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

Shaffer SM, Emert BL, Sizemore AE, Gupte R, Torre E,  Bassett DS, Raj A.

BioRxiv. doi: 10.1101/379016. PDF | BioRxiv


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