latest news & announcements

A web application for sample size and power calculation in case-control microbiome studies

When designing a case-control study to investigate differences in microbial composition, it is fundamental to assess the sample sizes needed to detect an hypothesised difference with sufficient statistical power. Our application includes power calculation for (i) a recoded version of the two-sample generalised Wald test of the “HMP” R-package for comparing community composition, and (ii) the Wilcoxon-Mann-Whitney test for comparing OTU-specific abundances between two samples (optional).

Pieter Mestdagh nominated for 'New Scientist Wetenschapstalent 2016'

Colleague Pieter Mestdagh has been nominated for the biggest Science Talent of Belgium and The Netherlands by the New Scientist. Out of those 25 nominated people, 5 candidates will be for the final election in Amsterdam. Selection is based on the opinion of both jury and public.
Taken in mind Pieter’s contributions to BIG N2N, please support him with your vote:

Epigenetics for renal cancer diagnostics

Background: Genetic intratumoral heterogeneity (ITH) hinders biomarker development in metastatic clear cell renal cancer (mccRCC). Epigenetic relative to genetic ITH or the presence of consistent epigenetic changes following targeted therapy in mccRCC have not been evaluated. The aim of this study was to determine methylome/genetic ITH and to evaluate specific epigenetic and genetic changes associated with sunitinib therapy.

Unipept web services for metaproteomics analysis

Unipept is an open source web application that is designed for metaproteomics analysis with a focus on interactive datavisualization. It is underpinned by a fast index built from UniProtKB and the NCBI taxonomy that enables quick retrieval of all UniProt entries in which a given tryptic peptide occurs. Unipept version 2.4 introduced web services that provide programmatic access to the metaproteomics analysis features. This enables integration of Unipept functionality in custom applications and data processing pipelines.

A Pipeline for Differential Proteomics in Unsequenced Species

Shotgun proteomics experiments often take the form of a differential analysis, where two or more samples are compared against each other. The objective is to identify proteins that are either unique to a specific sample or a set of samples (qualitative differential proteomics), or that are significantly differentially expressed in one or more samples (quantitative differential proteomics). However, the success depends on the availability of a reliable protein sequence database for each sample.

Elucidation of the Mode of Action of a New Antibacterial Compound Active against Staphylococcus aureus and Pseudomonas aeruginosa

Nosocomial and community-acquired infections caused by multidrug resistant bacteria represent a major human health problem. Thus, there is an urgent need for the development of antibiotics with new modes of action. In this study, we investigated the antibacterial characteristics and mode of action of a new antimicrobial compound, SPI031 (N-alkylated 3, 6-dihalogenocarbazol 1-(sec-butylamino)-3-(3,6-dichloro-9H-carbazol-9-yl) propan-2-ol), which was previously identified in our group.

Statistical explorative method for early drug development

We propose a statistical explorative method for data integration. It is developed in the context of early drug development for which it enables the detection of chemical substructures and the identification of genes that mediate their association with the bioactivity (BA). The core of the method is a sparse singular value decomposition for the identification of the gene set and a permutation-based method for the control of the false discovery rate. The method is illustrated using a real dataset, and its properties are empirically evaluated by means of a simulation study.