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SIMBA: single-cell embedding along with features.
Nat Methods. 2023 May 29. doi: 10.1038/s41592-023-01899-8. Online ahead of print.
Nat Methods. 2023.
PMID: 37248389
CRISPR-suppressor scanning reveals a nonenzymatic role of LSD1 in AML.
Vinyard ME, Su C, Siegenfeld AP, Waterbury AL, Freedy AM, Gosavi PM, Park Y, Kwan EE, Senzer BD, Doench JG, Bauer DE, Pinello L, Liau BB.
Vinyard ME, et al.
Nat Chem Biol. 2019 May;15(5):529-539. doi: 10.1038/s41589-019-0263-0. Epub 2019 Apr 15.
Nat Chem Biol. 2019.
PMID: 30992567
Free PMC article.
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Assessment of computational methods for the analysis of single-cell ATAC-seq data.
Chen H, Lareau C, Andreani T, Vinyard ME, Garcia SP, Clement K, Andrade-Navarro MA, Buenrostro JD, Pinello L.
Chen H, et al. Among authors: vinyard me.
Genome Biol. 2019 Nov 18;20(1):241. doi: 10.1186/s13059-019-1854-5.
Genome Biol. 2019.
PMID: 31739806
Free PMC article.
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Current progress and potential opportunities to infer single-cell developmental trajectory and cell fate.
Wang L, Zhang Q, Qin Q, Trasanidis N, Vinyard M, Chen H, Pinello L.
Wang L, et al.
Curr Opin Syst Biol. 2021 Jun;26:1-11. doi: 10.1016/j.coisb.2021.03.006. Epub 2021 Mar 26.
Curr Opin Syst Biol. 2021.
PMID: 33997529
Free PMC article.
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singlecellVR: Interactive Visualization of Single-Cell Data in Virtual Reality.
Stein DF, Chen H, Vinyard ME, Qin Q, Combs RD, Zhang Q, Pinello L.
Stein DF, et al. Among authors: vinyard me.
Front Genet. 2021 Oct 28;12:764170. doi: 10.3389/fgene.2021.764170. eCollection 2021.
Front Genet. 2021.
PMID: 34777482
Free PMC article.
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Integrative dissection of gene regulatory elements at base resolution.
Chen Z, Javed N, Moore M, Wu J, Sun G, Vinyard M, Collins A, Pinello L, Najm FJ, Bernstein BE.
Chen Z, et al.
Cell Genom. 2023 Apr 28;3(6):100318. doi: 10.1016/j.xgen.2023.100318. eCollection 2023 Jun 14.
Cell Genom. 2023.
PMID: 37388913
Free PMC article.
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Defining and benchmarking open problems in single-cell analysis.
Luecken MD, Gigante S, Burkhardt DB, Cannoodt R, Strobl DC, Markov NS, Zappia L, Palla G, Lewis W, Dimitrov D, Vinyard ME, Magruder DS, Andersson A, Dann E, Qin Q, Otto DJ, Klein M, Botvinnik OB, Deconinck L, Waldrant K; Open Problems Jamboree Members; Bloom JM, Pisco AO, Saez-Rodriguez J, Wulsin D, Pinello L, Saeys Y, Theis FJ, Krishnaswamy S.
Luecken MD, et al. Among authors: vinyard me.
Res Sq [Preprint]. 2024 Apr 4:rs.3.rs-4181617. doi: 10.21203/rs.3.rs-4181617/v1.
Res Sq. 2024.
PMID: 38645152
Free PMC article.
Preprint.
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A molecular glue approach to control the half-life of CRISPR-based technologies.
Sreekanth V, Jan M, Zhao KT, Lim D, Davis JR, McConkey M, Kovalcik V, Barkal S, Law BK, Fife J, Tian R, Vinyard ME, Becerra B, Kampmann M, Sherwood RI, Pinello L, Liu DR, Ebert BL, Choudhary A.
Sreekanth V, et al. Among authors: vinyard me.
bioRxiv [Preprint]. 2023 Mar 20:2023.03.12.531757. doi: 10.1101/2023.03.12.531757.
bioRxiv. 2023.
PMID: 36945568
Free PMC article.
Preprint.
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