Selected Publications
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; 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 algorithm, STELLAR, for cell type label transfer in spatial single-cell data [Nature Methods, 2022].
Technique and protocol for CODEX multiplexed imaging [EJI, 2021; Nature Protocols, 2021]
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] and inflammation-associated cancers [bioRxiv, 2023].
Comparison of 21 normalization strategies combined with different unsupervised clustering algorithms to produce an accurate pipeline of identification of cell types [Frontiers Immunology, 2021].
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].