Non-genetic differences underlie variability in proliferation among esophageal epithelial clones

Reyes Hueros RA, Gier RA, Shaffer SM

BioRxiv. 2023 June. doi: https://doi.org/10.1101/2023.05.31.543080

Clonal differences underlie variable responses to sequential and prolonged treatment

Schaff DL*, Fasse AJ*, White PE, Vander Velde R, Shaffer SM *equal contributions

Cell Systems. 2024 March. doi: https://doi.org/10.1016/j.cels.2024.01.011 PDF

Clonal cell states link Barrett’s esophagus and esophageal adenocarcinoma

Gier RA, Reyes Hueros RA, Rong J, DeMarshall M, Karakasheva TA, Muir AB, Falk GW, Zhang NR, Shaffer SM

BioRxiv. 2023 Jan. doi: https://doi.org/10.1101/2023.01.26.525564

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. 2023 November. doi: 10.1038/s41467-023-41811-8 PDF | pubmed

Integrating mutational and nonmutational mechanisms of acquired therapy resistance within the Darwinian paradigm

Vander Velde R, Shaffer SM, Marusyk A

Trends in Cancer. 2022 June. doi: https://doi.org/10.1016/j.trecan.2022.02.004

Subcellular Detection of SARS-CoV-2 RNA in Human Tissue Reveals Distinct Localization in Alveolar Type 2 Pneumocytes and Alveolar Macrophages.

Acheampong KK, Schaff DL, Emert BL, Lake J, Reffsin S, Shea EK, Comar CE, Litzky LA, Khurram NA, Linn RL, Feldman M, Weiss SR, Montone KT, Cherry S, Shaffer SM

mBio. 2022 February 8. doi: 10.1128/mbio.03751-21 PDF | pubmed

Variability within rare cell states enables multiple paths toward drug resistance.

Emert BL, Cote CJ, Torre EA, Dardani IP, Jiang CL, Jain N, Shaffer SM & Raj A

Nature Biotechnology. 2021. PDF | pubmed

Genetic Screening for Single-cell Variability Modulators Driving Therapy Resistance.

Torre EA, Arai E, Bayatpour S, Jiang CL, Beck LE, Emert BL, Shaffer SM, Mellis IA, Fane M, Alicea G, Budinich KA, Weeraratna A, Shi J, Raj A

Nature Genetics. 2021. journal | pubmed

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Memory sequencing reveals 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 *equal contributions

Cell. 2020 August 20. doi: 10.1016/j.cell.2020.07.003 PDF | pubmed

TooManyCells identifies and visualizes relationships of single-cell clades.

Schwartz GW, Zhou Y, Petrovic J, Xu L, Shaffer SM, Pear WS, Vahedi G, Faryabi RB.

Nature Methods. 2020. journal | pubmed

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

Sussman RT*, Shaffer S*, Azzato EM*, DeSloover D, Farooqi MS, Meyer A, Lieberman DB, Bigdeli A, Paolillo C, Ganapathy K, Sukhadia S, Rosenbaum JN, Daber RD, Morrissette JJD. *equal contributions

Cancer Genetics. 2018 December. journal website

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Gene expression distribution deconvolution in single-cell RNA sequencing.

Wang J, Huang M, Torre E. Dueck H, Shaffer S, Murray J, Raj A, Li M, and Zhang NR.

PNAS. 2018 June 26. PDF | pubmed

SAVER: Gene expression recovery for single-cell RNA sequencing.

Huang M, Wang J, Torre E, Dueck H, Shaffer S, Bonasio R, Murray JI, Raj A, Li M, and Zhang NR.

Nature Methods. 2018 June 25. pubmed

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

M Perego, M Maurer, JX Wang, S Shaffer, AC Müller, K Parapatics, L Li, D Hristova, S Shin, F Keeney, S Liu, X Xu, A Raj, JK Jensen, KL Bennett, SN Wagner, R Somasundaram, M Herlyn.

Oncogene. 2018 Jan. PDF | pubmed

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Rare Cell Detection by Single-Cell RNA Sequencing as Guided by Single-Molecule RNA FISH.

Torre E, Dueck H, Shaffer S, Gospocic J, Gupte R, Bonasio R, Kim J, Murray J, Raj A.

Cell Systems. 2018 Feb 28. PDF | pubmed

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Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance.

Shaffer SM, Dunagin MC, Torborg SR, Torre EA, Emert B, Krepler C, Beqiri M, Sproesser K, Brafford PA, Xiao M, Eggan E, Anastopoulos IN, Vargas-Garcia CA, Singh A, Nathanson KL, Herlyn M, Raj A.

Nature. 2017 Jun 7. PDF | pubmed

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Transcriptional Bursting Explains the Noise-Versus-Mean Relationship in mRNA and Protein Levels.

Dar RD, Shaffer SM, Singh A, Razooky BS, Simpson ML, Raj A, Weinberger LS.

PLoS One. 11, e0158298 (2016). PDF | pubmed

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Multiplexed detection of viral infections using rapid in situ RNA analysis on a chip.

Shaffer SM*, Joshi RP*, Chambers BS, Sterken D, Biaesch AG, Gabrieli DJ, Li Y, Feemster KA, Hensley SE#, Issadore D#, Raj A#. * equal contributions, # corresponding author.

Lab on a Chip. 2015. PDF | pubmed

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Turbo FISH: A method for rapid single molecule RNA FISH.

Shaffer SM, Wu M, Levesque MJ, Raj A.

PLoS ONE. 8(9): e75120, 2013. PDF | pubmed