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Jean‐Philippe Vert

institut paoli-calmette (ipc)

65H-index
282Paper Count
1.9WCitation Count
Published Papers 34
Publication Date
Multicondition and multimodal temporal profile inference during mouse embryonic development
err2025-10-01
err0
errOAAI
errZhang, Ran; Qiu, Chengxiang; Filippova, Galina N.; Li, Gang; Shendure, Jay; Vert, Jean-Philippe; Deng, Xinxian; Noble, William Stafford; Disteche, Christine M.
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Causal Inference Methods for Combining Randomized Trials and Observational Studies: A Review
err2024-02-01
err20
errOAAI
errColnet, Benedicte; Mayer, Imke; Chen, Guanhua; Dieng, Awa; Li, Ruohong; Varoquaux, Gael; Vert, Jean -Philippe; Josse, Julie; Yang, Shu
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A benchmark of computational pipelines for single-cell histone modification data
err2023-06-20
err5
errOAAI
errRaimundo, Felix; Prompsy, Pacome; Vert, Jean-Philippe; Vallot, Celine
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Deep embedding and alignment of protein sequences
err2022-12-15
err18
errOAAI
errLlinares-Lopez, Felipe; Berthet, Quentin; Blondel, Mathieu; Teboul, Olivier; Vert, Jean-Philippe
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DeepConsensus improves the accuracy of sequences with a gap-aware sequence transformer
err2022-09-01
err56
PREAI
errBaid, Gunjan; Cook, Daniel E.; Shafin, Kishwar; Yun, Taedong; Llinares-Lopez, Felipe; Berthet, Quentin; Belyaeva, Anastasiya; Topfer, Armin; Wenger, Aaron M.; Rowell, William J.; Yang, Howard; Kolesnikov, Alexey; Ammar, Waleed; Vert, Jean-Philippe; Vaswani, Ashish; McLean, Cory Y.; Nattestad, Maria; Chang, Pi-Chuan; Carroll, Andrew
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AI-based mobile application to fight antibiotic resistance
err2021-02-19
err42
errOAAI
errPascucci, Marco; Royer, Guilhem; Adamek, Jakub; Al Asmar, Mai; Aristizabal, David; Blanche, Laetitia; Bezzarga, Amine; Boniface-Chang, Guillaume; Brunner, Alex; Curel, Christian; Dulac-Arnold, Gabriel; Fakhri, Rasheed M.; Malou, Nada; Nordon, Clara; Runge, Vincent; Samson, Franck; Sebastian, Ellen; Soukieh, Dena; Vert, Jean-Philippe; Ambroise, Christophe; Madoui, Mohammed-Amin
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Tuning parameters of dimensionality reduction methods for single-cell RNA-seq analysis
err2020-08-24
err12
errOAAI
errRaimundo, Felix; Vallot, Celine; Vert, Jean-Philippe
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Measuring significant changes in chromatin conformation with ACCOST
err2020-02-08
err17
errOAAI
errCook, Kate B.; Hristov, Borislav H.; Le Roch, Karine G.; Vert, Jean Philippe; Noble, William Stafford
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Transcriptional Programs Define Intratumoral Heterogeneity of Ewing Sarcoma at Single-Cell Resolution
err2020-02-01
err102
errOAAI
errAynaud, Marie-Ming; Mirabeau, Olivier; Gruel, Nadege; Grossetete, Sandrine; Boeva, Valentina; Durand, Simon; Surdez, Didier; Saulnier, Olivier; Zaidi, Sakina; Gribkova, Svetlana; Fouche, Aziz; Kairov, Ulykbek; Raynal, Virginie; Tirode, Franck; Gruenewald, Thomas G. P.; Bohec, Mylene; Baulande, Sylvain; Janoueix-Lerosey, Isabelle; Vert, Jean-Philippe; Barillot, Emmanuel; Delattre, Olivier; Zinovyev, Andrei
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A general and flexible method for signal extraction from single-cell RNA-seq data (vol 9, 284, 2018)
err2019-02-04
err9
errOAAI
errRisso, Davide; Perraudeau, Fanny; Gribkova, Svetlana; Dudoit, Sandrine; Vert, Jean-Philippe
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Changes in genome organization of parasite-specific gene families during the Plasmodium transmission stages
err2018-05-15
err78
errOAAI
errBunnik, Evelien M.; Cook, Kate B.; Varoquaux, Nelle; Batugedara, Gayani; Prudhomme, Jacques; Cort, Anthony; Shi, Lirong; Andolina, Chiara; Ross, Leila S.; Brady, Declan; Fidock, David A.; Nosten, Francois; Tewari, Rita; Sinnis, Photini; Ay, Ferhat; Vert, Jean-Philippe; Noble, William Stafford; Le Roch, Karine G.
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Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications
err2018-02-26
err96
errOAAI
errVan den Berge, Koen; Perraudeau, Fanny; Soneson, Charlotte; Love, Michael I.; Risso, Davide; Vert, Jean-Philippe; Robinson, Mark D.; Dudoit, Sandrine; Clement, Lieven
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A general and flexible method for signal extraction from single-cell RNA-seq data
err2018-01-18
err452
errOAAI
errRisso, Davide; Perraudeau, Fanny; Gribkova, Svetlana; Dudoit, Sandrine; Vert, Jean-Philippe
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HiC-Pro: an optimized and flexible pipeline for Hi-C data processing
err2015-12-01
err1.6K
errOAAI
errServant, Nicolas; Varoquaux, Nelle; Lajoie, Bryan R.; Viara, Eric; Chen, Chong-Jian; Vert, Jean-Philippe; Heard, Edith; Dekker, Job; Barillot, Emmanuel
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Changes in correlation between promoter methylation and gene expression in cancer
err2015-10-28
err134
errOAAI
errMoarii, Matahi; Boeva, Valentina; Vert, Jean-Philippe; Reyal, Fabien
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Φ-score: A cell-to-cell phenotypic scoring method for sensitive and selective hit discovery in cell-based assays
err2015-09-18
err4
errOAAI
errGuyon, Laurent; Lajaunie, Christian; Fer, Frederic; Bhajun, Ricky; Sulpice, Eric; Pinna, Guillaume; Campalans, Anna; Radicella, J. Pablo; Rouillier, Philippe; Mary, Melissa; Combe, Stephanie; Obeid, Patricia; Vert, Jean-Philippe; Gidrol, Xavier
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Prediction of human population responses to toxic compounds by a collaborative competition
err2015-09-01
err81
PREAI
errEduati, Federica; Mangravite, Lara M.; Wang, Tao; Tang, Hao; Bare, J. Christopher; Huang, Ruili; Norman, Thea; Kellen, Mike; Menden, Michael P.; Yang, Jichen; Zhan, Xiaowei; Zhong, Rui; Xiao, Guanghua; Xia, Menghang; Abdo, Nour; Kosyk, Oksana; Friend, Stephen; Dearry, Allen; Simeonov, Anton; Tice, Raymond R.; Rusyn, Ivan; Wright, Fred A.; Stolovitzky, Gustavo; Xie, Yang; Saez-Rodriguez, Julio; Aittokallio, Tero; Alaimo, Salvatore; Amadoz, Alicia; Ammad-ud-din, Muhammad; Azencott, Chloe-Agathe; Bacardit, Jaume; Barron, Pelham; Bernard, Elsa; Beyer, Andreas; Bin, Shao; van Boemmel, Alena; Borgwardt, Karsten; Brys, April M.; Caffrey, Brian; Chang, Jeffrey; Chang, Jungsoo; Chheda, Himanshu; Christodoulou, Eleni G.; Clement-Ziza, Mathieu; Cohen, Trevor; Cowherd, Marianne; Demeyer, Sofie; Dopazo, Joaquin; Elhard, Joel D.; Falcao, Andre O.; Ferro, Alfredo; Friedenberg, David A.; Giugno, Rosalba; Gong, Yunguo; Gorospe, Jenni W.; Granville, Courtney A.; Grimm, Dominik; Heinig, Matthias; Hernansaiz, Rosa D.; Hintsanen, Petteri; Hochreiter, Sepp; Huang, Liang-Chin; Huska, Matthew; Jaiswal, Alok; Jiao, Yunlong; Kaski, Samuel; Kaur, Ismeet; Khan, Suleiman Ali; Klambauer, Guenter; Krasnogor, Natalio; Kuhn, Michael; Kursa, Miron Bartosz; Kutum, Rintu; Lazzarini, Nicola; Lee, Inhan; Leung, Michael K. K.; Lim, Weng Khong; Liu, Charlie; Lopez, Felipe Llinares; Mammana, Alessandro; Mayr, Andreas; Michoel, Tom; Mongiovi, Misael; Moore, Jonathan D.; Mpindi, John-Patrick; Narasimhan, Ravi; Opiyo, Stephen O.; Pandey, Gaurav; Peabody, Andrea L.; Perner, Juliane; Poso, Antti; Pulvirenti, Alfredo; Rawlik, Konrad; Reinhardt, Susanne; Riffle, Carol G.; Ruderfer, Douglas; Sander, Aaron J.; Savage, Richard S.; Scornet, Erwan; Sebastian-Leon, Patricia; Sharan, Roded; Simon-Gabriel, Carl Johann; Stoven, Veronique; Sun, Jingchun; Tang, Jing; Teixeira, Ana L.; Tenesa, Albert; Vert, Jean-Philippe; Vingron, Martin; Walter, Thomas; Wennerberg, Krister; Whalen, Sean; Wisniewska, Zofia; Wu, Yonghui; Xu, Hua; Zhang, Shihua; Zhao, Junfei; Zheng, W. Jim; Dai Ziwei
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