Author

Akshay Agarwal

IBM (United States)ORCID 0000-0002-3075-0916Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Approach:statistical model· 3 Assay:whole-genome sequencing· 3 Research Focus:benchmarking· 2 Research Focus:gene regulatory network inference· 2 Approach:machine learning (classical)· 2 Organism:virus· 2 Organism:bacteria (other)· 1 Research Focus:differential expression· 1

Frequent Co-Authors

James H. KaufmaniD· 5 shared Ed SeaboltiD· 4 shared Gowri NayariD· 4 shared Kristen L. BeckiD· 4 shared Vandana V. MukherjeeiD· 4 shared Mark KunitomiiD· 2 shared Simone BiancoiD· 2 shared Alison Laufer HalpiniD· 1 shared

Activity by Year

2019-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 36 mutual co-author links

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5 shared papersBioinformatics

James H. KaufmanORCID

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5 papers

Recent·Most cited

Commensal or pathogen: computational vectorizing microbial genomes for de novo risk assessment and virulence feature discovery in Klebsiella pneumoniae

Kristen L. Beck, Akshay Agarwal, Alison Laufer Halpin, L. Clifford McDonald, Susannah L. McKay, Alyssa G. Kent, James H. Kaufman, Vandana V. Mukherjee, Christopher A. Elkins, Ed Seabolt

This paper predicts virulence in Klebsiella pneumoniae using expanded gene function discoveries and machine learning, achieving higher accuracy than traditional methods.

Communications Biology · Apr 17, 2025Peer-reviewedMicrobiology

Predicting Epitope Candidates for SARS-CoV-2

Akshay Agarwal, Kristen L. Beck, Sara Capponi, Mark Kunitomi, Gowri Nayar, Ed Seabolt, Gandhar K. Mahadeshwar, Simone Bianco, Vandana V. Mukherjee, James H. Kaufman

The paper predicts epitope candidates for SARS-CoV-2 by analyzing epitope sequences from related coronaviruses and identifying conserved and diverse antigen regions across 62k genomes.

Viruses · Aug 21, 2022Peer-reviewedBioinformatics

Semi-supervised identification of SARS-CoV-2 molecular targets

Kristen L. Beck, Ed Seabolt, Akshay Agarwal, Gowri Nayar, Simone Bianco, Harsha Krishnareddy, Vandana V. Mukherjee, James H. Kaufman

The paper develops a semi-supervised pipeline to annotate SARS-CoV-2 genomes, identifying molecular targets with high accuracy and scalability.

bioRxiv · May 3, 2021 · PreprintBioinformatics

Analysis and Forecasting of Global RT-PCR Primers for SARS-CoV-2

Gowri Nayar, Ed Seabolt, Mark Kunitomi, Akshay Agarwal, Kristen L. Beck, Vandana V. Mukherjee, James H. Kaufman

The paper analyzes how SARS-CoV-2 mutations affect RT-PCR primer specificity and finds a 2% monthly increase in mismatches and geographic-specific virus detection.

Scientific Reports · Apr 26, 2021Peer-reviewedBioinformatics

Survey of Public Assay Data: Opportunities and Challenges to Understanding Antimicrobial Resistance

Akshay Agarwal, Gowri Nayar, James H. Kaufman

This paper analyzes antimicrobial resistance assay data to identify biases and contradictions in training data for machine learning models.

bioRxiv · Dec 13, 2019 · PreprintBioinformatics