Author

A. Patrick McDeed

Fred Hutch Cancer CenterORCID 0000-0003-3380-4112Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Research Focus:differential expression· 2 Organism:human· 2 Approach:statistical model· 2 Approach:deep learning· 1 Assay:DNA methylation· 1 Research Focus:drug response / drug discovery· 1 Research Focus:gene regulatory network inference· 1 Assay:whole-genome sequencing· 1

Frequent Co-Authors

Aditya Pawar· 1 shared Akira Nair· 1 shared Alexander KroemeriD· 1 shared Alexander Netzley· 1 shared Alireza GhodsiiD· 1 shared Amber J. KilitiiD· 1 shared Amir IravaniiD· 1 shared Andrew Caleb HsiehiD· 1 shared

Activity by Year

2025-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 21 mutual co-author links

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1 shared paperBioinformatics

Aditya Pawar

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2 papers

Recent·Most cited

BioinformaticsbioRxivPreprintAug 28, 2026

Gene expression inference from cell-free DNA using uncertainty-aware deep learning

Robert D. Patton, A. Patrick McDeed, Alexander Netzley…·Gavin Ha

This paper develops a deep learning framework to infer gene expression from cell-free DNA, improving reliability and enabling functional genomics in precision oncology.

DOI 10.64898/2026.02.10.705188

humanwhole-genome sequencing

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Molecular BiologyNature CommunicationsPeer-reviewedJun 17, 2025

Circulating, cell-free methylated DNA indicates cellular sources of allograft injury after liver transplant

Megan E. McNamara, Sidharth S Jain, Kesha Oza…·Anton Wellstein

The paper uses cfDNA methylation patterns to detect allograft injury after liver transplants and identifies early-onset injury through sustained cfDNA elevation.

12 citationstop 1%

humanDNA methylation

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