Research Topics
Genomes and GenesSpecies | Stein AertsSummaryAffiliation: Katholieke Universiteit Leuven Country: Belgium Publications
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Detail Information
Publications
Toucan: deciphering the cis-regulatory logic of coregulated genesStein Aerts
Department of Electrical Engineering ESAT SCD, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, 3001 Heverlee, Leuven, Belgium
Nucleic Acids Res 31:1753-64. 2003..Software available at http://www.esat.kuleuven.ac. be/ approximately dna/BioI/Software.html...- Comprehensive analysis of the base composition around the transcription start site in MetazoaStein Aerts
Department of Electrical Engineering ESAT SCD, Katholieke Universiteit Leuven, Belgium
BMC Genomics 5:34. 2004..Now that several sequenced metazoan genomes have been annotated, we have been able to compare the base composition around the transcription start site for all annotated genes across multiple genomes... - A genetic algorithm for the detection of new cis-regulatory modules in sets of coregulated genesStein Aerts
Department of Electrical Engineering ESAT SCD, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, 3001 Heverlee Leuven, Belgium
Bioinformatics 20:1974-6. 2004..Toucan can be accessed at http://www.esat.kuleuven.ac.be/~saerts/software/toucan.php. A standalone version of the software is available upon request... - Computational detection of cis -regulatory modulesStein Aerts
Department of Electrical Engineering ESAT SCD, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, Leuven, Belgium
Bioinformatics 19:ii5-14. 2003..By integrating multiple signals, CRMs confer an organism specific spatial and temporal rate of transcription... - Robust target gene discovery through transcriptome perturbations and genome-wide enhancer predictions in Drosophila uncovers a regulatory basis for sensory specificationStein Aerts
Laboratory of Neurogenetics, Department of Molecular and Developmental Genetics, VIB, Leuven, Belgium
PLoS Biol 8:e1000435. 2010..The validated set of novel Ato targets exhibit functional enrichment of signaling molecules and a subset is predicted to be coregulated by other TFs within the retinal gene regulatory network... - Integrating computational biology and forward genetics in DrosophilaStein Aerts
Department of Molecular and Developmental Genetics, Laboratory of Neurogenetics, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
PLoS Genet 5:e1000351. 2009..A systems genetics approach that combines the power of computational predictions with in vivo genetic screens strongly enhances the process of gene function and gene-gene association discovery... - INCLUSive: A web portal and service registry for microarray and regulatory sequence analysisBert Coessens
ESAT SCD, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, 3001 Leuven, Belgium
Nucleic Acids Res 31:3468-70. 2003..All services are catalogued and described in a web service registry. The INCLUSive web portal is available for academic purposes at http://www.esat.kuleuven.ac.be/inclusive... - ENDEAVOUR update: a web resource for gene prioritization in multiple speciesLeon Charles Tranchevent
Department of Electrical Engineering ESAT SCD, Katholieke Universiteit Leuven, Belgium
Nucleic Acids Res 36:W377-84. 2008..Additionally, we describe a number of recent independent studies that made use of Endeavour to prioritize candidate genes for obesity and Type II diabetes, cleft lip and cleft palate, and pulmonary fibrosis... - Comparison and meta-analysis of microarray data: from the bench to the computer deskYves Moreau
Department of Electrical Engineering ESAT SCD, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, 3001, Heverlee Leuven, Belgium
Trends Genet 19:570-7. 2003.... - Whole-genome prediction of cis-regulatory modules and target genes yields insight into gene regulatory networks underlying sensory differentiationStein Aerts
Laboratory of Computational Biology, KU Leuven School of Medicine, Leuven, Belgium
Fly (Austin) 5:221-3. 2011..We discuss the biological functions of the proneural targetome in the light of signaling pathways, and the recent progress on computational target gene predictions using cisTargetX... - The atonal proneural transcription factor links differentiation and tumor formation in DrosophilaWouter Bossuyt
Laboratory of Neurogenetics, Department of Molecular and Developmental Genetics, VIB, Leuven, Belgium
PLoS Biol 7:e40. 2009..Combined with evidence that atonal's mammalian homolog, ATOH1, is a tumor suppressor gene, our data support a critical, evolutionarily conserved, function for ato in oncogenesis... - Gene profiling of hippocampal neuronal cultureMichal Dabrowski
Laboratory for Neuronal Cell Biology, Center for Human Genetics, and Department of Electrical Engineering ESAT-SCD, Katholieke Universiteit Leuven and VIB (Flemish Interuniversity Institute for Biotechnology, Leuven, Belgium
J Neurochem 85:1279-88. 2003..Our results also demonstrate that a comparison across the two experimental platforms (cDNA microarrays and oligonucleotide chips) and across different biological paradigms is feasible... - Fine-tuning enhancer models to predict transcriptional targets across multiple genomesStein Aerts
Laboratory of Neurogenetics, Department of Molecular and Developmental Genetics, Vlaams Instituut voor Biotechnologie VIB, Leuven, Belgium
PLoS ONE 2:e1115. 2007..The ability to model known TF-TG relations, together with the use of multiple genomes, results in a significant step forward in solving the architecture of gene regulatory networks... - TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysisStein Aerts
Laboratory of Neurogenetics, Department of Human Genetics, Flanders Interuniversity Institute for Biotechnology and K U Leuven Belgium
Nucleic Acids Res 33:W393-6. 2005..TOUCAN can be launched from this location: http://www.esat.kuleuven.ac.be/~saerts/software/toucan.php... - Text-mining assisted regulatory annotationStein Aerts
Laboratory of Neurogenetics, Department of Molecular and Developmental Genetics, VIB, Leuven, B 3000, Belgium
Genome Biol 9:R31. 2008.... - Computational strategies for the genome-wide identification of cis-regulatory elements and transcriptional targetsStein Aerts
Laboratory of Computational Biology, Center for Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
Curr Top Dev Biol 98:121-45. 2012.... - ORegAnno: an open-access community-driven resource for regulatory annotationObi L Griffith
Canada s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 4S6, Canada
Nucleic Acids Res 36:D107-13. 2008..All data are freely available through search pages, XML data dumps or web services at: http://www.oreganno.org... - Discovery of functional elements in 12 Drosophila genomes using evolutionary signaturesAlexander Stark
The Broad Institute, Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02140, USA
Nature 450:219-32. 2007..We also study how discovery power scales with the divergence and number of species compared, and we provide general guidelines for comparative studies... - Sequencing the regulatory genomeStein Aerts
Department of Molecular and Developmental Genetics, Laboratory of Neurogenetics, VIB, Leuven B 3000, Belgium
Genome Biol 9:313. 2008..A report on the Cold Spring Harbor Laboratory meeting 'Systems Biology: Global Regulation of Gene Expression', Cold Spring Harbor, USA, 27-30 March 2008... - Gene prioritization through genomic data fusionStein Aerts
Laboratory of Neurogenetics, Department of Human Genetics, Flanders Interuniversity Institute for Biotechnology VIB, University of Leuven, Herestraat 49, bus 602, 3000 Leuven, Belgium
Nat Biotechnol 24:537-44. 2006..The approach described here offers an alternative integrative method for gene discovery... - Prediction of a key role of motifs binding E2F and NR2F in down-regulation of numerous genes during the development of the mouse hippocampusMichal Dabrowski
Laboratory of Transcription Regulation, Department of Cell Biology, The Nencki Institute of Experimental Biology, Pasteura 3, 02 093 Warsaw, Poland
BMC Bioinformatics 7:367. 2006..In either dataset, the expression vectors of all the genes form two large clusters that differ in the sign of the contribution of Mode 2, which for the majority of them reflects the difference between down- or up-regulation... - Identification of conserved modes of expression profiles during hippocampal development and neuronal differentiation in vitroMichal Dabrowski
Laboratory of Transcription Regulation, Department of Cell Biology, The Nencki Institute of Experimental Biology, Warsaw, Poland
J Neurochem 97:87-91. 2006..Our results also indicate that the magnitude of expression, and the direction of change in expression during hippocampal development, are uncorrelated, suggesting that they are regulated by largely independent mechanisms... - Identification of IGFBP-6 as a significantly downregulated gene by beta-catenin in desmoid tumorsHannelore Denys
Center for Human Genetics, University of Leuven, Leuven B-3000, Belgium
Oncogene 23:654-64. 2004..These findings suggest that IGFBP-6 is directly downregulated by the beta-catenin/TCF complex in desmoid tumors, and imply a role for the IGF axis in the proliferation of desmoid tumors...