Author

Vignesh Shanmugam

Broad InstituteORCID 0000-0002-2005-9080Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Research Focus:database / resource· 2 Research Focus:differential expression· 2 Organism:human· 2 Organism:mouse· 2 Research Focus:software / tool· 2 Assay:spatial transcriptomics· 2 Assay:ATAC-seq· 1 Research Focus:benchmarking· 1

Frequent Co-Authors

Evan Z. MacoskoiD· 3 shared Fei CheniD· 3 shared Dylan M. CableiD· 2 shared Jackson A. WeiriD· 2 shared Naeem M. NadafiD· 2 shared Abner LouissaintiD· 1 shared Andrew J. C. RusselliD· 1 shared Caroline UhleriD· 1 shared

Activity by Year

2022-2025 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 36 mutual co-author links

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3 shared papersGenomics

Evan Z. MacoskoORCID

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3 papers

Recent·Most cited

Genome-scale spatial mapping of the Hodgkin lymphoma microenvironment identifies tumor cell survival factors

Vignesh Shanmugam, Neriman Tokcan, Daniel Chafamo, Sean Sullivan, Mehdi Borji, Haley K. Martin, Gail A. Newton, Naeem M. Nadaf, Saoirse Hanbury, Irving Barrera, Dylan M. Cable, Jackson A. Weir, Orr Ashenberg, Geraldine Pinkus, Scott J. Rodig, , Todd R. Golub

This study identifies IL13 as a survival factor for Hodgkin lymphoma cells by analyzing the tumor microenvironment with spatial and single-cell resolution.

Nature Communications · Dec 20, 2025Peer-reviewedCancer Biology

Slide-tags: scalable, single-nucleus barcoding for multi-modal spatial genomics

Andrew J. C. Russell, Jackson A. Weir, Naeem M. Nadaf, Matthew Shabet, Vipin Kumar, Sandeep Kambhampati, Ruth Raichur, Giovanni J. Marrero, Sophia Liu, Karol S. Balderrama, Charles R. Vanderburg, Vignesh Shanmugam, Luyi Tian, Catherine J. Wu, Charles H. Yoon, , Fei Chen

Slide-tags enables spatial localization of single nuclei for multi-modal spatial genomics, achieving high-resolution mapping and multiomic profiling in various tissues.

bioRxiv · Apr 1, 2023 · PreprintGenomics

Cell type-specific inference of differential expression in spatial transcriptomics

Dylan M. Cable, Evan M. Murray, Vignesh Shanmugam, Simon Zhang, Luli S. Zou, Michael Diao, Haiqi Chen, Evan Z. Macosko, Rafael A. Irizarry, Fei Chen

The paper introduces a statistical method to detect cell type-specific differential gene expression in spatial transcriptomics data and validates it using simulations and real datasets.

Nature Methods · Sep 1, 2022Peer-reviewedGenomics