Data integration & Biological Networks

Publications

Papers

(133) Thilakarathne, P.J., Verbeke, G., Engelen, K., Marchal, K., Lin, D. (2013) Identifying differentially expressed genes in the absence of replication Int J Bioinform Res Appl. 9(1):71-90

(132) Tytgat, HL., Sanchez-Rodriguez, A., Schoofs, G., Verhoeven, G., De Keersmaecker, S., Marchal, K., Vanderleyden, J., Lebeer, S. (2012) A combined approach to study the protein glycosylation potential of Lactobacillus rhamnosus GG (LGG). Commun. Agric. Appl. Biol. Sci. 77, 15-19

(131) Sun, H., Guns, T., Fierro, A.C., Thorrez, L., Nijssen, S., Marchal, K. (2012) Unveiling combinatorial regulation through the combination of ChIP information and in silico cis-regulatory module detection. Nucleic Acids Res. 40, e90

(130) Fu, Q., Lemmens, K., Sanchez-Rodriguez, A., Thijs, G., Meysman, P., Sun, H., Fierro, A.C., Engelen, K., Marchal, K. (2012) Directed module detection in a large-scale expression compendium. Methods Mol. Biol. 804,131-165

(129) Wu, W., Cai, H., Sun, H., Lu, J., Zhao, D., Qin, B., Han, B., Niu, X., Lu, C., Xia, Y., Wang, X., De Moor, B., Marchal, K., Wang, X. (2012) Follicle stimulating hormone receptor G-29A, 919A>G, 2039A>G polymorphism and the risk of male infertility: A meta-analysis. Gene 505, 388-92

(128) Claeys, M., Storms, V., Sun, H., Michoel, T., Marchal, K. (2012) MotifSuite: workflow for probabilistic motif detection and assessment Bioinformatics 28, 1931-1932

(127) Meysman, P., Marchal, K., Engelen, K. (2012) Identifying common structural DNA properties in transcription factor binding site sets of the LacI-GalR family Curr. Bioinform. In press

(126) Sanchez-Rodriguez, A., Cloots, L., Marchal, K. (2012) Omics derived networks in bacteria Curr. Bioinform. In press

(125) Sun, H., Guns, T., C. Fierro, A., Thorrez, L., Nijssen, S., Marchal, K. (2012) Unveiling combinatorial regulation through the combination of ChIP information and in silico cis-regulatory module detection Nucleic Acids Res. 40, e90

(124) Aslankoohi, E., Voordeckers, K., Sun, H., Sanchez Rodriguez, A., van der Zande, E., Marchal, K., Verstrepen, K.J. (2012) Nucleosomes affect local transformation efficiency Nucleic Acids Research 40(19), 9506-9512

(123) Meysman, P., Marchal, K., Engelen, K. (2012) DNA structural properties in the classification of genomic transcription regulation elements Bioinform Biol Insights 6:155-68

(122) Voordeckers, K., De Maeyer, L., van der Zande, E., Vinces, M.D., Meert, W., Cloots, L., Ryan, O., Marchal, K., Verstrepen, K.J. (2012) Identification of a complex genetic network underlying Saccharomyces cerevisiae colony morphology Molecular Microbiology in press

(121) Le Van, T., Fierro Gutiérrez, A., Guns, T., Van Leeuwen, T., Nijssen, S., De Raedt, L., Marchal, K. (2012) Mining local staircase patterns in noisy data International workshop on Co-Clustering and Applications (CoClus’12) in conjunction with IEEE ICDM 2012. Brussels, 10 December 2012 pp. 1-8

(120) Vercruysse, M., Fauvart, M., Beullens, S., Braeken, K., Cloots, L., Engelen, K., Marchal, K., Michiels, J. (2011) A Comparative Transcriptome Analysis of Rhizobium etli Bacteroids: Specific Gene Expression During Symbiotic Nongrowth Mol. Plant Microbe In. 24, 1553-1561

(119) Aguero-Chapin, G., Sanchez-Rodriguez, A., I. Hidalgo-Yanes, P., Perez-Castillo, Y., Molina-Ruiz, R., Marchal, K., Vasconcelos, V., Antunes, A. (2011) An Alignment-Free Approach for Eukaryotic ITS2 Annotation and Phylogenetic Inference PLOS One 6, e26638

(118) Cloots, L., Marchal, K. (2011) Network-based functional modeling of genomics, transcriptomics and metabolism in bacteria Curr. Opin. Microbiol. 14, 599-607

(117) Vercruysse, M., Fauvart, M., Jans, A., Beullens, S., Braeken, K., Cloots, L., Engelen, K., Marchal, K., Michiels, J. (2011) Stress response regulators identified through genome-wide transcriptome analysis of the (p) ppGpp-dependent response in Rhizobium etli Genome Biol. 12, 23

(116) De Smet, R., Marchal, K. (2011) An ensemble biclustering approach for querying gene expression compendia with experimental lists Bioinformatics 27, 1948-1956

(115) Engelen, K., Fu, Q., Meysman, P., Sanchez-Rodriguez, A., De Smet, R., Lemmens, K., C. Fierro, A., Marchal, K. (2011) COLOMBOS: Access Port for Cross-Platform Bacterial Expression Compendia PLOS One 6, 1948-1956

(114) Fauvart, M., Sanchez-Rodriguez, A., Beullens, S., Marchal, K., Michiels, J. (2011) Genome Sequence of Rhizobium etli CNPAF512, a Nitrogen-Fixing Symbiont Isolated from Bean Root Nodules in Brazil J. Bacteriol. 193, 3158-3159

(113) Van Puyvelde, S., Cloots, L., Engelen, K., Das, F., Marchal, K., Vanderleyden, J., Spaepen, S. (2011) Transcriptome Analysis of the Rhizosphere Bacterium Azospirillum brasilense Reveals an Extensive Auxin Response Microb. Ecol. 61, 723-728

(112) Zarrineh, P., C. Fierro, A., Sanchez-Rodriguez, A., De Moor, B., Engelen, K., Marchal, K. (2011) COMODO: an adaptive coclustering strategy to identify conserved coexpression modules between organisms Nucleic Acids Res. 39, E41-U45

(111) Zhao, Q., Cloots, L., Van den Bulcke, T., Wu, H.-J., De Smet, R., Storms, V., Meysman, P., Engelen, K., Marchal, K. (2011) Query-based biclustering of gene expression data using Probabilistic Relational Models. BMC Bioinformatics 12, S37

(110) Meysman, P., D. Thanh, H., Laukens, K., De Smet, R., Wu, Y., Marchal, K., Engelen, K. (2011) Use of structural DNA properties for the prediction of transcription-factor binding sites in Escherichia coli Nucleic Acids Res. 39, 1245

(109) Thiele, I., R. Hyduke, D., Steeb, B., Fankam, G., K. Allen, D., Bazzani, S., Charusanti, P., C. Chen, F., M. T. Fleming, R., A. Hsiung, C., C. J. De Keersmaecker, S., C. Liao, Y., Marchal, K., L. Mo, M., Ozdemir, E., Raghunathan, A., L. Reed, J., I. Shin, S., Sigurbjornsdottir, S., Steinmann, J., Sudarsan, S., Swainston, N., M. Thijs, I., Zengler, K., O. Palsson, B., N. Adkins, J., Bumann, D. (2011) A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2 BMC Syst. Biol. 5, 221

(108) Meysman, P., Dang, T. H., Laukens, K., De Smet, R., Wu, H.-J., Marchal, K., Engelen, K. (2011) Use of structural DNA properties for the prediction of transcription factor binding sites Nucleic Acids Res. 39, 6

(107) Cloots, L., De Maeyer, L., Marchal, K. (2011) Path Finding in Biological Networks to Interpret Functional Data

(106) Cloots, L., Zhao, H., Van den Bulcke, T., Wu, Y., De Smet, R., Storms, V., Meysman, P., Engelen, K., Marchal, K. (2011) Query?based biclustering of gene expression data using Probabilistic Relational Models

(105) De Smet, R., Marchal, K. (2010) An ensemble method for querying gene expression compendia with experimental lists. Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM2010) 314-318, Hong Kong, China

(104) Kint, G., De Coster, D., Marchal, K., Vanderleyden, J., C. J. De Keersmaecker, S. (2010) The small regulatory RNA molecule MicA is involved in Salmonella enterica serovar Typhimurium biofilm formation BMC Microbiol. 10, 4919-4926

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

(102) De Smet, R., Marchal, K. (2010) Advantages and limitations of current network inference methods. Nat. Rev. Microbiol. 8, 717-729

(101) Engelen, K., Sifrim, A., Van de Plas, B., Laukens, K., Arckens, L., Marchal, K. (2010) Alternative Experimental Design with an Applied Normalization Scheme Can Improve Statistical Power in 2D-DIGE Experiments J. Proteome Res. 9, 4919-4926

(100) M. Thijs, I., Zhao, H., De Weerdt, A., Engelen, K., De Coster, D., Schoofs, G., McClelland, M., Vanderleyden, J., Marchal, K., C. D. De Keersmaecker, S. (2010) The AI-2-dependent regulator LsrR has a limited regulon in Salmonella Typhimurium Cell Res. 20, 966-969

(99) Bonnet, E., Tatari, M., Joshi, A., Michoel, T., Marchal, K., Berx, G., Van de Peer, Y. (2010) Module network inference from a cancer gene expression data set identifies microRNA regulated modules. PLOS One 5, e10162

(98) Kriebitzsch, C., Verlinden, L., Eelen, G., Marchal, K., DeMoor, B., Beullens, I., Van Camp, M., Bouillon, R., Verstuyf, A. (2010) Regulation of Cystathionine Beta Synthase by 1 Alpha,25-Dihydroxyvitamin D(3) Bone 46, S51-S51

(97) Verlinden, L., Kriebitzsch, C., Eelen, G., Beullens, I., Van Camp, M., K. Tan, B., De Moor, B., Marchal, K., Bouillon, R., Verstuyf, A. (2010) Regulation of semaphorin 3 family members and their receptors by 1 alpha,25-dihydroxyvitamin D(3) Bone 46, S66-S66

(96) Kint, G., Fierro, C., Marchal, K., Vanderleyden, J., C. J. De Keersmaecker, S. (2010) Integration of omics data: does it lead to new insights into host-microbe interactions? Future Microbiol. 5, 313-328

(95) Storms, V., Claeys, M., Sanchez, A., De Moor, B., Verstuyf, A., Marchal, K. (2010) The Effect of Orthology and Coregulation on Detecting Regulatory Motifs PLOS One 5, e8938

(94) Vercruysse, M., Fauvart, M., Cloots, L., Engelen, K., M. Thijs, I., Marchal, K., Michiels, J. (2010) Genome-wide detection of predicted non-coding RNAs in Rhizobium etli expressed during free-living and host-associated growth using a high-resolution tiling array BMC Genomics 11, 1

(93) De Smet, R., Lemmens, K., Fierro, A.C., Marchal, K. (2010) Systems Microbiology: Gaining Insights in Transcriptional Networks. Infectious Disease Informatics (Book Chapter, Ed. Sintchenko V.),93-122

(92) Guns, T., Sun, H., Marchal, K., Nijssen, S. (2010) Cis-regulatory module detection using constraint programming

(91) Fadda, A., C. Fierro, A., Lemmens, K., Monsieurs, P., Engelen, K., Marchal, K. (2009) Inferring the transcriptional network of Bacillus subtilis Mol. BioSyst. 5, 1840-1852

(90) H. Dang, T., Engelen, K., Meysman, P., Marchal, K., Verschoren, A., Laukens, K. (2009) Conditional Random Fields feature subset selection based on Genetic Algorithms for phosphorylation site prediction International Conference on Knowledge and Systems Engineering (Kse 2009) 28, 7-12

(89) Sun, H., Lemmens, K., Van den Bulcke, T., Engelen, K., De Moor, B., Marchal, K. (2009) ViTraM: visualization of transcriptional modules Bioinformatics 25, 2450-2451

(88) Vanoirbeek, E., Eelen, G., Verlinden, L., Marchal, K., Engelen, K., De Moor, B., Beullens, I., Marcelis, S., De Clercq, P., Bouillon, R., Verstuyf, A. (2009) Microarray Analysis of MCF-7 Breast Cancer Cells Treated with 1,25-Dihydroxyvitamin D(3) or a 17-Methyl-D-ring Analog Anticancer Res. 29, 3585-3590

(87) Lemmens, K., De Bie, T., Dhollander, T., Monsieurs, P., De Moor, B., Collado-Vides, J., Engelen, K., Marchal, K. (2009) The Condition-Dependent Transcriptional Network in Escherichia coli Ann. Ny. Acad. Sci. 1158, 29-35

(86) Michoel, T., De Smet, R., Joshi, A., Van de Peer, Y., Marchal, K. (2009) Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks. BMC Systems Biology 3, 49

(85) Michoel, T., De Smet, R., Joshi, A., Marchal, K., Van de Peer, Y. (2009) Reverse-engineering transcriptional modules from gene expression data Annals of the New York Academy of Sciences 1158, 36-43

(84) J. Thilakarathne, P., Verbeke, G., Engelen, K., Marchal, K. (2009) A Nonlinear Mixed-Effects Model for Estimating Calibration Intervals for Unknown Concentrations in Two-Color Microarray Data with Spike-Ins Stat. Appl. Genet. Mo. B. 8, 14

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

(82) Sun, H., Van den Bulcke, T., De Moor, B., Lemmens, K., Engelen, K., Marchal, K. (2009) Layout and Post-Processing of Transcriptional Modules 2009 International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing, Proceedings 25, 116-121

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

(80) Sun, H., De Bie, T., Storms, V., Fu, Q., Dhollander, T., Lemmens, K., Verstuyf, A., De Moor, B., Marchal, K. (2009) ModuleDigger: an itemset mining framework for the detection of cis-regulatory modules BMC Bioinformatics 10, 36-43

(79) Thilakarathne, P.J., Verbeke, G., Engelen, K., Marchal, K. (2009) The Use of Mixed Models to Identify Differentially Expressed Genes when a Single Replicate per Biological Condition is Present In : The 2009 Intenational Conference on Bioinformatics & Computational biology, 1, (Arabnia, H., Yang, M. (Eds.)). BIOCOMP09. Las Vegas Nevada, USA, 13-16 July 2009 pp. 186-190. CSREA press

(78) Sun, H., De Bie, T., Storms, V., Fu, Q., Dhollander, T., Lemmens, K., Verstuyf, A., De Moor, B., Marchal, K. (2009) ModuleDigger: an itemset mining framework for the detection of cis-regulatory modules In : Proceedings of 7th Asia-Pacific Bioinformatics Conference APBC2009, (Zhang, M., Waterman, M., Zhang, X. (Eds.)). 7th Asia-Pacific Bioinformatics Conference APBC2009, Beijing, China, 2009 pp. 345-369. Tsinghua University Press

(77) Fierro, A.C., Vandenbussche, M., Engelen, K., Van de Peer, Y., Marchal, K. (2008) Meta Analysis of Gene Expression Data within and Across Species Current Genomics 9, 525-34

(76) Smets, B., De Snijder, P., Engelen, K., Joossens, E., Ghillebert, R., Thevissen, K., Marchal, K., Winderickx, J. (2008) Genome-wide expression analysis reveals TORC1-dependent and -independent functions of Sch9 Fems Yeast Res. 8, 1276-1288

(75) Van Leemput, K., Van den Bulcket, T., Dhollander, T., De Moor, B., Marchal, K., van Remortel, P. (2008) Exploring the operational characteristics of inference algorithms for transcriptional networks by means of synthetic data Artif. Life 14, 49-63

(74) C. A. Janssens, J., Steenackers, H., Robijns, S., Gellens, E., Levin, J., Zhao, H., Hermans, K., De Coster, D., L. Verhoeven, T., Marchal, K., Vanderleyden, J., E. De Vos, D., C. J. De Keersmaecker, S. (2008) Brominated Furanones Inhibit Biofilm Formation by Salmonella enterica Serovar Typhimurium Appl. Environ. Microb. 74, 6639-6648

(73) Marchal, K., C. De Keersmaecker, S. (2008) Bacterial networking Genome Biol. 9, 327

(72) Vanoirbeek, E., Eelen, G., Beullens, I., Van Camp, M., Engelen, K., Marchal, K., De Clercq, P., Bouillon, R., Verstuyf, A. (2008) Microarray Analysis of Mcf-7 Breast Cancer Cells Treated with 1,25-Dihydroxyvitamin D(3) or the Seco-9,11-Bisnor-17-Methyl Analog Wy1112 Anticancer Res. 28, 3526-3526

(71) Eelen, G., V. Bempt, I., Verlinden, L., Drijkoningen, M., Smeets, A., Neven, P., R. Christiaens, M., Marchal, K., Bouillon, R., Verstuyf, A. (2008) Expression of the BRCA1-interacting protein Brip1/BACH1/FANCJ is driven by E2F and correlates with human breast cancer malignancy Oncogene 27, 4233-4241

(70) Vanoirbeek, E., Eelen, G., Beullens, I., Van Camp, M., Engelen, K., Marchal, K., De Clercq, P., Vandewalle, M., Bouillon, R., Verstuyf, A. (2008) Microarray analysis of MCF-7 breast cancer cells treated with 1,25-(OH)(2)D-3 or the analog WY1112 Anticancer Res. 28, 1625-1626

(69) Thorrez, L., Van Deun, K., C. Tranchevent, L., Van Lommel, L., Engelen, K., Marchal, K., Moreau, Y., Van Mechelen, I., Schuit, F. (2008) Using Ribosomal Protein Genes as Reference: A Tale of Caution PLOS One 3, S11

(68) C. Fierro, A., Thuret, R., Engelen, K., Bernot, G., Marchal, K., Pollet, N. (2008) Evaluation of time profile reconstruction from complex two-color microarray designs BMC Bioinformatics 9, 4233-4241

(67) Michoel, T., Maere, S., Bonnet, E., Joshi, A., Saeys, Y., Van den Bulcke, T., Van Leemput, K., van Remortel, P., Kuiper, M., Marchal, K., Van de Peer, Y. (2007) Validating module network learning algorithms using simulated data BMC Bioinformatics 8, 860-871

(66) Dhollander, T., Z. Sheng, Q., Lemmens, K., De Moor, B., Marchal, K., Moreau, Y. (2007) Query-driven module discovery in microarray data Bioinformatics 23, 2573-2580

(65) Van Hellemont, R., Blomme, T., Van de Peer, Y., Marchal, K. (2007) Divergence of regulatory sequences in duplicated fish genes. Genome Dyn 3, 81-100

(64) M. V. Thijs, I., C. J. De Keersmaecker, S., Fadda, A., Engelen, K., Zhao, H., McClelland, M., Marchal, K., Vanderleyden, J. (2007) Delineation of the Salmonella enterica serovar typhimurium HilA regulon through genome-wide location and transcript analysis J. Bacteriol. 189, 4587-4596

(63) Verlinden, L., V. Bempt, I., Eelen, G., Drijkoningen, M., Verlinden, I., Marchal, K., De Wolf-Peeters, C., R. Christiaens, M., Michiels, L., Bouillon, R., Verstuyf, A. (2007) The E2F-regulated gene Chk1 is highly expressed in triple-negative estrogen receptor-/progesterone receptor-/HER-2- Breast carcinomas Cancer Res. 67, 6574-6581

(62) Zhao, H., Engelen, K., De Moor, B., Marchal, K. (2007) CALIB: a Bioconductor package for estimating absolute expression levels from two-color microarray data Bioinformatics 23, 1700-1701

(61) Van Deun, K., Marchal, K., J. Heiser, W., Engelen, K., Van Mechelen, I. (2007) Joint mapping of genes and conditions via multidimensional unfolding analysis BMC Bioinformatics 8, 4587-4596

(60) * Michoel, T., * Maere, S., Bonnet, E., Joshi, A., Saeys, Y., Van den Bulcke, T., Van Leemput, K., van Remortel, P., Kuiper, M., Marchal, K., Van de Peer, Y. (2007) Validating module networks learning algorithms using simulated data. BMC Bioinformatics 8, S5

(59) Verlinden, L., Eelen, G., Van Hellemont, R., Engelen, K., Beullens, I., Van Camp, M., Marchal, K., Mathieu, C., Bouillon, R., Verstuyf, A. (2007) 1 alpha,25-dihydroxyvitamin D-3-induced down-regulation of the checkpoint proteins, Chk1 and Claspin, is mediated by the pocket proteins p107 and p 130 J. Steroid Biochem. 103, 411-415

(58) Lebeer, S., C. J. De Keersmaecker, S., L. A. Verhoeven, T., A. Fadda, A., Marchal, K., Vanderleyden, J. (2007) Functional analysis of luxS in the probiotic strain Lactobacillus rhamnosus GG reveals a central metabolic role important for growth and Biofilm formation J. Bacteriol. 189, 860-871

(57) Pastor, D., Lemmens, K., Cortés-Calabuig, A., Marchal, K., Denecker, M., De Moor, B. (2007) GeneReg: Integration of experimental data on the DNA transcription process In : Proceedings of the 19th Belgian-Dutch Conference on Artificial Intelligence, (Dastani, M., de Jong, E. (Eds.)). The 19th Belgian-Dutch Conference on Artificial Intelligence, Utrecht, The Netherlands, November 5-6, 2007 pp. 260-267

(56) C. J. De Keersmaecker, S., M. V. Thijs, I., Vanderleyden, J., Marchal, K. (2006) Integration of omics data: how well does it work for bacteria? Mol. Microbiol. 62, 1239-1250

(55) C. J. De Keersmaecker, S., L. A. Verhoeven, T., Desair, J., Marchal, K., Vanderleyden, J., Nagy, I. (2006) Strong antimicrobial activity of Lactobacillus rhamnosus GG against Salmonella typhimurium is due to accumulation of lactic acid Fems Microbiol. Lett. 259, 89-96

(54) Lemmens, K., Dhollander, T., De Bie, T., Monsieurs, P., Engelen, K., Smets, B., Winderickx, J., De Moor, B., Marchal, K. (2006) Inferring transcriptional modules from ChIP-chip, motif and microarray data Genome Biol. 7, 1251-1258

(53) Engelen, K., Naudts, B., De Moor, B., Marchal, K. (2006) A calibration method for estimating absolute expression levels from microarray data Bioinformatics 22, 1251-1258

(52) Monsieurs, P., Thijs, G., A. Fadda, A., C. J. De Keersmaecker, S., Vanderleyden, J., De Moor, B., Marchal, K. (2006) More robust detection of motifs in coexpressed genes by using phylogenetic information BMC Bioinformatics 7, 1251-1258

(51) Denolet, E., De Gendt, K., Allemeersch, J., Engelen, K., Marchal, K., Van Hummelen, P., A. L. Tan, K., M. Sharpe, R., T. K. Saunders, P., V. Swinnen, J., Verhoeven, G. (2006) The effect of a sertoli cell-selective knockout of the androgen receptor on testicular gene expression in prepubertal mice Mol. Endocrinol. 20, 321-334

(50) Van den Bulcke, T., Van Leemput, K., Naudts, B., van Remortel, P., W. Ma, H., Verschoren, A., De Moor, B., Marchal, K. (2006) SynTReN: a generator of synthetic gene expression data for design and analysis of structure learning algorithms BMC Bioinformatics 7, 301-313

(49) Van den Bulcke, T., Lemmens, K., Van de Peer, Y., Marchal, K. (2006) Inferring transcriptional networks by mining 'omics' data. Current Bioinformatics 1, 301-313

(48) De Smet, F., Pochet, N., Engelen, K., Van Gorp, T., Van Hummelen, P., Marchal, K., Amant, F., Timmerman, D., De Moor, B., Vergote, I. (2006) Predicting the clinical behaviour of ovarian cancer from gene expression profiles International Journal of Gynecological Cancer 16, 147-151

(47) Van Gorp, T., De Smet, F., Pochet, N., Engelen, K., Van Hummelen, P., Suykens, J., Marchal, K., Amant, F., Moreau, Y., Timmerman, D., De Moor, B., Vergote, I. (2005) Predicting the clinical behavior of ovarian cancer from gene expression profiles. International Journal of Gynecological Cancer (ESGO) 15, 66

(46) De Bie, T., Monsieurs, P., Engelen, K., De Moor, B., Cristianini, N., Marchal, K. (2005) Discovering transcriptional modules from motif, chip-chip and microarray data Pacific Symposium on Biocomputing 2005 15, 483-494

(45) Verlinden, L., Eelen, G., Beullens, I., Van Camp, M., Van Hummelen, P., Engelen, K., Van Hellemont, R., Marchal, K., De Moor, B., Foijer, F., T. Riele, H., Beullens, M., Bollen, M., Mathieu, C., Bouillon, R., Verstuyf, A. (2005) Characterization of the condensin component Cnap1 and protein kinase Melk as novel E2F target genes down-regulated by 1,25-dihydroxyvitamin D(3) J. Biol. Chem. 280, 37319-37330

(44) C. J. De Keersmaecker, S., Marchal, K., L. A. Verhoeven, T., Engelen, K., Vanderleyden, J., S. Detweiler, C. (2005) Microarray analysis and motif detection reveal new targets of the Salmonella enterica serovar typhimurium HilA regulatory protein, including hilA itself J. Bacteriol. 187, 4381-4391

(43) C. J. De Keersmaecker, S., Varszegi, C., van Boxel, N., W. Habel, L., Metzger, K., Daniels, R., Marchal, K., De Vos, D., Vanderleyden, J. (2005) Chemical synthesis of (S)-4,5-dihydroxy-2,3-pentanedione, a bacterial signal molecule precursor, and validation of its activity in Salmonella typhimurium J. Biol. Chem. 280, 19563-19568

(42) Monsieurs, P., De Keersmaecker, S., W. Navarre, W., W. Bader, M., De Smet, F., McClelland, M., C. Fang, F., De Moor, B., Vanderleyden, J., Marchal, K. (2005) Comparison of the PhoPQ regulon in Escherichia coli and Salmonella typhimurium J. Mol. Evol. 60, 462-474

(41) Roosen, J., Engelen, K., Marchal, K., Mathys, J., Griffioen, G., Cameroni, E., M. Thevelein, J., De Virgilio, C., De Moor, B., Winderickx, J. (2005) PKA and Sch9 control a molecular switch important for the proper adaptation to nutrient availability Mol. Microbiol. 55, 862-880

(40) Van Hellemont, R., Monsieurs, P., Thijs, G., De Moor, B., Van de Peer, Y., Marchal, K. (2005) A novel approach to identifying regulatory motifs in distantly related genomes. Genome Biol. 6, R113

(39) Pochet, N., Janssens, F., De Smet, F., Marchal, K., Suykens, J., De Moor, B. (2005) M@CBETH: a microarray classification benchmarking tool Bioinformatics 21, 3185-3186

(38) Sheng, Q., Moreau, Y., De Smet, R., Marchal, K., De Moor, B. (2005) Advances in cluster analysis of microarray data In: Azuaje F., Dopazo J. (Eds.), Data analysis and visualization in genomics and proteomics, Chapt. 10. Chichester, UK: John Wiley & Sons Ltd. 153-173

(37) De Moor, B., Marchal, K., Mathys, J., Moreau, Y. (2005) Bioinformatics : Organisms from Venus, Technology from Jupiter, Algorithms from Mars In : Mathematics and Genomics pp. 37-102

(36) Smets, I., Cappuyns, A., Bernaerts, K., van Boxel, N., Sonck, K., De Keersmaecker, S., Monsieurs, P., Van den Bulcke, T., Marchal, K., Mathys, J., De Moor, B., Vanderleyden, J., Van Impe, J. (2005) Identifying new drug targets to combat pathogenic infections: An interdisciplinary approach In : Proceedings of the 16th IFAC World Congress. 16th IFAC World Congress, Prague (Czech Republic), July 4-8, 2005 pp. ID 03952

(35) Pochet, N., Janssens, F., De Smet, F., Marchal, K., Vergote, I., Suykens, J., De Moor, B. (2005) M@CBETH: optimizing clinical microarray classification In : Proc. of the 2005 IEEE Computational Systems Bioinformatics Conference (CSB2005). 2005 IEEE Computational Systems Bioinformatics Conference (CSB2005), Stanford, California (US), Aug. 2005 pp. 89-90

(34) Marchal, K., De Keersmaecker, S., Monsieurs, P., van Boxel, N., Lemmens, K., Thijs, G., Vanderleyden, J., De Moor, B. (2004) In silico identification and experimental validation of PmrAB targets in Salmonella typhimurium by regulatory motif detection Genome Biol. 5, 211

(33) Dirix, G., Monsieurs, P., Dombrecht, B., Daniels, R., Marchal, K., Vanderleyden, J., Michiels, J. (2004) 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 Peptides 25, 1425-1440

(32) R. Brants, J., A. Y. Ayoubi, T., Chada, K., Marchal, K., J. M. Van de Ven, W., M. R. Petit, M. (2004) Differential regulation of the insulin-like growth factor II mRNA-binding protein genes by architectural transcription factor HMGA2 FEBS Lett. 569, 277-283

(31) Vanbleu, E., Marchal, K., Vanderleyden, J. (2004) Genetic and physical map of the pLAFR1 vector DNA Sequence 15, 225-227

(30) Dirix, G., Monsieurs, P., Marchal, K., Vanderleyden, J., Michiels, J. (2004) Screening genomes of gram-positive bacteria for double-glycine-motif-containing peptides Microbiology-Sgm 150, 1121-1126

(29) Vanbleu, E., Marchal, K., Lambrecht, M., Mathys, J., Vanderleyden, J. (2004) Annotation of the pRhico plasmid of Azospirillum brasilense reveals its role in determining the outer surface composition Fems Microbiol. Lett. 232, 165-172

(28) Eelen, G., Verlinden, L., Van Camp, M., Van Hummelen, P., Marchal, K., De Moor, B., Mathieu, C., Carmeliet, G., Bouillon, R., Verstuyf, A. (2004) The effects of 1 alpha,25-dihydroxyvitamin D-3 on the expression of DNA replication genes J. Bone Miner. Res. 19, 133-146

(27) Thijs, G., De Smet, F., Moreau, Y., Marchal, K., De Moor, B. (2004) Gene regulation bioinformatics of microarray data In: Metin A (Eds.) Genomics and Proteomics Engineering 1-41

(26) Marchal, K., De Smet, F., Engelen, K., De Moor, B. (2004) Computational biology and toxicogenomics In: Helma C. (Eds.), Predictive toxicology 37-85

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

(24) Engelen, K., Coessens, B., Marchal, K., De Moor, B. (2003) MARAN: normalizing micro-array data Bioinformatics 19, 893-894

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

(22) De Moor, B., Marchal, K., Mathys, J., Moreau, Y. (2003) Bioinformatics: Organisms from Venus, technology from Jupiter, algorithms from Mars Eur. J. Control 9, 237-278

(21) * Rombauts, S., * Florquin, K., Lescot, M., Marchal, K., Rouzé, P., Van de Peer, Y. (2003) Computational approaches to identify promoters and cis-regulatory elements in plant genomes. Plant Physiol. 132, 1162-76

(20) Marchal, K., Engelen, K., De Brabanter, J., Aert, S., De Moor, B., Ayoubi, T., Van Hummelen, P. (2002) Comparison of different methodologies to identify differentially expressed genes in two-sample cDNA microarrays J. Biol. Syst. 10, 409-430

(19) Moreau, Y., De Smet, F., Thijs, G., Marchal, K., De Moor, B. (2002) Functional bioinformatics of microarray data: From expression to regulation P. IEEE 90, 1722-1743

(18) Smets, I., Bernaerts, K., Sun, J., Marchal, K., Vanderleyden, J., Van Impe, J. (2002) Sensitivity function-based model reduction - A bacterial gene expression case study Biotechnol. Bioeng. 80, 195-200

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

(16) Thijs, G., Moreau, Y., De Smet, F., Mathys, J., Lescot, M., Rombauts, S., Rouzé, P., De Moor, B., Marchal, K. (2002) INCLUSive: INtegrated clustering, upstream of sequence retrieval and motif sampling Bioinformatics 18, 331-332

(15) Dombrecht, B., Marchal, K., Vanderleyden, J., Michiels, J. (2002) Prediction and overview of the RpoN-regulon in closely related species of the Rhizobiales Genome Biol. 3, 735-746

(14) Thijs, G., Marchal, K., Lescot, M., Rombauts, S., De Moor, B., Rouzé, P., Moreau, Y. (2002) A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes. J. Comput Biol. 9, 447-64

(13) Thijs, G., Moreau, Y., De Smet, F., Mathys, J., Lescot, M., Rombauts, S., Rouzé, P., De Moor, B., Marchal, K. (2002) INCLUSive: integrated clustering, upstream sequence retrieval and motif sampling. Bioinformatics 18, 331-2

(12) Smets, I., Bernaerts, K., Sun, J., Marchal, K., Vanderleyden, J., Van Impe, J. (2002) Sensitivity function based model reduction: a bacterial gene expression case study

(11) Thijs, G., Lescot, M., Marchal, K., Rombauts, S., De Moor, B., Rouzé, P., Moreau, Y. (2001) A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling Bioinformatics 17, 1113-1122

(10) Sun, J., Smets, I., Bernaerts, K., Van Impe, J., Vanderleyden, J., Marchal, K. (2001) Quantitative analysis of bacterial gene expression by using the gusA reporter gene system Appl. Environ. Microb. 67, 3350-3357

(9) Thijs, G., Lescot, M., Rombauts, S., Marchal, K., De Moor, B., Moreau, Y., Rouzé, P. (2001) A higher order background model improves the detection by Gibbs sampling of potential promoter regulatory elements in DNA sequences. Bioinformatics 17, 1113-22

(8) Thijs, G., Marchal, K., Lescot, M., Rombauts, S., De Moor, B., Rouzé, P., Moreau, Y. (2001) A Gibbs Sampling method to detect over-represented motifs in upstream regions of co-expressed genes In : 5th Annual International Conference on Computational Biology (RECOMB 2001). 5th Annual International Conference on Computational Biology (RECOMB 2001), Montreal, Canada, Apr. 2001 pp. 296-302

(7) Thijs, G., Marchal, K., Lescot, M., Rombauts, S., De Moor, B., Rouzé, P., Moreau, Y. (2001) A Gibbs Sampling method to detect over-represented motifs in upstream regions of co-expressed genes In : Proc. of the 5th Annual International Conference on Computational Biology (RECOMB’2001). 5th Annual International Conference on Computational Biology (RECOMB 2001), Montreal, Canada, Apr. 2001 pp. 305-312

(6) Marchal, K., Vanderleyden, J. (2000) The "oxygen paradox" of dinitrogen-fixing bacteria Biol. Fert. Soils 30, 363-373

(5) F. Revers, L., M. P. Passaglia, L., Marchal, K., Frazzon, J., G. Blaha, C., Vanderleyden, J., S. Schrank, I. (2000) Characterization of an Azospirillum brasilense Tn5 mutant with enhanced N-2 fixation: the effect of ORF280 on nifH expression Fems Microbiol. Lett. 183, 23-29

(4) Thijs, G., Rombauts, S., Lescot, M., Marchal, K., De Moor, B., Moreau, Y., Rouzé, P. (2000) Detection of cis-acting regulatory elements in plants: a Gibbs sampling approach In : Proc. of Bioinformatics of Gene regularisation and structure (BGRS’2000). The second international conference on bioinformatics, genome regulation and structure, Novosibirsk, Russia, Aug. 2000 pp. 119-123

(3) Marchal, K., Sun, J., Keijers, V., Haaker, H., Vanderleyden, J. (2000) The cytochrome cbb3 (cytochrome C) terminal oxidase of A. brasilense Sp7 Nitrogen Fixation: from molecules to crop productivity

(2) Marchal, K., Sun, J., Keijers, V., Haaker, H., Vanderleyden, J. (1998) A cytochrome cbb(3) (Cytochrome c) terminal oxidase in Azospirillum brasilense Sp7 supports microaerobic growth J. Bacteriol. 180, 5689-5696

(1) Marchal, K., Keijers, V., Haaker, H., Vanderleyden, J. (1997) Evidence for a cbb 3 -type cytochrome c terminal oxidase in Azospirillum brasilense Sp7 In : Proceedings 11 th International Congress on Nitrogen Fixation pp. 164.