Author

Bradley K. Broyles

Purdue University West LafayetteORCID 0000-0002-3608-4491Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 2 Molecular Biology· 1

Signature Assays, Organisms & Methods

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Research Focus:differential expression· 2 Research Focus:gene regulatory network inference· 2 Assay:protein sequence· 2 Research Focus:benchmarking· 1 Approach:experimental assay· 1 Approach:graph neural network· 1 Approach:machine learning (classical)· 1 Research Focus:sequence-to-function modeling· 1

Frequent Co-Authors

Alexandre M. ErkineiD· 2 shared Andrew T. Gutierrez· 1 shared Caleb A. ClassiD· 1 shared Daisuke KiharaiD· 1 shared Daniel A. Coil· 1 shared Farhanaz FarheeniD· 1 shared Nabil IbtehaziD· 1 shared Qixin HeiD· 1 shared

Activity by Year

2023-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 21 mutual co-author links

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2 shared papersBioinformatics

Alexandre M. ErkineORCID

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3 papers

Recent·Most cited

evo3D R package: a spatial haplotype framework for structure-informed analysis of molecular evolution

Bradley K. Broyles, Qixin He

The paper introduces evo3D, an R package for structure-informed evolutionary analysis, enabling spatial haplotype extraction and diverse downstream analyses in 3D structural contexts.

Molecular Biology and Evolution · Apr 30, 2026Peer-reviewedBioinformatics

Predicting transcriptional activation domain function using Graph Neural Networks

Farhanaz Farheen, Bradley K. Broyles, Yuanyuan Zhang, Nabil Ibtehaz, Alexandre M. Erkine, Daisuke Kihara

The paper predicts transcriptional activation domain function using graph neural networks, achieving high accuracy and outperforming existing methods.

bioRxiv · May 8, 2024 · PreprintBioinformatics

Sequence features of transcriptional activation domains are consistent with the surfactant mechanism of gene activation

Bradley K. Broyles, Tamara Y. Erkina, Theodore P. Maris, Andrew T. Gutierrez, Daniel A. Coil, Thomas M. Wagner, Caleb A. Class, Alexandre M. Erkine

The paper identifies sequence features of transcriptional activation domains that enable gene activation through an amphiphilic surfactant-like mechanism.

bioRxiv · Jun 18, 2023 · PreprintMolecular Biology