latest news & announcements

N2N developed a parallel, distributed-memory framework for comparative motif discovery

The increasing number of sequenced organisms has opened new possibilities for the computational discovery of cis-regulatory elements ('motifs') based on phylogenetic footprinting. Word-based, exhaustive approaches are among the best performing algorithms, however, they pose significant computational challenges as the number of candidate motifs to evaluate is very high. In this contribution, we describe a parallel, distributed-memory framework for de novo comparative motif discovery.

PeptideShaker enables reanalysis of MS-derived proteomics data sets

Mass spectrometry (MS)-based proteomics is commonly used to identify and quantify the hundreds to thousands of proteins that are present in complex biological samples. Widespread data sharing via publicly accessible repositories, such as PRIDE1, has now become standard practice, aided by robust user-oriented tools for data submission and inspection and bolstered by the advent of the ProteomeXchange initiative.

Bringing bioinformatics to primary school: 'Wetenschap op stap' VIB-project

N2N participated in the VIB project 'Wetenschap op stap' in which scientists visit a primary school class during half a day and tell the children about their research in a very interactive way. Of course, a real experiment was part of it. The children decoded a piece of DNA sequence, first manually and then with bio-informatics tools to feel the difference. Their many questions about cloning, genetics, biology, GGOs and personalized medicine got answered and they were very enthusiastic about the impact of bioinformatics research!
An impression is given in the attached document.

Drought Tolerance Conferred to Sugarcane by Association with Gluconacetobacter diazotrophicus: A Transcriptomic View of Hormone Pathways

Sugarcane interacts with particular types of beneficial nitrogen-fixing bacteria that provide fixed-nitrogen and plant growth hormones to host plants, promoting an increase in plant biomass. Other benefits, as enhanced tolerance to abiotic stresses have been reported to some diazotrophs. Here we aim to study the effects of the association between the diazotroph Gluconacetobacter diazotrophicus PAL5 and sugarcane cv. SP70-1143 during water depletion by characterizing differential transcriptome profiles of sugarcane.

New N2N tool VirVarSeq: a low-frequency virus variant detection pipeline for Illumina sequencing using adaptive base-calling accuracy filtering

Motivation: In virology, massively parallel sequencing (MPS) opens many opportunities for studying viral quasi-species, e.g. in HIV-1- and HCV-infected patients. This is essential for understanding pathways to resistance, which can substantially improve treatment. Although MPS platforms allow in-depth characterization of sequence variation, their measurements still involve substantial technical noise. For Illumina sequencing, single base substitutions are the main error source and impede powerful assessment of low-frequency mutations.

Spotlight on recent top publications

Ghent University incites its researchers to publish the results of scientific research in the best scientific media. This is one of the ruling principles of Ghent University's Publication Policy.

The government and the university have implemented an incentive policy to stimulate this dissemination of scientific literature through the distribution of research resources based on publication and citation numbers. However, it is important that researchers select the best journals and publishers for their scientific work to best support the above goals.

The Notch driven long non-coding RNA repertoire in T-cell acute lymphoblastic leukemia

Genetic studies in T-cell acute lymphoblastic leukemia have uncovered a remarkable complexity of oncogenic and loss-of-function mutations. Amongst this plethora of genetic changes, NOTCH1 activating mutations stand out as the most frequently occurring genetic defect, identified in more than 50% of T-cell acute lymphoblastic leukemias, supporting a role as an essential driver for this gene in T-cell acute lymphoblastic leukemia oncogenesis. In this study, we aimed to establish a comprehensive compendium of the long non-coding RNA transcriptome under control of Notch signaling.

CASP8 SNP D302H (rs1045485) Is Associated with Worse Survival in MYCN-Amplified Neuroblastoma Patients

Background: Neuroblastoma is a pediatric cancer that exhibits a wide clinical spectrum ranging from spontaneous regression in low-risk patients to fatal disease in high-risk patients. The identification of single nucleotide polymorphisms (SNPs) may help explain the heterogeneity of neuroblastoma and assist in identifying patients at higher risk for poor survival. SNPs in the TP53 pathway are of special importance, as several studies have reported associations between TP53 pathway SNPs and cancer. Of note, less than 2% of neuroblastoma tumors have a TP53 mutation at diagnosis.

An improved toolbox to unravel the plant cellular machinery by tandem affinity purification of Arabidopsis protein complexes

Tandem affinity purification coupled to mass spectrometry (TAP-MS) is one of the most advanced methods to characterize protein complexes in plants, giving a comprehensive view on the protein-protein interactions (PPIs) of a certain protein of interest (bait). The bait protein is fused to a double affinity tag, which consists of a protein G tag and a streptavidin-binding peptide separated by a very specific protease cleavage site, allowing highly specific protein complex isolation under near-physiological conditions.