TITLE: "Algorithms or experiments? How to improve transcriptome analysis” Hosted Jingyi Jessica Li for Bioinformatics
MATLAB is a powerful, high-level programing language for numerical computation, visualization, and application development. This workshop will start by introducing the MATLAB environment and then cover working with arrays and matrices, loops and conditional statements, writing your own functions, working with files and visualizing your data. The final day will briefly introduce utilizing MATLAB to […]
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 […]
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 […]
