Events

During cancer metastasis, cells move from the primary tumor, traversing heterogeneous terrain before seeding within a secondary site. Quantitative systems biology observes this terrain, including changes in tissue stiffness and architecture which can affect cell behavior and metastatic potential. In this talk, I will describe my lab’s efforts to understand the forces driving cell movements […]

Based on optimal transport theory, transport transforms are non-linear transforms that are well suited for many applications in data analysis, classification, and processing. In many situations, ranging from machine learning and signal processing, transport-based algorithms have outperformed state-of-the-art methods. In this talk, we will describe the Cumulative Distribution Transform (CDT), the Radon-CDT, and some of […]

Biological 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 makes it difficult to draw confident conclusions without automated and quantitative measurement strategies. Traditionally, digital image processing has relied on engineering mathematical models of e.g. […]

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 into adjacent cells over ~20 s, and appears in a much larger set of surrounding cells via a delayed second expansion over 40-300 s – […]

A 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 significantly over the past several decades, but particularly so in industrialized nations where environmental exposures and lifestyles have rapidly diverged from those with which humans […]

A 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 (e.g. time-lapse imaging of fluorescent cell cycle biosensors) has revealed that cells do not always take the same molecular path through the cell cycle. This […]

Negative 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 loops, leaving unknown whether other common biochemical reactions can produce oscillatory or switch-like dynamics. We used mass-action-based models to show that regulated RNA degradation involving […]

Single-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 us to study cell neighborhoods in unprecedented detail. In this talk, I will provide an overview of highly-multiplexed tissue imaging, a particular class of methods that uses fluorescence […]

A 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 of biological processes is often not clear. In this presentation, I will address the link between data and knowledge across multiple data types and explore […]

In 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 individual cells regulate insulin availability and secretion in response to glucose stimulation is of utmost importance. I will focus on the intra-cellular (rather than systemic) […]

Early 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 which stays on throughout a worm's life and directs gut differentiation and maintenance. Although the network is robust to deletions of some of its trans-activators, […]

Bactericidal 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 physiology may also play a decisive, causal role. Yet, the interplay between bacterial metabolism and bactericidal antibiotic lethality is challenging to study due to the […]

Papers 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 where they are published is often used as a proxy for a researcher’s worthiness of grants and promotion. Today, commercial publication is handled by five […]

In 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. In this talk, I will illustrate how interpretable deep learning models can achieve both high prediction accuracy and transparency. First, I will introduce multi-modal deep […]