Sonographic visibility of cannulas using convex ultrasound transducers.

The key for safe ultrasound (US)-guided punctures is a good visibility of the cannula. When using convex transducers for deep punctures, the incident angle between US beam and cannula varies along the cannula leading to a complex visibility pattern. Here, we present a method to systematically investigate the visibility throughout the US image.

VARiD: a variation detection framework for color-space and letter-space platforms.

Motivation: High-throughput sequencing (HTS) technologies are transforming the study of genomic variation. The various HTS technologies have different sequencing biases and error rates, and while most HTS technologies sequence the residues of the genome directly, generating base calls for each position, the Applied Biosystem's SOLiD platform generates dibase-coded (color space) sequences. While combining data from the various platforms should increase the accuracy of variation detection, to date there are only a few tools that can identify variants from color space data, and none that can analyze color space and regular (letter space) data together.

SHRiMP: accurate mapping of short color-space reads.

The development of Next Generation Sequencing technologies, capable of sequencing hundreds of millions of short reads (25-70 bp each) in a single run, is opening the door to population genomic studies of non-model species. In this paper we present SHRiMP - the SHort Read Mapping Package: a set of algorithms and methods to map short reads to a genome, even in the presence of a large amount of polymorphism. Our method is based upon a fast read mapping technique, separate thorough alignment methods for regular letter-space as well as AB SOLiD (color-space) reads, and a statistical model for false positive hits.