Author

Zachary D. Stephens

Mayo Clinic

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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Bioinformatics· 2 Cancer Biology· 1 Molecular Biology· 1

Signature Assays, Organisms & Methods

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Organism:human· 4 Approach:experimental assay· 3 Assay:whole-genome sequencing· 3 Research Focus:variant calling· 2 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1 Research Focus:cancer & tumor microenvironment· 1 Research Focus:cell type annotation· 1

Frequent Co-Authors

Jean‐Pierre KocheriD· 2 shared Abbas Abdallah· 1 shared Alireza EdrakiiD· 1 shared Annapoorna VenkatachalamiD· 1 shared Arvind PandayiD· 1 shared Aydan KahrimaniD· 1 shared Brad A. Chapman· 1 shared C. Victor Jongeneel· 1 shared

Activity by Year

2015-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 17 mutual co-author links

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2 shared papersMolecular Biology

Jean‐Pierre KocherORCID

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Author profile →

4 papers

Recent·Most cited

FANCM restrains structural genome evolution and defines a synthetic lethal dependency in BRCA1-deficient breast cancer

Farah Ramadan, Sameer Bikram Shah, Ujwal Subedi, Zachary D. Stephens, Annapoorna Venkatachalam, Neelima Yadav, Vickky Pandit, Sadhana Dubey, Sarah Latka, Hugo Villanueva, Scott H. Kaufmann, Arvind Panday

This study identifies FANCM as a synthetic lethal target in BRCA1-deficient breast cancer, showing it restricts structural genome instability and links replication stress to transcriptional changes.

bioRxiv · Sep 10, 2026 · PreprintCancer Biology

CRISPR/Cas9-Mediated Excision of ALS/FTD-Causing Hexanucleotide Repeat Expansion in C9ORF72 rescues major disease mechanisms in vivo and in vitro

Katharina E. Meijboom, Abbas Abdallah, Nicholas P. Fordham, Hiroko Nagase, Tomás Rodríguez, Carolyn Kraus, Tania F. Gendron, Gopinath Krishnan, Rustam Esanov, Nadja S. Andrade, Matthew J. Rybin, Melina Ramic, Zachary D. Stephens, Alireza Edraki, Meghan Blackwood, , Christian Mueller

This study removes a hexanucleotide repeat expansion in C9ORF72 using CRISPR/Cas9 in cell and animal models, reducing disease hallmarks.

Nature Communications · Oct 21, 2022Peer-reviewedMolecular Biology

Exogene: A performant workflow for detecting viral integrations from paired-end next-generation sequencing data

Zachary D. Stephens, Daniel R. O’Brien, Mrunal K. Dehankar, Lewis Rowland Roberts, Ravishankar K. Iyer, Jean‐Pierre Kocher

Exogene detects viral integrations from paired-end sequencing data with high concordance to long-read validation, identifying new integrations in HCC samples.

PLoS ONE · Sep 22, 2021Peer-reviewedBioinformatics

Validation of Illumina’s Isaac variant calling workflow

Liudmila S. Mainzer, Brad A. Chapman, Oliver Hofmann, Gloria Rendon, Zachary D. Stephens, C. Victor Jongeneel

This paper evaluates Illumina's Isaac variant calling workflow, finding it fast with improved accuracy but noting high false positives in exomes and inability to reproduce claimed 99% sensitivity and specificity.

bioRxiv · Nov 26, 2015 · PreprintBioinformatics