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Simultaneous Single-Cell Profiling of the Transcriptome and Accessible Chromatin Using SHARE-seq.
Methods Mol Biol. 2023;2611:187-230. doi: 10.1007/978-1-0716-2899-7_11.
Methods Mol Biol. 2023.
PMID: 36807070
Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer's and Parkinson's diseases.
Corces MR, Shcherbina A, Kundu S, Gloudemans MJ, Frésard L, Granja JM, Louie BH, Eulalio T, Shams S, Bagdatli ST, Mumbach MR, Liu B, Montine KS, Greenleaf WJ, Kundaje A, Montgomery SB, Chang HY, Montine TJ.
Corces MR, et al. Among authors: bagdatli st.
Nat Genet. 2020 Nov;52(11):1158-1168. doi: 10.1038/s41588-020-00721-x. Epub 2020 Oct 26.
Nat Genet. 2020.
PMID: 33106633
Free PMC article.
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ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis.
Granja JM, Corces MR, Pierce SE, Bagdatli ST, Choudhry H, Chang HY, Greenleaf WJ.
Granja JM, et al. Among authors: bagdatli st.
Nat Genet. 2021 Mar;53(3):403-411. doi: 10.1038/s41588-021-00790-6. Epub 2021 Feb 25.
Nat Genet. 2021.
PMID: 33633365
Free PMC article.
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Author Correction: ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis.
Granja JM, Corces MR, Pierce SE, Bagdatli ST, Choudhry H, Chang HY, Greenleaf WJ.
Granja JM, et al. Among authors: bagdatli st.
Nat Genet. 2021 Jun;53(6):935. doi: 10.1038/s41588-021-00850-x.
Nat Genet. 2021.
PMID: 33790476
Free PMC article.
No abstract available.
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CasKAS: direct profiling of genome-wide dCas9 and Cas9 specificity using ssDNA mapping.
Marinov GK, Kim SH, Bagdatli ST, Higashino SI, Trevino AE, Tycko J, Wu T, Bintu L, Bassik MC, He C, Kundaje A, Greenleaf WJ.
Marinov GK, et al. Among authors: bagdatli st.
Genome Biol. 2023 Apr 21;24(1):85. doi: 10.1186/s13059-023-02930-z.
Genome Biol. 2023.
PMID: 37085898
Free PMC article.
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Systematic benchmarking of single-cell ATAC-sequencing protocols.
De Rop FV, Hulselmans G, Flerin C, Soler-Vila P, Rafels A, Christiaens V, González-Blas CB, Marchese D, Caratù G, Poovathingal S, Rozenblatt-Rosen O, Slyper M, Luo W, Muus C, Duarte F, Shrestha R, Bagdatli ST, Corces MR, Mamanova L, Knights A, Meyer KB, Mulqueen R, Taherinasab A, Maschmeyer P, Pezoldt J, Lambert CLG, Iglesias M, Najle SR, Dossani ZY, Martelotto LG, Burkett Z, Lebofsky R, Martin-Subero JI, Pillai S, Sebé-Pedrós A, Deplancke B, Teichmann SA, Ludwig LS, Braun TP, Adey AC, Greenleaf WJ, Buenrostro JD, Regev A, Aerts S, Heyn H.
De Rop FV, et al. Among authors: bagdatli st.
Nat Biotechnol. 2023 Aug 3. doi: 10.1038/s41587-023-01881-x. Online ahead of print.
Nat Biotechnol. 2023.
PMID: 37537502
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The chromatin landscape of the euryarchaeon Haloferax volcanii.
Marinov GK, Bagdatli ST, Wu T, He C, Kundaje A, Greenleaf WJ.
Marinov GK, et al. Among authors: bagdatli st.
Genome Biol. 2023 Nov 6;24(1):253. doi: 10.1186/s13059-023-03095-5.
Genome Biol. 2023.
PMID: 37932847
Free PMC article.
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