latest news & announcements

PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration

An increasing amount of studies integrate mRNA sequencing data into MS-based proteomics to complement the translation product search space. However, several factors, including extensive regulation of mRNA translation and the need for three- or six-frame-translation, impede the use of mRNA-seq data for the construction of a protein sequence search database.

ViVaMBC: estimating viral sequence variation in complex populations from illumina deep-sequencing data using model-based clustering

Background: Deep-sequencing allows for an in-depth characterization of sequence variation in complex populations. However, technology associated errors may impede a powerful assessment of low-frequency mutations. Fortunately, base calls are complemented with quality scores which are derived from a quadruplet of intensities, one channel for each nucleotide type for Illumina sequencing. The highest intensity of the four channels determines the base that is called. Mismatch bases can often be corrected by the second best base, i.e. the base with the second highest intensity in the quadruplet.

(Article in Flanders Today) Q&A: Biologist Katrijn Vannerum on a unique new Master’s degree

Summary

Biologist Katrijn Vannerum explains why the new qualification in bioinformatics at Ghent University could have positive consequences for pest control in valuable crops

Keeping both parties happy

Katrijn Vannerum is project manager of the Bioinformatics Institute Ghent N2N at Ghent University. She’s one of the organisers of the new MSc in bioinformatics – the development of methods and software for understanding biological data – at Ghent University, a brand new curriculum in Flanders.

Sensor Function Virtualization to Support Distributed Intelligence in the Internet of Things

It is estimated that-by 2020-billion devices will be connected to the Internet. This number not only includes TVs, PCs, tablets and smartphones, but also billions of embedded sensors that will make up the "Internet of Things" and enable a whole new range of intelligent services in domains such as manufacturing, health, smart homes, logistics, etc. To some extent, intelligence such as data processing or access control can be placed on the devices themselves. Alternatively, functionalities can be outsourced to the cloud. In reality, there is no single solution that fits all needs.

We are all individuals ... bioinformatics in the personalized medicine era

The medical landscape is evolving at a rapid pace, creating the opportunity for more personalized patient treatment and shifting the way healthcare is approached and thought about. With the availability of (epi)genome-wide, transcriptomic and proteogenomic profiling techniques detailed characterization of a disease at the level of the individual is now possible, offering the opportunity for truly tailored approaches for treatment and patient care.

Increasing the power of the Mann-Whitney test in randomized experiments through flexible covariate adjustment

The Mann-Whitney U test is frequently used to evaluate treatment effects in randomized experiments with skewed outcome distributions or small sample sizes. It may lack power, however, because it ignores the auxiliary baseline covariate information that is routinely collected. Wald and score tests in so-called probabilistic index models generalize the Mann-Whitney U test to enable adjustment for covariates, but these may lack robustness by demanding correct model specification and do not lend themselves to small sample inference.

Genome wide expression profiling of p53 regulated miRNAs in neuroblastoma

Restoration of the antitumor activity of p53 could offer a promising approach for the treatment of neuroblastoma. MicroRNAs (miRNAs) are important mediators of p53 activity, but their role in the p53 response has not yet been comprehensively addressed in neuroblastoma. Therefore, we set out to characterize alterations in miRNA expression that are induced by p53 activation in neuroblastoma cells. Genome-wide miRNA expression analysis showed that miR-34a-5p, miR-182-5p, miR-203a, miR-222-3p, and miR-432-5p are upregulated following nutlin-3 treatment in a p53 dependent manner.

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