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Text-mining assisted regulatory annotation

Stein Aerts, Maximilian Haeussler, Steven van Vooren, Obi L Griffith, Paco Hulpiau, Steven JM Jones, Stephen B Montgomery, Casey M Bergman, The Open Regulatory Annotation Consortium
2008 Genome Biology  
doi:10.1186/gb-2008-9-2-r31 pmid:18271954 pmcid:PMC2374703 fatcat:rplmnumegze4hg3kdc37tykuim

TXTGate: profiling gene groups with text-based information

Patrick Glenisson, Bert Coessens, Steven Van Vooren, Janick Mathys, Yves Moreau, Bart De Moor
2004 Genome Biology  
GOA-Mefisto-666, GOA-Ambiorics, IDO), the Fonds voor Wetenschappelijk Onderzoek -Vlaanderen (G.0115.01, G.0240.99, G.0407.02, G.0413.03, G.0388.03, G.0229.03, G.0241.04), the Instituut voor de aanmoediging van  ... 
doi:10.1186/gb-2004-5-6-r43 pmid:15186494 pmcid:PMC463076 fatcat:iijxrcxvr5hffkpfnpwl4hbhvq

Collaboratively charting the gene-to-phenotype network of human congenital heart defects

Roland Barriot, Jeroen Breckpot, Bernard Thienpont, Sylvain Brohée, Steven Van Vooren, Bert Coessens, Leon-Charles Tranchevent, Peter Van Loo, Marc Gewillig, Koenraad Devriendt, Yves Moreau
2010 Genome Medicine  
These data complement at a much higher resolution the CHD regions identified by Van Karnebeek et al. [14] , which were based on reported cytogenetically visible chromosomal aberrations.  ...  Features CHD Genes 193 Linkage regions 14 Balanced chromosomal aberrations 21 Van Karnebeek and Hennekam 1999 regions 85 Patients 281 Studies (mutation screens) 297 Mutations  ... 
doi:10.1186/gm137 pmid:20193066 pmcid:PMC2873794 fatcat:uwdxak5uafbmnoclveb4edbkwu

Waarnemingen.be – Plant occurrences in Flanders and the Brussels Capital Region, Belgium

Roosmarijn Steeman, Wouter Vanreusel, Rutger Barendse, Filip Verloove, Nico Wysmantel, Walter Van den Bussche, Thomas Gyselinck, Pieter Hendrickx, Arnout Zwaenepoel, Pierre Van Vooren, Steven Jacobs, Peter Desmet (+3 others)
2017 PhytoKeys  
Together with the datasets Florabank1 (Van Landuyt and Brosens 2017) and the Belgian IFBL (Instituut voor Floristiek van België en Luxemburg) Flora Checklists (Van Landuyt and Noé 2015) , the dataset  ...  This species was in Van Landuyt et al. (2006) also the most widespread plant.  ... 
doi:10.3897/phytokeys.85.14925 pmid:29033655 pmcid:PMC5624210 fatcat:be4iuu5smbgy7oqidyhiuwgblu

Diagnostic interpretation of array data using public databases and internet sources

Nicole de Leeuw, Trijnie Dijkhuizen, Jayne Y. Hehir-Kwa, Nigel P. Carter, Lars Feuk, Helen V. Firth, Robert M. Kuhn, David H. Ledbetter, Christa Lese Martin, Conny M. A. van Ravenswaaij-Arts, Steven W. Scherer, Soheil Shams (+4 others)
2012 Human Mutation  
The range of commercially available array platforms and analysis software packages is expanding and their utility is improving, making reliable detection of copy-number variants (CNVs) relatively straightforward. Reliable interpretation of CNV data, however, is often difficult and requires expertise. With our knowledge of the human genome growing rapidly, applications for array testing continuously broadening, and the resolution of CNV detection increasing, this leads to great complexity in
more » ... rpreting what can be daunting data. Correct CNV interpretation and optimal use of the genotype information provided by single-nucleotide polymorphism probes on an array depends largely on knowledge present in various resources. In addition to the availability of host laboratories' own datasets and national registries, there are several public databases and Internet resources with genotype and phenotype information that can be used for array data interpretation. With so many resources now available, it is important to know which are fit-for-*
doi:10.1002/humu.22049 pmid:26285306 pmcid:PMC5027376 fatcat:hqvlbupy2faw7njm7ppq52hifa

An experimental loop design for the detection of constitutional chromosomal aberrations by array CGH

Joke Allemeersch, Steven Van Vooren, Femke Hannes, Bart De Moor, Joris Vermeesch, Yves Moreau
2009 BMC Bioinformatics  
Comparative genomic hybridization microarrays for the detection of constitutional chromosomal aberrations is the application of microarray technology coming fastest into routine clinical application. Through genotype-phenotype association, it is also an important technique towards the discovery of disease causing genes and genomewide functional annotation in human. When using a two-channel microarray of genomic DNA probes for array CGH, the basic setup consists in hybridizing a patient against
more » ... normal reference sample. Two major disadvantages of this setup are (1) the use of half of the resources to measure a (little informative) reference sample and (2) the possibility that deviating signals are caused by benign copy number variation in the "normal" reference instead of a patient aberration. Instead, we apply an experimental loop design that compares three patients in three hybridizations. Results: We develop and compare two statistical methods (linear models of log ratios and mixed models of absolute measurements). In an analysis of 27 patients seen at our genetics center, we observed that the linear models of the log ratios are advantageous over the mixed models of the absolute intensities. Conclusion: The loop design and the performance of the statistical analysis contribute to the quick adoption of array CGH as a routine diagnostic tool. They lower the detection limit of mosaicisms and improve the assignment of copy number variation for genetic association studies.
doi:10.1186/1471-2105-10-380 pmid:19925645 pmcid:PMC2791104 fatcat:tbqclklz3vh7xi3haohgvgmzwi

Mapping biomedical concepts onto the human genome by mining literature on chromosomal aberrations

Steven Van Vooren, Bernard Thienpont, Björn Menten, Frank Speleman, Bart De Moor, Joris Vermeesch, Yves Moreau
2007 Nucleic Acids Research  
Biomedical literature provides a rich but unstructured source of associations between chromosomal regions and biomedical concepts. By mining MEDLINE abstracts, we annotate the human genome at the level of cytogenetic bands. Our method creates a set of chromosomal aberration maps that associate cytogenetic bands to biomedical concepts from a variety of controlled vocabularies, including disease, dysmorphology, anatomy, development and Gene Ontology branches. The association between a band (e.g.
more » ... p16.3) and a concept (e.g. microcephaly) is assessed by the statistical overrepresentation of this concept in the abstracts relating to this band. Our method is validated using existing genome annotation resources and known chromosomal aberration maps and is further illustrated through a case study on heart disease. Our chromosomal aberration maps provide diagnostics support to clinical geneticists, aid cytogeneticists to interpret and report cytogenetic findings and support researchers interested in human gene function. The method is available as a web application, aBandApart, at
doi:10.1093/nar/gkm054 pmid:17403693 pmcid:PMC1885641 fatcat:6ni5eyuswzcnfpa62yrnjaza5y

Comparison of vocabularies, representations and ranking algorithms for gene prioritization by text mining

Shi Yu, Steven Van Vooren, Leon-Charles Tranchevent, Bart De Moor, Yves Moreau
2008 Computer applications in the biosciences : CABIOS  
GeneSeeker (Van Driel et al., 2005) provides a web interface that filters candidate disease genes on the basis of cytogenetic location, phenotypes and expression patterns.  ... 
doi:10.1093/bioinformatics/btn291 pmid:18689812 fatcat:6osfcq6xlzb3fiulgl2s6q2yvu

arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays

Björn Menten, Filip Pattyn, Katleen De Preter, Piet Robbrecht, Evi Michels, Karen Buysse, Geert Mortier, Anne De Paepe, Steven van Vooren, Joris Vermeesch, Yves Moreau, Bart De Moor (+3 others)
2005 BMC Bioinformatics  
The availability of the human genome sequence as well as the large number of physically accessible oligonucleotides, cDNA, and BAC clones across the entire genome has triggered and accelerated the use of several platforms for analysis of DNA copy number changes, amongst others microarray comparative genomic hybridization (arrayCGH). One of the challenges inherent to this new technology is the management and analysis of large numbers of data points generated in each individual experiment. We
more » ... developed arrayCGHbase, a comprehensive analysis platform for arrayCGH experiments consisting of a MIAME (Minimal Information About a Microarray Experiment) supportive database using MySQL underlying a data mining web tool, to store, analyze, interpret, compare, and visualize arrayCGH results in a uniform and user-friendly format. Following its flexible design, arrayCGHbase is compatible with all existing and forthcoming arrayCGH platforms. Data can be exported in a multitude of formats, including BED files to map copy number information on the genome using the Ensembl or UCSC genome browser. ArrayCGHbase is a web based and platform independent arrayCGH data analysis tool, that allows users to access the analysis suite through the internet or a local intranet after installation on a private server. ArrayCGHbase is available at http://medgen.ugent.be/arrayCGHbase/.
doi:10.1186/1471-2105-6-124 pmid:15910681 pmcid:PMC1173083 fatcat:o23fqjhs2vafnfykt5w3hyif7e

DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources

Helen V. Firth, Shola M. Richards, A. Paul Bevan, Stephen Clayton, Manuel Corpas, Diana Rajan, Steven Van Vooren, Yves Moreau, Roger M. Pettett, Nigel P. Carter
2009 American Journal of Human Genetics  
Many patients suffering from developmental disorders harbor submicroscopic deletions or duplications that, by affecting the copy number of dosage-sensitive genes or disrupting normal gene expression, lead to disease. However, many aberrations are novel or extremely rare, making clinical interpretation problematic and genotype-phenotype correlations uncertain. Identification of patients sharing a genomic rearrangement and having phenotypic features in common leads to greater certainty in the
more » ... ogenic nature of the rearrangement and enables new syndromes to be defined. To facilitate the analysis of these rare events, we have developed an interactive web-based database called DECIPHER (Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources) which incorporates a suite of tools designed to aid the interpretation of submicroscopic chromosomal imbalance, inversions, and translocations. DECIPHER catalogs common copy-number changes in normal populations and thus, by exclusion, enables changes that are novel and potentially pathogenic to be identified. DECIPHER enhances genetic counseling by retrieving relevant information from a variety of bioinformatics resources. Known and predicted genes within an aberration are listed in the DECIPHER patient report, and genes of recognized clinical importance are highlighted and prioritized. DECIPHER enables clinical scientists worldwide to maintain records of phenotype and chromosome rearrangement for their patients and, with informed consent, share this information with the wider clinical research community through display in the genome browser Ensembl. By sharing cases worldwide, clusters of rare cases having phenotype and structural rearrangement in common can be identified, leading to the delineation of new syndromes and furthering understanding of gene function.
doi:10.1016/j.ajhg.2009.03.010 pmid:19344873 pmcid:PMC2667985 fatcat:b62ezm5vfvc63fh5yhtbzrzdbe

Array comparative genomic hybridization and computational genome annotation in constitutional cytogenetics: suggesting candidate genes for novel submicroscopic chromosomal imbalance syndromes

Steven Van Vooren, Bert Coessens, Bart De Moor, Yves Moreau, Joris R Vermeesch
2007 Genetics in Medicine  
Van Vooren et al. in a set of MEDLINE abstracts of MeSH terms in the Diseases and Chemical and Drugs categories with the gene's gene ontology annotations.  ...  The approach taken by Van Vooren et al. 27 uses overrepresentation statistics to correlate specific biomedical terms from various targeted biomedical vocabularies with cytogenetic bands cited in MEDLINE  ... 
doi:10.1097/gim.0b013e318145b27b pmid:17873653 fatcat:76u2kxhadnh2nb3y3q66e3galu

A novel genomic disorder: a deletion of the SACS gene leading to Spastic Ataxia of Charlevoix–Saguenay

Jeroen Breckpot, Yoshihisa Takiyama, Bernard Thienpont, Steven Van Vooren, Joris Robert Vermeesch, Els Ortibus, Koenraad Devriendt
2008 European Journal of Human Genetics  
doi:10.1038/ejhg.2008.58 pmid:18398442 fatcat:pudd6vrih5aztituqjlj3ur7re

Data-driven Summarization of Broadcasted Cycling Races by Automatic Team and Rider Recognition

Steven Verstockt, Alec Van den broeck, Brecht Van Vooren, Simon De Smul, Jelle De Bock
2020 Proceedings of the 8th International Conference on Sport Sciences Research and Technology Support  
The number of spectators for cycling races broadcasted on television is decreasing each year. More dynamic and personalized reporting formats are needed to keep the viewer interested. In this paper, we propose a methodology for data-driven summarization, which allows end-users to query for personalized stories of a race, tailored to their needs (such as the length of the clip and the riders and/or teams that they are interested in). The automatic summarization uses a combination of
more » ... d rider pose detection and pose-based recognition algorithms of the team jerseys and rider faces/numbers. Evaluation on both cyclocross and road cycling races show that there is certainly potential in this novel methodology.
doi:10.5220/0010016900130021 dblp:conf/icsports/VerstocktbVSB20 fatcat:umxjgz5wzjgx5avs3qsjodr25u

Critical points for an accurate human genome analysis

Stefan J. White, Jeroen F.J. Laros, Egbert Bakker, Anne Cambon-Thomsen, Martin Eden, Samantha Leonard, Hanns Lochmüller, Gert Matthijs, Christopher Mattocks, Simon Patton, Katherine Payne, Hans Scheffer (+7 others)
2017 Human Mutation  
Disclosure of Conflicts of Interest Stefan Van Vooren is employed by Agilent Technologies. Bart Janssen is employed by GenomeScan B.V. This article is protected by copyright. All rights reserved.  ...  ., 2009; van Dijk, et al., 2014) . Read alignment The two main variables in read alignment are the choice of aligner and the choice of reference genome.  ...  SOX9 with disorders of sex development, campomelic dysplasia, and / or craniofacial disorders (Gordon, et al., 2009; Kleinjan and van Heyningen, 2005) .  ... 
doi:10.1002/humu.23238 pmid:28471515 fatcat:3mt4di2c2recjnj6cxzbizb3vm

Reliable and Scalable SARS-CoV-2 qPCR Testing at a High Sample Throughput: Lessons Learned from the Belgian Initiative

Steven Van Vooren, James Grayson, Marc Van Ranst, Elisabeth Dequeker, Lies Laenen, Reile Janssen, Laurent Gillet, Fabrice Bureau, Wouter Coppieters, Nathalie Devos, Benjamin Hengchen, Pierre Wattiau (+24 others)
2022 Life  
We present our approach to rapidly establishing a standardized, multi-site, nation-wide COVID-19 screening program in Belgium. Under auspices of a federal government Task Force responsible for upscaling the country's testing capacity, we were able to set up a national testing initiative with readily available resources, putting in place a robust, validated, high-throughput, and decentralized qPCR molecular testing platform with embedded proficiency testing. We demonstrate how during an acute
more » ... rcity of equipment, kits, reagents, personnel, protective equipment, and sterile plastic supplies, we introduced an approach to rapidly build a reliable, validated, high-volume, high-confidence workflow based on heterogeneous instrumentation and diverse assays, assay components, and protocols. The workflow was set up with continuous quality control monitoring, tied together through a clinical-grade information management platform for automated data analysis, real-time result reporting across different participating sites, qc monitoring, and making result data available to the requesting physician and the patient. In this overview, we address challenges in optimizing high-throughput cross-laboratory workflows with minimal manual intervention through software, instrument and assay validation and standardization, and a process for harmonized result reporting and nation-level infection statistics monitoring across the disparate testing methodologies and workflows, necessitated by a rapid scale-up as a response to the pandemic.
doi:10.3390/life12020159 pmid:35207446 pmcid:PMC8879918 fatcat:li3fff3zjrga7jyfblj5fkp7mu
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