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Motivation: Next-generation sequencing has become an important tool for genome-wide quantification of DNA and RNA. However, a major technical hurdle lies in the need to map short sequence reads back to their correct locations in a reference genome. Here, we investigate the impact of SNP variation...
Motivation: The recent development of methods for modeling RNA 3D structures using coarse-grain approaches creates a need to bridge low- and high-resolution modeling methods. Although they contain topological information, coarse-grain models lack atomic detail, which limits their utility for some...
Summary: Large numbers of genomes are being sequenced regularly and the rate will go up in future due to availability of new genome sequencing techniques. In order to understand genotype to phenotype relationships, it is necessary to identify sequence variations at the genomic level. Alignment of...
Motivation: The need to align spectra to correct for mass-to-charge experimental variation is a problem that arises in mass spectrometry (MS). Most of the MS-based proteomic data analysis methods involve a two-step approach, identify peaks first and then do the alignment and statistical inference...
Motivation: All metabolic networks contain metabolites, such as ATP and NAD, known as currency metabolites, which take part in many reactions. These are often removed in the study of these networks, but no consensus exists on what actually constitutes a currency metabolite, and it is also unclear...