Author

Kathryn O’Neill

Cold Spring Harbor LaboratoryORCID 0000-0002-5247-6428Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Research Focus:differential expression· 3 Organism:human· 3 Assay:bulk RNA-seq· 2 Assay:scRNA-seq· 2 Approach:statistical model· 2 Research Focus:cell type annotation· 1 Research Focus:clustering· 1 Approach:deep learning· 1

Frequent Co-Authors

Molly HammelliD· 3 shared Hemali P. PhatnaniiD· 2 shared Isobel Bolger· 2 shared Oliver H. TamiD· 2 shared Regina Shaw· 2 shared Ami K. PateliD· 1 shared Christopher A. JacksoniD· 1 shared Cláudio Gouveia RoqueiD· 1 shared

Activity by Year

2018-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 37 mutual co-author links

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3 shared papersGenomics

Molly HammellORCID

Mutual co-authors in cluster

Author profile →

3 papers

Recent·Most cited

TDP-43 dysfunction leads to the accumulation of cryptic transposable element-derived exons, crypTEs, in iPSC derived neurons and ALS/FTD patient tissues

Isobel Bolger, Regina Shaw, Oliver H. Tam, Cláudio Gouveia Roque, Christopher A. Jackson, Kathryn O’Neill, Colin M. Smith, Hemali P. Phatnani, Karthick Natarajan, Molly Hammell

This study identifies TDP-43-dependent cryptic gene-TE fusions (crypTEs) in neurons and ALS/FTD tissues, showing their association with altered gene expression and potential pathogenic effects.

bioRxiv · Jan 9, 2026 · PreprintGenomics

ALS molecular subtypes are a combination of cellular, genetic, and pathological features learned by deep multiomics classifiers

Kathryn O’Neill, Regina Shaw, Isobel Bolger, Oliver H. Tam, Hemali P. Phatnani, Molly Hammell

This study introduces DANcer, a deep learning classifier that identifies robust ALS molecular subtypes across bulk and single-cell datasets, showing they correlate with clinical features and cellular mechanisms.

Cell Reports · Mar 1, 2025Peer-reviewedGenomics

TEsmall identifies small RNAs associated with targeted inhibitor resistance in melanoma

Kathryn O’Neill, Wen‐Wei Liao, Ami K. Patel, Molly Hammell

TEsmall identifies small RNAs associated with targeted inhibitor resistance in melanoma by analyzing multiple small RNA classes in an integrated workflow.

Frontiers in Genetics · Oct 5, 2018Peer-reviewedGenomics