Sydney M Shaffer, M.D., Ph.D.

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Assistant Professor of Pathology and Laboratory Medicine
Assistant Investigator, Abramson Family Cancer Research Institute
Assistant Professor, Department of Pathology and Laboratory Medicine
Assistant Professor, Department of Bioengineering
Department: Pathology and Laboratory Medicine

Contact information
University of Pennsylvania
Philadelphia, PA 19104
B.S. (Chemical and Biomolecular Engineering)
Georgia Institute of Technology , 2010.
Ph.D. (Bioengineering)
University of Pennsylvania, 2017.
M.D. (Medicine)
Perelman School of Medicine, University of Pennsylvania, 2018.
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Selected Publications

Hailong Song, Alexandra Tomasevich, Kofi K Acheampong, Dylan L Schaff, Sydney M Shaffer, Jean-Pierre Dolle, Victoria E Johnson, Bailey Mikytuck, Edward B Lee, Amber Nolan, C Dirk Keene, Susan R Weiss, William Stewart, Douglas H Smith: Detection of blood–brain barrier disruption in brains of patients with COVID-19, but no evidence of brain penetration by SARS-CoV-2. Acta Neuropathologica August 2023 Notes:

Reyes Hueros RA, Gier RA, Shaffer SM: Non-genetic differences underlie variability in proliferation among esophageal epithelial clones. BioRxiv [Pre-print] June 2023 Notes:

Raymond W S Ng, Sydney M Shaffer: Patterns of tumour transcriptional variability. Nature June 2023.

Schaff DL*, Fasse AJ*, White PE, Vander Velde R, Shaffer SM: Clonal differences underlie variable responses to sequential and prolonged treatment. BioRxiv [Pre-print] March 2023 Notes:

Gier RA, Reyes Hueros RA, Rong J, DeMarshall M, Karakasheva TA, Muir AB, Falk GW, Zhang NR, Shaffer SM: Clonal cell states link Barrett’s esophagus and esophageal adenocarcinoma. BioRxiv [Pre-print] Jan 2023 Notes:

Harmange G, Reyes Hueros RA, Schaff D, Emert B, Saint-Antoine M, Nellore S, Fane ME, Alicea GM, Weeraratna AT, Singh A, Shaffer SM: Disrupting cellular memory to overcome drug resistance. Nature Communications (Accepted Sept 2023) June 2022 Notes: Pre-print available at

Robert Vander Velde, Sydney Shaffer, Andriy Marusyk: Integrating mutational and nonmutational mechanisms of acquired therapy resistance within the Darwinian paradigm. Trends in Cancer June 2022.

Benjamin L Emert, Christopher J Cote, Eduardo A Torre, Ian P Dardani, Connie L Jiang, Naveen Jain, Sydney M Shaffer, Arjun Raj: Variability within rare cell states enables multiple paths toward drug resistance. Nature Biotechnology July 2021.

Kofi K Acheampong, Dylan L Schaff, Benjamin L Emert, Jonathan Lake, Sam Reffsin, Emily K Shea, Courtney E Comar, Leslie A Litzky, Nigar A Khurram, Rebecca L Linn, Michael Feldman, Susan R Weiss, Kathleen T Montone, Sara Cherry, Sydney M Shaffer: Subcellular Detection of SARS-CoV-2 RNA in Human Tissue Reveals Distinct Localization in Alveolar Type 2 Pneumocytes and Alveolar Macrophages. mBio Feb 2021.

Eduardo A Torre, Eri Arai, Sareh Bayatpour, Connie L Jiang, Lauren E Beck, Benjamin L Emert, Sydney M Shaffer, Ian A Mellis, Mitchell E Fane, Gretchen M Alicea, Krista A Budinich, Ashani T Weeraratna, Junwei Shi, Arjun Raj: Genetic screening for single-cell variability modulators driving therapy resistance. Nature Genetics January 2021.

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Last updated: 09/29/2023
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