Author

Matthew T. Nguyen

Virginia Commonwealth UniversityORCID 0000-0001-8826-8658Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 1

Signature Assays, Organisms & Methods

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Research Focus:benchmarking· 1 Assay:ChIP-seq· 1 Assay:DNA methylation· 1 Approach:experimental assay· 1 Research Focus:gene regulatory network inference· 1 Approach:statistical model· 1 Research Focus:variant calling· 1 Assay:whole-genome sequencing· 1

Frequent Co-Authors

Amy L. OlexiD· 1 shared Anthony C. FaberiD· 1 shared Brydon P. G. Wall· 1 shared Jonathan D. OgataiD· 1 shared Joseph L. McClayiD· 1 shared Joshua Chuck HarrelliD· 1 shared Konstantinos V. FlorosiD· 1 shared Mikhail G. DozmoroviD· 1 shared

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Amy L. OlexORCID

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1 paper

Recent·Most cited

BioinformaticsBioinformaticsPeer-reviewedFeb 28, 2026

Beyond Blacklists: A Critical Assessment of Exclusion Set Generation Strategies and Alternative Approaches

Brydon P. G. Wall, Jonathan D. Ogata, Matthew T. Nguyen…·Mikhail G. Dozmorov

The paper evaluates exclusion set generation strategies in short-read sequencing, finding that pre-generated Blacklists are hard to reproduce and proposes sponge sequences as an alternative to reduce artifacts.

DOI 10.1093/bioinformatics/btag110

ChIP-seqDNA methylation

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