Sydney M. Shaffer, MD, PhD

Assistant Professor of Pathology and Laboratory Medicine
Assistant Professor of Bioengineering
Perelman School of Medicine at the University of Pennsylvania

Contact InformationUniversity of Pennsylvania
Philadelphia, PA, 19104

Specialty Division

Immunobiology and Experimental Pathology

Itmat Expertise

Biomedical engineering
Systems Biology
Tissue engineering

Graduate Groups

Biochemistry and Molecular Biophysics
Cell and Molecular Biology


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

Specialty Certification

Postgraduate Training

Research Intern, Eli, Lilly and Company, Research and Development, 2007-2008
Hartwell Foundation Postdoctoral Fellowship, University of Pennsylvania, 2018-2019

Awards and Honors

John G. Clark Research Paper Award, University of Pennsylvania, 2014
NIH Ruth L. Kirschstein National Research Service Award (F30), 2015-2018
Solomon R. Pollack Award for Excellence in Graduate Bioengineering Research/University of Pennsylvania, 2018
NIH Director's Early Independence Award DP5, 2019

Memberships and Professional Organizations

Biomedical Engineering Society, Member, 2017 - Present
American Association for Cancer Research, Associate Member, 2018 - Present

Web Links

Selected Publications

Variability within rare cell states enables multiple paths toward drug resistance

Benjamin L Emert, Christopher J Cote, Eduardo A Torre, Ian P Dardani, Connie L Jiang, Naveen Jain, Sydney M Shaffer, Arjun Raj, Nature Biotechnology, 2021

Genetic screening for single-cell variability modulators driving therapy resistance

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, Nature Genetics, 2021

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

Shaffer SM*, Emert B*, Reyes-Hueros RA, Cote C, Harmange G, Schaff G, Sizemore AE, Gupte R, Torre E, Singh A, Basset DS, Raj A, Cell, 2020, PMID:32735851

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TooManyCells identifies and visualizes relationships of single-cell clades

Gregory W Schwartz, Yeqiao Zhou, Jelena Petrovic, Maria Fasolino, Lanwei Xu, Sydney M Shaffer, Warren S Pear, Golnaz Vahedi, Robert B Faryabi, Nature Methods, 2020, PMID:32123397

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Abstract LB-050: Memory sequencing reveals heritable single cell gene expression programs associated with therapy resistance

Sydney Shaffer, Benjamin Emert, Eduardo Torre, Arjun Raj, American Association for Cancer Research, Cancer Research 79(): LB-050-LB-050, 2019

Validation of a next-generation sequencing oncology panel optimized for low input DNA.

Sussman RT, Shaffer SM, Azzato EM, DeSloover D, Farooqi MS, Meyer A, Liebeman DB, Bigdeli A, Paolillo C, Sukhadia S, Rosenbaum JN, Daber RD, Morrissette JD, Cancer Genetics 228-229(): 55-63, 2018

SAVER: Gene expression recovery for single cell RNA sequencing

Huang M, Wang J, Torre EA, Dueck H, Shaffer SM, Bonasio R, Murray J, Raj A, Li M, Zhang NR., Nature Methods, 2018

Gene expression distribution deconvolution in single cell RNA sequencing.

Wang J, Huang M, Torre E, Dueck H, Shaffer SM, Murray J, Raj A, LI M, Zhang NR, Proceedings of National Academy of Sciences 115(28): E6437-E6446, 2018

Rare cell detection by single-cell RNA sequencing as guided by single-molecule RNA FISH.

Torre EA, Dueck H, Shaffer SM, Gospocic J, Gupte R, Bonasio R, Kim J, Murray J, Raj A., Cell Systems 6(2): 171-179.e5, 2018

A slow-cycling subpopulation of melanoma cells with highly invasive properties.

Perego M, Maurer M, Wang J, Shaffer SM, Muller A, Parapatics K, Li L, Hristova D, Shin S, Keeney F, Liu S, Xu X, Raj A, Jensen J, Bennett K, Wagner S, Somasundaram R, Herlyn M., Oncogene 37(3): 302-312, 2017