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
Microfludics
Diagnostics
Graduate Groups
Biochemistry and Molecular Biophysics
Cell and Molecular Biology
Education
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
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
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
