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BACKGROUND: Gene set enrichment (GSE) analysis is a popular framework for condensing information from gene expression profiles into a pathway or signature summary. The strengths of this approach over single gene analysis...

Although genomewide RNA expression analysis has become a routine tool in biomedical research, extracting biological insight from such information remains a major challenge. Here, we describe a powerful analytical method ...

PAML, currently in version 4, is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML). The programs may be used to compare and test phylogenetic trees, but their main...

BACKGROUND: RNA-Seq is revolutionizing the way transcript abundances are measured. A key challenge in transcript quantification from RNA-Seq data is the handling of reads that map to multiple genes or isoforms. This issu...

The standard bootstrap (SBS), despite being computationally intensive, is widely used in maximum likelihood phylogenetic analyses. We recently proposed the ultrafast bootstrap approximation (UFBoot) to reduce computing t...

limma is an R/Bioconductor software package that provides an integrated solution for analysing data from gene expression experiments. It contains rich features for handling complex experimental designs and for informatio...

Materias / palabras clave: soft computing in real-world systems, computational intelligence, learning theory, probability theory, hybrid methods, rough sets; Technology: Technology (General): Industrial engineering. Management engineering: Informa...

Materias / palabras clave: fuzzy information, soft computing, fuzzy engineering, fuzzy operations research, artificial intelligence, fuzzy sets and systems; Technology: Engineering (General). Civil engineering (General); Science: Mathematics