Image analysis and AI in microscopy-based life science research
ZoomBiological processes can be observed both in space and over time using imaging. Visual assessment becomes limiting as datasets grow, and complexity of data as well as subtleness of processes […]
“From games in Cancer to endless evolution: a view through the algorithmic lens”
Any process can be framed as an algorithm; its power and its limits can then be analysed with the techniques of theoretical computer science. To analyse algorithms, we divide the […]
Moving the message: how mRNA transcripts are spatially patterned to direct developmental outcomes
ZoomEvent Zoom Link Gene expression involves the precise regulation of messenger RNA (mRNA) transcripts in space and time. In developing embryos, this process must be precisely executed to ensure cells […]
Something’s Wrong in the (cellular) neighborhood: Mechanisms of epithelial wound detection”
The first response of epithelial cells to local wounds is a dramatic increase in cytosolic calcium. This increase occurs quickly – calcium floods into damaged cells within 0.1 s, moves […]
Early life microbiota development and childhood asthma – microbes to mechanisms
ZoomA presentation by Susan Lynch Professor of Medicine, Director, Benioff Center for Microbiome Medicine, University of California: San Francisco Zoom link https://us02web.zoom.us/j/87550168229 The prevalence of allergy and asthma has increased […]
Using Single-Cell Multiplexed Imaging and Manifold Learning to Visualize Cell Cycle Plasticity in Health and Disease
ZoomA Presentation by Wayne Michael Stallaert, Ph.D. Postdoctoral Researcher in Computational Medicine, University of North Carolina at Chapel Hill The recent development of single-cell approaches to study the cell cycle […]
Precision and Plasticity in Animal Transcription
Over the past decade, our group has focused on discerning the molecular mechanisms that can reconcile how transcriptional control during animal development can be simultaneously precise (e.g. sharp in response […]
A Model of Non-modular Biochemical Oscillator and Switch
ZoomNegative and positive feedback loops have been considered essential components for biological rhythms and switches, respectively. Research in systems biology focused on gene regulatory networks with intuitive appearances of feedback […]
Highly-multiplexed tissue imaging at the Laboratory of Systems Pharmacology and beyond
ZoomSingle-cell technologies have revolutionized our ability to characterize biological systems. An exciting direction for quantitative biology is the recent emergence of spatial -omics technologies, which promise to spatially resolve single-cell measurements and allow […]
From Data to Knowledge in Network-Driven Cellular Processes
ZoomA mechanistic understanding of cellular processes continues to be an elusive goal of quantitative biology. Measurements across multiple spatiotemporal resolutions are routinely collected but how these data impact our understanding […]
Modeling intra-cellular insulin dynamics in pancreatic Beta cells
ZoomIn this talk, I will discuss the role of cytoskeletal processes in regulating insulin dynamics in pancreatic cells. Due to the increasing prevalence of diabetes and related disorders, understanding how […]
Redundancy and fragility in a young but essential gene regulatory network
ZoomEarly in embryogenesis, C. elegans worms use a short network of interacting and related transcription factors to establish gut cell identity. The goal is to activate a downstream master regulator […]
Systems Biology Insights into Antimicrobial Resistance Physiology
ZoomBactericidal antibiotics are conventionally understood to kill bacteria through a target-dependent process mediated by antibiotic inhibition of replicative machinery. However, several lines of evidence suggest that other aspects of bacterial […]
Demystifying Scientific Publishing from the Perspective of a Researcher Turned Editor
ZoomPapers are the core currency of scientific research; not only are they the primary medium researchers use to communicate their work, but the number of papers a researcher publishes and […]
Expanding the Genomechanics Toolbox: New Techniques to Investigate Metastatic Mechanical and Genetic Data at Single Cell Level across the Genome
Engineering & Science Building 048 Vanderbilt University, Nashville, United StatesNine out of every ten cancer-related deaths is caused by metastasis, but the molecular mechanisms driving this process are still not fully understood. Several studies have implicated that as a […]
Building the Cell from Unreliable Parts: the Case of Stochastic Organelle Biogenesis
Engineering & Science Building 048 Vanderbilt University, Nashville, United StatesPerhaps the defining feature of the eukaryotic cell is its organization into membrane-bound compartments known as organelles. While the processes underlying the biogenesis of individual organelles are often well-known the […]
Interpretable Deep Learning for Cancer Personalized Medicine
Engineering & Science Building 048 Vanderbilt University, Nashville, United StatesIn recent years, deep learning models have resulted in outstanding breakthrough performances. However, many models behave as black boxes that can hide data biases, incorrect hypotheses or even software errors. […]
Modeling Transcriptional Dynamics from Single-Cell Genomics Data
Engineering & Science Building 048 Vanderbilt University, Nashville, United StatesSingle-cell genomics technologies have been lauded for their potential to probe biological systems with cell type specificity, and to elucidate cellular differentiation trajectories. However, the analysis of single-cell genomics data […]
A Computational Model of Crosstalk Between MAPK Signaling and Store-Operated Calcium Entry in Melanoma Cells
Engineering & Science Building 048 Vanderbilt University, Nashville, United StatesBRAF-mutant melanoma cells under prolonged BRAF inhibition have been shown to enter a state of balanced division and death, termed "idling."It is hypothesized that the idling state acts as a […]
Exploring Bacterial Phenotypic Heterogeneity with Single-Cell Transcriptomics
Engineering & Science Building 048 Vanderbilt University, Nashville, United StatesEven isogenic bacteria may heterogeneously express different subsets of genes, assuming distinct roles for the survival of the community. There is limited knowledge about the diversity of phenotypic states within […]
