Author

Brooke Felsheim

University of North Carolina at Chapel HillORCID 0000-0001-8421-8290Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 1 Cancer Biology· 1 Genomics· 1

Signature Assays, Organisms & Methods

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Research Focus:gene regulatory network inference· 2 Organism:human· 2 Approach:statistical model· 2 Assay:bulk RNA-seq· 1 Research Focus:database / resource· 1 Research Focus:differential expression· 1 Assay:DNA methylation· 1 Approach:machine learning (classical)· 1

Frequent Co-Authors

Charles M. PerouiD· 2 shared A ArnesoniD· 1 shared Aatish ThennavaniD· 1 shared Adam D. PfefferleiD· 1 shared Alexander LobanoviD· 1 shared Anna R. MichmerhuizeniD· 1 shared Christian BruefferiD· 1 shared Daniel P. HollerniD· 1 shared

Activity by Year

2020-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 29 mutual co-author links

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2 shared papersCancer Biology

Charles M. PerouORCID

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3 papers

Recent·Most cited

Cancer BiologyCancer ResearchPeer-reviewedAug 14, 2026

Transcriptomic profiling of mouse mammary tumors enables prognostic and predictive biomarker discovery for human breast cancers

Matthew D. Sutcliffe, Kevin Raynard Mott, Tulay Yilmaz-Swenson…·Charles M. Perou

This paper uses mouse mammary tumor data to train machine learning models predicting human breast cancer survival and treatment response.

DOI 10.1158/0008-5472.can-26-0855

mousebulk RNA-seq

𝕏 PostBluesky

GenomicsCell GenomicsPeer-reviewedFeb 1, 2025

Defining the Regulatory Logic of Breast Cancer Using Single-Cell Epigenetic and Transcriptome Profiling

Matthew J. Regner, Susana García‐Recio, Aatish Thennavan…·Hector L. Franco

This study identifies regulatory elements that switch from silencers to enhancers in breast cancer cells using single-cell ATAC-seq and RNA-seq data.

16 citationstop 4%

humanscATAC-seq

𝕏 PostBluesky

BioinformaticsNAR Genomics and BioinformaticsPeer-reviewedDec 1, 2020

ConsHMM Atlas: conservation state annotations for major genomes and human genetic variation

A Arneson, Brooke Felsheim, Jennifer Chien, Jason Ernst

The paper extends the ConsHMM method to annotate conservation states for multiple genomes and human genetic variation, providing a web interface for visualization.

5 citations

humanmultiple species

𝕏 PostBluesky