Selected Publications

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 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.

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 : Memory sequencing heritable single cell gene expression programs associated with distinct cellular behaviors. Cell August 2020 Notes: doi: 10.1016/j.cell.2020.07.003.

Gregory W Schwartz, Yeqiao Zhou, Jelena Petrovic, Maria Fasolino, Lanwei Xu, Sydney M Shaffer, Warren S Pear, Golnaz Vahedi, Robert B Faryabi: TooManyCells identifies and visualizes relationships of single-cell clades. Nature Methods April 2020 Notes: https://doi.org/10.1038/s41592-020-0748-5.

Sydney Shaffer, Benjamin Emert, Eduardo Torre, Arjun Raj: Abstract LB-050: Memory sequencing reveals heritable single cell gene expression programs associated with therapy resistance. American Association for Cancer Research, Cancer Research 79: LB-050-LB-050, July 2019 Notes: Abstract from American Association for Cancer Research Annual Meeting.

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: Validation of a next-generation sequencing oncology panel optimized for low input DNA. Cancer Genetics 228-229: 55-63, Dec 2018.

Huang M, Wang J, Torre EA, Dueck H, Shaffer SM, Bonasio R, Murray J, Raj A, Li M, Zhang NR.: SAVER: Gene expression recovery for single cell RNA sequencing. Nature Methods June 2018.

Wang J, Huang M, Torre E, Dueck H, Shaffer SM, Murray J, Raj A, LI M, Zhang NR: Gene expression distribution deconvolution in single cell RNA sequencing. Proceedings of National Academy of Sciences 115(28): E6437-E6446, June 2018 Notes: published ahead of print June 26, 2018

Torre EA, Dueck H, Shaffer SM, Gospocic J, Gupte R, Bonasio R, Kim J, Murray J, Raj A.: Rare cell detection by single-cell RNA sequencing as guided by single-molecule RNA FISH. Cell Systems 6(2): 171-179.e5, February 2018 Notes: doi: 10.1016/j.cels.2018.01.014. Epub 2018 Feb 14.

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.: A slow-cycling subpopulation of melanoma cells with highly invasive properties. Oncogene 37(3): 302-312, September 2017 Notes: doi: 10.1038/onc.2017.341. Epub 2017 Sep 18.