We consider topology based criteria for the selection of optimal beam orientations for conformal external radiotherapy. The advantage of such an approach is that computation time is considerably reduced since no dose calculation is required. The algorithm preclassifies all possible irradiation directions by assigning to each a fitness measure, the geometry fitness factor (GFF). This factor is a...

All ribosome profiling experiments analyzed involve attaching a known sequence to the 3′ end of RNA footprints to which a reverse transcription primer can be annealed. Some experiments use polyA tailing for this purpose, while others attach an oligonucleotide linker sequence. For experiments using polyA tailing, reads were trimmed from the end back to the first base that wasn’t an A or an N. Fo...

Objectives: Human lung sounds are important indicators of underlying lung pathology. The prime objective of this work is to classify normal and adventitious lung sounds in paediatric population using spectral features and artificial neural networks. Material and Method: 3M Littmann 3200 electronic stethoscope was used to record the lung sounds. After pre-processing ten spectral features were ex...

Alternative splicing plays a key role in the regulation of the central dogma. Four major types of alternative splicing have been classified as intron retention, exon skipping, alternative 5 splice sites or alternative donor sites, and alternative 3 splice sites or alternative acceptor sites. A few algorithms have been developed to detect splice junctions from RNA-Seq reads. However, there are f...

UNLABELLED ChIP-based technology is becoming the leading technology to globally profile thousands of transcription factors and elucidate the transcriptional regulation mechanisms in living cells. It has evolved rapidly in recent years, from hybridization with spotted or tiling microarray (ChIP-chip), to pair-end tag sequencing (ChIP-PET), to current massively parallel sequencing (ChIP-seq). Alt...

Many tools are available for visualizing RNA or DNA secondary structures, but there is scarce implementation in JavaScript that provides seamless integration with the increasingly popular web computational platforms. We have developed JNSViewer, a highly interactive web service, which is bundled with several popular tools for DNA/RNA secondary structure prediction and can provide precise and in...

SUMMARY Insertional mutagenesis is a powerful method for gene discovery. To identify the location of insertion sites in the genome linker based polymerase chain reaction (PCR) methods (such as splinkerette-PCR) may be employed. We have developed a web application called iMapper (Insertional Mutagenesis Mapping and Analysis Tool) for the efficient analysis of insertion site sequence reads agains...

Starr is an extension of the Ringo [6] package for the analysis of ChIP-chip projects. Whereas the latter is specialized to the processing of Nimblegen and Agilent arrays, the former provides all corresponding features for Affymetrix arrays. Data can be read in from Affymetrix CEL-files, or from text files in gff format. Standard quality assessment and data normalization tools are available. St...

The latest supercomputers incorporate a high number of compute units under the form of manycore accelerators. Such accelerators, like GPUs, have integrated processors where a massively high number of threads, in the order of thousands, execute concurrently. Compared to single-CPU throughput performance, they offer higher levels of parallelism. Therefore, they represent an indispensable technolo...