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This paper reports an integrated solution, called BALSA, for the secondary analysis of next generation sequencing data; it exploits the computational power of GPU and an intricate memory management to give a fast and accurate analysis. From raw reads to variants...

["Bioinformatics","Computational Biology","Genomics","Computational Science"]

The neXtProt database is a comprehensive knowledge platform recently adopted by the Chromosome-centric Human Proteome Project as the main reference database. The primary goal of the project is to identify and catalog every human protein encoded in the human genome....

["Bioinformatics","Computational Biology"]

Background: The individual running style has an impact on the running performance as well as the running injury risk. In order to increase the performance and lower the injury risk, runners should be educated towards a healthy running style. But before advices...

["Bioinformatics","Anatomy and Physiology","Orthopedics","Computational Science"]

In ChIP-Seq and DNase-Seq experiments the density of background reads can vary from sample to sample. Differences in background read densities between samples do not necessarily correspond to proportional changes of read densities in true ChIP-Seq peaks. Therefore,...


The vision of the Human Motion Project is to become a successful analogue of the Human Genome Project: improving human health by an open collaborative technology platform for the mobile medical monitoring of human motion. The basis is a growing “critical path toolbox”...

["Bioinformatics","Clinical Trials","Evidence Based Medicine","Kinesiology","Science and Medical Education"]

Background: Unlike full reading, 'skim-reading' involves the process of looking quickly over information in an attempt to cover more material whilst still being able to retain a superficial view of the underlying content. Within this work, we specifically emulate...

["Bioinformatics","Computational Science","Science and Medical Education"]

scikit-image is an image processing library that implements algorithms and utilities for use in research, education and industry applications. It is released under the liberal "Modified BSD" open source license, provides a well-documented API in the Python programming...

["Bioinformatics","Computational Biology","Computational Science","Human-Computer Interaction","Science and Medical Education"]

Background. As whole genome sequence data from bacterial isolates becomes cheaper to generate, computational methods are needed to correlate sequence data with biological observations. Here we present the large-scale BLAST score ratio (LS-BSR) pipeline, which rapidly...

["Bioinformatics","Computational Biology","Genomics","Microbiology"]

Multiple cell types form specialized protein complexes, podosomes or invadopodia and collectively referred to as invadosomes, which are used by the cell to actively degrade the surrounding extracellular matrix. Due to their potential importance in both healthy...

["Bioengineering","Bioinformatics","Cell Biology","Computational Biology","Computational Science"]

Restriction-site associated DNA sequencing (RADseq) has become a powerful and useful approach for population genomics. Currently, no software exists that utilizes both paired-end reads from RADseq data to efficiently produce population-informative variant calls,...

["Bioinformatics","Genomics","Marine Biology","Molecular Biology"]

Classification of antibody Complementarity-Determining Region (CDR) conformations is an important step that drives antibody modelling and engineering, prediction from sequence, directed mutagenesis and induced-fit studies, and allows inferences on sequence-to-structure...

["Bioinformatics","Computational Biology","Molecular Biology","Immunology"]

The accurate prediction of the conformation of Complementarity-Determining Regions (CDRs) is important in modelling antibodies for protein engineering applications. Specifically, the Canonical paradigm has proved successful in predicting the CDR conformation in...

["Bioinformatics","Computational Biology","Molecular Biology","Immunology"]

Many protein domains bind to short peptide sequences, called linear motifs. Data on their sequence specificities is sparse, which is why biologists usually resort to basic pattern searches to identify new putative binding sites for experimental follow-up. Most...

["Bioinformatics","Computational Biology"]

Background. Semantic Web technologies are increasingly used in biological database systems. The improved expressiveness shows advantages in tracking provenance and allowing knowledge to be more explicitly annotated. The list of semantic web standards needs a complementary...

["Bioinformatics","Computational Science"]

While numerous effective peak finders have been developed for eukaryotic systems, we have found that the approaches used can be error prone when run on high coverage bacterial and archaeal ChIP-Seq datasets. We have developed Pique, an easy to use ChIP-Seq peak...


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