Farouni R - Search Results

1

ALTRE: workflow for defining ALTered Regulatory Elements using chromatin accessibility data.

Baskin E, Farouni R, Mathé EA. Baskin E, et al. Among authors: farouni r. Bioinformatics. 2017 Mar 1;33(5):740-742. doi: 10.1093/bioinformatics/btw688. Bioinformatics. 2017. PMID: 28011773 Free PMC article.

2

ALTRE: workflow for defining ALTered regulatory elements using chromatin accessibility data.

Baskin E, Farouni R, Mathé EA. Baskin E, et al. Among authors: farouni r. Bioinformatics. 2017 Aug 15;33(16):2609. doi: 10.1093/bioinformatics/btx386. Bioinformatics. 2017. PMID: 28666331 Free PMC article. No abstract available.

3

Haystack: systematic analysis of the variation of epigenetic states and cell-type specific regulatory elements.

Pinello L, Farouni R, Yuan GC. Pinello L, et al. Among authors: farouni r. Bioinformatics. 2018 Jun 1;34(11):1930-1933. doi: 10.1093/bioinformatics/bty031. Bioinformatics. 2018. PMID: 29360936 Free PMC article.

4

AmpUMI: design and analysis of unique molecular identifiers for deep amplicon sequencing.

Clement K, Farouni R, Bauer DE, Pinello L. Clement K, et al. Among authors: farouni r. Bioinformatics. 2018 Jul 1;34(13):i202-i210. doi: 10.1093/bioinformatics/bty264. Bioinformatics. 2018. PMID: 29949956 Free PMC article.

5

CRISPR-SURF: discovering regulatory elements by deconvolution of CRISPR tiling screen data.

Hsu JY, Fulco CP, Cole MA, Canver MC, Pellin D, Sher F, Farouni R, Clement K, Guo JA, Biasco L, Orkin SH, Engreitz JM, Lander ES, Joung JK, Bauer DE, Pinello L. Hsu JY, et al. Among authors: farouni r. Nat Methods. 2018 Dec;15(12):992-993. doi: 10.1038/s41592-018-0225-6. Nat Methods. 2018. PMID: 30504875 Free PMC article.

6

CRISPResso2 provides accurate and rapid genome editing sequence analysis.

Clement K, Rees H, Canver MC, Gehrke JM, Farouni R, Hsu JY, Cole MA, Liu DR, Joung JK, Bauer DE, Pinello L. Clement K, et al. Among authors: farouni r. Nat Biotechnol. 2019 Mar;37(3):224-226. doi: 10.1038/s41587-019-0032-3. Nat Biotechnol. 2019. PMID: 30809026 Free PMC article. No abstract available.

7

TAF5L and TAF6L Maintain Self-Renewal of Embryonic Stem Cells via the MYC Regulatory Network.

Seruggia D, Oti M, Tripathi P, Canver MC, LeBlanc L, Di Giammartino DC, Bullen MJ, Nefzger CM, Sun YBY, Farouni R, Polo JM, Pinello L, Apostolou E, Kim J, Orkin SH, Das PP. Seruggia D, et al. Among authors: farouni r. Mol Cell. 2019 Jun 20;74(6):1148-1163.e7. doi: 10.1016/j.molcel.2019.03.025. Epub 2019 Apr 17. Mol Cell. 2019. PMID: 31005419 Free PMC article.

8

Model-based analysis of sample index hopping reveals its widespread artifacts in multiplexed single-cell RNA-sequencing.

Farouni R, Djambazian H, Ferri LE, Ragoussis J, Najafabadi HS. Farouni R, et al. Nat Commun. 2020 Jun 1;11(1):2704. doi: 10.1038/s41467-020-16522-z. Nat Commun. 2020. PMID: 32483174 Free PMC article.

9

Legacy Data Confound Genomics Studies.

Anderson-Trocmé L, Farouni R, Bourgey M, Kamatani Y, Higasa K, Seo JS, Kim C, Matsuda F, Gravel S. Anderson-Trocmé L, et al. Among authors: farouni r. Mol Biol Evol. 2020 Jan 1;37(1):2-10. doi: 10.1093/molbev/msz201. Mol Biol Evol. 2020. PMID: 31504792 Review.

10

Transcriptional linkage analysis with in vivo AAV-Perturb-seq.

Santinha AJ, Klingler E, Kuhn M, Farouni R, Lagler S, Kalamakis G, Lischetti U, Jabaudon D, Platt RJ. Santinha AJ, et al. Among authors: farouni r. Nature. 2023 Oct;622(7982):367-375. doi: 10.1038/s41586-023-06570-y. Epub 2023 Sep 20. Nature. 2023. PMID: 37730998 Free PMC article.

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