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
Cancer and Immunobiology
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
Hartwell Foundation Postdoctoral Fellowship, 2018
NIH Director's Early Independence Award DP5, 2019
Society for Melanoma Research, Christopher Marshall Award, 2023
American Cancer Society Research Scholar Grant, 2024
Damon Runyon-Rachleff Innovation Award, 2024
Memberships and Professional Organizations
Biomedical Engineering Society, Member, 2017 - Present
American Association for Cancer Research, Associate Member, 2018 - Present
Web Links
Selected Publications
Recurrent ERBB2 alterations are associated with esophageal adenocarcinoma brain metastases
NM Lawson, L Ye, CY Cho, B Zhao, T Mitchell, I MartÃn-Barrio, B Beernaert, A Gupta, M Banu, Y Lissanu, S Shaffer, H Tawbi, J Li, MK Gule-Monroe, CA Alvarez-Breckenridge, JT Huse, MB Murphy, F Yin, FF Lang, EE Parkes, JS Weinberg, KC Akdemir, medRxiv, 2025
SpaceBar enables clone tracing in spatial transcriptomic data
Grant Kinsler, C Fagan, H Li, J Kaster, M Dunne, RJ Vander Velde, RH Boe, S Shaffer, M Herlyn, A Raj, Y Heyman, bioRxiv, 2025
Unveiling heterogeneity in rare cells by combining RNA-based sorting and scRNA-seq
M Wahlsten, SM Shaffer, Nature Genetics 57(): 283-284, 2025
Cancer-associated fibroblasts maintain critical pancreatic cancer cell lipid homeostasis in the tumor microenvironment
Han X, Burrows M, Kim LC, Xu JP, Vostrejs W, Le TNV, Poltorack C, Jiang Y, Cukierman E, Stanger BZ, Reiss KA, Shaffer SM, Mesaros C, Keith B, Simon MC, Cell Reports 43(11): 8-9, 2024, PMID:114972
Non-genetic differences underlie variability in proliferation among esophageal epithelial clones
Reyes Hueros RA, Gier RA, Shaffer SM, PLOS Computational Biology, 2024
Development of a functional beige fat cell line uncovers independent subclasses of cells expressing UCP1 and the futile creatine cycle
Vargas-Castillo A, Sun Y, Smythers AL, Grauvogel L, Dumesic PA, Emont MP, Tsai LT, Rosen ED, Zammit NW, Shaffer SM, Ordonez M, Chouchani ET, Gygi SP, Wang T, Sharma AK, Balaz M, Wolfrum C, Spiegelman BM, Cell Metabolism, 2024, PMID:39084217
Clonal differences underlie variable responses to sequential and prolonged treatment
Schaff DL*, Fasse AJ*, White PE, Vander Velde R, Shaffer SM, Cell Systems, 2024
Breaking reflection symmetry: evolving long dynamical cycles in Boolean systems
Ouellet M, Kim JZ, Guillaume H, Shaffer SM, Bassett LC, Bassett DS, New Journal of Physics, 2024, PMID:23006
IGF2BP1/IMP1 Deletion Enhances a Facultative Stem Cell State via Regulation of MAP1LC3B
Parham LR, Williams PA, Katada K, Nettleford SK, Chatterji P, Acheampong KK, Danan CH, Ma X, Simon LA, Naughton KE, Mizuno R, Karakasheva T, McMillan EA, Whelan KA, Brady DC, Shaffer SM, Hamilton KE, Cellular and Molecular Gastroenterology and Hepatology, 2024
Disrupting cellular memory to overcome drug resistance
Harmange G, Reyes Hueros RA, Schaff D, Emert B, Saint-Antoine M, Nellore S, Fane ME, Alicea GM, Weeraratna AT, Singh A, Shaffer SM, Nature Communications 14(7130): , 2023
