Author

James L. Manley

Columbia UniversityORCID 0000-0002-8341-1459Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Molecular Biology· 4

Signature Assays, Organisms & Methods

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Assay:bulk RNA-seq· 4 Research Focus:differential expression· 4 Organism:human· 4 Approach:statistical model· 3 Research Focus:gene regulatory network inference· 2 Research Focus:cell-cell communication· 1 Approach:experimental assay· 1 Research Focus:spatial domain detection· 1

Frequent Co-Authors

Pedro Bak‐GordoniD· 2 shared Zhaoqi LiuiD· 2 shared Andrey DamianoviD· 1 shared Chia-Ho LiniD· 1 shared Douglas L. BlackiD· 1 shared Elizabeth ValenzuelaiD· 1 shared Jian ZhangiD· 1 shared Jian ZhangiD· 1 shared

Activity by Year

2024-2025 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 13 mutual co-author links

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2 shared papersMolecular Biology

Pedro Bak‐GordonORCID

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4 papers

Recent·Most cited

Multiple human enhancer RNAs contain long translated open reading frames

Pavel A. Vlasov, Koichi Ogami, Elizabeth Valenzuela, Risa Karakida Kawaguchi, Marko Jovanovic, James L. Manley

The paper identifies that ~12% of human intergenic enhancer RNAs contain long open reading frames that can be translated into proteins.

Genes & Development · Dec 1, 2025Peer-reviewedMolecular Biology

Cancer-associated SF3B1 mutation K700E causes widespread changes in U2/branchpoint recognition without altering splicing.

Andrey Damianov, Chia-Ho Lin, Jian Zhang, James L. Manley, Douglas L. Black

This study shows that the SF3B1 K700E mutation causes widespread changes in U2/branchpoint recognition without altering 3' splice site selection.

Proceedings of the National Academy of Sciences · Mar 26, 2025Peer-reviewedMolecular Biology

SUGP1 loss is the sole driver of SF3B1 hotspot mutant missplicing in cancer

Peiqi Xing, Pedro Bak‐Gordon, Jindou Xie, Jian Zhang, Zhaoqi Liu, James L. Manley

The paper identifies SUGP1 loss as the sole driver of SF3B1 hotspot mutant missplicing in cancer, while AQR loss has an indirect effect.

bioRxiv · Feb 17, 2025 · PreprintMolecular Biology

Splicing dysregulation in glioblastoma alters the function of cell migration-related genes

Minu Seong, Pedro Bak‐Gordon, Zhaoqi Liu, Peter Canoll, James L. Manley

The paper introduces a novel AS analysis method, Semi-Q, to identify GBM-specific splicing events and shows that dysregulated splicing of cell migration-related genes contributes to tumor growth and invasiveness.

Glia · Oct 24, 2024Peer-reviewedMolecular Biology