163 results found
    1. Cancer Biology
    2. Computational and Systems Biology

    Robust estimation of cancer and immune cell-type proportions from bulk tumor ATAC-Seq data

    Aurélie Anne-Gaëlle Gabriel, Julien Racle ... David Gfeller
    EPIC-ATAC accurately quantifies cell-type heterogeneity in tumor bulk ATAC-Seq samples using reliable cell-type specific chromatin accessibility markers for the major cell types found in tumor microenvironments.
    1. Genetics and Genomics
    2. Immunology and Inflammation

    Simultaneous trimodal single-cell measurement of transcripts, epitopes, and chromatin accessibility using TEA-seq

    Elliott Swanson, Cara Lord ... Peter J Skene
    Simultaneous multimodal measurement of chromatin accessibility, gene expression, and protein expression provides a unified view of the molecular underpinnings of immune cell state in health and disease.
    1. Microbiology and Infectious Disease

    Longitudinal transcriptional changes reveal genes from the natural killer cell-mediated cytotoxicity pathway as critical players underlying COVID-19 progression

    Matias A Medina, Francisco Fuentes-Villalobos ... Maria Ines Barria
    Longitudinal transcriptomic analysis of unvaccinated patients reveals that early NK cell cytotoxicity activation distinguishes mild from severe COVID-19, supporting the relevance of concerted innate–adaptive immune responses against the virus.
    1. Microbiology and Infectious Disease

    Monocyte-derived transcriptome signature indicates antibody-dependent cellular phagocytosis as a potential mechanism of vaccine-induced protection against HIV-1

    Shida Shangguan, Philip K Ehrenberg ... Rasmi Thomas
    Using single-cell CITE-seq to implicate monocytes as the cellular origin of a protective HIV vaccine gene signature.
    1. Genetics and Genomics
    2. Immunology and Inflammation

    Improving oligo-conjugated antibody signal in multimodal single-cell analysis

    Terkild B Buus, Alberto Herrera ... Sergei B Koralov
    Oligo-conjugated antibodies are a powerful tool but require thorough optimization to reduce background signal, increase sensitivity, and reduce sequencing costs.
    1. Computational and Systems Biology
    2. Medicine

    Identification of human glucocorticoid response markers using integrated multi-omic analysis from a randomized crossover trial

    Dimitrios Chantzichristos, Per-Arne Svensson ... Gudmundur Johannsson
    A human experimental model for physiological glucocorticoid exposure and glucocorticoid withdrawal identifies a multi-omic cluster, including microRNA miR-122-5p and metabolites, associated with glucocorticoid-responsive genes.
    1. Immunology and Inflammation
    2. Medicine

    Innate lymphoid cells and COVID-19 severity in SARS-CoV-2 infection

    Noah J Silverstein, Yetao Wang ... Jeremy Luban
    Homeostatic innate lymphoid cell abundance, adjusted for age and sex, correlates inversely with COVID-19 severity in adults and children.
    1. Microbiology and Infectious Disease

    Establishment and stability of the latent HIV-1 DNA reservoir

    Johanna Brodin, Fabio Zanini ... Jan Albert
    Building on previous work (Zanini et al, 2015), deep-sequencing is used to show that HIV persistence during suppressive antiretroviral therapy, the main hurdle for HIV cure, is due to homeostatic proliferation and longevity of infected cells rather than ongoing virus replication.
    1. Cancer Biology

    Cancer immunotherapy by NC410, a LAIR-2 Fc protein blocking human LAIR-collagen interaction

    M Ines Pascoal Ramos, Linjie Tian ... Linde Meyaard
    NC410, a LAIR-2 Fc protein blocking LAIR-collagen interaction, might be a powerful new strategy for cancer immunotherapy for collagen-rich immune-excluded tumors.
    1. Cancer Biology

    Systematic identification of cancer cell vulnerabilities to natural killer cell-mediated immune surveillance

    Matthew F Pech, Linda E Fong ... Jeffrey Settleman
    CRISPR/Cas9 screens reveal a role for the ubiquitin ligase substrate adaptor DCAF15 in the immune surveillance of cancer cells by natural killer cells.

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