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We like to introduce sORF.org, a public repository for sORFs. The main purpose is to allow researchers to examine individual sORFs or to perform searches based on several criteria for further large-scale studies. Different data sources, both experimental and in silico (based on various bioinformatics tools), are collected. sORF.org currently holds 3551506 sORFs across three different species (human, mouse and fruit fly), derived from multiple RIBO-seq experiments and is expanding as more data becomes available.
Methyl Binding Domain based purification of methylated DNA-fragments, followed by second-generation sequencing (MethylCap, also called MiGS and MBDSeq), is one of the most cost-efficient and sensitive methods for completely genome-wide DNA-methylation profiling. This methodology is therefore rapidly gaining interest in the Epigenetics community. Over the course of the last two years, our lab has optimized this technique and the corresponding data analysis. A special peak-calling algorithm was created which involved the indirect use of the underlying CpG-density, and therefore yields far more relevant information than the application of e.g. ChIP-seq peak calling algorithms. On this website, you’ll find current and former releases, in addition. A Genome Browser is available to study our human methylome by browsing to genes and genomic regions.
MaelstRom is the Modeller of Allele-Specific Transcriptomics, an R package providing extensive functions for various RNAseq-based allelic analyses. This ranges from basic tasks such as (solely) RNAseq-based genotyping, to the analysis of more complex population-level phenomena such as (differential) allelic bias, allellic divergence and (loss of) imprinting analyses. More information about what these are and how to model them using maelstRom can be found in the package vignette.
DeepRibo is a deep neural network created by Clauwaert. J et. al. for the annotation of Open Reading Frames (ORF) in prokaryotes using ribosome profiling data and short DNA sequences (Shine-Dalgarno region). The package is written in python 3 and uses the PyTorch library for deep learning purposes. A model has been trained and evaluated using seven ribo-seq datasets.
MappingQC is a tool to easily generate some figures which give a nice overview of the quality of the mapping of ribosome profiling data. More specific, it gives an overview of the P site offset calculation, the gene distribution and the metagenic classification. Furthermore, MappingQC does a thorough analysis of the triplet periodicity and the linked triplet phase (typical for ribosome profiling) in the canonical transcript of your data. Especially, the link between the phase distribution and the RPF length, the relative sequence position and the triplet identity are taken into account.
proBAMconvert is a conversion tool to convert common peptide identification files (mzIdentML, pepXML, mzTAB) to the proBAM or proBED format, as defined by the HUPO Proteomics Standards Initiative. In essence, proBAMconvert reads peptide identification files, maps identified peptides onto the genome and writes output into the proBAM/proBED format.
RiboZinB: A tool to identifying actively translated isoform(s) from ribosome profiling data. The case of the Zero-inflated model.
REPARATION (Ribosome Profiling Assisted (Re-)Annotation of Bacterial genomes) is a pipeline that uses ribosome profiling data for a de novo open reading frame delineation in prokaryotic (bacterial) genomes.
In recent years, increasing amounts of genomic and clinical cancer data have become publicly available through large-scale collaborative projects such as The Cancer Genome Atlas (TCGA). However, as long as these datasets are difficult to access and interpret, they are essentially useless for a major part of the research community and their scientific potential will not be fully realized. To address these issues we developed MEXPRESS, a straightforward and easy-to-use web tool for the integration and visualization of the expression, DNA methylation and clinical TCGA data on a single-gene level (https://mexpress.be).
PROTEOFORMER is a proteogenomic pipeline that delineates true in vivo proteoforms and generates a protein sequence search space for peptide to MS/MS matching.
Monoallelic gene expression is typically initiated early in the development of an organism. Dysregulation of monoallelic gene expression has already been linked to several non-Mendelian inherited genetic disorders. In humans, monoallelic DNA-methylation (MAM) is deemed to be an important regulator of monoallelic gene expression, but only few examples are known.