Author

Jonathan M. Shaffer

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Bioinformatics· 1 Molecular Biology· 1

Signature Assays, Organisms & Methods

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Research Focus:benchmarking· 2 Assay:bulk RNA-seq· 2 Organism:human· 2 Approach:statistical model· 2 Research Focus:differential expression· 1

Frequent Co-Authors

Amanda M. McNulty· 1 shared Andrew A. FarmeriD· 1 shared Arvind Y. M. SundaramiD· 1 shared Benedicte Alexandra LieiD· 1 shared Daniel Kim· 1 shared Fatima HeinickeiD· 1 shared Gregor D. GilfillaniD· 1 shared Hoichong Karen Yip· 1 shared

Activity by Year

2019-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 29 mutual co-author links

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1 shared paperBioinformatics

Amanda M. McNulty

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2 papers

Recent·Most cited

Pre-analytical delay as a dominant confounder in blood RNA-seq: Rapid ex vivo gene expression changes in EDTA blood

Kalle Günther, Ioanna Andreou, Daniel Kim, Jonathan M. Shaffer, Markus Sprenger‐Haussels

The paper investigates how pre-analytical delay affects gene expression in EDTA blood compared to stabilized PAXgene blood using RNA-seq.

bioRxiv · Jun 29, 2026 · PreprintMolecular Biology

Systematic assessment of commercially available low-input miRNA library preparation kits

Fatima Heinicke, Xiangfu Zhong, Manuela Zucknick, Johannes Breidenbach, Arvind Y. M. Sundaram, Siri T. Flåm, Magnus Leithaug, Marianne Dalland, Andrew A. Farmer, Jordana M. Henderson, Melanie Hussong, Pamela Renate Moll, Loan Nguyen, Amanda M. McNulty, Jonathan M. Shaffer, , Gregor D. Gilfillan

This study evaluates six commercial low-input miRNA library prep kits, finding differences in detection sensitivity and differential expression but no kit fully captures all expected miRNAs.

RNA Biology · Sep 27, 2019Peer-reviewedBioinformatics