Author

Harsh Vardhan Dubey

University of Massachusetts AmherstORCID 0009-0003-8709-7844Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 3

Signature Assays, Organisms & Methods

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Research Focus:benchmarking· 2 Research Focus:differential expression· 2 Approach:statistical model· 2 Assay:bulk RNA-seq· 1 Research Focus:gene regulatory network inference· 1 Organism:human· 1 Assay:metabolomics· 1 Approach:simulation· 1

Frequent Co-Authors

Patrick FlahertyiD· 2 shared Collin Giguere· 1 shared Gregory FarageiD· 1 shared Guangyu ZhuiD· 1 shared Hachem SaddikiiD· 1 shared Śaunak SeniD· 1 shared Shai He· 1 shared Tingting ZhaoiD· 1 shared

Activity by Year

2020-2026 · peak 1/yr

Co-Author Collaboration Network

9 top collaborators · 14 mutual co-author links

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2 shared papersBioinformatics

Patrick FlahertyORCID

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3 papers

Recent·Most cited

BioinformaticsbioRxivPreprintAug 6, 2026

Using Shared Features Improves Metabolite Effect Estimation

Harsh Vardhan Dubey, Gregory Farage, Śaunak Sen

The paper improves metabolite effect estimation by incorporating external biological knowledge through a Bayesian hierarchical framework, showing consistent gains in both simulated and real datasets.

DOI 10.64898/2026.07.31.742124

metabolomicsstatistical model

𝕏 PostBluesky

BioinformaticsBriefings in BioinformaticsPeer-reviewedFeb 18, 2023

Identification of Significant Gene Expression Changes in Multiple Perturbation Experiments using Knockoffs

Tingting Zhao, Guangyu Zhu, Harsh Vardhan Dubey, Patrick Flaherty

The paper introduces a method to identify significant gene expression changes in multiple perturbation experiments using knockoffs and applies it to data from the LINCS program.

5 citations

humanbulk RNA-seq

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BioinformaticsBMC BioinformaticsPeer-reviewedMay 26, 2020

SCSIM: Jointly simulating correlated single-cell and bulk next-generation DNA sequencing data

Collin Giguere, Harsh Vardhan Dubey, Vishal Sarsani…·Patrick Flaherty

SCSIM simulates correlated single-cell and bulk DNA sequencing data for testing variant callers and analysis tools.

8 citations

whole-genome sequencingwhole-exome sequencing

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