1. Van Loo P., Systems biology: identification of regulatory regions and disease causing genes and mechanisms

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International Journal Paper

1. Epstein E., Van Holsbeke C., Mascilini F., M?sb?ck A., Kannisto P., Ameye L., Fischerova D., Zannoni G., Vellone V., Timmerman D., Testa A.C., "Gray-scale and color Doppler ultrasound characteristics of endometrial cancer in relation to stage, grade and tumor size", Ultrasound in Obstetrics and Gynecology, vol. 38, no. 5, Nov. 2011, pp. 586-593.


2. Welkenhuysen M., Andrei A., Ameye L., Eberle W., Nuttin B., "Effect of insertion speed on tissue response and insertion mechanics of a chronically implanted silicon-based neural probe", IEEE Transactions on Biomedical Engineering , vol. 58, no. 11, Nov. 2011, pp. 3250-3259.


3. Dancet E.A., Ameye L., Sermeus W., Welkenhuysen M., Nelen W.L., Tully L., De Bie B., Veit J., Vedsted-Hansen H., Zondervan K.T., De Cicco C., Kremer J.A., Timmerman D., D'Hooghe T.M., "The ENDOCARE questionnaire (ECQ): a valid and reliable instrument to measure the patient-centeredness of endometriosis care in Europe", Human Reproduction, vol. 26, no. 11, Sep. 2011, pp. 2988-2999.


4. Secrier M., Pavlopoulos GA., Aerts J., Schneider R., "Arena3D: visualizing time-driven phenotypic differences in biological systems", BMC Bioinformatics, vol. In Press, Mar. 2012, pp. .


5. Soldatos TG., O'Donoghue SI., Satagopam VP., Barbosa-Silva A., Pavlopoulos GA., Wanderley-Nogueira AC., Soares-Cavalcanti NM., Schneider R., "Caipirini: using gene sets to rank literature.", BioData Mining, vol. 5, no. 1, Feb. 2012, pp. .


6. Van Houdt J., Nowakowska B., Sousa S., van Schaik B., Seuntjens E., Avonce N., Sifrim A., Abdul-Rahman O., van den Boogaard M., Bottani A., Castori M., Cormier-Daire V., Deardorff M., Filges I., Fryer A., Fryns J., Gana S., Garavelli L., Gillessen-Kaesbach G., Hall B., Horn D., Huylebroeck D., Klapecki J., Krajewska-Walasek M., Kuechler A., Lines M., Maas S., MacDermot K., McKee S., Magee A., de Man S., Moreau Y., Morice-Picard F., Obersztyn E., Pilch J., Rosser E., Shannon N., Stolte-Dijkstra I., Van Dijck P., Vilain C., Vogels A., Wakeling E., Wieczorek D., Wilson L., Zuffardi O., van Kampen A., Devriendt K., Hennekam R., Vermeesch J., "Heterozygous missense mutations in SMARCA2 cause Nicolaides-Baraitser syndrome", Nature Genetics, Epub ahead of print, vol. 44, no. 4, Feb. 2012, pp. 1-6.


7. Put N., Van Roosbroeck K., Konings P., Meeus P., Brusselmans C., Rack K., Gervais C., Nguyen-Khac F., Chapiro E., Radford-Weiss I., Struski S., Dastugue N., Gachard N., Lefebvre C., Barin C., Eclache V., Fert-Ferrer S., Laibe S., Mozziconacci M.-J., Quilichini B., Poirel H.A., Wlodarska I., Hagemeijer A., Moreau Y., Vandenberghe P., Michaux L., "Chronic lymphocytic leukemia and prolymphocytic leukemia with MYC translocations: a subgroup with an aggressive disease course", Annals of Hematology, vol. online first, Dec. 2011, pp. 1-11.


8. Fassbender A., Waelkens W., Verbeeck N., Kyama C.M., Bokor A., Vodolazkaia A., Van de Plas R., Meuleman C., Peeraer K., Tomassetti C., Gevaert O., Ojeda F., De Moor B., DHooghe T., "Proteomics Analysis of Plasma for Early Diagnosis of Endometriosis.", Obstetrics & Gynecology, vol. 119, no. 2, part 1, Feb. 2012, pp. 276-285.


9. Iacucci E., Zingg H., Perkins T., "Methods for Determining the Statistical Significance of Enrichment or Depletion of Gene Ontology Classifications under Weighted Membership", Frontiers in Systems Biology, vol. 3, no. 24, Feb. 2012, pp. 1-12.


10. Moschopoulos CN., Pavlopoulos GA., Iacucci E., Aerts J., Likothanassis S., Schneider R., Kossida S., "Which clustering algorithm is better for predicting protein complexes?", BMC Research Notes, vol. 4, no. 1, Dec. 2011, pp. 549-555.


11. Pavlopoulos GA., Hooper SD., Sifrim A., Schneider R., Aerts J., "Medusa: A tool for exploring and clustering biological networks.", BMC Res Notes. , vol. 4, no. 1, Oct. 2011, pp. 384-390.


12. Fassbender A., Simsa P., Kyama C.M., Waelkens E., Mihalyi A., Meuleman C., Gevaert O., Van de Plas R., de Moor B., D'Hooghe TM., "TRIzol treatment of secretory phase endometrium allows combined proteomic and mRNA microarray analysis of the same sample in women with and without endometriosis", Reproductive Biology and Endocrinology, vol. 9, no. 44, Apr. 2010, pp. 1-6.


13. Engelen K., Sifrim A., van der 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, vol. 9, no. 10, Aug. 2010, pp. 4919-4926.


14. Fassbender A., Verbeeck N., Boernigen D., Kyama C.M., Bokor A., Vodolazkaia A., Peeraer K., Tomassetti C., Meuleman C., Gevaert O., Van de Plas R., Ojeda F., De Moor B., Moreau Y., Waelkens E., D'Hooghe T., "Combined mRNA Microarray and Proteomic analysis of eutopic endometrium of women with and without endometriosis.", Human Reproduction, May 2012, pp. 1-10.


15. Valentin L., Ameye L., Savelli L., Fruscio R., Leone F.P.G., Czekierdowski A., Lissoni A.A., Fischerova D., Guerriero S., Van Holsbeke C., Van Huffel S., Timmerman D., "Adnexal masses difficult to classify as benign or malignant using subjective assessment of gray scale and Doppler ultrasound findings : logistic regression models do not help", Ultrasound in Obstetrics and Gynecology, vol. 38, no. 4, Oct. 2011, pp. 456-465.


16. Yazbek J., Ameye L., Timmerman D., Testa A.C., Valentin L., Holland T.K., Van Holsbeke C., Jurkovic D., "Use of ultrasound pattern recognition by expert operators to identify borderline ovarian tumors: a study of diagnostic performance and interobserver agreement.", Ultrasound in Obstetrics and Gynecology, vol. 35, no. 1, Jan. 2010, pp. 84-88.


17. Timmerman D., Ameye L., Fischerova D., Epstein E., Melis G.B., Guerriero S., Van Holsbeke C., Savelli L., Fruscio R., Lissoni A.A., Testa A.C., Veldman J., Vergote I., Van Huffel S., Bourne T., Valentin L., "Simple ultrasound rules to distinguish between benign and malignant adnexal masses before surgery: prospective validation by IOTA group", British Medical Journal, doi: 10.1136/bmj.c6839., vol. 341, Dec. 2010, pp. c6839-.


18. Breckpot J., Thienpont B., Tranchevent LC., Gewillig M., Allegaert K., Vermeesch JR., Moreau Y., Devriendt K., "Challenges of Interpreting Copy Number Variation in Syndromic and Non-Syndromic Congenital Heart Defects", Cytogenetic and genome research e-pub ehead of print, 7 p.


19. Schraenen A., de Faudeur G., Thorrez L., Lemaire K., Van Wichelen G., Granvik M., Van Lommel L., in 't Veld P., Schuit F., "mRNA expression analysis of cell cycle genes in islets of pregnant mice", Diabetologia, vol. Epub ahead of print, Oct. 2010, pp. .


20. Denayer S., Helsen C., Thorrez L., Haelens A., Claessens F., "The rules of DNA recognition by the androgen receptor", Molecular Endocrinology, vol. 5, no. 24, May 2010, pp. 898-913.


21. Smeets A., Daemen A., Van den Bempt I., Gevaert O., Claes B., Wildiers H., Drijkoningen R., Van Hummelen P., Lambrechts D., De Moor B., Neven P., Sotiriou C., Van Dorpe T., Paridaens R., Christiaens MR., "Prediction of lymph node involvement in breast cancer from primary tumor tissue using gene expression profiling and miRNAs", Breast Cancer Research and Treatment, vol. 129, no. 3, Oct. 2011, pp. 767-76.


22. Put N., Lemmens H., Wlodarska I., Konings P., Moreau Y., Hagemeijer A., Vandenberghe P., Michaux L., "Interphase fluorescence in situ hybridization on selected plasma cells is superior in the detection of cytogenetic aberrations in plasma cell dyscrasia", Genes, Chromosomes and Cancer, vol. 49, no. 11, Jul. 2010, pp. 991-997.


23. Alzate C., Suykens J.A.K., "Sparse Kernel Spectral Clustering Models for Large-Scale Data Analysis", Neurocomputing, Special Issue on Advances in Artificial Neural Networks, Machine Learning and Computational Intelligence (ESANN 2010), vol. 74, no. 9, Apr. 2011, pp. 1382-1390.


24. Van Gorp T., Cadron I., Despierre E., Daemen A., Leunen K., Amant F., Timmerman D., De Moor B., Vergote I., "HE4 and CA125 as a diagnostic test in ovarian cancer: prospective validation of the Risk of Ovarian Malignancy Algorithm", British Journal of Cancer, vol. 104, no. 5, 2011, pp. 863-870.


25. Nitsch D., Goncalves JP., Ojeda F., De Moor B., Moreau Y., "Candidate Gene Prioritization by Network Analysis of Differential Expression using Machine Learning Approaches", BMC Bioinformatics, vol. 11, no. 460, Sep. 2010, pp. 1-.


26. Podo F., Buydens L.M.C., Degani H., Hilhorst R., Klipp E., Gribbestad I., Van Huffel S., van Laarhoven H., Luts J., Monleon D., Postma G.J., Schneiderrham-Marra N., Russness H., Santoro F., Wouters H., Sorlie T., Tagliabue E., Borresen-Dale A.-L., "Triple-negative breast cancer: present challenges and new perspectives", Triple-negative breast cancer: present challenges and new perspectives, Thematic Issue: The Molecular Biology of Breast Cancer, vol. 4, no. 3, Jun. 2010, pp. 209-229.


27. Postma G., Luts J., Idema A.J., Julia-Sape M., Moreno-Torres A., Gajewicz W., Suykens J.A.K., Heerschap A., Van Huffel S., Buydens L.M.C., "On the relevance of automatically selected single voxel MRS and multimodal MRI and MRSI features for brain tumor differentiation", Computers in Biology and Medicine, vol. 41, no. 2, Feb. 2011, pp. 87-97.


28. De Bruyne E., Bos T.J., Schuit F., Van Valckenborgh E., Menu E., Thorrez L., Atadja P., Jernberg-Wiklund H., Vanderkerken K., "IGF-1 suppresses Bim expression in multiple myeloma via epigenetic and posttranslational mechanisms", Blood, vol. 12, no. 115, Mar. 2010, pp. 2430-2440.


29. 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, vol. 5, no. 2, Feb. 2010, e8938 p.


30. Liu X.H., Yu S., Janssens F., Gl$\ddot{a} W., Moreau Y., De moor B., "Weighted Hybrid Clustering by Combining Text Mining and Bibliometrics on Large-Scale Journal Database", Journal of the American Society for Information Science and Technology, vol. 61, no. 6, Jun. 2010, pp. 1105-1119.


31. Luts J., Ojeda F., Van de Plas R., De Moor B., Van Huffel S., Suykens J.A.K, "A tutorial on support vector machine-based methods for classification problems in chemometrics", Analytica Chimica Acta, vol. 665, no. 2, Apr. 2010, pp. 129-145.


32. Van den Bosch T., Daemen A., Gevaert O., De Moor B., Timmerman D., "Building decision trees for diagnosing intracavitary uterine pathology", Facts, Views & Vision in ObGyn, vol. 1, no. 3, Dec. 2009, pp. 182-188.


33. Sarris I., Bottomley C., Daemen A., Pexsters A., Timmerman D., Bourne T., Papageorghiou A., "No influence of body mass index on first trimester fetal growth", Human Reproduction, vol. 25, no. 8, Aug. 2010, pp. 1895-1899.


34. Yazbek J., Ameye L., Testa A.C., Valentin L., Timmerman D., Holland T.K., Van Holsbeke C., Jurkovic D., "Confidence of expert ultrasound operators in making a diagnosis of adnexal tumor: effect on diagnostic accuracy and interobserver agreement", Ultrasound in Obstetrics and Gynecology, vol. 35, no. 1, Jan. 2010, pp. 89-93.


35. Daemen A., Signoretto M., Gevaert O., Suykens JAK., De Moor B., "Improved microarray-based decision support with graph encoded interactome data", PLoS ONE, vol. 5, no. 4, Apr. 2010, pp. 1-16.


36. Yu S., Falck T., Daemen A., Tranchevent L.C., Suykens J., De Moor B., Moreau Y., "L2-norm multiple kernel learning and its application to biomedical data fusion", BMC Bioinformatics, vol. 11, no. 309, Jun. 2010, pp. 1-53.


37. Zhang L., Liu X.H., Janssens F., Linag L., Glanzel W., "Subject clustering analysis based on ISI category classification", Journal of Informetrics, vol. 4, no. 2, Apr. 2010, pp. 185-193.


38. Schuierer S., Tranchevent L., Dengler U., Moreau Y., "Large-scale benchmark of Endeavour using MetaCore maps", Bioinformatics, vol. 26, no. 15, Aug. 2010, pp. 1922-3.


39. Tranchevent L., Capdevila F.B., Nitsch D., De Moor B., De Causmaecker P., Moreau Y., "A guide to web tools to prioritize candidate genes", Briefings in Bioinformatics, Jan. 2011, pp. 22-32.


40. Vergote I., Amant F., Ameye L., Timmerman D., "Screening for ovarian carcinoma: not quite there yet", Lancet Oncology, vol. 10, Apr. 2009, pp. 308-309.


41. Gevaert O., Daemen A., De Moor B., Libbrecht L., "A Taxonomy of Epithelial Human Cancer and their Metastases", BMC Medical Genomics, vol. 2, no. 69, Dec. 2009, pp. 1-33.


42. Lemaire K., Ravier M.A., Schraenen A., Creemers J.W.M., Van de Plas R., Granvik M., Van Lommel L., Waelkens E., Chimienti F., Rutter G.A., Gilon P., in't Veld P.A., Schuit F.C., "Insulin crystallisation depends on zinc transporter ZnT8 expression, but is not required for normal glucose homeostasis in mice", Proceedings of the National Academy of Sciences, vol. 106, no. 35, Sep. 2009, pp. 14872-14877.


43. Arijs I., Li K., Toedter G., Quintens R., Van Lommel L., Van Steen K., Leemans P., De Hertogh G., Lemaire K., Ferrante M., Schnitzler F., Thorrez L., Ma K., Song X.Y., Marano C., Van Assche G., Vermeire S., Geboes K., Schuit F., Baribaud F., Rutgeerts P., "Mucosal gene signatures to predict response to infliximab in patients with ulcerative colitis", Gut, vol. 58, no. 12, Dec. 2009, pp. 1612-9.


44. Janssens F., Zhang L., De Moor B., Glanzel W., "Hybrid Clustering for Validation and Improvement of Subject-Classification Schemes", Information Processing & Management, vol. 45, no. 6, Nov. 2009, pp. 683-702.


45. Sun H., Lemmens K., Van den Bulcke T., Engelen K., De Moor B., Marchal K., "ViTraM: Visualization of Transcriptional Modules", Bioinformatics, vol. 25, no. 18, Jul. 2009, pp. 2450-2451.


46. Habayeb O., Daemen A., Timmerman D., De Moor B., Hackett GA., Bourne T., Lees CC., "The relationship between first trimester fetal growth, pregnancy associated plasma protein A levels and birthweight", Prenatal Diagnosis, vol. 30, no. 9, Sep. 2010, pp. 873-878.


47. van Malenstein H., Gevaert O., Libbrecht L., Daemen A., Allemeersch J., Nevens F., Van Cutsem E., Cassiman D., De Moor B., Verslype C., van Pelt J., "A Seven-Gene Set Associated with Chronic Hypoxia of Prognostic Importance in Hepatocellular Carcinoma", Clinical Cancer Research, vol. 16, no. 16, Aug. 2010, pp. 4278-4288.


48. Put N., Konings P., Rack K., Jamar M., Van Roy N., Libouton J-M., Vannuffel P., Sartenaer D., Ameye G., Speleman F., Herens C., Poirel H.A., Moreau Y., Vandenberghe P., Michaux L., "Improved Detection of Chromosomal Abnormalities in Chronic Lymphocytic Leukemia by Conventional Cytogenetics Using CpG Oligonucleotide and Interleukin-2 Stimulation. A Belgian Multicentric Study", Genes Chromosomes and Cancer, vol. 48, no. 10, Oct. 2009, pp. 843-853.


49. Sun H., Lemmens K., Van den Bulcke T., Engelen K., De Moor B., Marchal K., "Layout and Post-Processing of Transcriptional Modules", IEEE Computer Society, in the proceedings of IJCBS 2009, vol. 1, no. 1, Aug. 2009, pp. 1-6.


50. Tipney H.J., Leach S.M., Feng W., Spritz R., Williams T., Hunter L., "Leveraging existing biological knowledge in the identification of candidate genes for facial dysmorphology", BMC Bioinformatics, vol. 10 Suppl2, Feb. 2009, pp. S12-.


51. Leach S.M., Tipney H., Feng W., Baumgartner W.A., Kasliwal P., Schuyler R.P., Willliams T., Spritz R.A., Hunter L., "Biomedical Discovery Acceleration, with Applications to Craniofacial Development", PLoS Computational Biology, vol. 5, no. 3, Mar. 2009, pp. e1000215-.


52. Karimpour-Fard A., Leach S.M., Gill R.T., Hunter L.E., "Predicting protein linkages in bacteria : Which method is best depends on task", BMC Bioinformatics, vol. 9, Sep. 2008, pp. 1-21.


53. Sun H., De Bie T., Storms V., Fu Q., Dhollander T., Lemmens K., Verstuyf A., De Moor B., Marchal K., "ModuleDigger: an itemset mining framework for the detection of cis-regulatory modules.", BMC Bioinformatics, vol. 10, no. Suppl 1, Jan. 2009, pp. S30-.


54. Yu S., Tranchevent L.C., De Moor B., Moreau Y., "Gene prioritization and clustering by multi-view text mining", BMC Bioinformatics, doi:10.1186/1471-2105-11-28, vol. 11, no. 28, Jan. 2010, pp. 1-48.


55. Ameye L., Valentin L., Testa A.C., Van Holsbeke C., Domali E., Van Huffel S., Vergote I., Bourne T., Timmerman D., "A scoring system to differentiate malignant from benign masses in specific ultrasound-based subgroups of adnexal masses", Ultrasound in Obstetrics and Gynecology, vol. 33, Jan. 2009, pp. 92-101.


56. Daemen A., Jurkovic D., Van Holsbeke C., Guerriero S., Testa AC., Czekierdowski A., Fruscio R., Paladini D., Neven P., Rossi A., Bourne T., De Moor B., Timmerman D., "The effect of cancer prevalence on the use of different cut-off levels and the performance of mathematical models to distinguish benign from malignant adnexal masses", Ultrasound in Obstetrics and Gynecology, vol. 37, no. 2, 2010, pp. 226-231.


57. Daemen A., Valentin L., Fruscio R., Van Holsbeke C., Melis GB., Guerriero S., Czekierdowski A., Jurkovic D., Ombelet W., Rossi A., Vergote I., Bourne T., De Moor B., Timmerman D., "Improving the preoperative classification of adnexal masses as benign or malignant by second stage tests", Ultrasound in Obstetrics and Gynecology, vol. 37, no. 1, 2011, pp. 100-106.


58. Leunen K., Gevaert O., Daemen A., Vanspauwen V., Michils G., De Moor B., Moerman P., Vergote I. and Legius E., "Recurrent copy number alterations in BRCA1-mutated ovarian tumors alter biological pathways", Human Mutation, vol. 30, no. 12, Dec. 2009, pp. 1693-1702.


59. Barriot R., Breckpot J., Thienpont B., Brohee S., Van Vooren S., Coessens B., Tranchevent L., Van Loo P., Gewillig M., Devriendt K., Moreau Y., "Collaboratively charting the gene-to-phenotype network of human congenital heart defects", Genome Medicine, vol. 2, no. 3, Mar. 2010, pp. 1-9.


60. Karimpour-Fard A., Leach SM., Hunter LE., Gill RT., "The topology of the bacterial co-conserved protein network and its implications for predicting protein function", BMC Genomics, vol. 9, Jun. 2008, pp. 313-.


61. Gabow A.P., Leach S.M., Baumgartner W.A., Hunter L.E., Goldberg D.S., "Improving protein function prediction methods with integrated literature data", BMC Bioinformatics, vol. 9, Apr. 2008, pp. 1-16.


62. Thorrez L., Tranchevent L., Chang H.J., Moreau Y., Schuit F., "Detection of novel 3'UTR extensions with 3' expression microarrays", BMC Bioinformatics, vol. 11, Mar. 2010, 205 p.


63. Aerts S., Vilain S., Hu S., Tranchevent L., Barriot R., Yan J., Moreau Y., Hassan B., Quan X., "Integrating Computational Biology and Forward Genetics in Drosophila", PLoS Genetics, vol. 5, no. 1, Jan. 2009, pp. 351.


64. Bottomley C., Daemen A., Mukri F., Kirk E., Papageorghiou A.T., Timmerman D., De Moor B., Bourne T., "Revisiting very early first trimester growth - influence of ethnic background and maternal age using transvaginal ultrasonography (TVS)", Human Reproduction, Abstract Book of the 24th ESHRE Annual Meeting, Spain July 2008, vol. 23, no. Suppl 1, Jul. 2008, pp. i43-i45.


65. Daemen A., Bottomley C., Mukri F., Kirk E., Papageorghiou A., Timmerman D., De Moor B., Bourne T., "A new statistical method for longitudinal assessment of early fetal growth - prospective testing of a functional linear discriminant analysis model", Human Reproduction, Abstract Book of the 24th ESHRE Annual Meeting, Spain July 2008, vol. 23, no. Suppl 1, Jul. 2008, pp. i43-i45.


66. Vertommen J., Janssens F., De Moor B., Duflou J. R., "Multiple-vector user profiles in support of knowledge sharing", Information Sciences, vol. 178, no. 17, Sep. 2008, pp. 3333-3346.


67. Van Holsbeke C., Daemen A., Yazbek J., Holland T.K., Bourne T., Mesens T., Lannoo L., De Moor B., de Jonge E., Testa A.C., Valentin L., Jurkovic D., Timmerman D., "Ultrasound methods to distinguish between malignant and benign adnexal masses in the hands of examiners with different levels of experience", Ultrasound in Obstetrics and Gynecology, vol. 34, no. 4, Oct. 2009, pp. 454-461.


68. Van den Bosch T., Verguts J., Daemen A., Gevaert O., Domali E., Claerhout F., Vandenbroucke V., De Moor B., Deprest J., Timmerman D., "Reply to Re: Pain experienced during transvaginal ultrasound, saline contrast sonohysterography, hysteroscopy and office sampling: a comparative study", Ultrasound in Obstetrics and Gynecology, vol. 32, no. 1, Jul. 2008, pp. 118-119.


69. Machiels J.-P., Debucquoy A., Gevaert O., Daemen A., Sempoux C., McBride W., Stroh C., Vlassak S., Haustermans K., "Prediction of pathological response to preoperative chemoradiotherapy with cetuximab in rectal cancer.", J Clin Oncol, Suppl, ASCO annual meeting, Chicago, Illinois, vol. 26, no. 20, May 2008, pp. 4095-96.


70. Mihalyi A., Gevaert O., Kyama C., Simsa P., Pochet N., De Smet F., De Moor B., Meuleman C., Billen J., Blanckaert N., Vodolazkaia A., Fulop V., D'Hooghe T., "Non-invasive diagnosis of endometriosis based on a combined analysis of six plasma biomarkers", Human Reproduction, vol. 25, no. 3, 2010, pp. 654-664.


71. Kyama C.M., Mihalyi A., Gevaert O., Waelkens E., Simsa P., Van de Plas R., Meuleman C., De Moor B., D'Hooghe T.M., "Evaluation of endometrial biomarkers for semi-invasive diagnosis of endometriosis", Fertility and Sterility, vol. 95, no. 4, Mar. 2011, pp. 1338-43.


72. Cadron I., Van Gorp T., Amant F., Vergote I., Moerman P., Waelkens E., Daemen A., Van de Plas R., De Moor B., Zeillinger R., "The use of laser microdissection and SELDI-TOF MS in ovarian cancer tissue to identify protein profiles", Anticancer Research, vol. 29, no. 4, Apr. 2009, pp. 1039-1046.


73. Bottomley C., Daemen A., Mukri F., Papageorghiou A.T., Kirk E., Pexsters A., De Moor B., Timmerman D., Bourne T., "Functional linear discriminant analysis: a new longitudinal approach to the assessment of embryonic growth", Human Reproduction, vol. 24, no. 2, Feb. 2009, pp. 278-283.


74. Van den Bosch T., Betsas G., Van Schoubroeck D., Daemen A., Vandenbroucke V., Cornelis A., De Moor B., Deprest J., Timmerman D., "Gel infusion sonography in the evaluation of the uterine cavity", Ultrasound in Obstetrics and Gynecology, vol. 34, no. 6, Dec. 2009, pp. 711-714.


75. Van Loo P., Aerts S., Thienpont B., De Moor B., Moreau Y., Marynen P., "ModuleMiner: improved computational detection of cis-regulatory modules. Different modes of gene regulation in embryonic development and adult tissues?", Genome Biology, vol. 9, Apr. 2008, pp. R66-.


76. Bottomley C., Daemen A., Mukri F., Papageorghiou A.T., Kirk E., Pexsters A., De Moor B., Timmerman D., Bourne T., "Assessing first trimester growth: the influence of ethnic background and maternal age", Human Reproduction, vol. 24, no. 2, Feb. 2009, pp. 284-290.


77. Neven P., Van Belle V., Brouckaert O., Pintens S., Paridaens R., Christiaens M-R., Deraedt K., Moerman P., "Are gene signatures better than traditional clinical factors?", The Lancet Oncology, vol. 9, Mar. 2008, pp. 197-198.


78. Tranchevent L., Barriot R., Yu S., Van Vooren S., Van Loo P., Coessens B., Aerts S., De Moor B., Moreau Y., "ENDEAVOUR update: a web resource for gene prioritization in multiple species", Nucleic Acids Research, Web Server issue, vol. 36, no. 1, Jun. 2008, pp. 377-384.


79. Kirk E., Daemen A., Papageorghiou AT., Bottomley C., Condous G., De Moor B., Timmerman D., Bourne T., "Why are some ectopic pregnancies characterized as pregnancies of unknown location at the initial transvaginal ultrasound examination?", Acta Obstetricia et Gynecologica Scandinavica, vol. 87, no. 11, Nov. 2008, pp. 1150-1154.


80. Alzate C., Suykens J. A. K., "Multiway Spectral Clustering with Out-of-Sample Extensions through Weighted Kernel PCA", IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 32, no. 2, Feb. 2010, pp. 335-347.


81. 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", Annals New York Academie of Science, vol. 1158, Mar. 2009, pp. 29-35.


82. De Preter K., Barriot R., Speleman F., Vandesompele J., Moreau Y., "Positional gene enrichment analysis of gene sets for high resolution identification of overrepresented chromosomal regions", Nucleic Acids Research, vol. 36, no. 7, Mar. 2008, e43 p.


83. Yu S., Van Vooren S., Tranchevent L.C., De Moor B., Moreau Y., "Comparison of vocabularies, representations and ranking algorithms for gene prioritization by text mining", Bioinformatics, vol. 24, no. 16, Aug. 2008, pp. i119-125.


84. Van Holsbeke C., Yazbek J., Holland T.K., Daemen A., De Moor B., Testa A.C., Valentin L., Jurkovic D., Timmerman D., "Real-time ultrasound vs. evaluation of static images in the preoperative assessment of adnexal masses", Ultrasound in Obstetrics and Gynecology, vol. 32, no. 6, Nov. 2008, pp. 828-831.


85. Ojeda F., Suykens J.A.K, De Moor B., "Low rank updated LS-SVM classifiers for fast variable selection", Neural Networks, Special Issue on Advances in Neural Networks Research: IJCNN 2007, vol. 21, no. 2-3, Mar.-Apr. 2008, pp. 437-449.


86. Glanzel W., Janssens F., Thijs B., "A comparative analysis of publication activity and citation impact based on the core literature in bioinformatics", Scientometrics, vol. 79, no. 1, Apr. 2009, pp. 109-129.


87. Janssens F., Glanzel W., De Moor B., "A hybrid mapping of information science", Scientometrics, vol. 75, no. 3, Jun. 2008, pp. 607-631.


88. Thorrez L., Van Deun K., Tranchevent L., Van Lommel L., Engelen K., Marchal K., Moreau Y., Van Mechelen I., Schuit F., "Using ribosomal protein genes as reference: a tale of caution", PLoS One, vol. 3, no. 3, Mar. 2008, pp. e1854.


89. Van Vooren S., Coessens B., De Moor B., Moreau Y., Vermeesch J. R., "Array comparative genomic hybridization and computational genome annotation in constitutional cytogenetics: suggesting candidate genes for novel submicroscopic chromosomal imbalance syndromes", Genetics in Medicine, vol. 9, no. 9, Sep. 2007, pp. 642-649.


90. Balikova I., Martens K., Melotte C., Amyere M., Van Vooren S., Moreau Y., Vetrie D., Fiegler H., Carter N.P., Liehr T., Vikkula M., Matthijs G., Fryns J.P., Casteels I., Devriendt K., Vermeesch J.R., "Autosomal dominant microtia linked to five tandem copies of a copy number variable region at chromosome 4pter", American Journal of Human Geneticts, vol. 81, no. 1, 2008, pp. 181-187.


91. Gevaert O., De Moor B., Timmerman D., "Optimizing variable selection and cost using a genetic algorithm for modelling adnexal masses with Bayesian networks", Ultrasound in Obstetrics and Gynecology, Special Issue: 17th World Congress on Ultrasound in Obstetrics and Gynecology, vol. 30, no. 4, Oct. 2007, pp. 412.


92. De Bie T., Tranchevent L., van Oeffelen L., Moreau Y., "Kernel-based data fusion for gene prioritization", Bioinformatics, vol. 23, no. 13, Jul. 2007, pp. i125-32.


93. Gevaert O., Van Vooren S., De Moor B., "A framework for elucidating regulatory networks based on prior information and expression data", Annals of the New York Academy of Sciences, vol. 1115, Dec. 2007, pp. 240-248.


94. Kyama CM., Mihalyi A., Gevaert O., Simsa P., Waelkens E., Van de Plas R., Mwenda JM., Meuleman C., De Moor B., D'Hooghe TM., "Endometrial biomarkers for semi-invasive diagnosis of endometriosis", Human Reproduction, Abstracts of the 23rd Annual Meeting of the European Society of Human Reproduction and Embryology, vol. 22, no. Supplement 1, Jul. 2007, pp. i106-i108.


95. van Oeffelen L., Cornelis P., Van Delm W., De Ridder F., De Moor B., Moreau Y., "Detecting cis-regulatory binding sites for cooperatively binding proteins", Nucleic Acids Research, vol. 36, no. 8:e46, May 2008, pp. 1-6.


96. Dhollander T., Sheng Q., Lemmens K., De Moor B., Marchal K., Moreau Y., "Query-driven module discovery in microarray data", Bioinformatics, vol. 23, no. 19, Oct. 2007, pp. 2573-2580.


97. Gevaert O., Pochet N., De Smet F., Engelen K., Van Gorp T., Amant F., De Moor B., Timmerman D., Vergote I., "Expression profiling to predict the clinical behaviour of ovarian cancer fails independent evaluation", BMC Cancer, vol. 8, no. 18, Jan. 2008, pp. 1-26.


98. Van den Bosch T., Verguts J., Daemen A., Gevaert O., Domali E., Claerhout P., Vandenbroucke V., De Moor B., Deprest J., Timmerman D., "Experienced pain during vaginal ultrasound, hydrosonography, hysteroscopy and office sampling: a comparative study", Ultrasound in Obstetrics and Gynecology, vol. 31, no. 3, Feb. 2008, pp. 346-351.


99. Verlinden L., Eelen G., Van Hellemont R., Engelen K., Buellens I., Van Camp M., Marchal K., Mathieu C., Bouillon R., Verstuyf A., "1alpha,25-dihydroxyvitamin D(3)-induced down-regulation of the checkpoint proteins. Chk1 and Claspin, is mediated by the pocket proteins", J. Steroid Biochem. Mol. Biol., vol. 103, no. 3-5, Mar. 2007, pp. 411-5.


100. Van Leemput K., Van den Bulcke T., Dhollander T., De Moor B., Marchal K., van Remortel P., "Exploring the operational characteristics of inference algorithms for transcriptional networks by means of synthetic data", Artificial Life, Special Issue on Systems Biology, vol. 14, no. 1, Jan. 2008, pp. 49--63.


101. De Keersmaecker S., Thijs I., Vanderleyden J., Marchal K., "Integration of onmic data : how well does it work for bacteria ?", Molecular Microbiology, Oct. 2006, pp. 1-12.


102. Allemeersch J., Van Vooren S., Hannes F., De Moor B., Vermeesch J., Moreau Y., "An experimental loop design for the detection of constitutional chromosomal aberrations by array CGH", \em{BMC Bioinformatics}, vol. 10, no. 380, 2009, 29 p.


103. Deforche K., Silander T., Camacho R., Grossman Z., Soares M., Van Laethem K., Kantor R., Moreau Y., Vandamme A.M., "Analysis of HIV-1 pol sequences using Bayesian networks : implications for drug resistance", Bioinformatics, 4 Oct. 2006.


104. Pochet N.L.M.M., Suykens J.A.K., "Support vector machines versus logistic regression: improving prospective performance in clinical decision-making", Ultrasound in Obstetrics & Gynecology, Opinion, vol. 27, no. 6, Jun. 2006, pp. 607-608.


105. De Keersmaecker S.C., Marchal K., Verhoeven T.L.A., Engelen K., Vanderleyden J., Detweiler S., "Microarray analysis and motif detection reveal new targets of the salmonella enterica serovar typhimurium hila regulatory protein, including hila itself", Journal of Bacteriology, vol. 187, no. 13, Jul. 2006, pp. 4381-4391.


106. Engelen K., Naudts B., De Moor B., Marchal K., "A calibration method for estimating absolute expression levels from microarray data", Bioinformatics, vol. 22, no. 10, May 2006, pp. 1251-8.


107. De Keersmacker S.C., Verhoeven T.L., Desair J., Marchal K., Vanderleyden J., Nagy I., "Strong antimicrobial activity of Lactobacillus rhamnosus GG against Salmonella typhimurium is due to accumulation of lactic acid", FEMS Microbiol. Lett., vol. 259, no. 1, 2006, pp. 89-96.


108. Menten B., Maas N., Thienpont B., Buysse K., Vandesompele J., Melotte C., de Ravel T., Van Vooren S., Balikova I., Backx L., Janssens S., De Paepe A., De Moor B., Moreau Y., Marynen P., Fryns JP., Mortier G., Devriendt K., Speleman F., Vermeesch JR., "Emerging patterns of cryptic chromosomal imbalances in patients with idiopathic mental retardation and multiple congenital anomalies: a new series of 140 patients and review of the literature", J Med Genet, vol. 43, no. 8, Feb. 2006, pp. 625-633.


109. Le Caignec C., Spits C., Sermon K., De Rycke M., Thienpont B., Debrock S., Staessen C., Moreau Y., Fryns J.-P., Van Steirteghem A., Liebaers I., Vermeesch J., "Single-cell chromosomal imbalances detection by array CGH", Nucleic Acids Research, vol. 34, no. 9, 2006, e68 p.


110. Gevaert O., De Smet F., Timmerman D., Moreau Y. and De Moor B., "Predicting the prognosis of breast cancer by integrating clinical and microarray data with Bayesian networks", Bioinformatics, ISMB 2006 Conference Proceedings, August 6-10, Fortaleza, Brazil, vol. 22, no. 14, Jul. 2006, pp. e184-e190.


111. Van Vooren S., Thienpont B., Menten B., Speleman F., De Moor B., Vermeesch J. R., Moreau Y., "Mapping Biomedical Concepts onto the Human Genome by Mining Literature on Chromosomal Aberrations", Nucleic Acids Research, vol. 35, no. 8, Apr. 2007, pp. 2533-2543.


112. Gevaert O., Pochet N., De Smet F., Van Gorp T., De Moor B., Timmerman D., Amant F., Vergote I., "Molecular profiling of platinum resistant ovarian cancer: use of the model in clinical practice", International Journal of Cancer, vol. 119, no. 6, Sep. 2006, pp. 1511-1512.


113. Monsieurs P.; Thijs G.; Fadda A.; De Keersmaecker S.; Vanderleyden J.; De Moor B.; Marchal K., "More robust detection of motifs in coexpressed genes by using phylogenetic information", BMC Bioinformatics, vol. 20, no. 7(1), Mar. 2006, 160 p.


114. Dabrowski M., Adach A., Aerts S., Moreau Y., Kaminska B., "Identification of conserved modes of expression profiles during hippocampal development and neuronal differentiation in vitro", Journal Neurochemistry, vol. 29, 2005, pp. 87-91.


115. Valentin L., Ameye L., Testa F., Lecuru F., Bernard J.P., Paladini D., Van Huffel S., Timmerman D., "Ultrasound characteristics of different types of adnexal malignancies", Gynecologic Oncology, vol. 102, no. 1, Jul. 2006, pp. 41-48.


116. Mukherjee G., Abeygunawardena N., Parkinson H., Contrino S., Durinck S., Farne A., Holloway E., Lilja P., Moreau Y., Oezcimen A., Rayner T., Sharma A., Brazma A., Sarkans U., Shojatalab M., "Plant-Based Microarray Data at the European Bioinformatics Institute. Introducing AtMIAMExpress, a Submission Tool for Arabidopsis Gene Expression Data to ArrayExpress.", Plant Physiology, vol. 139, Oct. 2005, pp. 632-636.


117. Janssens F., Leta J., Glanzel W., De Moor B., "Towards Mapping Library and Information Science", Information Processing & Management, Special Issue on Informetrics, vol. 42, no. 6, Dec. 2006, pp. 1614-1642.


118. Neven P., Pochet N., Drijkoningen M., Amant F., De Smet F., Paridaens R., Christiaens M.R., Vergote I., "Progesterone Receptor in Estrogen Receptor?Positive Breast Cancer: The Association Between HER-2 and Lymph Node Involvement Is Age Related", Journal of Clinical Oncology, vol. 24, no. 16, Jun. 2006, pp. 2595-2597.


119. Denolet E., De Gendt K., Allemeersch J., Engelen K., Marchal K., Van Hummelen P., Tan K. A. L., Sharpe R. M., Saunders P. T. K., Swinnen J. V., Verhoeven G., "The effect of a Sertoli cell-selective knockout of the androgen", Molecular Endocrinology, vol. 20, no. 2, Feb. 2006, pp. 321-334.


120. Gevaert O., De Smet F., Kirk E., Van Calster B., Bourne T., Van Huffel S., Moreau Y., Timmerman D., De Moor B and Condous G., "Predicting the outcome of pregnancies of unknown location: Bayesian networks with expert prior information compared to logistic regression", Human Reproduction, vol. 21, no. 7, Jul. 2006, pp. 1824-1831.


121. Lemmens K., Dhollander T., De Bie T., Monsieurs P., Engelen K., Smets B., Winderickx J., De Moor B., Marchal K., "Inferring transcriptional module networks from ChIP-chip-, motif- and microarray data", Genome Biology, vol. 7, no. 5, May 2006, pp. R37.1-R37.14.


122. Van den Bulcke T., Lemmens K., Van de Peer Y., Marchal K., "Inferring Transcriptional Networks by Mining Omics Data", Current Bioinformatics, vol. 1, no. 3, Aug. 2006, pp. 301--313.


123. Valentin L., Ameye L., Jurkovic D., Metzger U., L'Ecuru F., Van Huffel S., Timmerman D., "Which extrauterine pelvic masses are difficult to correctly classify as benign or malignant on the basis of ultrasound findings, and is there a way of making a correct diagnosis ?", Ultrasound in Obstetrics and Gynecology, vol. 27, no. 4, Apr. 2006, pp. 438-444.


124. Van den Bulcke T., Van Leemput K., Naudts B., van Remortel P., Ma H., Verschoren A., De Moor B., Marchal K., "SynTReN: a generator of synthetic gene expression data for design and analysis of structure learning algorithms", BMC Bioinformatics, vol. 7, no. 43, Jan. 2006, pp. 7-43.


125. Verlinden L., Eelen G., Beullens I., Van Camp M., Van Hummelen P., Engelen K., Van Hellemont R., Marchal K., De Moor B., Beullens M., Bollen M., Mathieu C., Bouillon R., Verstuyf A., "Characterization of the Condensin Component Cnap1 and the Protein Kinase Melk as E2F-Target Genes", J. Biol. Chem., vol. 280, no. 45, 2005, pp. 37319-37330.


126. Van Gorp T., De Smet F., Pochet N., Engelen K., Van Hummelen P., Suykens J.A.K., Marchal K., Amant F., Moreau Y., Timmerman D., De Moor B., Vergote I., "Predicting the clinical behavior of ovarian cancer from gene expression profiles", International Journal of Gynecological Cancer, 14th International meeting of the ESGO (ESGO 14), Istanbul, Turkey, vol. 15, no. S2, Sep. 2005, pp. 66.


127. De Smet F., Pochet N.L.M.M., De Moor B.L.R., Van Gorp T., Timmerman D., Vergote I.B., Hartmann L.C., Damokosh A.I., Hoersch S., "Independent test set performance in the prediction of early relapse in ovarian cancer with gene expression profiles", Clinical Cancer Research, vol. 11, no. 21, Nov. 2005, pp. 7958-7959.


128. Condous G., Kirk E., Lu C., Van Huffel S., Gevaert O., De Moor B., De Smet F., Timmerman D., Bourne T., "Diagnostic accuracy of varying discriminatory zones for the prediction of ectopic pregnancy in women with a pregnancy of unknown location", Ultrasound in Obstetrics and Gynecology, vol. 26, no. 7, Dec. 2005, pp. 770-775.


129. Rovas L., Sladkevicius P., Strobel E., De Smet F., De Moor B., Valentin L., "Three-dimensional ultrasound assessment of the cervix for predicting time to spontaneous onset of labor and time to delivery in prolonged pregnancy.", Ultrasound in Obstetrics and Gynecology, vol. 28, no. 2, 2006, pp. 306-311.


130. Durinck S., Moreau Y., Kasprzyk A., De Moor B., Brazma A., Huber W., "BioMart and Bioconductor: A powerful link between biological databases and microarray data analysis", Bioinformatics, vol. 21, no. 16, May 2005, pp. 3439-3440.


131. Van Hellemont R., Monsieurs P., Thijs G., De Moor B., Van de Peer Y., Marchal K., "A novel approach to identifying regulatory motifs in distantly related genomes.", Genome Biology, vol. 6, no. R113, Dec. 2005, pp. R113.1-R113.19.


132. De Smet F., De Brabanter J., Konstantinovic M.L., Pochet N., Van den Bosch T., Moerman P., De Moor B., Vergote I., Timmerman D., "New models to predict depth of infiltration in endometrial carcinoma based on transvaginal sonography", Ultrasound in Obstetrics and Gynecology, vol. 27, no. 6, May 2006, pp. 664-671.


133. Fruscella E., Testa A., Ferrandina G., De Smet F., Van Holsbeke C., Scambia G., Zannoni G.F., Ludovisi M., Achten R., Amant F., Vergote I., Timmerman D., "Ultrasound features of different histopathological subtypes of borderline ovarian tumors", Ultrasound Obstetrics Gynecology, vol. 26, 2005, pp. 644-650.


134. Boets J., De Cock K., Espinoza M., De Moor B., "Clustering time series, subspace identification and cepstral distances", Communications in Information and Systems, Special Issue Dedicated to the 70th Birthday of Thomas Kailath: Part I, vol. 5, no. 1, 2005, pp. 69-96.


135. De Moor B., Marchal K., Mathys J., Moreau Y., "Bioinformatics : Organisms from Venus, Technology from Jupiter, Algorithms from Mars", Mathematics and Genomics, (Eds. Bultheel, Teugels, Thas), Koninklijke Vlaamse Academie van Belgie voor Wetenschappen en Kunsten, 2005., pp. 37-102.


136. Condous G., Okaro E., Khalid A., Lu C., Van Huffel S., Bourne T., "The accuracy of transvaginal ultrasonography for the diagnosis of ectopic pregnancy prior to surgery", Human Reproduction, vol. 20, no. 5, 2005, pp. 1404-1409.


137. Van den Bosch T., Van Schoubroeck D., Ameye L., Van Huffel S., Timmerman D., "Ultrasound examination of the endometrium before and after Pipelle endometrial sampling", Ultrasound in Obstetrics and Gynecology, vol. 26, no. 3, Sep. 2005, pp. 283-286.


138. Timmerman D., Testa A.C., Bourne T., Ferrazzi E., Ameye L., Konstantinovic M.L., Van Calster B., Collins W.P., Vergote I., Van Huffel S., Valentin L., "Logistic regression model to distinguish between the benign and malignant adnexal mass before surgery: a multicenter study by the International Ovarian Tumor Analysis Group", Journal of Clinical Oncology, vol. 23, no. 34, Dec. 2005, pp. 8794-8801.


139. Aerts S., Van Loo P., Thijs G., Mayer H., de Martin R., Moreau Y., De Moor B., "TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis", Nucleic Acids Research (Web Server Issue), vol. 33, 2005, pp. W393-W396.


140. Glenisson P., Gl?nzel W., Janssens F., De Moor B., "Combining full-text and bibliometric information in mapping scientific disciplines", Information Processing and Management, Special Issue on Informetrics, vol. 41, no. 6, Dec. 2005, pp. 1548-1572.


141. Aerts S., Lambrechts D., Maity S., Van Loo P., Coessens B., De Smet F., Tranchevent L., De Moor B., Marynen P., Hassan B., Carmeliet P., Moreau Y., "Gene prioritization through genomic data fusion", Nature Biotechnology, vol. 24, no. 5, May 2006, pp. 537-544.


142. Pochet N.L.M.M., Janssens F.A.L., De Smet F., Marchal K., Suykens J.A.K., De Moor B.L.R., "M@CBETH: a microarray classification benchmarking tool", Bioinformatics, vol. 21, no. 14, Jul. 2005, pp. 3185-3186.


143. 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., "ArrayCGHbase : an analysis platform for comparative genomic hybridization microarrays", BMC Bioinformatics, vol. 6, no. 124, May 2005, pp. 1-20.


144. Vermeesch J., 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., "Molecular Karyotyping: Towards Improved Pre- and Postnatal Genetic Diagnosis", J. Histochem. Cytochem, vol. 53, no. 3, 2005, pp. 413-422.


145. Roosen J., Engelen K., Marchal K., Mathys J., Griffioen G., Cameroni E., Thevelein J.M., De Virgilio C., De Moor B. and Winderickx J., "PKA and Sch9 Control a Molecular Switch Important for the Proper Adaptation to Nutrient Availability.", Molecular Microbiology, vol. 55, no. 3, Dec. 2004, pp. 862-880.


146. Brants JR., Ayoubi TA., Chada K., Marchal K., Van de Ven W.J., Petit. M.M., "Differential regulation of the insulin-like growth factor II mRNA-binding protein genes by architectural transcription factor HMGA2.", FEBS Letters, vol. 569, no. 1-3, Jul. 2004, pp. 277-283.


147. Lu C., Devos A., Suykens J.A.K., Arus C., Van Huffel S., "Bagging linear sparse Bayesian learning models for variable selection in cancer diagnosis", IEEE Transactions on information technology in biomedicine, vol. 11, no. 3, May 2007, pp. 338-347.


148. Condous G., Okaro E., Khalid A., Lu C., Van Huffel S., Timmerman D., Bourne1 T., "A prospective evaluation of a single visit strategy to manage pregnancies of unknown location (PUL)", Human Reproduction, vol. 20, no. 5, 2005, pp. 1398-1403.


149. Monsieurs P., Dirix G., Marchal K., Vanderleyden J., Michiels J., "Screening genomes of Gram-positive bacteria for double-glycine-motif-containing peptides.", Microbiology, vol. 150, no. 5, May 2004, pp. 1121-26.


150. Monsieurs P., De Keersmaecker S., Navarre W.W., Bader M.W., De Smet F., McClelland M., Fang F.C., De Moor B., Vanderleyden J., Marchal K., "Comparison of the PhoPQ regulon in Escherichia coli and Salmonella typhimurium", Journal of Molecular Evolution, vol. 60, no. 4, Apr. 2005, pp. 462-474.


151. 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., "An Assessment of Computational Tools for the Discovery of Transcription Factor Binding Sites", Nature Biotechnology, vol. 23, no. 1, Jan. 2005, pp. 137-144.


152. 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., "Benchmarking the CATMA microarray: a novel tool for Arabidopsis transcriptome analysis.", Plant Physiology, vol. 137, Feb. 2005, pp. 588-601.


153. Morales L., Neven P., Timmerman D., Christiaens M.-R., Vergote I., Van Limbergen E., Carbonez A., Van Huffel S., Ameye L., Paridaens R., "Acute effects of tamoxifen and third generation aromatase inhibitors on menopausal symptoms of breast cancer patients", Anti-Cancer Drugs, vol. 15, no. 8, Sep. 2004, pp. 753-760.


154. Durinck S., Allemeersch J., Carey V.J., Moreau Y., De Moor B., "Importing MAGEML format microarray data into BioConductor", Bioinformatics, vol. 20, no. 18, Dec. 2004, pp. 3641-3642.


155. Kapushesky M., Kemmeren P., Culhane A.C., Durinck S., Ihmels J., Korner C., Kull M., Torrente A., Sarkans U., Vilo J. and Brazma A., "Expression Profiler: next generation - an online platform for analysis of microarray data", Nucleic Acids Research, vol. 32, Apr. 2004, pp. W465-470.


156. Hilson P., Allemeersch J., Altmann T., Aubourg S., Avon A., Beynon J., Bhalero R.P., Bitton F., Caboche M., Cannoot B., Chardakov V., Cognet-Holliger C., Colot V., Crowe M., Darimont C., Durinck S., Eickhoff H., Falcon de Languevialle A., Farmer E.E., Grant M., Kuiper M.T.R., Lehrach H., Leon C., Leyva A., Lundenberg J., Lurin C., Moreau Y., Nietfeld W., Serizet C., Tabrett A., Taconnat L., Thareau V., Van Hummelen P., Vercruysse S., Vuylsteke M., Weingartner M., Weisbeek P.J., Wirta V., Wittink F.R.A., Zabeau M., Small I., "Versatile Gene-specific sequence tages for arabidopsis functional genomics : Transcript profiling and reverse genetics applications.", Genome Research, vol. 14, no. 10b, Oct. 2004, pp. 2176-2189.


157. Lanckriet G., De Bie T., Cristianini N., Jordan M., Stafford Noble W., "A Framework for Genomic Data Fusion and its Application to Membrane Protein Prediction", Bioinformatics, vol. 20, no. 16, Nov. 2004, pp. .


158. Condous G., Okaro E., Khalid A., Timmerman D., Lu C., Zhou Y., Van Huffel S., Collins W., Bourne T., "The use of a new logistic regression model for predicting the outcome of pregnancies of unknown location", Human Reproduction, vol. 19, no. 8, Aug. 2004, pp. 1900-1910.


159. Pelckmans K., De Brabanter J., Suykens J.A.K., De Moor B., "The differogram : Nonparametric noise variance estimation and its use for model", Neurocomputing, Special Issue on Signal Processing, vol. 69, no. 1-3, Dec. 2005, pp. 100-122.


160. Van Bleu E., Marchal K., Lambrecht M., Mathys J., Vanderleyden J., "Annotation of the pRhico plasmid of Azospirillum brasilense reveals its role in determining the outer surface composition", FEMS Microbiology Letters, vol. 232, no. 2, Mar. 2004, pp. 165-172.


161. Dirix G., Monsieurs P., Dombrecht B., Daniels R., Marchal K., Vanderleyden J., Michiels J., "Peptide signal molecules and bacteriocins in Gramnegative bacteria : a genome-wide in silico screening for peptides containing a double-glycine leader sequence and their cognate transporters.", Peptides, vol. 25, no. 9, Sep. 2004, pp. 1425-1440.


162. Aerts S., Thijs G., Dabrowski M., Moreau Y., De Moor B., "Comprehensive analysis of the base composition around the transcription start site in Metazoa", BMC Genomics, vol. 5, no. 34, Jun. 2004, pp. 1-10.


163. De Smet F., Moreau Y., Engelen K., Timmerman D., Vergote I., De Moor B., "Balancing false positives and false negatives for the detection of differential expression in malignancies", British Journal of Cancer, vol. 91, no. 6, Sep. 2004, pp. 1160-1165.


164. 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, voL 5, no. 2, Epub, Jan. 2004, 20 p.


165. Pochet N., De Smet F., Suykens J.A.K., De Moor B., "Systematic benchmarking of micorarray data classification : assessing the role of nonlinearity and dimensionality reduction", Bioinformatics, vol. 20, no. 17, Nov. 2004, pp. 3185-3195.


166. Glenisson P.,Coessens B., Van Vooren S., Mathys J., Moreau Y., De Moor B., "TXTGate : Profiling gene groups with text-based information", Genome Biology, vol. 5, no. 6, May 2004, pp. R43.1-R43.12.


167. Glenisson P., Mathijs J., Moreau Y., De Moor B., "Meta-clustering of gene expression data and literature-extracted information", SIGKDD Explorations, Special Issue on Microarray Data Mining, vol. 5, no. 2, Dec. 2003, pp. 101-112.


168. Condous G., Lu C., Van Huffel S., Timmerman D., Bourne T., "Human chorionic gonadotrophin and progesterone levels for the investigation of pregnancies of unknown location", International Journal of Gynecology and Obstetrics, vol. 86, 2004, pp. 351-357.


169. Eelen G., Verlinden L., Van Camp M., Van Hummelen P., Marchal K., De Moor B., Mathieu C., Carmeliet G., Bouillon R., Verstuyf A., "The effects of 1a,25-dihydroxyvitamin D3 on the expression of DNA replication genes.", Journal of bone and mineral research, vol. 19, 2004, pp. 133-146.


170. Aerts S., Van Loo P., Moreau Y., De Moor B., "A genetic algorithm for the detection of new cis-regulatory modules in sets of coregulated genes", Bioinformatics, vol. 20, no. 12, Aug. 2004, pp. 1974-1976.


171. Rombauts S., Florquin K., Lescot M., Marchal K., Rouze P., Van de Peer Y., "Computational approaches to identify promoters and cis-regulatory elements in plant genomes", Plant Physiology, vol. 132, no. 3, Jul. 2003, pp. 1162-1176.


172. Lukas L., Devos A., Suykens J.A.K., Vanhamme L., Howe F.A., Majos C., Moreno-Torres A., Van der Graaf M., Tate A.R., Arus C., Van Huffel S., "Brain Tumour Classification based on long echo proton MRS signals", Artificial Intelligence in Medicine, vol. 31, 2004, pp. 73-89.


173. Aerts S., Van Loo P., Thijs G., Moreau Y., De Moor B., "Computational detection of cis-regulatory modules", Bioinformatics, Special Issue on ECCB 2003, vol. 19, no. Suppl. 2, Oct. 2003, pp. ii5-ii14.


174. 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, vol. 19, no. 10, Oct. 2003, pp. 570-577.


175. Coessens B., Thijs G., Aerts S., Marchal K., De Smet F. Engelen K., Glenisson P., Moreau Y., Mathys J., De Moor B., "INCLUSive : a web portal and service registry for microarray and regulatory sequence analysis", Nucleic Acids Research, web server issue 2003, vol. 31, no. 13, Jul. 2003, pp. 3468-3470.


176. Sheng Q., Moreau Y., De Moor B., "Biclustering Microarray data by Gibbs sampling", Bioinformatics, ECCB 2003 Proceedings, vol. 19, Sep. 2003, pp. ii196-ii205.


177. Van Schoubroeck D., Van den Bosch T., Scharpe K., Lu C., Van Huffel S. Timmerman D., "Prospective evaluation of blood flow in the myometrium and in the uterine arteries in the puerperium", Ultrasound in Obstetrics and Gynecology, vol. 23, no. 4, Apr. 2004, pp. 378-381.


178. Smets I., Bernaerts K., Sun J., Marchal K., Vanderleyden J., Van Impe J., "Sensitivity function based model reduction : a bacterial gene expression case study", Biotechnology and Bioengineering, vol. 80, No. 2, Oct. 2002, pp. 195-200.


179. Denys H., Jadidizadeh A., Amini Nik S., Vandam K., Tejpar S., Aerts S., Moreau Y., De Moor B., Alman B., Cassiman J.J., "Identification of IGFBP-6 as a significantly down-regulated gene by beta-catenin in desmoid tumors", Oncogene, vol. 23, Jan. 2004, pp. 654-664.


180. Dombrecht B., Marchal K., Vanderleyden J., Michiels J., "Prediction and overview of the RpoN-regulon in closely related species of the Rhizobiales", Genome Biology, Research0076, vol. 3, no. 12, 2002.


181. 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, vol. 11, no. 2, Feb. 2003, pp. 61-66.


182. Engelen K., Coessens B., Marchal K., De Moor B., "MARAN: normalizing micro-array data", Bioinformatics, vol. 19, no. 7, May 2003, pp. 893-894.


183. 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, vol. 31, no. 6, Mar. 2003, pp. 1753-1764.


184. 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, vol. 85, no. 5, Jun. 2003, pp. 1279-1288.


185. Marchal K., Engelen K., De Brabanter J., De Moor B., "A guideline for the analysis of two sample microarray data", Journal of Biological Systems, vol. 10, no. 4, Dec. 2002, pp. 409-430.

Top

International Conference Paper

1. Soldatos TG., Pavlopoulos GA., "Mining cell literature using support vector machines", in Lecture Notes in Artificial Intelligence (SETN2012), Lamia, Greece, May 2012.


2. Iacucci E., Popovic D., Pavlopoulos G., Tranchevent L-C., De Moor B., Morea Y., "Towards Better Prioritization of Epigenetically Modified DNA Regions", in Springer's Lecture Notes in Computer Science / Lecture Notes in Artificial Intelligence (SETN 2012), Lamia, Greece, May 2012.


3. Breckpot J., Tranchevent L., Thienpont B., Bauters M., Troost E., Gewillig M., Vermeesch J., Moreau Y., Devriendt K., Van Esch H., "BMPRIA is a candidate gene for congenital heart defects associated with the recurrent 10q22q23 deletion syndrome"


4. Gligorijevic I., De Vos M., Blok J.H., Mijovic B., van Dijk J.P., Van Huffel S., "Automated way to obtain motor units? signatures and estimate their firing patterns during voluntary contractions using HD-sEMG", in Proc. of the 33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society (IEEE EMBS Boston), Boston, Massachusetts, Aug. 2011, pp. 4090-4093.


5. Adefioye A., Lui X., DeMoor B., "Multi-view Spectral Clustering and its Chemical Application", in Proc. of the International Conference on Intelligent Biology and Medicine (ICIBM), Nashville, United States of America, Apr. 2012, pp. 1-26.


6. Iacucci E., Moreau Y., "Towards Better Receptor-Ligand Prioritization: How Machine Learning on Protein-Protein Interaction Data Can Provide Insight Into Receptor-Ligand Pairs.", in Proc. of the 20th International Conference on Artificial Neural Networks (ICANN 2010), Thessaloniki, Greece, Sep. 2010, pp. 267-271.


7. Langone R., Alzate C., Suykens J.A.K., "Modularity-based model selection for kernel spectral clustering", in Proc. of the International Joint Conference on Neural Networks (IJCNN 2011), San Jose, U.S.A., Aug. 2011, pp. 1849-1856.


8. Alzate C., Suykens J.A.K., "Out-of-Sample Eigenvectors in Kernel Spectral Clustering", in Proc. of the International Joint Conference on Neural Networks (IJCNN 2011), San Jose, U.S.A., Aug. 2011, pp. 2349-2356.


9. Guns T., Sun H., Nijssen S., Marchal K., De Raedt L., "Cis-regulatory Module Detection using Constraint Programming", in Proc. of the IEEE International Conference on bioinformatics and Biomedicine, Hong, Kong, Dec. 2010, pp. 363-368.


10. Gligorijevic I., Welkenhuysen M., Prodanov D., Eberle W., Nuttin B., Bartic C., Van Huffel S., "Statistical analysis of neural spike trains for evaluation of functional differences in brain activity", in Proc. of the BIOSIGNAL 2010 conference (BIOSIGNAL 2010), Berlin, Germany, Jul. 2010.


11. Ojeda F., Signoretto M., Van de Plas R., Waelkens E., De Moor B., Suykens J.A.K., "Semi-supervised Learning of Sparse Linear Models in Mass Spectral Imaging", in Pattern Recongintion in Bioinformatics, (Dijkstra T.M.H, Tsivtsivadze E., Marchiori E., and Heskes T., eds.), 5th IAPR International Conference, PRIB 2010 Nijmegen, The Netherlands, September 2010, vol. 6282 of Lecture Notes in Bioinformatics. Subseries of Lecture Notes in Computer Science, Springer-Verlag, 2010, pp. 325-334.


12. Alzate C., Suykens J.A.K., "Highly Sparse Kernel Spectral Clustering with Predictive Out-of-Sample Extensions", in Proc. of the 18th European Symposium on Artificial Neural Networks (ESANN 2010), Bruges, Belgium, Apr. 2010, pp. 235-240.


13. Signoretto M., Daemen A., Savorgnan C., Suykens J. A. K., "Variable Selection and Grouping with Multiple Graph Priors", in Proc. of the 2nd NIPS Workshop on Optimization for Machine Learning, Whistler, Canada , Dec. 2009.


14. Liu X.H., Yu S. Moreau Y.. De moor B., Glanzel W., Janssens F., "Hybrid Clustering by Integrating Text and Citation based Graphs in Journal Database Analysis", in Proc. of the 2009 IEEE International Conference on Data Mining Workshops (ICDMW2009), Miami, Florida, Dec. 2009, pp. 521-526.


15. Talmor AJ., Daemen A., Murdoch E., Missfelder-Lobos H., De Moor B., Timmerman D., Bourne T., Lees C., "The relationship between abdominal circumference and middle cerebral artery Doppler z-scores in severe early onset fetal growth restriction", in Proc. of the 20th World Congress on Ultrasound in Obstetrics and Gynecology (ISUOG), Hamburg, Germany, Sep. 2009, 257 p.


16. Talmor AJ., Daemen A., Murdoch E., De Moor B., Missfelder-Lobos H., Timmerman D., Bourne T., Lees C., "The relationship between abdominal circumference and umbilical artery Doppler z-scores in severe early onset fetal growth restriction", in Proc. of the 20th World Congress on Ultrasound in Obstetrics and Gynecology (ISUOG), Hamburg, Germany, Sep. 2009, 151 p.


17. Habayeb O., Daemen A., Timmerman D., De Moor B., Bourne T., Hackett G., Lees C., "The relationship between fetal growth in the first trimester, PAPP-A and birthweight percentiles", in Proc. of the 20th World Congress on Ultrasound in Obstetrics and Gynecology (ISUOG), Hamburg, Germany, Sep. 2009, 95 p.


18. Habayeb O., Daemen A., Timmerman D., De Moor B., Bourne T., Hackett G., Lees C., "The relationship between early first trimester PAPP-A and birthweight percentiles", in Proc. of the 20th World Congress on Ultrasound in Obstetrics and Gynecology (ISUOG), Hamburg, Germany, Sep. 2009, 253 p.


19. Sarris I., Daemen A., Bottomley C., Pexsters A., Timmerman D., Bourne T., Papageorghiou A., "The influence of body mass index on first trimester fetal growth", in Proc. of the 20th World Congress on Ultrasound in Obstetrics and Gynecology (ISUOG), Hamburg, Germany, Sep. 2009, pp. 92-93.


20. Bottomley C., Daemen A., Bourne T., Pexsters A., Timmerman D., Thilaganathan B., Papageorghiou A., "The influence of maternal demographic features on fetal size in the first trimester", in Proc. of the 20th World Congress on Ultrasound in Obstetrics and Gynecology (ISUOG), Hamburg, Germany, Sep. 2009, 92 p.


21. Pexsters A., Daemen A., Frijns JP., Bottomley C., Van Schoubroeck D., De Catte L., De Moor B., D'Hooghe T., Timmerman D., Bourne T., "Crown-rump length in genetically abnormal pregnancies compared to a CRL curve for normal pregnancies", in Proc. of the 20th World Congress on Ultrasound in Obstetrics and Gynecology (ISUOG), Hamburg, Germany, Sep. 2009, 85 p.


22. Pexsters A., Daemen A., Bottomley C., Van Schoubroeck D., De Catte L., De Moor B., D'Hooghe T., Lees C., Timmerman D., Bourne T., "A new crown-rump length curve based on over 3500 pregnancies", in Proc. of the 20th World Congress on Ultrasound in Obstetrics and Gynecology (ISUOG), Hamburg, Germany, Sep. 2009, pp. 11-12.


23. Alzate C., Espinoza M., De Moor B., Suykens J.A.K., "Identifying Customer Profiles in Power Load Time Series Using Spectral Clustering", in Proc. of the 19th International Conference on Artificial Neural Networks (ICANN 2009), Limassol, Cyprus, Sep. 2009, pp. 315-324.


24. Alzate C., Suykens J.A.K., "A Regularized Formulation for Spectral Clustering with Pairwise Constraints", in Proc. of the 2009 International Joint Conference on Neural Networks (IJCNN'09), Atlanta, U.S.A, Jun. 2009, pp. 141-148.


25. Liu X.H., Yu S., Moreau Y., De Moor B., Glanzel W., Janssens F., "Hybrid Clustering of Text Mining and Bibliometrics Applied to Journal Sets", in Proc. of the SIAM Data Mining Conference 09 (SIAM DM 09), Sparks, Nevada USA, May 2009, pp. 46-60.


26. Yu S., De Moor B., Moreau Y., "Clustering by heterogeneous data fusion: framework and applications", in Neural Information Processing 2009 workshop learning from multiple sources (NIPS 2009 workshop), Whistler, Canada, Dec. 2008.


27. Daemen A., Gevaert O., Leunen K., Legius E., Vergote I., De Moor B., "Supervised classification of array CGH data with HMM-based feature selection", in Pacific Symposium on Biocomputing (PSB), Big Island, Hawaii, Jan. 2009, pp. 468-479.


28. Kirk E., Papageorghiou A.T., Daemen A., Condous G., Timmerman D., Bourne T., "The appearance and behaviour of ectopic pregnancies in the 'pregnancy of unknown location' population", in Proc. of the 18th World Congress on Ultrasound in Obstetrics and Gynecology (ISUOG), Chicago, Illinois, Aug. 2008, 273 p.


29. Van den Bosch T., Vandenbroucke V., Daemen A., Domali E., Van Schoubroeck D., De Moor B., Deprest J., Timmerman D., "Removal of focal intracavity lesions results in cessation of abnormal uterine bleeding in the vast majority of women", in Proc. of the 18th World Congress on Ultrasound in Obstetrics and Gynecology (ISUOG), Chicago, Illinois, Aug. 2008, 258 p.


30. Van Holsbeke C., Daemen A., Lannoo L., Mesens T., de Jonge E., Valentin L., Jurkovic D., Yazbek J., Holland T., Timmerman D., "Pattern recognition by less experienced examiners and use of mathematical models to discriminate between static ultrasound images of benign and malignant adnexal masses", in Proc. of the 18th World Congress on Ultrasound in Obstetrics and Gynecology (ISUOG), Chicago, Illinois, Aug. 2008, 292 p.


31. Daemen A., Gevaert O., Leunen K., Vanspauwen V., Michils G., Legius E., Vergote I., De Moor B., "Classification of sporadic and BRCA1 ovarian cancer based on a genome-wide study of copy number variations", in Knowledge-Based Intelligent Information and Engineering Systems, (Lovrek I., Howlett R.J., and Jain L.C., eds.), vol. 5178 of mph{Lecture Notes in Artificial Intelligence}, Springer, 2008, pp. 165-172.


32. Pexsters A., Daemen A., Frijns J.P., Bottomley C., Van Schoubroeck D., De Catte L., Timmerman D., Bourne T., "A cross-sectional analysis of embryonic growth in normal and genetically abnormal pregnancies", in Proc. of the 18th World Congress on Ultrasound in Obstetrics and Gynecology (ISUOG), Chicago, Illinois, Aug. 2008, 337 p.


33. Pexsters A., Daemen A., Bottomley C., Van Schoubroeck D., De Catte L., Timmerman D., Bourne T., "Validation of the Robinson growth curve with data of transvaginal ultrasound assessments in early pregnancy from a large Caucasian population", in Proc. of the 18th World Congress on Ultrasound in Obstetrics and Gynecology (ISUOG), Chicago, Illinois, Aug. 2008, 278 p.


34. Bottomley C., Daemen A., Mukri F., Papageorghiou A.T., Kirk E., Pexsters A., De Moor B., Timmerman D., Bourne T., "Growth delay in the first trimester: sensitivity and specificity of using serial measurements of embryonic growth for the prediction of early pregnancy loss", in Proc. of the 18th World Congress on Ultrasound in Obstetrics and Gynecology (ISUOG), Chicago, Illinois, Aug. 2008, 278 p.


35. Bottomley C., Daemen A., Mukri F., Papageorghiou A.T., Kirk E., Pexsters A., De Moor B., Timmerman D., Bourne T., "The influence of maternal age on early first trimester growth assessed by ultrasound", in Proc. of the 18th World Congress on Ultrasound in Obstetrics and Gynecology (ISUOG), Chicago, Illinois, Aug. 2008, 355 p.


36. Bottomley C., Daemen A., Mukri F., Kirk E., Papageorghiou A.T., Pexsters A., De Moor B., Timmerman D., Bourne T., "Assessing early first trimester growth with ultrasonography: the influence of ethnic background", in Proc. of the 18th World Congress on Ultrasound in Obstetrics and Gynecology (ISUOG), Chicago, Illinois, Aug. 2008, 354 p.


37. Daemen A., Van Holsbeke C., Fruscio R., Guerriero S., Czekierdowski A., Valentin L., Savelli L., Testa A., Colombo N., Bourne T., Vergote I., De Moor B., Timmerman D., "Prevalence of cancer and optimal cut-off levels for mathematical models to distinguish between benign and malignant adnexal masses", in Proc. of the 18th World Congress on Ultrasound in Obstetrics and Gynecology (ISUOG), Chicago, Illinois, Aug. 2008, pp. 292-293.


38. Daemen A., Van Holsbeke C., Gevaert O., Fruscio R., Guerriero S., Czekierdowski A., Valentin L., Savelli L., Testa A., Fischerova D., Bourne T., Vergote I., De Moor B., Timmerman D., "Prospective comparison of one-step and two-step models for the classification of adnexal masses as benign or malignant", in Proc. of the 18th World Congress on Ultrasound in Obstetrics and Gynecology (ISUOG), Chicago, Illinois, Aug. 2008, 368 p.


39. Gevaert O., Testa A., Daemen A., Van Holsbeke C., Fruscio R., Epstein E., Leone FPG., Czerkierdowski A., Valentin L., Savelli L., Bourne T., Amant F., De Moor B., Timmerman D., "Investigation of the performance of mathematical models on small ovarian masses on IOTA phase 1 and 2 data.", in 18th World Congress on Ultrasond in Obstetrics and Gynecology (ISUOG 2008), Chicago, Illinois, Aug. 2008, 1 p.


40. Gevaert O., Van Holsbeke C., Fruscio R., Guerriero S., Czekierdowski A., Savelli L., Testa A., Fischerova D., Jurkovic D., Bourne T., Neven P., Valentin L., De Moor B., Timmerman D., "Multicenter prospective testing to predict malignancy in adnexal masses using Bayesian network models", in 18th World Congress on Ultrasond in Obstetrics and Gynecology (ISUOG 2008), Chicago, Illinois, Aug. 2008, 1 p.


41. Alzate C., Suykens J. A. K., "Sparse Kernel Models for Spectral Clustering Using the Incomplete Cholesky Decomposition", in Proc. of the 2008 International Joint Conference on Neural Networks (IJCNN 2008), Hong Kong, China, Jun. 2008, pp. 3555-3562.


42. Willems J., "Stability and quadratic Lyapunov functions for nD Systems", in Proc. of the International Conference on Multidimensional (nD) Systems, Aveiro, Portugal, 2007, pp. 41-45.


43. Van Belle V., Pelckmans K., Suykens J.A.K., Van Huffel S., "Survival SVM: a Practical Scalable Algorithm", in Proc. of the 16th European Symposium on Artificial Neural Networks (ESANN2008), Bruges, Belgium, Apr. 2008, pp. 89-94.


44. Van de Plas R., Pelckmans K., De Moor B., Waelkens E., "Spatial Querying of Imaging Mass Spectrometry Data: A Nonnegative Least Squares Approach", in The NIPS workshop on Machine Learning in Computational Biology (NIPS MLCB), Whistler (B.C.), Canada, Dec. 2007.


45. Van de Plas R., De Moor B., Waelkens E., "Discrete Wavelet Transform-based Multivariate Exploration of Tissue via Imaging Mass Spectrometry", in Proc. of the 23rd Annual ACM Symposium on Applied Computing (ACM SAC), Fortaleza, Brazil, Mar. 2008.


46. Van de Plas R., De Moor B., Waelkens E., "Imaging Mass Spectrometry Based Exploration of Biochemical Tissue Composition using Peak Intensity Weighted PCA", in Proceedings of the Third IEEE/NIH BISTI Life Science Systems and Applications Workshop 2007 (LISSA 2007), Bethesda, Maryland USA, Nov. 2007.


47. Pastor D., Cortes-Calabuig A., Lemmens K., De Moor B., Marchal K., Denecker M., "GeneReg: Integration of Experimental Data on the DNA Transcription Process", in Proc. of the 19th Belgian-Dutch Conference on Artificial Intelligence (BNAIC), Utrecht, Netherlands, Nov. 2007, pp. 1-8.


48. Gevaert O., Van Vooren S., De Moor B., "Integration of microarray and textual data improves the prognosis prediction of breast, lung and ovarian cancer patients", in Pacific Symposium on Biocomputing (Pac Symp Biocomput. ), Kohala Coast, Hawaii, Jan. 2008, pp. 279-290.


49. Daemen A., Gevaert O., De Bie T., Debucquoy A., Machiels J.-P., De Moor B., Haustermans K., "Integrating microarray and proteomics data to predict the response on cetuximab in patients with rectal cancer", in Pacific Symposium on Biocomputing (Pac Symp Biocomput. ), Kohala Coast, Hawaii, Jan. 2008, pp. 166-177.


50. Daemen A., Bottomley C., Gevaert O., De Moor B., Timmerman D., Bourne T., "Predicting early pregnancy loss with Functional Linear Discriminant Analysis (FLDA)", in Proc. of the 17th World Congress on Ultrasound in Obstetrics and Gynecology (ISUOG), Florence, Italy, Oct. 2007, 469 p.


51. Daemen A., Gevaert O., De Moor B., "Integration of clinical and microarray data with kernel methods", in Proc. of the 29th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), Lyon, France, Aug. 2007, pp. 5411-5415.


52. Ojeda F., Suykens J.A.K, De Moor B., "Variable selection by rank-one updates for least squares support vector machines", in Proc. of the 2007 International Joint Conference on Neural Networks (IJCNN), Orlando, FL. U.S.A., Aug. 2007, pp. 2283-2288.


53. Janssens F., Glanzel W., De Moor B., "Dynamic hybrid clustering of bioinformatics by incorporating text mining and citation analysis", in Proc. of the 13th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD˘07), San Jose, California, Aug. 2007, pp. 360--369.


54. Garcia-Gomez J.M., Tortajada S., Vicente J., Saez C., Castells X., Luts J., Julia-Sape M., Juan-Ciscar A., Van Huffel S., Arus C., Robles M., "Genomics and metabolomics research of Brain Tumours based on Machine Learning", in Proc. of the 9th International Work-Conference on Artificial Neural Networks (IWANN'07), San Sebastian, Spain, Jun. 2007, pp. 1012-1019.


55. Rodriguez V., Janssens F., Ghazanchian M., Debackere K., De Moor B., "On material transfer agreements and visibility of researchers in biotechnology", in Proc. of the 11th International Conference of the International Society for Scientometrics and Informetrics (ISSI2007), Madrid, Spain, Jun. 2007, pp. 659-671.


56. Glanzel W., Janssens F., Thijs B., "A comparative analysis of publication activity and citation impact based on the core literature in bioinformatics", in Proc. of the 11th International Conference of the International Society for Scientometrics and Informetrics (ISSI2007), Madrid, Spain, Jun. 2007, pp. 321--334.


57. Van de Plas R., Ojeda F., Dewil M., Van Den Bosch L., De Moor B., Waelkens E., "Prospective Exploration of Biochemical Tissue Composition via Imaging Mass Spectrometry Guided by Principal Component Analysis", in Proceedings of the Pacific Symposium on Biocomputing 12 (PSB), Maui, Hawaii, Jan. 2007, pp. 458-469.


58. Janssens F., Glanzel W., De Moor B., "A hybrid mapping of information science", in Proc. of the 11th International Conference of the International Society for Scientometrics and Informetrics (ISSI2007), Madrid, Spain, Jun. 2007, pp. 408--420.


59. Pelckmans K., Shawe-Taylor J., Suykens J.A.K., De Moor B., "Margin based Transductive Graph Cuts using Linear Programming", in Proc. of the 11th International Conference on Artificial Intelligence (AISTATS 2007), San Juan, Puerto Rico, Apr. 2007, pp. 360-367.


60. Pelckmans K., Suykens J.A.K., De Moor B., "The Kingdom-Capacity of a Graph: On the Difficulty of Learning a Graph Labelling", in Proc. of the workshop Mining and Learning with graphs (MLG 2006), Berlin, Germany, Sep. 2006.


61. Janssens F., Tran Quoc V., Glanzel W., De Moor B., "Integration of textual content and link information for accurate clustering of science fields", in Proc. of the 1st International Conference on Multidisciplinary Information Sciences and Technologies (InSciT2006), Mérida, Spain, Oct. 2006, pp. 615-619.


62. Coessens B., Christiaens S., Verlinden R., Moreau Y., Meersman R., De Moor B., "Ontology-Guided Data Integration for Computational Prioritization of Disease Genes", in On the Move to Meaningful Internet Systems 2006: OTM 2006 Workshops, (Meersman R., Tari Z., and and Herrero P., eds.), vol. 4277 of mph{Lecture Notes in Computer Science}, Springer-Verlag, 2006, pp. 689-698.


63. Gevaert O., Ojeda F., Timmerman D., De Moor B., "Integrating proteomics in medical decision support systems using Bayesian networks", in Proc. of the conference on In-Silico Analysis of Proteins - Swiss-Prot (Swiss-Prot), Fortaleza, Brazil, Aug. 2006, pp. 1-2.


64. Pelckmans K., Van Vooren S., Coessens B., Suykens J.A.K., De Moor B., "Mutual Spectral Clustering: Microarray Experiments Versus Text Corpus", in Proc. of the workshop on Probabilistic Modeling and Machine Learning in Structural and Systems Biology (PMSB 2006), Helsinki, Finland, Jun. 2006.


65. Gevaert O., Van Vooren S., De Moor B., "The use of prior distributions for learning genetic networks", in Proc. of the workshop on Probabilistic Modeling and Machine Learning in Structural and Systems Biology (PMSB), Helsinki, Finland, Jun. 2006, pp. 103-107.


66. Yu S., Van Vooren S., Coessens B., De Moor M., "Interpreting gene profiles from biomedical literature minging with self organization maps", in Lecture Notes in Computer Science: Advances in Neural Networks - ISNN 2006: Third International Symposium on Neural Networks (ISNN 2006), ChenDu, China, May 2006, pp. 635-641.


67. Pelckmans K., Suykens J.A.K., De Moor B., "Clustering and Staircases", in NIPS 2005 workshop on Theoretical Foundations on Clustering, 2 p.


68. Gevaert O., De Smet F., Timmerman D., Moreau Y. and De Moor B., "Integration of clinical and microarray data using Bayesian networks", in Proc. of the 14th IFAC Symposium on System Identification (SYSID), Newcastle, Australia, Mar. 2006, pp. 1-6.


69. De Smet F., Vergote I., De Brabanter J., Konstantinovic M.L., Van den Bosch T., Moerman P., De Moor B., Amant F., Timmerman D., "New models to predict depth of infiltration in endometrial carcinoma based on transvaginal sonography", in International Journal of Gynecological Cancer (14th International meeting of the ESGO) (ESGO 14), Istanbul, Turkey, Sep. 2005, 2 p.


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


71. Pelckmans K., De Brabanter J. Suykens J.A.K., De Moor B., "Convex Clustering Shrinkage", in Workshop on Statistics and Optimization of Clustering Workshop (PASCAL), London, U.K., Jul. 2005, pp. .


72. Ameye L., De Brabanter J., Suykens J.A.K., Cadron I., Devlieger R., Timmerman D., Spitz B., Van Huffel S., "Predictive Models for Long Term Survival after Premature Rupture of Membranes", in Proc. of the 2005 IEEE Engineering in Medicine and Biology 27th Annual Conference (IEEE-EMB), Shanghai, China, Sep. 2005, pp. 572-575.


73. Boets J., De Cock K., De Moor B., "Distances between dynamical models for clustering time series", in Proc. of the 14th IFAC Symposium on System Identification (SYSID-2006), Newcastle, Australia, Mar. 2006, pp. 392-397.


74. Timmerman D., De Smet F., De Brabanter J., Moerman P., De Moor B., Moreau Y., Van Huffel S., Vergote I., "News on ultrasonographic techniques for pelvic malignancies", in Int J Gynecol Cancer 2003, 13 (Suppl. 1), ME04 (13th International meeting of the ESGO), Brussels, Belgium, Apr. 2003, pp. 120-121.


75. Vanspauwen R., Housmans S., Moreau Y., De Smet F., Drijkoningen M., Amant F., Berteloot P., Vergote I., Christiaens M.R., Neven P., "Which factor does predict axillary lymph node status best in operable breast cancers", in Int J Gynecol Cancer 2003, 13 (Suppl. 1), PO160 (13th International meeting of the ESGO), Brussels, Belgium, Apr. 2003, pp. 81.


76. Timmerman D., De Smet F., De Brabanter J., Thijs I., Moreau Y., De Moor B., Vergote I., "PRE-OPERATIVE PREDICTION OF DEPTH OF MYOMETRIAL INVASION IN PATIENTS WITH ENDOMETRIAL CANCER: EVALUATION OF ULTRASOUND PARAMETERS AND DEVELOPMENT OF A NEW LOGISTIC REGRESSION MODEL", in Int J Gynecol Cancer,13 (Suppl 1), OP064 ( 13th International Meeting of the ESGO), Brussels, Belgium, Apr. 2003, pp. 26.


77. Devos A., Lukas L., Suykens J.A.K., Vanhamme L., Howe F.A., Majos C., Moreno-Torres A., van der Graaf M., Tate A.R., Arus C., Van Huffel S., "Brain tumour classification using short echo time 1H MRS. Objective comparison of classification techniques (LDA, LS-SVM).", in Proc. of the 12th Scientific Meeting and Exhibition of the International Society for Magnetic Resonance in Medicine (ISMRM04), Kyoto, Japan, May 2004, 384 p.


78. Vertommen J., Janssens F., De Moor B., Duflou J., "Advanced Personalization and Document Retrieval Techniques in Support of Efficient Knowledge Management", in Proc. of the 2nd International Seminar on Digital Enterprise Technology (DET), Seattle, Washington, Sep. 2004.


79. De Bie T., Monsieurs P., Engelen K., De Moor B., Cristianini N., Marchal K., "Discovering transcriptional modules from Motif, Chip-chip and microarray data", in Proceedings of the Pacific Symposium on Biocomputing (PSB 2005), Hawaii, Jan. 2005, pp. 483-494.


80. Vertommen J., Vandermeulen B., Duflou J., Van Dromme D., De Moor B., "Testing methods and algorithms for the next generation of knowledge management systems", in Proc. of the Future Business Technology Conference 2004 (FUBUTEC 2004), Fontainebleau, France, Mar. 2004.


81. Timmerman D., De Smet F., De Brabanter J., Van Holsbeke C., Jermy K., Moreau Y., Bourne T., Vergote I., "OC118 : Mathematical models to evaluate ovarian masses - can they beat an expert operator ?", in Ultrasound Obstet Gynecol, 22(Suppl 1) (13th World Congress on Ultrasound in Obstetrics & Gynecology), Paris, France, Aug.-Sep. 2003, pp. 33.


82. Glenisson P., Coessens B., Van Vooren S., Moreau Y., De Moor B., "Text-based gene profiling with domain-specific views", in Proc. of the First International Workshop on Semantic Web and Databases (SWDB 2003), Berlin, Germany, Sep. 2003, pp. 15-31.

Top

Book

1. Yu S., Tranchevent L.C., De Moor B., Moreau Y., Kernel-based Data Fusion for Machine Learning, vol. 345 of Studies in Computational Intelligence, Springer, 2011, 200 p.

Top

Contribution to book

1. Iacucci E., Xavier de Souza S., Moreau Y., "Computational Approaches to Elucidating Transient Protein-Protein Interactions, Predicting Receptor-Ligand Pairings", in Chapter Protein Interaction , (Cai W., ed.), InTech (Rijeka, Croatia), 2011, pp. 1-16.


2. Luts J., Laudadio T., Idema A.J., Simonetti A.W., Heerschap A., Vandermeulen D., Suykens J.A.K., Van Huffel S., "Nosologic imaging of brain tumors using MRI and MRSI", in Chapter 16 Brain tumors (part 1), (Hayat M.A., ed.), vol. 3 of mph{Tumors of the central nervous system}, Springer, 2011, pp. 155-168.


3. Janssens F., Zhang L., Glanzel W., "Hybrid Clustering for Validation and Improvement of Subject-Classification Schemes", in Chapter 6 of Data Mining and Knowledge Discovery in Real Life Applications, (Ponce J., and Karahoca A., eds.), IN-TECH (Vienna, Austria), 2009, pp. 89-118.


4. Daemen A., Gevaert O., Leunen K., Vanspauwen V., Michils G., Legius E., Vergote I., De Moor B., "A genome-wide computational study of copy number variations: an example on ovarian cancer", in Chapter 9 of Investigating Human Cancer with Computational Intelligence Techniques, (Vellido A., and Lisboa PJG., eds.), Future Technology Press (Shoreham-by-sea, UK), 2009, pp. 107-118.


5. Van Lommel L., Moreau Y., Pipeleers D., Jonas J.-C., Schuit F., "mRNA profiling of pancreatic beta-cells: investigating mechanisms of diabetes", in Chapter 8 of Gene Expression Profiling by Microarrays - Clinical Implications, (Hofmann W.-K., ed.), Cambridge University Press (Cambridge, UK), 2006, pp. 187-211.


6. Pochet N.L.M.M., Ojeda F., De Smet F., De Bie T., Suykens J.A.K., De Moor B.L.R., "Kernel clustering for knowledge discovery in clinical microarray data analysis", in Chapter 3 Kernel methods in bioengineering, communications and image processing, (Camps-Valls G., Rojo-Alvarez J.L., and Martinez-Ramon M., eds.), Idea Group Inc (Hershey, Pennsylvania), 2005, pp. 64-92.


7. Marchal K., De Smet F., Engelen K., De Moor B., "Computational biology and toxicogenomics", in chapter 3 Predictive toxicology, (Helma C., ed.), Marcel Dekker (New York), 2004, pp. 37-85.


8. Sheng Q., Moreau Y., De Smet F., Marchal K., De Moor B., "Advances in cluster analysis of microarray data", in Chapter 10 of Data analysis and visualization in genomics and proteomics, (Azuaje F., and Dopazo J., eds.), Jonh Wiley & Sons Ltd. (Chichester, UK), 2005, pp. 153-173.


9. Thijs G., De Smet F., Moreau Y., Marchal K., De Moor B., "Gene regulation bioinformatics of microarray data", in chapter Genomics and Proteomics Engineering, (Metin A., ed.), WileyL/IEEE Press, 2004, pp. 1-41.

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Ph.D.-thesis

1. Liu X., Learning from multi-view data: clustering algorithm and text mining appliaction, PhD thesis, Faculty of Engineering, K.U.Leuven (Leuven, Belgium), Sep. 2011, 177 p.


2. Ojeda F., Kernel based Methods for Microarray and Mass Spectrometry Data Analysis, PhD thesis, Faculty of Engineering, K.U.Leuven (Leuven, Belgium), May 2011, 150 p.


3. Daemen A., Design of Clinical Decision Support Systems for Cancer based upon Clinical and Molecular Data, PhD thesis, Faculty of Engineering, K.U.Leuven (Leuven, Belgium), May 2010, 236 p.


4. Luts J., Classification of brain tumors based on magnetic resonance spectroscopy, PhD thesis, Faculty of Engineering, K.U.Leuven (Leuven, Belgium), Jan. 2010, 256 p.


5. Yu S., Kernel-based data fusion for machine learning: methods and applications in bioinformatics and text mining, PhD thesis, Faculty of Engineering, K.U.Leuven (Leuven, Belgium), Nov. 2009, 220 p.


6. Alzate C., Support Vector Methods for Unsupervised Learning, PhD thesis, Faculty of Engineering, K.U.Leuven (Leuven, Belgium), May 2009, 175 p.


7. Van den Bulcke T., Robust algorithms for inferring regulatory networks based on gene expression measurements and biological prior information, PhD thesis, Faculty of Engineering, K.U.Leuven (Leuven, Belgium), May 2009, 178 p.


8. Gevaert O., A Bayesian network integration framework for modeling biomedical data, PhD thesis, Faculty of Engineering, K.U.Leuven (Leuven, Belgium), Dec. 2008, 167 p.


9. Lemmens K., Reconstruction of regulatory modules based on heterogeneous data sources, PhD thesis, Faculty of Engineering, K.U.Leuven (Leuven, Belgium), Sep. 2008, 211 p.


10. Janssens F., Clustering of scientific fields by integrating text mining and bibliometrics, PhD thesis, Faculty of Engineering, K.U.Leuven (Leuven, Belgium), May 2007, 261 p.


11. Monsieurs P., Motif Detection in Prokaryotes based on Comparative Genomics, PhD thesis, Faculty of Engineering, K.U.Leuven (Leuven, Belgium), Dec. 2006, 212 p.


12. Van Hellemont R., Motif detection in vertebrates based on comparative genomics, PhD thesis, Faculty of Engineering, K.U.Leuven (Leuven, Belgium), Mar. 2007, 249 p.


13. Allemeersch J., Statistical analysis of microarray data: Applications in platform comparison, compendium data, and array CGH, PhD thesis, Faculty of Engineering, K.U.Leuven (Leuven, Belgium), Dec. 2006, xxiv+183 p.


14. Pochet N., Microarray data analysis using support vector machines and kernel methods, PhD thesis, Faculty of Engineering, K.U.Leuven (Leuven, Belgium), May 2006, 238 p.


15. Coessens B., Data Integration Techniques for Molecular Biology Research, PhD thesis, Faculty of Engineering, K.U.Leuven (Leuven, Belgium), Jun. 2006, 195 p.


16. Durinck S., Microarray compendia and their implications for bioinformatics software development, PhD thesis, Faculty of Engineering, K.U.Leuven (Leuven, Belgium), May 2006, 197 p.


17. Engelen K., Normalizing microarray data: estimating absolute expression levels, PhD thesis, Faculty of Engineering, K.U.Leuven (Leuven, Belgium), Dec. 2005, xlvi + 157 p.


18. Sheng Q., Gibbs sampling on Bayesian models for biclustering microarray data, PhD thesis, Faculty of Engineering, K.U.Leuven (Leuven, Belgium), Nov. 2005, 205 p.


19. Lu C., Probabilistic machine learning approaches to medical classification problems, PhD thesis, Faculty of Engineering, K.U.Leuven (Leuven, Belgium), Jan. 2005, 183 p.


20. 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.


21. 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.


22. Aerts S., Computational discovery of \emph{cis)-regulatory modules in animal genomes, PhD thesis, Faculty of Engineering, K.U.Leuven (Leuven, Belgium), May 2004, 200 p.


23. 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.

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To be published

1. Iacucci E., Tranchevent L.-C., Popovic D., Pavlopoulos G. A., De Moor B., Schneider R., Moreau Y., "A Bioinformatics E-dating Story: Computational Prediction and Prioritization of Receptor-Ligand Pairs", Internal Report 12-84, ESAT-SISTA, K.U.Leuven (Leuven, Belgium), 2012. Accepted for publication in Proc. of the International Conference on Intelligent Systems for Molecular Biology (ISMB SCS 2012)published in special issue of BMC Bioinformatics, Long Beach, California, Jul. 2012.


2. Liu X, Ji S., Glanzel W., De Moor B., "Multi-View Partitioning via Tensor Methods", Internal Report 12-79, ESAT-SISTA, K.U.Leuven (Leuven, Belgium), 2012. Accepted for publication in IEEE Transactions on Knowledge and Data Engineering.


3. Di Legge A., Testa A.C., Ameye L., Van Calster B., Lissoni A.A., Leone F.P.G., Savelli L., Franchi D., Czekierdowski A., Trio D., Van Holsbeke C., Ferrazzi E., Timmerman D., Valentin L., "Lesion size affects the diagnostic performance of the International Ovarian Tumor Analysis (IOTA) logistic regression models, the IOTA simple rules and the Risk of Malignancy Index to estimate the risk of malignancy in adnexal masses", Internal Report 12-70, ESAT-SISTA, K.U.Leuven (Leuven, Belgium), 2012. Accepted for publication in Ultrasound in Obstetrics and Gynecology.


4. Alzate C., Suykens J.A.K., "A Semi-Supervised Formulation to Binary Kernel Spectral Clustering", Internal Report 12-14, ESAT-SISTA, K.U.Leuven (Leuven, Belgium), 2012. Accepted for publication in \emph{2012 IEEE World Congress on Computational Intelligence (IEEE WCCI/IJCNN 2012), Brisbane, Australia, Jun. 2012.


5. Vodolazkaia A., El Aalamat Y., Popovic D., Mihalyi A., Bossuyt X., Kyama C., Fassbender A., Bokor A., Schols D., Huskens D., Meuleman C., Peeraer K., Tomassetti C., Gevaert O., Waelkens E., Kasran A., De Moor B., D'Hooghe T., "Evaluation of a panel of 28 biomarkers for a non-invasive diagnosis of endometriosis", Internal Report 12-03, ESAT-SISTA, K.U.Leuven (Leuven, Belgium), 2012. Accepted for publication in Human Reproduction.


6. Iacucci E., Popovic E., Tranchevent L-C., De Moor B., Moreau Y., "Critical Assessment of Receptor-Ligand Predictions", Internal Report 11-207, ESAT-SISTA, K.U.Leuven (Leuven, Belgium), 2011. Accepted for publication in Bioinformatics.


7. Gevaert O., Vergote I., "Book review: Outcome prediction in cancer, A. Taktak and A. Fisher (eds)", Internal Report 07-73, ESAT-SISTA, K.U.Leuven (Leuven, Belgium), 2007. Gynecologic Oncology.


8. Sheng Q., Thijs G., Moreau Y., and De Moor B., "Applications of Gibbs sampling in bioinformatics", Internal Report 05-65, ESAT-SISTA, K.U.Leuven (Leuven, Belgium), 2005. Accepted for publication in Optimization methods and software.

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