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2013
A rich internet application for remote visualization and collaborative annotation of digital slide images in histology and cytology  
Raphaël Marée, Benjamin Stevens, Loïc Rollus, Natacha Rocks, Xavier Moles-Lopez, Isabelle Salmon, Didier Cataldo, Louis Wehenkel
BMC Diagnostic Pathology (Proc. 12th European Congress on Telepathology and 5th International Congress on Virtual Microscopy), Volume 8 S1 - 2013
Structural Determinants of Specificity and Catalytic Mechanism in mammalian 25-kDa Thiamine Triphosphatase  
David Delvaux, Frédéric Kerff, Mamidanna R.V.S. Murty, Bernard Lakaye, Jan Czerniecki, Grégory Kohn, Pierre Wins, Raphaël Herman, Valérie Gabelica, Fabien Heuze, X. Tordoir, Raphaël Marée, André Matagne, Paulette Charlier, Edwin De Pauw, Lucien Bettendorff
Accepted for publication in Biochimica et Biophysica Acta - General Subjects - 2013
 
2011
Automatic localization of interest points in zebrafish images with tree-based methods   stern_prib2011-finalpreprint.pdf
Olivier Stern, Raphaël Marée, Jessica Aceto, Nathalie Jeanray, Marc Muller, Louis Wehenkel, Pierre Geurts
To appear Proc. 6th IAPR International Conference on Pattern Recognition in Bioinformatics - 2011
Discovery and biochemical characterisation of four novel biomarkers for osteoarthritis  
Dominique deSeny, Mohammed Sharif, Marianne Fillet, Gaël Cobraiville, Marie-Alice Meuwis, Raphaël Marée, Jean-Philippe Hauzeur, Louis Wehenkel, Edouard Louis, Marie-Paule Merville, John Kirwan, Clio Ribbens, Michel Malaise
Annals of the Rheumatic Diseases, Volume 70, page 1144-1152 - 2011
High-density lipoprotein proteome dynamics in human endotoxemia   1477-5956-9-34.pdf
Johannes H.M. Levels, Pierre Geurts, Helen Karlsson, Raphaël Marée, Stefan Ljunggren, Louise Fornander, Louis Wehenkel, Mats Lindahl, Erik S.G. Stroes, Jan Albert Kuivenhoven, Joost C. M. Meijers
Proteome Science, Volume 9, Number 34 - 2011
Phenotype Classification of Zebrafish Embryos by Supervised Learning   abstract_njeanray-Benelearn_postreview_V2.pdf
Nathalie Jeanray, Raphaël Marée, Benoît Pruvot, Olivier Stern, Pierre Geurts, Louis Wehenkel, Marc Muller
Extended Abstract at 20 th Machine Learning conference of Belgium and The Netherlands - may 2011
Zebra sh Skeleton Measurements using Image Analysis and Machine Learning Methods   stern-abstract-benelearn2011.pdf
Olivier Stern, Raphaël Marée, Jessica Aceto, Nathalie Jeanray, Marc Muller, Louis Wehenkel, Pierre Geurts
Extended Abstract at 20 th Machine Learning conference of Belgium and The Netherlands - may 2011
 
2010
A web-based framework for visualization, annotation, and automatic exploitation of whole-slide images   maree-tiga2010.pdf
Arnaud Babilone, Samuel Cop, Rafik Rassaa, Natacha Rocks, Loïc Rollus, Didier Cataldo, Raphaël Marée
Poster at 2nd European Workshop on Tissue Imaging and Analysis, Heidelberg - Jun 2010
Biomedical Imaging Modality Classification Using Bags of Visual and Textual Terms with Extremely Randomized Trees   maree-iclef2010.pdf
Raphaël Marée, Olivier Stern, Pierre Geurts
Working Notes, ImageCLEF LAB Notebook, Multilingual and Multimodal Information Access Evaluation (CLEF) - Sep 2010
Incremental Indexing and Distributed Image Search using Shared Randomized Vocabularies   maree-mir2010.pdf mir053-maree-author.pdf
Raphaël Marée, Philippe Denis, Louis Wehenkel, Pierre Geurts
Proc. 11th ACM International Conference on Multimedia Information Retrieval (MIR), page 91-100 - March 2010
Inferring regulatory networks from expression data using tree-based methods  
Vân Anh Huynh-Thu, Alexandre Irrthum, Louis Wehenkel, Pierre Geurts
Plos ONE, Volume 5, Number 9, page e12776 - sept 2010
Oligodendrocyte development and myelinogenesis are not impaired by high concentrations of phenylalanine or its metabolites   nihms261793.pdf
Renaud Schoemans, Marie-Stéphane Aigrot, Chaohong Wu, Raphaël Marée, Pengyu Hong, Shibeshi Belachew, Claire Josse, Catherine Lubetzki, Vincent Bours
Journal of Inherited Metabolism Disease, Volume 33, Number 2, page 113-120 - 2010
 
2009
Biomarker discovery in asthma-related inflammation and remodeling   2163_ftp.pdf
Florence Quesada Calvo, Marianne Fillet, Dominique deSeny, Marie-Alice Meuwis, Raphaël Marée, Celine Crahay, Genevieve Paulissen, Natacha Rocks, Maud Gueders, Louis Wehenkel, Marie-Paule Merville, Renaud Louis, Jean-Michel Foidart, Agnès Noel, Didier Cataldo
Proteomics, Volume 9, Number 8, page 2163-2170 - Apr 2009
P2X1 ion channels promote neutrophil chemotaxis through Rho kinase activation   2801.full.pdf
Christelle Lecut, Kim Frederix, D.M. Johnson, C. Deroanne, M. Thiry, C. Faccinetto, N. Ruzicka, Raphaël Marée, R.J. Evans, P. Volders, Vincent Bours, Cécile Oury
Journal of Immunology - 2009
Supervised learning with decision tree-based methods in computational and systems biology  
Pierre Geurts, Alexandre Irrthum, Louis Wehenkel
Molecular BioSystems, Volume 5, page 1593-1605 - dec 2009
 
2008
A novel formulation of inhaled doxycycline reduces allergen-induced inflammation, hyperresponsiveness and remodeling by matrix metalloproteinases and cytokines modulation   gueders-al-BP08.pdf
Maud Gueders, Pascal Bertholet, Fabienne Perin, Natacha Rocks, Raphaël Marée, Vincent Botta, Renaud Louis, Jean-Michel Foidart, Agnès Noel, Brigitte Evrard, Didier Cataldo
Biochemical Pharmacology, Volume 75, Number 2, page 514-526 - Jan 2008
Compositional protein analysis of HDL by SELDI-TOF MS during experimental endotoxemia  
Johannes H.M. Levels, Raphaël Marée, Pierre Geurts, Jan Albert Kuivenhoven, Louis Wehenkel, John J.P. Kastelein, Joost C. M. Meijers
77th European Atherosclerosis Society Congress (Poster) - April 2008
Exploiting tree-based variable importances to selectively identify relevant variables  
Vân Anh Huynh-Thu, Louis Wehenkel, Pierre Geurts
Proc. of FSDM08, ECML/PKDD Workshop on New challenges for feature selection in data mining and knowledge discovery - 2008
Exploiting tree-based variable importances to selectively identify relevant variables   huynhthu08a.pdf
Vân Anh Huynh-Thu, Louis Wehenkel, Pierre Geurts
JMLR: Workshop and Conference Proceedings, Volume 4, page 60-73 - 2008
Monomeric calgranulins determined by SELDI-TOF-MS compared with calprotectin measured by ELISA as biomarkers in arthritis  
Dominique deSeny, Marianne Fillet, Clio Ribbens, Raphaël Marée, Marie-Alice Meuwis, Laurence Lutteri, Jean-Paul Chapelle, Louis Wehenkel, Edouard Louis, Marie-Paule Merville, Michel Malaise
Clinical Chemistry, Volume 54, Number 6, page 1066-1075 - June 2008
Predicting gene essentiality from expression patterns in Escherichia coli  
Alexandre Irrthum, Louis Wehenkel
Proc. of MLSB 2008, second workshop on Machine Learning in Systems Biology - 2008
Proteomics for prediction and characterization of response to infliximab in Crohn Disease: a pilot study  
Marie-Alice Meuwis, Marianne Fillet, Laurence Lutteri, Raphaël Marée, Pierre Geurts, Dominique deSeny, Michel Malaise, Jean-Paul Chapelle, Louis Wehenkel, Jacques Belaiche, Marie-Paule Merville, Edouard Louis
Clinical Biochemistry, Volume 41, Number 12, page 960-967 - Aug 2008
Raw genotypes vs haplotype blocks for genome wide association studies by random forests  
Vincent Botta, Pierre Geurts, Sarah Hansoul, Louis Wehenkel
Proc. of MLSB 2008, second workshop on Machine Learning in Systems Biology - 2008
 
2007
A novel susceptibility locus for Crohn s disease identified by whole genome association maps to a gene desert on chromosome 5p13.1 and modulates the level of expression of the prostaglandin receptor EP4   Libioulle_2007.pdf
Cécille Libioulle, Edouard Louis, Sarah Hansoul, Cynthia Sandor, Frédéric Farnir, Denis Franchimont, Séverine Vermeire, Olivier de Wit, Martine de Vos, Anna Dixon, Bruno Demarche, Ivo Gut, Simon Heath, Liming Liang, Debby Laukens, Myriam Mni, Diana Zelinika, André Van Gossum, Paul Rutgeerts, Jacques Belaiche, Mark Lathrop, M. Georges
PLoS Genetics - 2007
Biomarker discovery for Inflammatory Bowel Disease, using proteomic serum profiling  
Marie-Alice Meuwis, Marianne Fillet, Pierre Geurts, Dominique deSeny, Laurence Lutteri, Jean-Paul Chapelle, Vincent Bours, Louis Wehenkel, Jacques Belaiche, Michel Malaise, Edouard Louis, Marie-Paule Merville
Biochemical Pharmacology, Volume 73, Number 9, page 1422--1433 - May 2007
Elucidating the Altered Transcriptional Programs in Breast Cancer using Independent Component Analysis  
Andrew Teschendorff, Michel Journée, Pierre-Antoine Absil, Rodolphe Sepulchre, Carlos Caldas
PLoS Computational Biology, Volume 3, Number 8, page 1539--1554 - August 2007
Inferring biological networks with output kernel trees   geurts-bmc2007.pdf
Pierre Geurts, Nizar Touleimat, Marie Dutreix, Florence d Alché-Buc
BMC Bioinformatics (PMSB06 special issue), Volume 8, Number Suppl 2, page S4 - 2007
Inferring biological networks with output kernel trees  
Pierre Geurts, Nizar Touleimat, Marie Dutreix, Florence d Alché-Buc
15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and 6th European Conference on Computational Biology (ECCB), Posters Track - 2007
Predetector: a new tool to identify regulatory elements in bacterial genomes   hiard2007-PREDetector.pdf
Samuel Hiard, Raphaël Marée, Séverine Colson, Paul A. Hoskinson, Fritz Titgemeyer, Gilles P. van Weeze, Bernard Joris, Louis Wehenkel, Sébastien Rigali
Biochemical and Biophysical Research Communications, Volume 357, Number 4, page 861-864 - June 2007
Random Subwindows and Extremely Randomized Trees for Image Classification in Cell Biology   maree-geurts-wehenkel-bmc-cell-biology-1471-2121-8-S1-S2.pdf
Raphaël Marée, Pierre Geurts, Louis Wehenkel
BMC Cell Biology supplement on Workshop of Multiscale Biological Imaging, Data Mining and Informatics, Volume 8, Number S1 - July 2007
Random Subwindows and Randomized Trees for Image Retrieval, Classification, and Annotation   maree-poster-ismb07.pdf
Raphaël Marée, Marie Dumont, Pierre Geurts, Louis Wehenkel
15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and 6th European Conference on Computational Biology (ECCB), Posters Track - 2007

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