Differential expression analysis (DEA) is one of the main instruments utilized for revealing molecular mechanisms in pathological and physiological conditions. DIANA-mirExTra v2.0 (http://www.microrna.gr/mirextrav2) performs a combined DEA of mRNAs and microRNAs (miRNAs...

Abstract Background The increasing volume and complexity of high-throughput genomic data make analysis and prioritization of variants difficult for researchers with limited bioinformatics skills. Variant Ranker allows researchers to rank identified variants and determin...

Summary: Identifying, amongst millions of publications available in MEDLINE, those that are relevant to specific microRNAs (miRNAs) of interest based on keyword search faces major obstacles. References to miRNA names in the literature often deviate from standard nomencl...

BACKGROUND: Recent advances in the field of high-throughput genomics have rendered possible the performance of genome-scale studies to define the nucleosomal landscapes of eukaryote genomes. Such analyses are aimed towards providing a better understanding of the process...

The advent of high-throughput genomic technologies is enabling analyses on thousands or even millions of single-nucleotide polymorphisms (SNPs). At the same time, the selection of a minimum number of SNPs with the maximum information content is becoming increasingly pro...

Background Understanding the topology and dynamics of the human protein-protein interaction (PPI) network will significantly contribute to biomedical research, therefore its systematic reconstruction is required. Several meta-databases integrate source PPI datasets, but...

It has been acknowledged that source databases recording experimentally supported human protein-protein interactions (PPIs) exhibit limited overlap. Thus, the reconstruction of a comprehensive PPI network requires appropriate integration of multiple heterogeneous primar...

microRNAs are short non-coding RNAs that post-transcriptionally regulate gene expression for which the identification of promoter and primary transcripts (pri-miRNAs) has been difficult. Here the authors describe microTSS, an algorithm that supports the precise identifi...

StRAnGER is a web application for the automated statistical analysis of annotated gene profiling experiments, exploiting controlled biological vocabularies, like the Gene Ontology or the KEGG pathways terms. Starting from annotated lists of differentially expressed gene...

Plan Nacional I+D+I of Spain [BFU2008-00366, BFU2011-23851 to J.R., BFU2010-21975-C03-01 to J.E.P.-O.]; Generalitat de Catalunya [2009SGR01222 to J.R.]; Generalitat Valenciana [Prometeo 088/2011 to J.E.P.-O.]. Funding for open access charge: Plan Nacional I + D + I of S...