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Community assessment of methods to deconvolve cellular composition from bulk gene expression
View ORCID ProfileBrian S. White, View ORCID ProfileAurélien de Reyniès, View ORCID ProfileAaron M. Newman, View ORCID ProfileJoshua J. Waterfall, Andrew Lamb, View ORCID ProfileFlorent Petitprez, View ORCID ProfileAlberto Valdeolivas, Yating Lin, Haojun Li, Xu Xiao, Shun Wang, Frank Zheng, View ORCID ProfileWenxian Yang, View ORCID ProfileRongshan Yu, View ORCID ProfileMartin E Guerrero-Gimenez, Carlos A Catania, View ORCID ProfileBenjamin J Lang, View ORCID ProfileSergii Domanskyi, Thomas J Bertus, View ORCID ProfileCarlo Piermarocchi, View ORCID ProfileGianni Monaco, Francesca P Caruso, View ORCID ProfileMichele Ceccarelli, Thomas Yu, Xindi Guo, John Coller, Holden Maecker, Caroline Duault, Vida Shokoohi, Shailja Patel, Joanna E Liliental, Stockard Simon, Tumor Deconvolution DREAM Challenge consortium, View ORCID ProfileJulio Saez-Rodriguez, Laura M. Heiser, View ORCID ProfileJustin Guinney, View ORCID ProfileAndrew J. Gentles
doi: https://doi.org/10.1101/2022.06.03.494221
Brian S. White
1Computational Oncology, Sage Bionetworks, Seattle, WA, USA
Aurélien de Reyniès
2Centre de Recherche des Cordeliers, INSERM U1138, Université Paris Cité, Paris, France
Aaron M. Newman
3Institute for Stem Cell Biology and Regenerative Medicine and Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
Joshua J. Waterfall
4INSERM U830 and Translational Research Department, Institut Curie, PSL Research University, Paris, France
Andrew Lamb
1Computational Oncology, Sage Bionetworks, Seattle, WA, USA
Florent Petitprez
5Programme Cartes d’Identité des Tumeurs, Ligue Nationale Contre le Cancer, Paris, France and MRC Centre for Reproductive Health, the Queen’s Medical Research Institute, University of Edinburgh, United Kingdom
Alberto Valdeolivas
6Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
Yating Lin
7Xiamen University, Xiamen, Fujian, China
Haojun Li
7Xiamen University, Xiamen, Fujian, China
Xu Xiao
7Xiamen University, Xiamen, Fujian, China
Shun Wang
8Aginome Scientific, Xiamen, Fujian, China
Frank Zheng
9AmoyDx, Xiamen, Fujian, China
Wenxian Yang
8Aginome Scientific, Xiamen, Fujian, China
Rongshan Yu
7Xiamen University, Xiamen, Fujian, China
Martin E Guerrero-Gimenez
10Institute of Biochemistry and Biotechnology, School of Medicine, National University of Cuyo, Mendoza, Argentina
Carlos A Catania
11Laboratory of Intelligent Systems (LABSIN), Engineering School, National University of Cuyo, Mendoza, Argentina
Benjamin J Lang
12Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
Sergii Domanskyi
13Michigan State University, East Lansing, MI, USA
Thomas J Bertus
13Michigan State University, East Lansing, MI, USA
Carlo Piermarocchi
13Michigan State University, East Lansing, MI, USA
Gianni Monaco
14BIOGEM Institute of Molecular Biology and Genetics, Ariano Irpino, AV, Italy
Francesca P Caruso
14BIOGEM Institute of Molecular Biology and Genetics, Ariano Irpino, AV, Italy
Michele Ceccarelli
15BIOGEM Institute of Molecular Biology and Genetics, Department of Electrical Engineering and Information Technology (DIETI), University of Naples “Federico II”, Ariano Irpino, AV, Italy
Thomas Yu
16Computational Oncology, Sage Bionetworks, Seattle, WA, USA
Xindi Guo
16Computational Oncology, Sage Bionetworks, Seattle, WA, USA
John Coller
17Stanford Functional Genomics Facility, Stanford University School of Medicine, Stanford, CA
Holden Maecker
18Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA
Caroline Duault
18Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA
Vida Shokoohi
19Stanford Functional Genomics Facility, Stanford University School of Medicine, Stanford, CA
Shailja Patel
20Translational Applications Service Center, Stanford University School of Medicine, Stanford, CA
Joanna E Liliental
20Translational Applications Service Center, Stanford University School of Medicine, Stanford, CA
Stockard Simon
21Sage Bionetworks, Seattle, WA, USA
Julio Saez-Rodriguez
22Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
Laura M. Heiser
23Department of Biomedical Engineering, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
Justin Guinney
16Computational Oncology, Sage Bionetworks, Seattle, WA, USA
Andrew J. Gentles
24Departments of Medicine, and Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
Posted June 07, 2022.
Community assessment of methods to deconvolve cellular composition from bulk gene expression
Brian S. White, Aurélien de Reyniès, Aaron M. Newman, Joshua J. Waterfall, Andrew Lamb, Florent Petitprez, Alberto Valdeolivas, Yating Lin, Haojun Li, Xu Xiao, Shun Wang, Frank Zheng, Wenxian Yang, Rongshan Yu, Martin E Guerrero-Gimenez, Carlos A Catania, Benjamin J Lang, Sergii Domanskyi, Thomas J Bertus, Carlo Piermarocchi, Gianni Monaco, Francesca P Caruso, Michele Ceccarelli, Thomas Yu, Xindi Guo, John Coller, Holden Maecker, Caroline Duault, Vida Shokoohi, Shailja Patel, Joanna E Liliental, Stockard Simon, Tumor Deconvolution DREAM Challenge consortium, Julio Saez-Rodriguez, Laura M. Heiser, Justin Guinney, Andrew J. Gentles
bioRxiv 2022.06.03.494221; doi: https://doi.org/10.1101/2022.06.03.494221
Community assessment of methods to deconvolve cellular composition from bulk gene expression
Brian S. White, Aurélien de Reyniès, Aaron M. Newman, Joshua J. Waterfall, Andrew Lamb, Florent Petitprez, Alberto Valdeolivas, Yating Lin, Haojun Li, Xu Xiao, Shun Wang, Frank Zheng, Wenxian Yang, Rongshan Yu, Martin E Guerrero-Gimenez, Carlos A Catania, Benjamin J Lang, Sergii Domanskyi, Thomas J Bertus, Carlo Piermarocchi, Gianni Monaco, Francesca P Caruso, Michele Ceccarelli, Thomas Yu, Xindi Guo, John Coller, Holden Maecker, Caroline Duault, Vida Shokoohi, Shailja Patel, Joanna E Liliental, Stockard Simon, Tumor Deconvolution DREAM Challenge consortium, Julio Saez-Rodriguez, Laura M. Heiser, Justin Guinney, Andrew J. Gentles
bioRxiv 2022.06.03.494221; doi: https://doi.org/10.1101/2022.06.03.494221
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