Jonathan Chen

Broad Institute — United States

Medicine · Health Sciences

26h-index7.7kcitations73works9.52yr avg
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Research Topics

Cancer Immunotherapy and Biomarkers(32), Single-cell and spatial transcriptomics(24), Cancer Genomics and Diagnostics(13), Immunotherapy and Immune Responses(12), Atherosclerosis and Cardiovascular Diseases(9)

Publications73 total

Spatially defined multicellular functional units in colorectal cancer revealed from single cell and spatial transcriptomics
eLife·2025· 1 citedOpen Access
Author response: Spatially defined multicellular functional units in colorectal cancer revealed from single cell and spatial transcriptomics
2025Open Access
498 Integrated scRNAseq, TCR repertoire and spatial transcriptomic analysis reveals immune remodeling induced by combined BRAF/MEK/PD-1 inhibition in metastatic BRAFV600E colorectal cancer
Regular and Young Investigator Award Abstracts·2025Open Access
Author response: Spatially defined multicellular functional units in colorectal cancer revealed from single cell and spatial transcriptomics
2025Open Access
Spatially defined multicellular functional units in colorectal cancer revealed from single cell and spatial transcriptomics
2025Open Access
Monitoring strategies for continuous evaluation of deployed clinical prediction models
Journal of Biomedical Informatics·2025
Abstract 664: Integrated scRNAseq and spatial transcriptomic analyses identify immune correlates of response to combined BRAF/MEK/PD-1 inhibition in metastatic colorectal cancer
Cancer Research·2025
Spatially defined multicellular functional units in colorectal cancer revealed from single cell and spatial transcriptomics
eLife·2025Open Access
Spatially defined multicellular functional units in colorectal cancer revealed from single cell and spatial transcriptomics
2025· 1 citedOpen Access
Author response: Spatially defined multicellular functional units in colorectal cancer revealed from single cell and spatial transcriptomics
2025Open Access
Batch correcting single-cell spatial transcriptomics count data with Crescendo improves visualization and detection of spatial gene patterns
Genome biology·2025· 6 citedOpen Access
Spatial biology captures the effects of neoadjuvant chemo-immunotherapy in lung cancer
Nature Genetics·2024· 1 citedOpen Access
PEARL: A Phase Ib/II Biomarker Study of Adding Radiation Therapy to Pembrolizumab Before Neoadjuvant Chemotherapy in Human Epidermal Growth Factor Receptor 2–Negative Breast Cancer
Journal of Clinical Oncology·2024· 20 citedOpen Access
Powerful microscopy technologies decode spatially organized cellular networks that drive response to immunotherapy in humans
Current Opinion in Immunology·2024Open Access
Single-cell transcriptomic analyses reveal distinct immune cell contributions to epithelial barrier dysfunction in checkpoint inhibitor colitis
Nature Medicine·2024· 42 citedOpen Access
Abstract 5492: Spatial organization and cellular composition of immunity hubs in human colorectal cancer
Cancer Research·2024
Abstract 6555: scRNAseq and TCR repertoire analysis identifies immune correlates of response to combined BRAF/MEK/PD1 inhibition in a phase 2 trial
Cancer Research·2024· 1 cited
Human lung cancer harbors spatially organized stem-immunity hubs associated with response to immunotherapy
Nature Immunology·2024· 107 citedOpen Access
Integrating spatial transcriptomics count data with Crescendo improves visualization and detection of spatial gene patterns
2024· 1 citedOpen Access
Intrarenal myeloid subsets associated with kidney injury are comparable in mice and patients with lupus nephritis
2023· 9 citedOpen Access
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Frequent Co-authors

Nir Hacohen(31), Genevieve M. Boland(19), Karin Pelka(18), Arnav Mehta(10), Moshe Sade-Feldman(9), David Lieb(9), Jason Reeves(9), Matan Hofree(9), Vjola Jorgji(9), Linda T. Nieman(9), Toni Delorey(8), Keren Yizhak(7), Dennie T. Frederick(7), Dejan Juric(7), Katherine Xu(7), Tatyana Sharova(7), Aviv Regev(7), Ryan J. Sullivan(6), Ryan B. Corcoran(6), Danielle Dionne(6)