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  1. Age-related nigral downregulation of the Parkinson’s risk factor FAM49B primes human microglia for inflammaging

    Publication
    Parkinson’s Disease (PD) is characterized by the loss of dopaminergic neurons in the substantia nigra pars compacta (SNpc), which is associated with changes in microglia function. While …

  2. 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 …

  3. 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 …

  4. NOVA1 acts as an oncogenic RNA-binding protein to regulate cholesterol homeostasis in human glioblastoma cells

    Publication
    NOVA1 is a neuronal RNA-binding protein identified as the target antigen of a rare autoimmune disorder associated with cancer and neurological symptoms, termed paraneoplastic opsoclonus-myoclonus ataxia …

  5. Shift in MSL1 alternative polyadenylation in response to DNA damage protects cancer cells from chemotherapeutic agent-induced apoptosis

    Publication
    DNA damage reshapes the cellular transcriptome by modulating RNA transcription and processing. In cancer cells, these changes can alter the expression of genes in the immune surveillance and …

  6. Tissue-specific enhancer functional networks for associating distal regulatory regions to disease

    Publication
    Systematic study of tissue-specific function of enhancers and their disease associations is a major challenge. We present an integrative machine-learning framework, FENRIR, that integrates thousands of …

  7. An automated framework for efficiently designing deep convolutional neural networks in genomics

    Publication
    Convolutional neural networks (CNNs) have become a standard for analysis of biological sequences. Tuning of network architectures is essential for a CNN’s performance, yet it requires substantial …

  8. Genome-wide landscape of RNA-binding protein target site dysregulation reveals a major impact on psychiatric disorder risk

    Publication
    Despite the strong genetic basis of psychiatric disorders, the underlying molecular mechanisms are largely unmapped. RNA-binding proteins (RBPs) are responsible for most post-transcriptional regulation, from splicing …

  9. A Multimodal and Integrated Approach to Interrogate Human Kidney Biopsies with Rigor and Reproducibility: Guidelines from the Kidney Precision Medicine Project

    Publication
    Comprehensive and spatially mapped molecular atlases of organs at a cellular level are a critical resource to gain insights into pathogenic mechanisms and personalized therapies for diseases. The …

  10. An automated framework for efficiently designing deep convolutional neural networks in genomics

    Publication
    Convolutional neural networks (CNNs) have become a standard for analysis of biological sequences. Tuning of network architectures is essential for CNN’s performance, yet it requires substantial knowledge …

  11. Specific viral RNA drives the SARS CoV-2 nucleocapsid to phase separate

    Publication
    A mechanistic understanding of the SARS-CoV-2 viral replication cycle is essential to develop new therapies for the COVID-19 global health crisis. In this study, we …

  12. Genome-wide landscape of RNA-binding protein dysregulation reveals a major impact on psychiatric disorder risk

    Publication
    Despite the strong genetic basis of psychiatric disorders, the molecular origins of these diseases are still largely unmapped. RNA-binding proteins (RBPs) are responsible for most post-transcriptional …

  13. Interpretation of an individual functional genomics experiment guided by massive public data

    Publication
    A key unmet challenge in interpreting omics experiments is inferring biological meaning in the context of public functional genomics data. We developed a computational framework, Your Evidence Tailored …