Genomes and Genes
Experts and Doctors on computational biology in Leuven, Flanders, Belgium
Locale: Leuven, Flanders, Belgium
Topic: computational biology
- 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. ..
- 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...
- 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. ..
- 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. ..
- 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...
- 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...
- 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. ..
- 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. ..
- 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. ..
- 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...
- 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. ..
- 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. ..
- 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. ..
- 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. ..
- 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. ..