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  1. Nuclear instance segmentation and tracking for preimplantation mouse embryos

    Publication
    For investigations into fate specification and morphogenesis in time-lapse images of preimplantation embryos, automated 3D instance segmentation and tracking of nuclei are invaluable. Low signal-to-noise …

  2. Single-cell gene regulatory network inference at scale: The Inferelator 3.0

    Publication
    Gene regulatory networks define regulatory relationships between transcription factors and target genes within a biological system, and reconstructing them is essential for understanding cellular growth and function. In …

  3. Shader-Like Computations in WebGL for Advanced Graphics and General Purposes

    Publication
    The feedWebGL2 software package enables parallel computations using a feature of HTML5/WebGL2 called Transform/Feedback. The Transform/Feedback mechanism can be used within Jupyter widgets or in …

  4. Identification of new therapeutic targets in CRLF2-overexpressing B-ALL through discovery of TF-gene regulatory interactions

    Publication
    Although genetic alterations are initial drivers of disease, aberrantly activated transcriptional regulatory programs are often responsible for the maintenance and progression of cancer. CRLF2-overexpression in B-ALL …

  5. Spatial Transcriptional Mapping of the Human Nephrogenic Program

    Publication
    defects affecting 3% of newborns. The human kidney develops over a 30-week period in which a nephron progenitor pool gives rise to around a million nephrons. To …

  6. A Comprehensive Map of the Monocyte-Derived Dendritic Cell Transcriptional Network Engaged upon Innate Sensing of HIV

    Publication
    Transcriptional programming of the innate immune response is pivotal for host protection. However, the transcriptional mechanisms that link pathogen sensing with innate activation remain poorly understood. During HIV …

  7. Learning representations of microbe-metabolite interactions

    Publication
    Integrating multiomics datasets is critical for microbiome research; however, inferring interactions across omics datasets has multiple statistical challenges. We solve this problem by using neural networks (https://github …

  8. Distinct Polysaccharide Utilization Profiles of Human Intestinal Prevotella copri Isolates

    Publication
    Gut-dwelling Prevotella copri (P. copri), the most prevalent Prevotella species in the human gut, have been associated with diet and disease. However, our understanding of their diversity …

  9. Characterization of Transcriptional Regulatory Networks that Promote and Restrict Identities and Functions of Intestinal Innate Lymphoid Cells

    Publication
    Innate lymphoid cells (ILCs) promote tissue homeostasis and immune defense but also contribute to inflammatory diseases. ILCs exhibit phenotypic and functional plasticity in response to environmental stimuli, yet …

  10. Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis

    Publication
    Amyotrophic lateral sclerosis (ALS) is a progressive motor neuron disease that affects nerve cells in the brain and the spinal cord. It has proven difficult to identify the …

  11. Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells

    Publication
    Transcriptional regulatory networks (TRNs) provide insight into cellular behavior by describing interactions between transcription factors (TFs) and their gene targets. The assay for transposase-accessible chromatin (ATAC)–seq …

  12. Marching Pentatopes for Continuous Morphing of Isosurfaces From Four Dimensional Data in HTML5/WebGL

    Publication
    Animations which show three dimensional volumes continuously changing over time facilitate the exploration and analysis of complex data sets such as calcium image data of neural activity and …

  13. Critical role of IRF1 and BATF in forming chromatin landscape during type 1 regulatory cell differentiation

    Publication
    Type 1 regulatory T cells (Tr1 cells) are induced by interleukin-27 (IL-27) and have critical roles in the control of autoimmunity and resolution of inflammation. We …