Author

F. S. Varn

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

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Cancer Biology· 7

Signature Assays, Organisms & Methods

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Organism:human· 7 Research Focus:cell type annotation· 6 Research Focus:differential expression· 6 Assay:bulk RNA-seq· 5 Approach:statistical model· 5 Research Focus:gene regulatory network inference· 3 Research Focus:clustering· 2 Assay:DNA methylation· 2

Frequent Co-Authors

H. Kim· 3 shared K. C. Johnson· 3 shared L. F. Stead· 3 shared R. G. Verhaak· 3 shared A. Chakrabarty· 2 shared A. Gusnanto· 2 shared A. Ismail· 2 shared F. P. Barthel· 2 shared

Activity by Year

2018-2023 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 28 mutual co-author links

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3 shared papersCancer Biology

H. Kim

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7 papers

Recent·Most cited

GBMdeconvoluteR accurately infers proportions of neoplastic and immune cell populations from bulk glioblastoma transcriptomics data

S. A. Ajaib, D. Lodha, S. Pollock, G. Hemmings, M. Finetti, A. Gusnanto, A. Chakrabarty, A. Ismail, E. Wilson, F. S. Varn, B. Hunter, A. Filby, A. A. Brockman, D. McDonald, R. Verhaak, , L. F. Stead

This paper develops GBMdeconvoluteR, a tool to accurately infer neoplastic and immune cell proportions in bulk glioblastoma RNAseq data, validated against imaging mass cytometry.

Neuro-Oncology · Jul 6, 2023Peer-reviewedCancer Biology

IDHwt glioblastomas can be stratified by their transcriptional response to standard treatment, with implications for targeted therapy

G. Tanner, R. Barrow, M. Finetti, S. Ajaib, N. Ahmed, S. Pollock, N. Rippaus, A. F. Bruns, K. Syed, J. Poulter, E. A. Wilson, C. A. Johnson, F. S. Varn, A. Bruning-Richardson, C. Hogg, , L. F. Stead

This study identifies two IDHwt glioblastoma subtypes based on transcriptional response to treatment, with distinct resistance mechanisms and potential therapeutic implications.

bioRxiv · Feb 3, 2023Cancer Biology

Longitudinal analysis of diffuse glioma reveals cell state dynamics at recurrence associated with changes in genetics and the microenvironment

F. S. Varn, K. C. Johnson, T. E. Wade, T. M. Malta, T. S. Sabedot, F. P. Barthel, H. Kim, N. Ahmed, I. Datta, J. S. Barnholtz-Sloan, S. Bakas, F. D'Angelo, H. K. Gan, L. Garofano, J. T. Huse, , The GLASS Consortium

This study analyzes longitudinal glioma data to identify recurrence-associated changes in genetics and microenvironment linked to therapy resistance.

bioRxiv · May 3, 2021Cancer Biology

CASCADES, a novel SOX2 super-enhancer associated long noncoding RNA, regulates cancer stem cell specification and differentiation in glioblastoma multiforme

U. Shahzad, C. Li, M. Johnston, J. J. Wang, N. Sabha, F. S. Varn, A. Riemenschneider, S. Krumholtz, P. Meda, C. Smith, J. Karamchandani, J. K. Watts, R. G. W. Verhaak, M. Gallo, J. T. Rutka, S. Das

This study identifies CASCADES, a lncRNA that regulates stemness in glioblastoma cancer stem cells by epigenetically controlling SOX2 expression.

bioRxiv · Sep 5, 2020 · PreprintCancer Biology

Single-cell multimodal glioma analyses reveal epigenetic regulators of cellular plasticity and environmental stress response

K. C. Johnson, K. J. Anderson, E. T. Courtois, F. Barthel, F. S. Varn, D. Luo, M. Seignon, E. Yi, H. Kim, M. Estecio, M. Tang, N. Navin, R. Maurya, C. Ngan, N. Verburg, , R. Verhaak

The paper integrates multi-omic data from gliomas to show that epigenetic instability and transcriptional disruption are linked to tumor aggressiveness and environmental stress response.

bioRxiv · Jul 22, 2020Cancer Biology

Comparative molecular life history of spontaneous canine and human gliomas

S. B. Amin, K. J. Anderson, C. E. Boudreau, E. Martinez-Ledesma, E. Kocavakuk, K. C. Johnson, F. P. Barthel, F. S. Varn, C. Kassab, X. Ling, H. Kim, M. Barter, C. Y. Ngan, M. Chapman, J. W. Koehler, , R. G. Verhaak

This study compares molecular profiles of canine and human gliomas to identify conserved mutational processes and similarities in tumor development.

bioRxiv · Jun 17, 2019Cancer Biology

Genomic characterization of six virus-associated cancers identifies changes in the tumor microenvironment and altered genetic programming

F. S. Varn, Y. Wang, C. Cheng

This study identifies how virus infection alters the tumor microenvironment and genetic programming in six virus-associated cancers using genomic data.

bioRxiv · Apr 21, 2018Cancer Biology