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NEAT: a framework for building fully automated NGS pipelines and analyses
Background: The analysis of next generation sequencing (NGS) has become a standard task for many laboratories in the life sciences. Though there exists several tools to support... -
Roar: detecting alternative polyadenylation with standard mRNA sequencing lib...
Background Post-transcriptional regulation is a complex mechanism that plays a central role in defining multiple cellular identities starting from a common genome. Modifications... -
"A scalability study of phylogenetic network inference methods using empirica...
Background Branching events in phylogenetic trees reflect bifurcating and/or multifurcating speciation and splitting events. In the presence of gene flow, a phylogeny cannot be... -
Cnidaria: fast, reference-free clustering of raw and assembled genome and tra...
Background: Identification of biological specimens is a major requirement for a range of applications. Reference-free methods analyse unprocessed sequencing data without relying... -
Bioinformatics identification of new targets for improving low temperature st...
Background Phenotypic studies in Triticeae have shown that low temperature-induced protective mechanisms are developmentally regulated and involve dynamic acclimation processes.... -
Combining location-and-scale batch effect adjustment with data cleaning by la...
Background In the context of high-throughput molecular data analysis it is common that the observations included in a dataset form distinct groups; for example, measured at... -
EchinoDB, an application for comparative transcriptomics of deeply-sampled cl...
Background One of our goals for the echinoderm tree of life project (http://echinotol.org) is to identify orthologs suitable for phylogenetic analysis from next-generation... -
A fast exact sequential algorithm for the partial digest problem
Background Restriction site analysis involves determining the locations of restriction sites after the process of digestion by reconstructing their positions based on the... -
Evaluation of logistic regression models and effect of covariates for case–co...
Background Next generation sequencing provides a count of RNA molecules in the form of short reads, yielding discrete, often highly non-normally distributed gene expression... -
SnoReport 2.0: new features and a refined Support Vector Machine to improve s...
Background snoReport uses RNA secondary structure prediction combined with machine learning as the basis to identify the two main classes of small nucleolar RNAs, the box H/ACA... -
AutoSOME: a clustering method for identifying gene expression modules without...
Abstract Background Clustering the information content of large high-dimensional gene expression datasets has widespread application in "omics" biology. Unfortunately, the... -
"CellProfiler Tracer: exploring and validating high-throughput, time-lapse mi...
Background Time-lapse analysis of cellular images is an important and growing need in biology. Algorithms for cell tracking are widely available; what researchers have been... -
QUADrATiC: scalable gene expression connectivity mapping for repurposing FDA-...
Background Gene expression connectivity mapping has proven to be a powerful and flexible tool for research. Its application has been shown in a broad range of research topics,...
