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BACKGROUND The growth of high-throughput technologies such as microarrays and next generation sequencing has been accompanied by active research in data analysis methodology, producing new analysis methods at a rapid pace. While most of the newly developed methods are freely available, their use requires substantial computational skills. In order to enable(More)
Vascular endothelial growth factor (VEGF) is a key regulator of endothelial growth and permeability. However, VEGF may also target nonendothelial cells, as VEGF receptors and responsiveness have been detected for example in monocytes, and high concentrations of VEGF have been reported in human semen. In this work we present evidence that overexpression of(More)
Structural biology, homology modelling and rational drug design require accurate three-dimensional macromolecular coordinates. However, the coordinates in the Protein Data Bank (PDB) have not all been obtained using the latest experimental and computational methods. In this study a method is presented for automated re-refinement of existing structure models(More)
MicroRNAs (miRNAs) are small regulatory molecules that cause post-transcriptional gene silencing. Although some miRNAs are known to have region-specific expression patterns in the adult brain, the functional consequences of the region-specificity to the gene regulatory networks of the brain nuclei are not clear. Therefore, we studied miRNA expression(More)
Hadoop-BAM is a novel library for the scalable manipulation of aligned next-generation sequencing data in the Hadoop distributed computing framework. It acts as an integration layer between analysis applications and BAM files that are processed using Hadoop. Hadoop-BAM solves the issues related to BAM data access by presenting a convenient API for(More)
SUMMARY Hadoop MapReduce-based approaches have become increasingly popular due to their scalability in processing large sequencing datasets. However, as these methods typically require in-depth expertise in Hadoop and Java, they are still out of reach of many bioinformaticians. To solve this problem, we have created SeqPig, a library and a collection of(More)
Programmatic access to data and tools through the web using so-called web services has an important role to play in bioinformatics. In this article, we discuss the most popular approaches based on SOAP/WS-I and REST and describe our, a cross section of the community, experiences with providing and using web services in the context of biological sequence(More)
P-selectin expressed on the surface of endothelium mediates leukocyte adhesion in vitro and rolling in vivo. Several inducers of cell-surface P-selectin expression on endothelial cells (EC) have previously been identified, all of which yield transient cell-surface expression of P-selectin lasting minutes to a few hours. We now show that a T-lymphocyte(More)
Sequence similarity/database searching is a cornerstone of molecular biology. PairsDB is a database intended to make exploring protein sequences and their similarity relationships quick and easy. Behind PairsDB is a comprehensive collection of protein sequences and BLAST and PSI-BLAST alignments between them. Instead of running BLAST or PSI-BLAST(More)
Identification of reliable molecular markers that show differential expression between distinct groups of samples has remained a fundamental research problem in many large-scale profiling studies, such as those based on DNA microarray or mass-spectrometry technologies. Despite the availability of a wide spectrum of statistical procedures, the users of the(More)