Author

J. R. Marks

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 Pathology· 1

Signature Assays, Organisms & Methods

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Organism:human· 6 Research Focus:cell type annotation· 4 Assay:bulk RNA-seq· 3 Research Focus:differential expression· 3 Approach:machine learning (classical)· 3 Approach:statistical model· 3 Research Focus:clustering· 2 Research Focus:gene regulatory network inference· 2

Frequent Co-Authors

E. S. Hwang· 4 shared R. B. West· 4 shared A. Hall· 3 shared G. A. Colditz· 3 shared S. H. Strand· 3 shared C. Maley· 2 shared C. Zhu· 2 shared K. Owzar· 2 shared

Activity by Year

2019-2023 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 44 mutual co-author links

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4 shared papersCancer Biology

E. S. Hwang

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Author profile →

6 papers

Recent·Most cited

Molecular subtypes of high grade serous ovarian cancer across racial groups and gene expression platforms

N. R. Davidson, M. E. Barnard, A. A. Hippen, A. Campbell, C. Johnson, G. P. Way, B. K. Dalley, A. Berchuck, L. A. Salas, L. C. Peres, J. R. Marks, J. M. Schildkraut, C. S. Greene, J. A. Doherty

This study identifies molecular subtypes of high-grade serous ovarian cancer across racial groups and gene expression platforms, finding similar subtype-specific survival rates despite differences in subtype prevalence.

bioRxiv · Nov 1, 2023Cancer Biology

Single Cell Expression Analysis of Ductal Carcinoma in Situ Identifies Alterations in Epithelial Integrity

X. Qin, S. H. Strand, M. R. Lee, D. G. P. van Ijzendoorn, C. Zhu, S. Vennam, S. Varma, A. Hall, L. King, L. Simpson, X. Luo, G. A. Colditz, S. Jiang, E. S. Hwang, J. R. Marks, , R. B. West

This study uses scRNA-seq to analyze DCIS and normal breast tissue, identifying clonal heterogeneity and cell state changes associated with progression to invasive cancer.

bioRxiv · Oct 10, 2023Cancer Biology

Analysis of ductal carcinoma in situ by self-reported race reveals molecular differences related to outcome.

S. H. Strand, K. E. Houlahan, V. Branch, T. Lynch, B. Harmon, F. Couch, K. Gallagher, M. Kilgore, S. Wei, A. DeMichele, T. King, P. McAuliffe, C. Curtis, K. Owzar, J. R. Marks, , R. B. West

The paper analyzes molecular differences in ductal carcinoma in situ (DCIS) by self-reported race and outcome groups, identifying variations in gene expression, tumor microenvironment, and copy number variations between Black and White women.

bioRxiv · Sep 28, 2023Cancer Biology

Transition to invasive breast cancer is associated with progressive changes in the structure and composition of tumor stroma

T. Risom, D. R. Glass, C. C. Liu, B. Rivero-Gutierrez, A. Baranski, E. F. McCaffrey, N. F. Greenwald, A. C. Kagel, S. H. Strand, S. Varma, A. Kong, L. Keren, S. Srivastava, C. Zhu, Z. Khair, , M. Angelo

The paper analyzes tumor microenvironment changes from normal to invasive breast cancer using imaging and machine learning, finding coordinated shifts in stromal cell location and function.

bioRxiv · Jan 5, 2021Cancer Biology

Minimal Barriers to Invasion During Human Colorectal Tumor Growth

M. D. Ryser, D. Mallo, A. Hall, T. Hardman, L. M. King, I. C. Sorribes, C. C. Maley, J. R. Marks, E. S. Hwang, D. Shibata

The paper examines intra-tumoral heterogeneity in colorectal tumors and finds that early multiclonal invasion occurs with minimal barriers to invasion.

bioRxiv · Nov 14, 2019Cancer Biology

Unmasking the tissue microecology of ductal carcinoma in situ with deep learning

P. L. Narayanan, S. E. A. Raza, A. Hall, J. R. Marks, L. King, R. B. West, L. Hernandez, M. Dowsett, B. Gusterson, C. Maley, S. E. Hwang, Y. Yuan

This paper develops a deep learning pipeline to detect and segment DCIS ducts, revealing that pure DCIS has more TILs but less co-localization with ducts compared to adjacent DCIS.

bioRxiv · Oct 28, 2019Pathology