Stein Aerts

Summary

Affiliation: Katholieke Universiteit Leuven
Country: Belgium

Publications

  1. pmc Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures
    Alexander Stark
    The Broad Institute, Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02140, USA
    Nature 450:219-32. 2007
  2. pmc High accuracy mutation detection in leukemia on a selected panel of cancer genes
    Zeynep Kalender Atak
    Center for Human Genetics, KU Leuven, Leuven, Belgium
    PLoS ONE 7:e38463. 2012
  3. pmc Prediction of a key role of motifs binding E2F and NR2F in down-regulation of numerous genes during the development of the mouse hippocampus
    Michal 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
  4. pmc Text-mining assisted regulatory annotation
    Stein Aerts
    Laboratory of Neurogenetics, Department of Molecular and Developmental Genetics, VIB, Leuven, B 3000, Belgium
    Genome Biol 9:R31. 2008
  5. ncbi request reprint Whole-genome prediction of cis-regulatory modules and target genes yields insight into gene regulatory networks underlying sensory differentiation
    Stein Aerts
    Laboratory of Computational Biology, KU Leuven School of Medicine, Leuven, Belgium
    Fly (Austin) 5:221-3. 2011
  6. pmc Fine-tuning enhancer models to predict transcriptional targets across multiple genomes
    Stein Aerts
    Laboratory of Neurogenetics, Department of Molecular and Developmental Genetics, Vlaams Instituut voor Biotechnologie VIB, Leuven, Belgium
    PLoS ONE 2:e1115. 2007
  7. pmc Robust target gene discovery through transcriptome perturbations and genome-wide enhancer predictions in Drosophila uncovers a regulatory basis for sensory specification
    Stein Aerts
    Laboratory of Neurogenetics, Department of Molecular and Developmental Genetics, VIB, Leuven, Belgium
    PLoS Biol 8:e1000435. 2010
  8. ncbi request reprint Gene prioritization through genomic data fusion
    Stein 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
  9. pmc Integrating computational biology and forward genetics in Drosophila
    Stein Aerts
    Department of Molecular and Developmental Genetics, Laboratory of Neurogenetics, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
    PLoS Genet 5:e1000351. 2009
  10. ncbi request reprint Computational detection of cis -regulatory modules
    Stein Aerts
    Department of Electrical Engineering ESAT SCD, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, Leuven, Belgium
    Bioinformatics 19:ii5-14. 2003

Collaborators

Detail Information

Publications28

  1. pmc Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures
    Alexander 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...
  2. pmc High accuracy mutation detection in leukemia on a selected panel of cancer genes
    Zeynep Kalender Atak
    Center for Human Genetics, KU Leuven, Leuven, Belgium
    PLoS ONE 7:e38463. 2012
    ..In conclusion, we established an optimized analysis pipeline for Roche/454 data that can be applied to accurately detect gene mutations in cancer, which led to the identification of several new candidate T-ALL driver mutations...
  3. pmc Prediction of a key role of motifs binding E2F and NR2F in down-regulation of numerous genes during the development of the mouse hippocampus
    Michal 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...
  4. pmc Text-mining assisted regulatory annotation
    Stein Aerts
    Laboratory of Neurogenetics, Department of Molecular and Developmental Genetics, VIB, Leuven, B 3000, Belgium
    Genome Biol 9:R31. 2008
    ....
  5. ncbi request reprint Whole-genome prediction of cis-regulatory modules and target genes yields insight into gene regulatory networks underlying sensory differentiation
    Stein 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...
  6. pmc Fine-tuning enhancer models to predict transcriptional targets across multiple genomes
    Stein 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...
  7. pmc Robust target gene discovery through transcriptome perturbations and genome-wide enhancer predictions in Drosophila uncovers a regulatory basis for sensory specification
    Stein 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...
  8. ncbi request reprint Gene prioritization through genomic data fusion
    Stein 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...
  9. pmc Integrating computational biology and forward genetics in Drosophila
    Stein 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...
  10. ncbi request reprint Computational detection of cis -regulatory modules
    Stein 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...
  11. pmc TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis
    Stein 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...
  12. pmc ModuleMiner - improved computational detection of cis-regulatory modules: are there different modes of gene regulation in embryonic development and adult tissues?
    Peter Van Loo
    Department of Molecular and Developmental Genetics, VIB, Herestraat 49, B 3000 Leuven, Belgium
    Genome Biol 9:R66. 2008
    ..Interestingly, CRM predictions for differentiated tissues exhibit strong enrichment close to the transcription start site, whereas CRM predictions for embryonic development gene sets are depleted in this region...
  13. pmc The atonal proneural transcription factor links differentiation and tumor formation in Drosophila
    Wouter 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...
  14. pmc Toucan: deciphering the cis-regulatory logic of coregulated genes
    Stein 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...
  15. pmc Comparative motif discovery combined with comparative transcriptomics yields accurate targetome and enhancer predictions
    Marina Naval-Sánchez
    Laboratory of Computational Biology, Department of Human Genetics, University of Leuven, 3000 Leuven, Belgium
    Genome Res 23:74-88. 2013
    ....
  16. ncbi request reprint Gene profiling of hippocampal neuronal culture
    Michal 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...
  17. doi request reprint TDP-43 loss-of-function causes neuronal loss due to defective steroid receptor-mediated gene program switching in Drosophila
    Lies Vanden Broeck
    Laboratory of Behavioral and Developmental Genetics, Center of Human Genetics, University of Leuven, B3000 Leuven, Belgium
    Cell Rep 3:160-72. 2013
    ..We propose that dTDP-43 neurotoxicity is caused by a loss of its normal function...
  18. doi request reprint Exome sequencing identifies mutation in CNOT3 and ribosomal genes RPL5 and RPL10 in T-cell acute lymphoblastic leukemia
    Kim De Keersmaecker
    Center for Human Genetics, KU Leuven, Leuven, Belgium
    Nat Genet 45:186-90. 2013
    ..Our data provide insights into the mutational landscape of pediatric versus adult T-ALL and identify the ribosome as a potential oncogenic factor...
  19. pmc Sequencing the regulatory genome
    Stein 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...
  20. pmc Comprehensive analysis of transcriptome variation uncovers known and novel driver events in T-cell acute lymphoblastic leukemia
    Zeynep Kalender Atak
    Laboratory of Computational Biology, Center for Human Genetics, KU Leuven, Leuven, Belgium
    PLoS Genet 9:e1003997. 2013
    ....
  21. doi request reprint Computational strategies for the genome-wide identification of cis-regulatory elements and transcriptional targets
    Stein Aerts
    Laboratory of Computational Biology, Center for Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
    Curr Top Dev Biol 98:121-45. 2012
    ....
  22. ncbi request reprint Identification of IGFBP-6 as a significantly downregulated gene by beta-catenin in desmoid tumors
    Hannelore 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...
  23. ncbi request reprint A genetic algorithm for the detection of new cis-regulatory modules in sets of coregulated genes
    Stein Aerts
    Department of Electrical Engineering ESAT SCD, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, 3001 Heverlee Leuven, Belgium
    Bioinformatics 20:1974-6. 2004
    ..The implementation of a genetic algorithm is described that provides a fast method of searching for the optimal combination of transcription factor binding sites in a set of regulatory sequences...
  24. pmc ENDEAVOUR update: a web resource for gene prioritization in multiple species
    Leon 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...
  25. pmc ORegAnno: an open-access community-driven resource for regulatory annotation
    Obi 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...
  26. pmc INCLUSive: A web portal and service registry for microarray and regulatory sequence analysis
    Bert 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...
  27. pmc Comprehensive analysis of the base composition around the transcription start site in Metazoa
    Stein 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...
  28. ncbi request reprint Identification of conserved modes of expression profiles during hippocampal development and neuronal differentiation in vitro
    Michal 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...