McCarthy DJ - Search Results

1

SSNIP-seq: A simple and rapid method for isolation of single-sperm nucleic acid for high-throughput sequencing.

Novakovic S, Tsui V, Semple T, Martelotto L, McCarthy DJ, Crismani W. Novakovic S, et al. Among authors: mccarthy dj. PLoS One. 2022 Sep 29;17(9):e0275168. doi: 10.1371/journal.pone.0275168. eCollection 2022. PLoS One. 2022. PMID: 36173986 Free PMC article.

2

Personalized genome structure via single gamete sequencing.

Lyu R, Tsui V, McCarthy DJ, Crismani W. Lyu R, et al. Among authors: mccarthy dj. Genome Biol. 2021 Apr 19;22(1):112. doi: 10.1186/s13059-021-02327-w. Genome Biol. 2021. PMID: 33874978 Free PMC article. Review.

3

sgcocaller and comapr: personalised haplotype assembly and comparative crossover map analysis using single-gamete sequencing data.

Lyu R, Tsui V, Crismani W, Liu R, Shim H, McCarthy DJ. Lyu R, et al. Among authors: mccarthy dj. Nucleic Acids Res. 2022 Nov 11;50(20):e118. doi: 10.1093/nar/gkac764. Nucleic Acids Res. 2022. PMID: 36107768 Free PMC article.

4

Classification of low quality cells from single-cell RNA-seq data.

Ilicic T, Kim JK, Kolodziejczyk AA, Bagger FO, McCarthy DJ, Marioni JC, Teichmann SA. Ilicic T, et al. Among authors: mccarthy dj. Genome Biol. 2016 Feb 17;17:29. doi: 10.1186/s13059-016-0888-1. Genome Biol. 2016. PMID: 26887813 Free PMC article.

5

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation.

McCarthy DJ, Chen Y, Smyth GK. McCarthy DJ, et al. Nucleic Acids Res. 2012 May;40(10):4288-97. doi: 10.1093/nar/gks042. Epub 2012 Jan 28. Nucleic Acids Res. 2012. PMID: 22287627 Free PMC article.

6

A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor.

Lun AT, McCarthy DJ, Marioni JC. Lun AT, et al. Among authors: mccarthy dj. F1000Res. 2016 Aug 31;5:2122. doi: 10.12688/f1000research.9501.2. eCollection 2016. F1000Res. 2016. PMID: 27909575 Free PMC article.

7

Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data.

Andrews TS, Kiselev VY, McCarthy D, Hemberg M. Andrews TS, et al. Nat Protoc. 2021 Jan;16(1):1-9. doi: 10.1038/s41596-020-00409-w. Epub 2020 Dec 7. Nat Protoc. 2021. PMID: 33288955 Review.

8

A comparison of marker gene selection methods for single-cell RNA sequencing data.

Pullin JM, McCarthy DJ. Pullin JM, et al. Among authors: mccarthy dj. Genome Biol. 2024 Feb 26;25(1):56. doi: 10.1186/s13059-024-03183-0. Genome Biol. 2024. PMID: 38409056 Free PMC article.

9

Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference.

Huang Y, McCarthy DJ, Stegle O. Huang Y, et al. Among authors: mccarthy dj. Genome Biol. 2019 Dec 13;20(1):273. doi: 10.1186/s13059-019-1865-2. Genome Biol. 2019. PMID: 31836005 Free PMC article.

10

Benchmarking single-cell RNA-sequencing protocols for cell atlas projects.

Mereu E, Lafzi A, Moutinho C, Ziegenhain C, McCarthy DJ, Álvarez-Varela A, Batlle E, Sagar, Grün D, Lau JK, Boutet SC, Sanada C, Ooi A, Jones RC, Kaihara K, Brampton C, Talaga Y, Sasagawa Y, Tanaka K, Hayashi T, Braeuning C, Fischer C, Sauer S, Trefzer T, Conrad C, Adiconis X, Nguyen LT, Regev A, Levin JZ, Parekh S, Janjic A, Wange LE, Bagnoli JW, Enard W, Gut M, Sandberg R, Nikaido I, Gut I, Stegle O, Heyn H. Mereu E, et al. Among authors: mccarthy dj. Nat Biotechnol. 2020 Jun;38(6):747-755. doi: 10.1038/s41587-020-0469-4. Epub 2020 Apr 6. Nat Biotechnol. 2020. PMID: 32518403

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