Gert Thijs

Summary

Affiliation: Katholieke Universiteit Leuven
Country: Belgium

Publications

  1. ncbi request reprint A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes
    Gert Thijs
    ESAT SCD, KULeuven, Kasteelpark Arenberg 10, 3001 Leuven, Belgium
    J Comput Biol 9:447-64. 2002
  2. 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
  3. pmc More robust detection of motifs in coexpressed genes by using phylogenetic information
    Pieter Monsieurs
    ESAT SCD SISTA, K U Leuven, Kasteelpark Arenberg 10, 3001 Leuven Heverlee, Belgium
    BMC Bioinformatics 7:160. 2006
  4. ncbi request reprint Adaptive quality-based clustering of gene expression profiles
    Frank De Smet
    ESAT SCD SISTA, K U Leuven, Kasteelpark Arenberg 10, 3001 Leuven Heverlee, Belgium
    Bioinformatics 18:735-46. 2002
  5. ncbi request reprint INCLUSive: integrated clustering, upstream sequence retrieval and motif sampling
    Gert Thijs
    ESAT_ SISTA COSIC, KULeuven, Kasteelpark Arenberg 10, 3001 Leuven Heverlee, Belgium
    Bioinformatics 18:331-2. 2002
  6. pmc In silico identification and experimental validation of PmrAB targets in Salmonella typhimurium by regulatory motif detection
    Kathleen Marchal
    ESAT SCD, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, 3001 Leuven Heverlee, Belgium
    Genome Biol 5:R9. 2004
  7. pmc A novel approach to identifying regulatory motifs in distantly related genomes
    Ruth Van Hellemont
    ESAT SCD, KU Leuven, Kasteelpark Arenberg 10, 3001 Leuven Heverlee, Belgium
    Genome Biol 6:R113. 2005
  8. 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
  9. 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
  10. ncbi request reprint Genome-specific higher-order background models to improve motif detection
    Kathleen Marchal
    ESAT SISTA SCD, K U Leuven, Kasteelpark Arenberg 10, 3001 Leuven Heverlee, Belgium
    Trends Microbiol 11:61-6. 2003

Detail Information

Publications14

  1. ncbi request reprint A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes
    Gert Thijs
    ESAT SCD, KULeuven, Kasteelpark Arenberg 10, 3001 Leuven, Belgium
    J Comput Biol 9:447-64. 2002
    ..Some other strong motifs do not have corresponding motifs in PlantCARE but are promising candidates for further analysis...
  2. 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...
  3. pmc More robust detection of motifs in coexpressed genes by using phylogenetic information
    Pieter Monsieurs
    ESAT SCD SISTA, K U Leuven, Kasteelpark Arenberg 10, 3001 Leuven Heverlee, Belgium
    BMC Bioinformatics 7:160. 2006
    ..Then we mutually compare all detected motifs and identify the ones that are shared by at least a few genes in the data set as potential candidates...
  4. ncbi request reprint Adaptive quality-based clustering of gene expression profiles
    Frank De Smet
    ESAT SCD SISTA, K U Leuven, Kasteelpark Arenberg 10, 3001 Leuven Heverlee, Belgium
    Bioinformatics 18:735-46. 2002
    ..In the following we describe a novel adaptive quality-based clustering algorithm that tackles some of these drawbacks...
  5. ncbi request reprint INCLUSive: integrated clustering, upstream sequence retrieval and motif sampling
    Gert Thijs
    ESAT_ SISTA COSIC, KULeuven, Kasteelpark Arenberg 10, 3001 Leuven Heverlee, Belgium
    Bioinformatics 18:331-2. 2002
    ....
  6. pmc In silico identification and experimental validation of PmrAB targets in Salmonella typhimurium by regulatory motif detection
    Kathleen Marchal
    ESAT SCD, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, 3001 Leuven Heverlee, Belgium
    Genome Biol 5:R9. 2004
    ..New targets of the system have recently been discovered that seem not to have a role in the well-described functions of PmrAB, suggesting that the PmrAB-dependent regulon might contain additional, unidentified targets...
  7. pmc A novel approach to identifying regulatory motifs in distantly related genomes
    Ruth Van Hellemont
    ESAT SCD, KU Leuven, Kasteelpark Arenberg 10, 3001 Leuven Heverlee, Belgium
    Genome Biol 6:R113. 2005
    ..The results on well-studied benchmark datasets indicate that the presented method outperforms other methods when the sequences become either too long or too heterogeneous in size...
  8. 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...
  9. 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...
  10. ncbi request reprint Genome-specific higher-order background models to improve motif detection
    Kathleen Marchal
    ESAT SISTA SCD, K U Leuven, Kasteelpark Arenberg 10, 3001 Leuven Heverlee, Belgium
    Trends Microbiol 11:61-6. 2003
    ..Therefore, we have developed complex background models for all prokaryotic species with available genome sequences...
  11. 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...
  12. 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...
  13. ncbi request reprint Assessing computational tools for the discovery of transcription factor binding sites
    Martin Tompa
    Department of Computer Science and Engineering, Box 352350, University of Washington, Seattle, Washington 98195 2350, USA
    Nat Biotechnol 23:137-44. 2005
    ..The purpose of the current assessment is twofold: to provide some guidance to users regarding the accuracy of currently available tools in various settings, and to provide a benchmark of data sets for assessing future tools...
  14. pmc PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences
    Magali Lescot
    Vakgroep Moleculaire Genetica, Departement Plantengenetica, Vlaams Interuniversitair Instituut voor Biotechnologie, Universiteit Gent, K L Ledeganckstraat 35, B 9000 Gent, Belgium
    Nucleic Acids Res 30:325-7. 2002
    ..New regulatory elements can be sent automatically and will be added to the database after curation. The PlantCARE relational database is available via the World Wide Web at http://sphinx.rug.ac.be:8080/PlantCARE/...