Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM.
Published in Bioinformatics
Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM.
The variant call format and VCFtools.
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Published in Bioinformatics (Oxford, England)
The variant call format (VCF) is a generic format for storing DNA polymorphism data such as SNPs, insertions, deletions and structural variants, together with rich annotations. VCF is usually stored in a compressed manner and can be indexed for fast data retrieval of variants from a range of positions on the reference genome. The format was develop...
Classifying G-protein coupled receptors with support vector machines.
Published in Bioinformatics
Motivation: The enormous amount of protein sequence data uncovered by genome research has increased the demand for computer software that can automate the recognition of new proteins. We discuss the relative merits of various automated methods for recognizing G-Protein Coupled Receptors (GPCRs), a superfamily of cell membrane proteins. GPCRs are fo...
Into the heart of darkness: large-scale clustering of human non-coding DNA.
Published in Bioinformatics
Site identification in high-throughput RNA-protein interaction data.
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Published in Bioinformatics
HAL: a hierarchical format for storing and analyzing multiple genome alignments.
Published in Bioinformatics
