TITLE: "Modeling the heterogenous NFκB dynamics of single immune cells." ABSTRACT: Macrophages function as immune sentinel cells, initiating appropriate and specialized immune responses to a great variety of pathogens.  The transcription factor NFκB controls macrophage gene expression responses, and its temporal dynamics enable stimulus-specificity of these responses.  Using a fluorescent reporter mouse our laboratory recently […]

TITLE: "The new culture of preprint peer-review"

TITLE: "TBD" Hosted by Grace Xiao for Bioinformatics

TITLE: "Characterization of Genomics Landscape and Natural History of Anaplastic Thyroid Cancer using High Depth WGS and Subclonal Reconstruction." ABSTRACT: Anaplastic thyroid cancer (ATC) is among the most lethal cancer types, with a median survival rate of approximately 12 weeks. ATC is resistant to both chemo- and radiotherapy, a characteristic attributed to its surrounding tissues […]

TITLE: "scGRNdb: A Cell Type Gene Regulatory Network Atlas for Human and Mouse." ABSTRACT: Gene regulatory networks (GRNs) elucidate the complex regulatory landscape in cells and tissues, making them powerful tools for understanding mechanisms in disease pathophysiology and identifying therapeutic targets. The advent of single cell RNA-sequencing (scRNAseq) enables a more granular study of disease mechanisms […]

TITLE: "TBD" Hosted by Jingyi Jessica Li for Bioinformatics

TITLE: "A Non-Invasive Epigenetic Measure of Inflammation." ABSTRACT: Existing epigenetic phenotype tests often lack mechanistic explanations of the observed correlations between specific methylation sites and phenotypes. This raises the crucial question: are these correlations primarily a result of marginal correlations, or do they stem from plausible biological mechanisms? To delve deeper into this question, we […]

TITLE: "scDEED: a statistical method for detecting dubious 2D single-cell embeddings and optimizing t-SNE and UMAP hyperparameters." ABSTRACT: Two-dimensional (2D) embedding methods are crucial for single-cell data visualization. Popular methods such as t-distributed stochastic neighbor embedding(t-SNE) and uniform manifold approximation and projection (UMAP) are commonly used for visualizing cell clusters; however, it is well known […]

TITLE: "An updated movement path randomization method to distinguish social and spatial drivers of animal interactions." ABSTRACT: Studying the spatial-social interface requires tools that distinguish between social and spatial drivers of interactions. Testing hypotheses regarding the factors determining animal interactions often involves comparing observed interactions with reference or ’null’ models. One approach to constructing reference models that account for spatial drivers […]

TITLE: "Detection of Symptoms of Depression Using Data From the iPhone and Apple Watch." ABSTRACT: Digital health data from consumer wearable devices and smartphones have the potential to improve our understanding of mental illness. However, in conditions like depression, there is not yet a consistent uniform measurement tool whose result can be reliably used as […]