available are approaching the scale of ten million tracks and this has posed a major challenge for searching, retrieving, and organizing music content. Research efforts in music information retrieval have involved experts from music perception, cognition, musicology, engineering, and computer science engaged in truly interdisciplinary activity that has resulted in many proposed algorithmic and methodological solutions to music search using content-based methods. This paper outlines the problems of content-based music information retrieval and explores the state-of-the-art methods using audio cues (e.g., query by humming, audio fingerprinting, content-based music retrieval) and other cues (e.g., music notation and symbolic representation), and identifies some of the major challenges for the coming years.

STRING 7—recent developments in the integration and prediction of protein interactions

Abstract: Information on protein–protein interactions is still mostly limited to a small number of model organisms, and originates from a wide variety of experimental and computational techniques The database and online resource STRING generalizes access to protein interaction data, by integrating known and predicted interactions from a variety of sources The underlying infrastructure includes a consistent body of completely sequenced genomes and exhaustive orthology classifications, based on which interaction evidence is transferred between organisms Although primarily developed for protein interaction analysis, the resource has also been successfully applied to comparative genomics, phylogenetics and network studies, which are all facilitated by programmatic access to the database backend and the availability of compact download files As of release 7, STRING has almost doubled to 373 distinct organisms, and contains more than 15 million proteins for which associations have been pre-computed Novel features include AJAX-based web-navigation, inclusion of additional resources such as BioGRID, and detailed protein domain annotation STRING is available at http:// stringemblde/

Genome phylogeny based on gene content

Abstract: Species phylogenies derived from comparisons of single genes are rarely consistent with each other, due to horizontal gene transfer, unrecognized paralogy and highly variable rates of evolution. The advent of completely sequenced genomes allows the construction of a phylogeny that is less sensitive to such inconsistencies and more representative of whole-genomes than are single-gene trees. Here, we present a distance-based phylogeny constructed on the basis of gene content, rather than on sequence identity, of 13 completely sequenced genomes of unicellular species. The similarity between two species is defined as the number of genes that they have in common divided by their total number of genes. In this type of phylogenetic analysis, evolutionary distance can be interpreted in terms of evolutionary events such as the acquisition and loss of genes, whereas the underlying properties (the gene content) can be interpreted in terms of function. As such, it takes a position intermediate to phylogenies based on single genes and phylogenies based on phenotypic characteristics. Although our comprehensive genome phylogeny is independent of phylogenies based on the level of sequence identity of individual genes, it correlates with the standard reference of prokarytic phylogeny based on sequence similarity of 16s rRNA. Thus, shared gene content between genomes is quantitatively determined by phylogeny, rather than by phenotype, and horizontal gene transfer has only a limited role in determining the gene content of genomes.