Kathleen Marchal

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INTERNATIONAL PEER REVIEWED ARTICLES - APPLICATIONS

INTERNATIONAL PEER REVIEWED ARTICLES


 

  • Cloots, L., Zhao,H., Van den Bulcke, T., Wu,Y., De Smet, R., Storms, V., Meysman, P., Engelen,K. and Marchal, K. Query-based Biclustering of Gene Expression Data Using Probabilistic Relational Models. 2011. BMC Bioinformatics. Feb 15;12 Suppl 1:S37.

  • Meysman P, Dang TH, Laukens K, De Smet R, Wu Y, Marchal K, Engelen K. Use of structural DNA properties for the prediction of transcription-factor binding sites in Escherichia coli. 2011. Nucleic Acids Res. Jan;39(2):e6.

  • Zarrineh P, Fierro AC, Sánchez-Rodríguez A, De Moor B, Engelen K, Marchal K. COMODO: an adaptive coclustering strategy to identify conserved coexpression modules between organisms. . 2011. Apr 1;39(7):e41.

  • Sanchez Rodriguez, A., Martens, C., Engelen, K., Van de Peer, Y., Marchal, K. The Potential for Pathogenicity was Present in the Ancestor of the Ascomycete subphylum Pezizomycotina. 2010. BMC Evolutionary Biology, 10(1), 318.

  • R. De Smet K. Marchal. Advantages and limitations of current network inference methods. 2010. Nat Rev Microbiol. 2010 Oct;8(10):717-29. Epub 2010 Aug 31. Review.

  • Engelen, K., Sifrim, A., Van de Plas, B., Laukens, K., Arckens, L., Marchal, K. Alternative experimental design with an applied normalization scheme can improve statistical power in 2D-DIGE experiments. Journal of Proteome Research, 9(10), 4919-4926.

  • V. Storms, M. Claeys, A. Sanchez, A. Verstuyf, B. De Moor, K. Marchal. The effect of orthology and coregulation on detecting regulatory motifs. 2010. PLoS One. 2010 Feb 3;5:e8938.

  • A. Fadda, A.C. Fierro, K. Lemmens, P. Monsieurs, K. Engelen, K. Marchal. Inferring the transcriptional network of Bacillus subtilis. 2009. Molecular Biosystems, 5:1840-52. Supplementary Info

  • H. Sun, K. Lemmens, T. Van den Buckle, K. Engelen, B. De Moor, K. Marchal. ViTraM: Visualization of Transcriptional Modules. 2009. Bioinformatics,15;25:2450-1. Jul 8.

  • T. Michoel, R. De Smet, A. Joshi, Y. Van de Peer and K. Marchal. Topological and evolutionary characterization of Escherichia coli transcriptional modules inferred from expression data. 2009. BMC Syst Biol. 7;3:49.

  • K. Lemmens, T. De Bie, T. Dhollander, S. De Keersmaecker, I. Thijs, G. Schoofs, A. De Weerdt, B. De Moor, J. Vanderleyden, J. Collado-Vides, K. Engelen, and K. Marchal. DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli. 2009. Genome biology, 6;10:R27.

  • P.J. Thilakarathne, G. Verbeke, K. Engelen, and K. Marchal. A nonlinear mixed-effects model for estimation of calibration intervals for unknown concentrations in spiked-in microarray data: an application to cDNA microarrays. 2009. Stat Appl Genet Mol Biol. 2009, 8: Article 5.

  • A. Joshi, R. De Smet, K. Marchal, Y. Van de Peer and T. Michoel Module networks revisited: computational assessment of model predictions. 2009. Bioinformatics 25:490-6.

  • K. Marchal, SC. De Keersmaecker. Bacterial networking. 2008. Genome Biol., 12;9:327.

  • T. Michoel, R. De Smet, A. Joshi, K. Marchal and Y. Van de Peer. Reverse-engineering transcriptional modules from gene expression data. 2009. Annals of the New York Academy of Sciences, Ann N Y Acad Sci. 1158:36-43.

  • Lemmens K, De Bie T, Dhollander T, Monsieurs P, De Moor B, Collado-Vides J, Engelen K, Marchal K. The condition-dependent transcriptional network in Escherichia coli. 2009. Annals of the New York Academy of Sciences, Ann N Y Acad Sci.1158:29-3.

  • H. Sun, T. De Bie, V. Storms, Q. Fu, T. Dhollander, K. Lemmens, K., A. Verstuyf, B. De Moor, and K. Marchal. ModuleDigger: an itemset mining framework for the detection of cis-regulatory modules. 2009. BMC Bioinformatics, in press.

  • A. C. Fierro, F. Vandenbussch, K. Engelen, Y. Van de Peer, K. Marchal. Meta Analysis of Gene Expression Data within and Across Species 2008. Current Genomics.

  • K. Van Leemput, T. Van den Bulcke, T. Dhollander, B. De Moor, K. Marchal, and P. van Remortel. Exploring the Operational Characteristics of Inference Algorithms for Transcriptional Networks by Means of Synthetic Data. 2008. Artificial Life, 14:49-63,.

  • L. Thorrez, K. Van Deun, L. C. Tranchevent, L. Van Lommel, K. Engelen, K. Marchal, Y. Moreau, M. Van, I, and F. Schuit. Using ribosomal protein genes as reference: a tale of caution. 2008. PLoS. ONE, 3:e1854.

  • K. Van Deun, K. Marchal, W.J. Heiser, K. Engelen, I.Van Mechelen. Joint mapping of genes and conditions via multidimensional unfolding analysis. 2008. BMC Bioinformatics, 8:181.

  • A. C. Fierro, R. Thuret, K. Engelen, G. Bernot, K. Marchal, and N. Pollet. Evaluation of time profile reconstruction from complex two-color microarray designs. 2008. BMC Bioinformatics, 9:1.

  • T. Dhollander, Q. Sheng, K. Lemmens, B. De Moor, K. Marchal, and Y. Moreau. Query-driven module discovery in microarray data. 2007. Bioinformatics,23:2573-80.

  • H. Zhao, K. Engelen, B. De Moor, and K. Marchal. CALIB: a Bioconductor package for estimating absolute expression levels from two-color microarray data. 2007. Bioinformatics.

  • T. Michoel, S. Maere, E. Bonnet, A. Joshi, Y. Saeys, B. T. Van den, K. Van Leemput, P. van Remortel, M. Kuiper, K. Marchal, and P. Y. Van de Peer. Validating module network learning algorithms using simulated data. 2007. BMC Bioinformatics, 8 Suppl 2:S5.

  • S.C.J. De Keersmaecker, I. M.V. Thijs, J. Vanderleyden and K. Marchal. Integration of omics data: How well does it work for bacteria? 2006. Mol. Microbiol., 62:1239-50.

  • K. Lemmens, T. Dhollander, T. De Bie, P. Monsieurs, K. Engelen, B. Smets, J. Winderickx, B. De Moor, and K. Marchal. Inferring transcriptional module networks from ChIP-chip-, motif- and microarray data. 2006. Genome Biology, 7:R37. Supplementary Information

  • P. Monsieurs, G. Thijs, A. A. Fadda, S. CJ De Keersmaecker, J. Vanderleyden, B. De Moor and K. Marchal. More robust detection of motifs in coexpressed genes by using phylogenetic information. 2006. BMC bioinformatics 20;7:160. Supplementary Information

  • K. Engelen, B. Naudts, B. De Moor, K. Marchal. A calibration method for estimating absolute expression levels from microarray data. 2006. Bioinformatics. 22:1251-8.

  • R. Van Hellemont, P. Monsieurs, G. Thijs, B. De Moor, Y. Van de Peer, K. Marchal. A novel approach to identify regulatory motifs in distantly related genomes. 2005. Genome Biology. 6:R113.1-R113.17, Epub. Supplementary Information

  • T.G. Van den Bulcke, K. MF. Van Leemput, B. Naudts, P. van Remortel, H. Ma, A. Verschoren, B. De Moor, K. Marchal SynTReN: A generator of synthetic gene expression data for design and analysis of structure learning algorithms 2006 BMC bioinformatics Supplementary Information

  • P. Monsieurs, G. Thijs, A. A. Fadda, S. CJ De Keersmaecker, J. Vanderleyden, B. De Moor and K. Marchal. More robust detection of motifs in coexpressed genes by using phylogenetic information 2006. BMC bioinformatics Supplementary Information

  • F. De Smet, N.L. Pochet, K. Engelen, T. Van Gorp, P. Van Hummelen, K. Marchal, F. Amant, D. Timmerman, B.L. De Moor, I.B. Vergote. Predicting the clinical behavior of ovarian cancer from gene expression profiles. 2006. Int. J. Gynecol. Cancer.

  • N.L. Pochet, F.A. Janssens, F. De Smet, K. Marchal, J.A. Suykens , B. De Moor. 2005. M@CBETH: a microarray classification benchmarking tool. Bioinformatics 21:3185-6.

  • T. De Bie, P. Monsieurs, K. Engelen, B. De Moor, N. Cristianini, and K. Marchal. Discovering regulatory modules from heterogeneous information sources. 2005. Pac. Symp. Biocomput. Supplementary Information

  • P. Monsieurs, S. De Keersmaecker, W. W. Navarre, M. W. Bader, F. De Smet, M. McClelland, F. C. Fang, B. De Moor, J. Vanderleyden, and K. Marchal. Comparison of the PhoPQ regulon in Escherichia coli and Salmonella typhimurium. 2005. J. Mol. Evol, 60:462-74.

  • E. Vanbleu, K. Marchal, and J. Vanderleyden. Genetic and physical map of the pLAFR1 vector. 2004. DNA Seq, 15:225-7.

  • G. Dirix, P. Monsieurs, K. Marchal, J. Vanderleyden, and J. Michiels. Screening genomes of Gram-positive bacteria for double-glycine-motif-containing peptides. 2004. Microbiology, 150:1121-6.

  • E. Vanbleu, K. Marchal, M. Lambrecht, J. Mathys, and J. Vanderleyden. Annotation of the pRhico plasmid of Azospirillum brasilense reveals its role in determining the outer surface composition. 2004. FEMS Microbiol. Lett., 232:165-72.

  • K. Marchal, S. De Keersmaecker, P. Monsieurs, N. Van Boxel, K. Lemmens, G. Thijs, J. Vanderleyden, and B. De Moor. In silico identification and experimental validation of PmrAB targets in Salmonella typhimurium by regulatory motif detection. 2004. Genome Biology. Supplementary Information.

  • G. Dirix, P. Monsieurs, B. Dombrecht, R. Daniels, K. Marchal, J. Vanderleyden, and J. Michiels. Peptide signal molecules and bacteriocins in Gram-negative bacteria: a genome-wide in silico screening for peptides containing a double-glycine leader sequence and their cognate transporters. 2004. peptides, 25:1425-40.

  • B. De Moor, K. Marchal, J. Mathys, and Y. Moreau. Bioinformatics: Organisms from Venus, technology from Jupiter, algorithms from Mars'. 2003. European Journal of Control, 9:237-278.

  • B. Coessens, G. Thijs, S. Aerts, J. Mathys, Y. Moreau, K. Marchal, F. De Smet, K. Engelen, P. Glenisson, and B. De Moor. INCLUSive-A web portal and service registry for microarray and regulatory sequence analysis. 2003. Nucleic Acids Research, 31:3468-3470.

  • S. Rombauts, K. Florquin, M. Lescot, K. Marchal, P. Rouz?, and Y. Van de Peer. Computational approaches to identify promoters and cis-regulatory elements in plant genomes. 2003. Plant Physiology, 132:1162-1176.

  • K. Marchal, G. Thijs, S. De Keersmaecker, P. Monsieurs, B. De Moor, and J. Vanderleyden. Genome-specific higher-order background models to improve motif detection. 2003. Trends in Microbiology, 11 (2): 61-66.

  • K. Engelen, B. Coessens, K. Marchal, and B. De Moor. MARAN: a web-based application for normalizing micro-array data. 2003. Bioinformatics 19(7):893-894.

  • B. Dombrecht, K. Marchal, J. Vanderleyden, and J. Michiels. Prediction and overview of the RpoN-regulon in closely related species of the Rhizobiales. 2002. Genome Biology, 3(12): research0076.1 - 0076.11.

  • K. Marchal, K. Engelen, J. De Brabanter, S. Aerts., B. De Moor, T. Ayoubi, and P. Van Hummelen. Comparison of different methodologies to identify differentially expressed genes in two-sample cDNA microarrays. 2002. Journal of Biological Systems, 10(4):409-430.

  • Y. Moreau, F. De Smet, G. Thijs, K. Marchal, and B. De Moor. Functional bioinformatics of microarray data: from expression to regulation. 2002. IEEE proceedings. 30 (11):1722-1743.

  • I. Smets, K. Bernaerts, J. Sun, K. Marchal, J. Vanderleyden, and J. Van Impe. Sensitivity function-based model reduction: A bacterial gene expression case study. 2002. Biotechnology Bioengineering, 80(2):195-200.

  • G. Thijs, K. Marchal, M. Lescot, S. Rombauts, B. De Moor, P. Rouz?, and Y. Moreau. A Gibbs Sampling method to detect over-represented motifs in the upstream regions of co-expressed genes. 2002. Journal of Computational Biology, 9 (3):447-464.

  • F. De Smet, J. Mathys, K. Marchal, G. Thijs, B. De Moor, and Y. Moreau. Adaptive quality-based clustering of gene expression profiles. 2002. Bioinformatics, 18(5):735-746.

  • M. Lescot, P. D?hais, G. Thijs, K. Marchal, Y. Moreau , Y. Van de Peer, P. Rouz?, and S. Rombauts. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. 2002. Nucleic Acids Research, 30(1):325-7.

  • G. Thijs, Y. Moreau, F. De Smet, J. Mathys, M. Lescot, S. Rombauts, P. Rouz?, B. De Moor, and K. Marchal. INCLUSive: INtegrated Clustering, Upstream sequence retrieval and motif Sampling. 2002. Bioinformatics, 18(2):331-2.

  • G. Thijs, M. Lescot, K. Marchal, S. Rombauts, B. De Moor, P. Rouz?, and Y. Moreau. A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling. 2001. Bioinformatics, 17(12):1113-22.

  • J. Sun, I. Smets, K. Bernaerts, J. Van Impe, J. Vanderleyden, and K. Marchal. Quantitative analysis of bacterial gene expression by using the gusA reporter gene system. 2001. Applied Environmental Microbiology, 67:3356-7.

    • APPLICATION


     

  • G. Eelen, B. Vanden, I, L. Verlinden, M. Drijkoningen, A. Smeets, P. Neven, M. R. Christiaens, K. Marchal, R. Bouillon, and A. Verstuyf. Expression of the BRCA1-interacting protein Brip1/BACH1/FANCJ is driven by E2F and correlates with human breast cancer malignancy. 2008. Oncogene,

  • I. M. Thijs, S. C. De Keersmaecker, A. Fadda, K. Engelen, H. Zhao, M. McClelland, K. Marchal, and I. Vanderleyden. Combining omics data to unravel the regulatory network controlling Salmonella invasion of epithelial cells. 2007. Commun. Agric. Appl Biol Sci., 72:55-9.

  • L. Verlinden, I. Vanden Bempt, G. Eelen, M. Drijkoningen, I. Verlinden, K. Marchal, C. Wolf-Peeters, M. R. Christiaens, L. Michiels, R. Bouillon, and A. Verstuyf. The E2F-regulated gene Chk1 is highly expressed in triple-negative estrogen receptor /progesterone receptor /HER-2 breast carcinomas. 2007. Cancer Research.,67:6574-81.

  • L. Verlinden, G. Eelen, R. Van Hellemont, K. Engelen, I. Beullens, M. Van Camp, K. Marchal, C. Mathieu, R. Bouillon, and A. Verstuyf. 1alpha,25-Dihydroxyvitamin D3-induced down-regulation of the checkpoint proteins, Chk1 and Claspin, is mediated by the pocket proteins p107 and p130. 2007. J Steroid Biochem. Mol Biol., 103:411-5.

  • I. M. Thijs, S. C. De Keersmaecker, A. Fadda, K. Engelen, H. Zhao, M. McClelland, K. Marchal, and J. Vanderleyden. Delineation of the Salmonella Typhimurium HilA regulon through genome-wide location and transcript analysis. 2007. J Bacteriol.

  • S. Lebeer, S. C. De Keersmaecker, T. L. Verhoeven, A. A. Fadda, K. Marchal, and J. Vanderleyden. Functional analysis of luxS in the probiotic strain Lactobacillus rhamnosus GG reveals a central metabolic role important for growth and biofilm formation. Journal of Bacteriology, 2007, 189:860-71.

  • F. De Smet, N.L. Pochet, K. Engelen, T. Van Gorp, P. Van Hummelen, K. Marchal, F. Amant, D. Timmerman, B.L. De Moor, I.B. Vergote. Predicting the clinical behavior of ovarian cancer from gene expression profiles. International Journal of Gynecological Cancer, 2006, 16 Suppl 1:147-51.

  • S.C. De Keersmaecker, T.L. Verhoeven, J. Desair, K. Marchal, J. Vanderleyden, and I. Nagy. Strong antimicrobial activity of Lactobacillus rhamnosus GG against Salmonella typhimurium is due to accumulation of lactic acid. FEMS Microbiological Letters, 2006, 259:89-96.

  • S.C. De Keersmaecker, K. Marchal, T.L. Verhoeven, K. Engelen, J. Vanderleyden, and C.S. Detweiler. 2005. Microarray analysis and motif detection reveal new targets of the Salmonella enterica serovar Typhimurium HilA regulatory protein, including hilA itself. J. Bacteriol. 187:4381-91.

  • L. Verlinden,G. Eelen,I. Beullens,M. Van Camp,P. Van Hummelen,K. Engelen ,R. Van Hellemont, K. Marchal, B. De Moor, F. Foijer, R.H. Te, M. Beullens, M. Bollen, C. Mathieu, R. Bouillon, A. Verstuyf. 2005. Characterization of the condensin component Cnap1 and the protein kinase Melk as novel E2F-target genes down-regulated by 1,25-dihydroxyvitamin D3. J Biol Chem. 280:37319-37330.

  • E. Denolet, K. De Gendt, J. Allemeersch, K. Engelen, K. Marchal, P. Van Hummelen, K. Tan, R. M Sharpe, P. TK Saunders, J. V. Swinnen, G. Verhoeven. The effect of a Sertoli cell-selective knockout of the androgen receptor on testicular gene expression in prepubertal mice, Mol Endocrinol.

  • J. Roosen, K. Engelen, K. Marchal, J. Mathys, G. Griffioen, E. cameroni, J.M. Thevelein, C. De Virgilio, B. De Moor, and J. Winderickx. PKA and Sch9 control a molecular switch important for the proper adaptation to nutrient availability. 2005. Mol. Microbiol. 55: 862-80. (SCI impact factor: 5.563)

  • E. Vanbleu, K. Marchal, and J. Vanderleyden. Genetic and physical map of the pLAFR1 vector. 2004. DNA Seq. 15:225-7. (SCI impact factor: 0.369)

  • S.C. De Keersmaecker, C. Varszegi, N. Van Boxel,L.W. Habel, K. Metzger, R. Daniels, K. Marchal, D. De Vos, and J. Vanderleyden. Chemical synthesis of (S)-4,5-dihydroxy-2,3-pentanedione, a bacterial signal molecule precursor, and validation of its activity in Salmonella typhimurium. 2005. J. Biol. Chem. 280:19563-8.

  • J. R. Brants, T. A. Ayoubi, K. Chada, K. Marchal, W. J. Van de Ven, and M. M. Petit. Differential regulation of the insulin-like growth factor II mRNA-binding protein genes by architectural transcription factor HMGA2. 2004. FEBS Lett., 569:277-83.

  • G. Eelen, L. Verlinden, M. Van Camp, P. Van Hummelen, K. Marchal, B. De Moor, C. Mathieu, G. Carmeliet, R. Bouillon, and A. Verstuyf. The effects of 1alpha,25-dihydroxyvitamin D3 on the expression of DNA replication genes. 2004. J. Bone Miner. Res., 19:133-46.

  • K. Marchal, K. Engelen, J. De Brabanter, S. Aerts., B. De Moor, T. Ayoubi, and P. Van Hummelen. Comparison of different methodologies to identify differentially expressed genes in two-sample cDNA microarrays. 2002. Journal of Biological Systems, 10(4):409-430.

  • L. Fernando Revers, L. M. Pereira Passaglia, K. Marchal, J. Frazzon, C. Galindo Blaha, J. Vanderleyden, and I. Silveira Schrank. Characterization of an Azospirillum brasilense Tn5 mutant with enhanced nitrogen fixation: the effect of ORF280 on nifH expression. 2000. FEMS Microbiology Letters, 183:23-9.

  • K. Marchal, and J. Vanderleyden. The O2-paradox of Azospirillum. 2000. Biology and Fertility of Soils, 30:363-373.

  • K. Marchal, J. Sun, V. Keijers, H. Haaker, and J. Vanderleyden. A Cytochrome cbb3 (cytochrome c) terminal oxidase in Azospirillum brasilense Sp7 supports microaerobic growth. 1998. Journal of Bacteriology, 180:5689-96.