Nathan Smits

@article{ewing_nanopore_2020,

title = {Nanopore Sequencing Enables Comprehensive Transposable Element Epigenomic Profiling},

author = {Adam D Ewing and Nathan Smits and Francisco J Sanchez-Luque and Jamila Faivre and Paul M Brennan and Sandra R Richardson and Seth W Cheetham and Geoffrey J Faulkner},

url = {http://www.sciencedirect.com/science/article/pii/S1097276520307310},

doi = {10.1016/j.molcel.2020.10.024},

issn = {1097-2765},

year  = {2020},

date = {2020-01-01},

urldate = {2020-11-30},

journal = {Molecular Cell},

abstract = {Transposable elements (TEs) drive genome evolution and are a notable source of pathogenesis, including cancer. While CpG methylation regulates TE activity, the locus-specific methylation landscape of mobile human TEs has to date proven largely inaccessible. Here, we apply new computational tools and long-read nanopore sequencing to directly infer CpG methylation of novel and extant TE insertions in hippocampus, heart, and liver, as well as paired tumor and non-tumor liver. As opposed to an indiscriminate stochastic process, we find pronounced demethylation of young long interspersed element 1 (LINE-1) retrotransposons in cancer, often distinct to the adjacent genome and other TEs. SINE-VNTR-Alu (SVA) retrotransposons, including their internal tandem repeat-associated CpG island, are near-universally methylated. We encounter allele-specific TE methylation and demethylation of aberrantly expressed young LINE-1s in normal tissues. Finally, we recover the complete sequences of tumor-specific LINE-1 insertions and their retrotransposition hallmarks, demonstrating how long-read sequencing can simultaneously survey the epigenome and detect somatic TE mobilization.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{beaton_community-led_2018,

title = {Community-led comparative genomic and phenotypic analysis of the aquaculture pathogen Pseudomonas baetica a390T sequenced by Ion semiconductor and Nanopore technologies},

author = {Ainsley Beaton and C\'{e}dric Lood and Edward Cunningham-Oakes and Alison MacFadyen and Alex J Mullins and Walid El Bestawy and Jo\~{a}o Botelho and Sylvie Chevalier and Shannon Coleman and Chloe Dalzell and Stephen K Dolan and Alberto Faccenda and Maarten G K Ghequire and Steven Higgins and Alexander Kutschera and Jordan Murray and Martha Redway and Talal Salih and Ana C da Silva and Brian A Smith and Nathan Smits and Ryan Thomson and Stuart Woodcock and Martin Welch and Pierre Cornelis and Rob Lavigne and Vera van Noort and Nicholas P Tucker},

url = {https://academic.oup.com/femsle/article/365/9/fny069/4951603},

doi = {10.1093/femsle/fny069},

issn = {0378-1097},

year  = {2018},

date = {2018-05-01},

urldate = {2019-06-26},

journal = {FEMS Microbiol Lett},

volume = {365},

number = {9},

abstract = {Here, we present the high-quality draft genome of Pseudomonas baetica, a bacterial pathogen that has been demonstrated to cause disease in fish cultivated in aq},

keywords = {},

pubstate = {published},

tppubtype = {article}

}