Author

Holly L. Allen

University of Colorado BoulderORCID 0000-0002-7014-1349Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Genomics· 3 Evolutionary Biology· 1

Signature Assays, Organisms & Methods

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Approach:experimental assay· 3 Research Focus:genome assembly· 2 Organism:human· 2 Assay:whole-genome sequencing· 2 Assay:bulk RNA-seq· 1 Research Focus:cell type annotation· 1 Research Focus:cell-cell communication· 1 Research Focus:differential expression· 1

Frequent Co-Authors

Edward B. ChuongiD· 4 shared Atma M. IvanceviciD· 3 shared Olivia Joyner· 2 shared Andrea D. OrdoneziD· 1 shared Arturo Barbachano-GuerreroiD· 1 shared Ashley AgyepongiD· 1 shared Benjamin Guy BitleriD· 1 shared Cody J. WarreniD· 1 shared

Activity by Year

2024-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 27 mutual co-author links

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4 shared papersGenomics

Edward B. ChuongORCID

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4 papers

Recent·Most cited

An ancient retrotransposon provides species-specific tuning of IL-18 inflammatory signaling

Andrea D. Ordonez, Holly L. Allen, Lynn Sanford, Atma M. Ivancevic, Ashley Agyepong, Mia Chaw, James P. Bridges, Tony Schountz, Edward B. Chuong

The paper identifies an ancient retrotransposon-derived IL18R1-Short isoform that modulates IL-18 signaling across species.

bioRxiv · May 26, 2026 · PreprintEvolutionary Biology

First whole genome assembly of Python regius (ball python), a model of extreme physiological and metabolic plasticity

Dakota R. Hunt, Holly L. Allen, Thomas G. Martin, Sophia N. Feghali, Edward B. Chuong, Leslie Anne Leinwand

The paper assembles and annotates the first whole genome of the ball python (Python regius), providing a high-quality resource for studying snake-specific traits and physiological adaptations.

G3 Genes Genomes Genetics · Sep 2, 2025Peer-reviewedGenomics

De novo genome assemblies of the dwarf honey bee subgenus Micrapis: Apis andreniformis and Apis florea

Atma M. Ivancevic, Madison Sankovitz, Holly L. Allen, Olivia Joyner, Edward B. Chuong, Samuel Ramsey

The paper presents high-quality de novo genome assemblies for two dwarf honey bee species using hybrid sequencing, showing improved contiguity and completeness compared to previous studies.

bioRxiv · Apr 1, 2025 · PreprintGenomics

Regulation of interferon signaling by transposon exonization

Giulia Irene Maria Pasquesi, Holly L. Allen, Atma M. Ivancevic, Arturo Barbachano-Guerrero, Olivia Joyner, Kejun Guo, David M. Simpson, Keala Gapin, Isabella Horton, Lily L. Nguyen, Qing Yang, Cody J. Warren, Liliana Florea, Benjamin Guy Bitler, Mario L. Santiago, , Edward B. Chuong

The paper identifies transposon exonization as a mechanism regulating interferon signaling by generating functional variants of immune genes, including a decoy receptor that inhibits interferon signaling.

Cell · Dec 1, 2024Peer-reviewedGenomics