Publications
Chosen filters:
Chosen filters:
In silico approaches to studying transcriptional gene regulation: prediction of transcription factor binding sites and applications thereof Ghent University
Developing algorithms for the in silico identification of transcription factor binding sites Ghent University
Modeling the specificity of transcription factors to the DNA is one of the challenges that has kept many bioinformatics researchers busy since the early beginnings. Initially it was expected that a universal recognition code describing the amino acid to base pair contacts would be able to describe protein-DNA complex formation. However, until this very day a universal recognition code has not yet been found and alternative methods became more ...
Use of structural DNA properties for the prediction of transcription-factor binding sites in Escherichia coli KU Leuven University of Antwerp Ghent University
Recognition of genomic binding sites by transcription factors can occur through base-specific recognition, or by recognition of variations within the structure of the DNA macromolecule. In this article, we investigate what information can be retrieved from local DNA structural properties that is relevant to transcription factor binding and that cannot be captured by the nucleotide sequence alone. More specifically, we explore the benefit of ...
Androgen receptor-binding sites are highly mutated in prostate cancer Hasselt University
Androgen receptor (AR) signalling is essential in nearly all prostate cancers. Any alterations to AR-mediated transcription can have a profound effect on carcinogenesis and tumor growth. While mutations of the AR protein have been extensively studied, little is known about those somatic mutations that occur at the non-coding regions where AR binds DNA. Using clinical whole genome sequencing, we show that AR binding sites have a dramatically ...
Androgen and glucocorticoid receptor direct distinct transcriptional programs by receptor-specific and shared DNA binding sites KU Leuven
The glucocorticoid (GR) and androgen (AR) receptors execute unique functions in vivo, yet have nearly identical DNA binding specificities. To identify mechanisms that facilitate functional diversification among these transcription factor paralogs, we studied them in an equivalent cellular context. Analysis of chromatin and sequence suggest that divergent binding, and corresponding gene regulation, are driven by different abilities of AR and GR ...
Evolution of DNA-binding sites of a floral master regulatory transcription factor KU Leuven
Flower development is controlled by the action of key regulatory transcription factors of the MADS-domain family. The function of these factors appears to be highly conserved among species based on mutant phenotypes. However, the conservation of their downstream processes is much less well understood, mostly because the evolutionary turnover and variation of their DNA-binding sites (BS) among plant species has not yet been experimentally ...
The cellular co-factor LEDGF/p75 determines lentiviral integration sites in the chromosome KU Leuven
BackgroundLentiviruses and the viral vectors derived thereof can insert their viral genome into the chromosome of a non-dividing cell. During this process the viral integrase is assisted by various cellular cofactors. Our group identifies and validates cellular cofactors of nuclear import and integration. LEDGF/p75 was originally identified in our group as a binding partner of HIV-1 integrase and as a chromosomal tether. Data suggest a role for ...
AliBiMotif : Integrating alignment and biclustering to unravel transcription factor binding sites in DNA sequences KU Leuven
Transcription Factors (TFs) control transcription by binding to specific sites in the promoter regions of the target genes, which can be modelled by structured motifs. In this paper we propose AliBiMotif, a method combining sequence alignment and a biclustering approach based on efficient string matching techniques using suffix trees to unravel approximately conserved sets of blocks (structured motifs) while straightforwardly disregarding ...
Nanobody-based chromatin immunoprecipitation/micro-array analysis for genome-wide identification of transcription factor DNA binding sites. Vrije Universiteit Brussel
Nanobodies are single-domain antibody fragments derived from camelid heavy-chain antibodies. Because of their small size, straightforward production in Escherichia coli, easy tailoring, high affinity, specificity, stability and solubility, nanobodies have been exploited in various biotechnological applications. A major challenge in the post-genomics and post-proteomics era is the identification of regulatory networks involving nucleic ...