Selected Publications

Gladstein AC, Solomon AMC, Poltorack CD, Venkatesh S, Adler KM, Robertson MR, Stransky S, Irizarry-Negron VM, Ruiz DA, Tao D, Freeburg NF, Sidoli S, Asangani IA, Shaffer SM, Feldser DM: Antagonistic roles of histone 3 lysine methyltransferases dictate tumor immune surveillance. Nature Communications August 2026 Notes: doi: 10.1038/s41467-026-76657-3. [Epub ahead of print]

Gupta M, Choi H, Karasic T, Furth EE, Shaffer S, Englander S, Pickup S, Clendenin C, Liu F, Cao Q, Song HK, Fan Y, Duda J, Gee JC, Rosen M, O'Dwyer PJ, Zhou R.: Co-Clinical Evaluation of Synthetic Vitamin D and Chemotherapy in Pancreatic Cancer by Integrated Imaging and Molecular Analyses. Cancer Research Communications August 2026 Notes: Online ahead of print, published August 10, 2026. Open access. doi: 10.1158/2767-9764.CRC-26-0443. Pilot clinical trial NCT03519308.

Buckley KH, Dungan ME, Dinh K, Kelly GM, Hausler R, Bennett KE, Clay DG, Youngman JE, Majer AD, Beyries KA, Niccum BA, Shaffer SM, Karakasheva TA, Hamilton KE, Kochman ML, Ginsberg GG, Ahmad N, Maxwell KN, Katona BW.: Gastric Epithelium from BRCA1 and BRCA2 Carriers Harbors Increased Double-Stranded DNA Damage and Enhanced Growth Potential. Molecular Cancer Research 24(7): 589–600, July 2026 Notes: doi: 10.1158/1541-7786.MCR-25-0970. Free full text in PMC.

Schaff DL, White PE, Cote CJ, Watterson GE, Lin KZ, Fasse AJ, Zhang NR, Shaffer SM: Pre-existing cell states predict resistance to multiple treatments. Cell Genomics 6(6): 101191, June 2026 Notes: doi: 10.1016/j.xgen.2026.101191.

Kinsler G, Fagan C, Li H, Kaster J, Dunne M, Vander Velde RJ, Boe RH, Shaffer S, Herlyn M, Raj A, Heyman Y: SpaceBar enables single-cell-resolution clone tracing with imaging-based spatial transcriptomics. Nature Methods 23(2): 328-333, February 2026 Notes: doi: 10.1038/s41592-025-02968-w. Epub 2025 Dec 18.

Vander Velde RJ, Ng RWS., Coté C, Shaffer, SM: Multiplexed enrichment and tracking of lineages with CloneSweeper. bioRxiv January 2026 Notes: Pre-Print https://doi.org/10.64898/2026.01.30.700779.

Bracht SA*, Rong J*, Gier RA, DeMarshall M, Golden H, Dhakal D, McDevitt JC, Mo F, Furth EE, Strauss Starling A, Muir AB, Falk GW, Katona BW, Stanger BZ, Zhang NR**, Shaffer SM** *equal contributions, **corresponding authors: Mitochondrial clone tracing within spatially intact human tissues. Nature Methods 2026 Notes: Accepted in Principle; BioRxiv available at doi: https://doi.org/10.1101/2025.07.11.664452.

Gier RA, Bracht SA, Rong J, Reyes Hueros RA, Wahlsten ML, Cote C, DeMarshall M, Karakasheva TA, Strauss Starling A, Muir AB, Falk GW, Zhang NR, Shaffer SM: Clonal cell states link Barrett’s esophagus and esophageal adenocarcinoma. Nature Communications 16: 10952, December 2025 Notes: doi: 10.1038/s41467-025-66302-w. Article number: 10952. Open access.

Sasaki M, Wang JX, Teranishi R, Itami T, Zhou Y, Kennedy KV, Semeao A, Ishikawa S, Hara T, McMillan EA, Mahon M, Golden H, Dhakal D, Baccarella A, Winters H, Umeweni CN, Wilkins BJ, Karakasheva TA, Whelan KA, Shaffer SM, Ruffner MA, Muir AB: FOXM1 inhibition reduces IL-13-induced epithelial remodelling and inflammation in eosinophilic oesophagitis. Gut Page: 1-15, May 2025 Notes: doi: 10.1136/gutjnl-2025-335163. Epub ahead of print 20 Nov 2025. Open access.

Lawson NM, Ye L, Cho CY, Zhao B, Mitchell T, Martín-Barrio I, Beernaert B, Gupta A, Banu M, Lissanu Y, Shaffer S, Tawbi H, Li J, Gule-Monroe MK, Alvarez-Breckenridge CA, Huse JT, Murphy MB, Yin F, Lang FF, Parkes EE, Weinberg JS, Akdemir KC: Recurrent ERBB2 alterations are associated with esophageal adenocarcinoma brain metastases. medRxiv February 2025.