Author

Daniela Q. James

Pennsylvania State UniversityORCID 0009-0008-1703-0536Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Genomics· 2 Bioinformatics· 1

Signature Assays, Organisms & Methods

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Assay:ChIP-seq· 3 Approach:deep learning· 2 Organism:human· 2 Organism:mouse· 2 Research Focus:differential expression· 1 Approach:experimental assay· 1 Research Focus:gene regulatory network inference· 1 Research Focus:variant calling· 1

Frequent Co-Authors

Shaun MahonyiD· 3 shared Alexis MorrisseyiD· 2 shared B. Franklin PughiD· 1 shared C Caiden Cannon· 1 shared Jeffrey ShiiD· 1 shared Jianyu YangiD· 1 shared Minoru S.H. KoiD· 1 shared Nitika Badjatia· 1 shared

Activity by Year

2023-2025 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 26 mutual co-author links

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3 shared papersGenomics

Shaun MahonyORCID

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3 papers

Recent·Most cited

GenomicsG3 Genes Genomes GeneticsPeer-reviewedNov 7, 2025

Optimized ChIP-exo for mammalian cells and patterned sequencing flow cells

Daniela Q. James, Sohini Mukherjee, C Caiden Cannon, Shaun Mahony

This paper introduces an optimized ChIP-exo protocol for mammalian cells, improving efficiency and compatibility with modern sequencing platforms.

2 citations

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BioinformaticsGenome ResearchPeer-reviewedJun 1, 2024

Allo: Accurate allocation of multi-mapped reads enables regulatory element analysis at repeats

Alexis Morrissey, Jeffrey Shi, Daniela Q. James, Shaun Mahony

Allo improves regulatory element analysis in repetitive regions by accurately allocating multi-mapped reads, leading to the discovery of new peaks and interactions in ChIP-seq data.

11 citations

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GenomicsbioRxivPreprintOct 6, 2023

Joint sequence & chromatin neural networks characterize the differential abilities of Forkhead transcription factors to engage inaccessible chromatin

Sonny Arora, Jianyu Yang, Tomohiko Akiyama…·Shaun Mahony

The paper investigates how sequence preferences and chromatin environments influence Fox TF binding using neural networks and mouse stem cells.

8 citations

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