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  1. Variant-resolved prediction of context-specific isoform variation with a graph-based attention model

    Publication
    Alternative splicing generates functional transcript diversity across human tissues. We present a graph-based neural attention architecture that predicts variant-resolved context-specific RNA isoform proportions directly from …

  2. HumanBase: an interactive AI platform for human biology

    Publication
    Increasing quantities of genomic data present an opportunity for uncovering functional and mechanistic insights. However, given the complexity and scale of the data, sophisticated analytical frameworks and integrative …

  3. Decomposition of phenotypic heterogeneity in autism reveals underlying genetic programs.

    Publication
    Unraveling the phenotypic and genetic complexity of autism is extremely challenging yet critical for understanding the biology, inheritance, trajectory and clinical manifestations of the many forms of the …

  4. CXCR4+ mammary gland macrophageal niche promotes tumor initiating cell activity and immune suppression during tumorigenesis

    Publication
    Tumor-initiating cells (TICs) share features and regulatory pathways with normal stem cells, yet how the stem cell niche contributes to tumorigenesis remains unclear. Here, we identify CXCR4 …

  5. Decomposition of phenotypic heterogeneity in autism reveals distinct and coherent genetic programs

    Publication
    Unraveling the phenotypic and genetic complexity of autism is extremely challenging yet critical for understanding the biology, inheritance, trajectory, and clinical manifestations of the many forms of the …

  6. Blood RNA alternative splicing events as diagnostic biomarkers for infectious disease

    Publication
    Assays detecting blood transcriptome changes are studied for infectious disease diagnosis. Blood-based RNA alternative splicing (AS) events, which have not been well characterized in pathogen infection, have …

  7. Pre-infection antiviral innate immunity contributes to sex differences in SARS-CoV-2 infection

    Publication
    Male sex is a major risk factor for SARS-CoV-2 infection severity. To understand the basis for this sex difference, we studied SARS-CoV-2 infection in …

  8. Asymptomatic SARS-CoV-2 Infection Is Associated With Higher Levels of Serum IL-17C, Matrix Metalloproteinase 10 and Fibroblast Growth Factors Than Mild Symptomatic COVID-19

    Publication
    … infections in young adults, including potential targets for developing new therapies and prognostic tests.

  9. Capturing the complexity of topologically associating domains through multi-feature optimization

    Publication
    The three-dimensional structure of human chromosomes is tied to gene regulation and replication timing, but there is still a lack of consensus on the computational and biological …