Research team

VIB CMN - Applied and Translational Neurogenomics

Expertise

In a previous position I set up a database of ribosomal RNA sequences and their structure, and wrote software for the management of this database and for predicting and visualizing the structure of RNA. I also used this database for phylogenetic analysis. My current work is focused on the design, development and implementation of work-flows and software tools to enhance the research of complex diseases. An iomportant part of this is the in-house LIMS (Laboratory Information Management System) managing the entire data-flow in the center from sample management and clinical data to experimental results. Over the years, I developed software covering the setup and analysis of a very diverse set of genotyping technologies, ranging from STR analysis and Sanger sequencing to next generation sequencing, and now also long-read sequencing. During the analysis of some of early complete genomes, I developed software for comparing, annotating, filtering and validating complete genome data (Genomecomb); which is now also used to integrate the in-house analysis of gene panel and exome sequencing using state of the art publicly available tools and local enhancements. We are further exploring new ways to extract meaning from the variants, by e.g. adding novel annotations/targets. For example we developed software for the discovery of novel miRNAs and for predicting the effect of genomic variants on their structure and biogenesis.

Development of the BioGraph technology for valorisation in life sciences industries. 01/03/2012 - 28/02/2013

Abstract

BioGraph is a data mining technology, developed at the University of Antwerp, for unsupervised biomedical knowledge discovery via automatically generated hypotheses in integrated knowledge databases. For this technology, we study business development opportunities and develop a specific off-the-shelf application for the interpretation of microarray studies.

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    Development for large data sets and their application to non-coding genetic information involved in psychiatric diseases. 01/01/2011 - 31/12/2012

    Abstract

    This project represents a research agreement between the UA and on the onther hand IWT. UA provides IWT research results mentioned in the title of the project under the conditions as stipulated in this contract.

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      Identification of causal variants for psychiatric diseases through massive parallel resequencing methods. 01/01/2010 - 31/12/2013

      Abstract

      The aim of this project is the identification of rare and/or common risk variants that are implicated in the development of SZ and BP disorder. Hereto we will use massive parallel resequencing approaches. During this project we will obtain expertise in generating large sequencing datasets as well as expertise in the analysis of these large sequence based datasets. The milestones of the project are: ¿ Exon based candidate gene resequencing ¿ Region specific resequencing ¿ Whole human genome resequencing

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        Text Mining on heterogeneous knowledge bases. An application to optimised discovery of disease relevant genetic variants 01/07/2007 - 30/06/2011

        Abstract

        The project proposes a methodology for text mining with heterogeneous information sources and its application to molecular genetics/genomics and knowledge management. State of the art text analysis and graph-based data mining techniques will be extended to make the methodology possible, and the methodology will be applied in a biomedical application (ranking of candidate disease-causing genes) and a knowledge management application (person profiling from www information).

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        Project website

        Molecular genetics/genomics of psychiatric diseases in an isolated population. 01/01/2007 - 31/12/2010

        Abstract

        Aims of the project : A. Identification of novel genes for psychiatric disorders in an isolated population from Northern Sweden B. Identification of novel loci for psychiatric disorders C. Development of neurophenomics research D. Development of genetic and genomic Multiplex PCR applications

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          Detection, identification and classification of genes in de analysis of genome sequences 01/10/1999 - 30/09/2002

          Abstract

          The complete genome sequence of several species has been determined, and several other sequences are expected to follow. The main objective of this project is finding and classifying possible coding sequences (CDS) and the determination of their structure and/or function. The similarity between postulated coding sequences will be calculated using a variety of scoring methods. The scores will then be used to detect gene groups or families using tree construction and other classification methods. The database will be scanned for additional members of the families. Using alignments and other computer sequence analysis methods the structure and function of these families will be studied.

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            Detection, identification and classification of genes in the analysis of genome sequences. 01/10/1996 - 30/09/1999

            Abstract

            The complete genome sequence of several species has been determined, and several other sequences are expected to follow. The main objective of this project is finding and classifying possible coding sequences (CDS) and the determination of their structure and/or function. The similarity between postulated coding sequences will be calculated using a variety of scoring methods. The scores will then be used to detect gene groups or families using tree construction and other classification methods. The database will be scanned for additional members of the families. Using alignments and other computer sequence analysis methods the structure and function of these families will be studied.

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              Optimization of a database for ribosomal RNA structure and application in structural and evolutionary research 01/10/1993 - 30/09/1995

              Abstract

              Ribosomal RNA sequences from different species can be aligned. In the comparative approach, secundary structure elements can be found by examining the alignement for comensatory base changes. The alignement is also used to study the evolution of different organisms on a molecular basis.

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                Optimization of a database for ribosomal RNA structure and application in structural and evolutionary research 01/10/1991 - 30/09/1993

                Abstract

                Ribosomal RNA sequences from different species can be aligned. In the comparative approach, secundary structure elements can be found by examining the alignement for comensatory base changes. The alignement is also used to study the evolution of different organisms on a molecular basis.

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                  01/10/1990 - 30/09/1991

                  Abstract

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