An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Authors: 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, Emily, Penfold-Brown, Duncan, Shasha, Dennis, Youngs, Noah, Bonneau, Richard, Lin, Alexandra, Sahraeian, Sayed ME, 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, C., Dukka B K., 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, Piovesan, Damiano, Tosatto, Silvio, del Pozo, Angela, Fernández, José M, Maietta, Paolo, Valencia, Alfonso, Tress, Michael L, Benso, Alfredo, Di Carlo, Stefano, Politano, Gianfranco, Savino, Alessandro, Rehman, Hafeez Ur, Re, Matteo, Mesiti, Marco, Valentini, Giorgio, Bargsten, Joachim W, van Dijk, Aalt DJ, Gemovic, Branislava, Glisic, Sanja, Perovic, Vladmir, Veljkovic, Veljko, Veljkovic, Nevena, Almeida-e-Silva, Danillo C, Vencio, Ricardo ZN, Sharan, Malvika, Vogel, Jörg, Kansakar, Lakesh, Zhang, Shanshan, Vucetic, Slobodan, Wang, Zheng, Sternberg, Michael JE, Wass, Mark N, Huntley, Rachael P, Martin, Maria J, O'Donovan, Claire, Robinson, Peter N, Moreau, Yves, Tramontano, Anna, Babbitt, Patricia C, Brenner, Steven E, Linial, Michal, Orengo, Christine A, Rost, Burkhard, Greene, Casey S, Mooney, Sean D, Friedberg, Iddo, Radivojac, Predrag

Subject Terms: Quantitative Biology - Quantitative Methods

Access URL: http://arxiv.org/abs/1601.00891

Interplay between coding and exonic splicing regulatory sequences

Authors: Fontrodona, Nicolas, Aubé, Fabien, Claude, Jean-Baptiste, Polvèche, Hélène, Lemaire, Sébastien, Tranchevent, Léon-Charles, Modolo, Laurent, Mortreux, Franck, Bourgeois, Cyril F., Auboeuf, Didier

Source: Genome research. 29(5):711-722

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN620188989&indx=1&recIds=ETOCRN620188989

Predicting clinical outcome of neuroblastoma patients using an integrative network-based approach

Authors: Tranchevent, Léon-Charles, Nazarov, Petr V., Kaoma, Tony, Schmartz, Georges P., Muller, Arnaud, Kim, Sang-Yoon, Rajapakse, Jagath C., Azuaje, Francisco

Source: Biology direct. 13(1):1-13

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100164863349.0x000001&indx=1&recIds=ETOCvdc_100164863349.0x000001

Identification of protein features encoded by alternative exons using Exon Ontology

Authors: Tranchevent, Léon-Charles, Aubé, Fabien, Dulaurier, Louis, Benoit-Pilven, Clara, Rey, Amandine, Poret, Arnaud, Chautard, Emilie, Mortada, Hussein, Desmet, François-Olivier, Chakrama, Fatima Zahra

Source: Genome research. 27(6):1087-1097

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN611588895&indx=1&recIds=ETOCRN611588895

RNA Helicases DDX5 and DDX17 Dynamically Orchestrate Transcription, miRNA, and Splicing Programs in Cell Differentiation

Authors: 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

Source: In Cell Reports 26 June 2014 7(6):1900-1913

A deep neural network approach to predicting clinical outcomes of neuroblastoma patients.

Authors: Tranchevent, Léon-Charles^1,2 (AUTHOR), Azuaje, Francisco^1,3 (AUTHOR), Rajapakse, Jagath C.⁴ (AUTHOR) asjagath@ntu.edu.sg

Source: BMC Medical Genomics. 12/20/2019 Supplement 8, Vol. 12, p1-11. 11p.

Subject Terms: *ARTIFICIAL neural networks, *FEATURE extraction, *SUPPORT vector machines, *FEATURE selection, *PROGNOSIS, *DEEP learning

Haploinsufficiency of TAB2 Causes Congenital Heart Defects in Humans

Authors: 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

Source: In The American Journal of Human Genetics 2010 86(6):839-849

Systems level analysis of sex-dependent gene expression changes in Parkinson's disease.

Authors: Tranchevent, Léon-Charles, Halder, Rashi, Glaab, Enrico

Source: NPJ Parkinson's Disease; 1/21/2023, Vol. 9 Issue 1, p1-16, 16p

CD47 is a direct target of SNAI1 and ZEB1 and its blockade activates the phagocytosis of breast cancer cells undergoing EMT

Authors: 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

Source: Oncoimmunology. 7(4)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100071857883.0x000001&indx=1&recIds=ETOCvdc_100071857883.0x000001

Community Assessment of the Predictability of Cancer Protein and Phosphoprotein Levels from Genomics and Transcriptomics

Authors: Aderinwale, Tunde, Afyounian, Ebrahim, Agrawal, Piyush, Ali, Mehreen, Amadoz, Alicia, Azuaje, Francisco, Bachman, John, Bae, Seohui, Bhalla, Sherry, Carbonell-Caballero, José, Chakraborty, Priyanka, Chaudhary, Kumardeep, Choi, Yonghwa, Choi, Yoonjung, Çubuk, Cankut, Dhanda, Sandeep Kumar, Dopazo, Joaquín, Elo, Laura L., Fóthi, Ábel, Gevaert, Olivier, Granberg, Kirsi, Greiner, Russell, Heo, Eunji, Hidalgo, Marta R., Jayaswal, Vivek, Jeon, Hwisang, Jeon, Minji, Kalmady, Sunil V., Kambara, Yasuhiro, Kang, Jaewoo, Kang, Keunsoo, Kaoma, Tony, Kaur, Harpreet, Kazan, Hilal, Kesar, Devishi, Kesseli, Juha, Kim, Daehan, Kim, Keonwoo, Kim, Sang-Yoon, Kim, Sunkyu, Kumar, Sajal, Lee, Bora, Lee, Heewon, Liu, Yunpeng, Luethy, Roland, Mahajan, Swapnil, Mahmoudian, Mehrad, Muller, Arnaud, Nazarov, Petr V., Nguyen, Hien, Nykter, Matti, Okuda, Shujiro, Park, Sungsoo, Pal Singh Raghava, Gajendra, Rajapakse, Jagath C., Rantapero, Tommi, Ryu, Hobin, Salavert, Francisco, Saraei, Sohrab, Sharma, Ruby, Siitonen, Ari, Sokolov, Artem, Subramanian, Kartik, Suni, Veronika, Suomi, Tomi, Tranchevent, Léon-Charles, Usmani, Salman Sadullah, Välikangas, Tommi, Vega, Roberto, Zhong, Hua, Yang, Mi, Petralia, Francesca, Li, Zhi, Li, Hongyang, Ma, Weiping, Song, Xiaoyu, Yu, Han, Kaczmarczyk, Jan, Stępniak, Piotr, Warchoł, Michał, Yu, Thomas, Calinawan, Anna P., Boutros, Paul C., Payne, Samuel H., Reva, Boris, Boja, Emily, Rodriguez, Henry, Stolovitzky, Gustavo, Guan, Yuanfang, Wang, Pei, Fenyö, David, Saez-Rodriguez, Julio

Source: In Cell Systems 26 August 2020 11(2):186-195

A bioinformatics e-dating story: computational prediction and prioritization of receptor-ligand pairs

Authors: Iacucci Ernesto, Tranchevent Léon-Charles, Popovic Dusan, Pavlopoulos Georgios A, De Moor Bart, Schneider Reinhard, Moreau Yves

Source: BMC Bioinformatics, Vol 13, Iss Suppl 18, p A7 (2012)

Subject Terms: Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1471-2105

Access URL: https://doaj.org/article/85ee348ca7f94ea19b45449b0edab11d

Computational tools for prioritizing candidate genes: boosting disease gene discovery.

Authors: Moreau, Yves¹, Tranchevent, Léon-Charles¹

Source: Nature Reviews Genetics. Aug2012, Vol. 13 Issue 8, p523-536. 14p. 4 Diagrams, 1 Chart.

Subject Terms: *BIOLOGISTS, *PROTEINS, *MEDICAL literature, *GENE expression, *DEVELOPMENTAL stability (Genetics)

Optimized data fusion for K-means Laplacian clustering.

Authors: Yu, Shi, Liu, Xinhai, Tranchevent, Léon-Charles

Source: Bioinformatics; January 1 2011, Vol. 27 Issue 1, p118-126, 9p

Network Analysis of Differential Expression for the Identification of Disease-Causing Genes.

Authors: Nitsch, Daniela¹ Daniela.Nitsch@esat.kuleuven.be, Tranchevent, Léon-Charles¹, Thienpont, Bernard², Thorrez, Lieven¹, Van Esch, Hilde², Devriendt, Koenraad², Moreau, Yves¹

Source: PLoS ONE. 2009, Vol. 4 Issue 5, p1-12. 12p. 1 Diagram, 2 Graphs.

Subject Terms: *GENES, *GENETICS, *CHROMOSOMES, *PHENOTYPES, *GENE expression, *PROTEINS, *PROTEIN-protein interactions, *LAPLACIAN operator, *RANDOM walks

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BMPR1A is a candidate gene for congenital heart defects associated with the recurrent 10q22q23 deletion syndrome

Authors: Breckpot, Jeroen, Tranchevent, Léon-Charles, Thienpont, Bernard, Bauters, Marijke, Troost, Els, Gewillig, Marc, Vermeesch, Joris R., Moreau, Yves, Devriendt, Koenraad, Van Esch, Hilde

Source: In European Journal of Medical Genetics January 2012 55(1):12-16

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