TITLE: "Quantification of Absolute Metabolite Concentrations in T cells by Shotgun Metabolomics." ABSTRACT: Quantitative understanding of immunometabolism underlies improving immune functions and developing successful immunotherapies. Kinetic and thermodynamic laws rely on absolute, not relative, metabolite concentrations to map metabolism. However, until now, comprehensive absolute metabolite quantification has been inaccessible due to the need for iterative analytical […]

TITLE: "Defining molecular dysregulation in Down Syndrome neocortex and neural progenitor cells." ABSTRACT: Down syndrome (DS) is the most common form of genetic, intellectual disability, which occurs 1 in 700 newborns and presents in patients as cognitive deficits, particularly diminished in learning, memory, and language development.1,2,3 DS symptoms result from impaired cortical development, which is […]

TITLE: "TBD" Hosted by William Hsu for Medical Informatics

TITLE: "Splicing-specific transcriptome-wide association uncovers novel genetic mechanisms for Schizophrenia." ABSTRACT: Recent studies have highlighted the essential role of RNA splicing, a key mechanism of alternative RNA processing, in establishing connections between genetic variations and disease. Genetic loci influencing RNA splicing variations show considerable influence on complex traits, possibly surpassing those affecting total gene expression. Dysregulated RNA […]

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 […]