Experts and Doctors on sequence alignment in Leuven, Flanders, Belgium

Summary

Locale: Leuven, Flanders, Belgium
Topic: sequence alignment

Top Publications

  1. Janssens S, Viaene T, Huysmans S, Smets E, Geuten K. Selection on length mutations after frameshift can explain the origin and retention of the AP3/DEF-like paralogues in Impatiens. J Mol Evol. 2008;66:424-35 pubmed publisher
    ..It is rather the length of the C-terminal domain that either is strictly conserved or varies strongly. This suggests a role for the length of the C-terminal domain in the retention of duplicated genes. ..
  2. Spasic D, Raemaekers T, Dillen K, Declerck I, Baert V, Serneels L, et al. Rer1p competes with APH-1 for binding to nicastrin and regulates gamma-secretase complex assembly in the early secretory pathway. J Cell Biol. 2007;176:629-40 pubmed
    ..We conclude that total cellular gamma-secretase activity is restrained by a secondary ER control system that provides a potential therapeutic value. ..
  3. 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. ..
  4. Kesters D, Thompson A, Brams M, van Elk R, Spurny R, Geitmann M, et al. Structural basis of ligand recognition in 5-HT3 receptors. EMBO Rep. 2013;14:49-56 pubmed publisher
    ..Our study offers the first structural perspective on recognition of serotonin and antagonism by anti-emetics in the 5-HT(3) receptor. ..
  5. Van Der Haegen A, Peigneur S, Tytgat J. Importance of position 8 in ?-conotoxin KIIIA for voltage-gated sodium channel selectivity. FEBS J. 2011;278:3408-18 pubmed publisher
    ..Replacement of Trp8 enables more selective blockers to be obtained for neuronal sodium channels. Trp is a key determinant for the reversibility of block of rNa(v)1.2. ..
  6. Vekemans D, Proost S, Vanneste K, Coenen H, Viaene T, Ruelens P, et al. Gamma paleohexaploidy in the stem lineage of core eudicots: significance for MADS-box gene and species diversification. Mol Biol Evol. 2012;29:3793-806 pubmed publisher
    ..We consider that the traits generated from this potential characterize extant core eudicots both chemically and morphologically. ..
  7. Breugelmans B, Simonet G, van Hoef V, Van Soest S, Broeck J. Identification, distribution and molecular evolution of the pacifastin gene family in Metazoa. BMC Evol Biol. 2009;9:97 pubmed publisher
  8. Van Doorslaer K, Sidi A, Zanier K, Rybin V, Deryck re F, Rector A, et al. Identification of unusual E6 and E7 proteins within avian papillomaviruses: cellular localization, biophysical characterization, and phylogenetic analysis. J Virol. 2009;83:8759-70 pubmed publisher
    ..Both constructs were highly soluble and well folded, according to nuclear magnetic resonance spectroscopy measurements...
  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

Publications42

  1. Bellon E, Luyten F, Tylzanowski P. delta-EF1 is a negative regulator of Ihh in the developing growth plate. J Cell Biol. 2009;187:685-99 pubmed publisher
    ..In summary, we have identified delta-EF1 as an in vivo negative regulator of Ihh expression in the growth plate. ..
  2. De Keersmaecker K, Atak Z, Li N, Vicente C, Patchett S, Girardi T, et al. Exome sequencing identifies mutation in CNOT3 and ribosomal genes RPL5 and RPL10 in T-cell acute lymphoblastic leukemia. Nat Genet. 2013;45:186-90 pubmed publisher
    ..Our data provide insights into the mutational landscape of pediatric versus adult T-ALL and identify the ribosome as a potential oncogenic factor. ..
  3. Vandendriessche T, Olamendi Portugal T, Zamudio F, Possani L, Tytgat J. Isolation and characterization of two novel scorpion toxins: The alpha-toxin-like CeII8, specific for Na(v)1.7 channels and the classical anti-mammalian CeII9, specific for Na(v)1.4 channels. Toxicon. 2010;56:613-23 pubmed publisher
    ..Since these effects have also been reported for the beta-toxin CssIV, the bioactive surfaces of the toxins have been compared to each other. ..
  4. Veugelers M, Vermeesch J, Watanabe K, Yamaguchi Y, Marynen P, David G. GPC4, the gene for human K-glypican, flanks GPC3 on xq26: deletion of the GPC3-GPC4 gene cluster in one family with Simpson-Golabi-Behmel syndrome. Genomics. 1998;53:1-11 pubmed
    ..The tight clustering of GPC3 and GPC4, with deletions that occasionally affect both genes, may be relevant for explaining the variability of the SGBS phenotype. ..
  5. 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...
  6. Naval Sanchez M, Potier D, Haagen L, Sánchez M, Munck S, Van De Sande B, et al. Comparative motif discovery combined with comparative transcriptomics yields accurate targetome and enhancer predictions. Genome Res. 2013;23:74-88 pubmed publisher
  7. Freson K, Thys C, Wittewrongel C, Vermylen J, Hoylaerts M, Van Geet C. Molecular cloning and characterization of the GATA1 cofactor human FOG1 and assessment of its binding to GATA1 proteins carrying D218 substitutions. Hum Genet. 2003;112:42-9 pubmed
    ..The identification of the human FOG1 gene will enable the genetic screening of patients with non X-linked thrombocytopenia and dyserythropoiesis. ..
  8. Claeys I, Simonet G, Poels J, Van Loy T, Vercammen L, De Loof A, et al. Insulin-related peptides and their conserved signal transduction pathway. Peptides. 2002;23:807-16 pubmed
  9. Hao Q, Van Damme E, Hause B, Barre A, Chen Y, Rouge P, et al. Iris bulbs express type 1 and type 2 ribosome-inactivating proteins with unusual properties. Plant Physiol. 2001;125:866-76 pubmed
  10. Van Veldhoven P, Gijsbers S, Mannaerts G, Vermeesch J, Brys V. Human sphingosine-1-phosphate lyase: cDNA cloning, functional expression studies and mapping to chromosome 10q22(1). Biochim Biophys Acta. 2000;1487:128-34 pubmed
    ..Northern analysis showed the presence of rare large-sized mRNAs of 6.7, 5.8 and 4 kb and the highest expression in liver. By fluorescent in situ hybridization, the gene was mapped to chromosome 10q22. ..
  11. Dillen S, Zels S, Verlinden H, Spit J, Van Wielendaele P, Vanden Broeck J. Functional characterization of the short neuropeptide F receptor in the desert locust, Schistocerca gregaria. PLoS ONE. 2013;8:e53604 pubmed publisher
    ..This is the first comprehensive study in which a clearly negative correlation is described between the sNPF signalling pathway and feeding, prompting a reconsideration of the diverse roles of sNPFs in the physiology of insects. ..
  12. Schulz J, Ceulemans H, Caussinus E, Baietti M, Affolter M, Hassan B, et al. Drosophila syndecan regulates tracheal cell migration by stabilizing Robo levels. EMBO Rep. 2011;12:1039-46 pubmed publisher
    ..We conclude that Sdc cell autonomously regulates Slit/Robo2 signalling in tracheal cells to guarantee ordered directional migration and branch fusion. ..
  13. Matthijnssens J, Joelsson D, Warakomski D, Zhou T, Mathis P, van Maanen M, et al. Molecular and biological characterization of the 5 human-bovine rotavirus (WC3)-based reassortant strains of the pentavalent rotavirus vaccine, RotaTeq. Virology. 2010;403:111-27 pubmed publisher
    ..The molecular and biologic characterization of RotaTeq adds to the significant body of clinical data supporting the consistent efficacy, immunogenicity, and safety of RotaTeq. ..
  14. Vleugels R, Lenaerts C, Baumann A, Vanden Broeck J, Verlinden H. Pharmacological characterization of a 5-HT1-type serotonin receptor in the red flour beetle, Tribolium castaneum. PLoS ONE. 2013;8:e65052 pubmed publisher
    ..castaneum facilitating functional research of 5-HT receptors in insects and other invertebrates. The pharmacological profiles may contribute to establish a reliable classification scheme for invertebrate 5-HT receptors...
  15. Bielejec F, Lemey P, Carvalho L, Baele G, Rambaut A, Suchard M. πBUSS: a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios. BMC Bioinformatics. 2014;15:133 pubmed publisher
    ..Applications are not restricted to the BEAST framework, or even time-measured evolutionary histories, and πBUSS can be connected to various other programs using standard input and output format. ..
  16. Fierens E, Gebruers K, Voet A, De Maeyer M, Courtin C, Delcour J. Biochemical and structural characterization of TLXI, the Triticum aestivum L. thaumatin-like xylanase inhibitor. J Enzyme Inhib Med Chem. 2009;24:646-54 pubmed publisher
    ..e. Triticum aestivum xylanase inhibitor (TAXI) and xylanase inhibitor protein (XIP). This high stability can probably be ascribed to the high number of disulfide bridges, much as seen for other thaumatin-like proteins...
  17. Rector A, Lemey P, Tachezy R, Mostmans S, Ghim S, Van Doorslaer K, et al. Ancient papillomavirus-host co-speciation in Felidae. Genome Biol. 2007;8:R57 pubmed
  18. Lebeer S, De Keersmaecker S, Verhoeven T, Fadda A, Marchal K, Vanderleyden J. Functional analysis of luxS in the probiotic strain Lactobacillus rhamnosus GG reveals a central metabolic role important for growth and biofilm formation. J Bacteriol. 2007;189:860-71 pubmed publisher
    ..Moreover, our data indicate that suppressor mutations are likely to occur in luxS mutants of L. rhamnosus GG. Therefore, results of luxS-related studies should be carefully interpreted...
  19. Huang Z, Depoortere I, De Clercq P, Peeters T. Sequence and characterization of cDNA encoding the motilin precursor from chicken, dog, cow and horse. Evidence of mosaic evolution in prepromotilin. Gene. 1999;240:217-26 pubmed
    ..Our study demonstrates that the N- and C-terminal regions of the motilin precursor have evolved at different rates, which is evidence for 'mosaic evolution'. ..
  20. Rector A, Mostmans S, Van Doorslaer K, McKnight C, Maes R, Wise A, et al. Genetic characterization of the first chiropteran papillomavirus, isolated from a basosquamous carcinoma in an Egyptian fruit bat: the Rousettus aegyptiacus papillomavirus type 1. Vet Microbiol. 2006;117:267-75 pubmed publisher
    ..This is the first time a papillomavirus has been isolated and characterized from a member of the Chiroptera order...
  21. De Keersmaecker S, Sonck K, Vanderleyden J. Let LuxS speak up in AI-2 signaling. Trends Microbiol. 2006;14:114-9 pubmed
    ..Ongoing attempts to dissect the metabolic and signaling roles of LuxS leave little doubt that unraveling the regulation of luxS expression and cellular LuxS activity is the key to understanding LuxS-based quorum sensing. ..
  22. Heykants L, Schollen E, Grunewald S, Matthijs G. Identification and localization of two mouse phosphomannomutase genes, Pmm1 and Pmm2. Gene. 2001;270:53-9 pubmed
    ..The most striking difference is the high expression of Pmm1 in brain tissue, whereas Pmm2 is only weakly expressed in this tissue. ..
  23. Ons E, Gertler A, Buyse J, Lebihan Duval E, Bordas A, Goddeeris B, et al. Visfatin gene expression in chickens is sex and tissue dependent. Domest Anim Endocrinol. 2010;38:63-74 pubmed publisher
    ..Our results showed that the visfatin gene is ubiquitously expressed in chickens with greater abundance in muscle, and that it is regulated in a tissue-specific manner by energy balance-related factors. ..
  24. Chávez Gutiérrez L, Tolia A, Maes E, Li T, Wong P, De Strooper B. Glu(332) in the Nicastrin ectodomain is essential for gamma-secretase complex maturation but not for its activity. J Biol Chem. 2008;283:20096-105 pubmed publisher
    ..Consequently, these studies indicate that the main role of the Glu(332) is in the maturation and assembly of gamma-secretase rather than in the recognition of the substrates. ..
  25. Simonet G, Breugelmans B, Proost P, Claeys I, Van Damme J, De Loof A, et al. Characterization of two novel pacifastin-like peptide precursor isoforms in the desert locust (Schistocerca gregaria): cDNA cloning, functional analysis and real-time RT-PCR gene expression studies. Biochem J. 2005;388:281-9 pubmed
  26. Matta S, Van Kolen K, da Cunha R, van den Bogaart G, Mandemakers W, Miskiewicz K, et al. LRRK2 controls an EndoA phosphorylation cycle in synaptic endocytosis. Neuron. 2012;75:1008-21 pubmed publisher
  27. Peeraer Y, Rabijns A, Collet J, van Schaftingen E, De Ranter C. How calcium inhibits the magnesium-dependent enzyme human phosphoserine phosphatase. Eur J Biochem. 2004;271:3421-7 pubmed
    ..The bidentate character of Asp20 towards Ca(2+) hampers the nucleophilic attack of one of the Asp20 side chain oxygen atoms on the phosphorus atom of the substrate phosphoserine. ..
  28. Meersseman G, Verschueren K, Nelles L, Blumenstock C, Kraft H, Wuytens G, et al. The C-terminal domain of Mad-like signal transducers is sufficient for biological activity in the Xenopus embryo and transcriptional activation. Mech Dev. 1997;61:127-40 pubmed
    ..We also mapped the MusMLP gene to a region on mouse chromosome 13 that corresponds to a region on human chromosome 5q that contains cancer-related genes. ..
  29. Wuyts A, D Haese A, Cremers V, Menten P, Lenaerts J, De Loof A, et al. NH2- and COOH-terminal truncations of murine granulocyte chemotactic protein-2 augment the in vitro and in vivo neutrophil chemotactic potency. J Immunol. 1999;163:6155-63 pubmed
    ..Taken together, these findings point to an important role of post-translationally modified GCP-2 to replace IL-8 in the mouse. ..
  30. Lavigne R, Burkal tseva M, Robben J, Sykilinda N, Kurochkina L, Grymonprez B, et al. The genome of bacteriophage phiKMV, a T7-like virus infecting Pseudomonas aeruginosa. Virology. 2003;312:49-59 pubmed
    ..Also, the strong virulence toward many clinical P. aeruginosa isolates and a short replication time make phiKMV attractive for phage therapy or a potential source for antimicrobial proteins...
  31. Van Houdt J, Nowakowska B, Sousa S, van Schaik B, Seuntjens E, Avonce N, et al. Heterozygous missense mutations in SMARCA2 cause Nicolaides-Baraitser syndrome. Nat Genet. 2012;44:445-9, S1 pubmed publisher
    ..These alterations likely do not impair SWI/SNF complex assembly but may be associated with disrupted ATPase activity. The identification of SMARCA2 mutations in humans provides insight into the function of the Snf2 helicase family...
  32. Cornelissen A, Ceyssens P, T Syen J, Van Praet H, Noben J, Shaburova O, et al. The T7-related Pseudomonas putida phage ?15 displays virion-associated biofilm degradation properties. PLoS ONE. 2011;6:e18597 pubmed publisher
    ..These data suggests that the addition of high initial titers of specifically selected phages with a proper EPS depolymerase are crucial criteria in the development of phage therapy. ..
  33. Maas N, Van de Putte T, Melotte C, Francis A, Schrander Stumpel C, Sanlaville D, et al. The C20orf133 gene is disrupted in a patient with Kabuki syndrome. J Med Genet. 2007;44:562-9 pubmed
    ..Both the finding of different of chromosomal rearrangements in patients with KS features and the absence of C20orf133 mutations in 19 additional patients with KS suggest that KS is genetically heterogeneous. ..