Selected Publications

NM Lawson, L Ye, CY Cho, B Zhao, T Mitchell, I Martín-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: Recurrent ERBB2 alterations are associated with esophageal adenocarcinoma brain metastases. medRxiv February 2025.

G Kinsler, C Fagan, H Li, J Kaster, M Dunne, RJ Vander Velde, RH Boe, S Shaffer, M Herlyn, A Raj, Y Heyman: SpaceBar enables clone tracing in spatial transcriptomic data. bioRxiv February 2025.

M Wahlsten, SM Shaffer : Unveiling heterogeneity in rare cells by combining RNA-based sorting and scRNA-seq. Nature Genetics 57: 283-284, February 2025.

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: Cancer-associated fibroblasts maintain critical pancreatic cancer cell lipid homeostasis in the tumor microenvironment. Cell Reports 43(11): 8-9, November 2024 Notes: doi: https://doi.org/10.1016/j.celrep.2024.114972.

Reyes Hueros RA, Gier RA, Shaffer SM: Non-genetic differences underlie variability in proliferation among esophageal epithelial clones. PLOS Computational Biology October 2024 Notes: doi: 10.1371/journal.pcbi.1012360.

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: Development of a functional beige fat cell line uncovers independent subclasses of cells expressing UCP1 and the futile creatine cycle. Cell Metabolism Page: 2146-2155, July 2024 Notes: doi: 10.1016/j.cmet.2024.07.002.

Schaff DL*, Fasse AJ*, White PE, Vander Velde R, Shaffer SM: Clonal differences underlie variable responses to sequential and prolonged treatment. Cell Systems Page: 213-226, March 2024 Notes: https://doi.org/10.1016/j.cels.2024.01.011.

Ouellet M, Kim JZ, Guillaume H, Shaffer SM, Bassett LC, Bassett DS: Breaking reflection symmetry: evolving long dynamical cycles in Boolean systems. New Journal of Physics February 2024.

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: IGF2BP1/IMP1 Deletion Enhances a Facultative Stem Cell State via Regulation of MAP1LC3B. Cellular and Molecular Gastroenterology and Hepatology Page: 439-451, January 2024.

Harmange G, Reyes Hueros RA, Schaff D, Emert B, Saint-Antoine M, Nellore S, Fane ME, Alicea GM, Weeraratna AT, Singh A, Shaffer SM: Disrupting cellular memory to overcome drug resistance. Nature Communications 14(7130), November 2023 Notes: https://doi.org/10.1038/s41467-023-41811-8.