An up-to-date list and links to publications can be found on Google Scholar. 

Highlighted Subset of Publications of Multiplexed Imaging

• In melanomas treated with immunotherapy, multiplexed imaging and computational analysis shows T cell phenotypes drive the formation of unique, inflamed tumor neighborhoods, with better therapies creating larger, interconnected regions of tumor and immune zones. [Cell Reports, 2023]

• Methods for integrating spatial-omics and multiscale agent-based modeling to create simulations of the tumor microenvironment [Cell Systems, 2024]

• Organization of the healthy human intestine at the single cell level incorporating integration of multiplexed imaging, snRNAseq, and snATACseq [Nature, 2023; Nature Cell Biology, 2023]

• Development of deep learning algorithms, such as STELLAR, for cell type label transfer in spatial single-cell data [Nature Methods, 2022] and MORPHE for generative tissue generation [bioRxiv, 2026]

• Technique and protocol for CODEX multiplexed imaging [EJI, 2021; Nature Protocols, 2021] and DIY spatial-omics [bioRxiv, 2025]

• As a part of global cell atlas initiatives (e.g.,  HuBMAP and HTAN) we created a primer to guide researchers entering the multiplexed imaging field [Nature Methods, 2021]. 

• Application of CODEX multiplexed imaging to understand the complex human tumor microenvironment for different macrophage subsets [Cancer Discovery, 2024], metastasis [Cancer Cell, 2026], and inflammation-associated cancers [Developmental Cell, 2025].

• Computational algorithms for analyzing spatial-omics data, with normalization and clustering selection for cell type annotation [Frontiers Immunology, 2021], SPACEc a python package for end-end spatial-omics data analysis [Nature Communications, 2026], and MINGL a method for identifying borders, gradients, and heterogeneity in cellular neighborhoods [bioRxiv, 2026] 

Highlighted Subset of Publications of Biomaterials for Cell Therapy

• Engineered extracellular matrix (ECM) hydrogel-based T cell stimulating biomaterial [Advanced Materials, 2019] that showed its stiffness influences T cell migration, stimulation, and memory phenotype affecting anti-tumor efficacy and could be used as in vivo stimulation agents [Advanced Materials, 2024]

• Engineered nanoparticles as artificial antigen presenting cells with controlled particle properties, shedding light on the mechanism of nano-scale organization on activation of T cell receptors that affected T cell phenotype [Nano Letters, 2017; Nano Letters, 2018]

• aAPCs engineered nanoparticles achieve 70% and 700-fold increase of antigen-specific T cells after 1 week [Biomaterials, 2018; Nano Letters, 2020], and  could use this to identify cross-reactivity between a cancer antigen and a peptide from the gut microbiota [JCI Insight, 2020]. 

• aAPC particles were extended to biodegradable formats having important implications for future injectable in vivo stimulating versions [Biomaterials, 2017; ACS App Mat & Int, 2021]. 

An up-to-date list and links to publications can be found on Google Scholar.