Ellis Patrick

2 months ago | nature.com | Chuhan Wang |Adam Chan |Xiaohang Fu |Shila Ghazanfar |Ellis Patrick

AbstractSpatial transcriptomics has enabled the quantification of gene expression at spatial coordinates across a tissue, offering crucial insights into molecular underpinnings of diseases. In light of this, several methods predicting spatial gene expression from paired histology images have provided the opportunity to enhance the utility of obtainable and cost-effective haematoxylin-and-eosin-stained histology images.

Apr 21, 2024 | biorxiv.org | Angela Ferguson |Thomas P. Beddow |Ellis Patrick |Elijah Willie

AbstractSurvival in recurrent/metastatic head and neck mucosal squamous cell carcinoma (HNmSCC) remains poor. Anti-programmed death (PD)-1 therapies have demonstrated improved survival with lower toxicity when compared to standard chemotherapy. However, response to anti-PD-1 therapy remains modest, at 13-17%. We evaluated the tumor microenvironment (TME) using Imaging Mass Cytometry (IMC) on 27 tumor specimens from 24 advanced HNmSCC patients prior to receiving anti-PD-1 based treatment.

Jul 17, 2023 | nature.com | Yingxin Lin |Ellis Patrick

scMerge2Single-cell grouping within one batchFollowing the same principals as scMerge, the scMerge2 approach begins by grouping the cells that share similar biological signals within each dataset or batch. We can approach this in two ways: one way is to perform unsupervised clustering; the other way is using results from supervised cell type classification. Clustering-based grouping: This is performed by default when no cell type label is used as input.

Jun 20, 2023 | biorxiv.org | Elijah Willie |Pengyi Yang |Ellis Patrick

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Mar 15, 2023 | rupress.org | Andrew Sawyer |Ellis Patrick

Tuberculosis (TB) remains a major cause of mortality, with 1.5 million deaths in 2020 (World Health Organization, 2021). Development of new TB vaccines and therapeutics remains a global priority and depends on a deep understanding of mechanisms mediating resistance to Mycobacterium tuberculosis (M.tb), the causative agent of TB (O’Garra et al., 2013; Orme et al., 2015; Libardo et al., 2018).