Author

J. M. Beechem

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· 4 Pathology· 1

Signature Assays, Organisms & Methods

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Organism:human· 5 Research Focus:cell type annotation· 4 Research Focus:cell-cell communication· 3 Approach:experimental assay· 3 Research Focus:spatial domain detection· 3 Assay:spatial transcriptomics· 3 Assay:bulk RNA-seq· 2 Research Focus:differential expression· 2

Frequent Co-Authors

D. R. Zollinger· 2 shared G. Geiss· 2 shared Y. Liang· 2 shared A. B. Haynes· 1 shared A. B. Rosenbloom· 1 shared A. R. Richman· 1 shared A. Regev· 1 shared A. Rininger· 1 shared

Activity by Year

2019-2023 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 21 mutual co-author links

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2 shared papersCancer Biology

D. R. Zollinger

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Author profile →

5 papers

Recent·Most cited

Therapy-associated remodeling of pancreatic cancer revealed by single-cell spatial transcriptomics and optimal transport analysis

C. Shiau, J. Cao, M. T. Gregory, D. Gong, X. Yin, J.-W. Cho, P. L. Wang, J. Su, S. Wang, J. W. Reeves, T. K. Kim, Y. Kim, J. A. Guo, N. A. Lester, N. Schurman, , W. L. Hwang

This study uses single-cell spatial transcriptomics and optimal transport analysis to reveal therapy-induced changes in pancreatic cancer microenvironment interactions.

bioRxiv · Jun 28, 2023 · PreprintCancer Biology

Ultra High-Plex Spatial Proteogenomic Investigation of Giant Cell Glioblastoma Multiforme Immune Infiltrates Reveals Distinct Protein and RNA Expression Profiles

S. A. Bonnett, A. B. Rosenbloom, G. Ong, M. Conner, A. Rininger, D. Newhouse, F. New, C. Phan, S. Ilcisin, H. Sato, J. Lyssand, G. Geiss, J. M. Beechem

This study develops and applies a spatial proteogenomic assay to analyze glioblastoma multiforme samples, revealing distinct RNA and protein expression profiles based on pathology and location.

bioRxiv · Oct 4, 2022Cancer Biology

Opposing immune and genetic forces shape oncogenic programs in synovial sarcoma

L. Jerby, C. Neftel, M. E. Shore, M. J. McBride, B. Haas, B. Izar, H. R. Weissman, A. Volorio, G. Boulay, L. Cironi, A. R. Richman, L. C. Broye, J. M. Gurski, C. C. Luo, R. Mylvaganam, , A. Regev

The paper profiles synovial sarcoma tumors to show that the SS18-SSX fusion drives oncogenic programs, which are repressed by immune cells and can be targeted with HDAC and CDK4/6 inhibitors.

bioRxiv · Aug 4, 2019 · PreprintCancer Biology

Defining the microenvironment landscape of bladder cancer using highly multiplexed spatial genomic and proteomic analysis

J. Reeves, Z. Zhang, Z. K. Norgaard, D. M. Zhou, J. Gong, Y. Liang, S. Das, S. E. Warren, M. Korpal, M. L. Hoang, J. M. Beechem, P. Kumar, V. Rimkunas

The paper uses spatial genomic and proteomic analysis to explore how PPARG signaling is linked to immune cell exclusion in bladder cancer.

bioRxiv · Jun 21, 2019 · PreprintCancer Biology

High multiplex, digital spatial profiling of proteins and RNA in fixed tissue using genomic detection methods

C. R. Merritt, G. T. Ong, S. Church, K. Barker, G. Geiss, M. Hoang, J. Jung, Y. Liang, J. McKay-Fleisch, K. Nguyen, K. Sorg, I. Sprague, C. Warren, S. Warren, Z. Zhou, , J. M. Beechem

This paper introduces Digital Spatial Profiling (DSP), a method for high-plex spatial analysis of proteins and RNA in tissue, and demonstrates its application in studying immune and cancer microenvironments.

bioRxiv · Feb 26, 2019 · PreprintPathology