SmartPhase: Accurate and fast phasing of heterozygous variant pairs for genetic diagnosis of rare diseases.

There is an increasing need to use genome and transcriptome sequencing to genetically diagnose patients suffering from suspected monogenic rare diseases. The proper detection of compound heterozygous variant combinations as disease-causing candidates is a challenge in diagnostic workflows as haplotype information is lost by currently used next-generation sequencing technologies. Consequently, computational tools are required to phase, or resolve the haplotype of, the high number of heterozygous variants in the exome or genome of each patient.

The bioinformatics of the yeast genome-A historical perspective.

From 1989 to 1997, the yeast genome was sequenced by a worldwide international consortium initiated and conducted by André Goffeau (1935-2018). The article describes the pioneering collaboration of yeast scientists from a bioinformatics perspective. Indeed, the yeast genome has turned bioinformatics from an exotic hobby of few nerds into a discipline indispensable for answering biological questions using computational methods.

PhenoDis: a comprehensive database for phenotypic characterization of rare cardiac diseases.

Background: Thoroughly annotated data resources are a key requirement in phenotype dependent analysis and diagnosis of diseases in the area of precision medicine. Recent work has shown that curation and systematic annotation of human phenome data can significantly improve the quality and selectivity for the interpretation of inherited diseases. We have therefore developed PhenoDis, a comprehensive, manually annotated database providing symptomatic, genetic and imprinting information about rare cardiac diseases.

KNIME4NGS: a comprehensive toolbox for next generation sequencing analysis.

Summary: Analysis of Next Generation Sequencing (NGS) data requires the processing of large datasets by chaining various tools with complex input and output formats. In order to automate data analysis, we propose to standardize NGS tasks into modular workflows. This simplifies reliable handling and processing of NGS data, and corresponding solutions become substantially more reproducible and easier to maintain.

Identification and Characterization of Carboxylesterases from Brachypodium distachyon Deacetylating Trichothecene Mycotoxins.

Increasing frequencies of 3-acetyl-deoxynivalenol (3-ADON)-producing strains of Fusarium graminearum (3-ADON chemotype) have been reported in North America and Asia. 3-ADON is nearly nontoxic at the level of the ribosomal target and has to be deacetylated to cause inhibition of protein biosynthesis. Plant cells can efficiently remove the acetyl groups of 3-ADON, but the underlying genes are yet unknown.