Author

Shawn A. Levy

HudsonAlpha Institute for Biotechnology

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· 2 Bioinformatics· 1 Genetic & Genomic Medicine· 1

Signature Assays, Organisms & Methods

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Organism:human· 3 Research Focus:variant calling· 3 Research Focus:gene regulatory network inference· 2 Assay:long-read sequencing· 2 Approach:statistical model· 2 Assay:whole-genome sequencing· 2 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1

Frequent Co-Authors

Chelsea Berngruber· 2 shared Donna Marie MuznyiD· 2 shared Evan E. EichleriD· 2 shared Fritz Joachim SedlazeckiD· 2 shared Hang SuiD· 2 shared Kimberly Floy DohenyiD· 2 shared Kiran V. GarimellaiD· 2 shared Namrata GuptaiD· 2 shared

Activity by Year

2022-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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2 shared papersBioinformatics

Chelsea Berngruber

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Author profile →

4 papers

Recent·Most cited

Himito: a Graph-based Toolkit for Mitochondrial Genome Analysis using Long Reads

Hang Su, Yongqing Huang, Timothy Durham, Nahyun Kong, Emma M. Casey, David I. Benjamin, Sheng Chih Jin, Namrata Gupta, Niall J. Lennon, Stacey Gabriel, Shawn A. Levy, Chelsea Berngruber, Jane Grimwood, Donna Marie Muzny, Richard A. Gibbs, , Kiran V. Garimella

Himito is a graph-based toolkit for analyzing mitochondrial genomes using long reads, achieving superior performance in assembly and variant calling and revealing age-related patterns in the All of Us dataset.

Nature Communications · Sep 9, 2026Peer-reviewedBioinformatics

Population-scale Long-read Sequencing in the All of Us Research Program

Kiran V. Garimella, Qiuhui Li, Julie Wertz, Samuel K. Lee, Fabio Cunial, Yongqing Huang, Yulia Mostovoy, Ryan Lorig-Roach, Adam C. English, Hang Su, Shawn A. Levy, Donna Marie Muzny, Chelsea Berngruber, Matt Christopher Danzi, William T. Harvey, , Evan E. Eichler

The paper analyzes long-read sequencing data from the All of Us Research Program to identify structural variants and their associations with diseases in a large cohort of Black or African American participants.

medRxiv · Oct 2, 2025 · PreprintGenetic & Genomic Medicine

A simplified hybrid capture approach retains high specificity and enables PCR-free workflow

Adeline Mah, Xiaodong Qi, Junhua Zhao, Kelly N. Wiseman, Laure Edoli, Kyle S. Metcalfe, Kyle Donohoe, Micah T. Ojeda, Sophie Billings, Juan Moreno, Marina McCowin, Ben Krajacich, Kevin Green, Ramkrishna Adhikary, Andrew M. Boddicker, , Michael J. R. Previte

This paper introduces a simplified hybrid capture method that eliminates PCR and bead-based steps while maintaining specificity and improving variant calling.

BMC Genomics · Sep 2, 2025Peer-reviewedGenomics

Betacoronavirus-specific alternate splicing

Guy Karlebach, Bruce J. Aronow, Stephen B. Baylin, Daniel Butler, Jonathan Foox, Shawn A. Levy, Cem Meydan, Christopher Mozsary, Amanda Saravia-Butler, Deanne M. Taylor, Eve Syrkin Wurtele, Christopher E. Mason, Afshin Beheshti, Peter N. Robinson

The paper investigates differential alternative splicing in cells infected by betacoronaviruses and finds characteristic patterns linked to viral load and gene function.

Genomics · Jan 22, 2022Peer-reviewedGenomics