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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

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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 […]

From Data to Knowledge in Network-Driven Cellular Processes

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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 […]

Systems Biology Insights into Antimicrobial Resistance Physiology

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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 […]

Interpretable Deep Learning for Cancer Personalized Medicine

Engineering & Science Building 048 Vanderbilt University, Nashville

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. […]

Modeling Transcriptional Dynamics from Single-Cell Genomics Data

Engineering & Science Building 048 Vanderbilt University, Nashville

Single-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 […]

Exploring Bacterial Phenotypic Heterogeneity with Single-Cell Transcriptomics

Engineering & Science Building 048 Vanderbilt University, Nashville

Even 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 […]