Author

Alexander T. Honkala

Oregon Health & Science UniversityORCID 0000-0002-7338-4039Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Genetics· 1 Systems Biology· 1

Signature Assays, Organisms & Methods

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Research Focus:clustering· 1 Approach:deep learning· 1 Approach:experimental assay· 1 Assay:long-read sequencing· 1 Assay:scRNA-seq· 1 Organism:virus· 1

Frequent Co-Authors

Benjamin A. PinskyiD· 1 shared Jennifer Li‐Pook‐ThaniD· 1 shared Malaya Kumar SahooiD· 1 shared Michael P. SnyderiD· 1 shared Sanjay V. MalhotraiD· 1 shared Selene BanuelosiD· 1 shared

Activity by Year

2021-2025 · peak 1/yr

Co-Author Collaboration Network

6 top collaborators · 10 mutual co-author links

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1 shared paperGenetics

Benjamin A. PinskyORCID

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2 papers

Recent·Most cited

Python Encoders for Archetypal Convex Hulls (PEACH): PyTorch-Based Archetypal Analysis

Alexander T. Honkala, Sanjay V. Malhotra

PEACH is a PyTorch-based archetype analysis tool for scRNA-seq data that identifies pure extremal cell states and their tradeoffs using a constrained autoencoder.

bioRxiv · Dec 29, 2025 · PreprintSystems Biology

Long-read sequencing of SARS-CoV-2 reveals novel transcripts and a diverse complex transcriptome landscape.

Jennifer Li‐Pook‐Than, Selene Banuelos, Alexander T. Honkala, Malaya Kumar Sahoo, Benjamin A. Pinsky, Michael P. Snyder

The paper uses long-read sequencing to identify novel SARS-CoV-2 transcripts and variants, revealing a complex transcriptome landscape.

bioRxiv · Mar 5, 2021 · PreprintGenetics