| Reference : Gene selection for optimal prediction of cell position in tissues from single-cell tr... |
| Scientific journals : Article | |||
| Life sciences : Biotechnology Life sciences : Multidisciplinary, general & others | |||
| Systems Biomedicine | |||
| http://hdl.handle.net/10993/44158 | |||
| Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics | |
| English | |
| Tanevski, Jovan [> >] | |
| Nguyen, Thin [> >] | |
| Truong, Buu [> >] | |
| Karaiskos, Nikolaos [> >] | |
| Eren, Mehmet [> >] | |
| Zhang, Xinyu [> >] | |
| Shu, Chang [> >] | |
| Hu, Ying [> >] | |
| Pham, Hoang V. V. [> >] | |
| Li, Xiaomei [> >] | |
| Le, Thuc [> >] | |
| Tarca, Adi [> >] | |
| Bhatti, Gaurav [> >] | |
| Romero, Roberto [> >] | |
| Karathanasis, Nestoras [> >] | |
| Loher, Phillipe [> >] | |
| Chen, Yang [> >] | |
| Ouyang, Zhengqing [> >] | |
| Mao, Disheng [> >] | |
| Zhang, Yuping [> >] | |
| Zand, Maryam [> >] | |
| Ruan, Jianhua [> >] | |
| Hafemeister, Christoph [> >] | |
| Qiu, Peng [> >] | |
| Tran, Duc [> >] | |
| Nguyen, Tin [> >] | |
| Gabor, Attila [> >] | |
| Yu, Thomas [> >] | |
Glaab, Enrico  [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > >] | |
| Krause, Roland [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) >] | |
| Banda, Peter [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) >] | |
| Stolovitzky, Gustavo [> >] | |
| Rajewsky, Nikolaus [> >] | |
| Saez-Rodriguez, Julio [> >] | |
| 2020 | |
| Life Science Alliance | |
| Life Science Alliance (LLC) | |
| 3 | |
| 11 | |
| e202000867 | |
| Yes (verified by ORBilu) | |
| International | |
| 2575-1077 | |
| Woodbury | |
| United States | |
| [en] transcriptomics ; single-cell ; prediction ; cell position ; 3D ; gene selection ; Drosophila ; scRNAseq ; challenge | |
| [en] Single-cell RNA-seq (scRNAseq) technologies are rapidly evolving. While very
informative, in standard scRNAseq experiments the spatial organization of the cells in the tissue of origin is lost. Conversely, spatial RNA-seq technologies designed to maintain cell localization have limited throughput and gene coverage. Mapping scRNAseq to genes with spatial information increases coverage while providing spatial location. However, methods to perform such mapping have not yet been benchmarked. To fill this gap, we organized the DREAM Single-Cell Transcriptomics challenge focused on the spatial reconstruction of cells from the Drosophila embryo from scRNAseq data, leveraging as silver standard, genes with in situ hybridization data from the Berkeley Drosophila Transcription Network Project reference atlas. The 34 participating teams used diverse algorithms for gene selection and location prediction, while being able to correctly localize clusters of cells. Selection of predictor genes was essential for this task. Predictor genes showed a relatively high expression entropy, high spatial clustering and included prominent developmental genes such as gap and pair-rule genes and tissue markers. Application of the Top-10 methods to a zebrafish embryo dataset yielded similar performance and statistical properties of the selected genes than in the Drosophila data. This suggests that methods developed in this challenge are able to extract generalizable properties of genes that are useful to accurately reconstruct the spatial arrangement of cells in tissues. | |
| Luxembourg Centre for Systems Biomedicine (LCSB): Biomedical Data Science (Glaab Group) ; Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) | |
| Researchers ; Professionals ; Students | |
| http://hdl.handle.net/10993/44158 | |
| The hyperlink to the original publication will be provided here once available. | |
| in press |
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