1. International Journal Papers
2. Books and Book Chapters
3. Conference Papers
4. National Publications
5. PhD Dissertations

1. International Journal Papers

• Durinck S., Moreau Y., Kasprzyk A., De Moor B., Brazma A., Huber W., 2005. BioMart and Bioconductor: A powerful link between biological databases and microarray data analysis. Accepted for publication in Bioinformatics.
• Pochet N, Janssens F, De Smet F, Marchal K, Suykens J, De Moor B., 2005. M@CBETH: a microarray classification benchmarking tool. Bioinformatics. in press.
• Monsieurs P, De Keersmaecker S, Navarre WW, Bader MW, De Smet F, McClelland M, Fang FC, De Moor B, Vanderleyden J, Marchal K., 2005. Comparison of the PhoPQ regulon in Escherichia coli and Salmonella typhimurium. J Mol Evol. 60(4):462-74.
• Vermeesch JR, Melotte C, Froyen G, Van Vooren S, Dutta B, Maas N, Vermeulen S, Menten B, Speleman F, De Moor B, Van Hummelen P, Marynen P, Fryns JP, Devriendt K., 2005. Molecular karyotyping: array CGH quality criteria for constitutional genetic diagnosis. J Histochem Cytochem. 53(3):413-22.
• Menten B, Pattyn F, De Preter K, Robbrecht P, Michels E, Buysse K, Mortier G, De Paepe A, Van Vooren S, Vermeesch J, Moreau Y, De Moor B, Vermeulen S, Speleman F, Vandesompele J., 2005. arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays. BMC Bioinformatics. 6(1):124
• Aerts S., Van Loo P., Thijs G., Mayer H., de Martin R., Moreau Y., De Moor B., 2005. TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis, Accepted for publication in Nucleic Acids Research (Web Server Issue).
• Allemeersch J., Durinck S., Vanderhaeghen R., Alard P., Maes R., Seeuws K., Bogaert T., Coddens K., Deschouwer K., Van Hummelen P., Vuylsteke M., Moreau Y., Kwekkeboom J., Wijfjes A. H. M., May S., Beynon J., Hilson P., Kuiper M.T.R., 2005. Benchmarking the CATMA microarray: a novel tool for Arabidopsis transcriptome analysis, Plant Physiology, 137, 588-601.
• Roosen J., Engelen K., Marchal K., Mathys J., Griffioen G., Cameroni E., Thevelein J.M., De Virgilio C., De Moor B. and Winderickx J., 2005. PKA and Sch9 Control a Molecular Switch Important for the Proper Adaptation to Nutrient Availability, Molecular Microbiology, 55(3), 855-860.
• Tompa M., Li N., Bailey T.L., Church G.M., De Moor B., Eskin E., Favorov A.V., Frith M.C., Fu Y., Kent J.W., Makeev V.J., Mironov A.A., Noble W.S., Pavesi G., Pesole G., Régnier M., Simonis N., Sinha S., Thijs G., van Helden J., Vandenbogaert M., Weng Z., Workman C., Ye C., Zhu Z., 2005. An Assessment of Computational Tools for the Discovery of Transcription Factor Binding Sites, Nature Biotechnology, 23(1), 137-144.

• Hilson P, Allemeersch J, Altmann T, Aubourg S, Avon A, Beynon J, Bhalerao RP, Bitton F, Caboche M, Cannoot B, Chardakov V, Cognet-Holliger C, Colot V, Crowe M, Darimont C, Durinck S, Eickhoff H, de Longevialle AF, Farmer EE, Grant M, Kuiper MT, Lehrach H, Leon C, Leyva A, Lundeberg J, Lurin C, Moreau Y, Nietfeld W, Paz-Ares J, Reymond P, Rouze P, Sandberg G, Segura MD, Serizet C, Tabrett A, Taconnat L, Thareau V, Van Hummelen P, Vercruysse S, Vuylsteke M, Weingartner M, Weisbeek PJ, Wirta V, Wittink FR, Zabeau M, Small I., 2004. Versatile gene-specific sequence tags for Arabidopsis functional genomics: transcript profiling and reverse genetics applications, Genome Res., 14(10B):2176-89.
• 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(9), 1425-1440.
• Dirix G., Monsieurs P., Marchal K., Vanderleyden J., Michiels J., 2004. Screening genomes of Gram-positive bacteria for double-glycine-motif-containing peptides, Microbiology, 150(5), 1121-1126.
• 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(2), 165-172.
• De Smet F., Moreau Y., Engelen K., Timmerman D., VergoteI., De Moor B., 2004. Balancing false positives and false negatives for the detection of differential expression in malignancies, Britisch Journal of Cancer, 91,1160-1165.
• Durinck S., Allemeersch J., Carey V.J., Moreau Y., De Moor B., 2004. Importing MAGE-ML format microarray data into BioConductor Bioinformatics. Advance Access published online on July 15, 2004.
• Pochet N., De Smet F., Suykens J., De Moor B., 2004. Systematic benchmarking of micorarray data classification : assessing the role of nonlinearity and dimensionality reduction. Bioinformatics. Advance Access published online on July 1, 2004.
• Aerts S, Van Loo P, Moreau Y, De Moor B., 2004. A genetic algorithm for the detection of new cis-regulatory modules in sets of coregulated genes. Bioinformatics. 20(12), 1974-6.
• Kapushesky M., Kemmeren P., Culhane A.C., Durinck S., Ihmels J., Korner C., Kull M., Torrente A., Sarkans U., Vilo J. and Brazma A., 2004. Expression Profiler: next generation - an online platform for analysis of microarray data, Nucleic Acids Research, 32, W465-470.
• Antal P., Fannes G., Timmerman D., Moreau Y., De Moor B., 2004. Using literature and data to learn Bayesian Networks as clinical models of ovarian tumors, Artificial Intelligence in Medicine, 30, 257-281. (preprint)
• Aerts S., Thijs G., Dabrowski M., Moreau Y., De Moor B., 2004. Comprehensive analysis of the base composition around the transcription start site in Metazoa, BMC Genomics, 5, 34.
• Glenisson P.,Coessens B., Van Vooren S., Mathys J., Moreau Y., De Moor B., 2004. TXTGate: Profiling gene groups with text-based information, Genome Biology, 5(6), R43.1-12.
• Denys H., Jadidizadeh A., Amini Nik S., Van Dam K., Aerts S., Alman B.A., Cassiman J.J., Tejpar S., 2004. Identification of IGFBP-6 as a significantly down-regulated gene by beta-catenin in desmoid tumors, Oncogene, 23(3), 654-664.
• Marchal K., De Keersmaecker S., Monsieurs P., van Boxel N., Lemmens K., Thijs G., Vanderleyden J., De Moor B., In silico identification and experimental validation of PmrAB targets in Salmonella typhimurium by regulatory motif detection, Genome Biology, 2004, 5(2), R9.
• Voz M.L., Mathys J., Hensen K., Pendeville H., Van Valckenborgh I., Van Huffel C., Chavez M., Van Damme B., De Moor B., Moreau Y., Van de Ven W.J., 2004. Microarray screening for target genes of the proto-oncogene PLAG1. Oncogene. 23(1), 179-191.
• 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 1alpha,25-dihydroxyvitamin D3 on the expression of DNA replication genes, J Bone Miner Res. 19(1):133-46.

• Glenisson P., Mathys J., Moreau Y., De Moor B., 2003. Meta-Clustering of Gene Expression Data and Literature-based Information. SIGKDD Explorations, 5(2), 101-112.
• Moreau Y., Aerts S., De Moor B., De Strooper B., Dabrowski M., Comparison and meta-analysis of microarray data: from the bench to the computer desk. Trends In Genetics, 2003, 19(10), 570-577.
• De Moor B., Marchal K., Mathys J., Moreau Y., Bioinformatics : Organisms from Venus, Technology from Jupiter, Algorithms from Mars, European Journal of Control, 9(2-3), 2003, 237-278.
• Coessens B., Thijs G., Aerts S., Mathys J., Moreau Y., Marchal K., De Smet F., Engelen K., Glenisson P., De Moor B. (2003) INCLUSive-A web portal and service registry for microarray and regulatory sequence analysis Nucleic Acids Research, 31: 3468-3470.
• Engelen K., Coessens B., Marchal K., De Moor B., MARAN: normalizing micro-array datas. Bioinformatics, 2003, 19(7), 893-894.
• Sheng Q., Moreau Y., and De Moor B., Biclustering microarray data by Gibbs sampling, Bioinformatics, Special issue ECCB'2003, 2003, 19(Suppl 2), ii196-ii205.
• Aerts S., Van Loo P., Thijs G., Moreau Y., De Moor B., 2003. Computational detection of cis-regulatory modules, Bioinformatics, Special issue ECCB'2003, 19(Suppl 2), ii5-ii14.
• Moreau Y., Antal P., Fannes G., De Moor B., Probabilistic graphical models for computational biomedicine. Methods of Information in Medicine, 2003, 42, 161-168.
• Aerts S., Thijs G., Coessens B., Staes M., Moreau Y., De Moor B Toucan : Deciphering the Cis-Regulatory Logic of Coregulated Genes. Nucleic Acids Research,, 2003, 31(6), 1753-1764.
• Dabrowski M., Aerts S., Van Hummelen P., Craessaerts K., De Moor B., Annaert W., Moreau Y., De Strooper B., Gene profiling of hippocampal neuronal culture, Journal of Neurochemistry, 2003, 85(5), 1279-1288.
• Marchal K., Thijs G., De Keersmaecker S., Monsieurs P., De Moor B., Vanderleyden J., "Genome-specific higher-order background models to improve motif detection", Trends in Microbiology, 2003, 11(2), 61-66.
• P. Antal, G. Fannes, D. Timmerman, Y. Moreau, B. De Moor, Bayesian application of belief networks and multilayer perceptrons for ovarian tumor classification with rejection, Artificial Intelligence in Medicine, Special Issue of AIME'01. (preprint)
• S. Rombauts, K. Florquin, M. Lescot, K. Marchal, P. Rouzé, Y. Van de Peer, Computational approaches to identify promoters and cis-regulatory elements in plant genomes, Plant Physiology, 2003, 132(3), 1162-1176.

• Marchal K., Engelen K., De Brabanter J., Aerts S., De Moor B., Comparison of different methodologies to identify differentially expressed genes in two-sample cDNA arrays. Journal of Biological Systems, 2002, 10(4), 409-430.
• Lescot M., Dehais P., Thijs G., Marchal K., Moreau Y., Van de Peer Y., Rouzé P., Rombauts S., PlantCARE : a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences, Nucleic Acids Research, Special Issue on databases, 2002, 30(1), 325-327.
• Thijs G., Moreau Y., De Smet F., Mathys J., Lescot M., Rombauts S., Rouzé P., De Moor B., Marchal K., INCLUSive: INtegrated CLustering, Upstream sequence retrieval and motif Sampling, Bioinformatics, 2002. 18(2), 331-332. (preprint)
• Thijs G., Marchal K., Lescot M., Rombauts S., De Moor B., Rouzé P., Moreau Y., A Gibbs Sampling method to detect over-represented motifs in upstream regions of coexpressed genes, Journal of Computational Biology, Special Issue RECOMB'2001, 2002, 9(2), 447-464. (preprint)
• De Smet F., Mathys J., Marchal K., Thijs G., De Moor B., Moreau Y., Adaptive quality-based clustering of gene expression profiles, Bioinformatics, 2002. 18(5),735-746.(preprint)
  Additional information and data sets.
• Epstein E., Skoog L., Isberg P., De Smet F., De Moor B., Olofsson P., Gudmundsson S., Valentin L., An algorithm including results of gray scale and power Doppler ultrasound examination to predict endometrial malignancy in women with postmenopausal bleeding, Ultrasound in Obstetrics and Gynecology, 2002. 20(10), 370-376. (reprint)
• Smets I., Bernaerts K., Sun J., Marchal K., Vanderleyden J., Van Impe J., Sensitivity function-based model reduction: A bacterial gene expression case study, Biotech. Bioeng., 2002, 80(2), 195-200.
• Dombrecht B., Marchal K., Vanderleyden J., Michiels J., Prediction and overview of the RpoN-regulon in closely related species of the Rhizobiales, Genome Biology, 2002, 3(12), research0076.1-0076.11
• Moreau Y., De Smet F., Thijs G., Marchal K., De Moor B., Functional bioinformatics of microarray data : from expression to regulation, Proceedings of the IEEE, 2002, 90(11), 1722-1743. (preprint)

• Thijs G., Lescot M., Marchal K., Rombauts S., De Moor B., Rouzé P., Moreau Y., A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling, Bioinformatics, 2001, 17(12),1113-1122. (preprint)
  Additional information and data sets.
• Brazma A., Hingamp P., Quakenbush J., Sherlock G., Spellman P., Stoeckert C., Aach J., Ansorge W., Ball C., Causton H., Gaasterland T., Glenisson P., Holstege F., Kim I., Markowitz V., Matese J., Parkinson H., Robinson A., Sarkans U., Schulze-Kremer S., Stewart J., Taylor R., Vilo J., Vingron M., Minimum information about a microarray experiment (MIAME) - towards standards for microarray data, Nature Genetics, 2001, 29, 365-371.
• Sun J., Smets I., Bernaerts K., Van Impe J., Vanderleyden J., Marchal K., Quantitative analysis of bacterial gene expression by using the gusA reporter gene system, Applied and Environmental Microbiology, 2001, 67(8), 3350-3357.

2. Books and Book Chapters (top)

• Sheng Q., Moreau Y., De Smet F., Marchal K., De Moor B., 2005. Advances in cluster analysis of microarray data, Chapter in Data analysis and visualization in genomics and proteomics, (Azuaje F., and Dopazo J., eds.), Jonh Wiley & Sons Ltd. (Chichester, UK), pp. 153-173.
• Thijs G., De Smet F., Moreau Y., Marchal K., De Moor B., 2005. Gene regulation bioinformatics of microarray data, Chapter in Genomics and Proteomics Engineering, (Metin A., ed.), WileyL/IEEE Press, in press.
• Marchal K., De Smet F., Engelen K., De Moor B., 2004. Computational biology and toxicogenomics, Chapter in Predictive toxicology, (Helma C., ed.), Marcel Dekker (New York), pp. 37-85.

3. International Conference papers (top)

• 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. In Proceedings of the Pacific Symposium Biocomputing 2005. p.483-94.

De Bie T., Cristianini N., 2004. Kernel methods for exploratory data analysis: a demonstration on text data, in Proc. of the joint IAPR international workshops on Syntactical and Structural Pattern Recognition and Statistical Pattern Recognition (SSSPR 2004), Lisbon, Portugal, Aug. 2004.

• Glenisson P., Coessens B., Van Vooren S., Moreau Y., De Moor B. 2003. Text-based gene profiling with domain-specific views, in Proceedings of the First International Workshop on Semantic Web and Databases, Berlin, Germany, pp. 15-31..
• Glenisson P., Antal P., Mathys J., Moreau Y., De Moor B. (2003) Evaluation of the vector space representation for text-based gene clustering, Proceedings of the Eighth Annual Pacific Symposium on Biocomputing (PSB 2003), 8, pp. 240-251.

• Antal P., Glenisson P., Fannes G., Mathys J., De Moor B., Moreau Y., On the potential of domain literature for clustering and Bayesian network learning, Internal Report 02-51, ESAT-SISTA, K.U.Leuven (Leuven,Belgium), 2002. in Proceedings of the 8th Int. Conf. on Knowledge Discovery and Datamining, (ACM-SIGKDD), Edmonton, Canada, Jul. 2002, pp. 405-414.
• Aerts S., Antal P., Timmerman D., De Moor B., Moreau Y., Web-based data collection for uterine adnexal tumors : a case study, 2002. in Proceedings of the 15th IEEE Symposium on Computer Based Medical Systems, Maribor, Slovenia, Jun. 2002, pp. 282-287.
• Antal P., De Moor B., Timmerman D., Meszaros T., Dobrowiecki T., Domain knowledge based information retrieval language : an , 2002. in Proceedings of the 15th IEEE Symposium on Computer Based Medical Systems, Maribor, Slovenia, Jun. 2002, pp. 213-218
• De Bie T., De Moor B., On two classes of alternatives to canonical correlation analysis, using mutual information and oblique projections, in Proc. of the 23rd symposium on information theory in the Benelux (ITB), Louvian-la-Neuve, Belgium, May 2002.
• Moreau Y., Thijs G., Marchal K., De Smet F., Mathys J., Lescot M., Rombauts M., Rouzé P., De Moor B., Integrating quality-based clustering of microarray data with Gibbs smapling for the discovery of regulatory motifs, in Journées Ouvertes Biologie Informatique Mathématiques (JOBIM), St. Malo, France, Jun. 2002, pp. 75-79.
• Lescot M., Thijs G., Rombauts S., Déhais P., Martin D., Thieffy D., Jacq B., Moreau Y., Rouzé P., Van Helden J., Deciphering cis-acting regulatory elements in plant and drosophila promoter, in Journées Ouvertes Biologie Informatique Mathématiques (JOBIM), St. Malo, France, Jun. 2002, pp. 349-350.
• Antal P., Fannes G., Moreau Y., De Moor B., Using Literature and Data to Annotate and Learn Bayesian Networks, 2002, in Proceedings of BNAIC-2002.

• Thijs G., Marchal K., Lescot M., Rombauts S., De Moor B., Rouzé P., Moreau Y., A Gibbs sampling method to detect over-represented motifs in the upstream regions of co-expressed genes,In proceedings RECOMB'2001, pp. 305-312.
• Antal P., Fannes G., De Moor B., Vandewalle J., Van Huffel S., Timmerman D., Bayesian predictive models for ovarian cancer classification : evalution of logistic regression, multi layer perceptron and belief network models in the Bayesian context, in Proc. of the Tenth Belgian-Dutch conference on Machine Learning (BENELEARN2000), Tilburg, The Netherlands, Dec. 2000, pp. 125-132.
• Antal P., Meszaros T., De Moor B., Dobrowiecki T., "Annotated Bayesian Networks : A tool to integrate textual and probabilistic medical knowledge", in Proc. of the Fourteenth IEEE Symposium on Computer-Based Medical Systems (CBMS 2001), Bethesda, MD, Jul. 2001.
• Antal P., Fannes G., De Smet F., De Moor B., "Ovarian cancer classification with rejection by Bayesian Belief Networks", in Proc. of the Bayesian Models in Medicine workshop, the European Conference on Artificial Intelligence in Medicine (AIME'01), Cascais, Portugal, Jul. 2001.
• Antal P., Fannes G., De Moor B., Vandewalle J., Moreau Y., Timmerman D., Extended Bayesian regression models : a symbiotic application of belief networks and multilayer perceptrons for the classification of ovarian tumors, in Proc. of the Eigth European Conference on Artificial Intelligence in Medicine (AIME'01), Cascais, Portugal, Jul. 2001.

• Thijs G., Rombauts S., Lescot M., Marchal K., De Moor B., Moreau Y., Rouzé P., Detection of cis-acting regulatory elements in plants : a Gibbs sampling approach, in Proc. of Bioinformatics of Gene regularisation and structure (BGRS'2000), Novosibirsk, Russia, Aug. 2000, .
• Antal P., Fannes G., Verrelst H., De Moor B., Vandewalle J., Incorporation of Prior Knowledge in Black-box Models : Comparison of Transformation Methods from Bayesian Network to Multilayer Perceptrons, in the Sixteenth conference on Uncertainty in Artificial Intelligence (UAI-2000).
• Antal P., Verrelst H., Timmerman D., Moreau Y., Van Huffel S., De Moor B., Vergote I., Bayesian Networks in Ovarian Cancer Diagnosis : Potentials and Limitations, in Proc. of the 13th IEEE Symposium on Computer-Based Medical Systems (CBMS 2000), Houston, US, Jun. 2000, pp. 103-108.

• Thijs G., Moreau Y., Rombauts G., De Moor B., Rouzé P., Recognition of gene regulatory sequences by bagging of neural networks, in Proc. of the ninth international conference on artificial neural networks (ICANN99), Edinburgh, Scotland, Sep. 1999, pp. 988-993.

4. National Publications (top)

• De Moor B., Bio-informatica : Hoe algoritmen tot leven brengen, Chapter in Lessen voor de XXIste eeuw. Universitaire Pers Leuven, Davidsfonds, Leuven, 2005.
• De Smet F., Marchal K., Timmerman D., De Moor B., Moreau Y., "Gebruik van microroosters in de klinische oncologie", Tijdschrift voor Geneeskunde, 2001. 57(8), 1225-1236.
• Moreau Y., Marchal K., Mathys J., "Computational biomedicine : a multidisciplinary crossroads", Siemens Prize, FWO (Flanders, Belgium), 2002, 89 p.

5. PhD Dissertations (top)

• De Bie T., Semi-supervised learning based on kernel methods and graph cut algorithms, PhD thesis, Faculty of Engineering, K.U.Leuven (Leuven, Belgium), May 2005, 216 p.
• Aerts S., Computational discovery of cis-regulatory modules in animal genomes, PhD thesis, Faculty of Engineering, K.U.Leuven (Leuven, Belgium), May 2004, 200 p.
• De Smet F., Microarrays : algorithms for knowledge discovery in oncology and molecular biology, PhD thesis, Faculty of Engineering, K.U.Leuven (Leuven, Belgium), May 2004, 242 p.
• Fannes G., Bayesian learning with expert knowledge: Transfroming informative priors between Bayesian networks and multilayer perceptrons, PhD thesis, Faculty of Engineering, K.U.Leuven (Leuven, Belgium), June 2004, 226 p.
• Glenisson P., Integrating scientific literature with large scale gene expression analysis, PhD thesis, Faculty of Engineering, K.U.Leuven (Leuven, Belgium), Jun. 2004, 252 p.
• Thijs G., Probabilistic methods to search for regulatory elements in sets of coregulated genes, PhD thesis, Faculty of Engineering, K.U.Leuven (Leuven, Belgium), Jun. 2003, 228 p.