Author

Simon Zhang

Broad Institute

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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Genomics· 1 Molecular Biology· 1 Synthetic Biology· 1

Signature Assays, Organisms & Methods

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Approach:experimental assay· 2 Organism:human· 2 Research Focus:benchmarking· 1 Research Focus:cell type annotation· 1 Research Focus:database / resource· 1 Research Focus:differential expression· 1 Assay:DNA methylation· 1 Organism:mouse· 1

Frequent Co-Authors

Fei CheniD· 2 shared Agnel J. SfeiriD· 1 shared Craig B. ThompsoniD· 1 shared Dylan M. CableiD· 1 shared Elim Choi· 1 shared Evan M. MurrayiD· 1 shared Evan Z. MacoskoiD· 1 shared George McDonald ChurchiD· 1 shared

Activity by Year

2022-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 17 mutual co-author links

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2 shared papersSynthetic Biology

Fei ChenORCID

Mutual co-authors in cluster

Author profile →

3 papers

Recent·Most cited

MTERF1 loss buffers against pathogenic mtDNA deletions through transcriptional regulation

Tamar Kavlashvili, Elim Choi, Ruobing Cui, Juan C. Landoni, Simon Zhang, R. Stefan Isaac, L. Stirling Churchman, Suliana Manley, Craig B. Thompson, Agnel J. Sfeir

The paper identifies MTERF1 as a suppressor of mtDNA deletion pathologies by showing its loss enhances mitochondrial function through transcriptional relief.

bioRxiv · Jul 17, 2026 · PreprintMolecular Biology

Cryptography in the DNA of living cells enabled by multi-site base editing

Verena Volf, Simon Zhang, Karen Song, Sharon Qian, Fei Chen, George McDonald Church

This paper develops a cryptographic encoding scheme called GSE to ensure information confidentiality and integrity in biological substrates using multi-site base editing in mammalian cells.

bioRxiv · Nov 15, 2023 · PreprintSynthetic Biology

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