Author

Nova Fong

University of Colorado Anschutz

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Molecular Biology· 5 Genomics· 2 Cell Biology· 1

Signature Assays, Organisms & Methods

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Approach:experimental assay· 6 Research Focus:differential expression· 4 Research Focus:gene regulatory network inference· 4 Assay:bulk RNA-seq· 3 Organism:human· 3 Approach:statistical model· 2 Research Focus:benchmarking· 1 Research Focus:cell type annotation· 1

Frequent Co-Authors

David L. BentleyiD· 8 shared Benjamin EricksoniD· 5 shared Ryan M. SheridaniD· 3 shared J. Matthew TaliaferroiD· 2 shared A. Barbara Dirac-SvejstrupiD· 1 shared Aaron A. HoskinsiD· 1 shared Amy DentoniD· 1 shared Anthony J. SaviolaiD· 1 shared

Activity by Year

2021-2026 · peak 4/yr

Co-Author Collaboration Network

10 top collaborators · 19 mutual co-author links

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8 shared papersMolecular Biology

David L. BentleyORCID

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Author profile →

8 papers

Recent·Most cited

AI discovery of sequence rules for RNA polymerase II pausing revises the pause-release model of gene activation

Nova Fong, Nicolas Huynh, Benjamin Erickson, Ryan M. Sheridan, Srinivas Ramachandran, Mihaela van der Schaar, David L. Bentley

The paper uses AI to discover sequence rules for RNA polymerase II pausing, challenging the pause-release model of gene activation by showing pausing is not required for certain activation responses.

bioRxiv · Sep 22, 2026 · PreprintMolecular Biology

Widespread exon definition is promoted by the U1 snRNP 70K subunit and requires sites of contact with RNA Polymerase II

Nova Fong, Ryan Sheridan, Benjamin Erickson, Rui Zhao, Aaron A. Hoskins, J. Matthew Taliaferro, David L. Bentley

The paper shows that U1-70K promotes exon definition by destabilizing U1-5' SS interactions, leading to exon skipping when depleted.

bioRxiv · Sep 9, 2026 · PreprintMolecular Biology

Dynamic interaction between tentacle-tethered microdomains in Integrator and NELF regulates the promoter-proximal pause checkpoint

Daniel Blears, Pernille Bech, David Lopez Martinez, Pengfei Dai, Riyaz Shah, Nova Fong, Zhong Han, Richard Mitter, Ryan M. Sheridan, Jens Vilstrup Johansen, A. Barbara Dirac-Svejstrup, David L. Bentley, Jesper Qualmann Svejstrup

The paper identifies a direct interaction between Integrator and NELF that regulates transcriptional pausing and premature termination.

bioRxiv · Jul 1, 2026 · PreprintCell Biology

A new phased assembly of the Antarctic spiny plunderfish provides novel insights into the evolution of the notothenioid radiation.

Jacopo Martelossi, Ksenia Krasheninnikova, Amy Denton, Jonathan M. D. Wood, Thomas C. Mathers, Richard Michael Durbin, Nova Fong, David L. Bentley, Melody Susan Clark, Iliana Bista

The paper presents a new phased assembly of the Antarctic spiny plunderfish and identifies genomic features linked to cold adaptation in notothenioids.

bioRxiv · Apr 23, 2026 · PreprintGenomics

CAR-SPLASH identifies nascent pre-mRNA structures implicated in kinetic coupling and alternative splicing

Hossein Shenasa, Nova Fong, Benjamin Erickson, Ira Alexandra Iosub, Jernej Ule, David L. Bentley

CAR-SPLASH identifies RNA kinetic switches that regulate alternative splicing based on transcription speed, with potential therapeutic applications using antisense oligonucleotides.

Proceedings of the National Academy of Sciences · Sep 29, 2025Peer-reviewedMolecular Biology

PP1 PNUTS binds the restrictor and dephosphorylates RNA pol II CTD Ser5 to stimulate transcription termination

Benjamin Erickson, Roman O Fedoryshchak, Nova Fong, Ryan M. Sheridan, Keira Y. Larson, Anthony J. Saviola, Stéphane Mouilleron, Kirk Charles Hansen, Richard Treisman, David L. Bentley

The paper identifies PP1 phosphatase activity in the PPWZ complex as essential for antisense transcription termination by dephosphorylating RNA pol II CTD Ser5.

bioRxiv · Jul 12, 2024 · PreprintMolecular Biology

Nucleotide level linkage of transcriptional elongation and polyadenylation

Joseph V. Geisberg, Zarmik Moqtaderi, Nova Fong, Benjamin Erickson, David L. Bentley, Kevin Struhl

The paper shows that Pol II elongation speed affects poly(A) site clustering and that poly(A) site clusters are linked to local elongation rates and DNA sequence elements.

eLife · Nov 24, 2022Peer-reviewedMolecular Biology

LABRAT reveals association of alternative polyadenylation with transcript localization, RNA binding protein expression, transcription speed, and cancer survival

Raeann Goering, Krysta L. Engel, Austin E. Gillen, Nova Fong, David L. Bentley, J. Matthew Taliaferro

LABRAT quantifies alternative polyadenylation (APA) and identifies its associations with RNA localization, transcription speed, cancer survival, and RNA-binding protein regulation.

BMC Genomics · Jun 26, 2021Peer-reviewedGenomics