Bioinformatics

Motivation: The β-barrel is a ubiquitous fold that is deployed to accomplish a wide variety of biological functions including membrane-embedded pores. Key influences of β-barrel lumen diameter include the number of β-strands ( n ) and the degree of ...

Motivation: The sequencing of over a thousand natural strains of the model plant Arabidopsis thaliana is producing unparalleled information at the genetic level for plant researchers. To enable the rapid exploitation of these data for functional ...

Motivation: In light of the increasing adoption of targeted resequencing (TR) as a cost-effective strategy to identify disease-causing variants, a robust method for copy number variation (CNV) analysis is needed to maximize the value of this ...

Motivation: Markov models are very popular for analyzing complex sequences such as protein sequences, whose sources are unknown, or whose underlying statistical characteristics are not well understood. A major problem is the computational complexity ...

Motivation: Ultra-high-throughput sequencing produces duplicate and near-duplicate reads, which can consume computational resources in downstream applications. A tool that collapses such reads should reduce storage and assembly complications and ...

Motivation: The identification of the sites at which transcription factors (TFs) bind to Deoxyribonucleic acid (DNA) is an important problem in molecular biology. Many computational methods have been developed for motif finding, most of them based on ...

Motivation: The expansion of DNA sequencing capacity has enabled the sequencing of whole genomes from a number of related species. These genomes can be combined in a multiple alignment that provides useful information about the evolutionary history ...

Motivation: Finding geometrically similar protein binding sites is crucial for understanding protein functions and can provide valuable information for protein–protein docking and drug discovery. As the number of known protein–protein interaction ...

Motivation: Expression quantitative trait loci (eQTL) analysis links variations in gene expression levels to genotypes. For modern datasets, eQTL analysis is a computationally intensive task as it involves testing for association of billions of ...

Motivation: It is becoming increasingly evident that the analysis of genotype data from recently admixed populations is providing important insights into medical genetics and population history. Such analyses have been used to identify novel disease ...

Motivation: DNA methylation is a molecular modification of DNA that plays crucial roles in regulation of gene expression. Particularly, CpG rich regions are frequently hypermethylated in cancer tissues, but not methylated in normal tissues. However, ...

Motivation: To improve the understanding of molecular regulation events, various approaches have been developed for deducing gene regulatory networks from mRNA expression data.

Results: We present a new score for network inference, η², that is ...

Motivation: Several measures have been recently proposed for quantifying the functional similarity between gene products according to well-structured controlled vocabularies where biological terms are organized in a tree or in a directed acyclic ...

Motivation: Modern automated laboratories need substantial data management solutions to both store and make accessible the details of the experiments they perform. To be useful, a modern Laboratory Information Management System (LIMS) should be flexible ...

Summary: GECA is a fast, user-friendly and freely-available tool for representing gene exon/intron organization and highlighting changes in gene structure among members of a gene family. It relies on protein alignment, completed with the ...

Motivation: Rknots is a flexible R package providing tools for the detection and characterization of topological knots in biological polymers. The package is well documented and provides a simple syntax for data import and preprocessing, structure ...

Motivation: Meta-analysis of large gene expression datasets obtained from public repositories requires consistently annotated data. Curation of such experiments, however, is an expert activity which involves repetitive manipulation of text. Existing ...

Motivation: Mass spectrometry-based iTRAQ protein quantification is a high-throughput assay for determining relative protein expressions and identifying disease biomarkers. Processing and analysis of these large and complex data involves a number of ...

Summary: Anuran tissues, and especially skin, are a rich source of bioactive peptides and their precursors. We here present a manually curated database of antimicrobial and other defense peptides with a total of 2571 entries, most of them in the ...

Summary: Progress in high-throughput genomic technologies has led to the development of a variety of resources that link genes to functional information contained in the biomedical literature. However, tools attempting to link small molecules to ...

Summary: Transcription and chromatin regulators, and histone modifications play essential roles in gene expression regulation. We have created CistromeMap as a web server to provide a comprehensive knowledgebase of all of the publicly available ChIP-Seq ...