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Structural and non-coding variants increase the diagnostic yield of clinical whole genome sequencing for rare diseases.
Genome Med. 2023 Nov 9;15(1):94. doi: 10.1186/s13073-023-01240-0.
Genome Med. 2023.
PMID: 37946251
Free PMC article.
CATCH-UP: A High-Throughput Upstream-Pipeline for Bulk ATAC-Seq and ChIP-Seq Data.
Riva SG, Georgiades E, Gur ER, Baxter M, Hughes JR.
Riva SG, et al.
J Vis Exp. 2023 Sep 22;(199). doi: 10.3791/65633.
J Vis Exp. 2023.
PMID: 37811941
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GTAC enables parallel genotyping of multiple genomic loci with chromatin accessibility profiling in single cells.
Turkalj S, Jakobsen NA, Groom A, Metzner M, Riva SG, Gür ER, Usukhbayar B, Salazar MA, Hentges LD, Mickute G, Clark K, Sopp P, Davies JOJ, Hughes JR, Vyas P.
Turkalj S, et al. Among authors: riva sg.
Cell Stem Cell. 2023 May 4;30(5):722-740.e11. doi: 10.1016/j.stem.2023.04.012.
Cell Stem Cell. 2023.
PMID: 37146586
Free article.
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MLL-AF4 cooperates with PAF1 and FACT to drive high-density enhancer interactions in leukemia.
Crump NT, Smith AL, Godfrey L, Dopico-Fernandez AM, Denny N, Harman JR, Hamley JC, Jackson NE, Chahrour C, Riva S, Rice S, Kim J, Basrur V, Fermin D, Elenitoba-Johnson K, Roeder RG, Allis CD, Roberts I, Roy A, Geng H, Davies JOJ, Milne TA.
Crump NT, et al.
Nat Commun. 2023 Aug 25;14(1):5208. doi: 10.1038/s41467-023-40981-9.
Nat Commun. 2023.
PMID: 37626123
Free PMC article.
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SMaSH: a scalable, general marker gene identification framework for single-cell RNA-sequencing.
Nelson ME, Riva SG, Cvejic A.
Nelson ME, et al. Among authors: riva sg.
BMC Bioinformatics. 2022 Aug 8;23(1):328. doi: 10.1186/s12859-022-04860-2.
BMC Bioinformatics. 2022.
PMID: 35941549
Free PMC article.
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MAGNETO: Cell type marker panel generator from single-cell transcriptomic data.
Tangherloni A, Riva SG, Myers B, Buffa FM, Cazzaniga P.
Tangherloni A, et al. Among authors: riva sg.
J Biomed Inform. 2023 Nov;147:104510. doi: 10.1016/j.jbi.2023.104510. Epub 2023 Oct 4.
J Biomed Inform. 2023.
PMID: 37797704
Free article.
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Integrative Single-Cell RNA-Seq and ATAC-Seq Analysis of Human Developmental Hematopoiesis.
Ranzoni AM, Tangherloni A, Berest I, Riva SG, Myers B, Strzelecka PM, Xu J, Panada E, Mohorianu I, Zaugg JB, Cvejic A.
Ranzoni AM, et al. Among authors: riva sg.
Cell Stem Cell. 2021 Mar 4;28(3):472-487.e7. doi: 10.1016/j.stem.2020.11.015. Epub 2020 Dec 21.
Cell Stem Cell. 2021.
PMID: 33352111
Free PMC article.
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