Author

Timothy Gilpatrick

Johns Hopkins University

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Genomics· 4 Cancer Biology· 1 Molecular Biology· 1

Signature Assays, Organisms & Methods

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Approach:experimental assay· 6 Organism:human· 6 Research Focus:variant calling· 4 Research Focus:differential expression· 3 Research Focus:gene regulatory network inference· 2 Assay:long-read sequencing· 2 Assay:whole-genome sequencing· 2 Assay:ATAC-seq· 1

Frequent Co-Authors

Winston TimpiD· 5 shared Fritz Joachim SedlazeckiD· 2 shared Isac LeeiD· 2 shared Jared T. SimpsoniD· 2 shared Norah SadowskiiD· 2 shared Roham RazaghiiD· 2 shared Alexander PayneiD· 1 shared Alexis L. NorrisiD· 1 shared

Activity by Year

2019-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 26 mutual co-author links

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5 shared papersGenomics

Winston TimpORCID

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Author profile →

6 papers

Recent·Most cited

Histologic variants in bladder cancer harbor aggressive molecular features including TM4SF1 expression and a CA125+ cell state

Heiko Yang, Hanbing Song, Elizabeth Yip, Timothy Gilpatrick, Kevin Chang, Paul Allegakoen, Kevin L. Lu, Keliana S F Hui, Julia H. Pham, Corynn Kasap, Vipul Kumar, Janae Gayle, Bradley A. Stohr, Chien‐Kuang Cornelia Ding, Arun P. Wiita, , Franklin W. Huang

Single cell RNA sequencing of bladder cancer subtypes identified a CA125+ cell state linked to aggressive features and TM4SF1 as a therapeutic target.

Nature Communications · Jun 17, 2025Peer-reviewedCancer Biology

IVT generation of guideRNAs for Cas9-enrichment Nanopore Sequencing

Timothy Gilpatrick, Josh Zhiyong Wang, David Weiss, Alexis L. Norris, James R. Eshleman, Winston Timp

The paper describes a method using in vitro transcribed guideRNAs for targeted nanopore sequencing to study structural variations in pancreatic cancer cell lines.

bioRxiv · Feb 7, 2023 · PreprintMolecular Biology

Long read mitochondrial genome sequencing using Cas9-guided adaptor ligation

Amy R. Vandiver, Brittany Pielstick, Timothy Gilpatrick, Austin N. Hoang, Hillary J. Vernon, Jonathan Wanagat, Winston Timp

This paper introduces a method to sequence mtDNA using Cas9-guided adaptor ligation and nanopore long reads, enabling mutation phasing and detection of age-induced deletions in a patient with mtDNA-linked syndrome.

Mitochondrion · Jul 1, 2022Peer-reviewedGenomics

Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing

Isac Lee, Roham Razaghi, Timothy Gilpatrick, Michael M. Molnar, Ariel Gershman, Norah Sadowski, Fritz Joachim Sedlazeck, Kasper D. Hansen, Jared T. Simpson, Winston Timp

This study introduces nanoNOMe, a method combining NOMe-seq and nanopore sequencing to profile chromatin accessibility and methylation in human cell lines, revealing phased methylation, large-scale patterns, and structural variations.

Nature Methods · Nov 23, 2020Peer-reviewedGenomics

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 Góes de Jesus, Karen L. Jones, Cameron M. Soulette, , Winston Timp

The paper uses nanopore sequencing to analyze poly(A) RNA from human cells, identifying long transcripts and modifications not captured by traditional methods.

Nature Methods · Nov 18, 2019Peer-reviewedGenomics

Targeted Nanopore Sequencing with Cas9 for studies of methylation, structural variants and mutations

Timothy Gilpatrick, Isac Lee, James E. Graham, Etienne Raimondeau, Rebecca Bowen, Andrew Heron, Fritz Joachim Sedlazeck, Winston Timp

The paper introduces a targeted nanopore sequencing method using Cas9 to profile methylation, structural variants, and mutations in cancer-related genes with high coverage and low cost.

bioRxiv · Jun 4, 2019 · PreprintGenomics