Boyle AP - Search Results

1

Multiplexed long-read plasmid validation and analysis using OnRamp.

Mumm C, Drexel ML, McDonald TL, Diehl AG, Switzenberg JA, Boyle AP. Mumm C, et al. Among authors: boyle ap. Genome Res. 2023 May;33(5):741-749. doi: 10.1101/gr.277369.122. Epub 2023 May 8. Genome Res. 2023. PMID: 37156622 Free PMC article.

2

Deciphering ENCODE.

Diehl AG, Boyle AP. Diehl AG, et al. Among authors: boyle ap. Trends Genet. 2016 Apr;32(4):238-249. doi: 10.1016/j.tig.2016.02.002. Epub 2016 Mar 5. Trends Genet. 2016. PMID: 26962025 Review.

3

Conserved and species-specific transcription factor co-binding patterns drive divergent gene regulation in human and mouse.

Diehl AG, Boyle AP. Diehl AG, et al. Among authors: boyle ap. Nucleic Acids Res. 2018 Feb 28;46(4):1878-1894. doi: 10.1093/nar/gky018. Nucleic Acids Res. 2018. PMID: 29361190 Free PMC article.

4

Predicting the effects of SNPs on transcription factor binding affinity.

Nishizaki SS, Ng N, Dong S, Porter RS, Morterud C, Williams C, Asman C, Switzenberg JA, Boyle AP. Nishizaki SS, et al. Among authors: boyle ap. Bioinformatics. 2020 Jan 15;36(2):364-372. doi: 10.1093/bioinformatics/btz612. Bioinformatics. 2020. PMID: 31373606 Free PMC article.

5

Transposable elements contribute to cell and species-specific chromatin looping and gene regulation in mammalian genomes.

Diehl AG, Ouyang N, Boyle AP. Diehl AG, et al. Among authors: boyle ap. Nat Commun. 2020 Apr 14;11(1):1796. doi: 10.1038/s41467-020-15520-5. Nat Commun. 2020. PMID: 32286261 Free PMC article.

6

CGIMP: Real-time exploration and covariate projection for self-organizing map datasets.

Diehl AG, Boyle AP. Diehl AG, et al. Among authors: boyle ap. J Open Source Softw. 2019;4(39):1520. doi: 10.21105/joss.01520. Epub 2019 Jul 10. J Open Source Softw. 2019. PMID: 32500114 Free PMC article. No abstract available.

7

MapGL: inferring evolutionary gain and loss of short genomic sequence features by phylogenetic maximum parsimony.

Diehl AG, Boyle AP. Diehl AG, et al. Among authors: boyle ap. BMC Bioinformatics. 2020 Sep 22;21(1):416. doi: 10.1186/s12859-020-03742-9. BMC Bioinformatics. 2020. PMID: 32962625 Free PMC article.

8

Cas9 targeted enrichment of mobile elements using nanopore sequencing.

McDonald TL, Zhou W, Castro CP, Mumm C, Switzenberg JA, Mills RE, Boyle AP. McDonald TL, et al. Among authors: boyle ap. Nat Commun. 2021 Jun 11;12(1):3586. doi: 10.1038/s41467-021-23918-y. Nat Commun. 2021. PMID: 34117247 Free PMC article.

9

The Inducible lac Operator-Repressor System Is Functional in Zebrafish Cells.

Nishizaki SS, McDonald TL, Farnum GA, Holmes MJ, Drexel ML, Switzenberg JA, Boyle AP. Nishizaki SS, et al. Among authors: boyle ap. Front Genet. 2021 Jun 18;12:683394. doi: 10.3389/fgene.2021.683394. eCollection 2021. Front Genet. 2021. PMID: 34220959 Free PMC article.

10

SquiggleNet: real-time, direct classification of nanopore signals.

Bao Y, Wadden J, Erb-Downward JR, Ranjan P, Zhou W, McDonald TL, Mills RE, Boyle AP, Dickson RP, Blaauw D, Welch JD. Bao Y, et al. Among authors: boyle ap. Genome Biol. 2021 Oct 27;22(1):298. doi: 10.1186/s13059-021-02511-y. Genome Biol. 2021. PMID: 34706748 Free PMC article.

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