Author

Benjamin J. Patty

University of PittsburghORCID 0000-0002-8244-5112Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Genomics· 1 Immunology· 1 Systems Biology· 1

Signature Assays, Organisms & Methods

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

Frequent Co-Authors

Sarah J. HaineriD· 2 shared Aamir Khan· 1 shared Ananda N. Rankin· 1 shared Andrew J. MonteithiD· 1 shared Ashley D. WiseiD· 1 shared Asya SmirnoviD· 1 shared Benjamin L. AllsupiD· 1 shared Braulio BonillaiD· 1 shared

Activity by Year

2025-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 29 mutual co-author links

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2 shared papersGenomics

Sarah J. HainerORCID

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3 papers

Recent·Most cited

ImmunologybioRxivPreprintMay 21, 2026

Neutrophils repurpose the nucleolus as a cytokine reservoir and secretory organelle

Shuying Xu, Asya Smirnov, Rachel L. Kinsella…·Christina M Stallings

The paper shows neutrophils store and release IFN-I from the nucleolus, revealing a new role for nucleolar stress in immune responses.

DOI 10.64898/2026.05.18.726057

humanproteomics

𝕏 PostBluesky

GenomicsGeneticsPeer-reviewedFeb 5, 2026

esBAF and INO80C fine-tune subcompartments and differentially regulate enhancer-promoter interactions

Braulio Bonilla, Benjamin J. Patty, Snehal Sambare…·Sarah Hainer

This study investigates the roles of esBAF and INO80C in shaping 3D genome organization in mouse embryonic stem cells, finding they influence subcompartment identity and enhancer-promoter interactions.

DOI 10.1093/genetics/iyag037

𝕏 PostBluesky

Systems BiologyCell ReportsPeer-reviewedMay 30, 2025

Widespread impact of nucleosome remodelers on transcription at cis-regulatory elements

Benjamin J. Patty, Rinku Dhungana, Sarah J. Hainer

The paper investigates how nucleosome remodelers affect transcription at cis-regulatory elements in murine ES cells, identifying novel roles and mechanisms of action for different remodelers.

13 citations

mousebulk RNA-seq

𝕏 PostBluesky