Author

Kaitlyn Brokaw

University of Massachusetts Chan Medical SchoolORCID 0000-0002-8056-7108Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Assay:bulk RNA-seq· 2 Research Focus:differential expression· 2 Research Focus:gene regulatory network inference· 2 Organism:human· 2 Approach:statistical model· 2 Research Focus:database / resource· 1

Frequent Co-Authors

Athma A. PaiiD· 2 shared Eraj Shafiq KhokhariD· 2 shared Jonathan K. WattsiD· 2 shared Zachary J. KartjeiD· 2 shared Adam K. HedgeriD· 1 shared Atish A. WaghiD· 1 shared Ayush KumariD· 1 shared Ezequiel Calvo-RoitbergiD· 1 shared

Activity by Year

2025-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 40 mutual co-author links

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2 shared papersGenomics

Athma A. PaiORCID

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2 papers

Recent·Most cited

CRYPTID-exon: streamlined detection of cryptic exons from RNA-seq data

Eraj Shafiq Khokhar, Kaitlyn Brokaw, Zachary J. Kartje, Marina Krykbaeva, Ezequiel Calvo-Roitberg, Adam K. Hedger, Jonathan Lee, Atish A. Wagh, Jonathan K. Watts, Athma A. Pai

CRYPTID-exon identifies cryptic exons in human RNA-seq data, showing their impact on mRNA stability and gene expression through ASO targeting.

bioRxiv · Dec 19, 2025 · PreprintGenomics

Pervasive noise in human splice site selection

Eraj Shafiq Khokhar, Kaitlyn Brokaw, Zachary J. Kartje, Valeria C. Sanabria, Nida Javeed, Ayush Kumar, Jonathan K. Watts, Athma A. Pai

The paper tracks splicing intermediates in human cells using ultra-deep sequencing and finds pervasive usage of low-fidelity splice sites associated with genomic features that promote splicing noise.

bioRxiv · Jul 16, 2025 · PreprintGenomics