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Metacells untangle large and complex single-cell transcriptome networks. BMC Bioinform. 23, 336 (2022). A paper that presents the methodology used by SCORPION to desparsify the single-cell RNA-seq data used as input.","journal-title":"BMC Bioinform."},{"key":"615_CR2","doi-asserted-by":"publisher","first-page":"e64832","DOI":"10.1371\/journal.pone.0064832","volume":"8","author":"K Glass","year":"2013","unstructured":"Glass, K. et al. Passing messages between biological networks to refine predicted interactions. PLoS One 8, e64832 (2013). This paper reports the PANDA algorithm used by SCORPION to integrate the information from single-cell RNA-seq and prior information on protein\u2013protein interaction and TF\u2013gene associations.","journal-title":"PLoS One"},{"key":"615_CR3","doi-asserted-by":"publisher","first-page":"147","DOI":"10.1038\/s41592-019-0690-6","volume":"17","author":"A Pratapa","year":"2020","unstructured":"Pratapa, A. et al. Benchmarking algorithms for gene regulatory network inference from single-cell transcriptomic data. Nat Methods. 17, 147\u2013154 (2020). This paper presents a standardized methodology to test the performance of methods for the construction of a gene regulatory network from single-cell RNA-seq data.","journal-title":"Nat Methods."},{"key":"615_CR4","doi-asserted-by":"publisher","first-page":"777","DOI":"10.1038\/s41588-019-0384-0","volume":"51","author":"L Chen","year":"2019","unstructured":"Chen, L. et al. A reinforcing HNF4-SMAD4 feed-forward module stabilizes enterocyte identity. Nat Genet. 51, 777\u2013785 (2019). This paper presents an experimental double knockout experiment used as input to validate the performance of SCORPION.","journal-title":"Nat Genet."},{"key":"615_CR5","doi-asserted-by":"publisher","first-page":"449","DOI":"10.1016\/j.stem.2022.01.014","volume":"29","author":"J Taubenschmid-Stowers","year":"2022","unstructured":"Taubenschmid-Stowers, J. et al. 8C-like cells capture the human zygotic genome activation program in vitro. Cell Stem Cell 29, 449\u2013459 (2022). This article reports an experimental transcription factor over-expression experiment used as input to validate the performance of SCORPION.","journal-title":"Cell Stem Cell"}],"container-title":["Nature Computational Science"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s43588-024-00615-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s43588-024-00615-6","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s43588-024-00615-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,3,26]],"date-time":"2024-03-26T17:04:18Z","timestamp":1711472658000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s43588-024-00615-6"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,3,8]]},"references-count":5,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2024,3]]}},"alternative-id":["615"],"URL":"https:\/\/doi.org\/10.1038\/s43588-024-00615-6","relation":{},"ISSN":["2662-8457"],"issn-type":[{"value":"2662-8457","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,3,8]]},"assertion":[{"value":"8 March 2024","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}]}}