Wim Van Criekinge

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Epigenetics, and more specifically DNA methylation is a fast evolving research area. In almost every cancer type, each month new publications confirm the differentiated regulation of specific genes due to methylation and mention the discovery of novel methylation markers. Therefore, it would be extremely useful to have an annotated, reviewed, sorted and(More)
We have developed a transcriptome-wide approach to identify genes affected by promoter CpG island DNA hypermethylation and transcriptional silencing in colorectal cancer. By screening cell lines and validating tumor-specific hypermethylation in a panel of primary human colorectal cancer samples, we estimate that nearly 5% or more of all known genes may be(More)
117 to find as intellectual property belonging to them and therefore decline to share the information. The problem is far greater when it comes to submission of the clinical information necessary to make genotype-phenotype correlations. First, few diagnostic labs even receive detailed clinical information upon submission of a test sample from the physician(More)
SUMMARY TreeIllustrator is a user-friendly application to visualize and customize phylogenetic trees. It has a broad range of functions and capabilities, such as dragging of nodes, different tree shapes, zooming and searching capabilities, and support for large trees. It acts as a solution that integrates the specificity of visualizing phylogenetic trees(More)
454 pyrosequencing is a commonly used massively parallel DNA sequencing technology with a wide variety of application fields such as epigenetics, metagenomics and transcriptomics. A well-known problem of this platform is its sensitivity to base-calling insertion and deletion errors, particularly in the presence of long homopolymers. In addition, the(More)
Next-generation amplicon sequencing enables high-throughput genetic diagnostics, sequencing multiple genes in several patients together in one sequencing run. Currently, no open-source out-of-the-box software solution exists that reliably reports detected genetic variations and that can be used to improve future sequencing effectiveness by analyzing the PCR(More)
With the rise of high throughput sequencing, new programs have been developed for dealing with the alignment of a huge amount of short read data to reference genomes. Recent developments in sequencing technology allow longer reads, but the mappers for short reads are not suited for reads of several hundreds of base pairs. We propose an algorithm for mapping(More)
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(More)
Purpose: To investigate how biologically relevant markers change in response to antiangiogenic therapy in metastatic clear cell renal cancer (mRCC) and correlate these changes with outcome. Experimental Design: The study used sequential tumor tissue and functional imaging (taken at baseline and 12–16 weeks) obtained from three similar phase II studies. All(More)