Author

D. N. Sidiropoulos

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Cancer Biology· 3 Immunology· 2

Signature Assays, Organisms & Methods

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Research Focus:cell type annotation· 4 Research Focus:cell-cell communication· 4 Organism:human· 4 Approach:deep learning· 3 Research Focus:differential expression· 3 Approach:experimental assay· 3 Assay:bulk RNA-seq· 2 Research Focus:clustering· 2

Frequent Co-Authors

E. J. Fertig· 4 shared E. M. Jaffee· 4 shared L. T. Kagohara· 4 shared A. Gupta· 2 shared J. T. Mitchell· 2 shared J. W. Zimmerman· 2 shared L. D. Wood· 2 shared L. Danilova· 2 shared

Activity by Year

2021-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 36 mutual co-author links

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4 shared papersImmunology

E. J. Fertig

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Author profile →

5 papers

Recent·Most cited

A generative reference grammar of healthy TCR repertoires reveals cancer-associated immune remodeling

A. Balan, Y. Elhanati, K. E. Meza Landeros, M. De Almeida Mendes, J. Lai, S. S. A. Zaidi, M. Unal, B. Y. S. Kim, C.-H. G. Lucas, E. Runco, V. K. Puduvalli, J. Gantchev, C. A. Whittaker, P. Sharma, V. Tabar, , R. Karchin

CRAFT, a transformer model, learns a generative grammar of healthy TCR repertoires to detect cancer-associated immune remodeling through structured deviations in sequence space.

bioRxiv · Jun 20, 2026 · PreprintCancer Biology

Immune landscape of tertiary lymphoid structures in hepatocellular carcinoma (HCC) treated with neoadjuvant immune checkpoint blockade

D. H. Shu, W. J. Ho, L. T. Kagohara, A. Girgis, S. M. Shin, L. Danilova, J. W. Lee, D. N. Sidiropoulos, S. Mitchell, K. Munjal, K. Howe, K. J. Bendinelli, H. Qi, G. Mo, J. Montagne, , M. Yarchoan

This study examines TLS in HCC treated with neoadjuvant immunotherapy, finding TLS correlate with better outcomes and show distinct morphological and functional features in tumor regression.

bioRxiv · Oct 16, 2023 · PreprintImmunology

PanIN and CAF Transitions in Pancreatic Carcinogenesis Revealed with Spatial Data Integration

A. T. F. Bell, J. T. Mitchell, A. L. Kiemen, K. Fujikura, H. Fedor, B. Gambichler, A. Deshpande, P.-H. Wu, D. N. Sidiropoulos, R. Erbe, J. Stern, R. Chan, S. Williams, J. M. Chell, J. W. Zimmerman, , L. T. Kagohara

This paper develops a new protocol for spatial transcriptomics analysis of FFPE PanIN specimens and integrates it with imaging and scRNA-seq to study the progression from PanIN to PDAC.

bioRxiv · Jul 16, 2022Cancer Biology

Inflammatory Signaling in Pancreatic Cancer Transfers Between a Single-cell RNA Sequencing Atlas and Co-Culture

B. Kinny-Koster, S. Guinn, J. A. Tandurella, J. T. Mitchell, D. N. Sidiropoulos, M. Loth, M. R. Lyman, A. B. Pucsek, T. T. Seppala, C. Cherry, R. Suri, H. Zlomke, J. He, C. L. Wolfgang, J. Yu, , J. W. Zimmerman

This paper integrates single-cell RNA sequencing data with organoid co-cultures to study inflammatory signaling in pancreatic cancer and validates findings through transfer learning and mechanistic experiments.

bioRxiv · Jul 14, 2022 · PreprintCancer Biology

Phenotypic shifts of tumor associated macrophages and STAT3 mediated suppression of myeloid derived suppressor cells drive sensitization of HER2+ tumor immunity.

D. N. Sidiropoulos, C. Rafie, B. J. Christmas, E. F. Davis-Marcisak, G. Sharma, E. Bigelow, A. Gupta, S. Yegnasubramanian, V. Stearns, R. M. Connolly, D. A. Gaykalova, L. T. Kagohara, E. M. Jaffee, E. J. Fertig, E. T. Roussos-Torres

The paper uses single-cell RNA-sequencing to show entinostat shifts tumor microenvironment cell states, reducing immunosuppression and enhancing immune checkpoint inhibitor responses in HER2+ breast tumors.

bioRxiv · Jan 29, 2021 · PreprintImmunology