Publications by authors named "Sydney Shaffer"

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Clonal cell states link gastroesophageal junction tissues with metaplasia and cancer.
Rodrigo A Gier, Sydney A Bracht, Jiazhen Rong, Raúl A Reyes Hueros, Madison L Wahlsten, Sydney M Shaffer

Nat Commun· December 2025

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SpaceBar enables single-cell-resolution clone tracing with imaging-based spatial transcriptomics.
Grant Kinsler, Caitlin Fagan, Haiyin Li, Jessica Kaster, Maggie Dunne, Sydney Shaffer

Nat Methods· December 2025

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FOXM1 inhibition reduces IL-13-induced epithelial remodelling and inflammation in eosinophilic oesophagitis.
Masaru Sasaki, Joshua X Wang, Ryugo Teranishi, Takefumi Itami, Yusen Zhou, Sydney M Shaffer

Gut· November 2025

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Gastric epithelium from and carriers harbors increased double-stranded DNA damage and augmented growth.
Kole H Buckley, Michaela E Dungan, Kevin Dinh, Gregory M Kelly, Ryan Hausler, Sydney M Shaffer

bioRxiv· October 2025

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Deciphering Cell Fate and Clonal Dynamics via Integrative Single-Cell Lineage Modeling.
Yuntian Fu, Divij Mathew, Mingshuang Wang, Xinyi E Chen, Kevin Z Lin, Sydney M Shaffer

bioRxiv· September 2025

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Deciphering Cell Fate and Clonal Dynamics via Integrative Single-Cell Lineage Modeling.
Yuntian Fu, Divij Mathew, Mingshuang Wang, Xinyi E Chen, Kevin Z Lin, Sydney M Shaffer

Res Sq· September 2025

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Mitochondrial clone tracing within spatially intact human tissues.
Sydney A Bracht, Jiazhen Rong, Rodrigo A Gier, Maureen DeMarshall, Hailey Golden, Sydney M Shaffer

bioRxiv· July 2025

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FOXM1 Modulation Alleviates Epithelial Remodeling and Inflammation in Eosinophilic Esophagitis.
Masaru Sasaki, Joshua X Wang, Yusen Zhou, Kanak V Kennedy, Ryugo Teranishi, Sydney M Shaffer

bioRxiv· May 2025

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The H3 oncohistone inhibits NSD2 to activate a SETD2-dependent antiviral-like immune response in KRAS-driven lung cancer.
Amy C Gladstein, Carson D Poltorack, Akino Mercy Charles Solomon, Sharan Venkatesh, Keren M Adler, Sydney M Shaffer

bioRxiv· May 2025

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Unveiling heterogeneity in rare cells by combining RNA-based sorting and scRNA-seq.
Madison Wahlsten, Sydney M Shaffer

Nat Genet· February 2025

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SpaceBar enables clone tracing in spatial transcriptomic data.
Grant Kinsler, Caitlin Fagan, Haiyin Li, Jessica Kaster, Maggie Dunne, Sydney Shaffer

bioRxiv· February 2025

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Recurrent alterations are associated with esophageal adenocarcinoma brain metastases.
Nora M Lawson, Lingqun Ye, Chae Yun Cho, Bo Zhao, Thomas Mitchell, Sydney Shaffer

medRxiv· February 2025

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Parent-identified intrinsic and extrinsic factors that influence performance across developmental domains and participation in their communities.
Rachel Bican, Sydney Shaffer, Jayna Kinkade, Quinn McAdams, Allyson S Hughes

Front Pediatr· February 2025

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Cancer-associated fibroblasts maintain critical pancreatic cancer cell lipid homeostasis in the tumor microenvironment.
Xu Han, Michelle Burrows, Laura C Kim, Jimmy P Xu, Will Vostrejs, Sydney M Shaffer

Cell Rep· November 2024

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Non-genetic differences underlie variability in proliferation among esophageal epithelial clones.
Raúl A Reyes Hueros, Rodrigo A Gier, Sydney M Shaffer

PLoS Comput Biol· October 2024

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Development of a functional beige fat cell line uncovers independent subclasses of cells expressing UCP1 and the futile creatine cycle.
Ariana Vargas-Castillo, Yizhi Sun, Amanda L Smythers, Louisa Grauvogel, Phillip A Dumesic, Sydney M Shaffer

Cell Metab· September 2024

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Author Correction: Disrupting cellular memory to overcome drug resistance.
Guillaume Harmange, Raúl A Reyes Hueros, Dylan L Schaff, Benjamin Emert, Michael Saint-Antoine, Sydney M Shaffer

Nat Commun· May 2024

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Clonal differences underlie variable responses to sequential and prolonged treatment.
Dylan L Schaff, Aria J Fasse, Phoebe E White, Robert J Vander Velde, Sydney M Shaffer

Cell Syst· March 2024

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IGF2BP1/IMP1 Deletion Enhances a Facultative Stem Cell State via Regulation of MAP1LC3B.
Louis R Parham, Patrick A Williams, Kay Katada, Shaneice K Nettleford, Priya Chatterji, Sydney M Shaffer

Cell Mol Gastroenterol Hepatol· February 2024

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Breaking reflection symmetry: evolving long dynamical cycles in Boolean systems.
Mathieu Ouellet, Jason Z Kim, Harmange Guillaume, Sydney M Shaffer, Lee C Bassett

New J Phys· February 2024

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Detection of blood-brain barrier disruption in brains of patients with COVID-19, but no evidence of brain penetration by SARS-CoV-2.
Hailong Song, Alexandra Tomasevich, Kofi K Acheampong, Dylan L Schaff, Sydney M Shaffer

Acta Neuropathol· November 2023

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Disrupting cellular memory to overcome drug resistance.
Guillaume Harmange, Raúl A Reyes Hueros, Dylan L Schaff, Benjamin Emert, Michael Saint-Antoine, Sydney M Shaffer

Nat Commun· November 2023

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Patterns of tumour transcriptional variability.
Raymond W S Ng, Sydney M Shaffer

Nature· June 2023

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Clonal differences underlie variable responses to sequential and prolonged treatment.
Dylan L Schaff, Aria J Fasse, Phoebe E White, Robert J Vander Velde, Sydney M Shaffer

bioRxiv· March 2023

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Clonal cell states link Barrett's esophagus and esophageal adenocarcinoma.
Rodrigo A Gier, Raúl A Reyes Hueros, Jiazhen Rong, Maureen DeMarshall, Tatiana A Karakasheva, Sydney M Shaffer

bioRxiv· February 2023

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