Author

David F. Jenkins

Boston UniversityORCID 0000-0002-7451-4288Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 2 Genetics· 1 Genomics· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 3 Approach:machine learning (classical)· 2 Research Focus:variant calling· 2 Research Focus:gene regulatory network inference· 1 Organism:human· 1 Organism:mouse· 1 Assay:scRNA-seq· 1 Research Focus:software / tool· 1

Frequent Co-Authors

William Evan JohnsoniD· 2 shared Zhongwu LaiiD· 2 shared Aleksandr Sidoruk· 1 shared Alexander M. Luong· 1 shared Brad ChapmaniD· 1 shared Brian Andrew DoughertyiD· 1 shared Britahny M. Baskin· 1 shared Camron D. BryantiD· 1 shared

Activity by Year

2017-2025 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 20 mutual co-author links

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2 shared papersGenetics

William Evan JohnsonORCID

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Author profile →

4 papers

Recent·Most cited

Atp1a2 and Kcnj9 are candidate genes underlying sensitivity to oxycodone-induced locomotor activation and withdrawal-induced anxiety-like behaviors in C57BL/6 substrains

Lisa R. Goldberg, Britahny M. Baskin, Yahia Adla, Jacob A. Beierle, Julia C. Kelliher, Emily J. Yao, Stacey L. Kirkpatrick, Eric R. Reed, David F. Jenkins, Jiayi Wu Cox, Alexander M. Luong, Kimberly P. Luttik, Julia L. Scotellaro, Timothy A. Drescher, Sydney B. Crotts, , Camron D. Bryant

Genes Brain & Behavior · Jan 13, 2025Peer-reviewedGenetics

Optimized data representation and convolutional neural network model for predicting tumor purity

Gerald J. Sun, David F. Jenkins, Pablo E. Cingolani, Jonathan R. Dry, Zhongwu Lai

Deep Purity (DePuty) uses convolutional neural networks to predict tumor purity from SNP-based copy number and minor allele frequency data without matched normals, outperforming existing methods with fewer samples.

bioRxiv · Oct 17, 2019 · PreprintBioinformatics

Interactive single cell RNA-Seq analysis with the Single Cell Toolkit (SCTK)

David F. Jenkins, Tyler Faits, Emma A. Briars, Sebastian Carrasco Pro, Steve Cunningham, Joshua David Campbell, Masanao Yajima, William Evan Johnson

The paper introduces SCTK, an interactive scRNA-Seq analysis tool with command-line and GUI interfaces for handling complex single-cell data.

bioRxiv · May 24, 2018 · PreprintBioinformatics

Prioritisation of Structural Variant Calls in Cancer Genomes

Miika J. Ahdesmaki, Brad Chapman, Pablo Cingolani, Oliver Hofmann, Aleksandr Sidoruk, Zhongwu Lai, Gennadii A. Zakharov, Mikhail Rodichenko, Mikhail Alperovich, David F. Jenkins, Thomas Hedley Carr, Daniel Stetson, Brian Andrew Dougherty, J. Carl Barrett, Justin H. Johnson

The paper introduces a tiered prioritisation approach to identify high-impact gene fusions in cancer genomes by improving variant annotation, interpretation, and visualisation.

PeerJ · Apr 4, 2017Peer-reviewedGenomics