Experts and Doctors on computational biology in Leuven, Flanders, Belgium

Summary

Locale: Leuven, Flanders, Belgium
Topic: computational biology

Top Publications

  1. Coemans B, Matsumura H, Terauchi R, Remy S, Swennen R, Sági L. SuperSAGE combined with PCR walking allows global gene expression profiling of banana (Musa acuminata), a non-model organism. Theor Appl Genet. 2005;111:1118-26 pubmed
    ..SuperSAGE in conjunction with 3'RACE and TAIL-PCR will be a powerful tool for transcriptomics of non-model, but otherwise important organisms. ..
  2. Bolander J, Ji W, Geris L, Bloemen V, Chai Y, Schrooten J, et al. The combined mechanism of bone morphogenetic protein- and calcium phosphate-induced skeletal tissue formation by human periosteum derived cells. Eur Cell Mater. 2016;31:11-25 pubmed
    ..This study presents further evidence for the potential of BMP-technology in the development of clinically relevant cell-based constructs for bone regenerative strategies. ..
  3. De Schutter T, Andrei G, Topalis D, Naesens L, Snoeck R. Cidofovir selectivity is based on the different response of normal and cancer cells to DNA damage. BMC Med Genomics. 2013;6:18 pubmed publisher
    ..Our findings underline the therapeutic potential of CDV for HPV-associated malignancies as well as other neoplasias. ..
  4. Meyfroidt G, Guiza F, Ramon J, Bruynooghe M. Machine learning techniques to examine large patient databases. Best Pract Res Clin Anaesthesiol. 2009;23:127-43 pubmed
    ..A general overview of machine learning techniques, with a more detailed discussion of some of these algorithms, is presented in this review. ..
  5. Vens C, Rosso M, Danchin E. Identifying discriminative classification-based motifs in biological sequences. Bioinformatics. 2011;27:1231-8 pubmed publisher
    ..The motif discovery tool and the proteins used in the experiments are available at http://dtai.cs.kuleuven.be/ml/systems/merci. ..
  6. Aerts S, Vilain S, Hu S, Tranchevent L, Barriot R, Yan J, et al. Integrating computational biology and forward genetics in Drosophila. PLoS Genet. 2009;5:e1000351 pubmed publisher
    ..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. ..
  7. Lemmens K, De Bie T, Dhollander T, De Keersmaecker S, Thijs I, Schoofs G, et al. DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli. Genome Biol. 2009;10:R27 pubmed publisher
    ..Surprisingly, the level of regulatory complexity seemed lower than that which would be expected from RegulonDB, indicating that complex regulatory programs tend to decrease the degree of modularity. ..
  8. van den Berg R, Van Mechelen I, Wilderjans T, Van Deun K, Kiers H, Smilde A. Integrating functional genomics data using maximum likelihood based simultaneous component analysis. BMC Bioinformatics. 2009;10:340 pubmed publisher
    ..Moreover, the maximum likelihood based approach underlying MxLSCA-P could be extended to custom-made solutions to specific problems encountered. ..
  9. Zwaenepoel K, Louis J, Goris J, Janssens V. Diversity in genomic organisation, developmental regulation and distribution of the murine PR72/B" subunits of protein phosphatase 2A. BMC Genomics. 2008;9:393 pubmed publisher
    ..We have integrated these results in a more consistent nomenclature of both human and murine PR72/B" genes and their transcripts/proteins. Our results provide a platform for the future generation of PR72/B" knockout mice. ..

More Information

Publications26

  1. Gazzo A, Raimondi D, Daneels D, Moreau Y, Smits G, Van Dooren S, et al. Understanding mutational effects in digenic diseases. Nucleic Acids Res. 2017;45:e140 pubmed publisher
    ..Together, our results show that digenic disease data generates novel insights, providing a glimpse into the oligogenic realm. ..
  2. Stevaert A, Dallocchio R, Dessì A, Pala N, Rogolino D, Sechi M, et al. Mutational analysis of the binding pockets of the diketo acid inhibitor L-742,001 in the influenza virus PA endonuclease. J Virol. 2013;87:10524-38 pubmed publisher
  3. Diego Garcia E, Peigneur S, Clynen E, Marien T, Czech L, Schoofs L, et al. Molecular diversity of the telson and venom components from Pandinus cavimanus (Scorpionidae Latreille 1802): transcriptome, venomics and function. Proteomics. 2012;12:313-28 pubmed publisher
    ..Expressed sequence tags from venom glands provide complementary information to MS and reveal undescribed components related to the biological activity of the venom...
  4. Van Deun K, Smilde A, van der Werf M, Kiers H, Van Mechelen I. A structured overview of simultaneous component based data integration. BMC Bioinformatics. 2009;10:246 pubmed publisher
    ..These types are shown to be linked to different specifications of the idea of a fair integration of the different coupled arrays. ..
  5. Lavigne R, Villegas A, Kropinksi A. In silico characterization of DNA motifs with particular reference to promoters and terminators. Methods Mol Biol. 2009;502:113-29 pubmed publisher
    ..Combining the available web-resources and literature data optimizes these predictions and can thus aid in a more directed experimental identification of these regulatory elements. ..
  6. Lavigne R, Darius P, Summer E, Seto D, Mahadevan P, Nilsson A, et al. Classification of Myoviridae bacteriophages using protein sequence similarity. BMC Microbiol. 2009;9:224 pubmed publisher
    ..It appears that horizontal gene transfer generally does not totally obliterate evolutionary relationships between phages...
  7. Gijsbers R, Ronen K, Vets S, Malani N, De Rijck J, McNeely M, et al. LEDGF hybrids efficiently retarget lentiviral integration into heterochromatin. Mol Ther. 2010;18:552-60 pubmed publisher
    ..Thus, engineered LEDGF/p75 chimeras provide technology for controlling integration site selection by lentiviral vectors...
  8. Thorrez L, Tranchevent L, Chang H, Moreau Y, Schuit F. Detection of novel 3' untranslated region extensions with 3' expression microarrays. BMC Genomics. 2010;11:205 pubmed publisher
    ..Since 3' UTR contain microRNA binding sites and other stability determining regions, identification of the full length 3' UTR is important to elucidate posttranscriptional regulation. ..
  9. Nitsch D, Tranchevent L, Thienpont B, Thorrez L, Van Esch H, Devriendt K, et al. Network analysis of differential expression for the identification of disease-causing genes. PLoS ONE. 2009;4:e5526 pubmed publisher
    ..Through a randomization procedure, we rank candidates by p-values. We illustrate our approach on four monogenic diseases and successfully prioritize the known disease causing genes. ..
  10. Froyen G, Belet S, Martinez F, Santos Rebouças C, Declercq M, Verbeeck J, et al. Copy-number gains of HUWE1 due to replication- and recombination-based rearrangements. Am J Hum Genet. 2012;91:252-64 pubmed publisher
    ..In summary, we showed that an increased dosage of HUWE1 causes nonsyndromic ID and demonstrated that the Xp11.22 region is prone to recombination- and replication-based rearrangements. ..
  11. Lemey P, Lott M, Martin D, Moulton V. Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning. BMC Bioinformatics. 2009;10:126 pubmed publisher
    ..We compare the quartet approach with triplet-based methods that employ additional heuristic tests to identify parental and recombinant sequences...
  12. Okbay A, Beauchamp J, Fontana M, Lee J, Pers T, Rietveld C, et al. Genome-wide association study identifies 74 loci associated with educational attainment. Nature. 2016;533:539-42 pubmed publisher
  13. Struyf J, Dobrin S, Page D. Combining gene expression, demographic and clinical data in modeling disease: a case study of bipolar disorder and schizophrenia. BMC Genomics. 2008;9:531 pubmed publisher
    ..Stratification can correct for such variables, but we show that this reduces the power of the statistical methods. ..
  14. Lemey P, Rambaut A, Drummond A, Suchard M. Bayesian phylogeography finds its roots. PLoS Comput Biol. 2009;5:e1000520 pubmed publisher
    ..From these analyses, we conclude that our phylogeographic framework will make an important asset in molecular epidemiology that can be easily generalized to infer biogeogeography from genetic data for many organisms. ..
  15. Schietgat L, Vens C, Struyf J, Blockeel H, Kocev D, Dzeroski S. Predicting gene function using hierarchical multi-label decision tree ensembles. BMC Bioinformatics. 2010;11:2 pubmed publisher
    ..Moreover, the ensemble method is computationally efficient and easy to use. Our results suggest that decision tree based methods are a state-of-the-art, efficient and easy-to-use approach to ORF function prediction. ..
  16. Storms V, Claeys M, Sanchez A, De Moor B, Verstuyf A, Marchal K. The effect of orthology and coregulation on detecting regulatory motifs. PLoS ONE. 2010;5:e8938 pubmed publisher
    ..Insights in this relation provide information useful to both developers and users. All benchmark datasets are available at http://homes.esat.kuleuven.be/~kmarchal/Supplementary_Storms_Valerie_PlosONE. ..
  17. Abrusan G, Grundmann N, DeMester L, Makalowski W. TEclass--a tool for automated classification of unknown eukaryotic transposable elements. Bioinformatics. 2009;25:1329-30 pubmed publisher
    ..It achieves 90-97% accuracy in the classification of novel DNA and LTR repeats, and 75% for LINEs and SINEs. http://www.compgen.uni-muenster.de/teclass, stand alone program upon request. ..