Author

Candace Savonen

Alex's Lemonade Stand FoundationORCID 0000-0001-6331-7070Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Genomics· 2 Genetics· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 3 Research Focus:benchmarking· 2 Assay:bulk RNA-seq· 2 Research Focus:differential expression· 2 Organism:human· 2 Research Focus:cell type annotation· 1 Research Focus:database / resource· 1 Approach:deep learning· 1

Frequent Co-Authors

Adam Cain ResnickiD· 1 shared Adam KrayaiD· 1 shared Alex David· 1 shared Alexander R. AbbasiD· 1 shared Alice M. WalshiD· 1 shared Alison I. BernsteiniD· 1 shared Allison P. HeathiD· 1 shared Andrew Stirn· 1 shared

Activity by Year

2019-2025 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 16 mutual co-author links

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1 shared paperGenomics

Adam Cain ResnickORCID

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3 papers

Recent·Most cited

Generative genomics accurately predicts future experimental results

Gregory Koytiger, Alice M. Walsh, Vaishali Marar, Kayla A Johnson, Max R. Highsmith, Alexander R. Abbas, Andrew Stirn, Ariel R. Brumbaugh, Alex David, Darren Hui, Jeffrey M. Kahn, Sheng-Yong Niu, Liza J. Ray, Candace Savonen, Stein Setvik, , Robert K. Bradley

This paper introduces GEM-1, a generative model that accurately predicts future gene expression experiments, achieving performance comparable to real lab experiments.

bioRxiv · Sep 8, 2025 · PreprintGenomics

OpenPBTA: An Open Pediatric Brain Tumor Atlas

Joshua A. Shapiro, Krutika Satish Gaonkar, Stephanie J. Spielman, Candace Savonen, Chanté J. Bethell, Run Jin, Komal S. Rathi, Yuankun Zhu, Laura E. Egolf, Bailey Farrow, Daniel P. Miller, Yang Yang, Tejaswi Koganti, Nighat Noureen, Mateusz Koptyra, , Jaclyn Taroni

OpenPBTA provides a collaborative platform to genomically characterize 1,074 pediatric brain tumors and 22 cell lines, offering analysis modules and somatic datasets for research and clinical applications.

Cell Genomics · May 31, 2023Peer-reviewedGenomics

Reconciling Base-Pair Resolution 5-methylcytosine and 5-hydroxymethylcytosine Data in Neuroepigenetics

Joseph J. Kochmanski, Candace Savonen, Alison I. Bernstein

The paper proposes a statistical method to analyze paired 5-mC and 5-hmC data at base-pair resolution to assess experimental treatment effects.

Frontiers in Genetics · Sep 10, 2019Peer-reviewedGenetics