Author

R. Karchin

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· 5 Immunology· 1

Signature Assays, Organisms & Methods

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Organism:human· 5 Approach:deep learning· 4 Research Focus:cell type annotation· 2 Research Focus:differential expression· 2 Research Focus:drug response / drug discovery· 2 Research Focus:gene regulatory network inference· 2 Approach:statistical model· 2 Research Focus:variant calling· 2

Frequent Co-Authors

R. H. Hruban· 3 shared V. Anagnostou· 3 shared A. Balan· 2 shared J. Lai· 2 shared L. Zheng· 2 shared N. J. Roberts· 2 shared X. M. Shao· 2 shared A. B. Riemer· 1 shared

Activity by Year

2019-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 21 mutual co-author links

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3 shared papersCancer Biology

R. H. Hruban

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Author profile →

6 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

Islands of genomic stability in the face of genetically unstable metastatic cancer

K. Bowland, J. Lai, A. Skaist, Y. Zhang, S. S. K. Teh, N. J. Roberts, E. Thompson, S. J. Wheelan, R. H. Hruban, R. Karchin, C. A. Iacobuzio-Donahue, J. R. Eshleman

The paper identifies genomically stable regions in metastatic pancreatic cancer that can be targeted by CRISPR-Cas9 due to preserved PAM sites, suggesting a potential gene therapy approach.

bioRxiv · Jan 26, 2024Cancer Biology

SpliceMutr enables pan-cancer analysis of splicing-derived neoantigen burden in tumors

T. Palmer, M. D. Kessler, X. M. Shao, A. Balan, M. Yarchoan, N. Zaidi, T. Y. Lopez-Vidal, A. Saeed, J. Gore, N. Azad, E. Jaffee, A. V. Favorov, V. Anagnostou, R. Karchin, D. Gaykalova, , E. J. Fertig

SpliceMutr quantifies splicing-derived neoantigens across cancers, finding correlations with immune biomarkers and treatment response.

bioRxiv · May 26, 2023Cancer Biology

Three-dimensional genomic mapping of human pancreatic tissue reveals striking multifocality and genetic heterogeneity in precancerous lesions

A. M. Braxton, A. L. Kiemen, M. P. Grahn, A. Forjaz, J. M. Babu, L. Zheng, L. Jiang, H. Cheng, Q. Song, R. Reichel, S. Graham, A. I. Damanakis, C. G. Fischer, S. Mou, C. Metz, , L. D. Wood

This study uses 3D imaging and genomic analysis to show that human pancreatic precancerous lesions (PanINs) are highly multifocal and genetically heterogeneous.

bioRxiv · Jan 27, 2023 · PreprintCancer Biology

High-throughput prediction of MHC Class I and Class II neoantigens with MHCnuggets

X. M. Shao, R. Bhattacharya, J. Huang, I. K. A. Sivakumar, C. Tokheim, L. Zheng, D. HIrsch, B. Kaminow, A. Omdahl, M. Bonsack, A. B. Riemer, V. Velculescu, V. Anagnostou, K. Pagel, R. Karchin

The paper introduces MHCnuggets, a deep learning method for predicting MHC class I and II neoantigen binding, showing improved performance and scalability across 26 cancer types.

bioRxiv · Oct 4, 2019Immunology

Assessing aneuploidy with repetitive element sequencing.

C. Douville, J. D. Cohen, J. Ptak, M. Popoli, J. Schaefer, N. Silliman, L. Dobbyn, R. E. Schoen, J. Tie, P. Gibbs, M. Goggins, C. L. Wolfgang, T.-L. Wang, I.-M. Shih, R. Karchin, , B. Vogelstein

The paper describes a PCR-based assay for detecting aneuploidy in low DNA samples, showing 49% prevalence in non-metastatic cancers and 80% sensitivity when combined with other biomarkers.

bioRxiv · Jun 5, 2019Cancer Biology