Computational tools for prioritizing candidate genes: boosting disease gene discovery von Moreau, Yves, Tranchevent, Léon-Charles

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Optimized Data Fusion for Kernel k-Means Clustering von Shi Yu, Tranchevent, Leon-Charles, Xinhai Liu, Glanzel, W., Suykens, J. A. K., De Moor, B., Moreau, Y.

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Systems level analysis of sex-dependent gene expression changes in Parkinson’s disease von Tranchevent, Léon-Charles, Halder, Rashi, Glaab, Enrico

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RNA Helicases DDX5 and DDX17 Dynamically Orchestrate Transcription, miRNA, and Splicing Programs in Cell Differentiation von Dardenne, Etienne, Polay Espinoza, Micaela, Fattet, Laurent, Germann, Sophie, Lambert, Marie-Pierre, Neil, Helen, Zonta, Eleonora, Mortada, Hussein, Gratadou, Lise, Deygas, Mathieu, Chakrama, Fatima Zahra, Samaan, Samaan, Desmet, François-Olivier, Tranchevent, Léon-Charles, Dutertre, Martin, Rimokh, Ruth, Bourgeois, Cyril F., Auboeuf, Didier

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Interplay between coding and exonic splicing regulatory sequences von Fontrodona, Nicolas, Aubé, Fabien, Claude, Jean-Baptiste, Polvèche, Hélène, Lemaire, Sébastien, Tranchevent, Léon-Charles, Modolo, Laurent, Mortreux, Franck, Bourgeois, Cyril F, Auboeuf, Didier

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Endeavour update: a web resource for gene prioritization in multiple species von Tranchevent, Léon-Charles, Barriot, Roland, Yu, Shi, Van Vooren, Steven, Van Loo, Peter, Coessens, Bert, De Moor, Bart, Aerts, Stein, Moreau, Yves

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CD47 is a direct target of SNAI1 and ZEB1 and its blockade activates the phagocytosis of breast cancer cells undergoing EMT von Noman, Muhammad Zaeem, Van Moer, Kris, Marani, Vanessa, Gemmill, Robert M, Tranchevent, Léon-Charles, Azuaje, Francisco, Muller, Arnaud, Chouaib, Salem, Thiery, Jean Paul, Berchem, Guy, Janji, Bassam

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Identification of protein features encoded by alternative exons using Exon Ontology von Tranchevent, Léon-Charles, Aubé, Fabien, Dulaurier, Louis, Benoit-Pilven, Clara, Rey, Amandine, Poret, Arnaud, Chautard, Emilie, Mortada, Hussein, Desmet, François-Olivier, Chakrama, Fatima Zahra, Moreno-Garcia, Maira Alejandra, Goillot, Evelyne, Janczarski, Stéphane, Mortreux, Franck, Bourgeois, Cyril F, Auboeuf, Didier

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An unbiased evaluation of gene prioritization tools von BÖRNIGEN, Daniela, TRANCHEVENT, Léon-Charles, BONACHELA-CAPDEVILA, Francisco, DEVRIENDT, Koenraad, DE MOOR, Bart, DE CAUSMAECKER, Patrick, MOREAU, Yves

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Using ribosomal protein genes as reference: a tale of caution von Thorrez, Lieven, Van Deun, Katrijn, Tranchevent, Léon-Charles, Van Lommel, Leentje, Engelen, Kristof, Marchal, Kathleen, Moreau, Yves, Van Mechelen, Iven, Schuit, Frans

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A guide to web tools to prioritize candidate genes von TRANCHEVENT, Léon-Charles, CAPDEVILA, Francisco Bonachela, NITSCH, Daniela, DE MOOR, Bart, DE CAUSMAECKER, Patrick, MOREAU, Yves

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Endothelial, epithelial, and fibroblast cells exhibit specific splicing programs independently of their tissue of origin von Mallinjoud, Pierre, Villemin, Jean-Philippe, Mortada, Hussein, Polay Espinoza, Micaela, Desmet, François-Olivier, Samaan, Samaan, Chautard, Emilie, Tranchevent, Léon-Charles, Auboeuf, Didier

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Haploinsufficiency of TAB2 Causes Congenital Heart Defects in Humans von Thienpont, Bernard, Zhang, Litu, Postma, Alex V., Breckpot, Jeroen, Tranchevent, Léon-Charles, Van Loo, Peter, Møllgård, Kjeld, Tommerup, Niels, Bache, Iben, Tümer, Zeynep, van Engelen, Klaartje, Menten, Björn, Mortier, Geert, Waggoner, Darrel, Gewillig, Marc, Moreau, Yves, Devriendt, Koen, Larsen, Lars Allan

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Kernel-based data fusion for gene prioritization von De Bie, Tijl, Tranchevent, Léon-Charles, van Oeffelen, Liesbeth M. M., Moreau, Yves

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Predicting clinical outcome of neuroblastoma patients using an integrative network-based approach von Tranchevent, Léon-Charles, Nazarov, Petr V, Kaoma, Tony, Schmartz, Georges P, Muller, Arnaud, Kim, Sang-Yoon, Rajapakse, Jagath C, Azuaje, Francisco

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Network analysis of differential expression for the identification of disease-causing genes von Nitsch, Daniela, Tranchevent, Léon-Charles, Thienpont, Bernard, Thorrez, Lieven, Van Esch, Hilde, Devriendt, Koenraad, Moreau, Yves

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Large-scale benchmark of Endeavour using MetaCore maps von Schuierer, Sven, Tranchevent, Léon-Charles, Dengler, Uwe, Moreau, Yves

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PINTA: a web server for network-based gene prioritization from expression data von Nitsch, Daniela, Tranchevent, Léon-Charles, Gonçalves, Joana P., Vogt, Josef Korbinian, Madeira, Sara C., Moreau, Yves

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An expanded evaluation of protein function prediction methods shows an improvement in accuracy von Jiang, Yuxiang, Oron, Tal Ronnen, Clark, Wyatt T, Bankapur, Asma R, D'Andrea, Daniel, Lepore, Rosalba, Funk, Christopher S, Kahanda, Indika, Verspoor, Karin M, Ben-Hur, Asa, Koo, Da Chen Emily, Penfold-Brown, Duncan, Shasha, Dennis, Youngs, Noah, Bonneau, Richard, Lin, Alexandra, Sahraeian, Sayed M E, Martelli, Pier Luigi, Profiti, Giuseppe, Casadio, Rita, Cao, Renzhi, Zhong, Zhaolong, Cheng, Jianlin, Altenhoff, Adrian, Skunca, Nives, Dessimoz, Christophe, Dogan, Tunca, Hakala, Kai, Kaewphan, Suwisa, Mehryary, Farrokh, Salakoski, Tapio, Ginter, Filip, Fang, Hai, Smithers, Ben, Oates, Matt, Gough, Julian, Törönen, Petri, Koskinen, Patrik, Holm, Liisa, Chen, Ching-Tai, Hsu, Wen-Lian, Bryson, Kevin, Cozzetto, Domenico, Minneci, Federico, Jones, David T, Chapman, Samuel, Bkc, Dukka, Khan, Ishita K, Kihara, Daisuke, Ofer, Dan, Rappoport, Nadav, Stern, Amos, Cibrian-Uhalte, Elena, Denny, Paul, Foulger, Rebecca E, Hieta, Reija, Legge, Duncan, Lovering, Ruth C, Magrane, Michele, Melidoni, Anna N, Mutowo-Meullenet, Prudence, Pichler, Klemens, Shypitsyna, Aleksandra, Li, Biao, Zakeri, Pooya, ElShal, Sarah, Tranchevent, Léon-Charles, Das, Sayoni, Dawson, Natalie L, Lee, David, Lees, Jonathan G, Sillitoe, Ian, Bhat, Prajwal, Nepusz, Tamás, Romero, Alfonso E, Sasidharan, Rajkumar, Yang, Haixuan, Paccanaro, Alberto, Gillis, Jesse, Sedeño-Cortés, Adriana E, Pavlidis, Paul, Feng, Shou, Cejuela, Juan M, Goldberg, Tatyana, Hamp, Tobias, Richter, Lothar, Salamov, Asaf, Gabaldon, Toni, Marcet-Houben, Marina, Supek, Fran, Gong, Qingtian, Ning, Wei, Zhou, Yuanpeng, Tian, Weidong, Falda, Marco, Fontana, Paolo, Lavezzo, Enrico, Toppo, Stefano, Ferrari, Carlo, Giollo, Manuel

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Optimized data fusion for K-means Laplacian clustering von Yu, Shi, Liu, Xinhai, Tranchevent, Léon-Charles, Glänzel, Wolfgang, Suykens, Johan A. K., De Moor, Bart, Moreau, Yves

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