Timothy Gilpatrick
Johns Hopkins University
9 Papers
48 Citations
Timothy Gilpatrick is an academic researcher from Johns Hopkins University. The author has contributed to research in topics: Nanopore sequencing & DNA methylation. The author has an hindex of 7, co-authored 9 publications. Previous affiliations of Timothy Gilpatrick include Johns Hopkins University School of Medicine.
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Papers
Nanopore native RNA sequencing of a human poly(A) transcriptome.
Rachael E. Workman,Alison D. Tang,Paul S. Tang,Miten Jain,John R. Tyson,Roham Razaghi,Philip C. Zuzarte,Timothy Gilpatrick,Alexander Payne,Joshua Quick,Norah Sadowski,Nadine Holmes,Jaqueline Goes de Jesus,Karen Jones,Cameron M. Soulette,Terrance P. Snutch,Nicholas J. Loman,Benedict Paten,Matthew Loose,Jared T. Simpson,Jared T. Simpson,Hugh E. Olsen,Angela N. Brooks,Mark Akeson,Winston Timp +24 more
TL;DR: This study generated 9.9 million aligned sequence reads for the human cell line GM12878, using thirty MinION flow cells at six institutions to identify 33,984 plausible RNA isoforms and describes strategies for assessing 3′ poly(A) tail length, base modifications and transcript haplotypes.
Targeted nanopore sequencing with Cas9-guided adapter ligation
Timothy Gilpatrick,Isac Lee,James E. Graham,Etienne Raimondeau,Rebecca Bowen,Andrew John Heron,Bradley M. Downs,Saraswati Sukumar,Fritz J. Sedlazeck,Winston Timp +9 more
TL;DR: N nanopore Cas9-targeted sequencing (nCATS), an enrichment strategy that uses targeted cleavage of chromosomal DNA with Cas9 to ligate adapters for nanopore sequencing, is described and shown that nCATS can simultaneously assess haplotype-resolved single-nucleotide variants, structural variations and CpG methylation.
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Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing.
Isac Lee,Roham Razaghi,Timothy Gilpatrick,Michael Molnar,Ariel Gershman,Norah Sadowski,Fritz J. Sedlazeck,Kasper D. Hansen,Jared T. Simpson,Jared T. Simpson,Winston Timp +10 more
TL;DR: This study uses nanopore sequencing to evaluate CpG methylation and chromatin accessibility simultaneously on long strands of DNA by applying GpC methyltransferase to exogenously label open chromatin, and applies this to a breast cancer model to evaluate differentialmethylation and accessibility between cancerous and non-cancerous cells.
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Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing
TL;DR: This study combines the ability of NOMe-seq to simultaneously evaluate CpG methylation and chromatin accessibility, with long-read nanopore sequencing technology, a method they call nanoNOMe.
Nanopore native RNA sequencing of a human poly(A) transcriptome
Rachael E. Workman,Alison D. Tang,Paul S. Tang,Miten Jain,John R. Tyson,Philip C. Zuzarte,Timothy Gilpatrick,Roham Razaghi,Joshua Quick,Norah Sadowski,Nadine Holmes,Jaqueline Goes de Jesus,Karen Jones,Terrance P. Snutch,Nicholas J. Loman,Benedict Paten,Matthew Loose,Jared T. Simpson,Jared T. Simpson,Hugh E. Olsen,Angela N. Brooks,Mark Akeson,Winston Timp +22 more
TL;DR: This study focused on poly(A) RNA from the human cell line GM12878, generating 9.9 million aligned sequence reads, which had an aligned N50 length of 1294 bases, and a maximum aligned length of over 21,000 bases.