Author

Dylan L. Schaff

University of PennsylvaniaORCID 0000-0002-3367-9270Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Research Focus:differential expression· 5 Organism:human· 5 Research Focus:cell type annotation· 4 Approach:statistical model· 4 Research Focus:clustering· 3 Approach:experimental assay· 3 Assay:scRNA-seq· 3 Assay:bulk RNA-seq· 2

Frequent Co-Authors

Sydney M. ShafferiD· 4 shared Abhyudai SinghiD· 2 shared Benjamin L. EmertiD· 2 shared Guillaume HarmangeiD· 2 shared Raúl A. Reyes HuerosiD· 2 shared Alexander F. KoeppeliD· 1 shared Ann E. SizemoreiD· 1 shared Aria J. FasseiD· 1 shared

Activity by Year

2019-2025 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 27 mutual co-author links

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4 shared papersSystems Biology

Sydney M. ShafferORCID

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5 papers

Recent·Most cited

Deciphering Cell Fate and Clonal Dynamics via Integrative Single-Cell Lineage Modeling

Yuntian Fu, Divij Mathew, Mingshuang Wang, Xinyi E. Chen, Kevin Lin, Dylan L. Schaff, Sydney M. Shaffer, Drew M. Pardoll, Christina Jackson, Nancy Ruonan Zhang

Clonotrace integrates gene expression and clonotype data to infer cell state transitions and fate biases, improving understanding of lineage dynamics in various biological systems.

bioRxiv · Sep 1, 2025 · PreprintBioinformatics

Clonal differences underlie variable responses to sequential and prolonged treatment

Dylan L. Schaff, Aria J. Fasse, Phoebe E. White, Robert Vander Velde, Sydney M. Shaffer

This study tracks resistant cancer clones through treatment using single-cell RNA-sequencing and barcoding, showing clones have distinct fates and gene expression states that predict survival.

Cell Systems · Feb 23, 2024Peer-reviewedSystems Biology

Disrupting cellular memory to overcome drug resistance

Guillaume Harmange, Raúl A. Reyes Hueros, Dylan L. Schaff, Benjamin L. Emert, Michael Saint-Antoine, Laura C. Kim, Zijian Niu, Shivani Nellore, Mitchell E. Fane, Gretchen Marie Alicea, Ashani T. Weeraratna, Marie Celeste Simon, Abhyudai Singh, Sydney M. Shaffer

The paper develops a method to quantify gene expression memory and identify regulators of cell state transitions, showing that modulating PI3K and TGF-β pathways can reduce drug resistance in melanoma.

Nature Communications · Nov 6, 2023Peer-reviewedSystems Biology

Memory sequencing reveals heritable single cell gene expression programs associated with distinct cellular behaviors

Sydney M. Shaffer, Benjamin L. Emert, Raúl A. Reyes Hueros, Christopher J. Cote, Guillaume Harmange, Dylan L. Schaff, Ann E. Sizemore, Rohit K. Gupte, Eduardo A. Torre, Abhyudai Singh, Danielle S. Bassett, Arjun Raj

The paper introduces MemorySeq, a method to identify gene expression fluctuations persisting across cell divisions, revealing non-genetic, heritable cellular behaviors in cancer cell lines.

Cell · Jul 30, 2020Peer-reviewedSystems Biology

In situ 10-cell RNA sequencing in tissue and tumor biopsy samples

Shambhavi Singh, Lixin Wang, Dylan L. Schaff, Matthew D. Sutcliffe, Alexander F. Koeppel, Jung‐Eun Kim, Suna Önengüt-Gümüşcü, Kwon-Sik Park, Hui Zong, Kevin A. Janes

This paper introduces 10cRNA-seq, an in situ method for sequencing 10 microdissected cells, showing improved sensitivity and reliability compared to scRNA-seq.

Scientific Reports · Mar 20, 2019Peer-reviewedSystems Biology