Theory and Computation in Biology
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The Shape of Life
We study embryonic morphogenesis. Our current interests are in finding physically inspired descriptions of live-imaging data, steps towards constructing a first mechanical atlas, and connecting the physical context of an embryo to its transcriptomic dynamics.
Representative studies:
An inverse problem approach to measuring the mechanical atlas of a gastrulating embryo
On the developmental constraints of phenotypic variation in the fly wing(David Lubensky's opinion piece on the work)
The coupled dynamics of mechano-chemistry give rise to multicellular patterning in the fly eye
The hypothesis of an active solid in the context of fly gastrulation
A confrontation between the predicted forces and chemistry during germ band extension in the fly
The Dynamics of Life
We envision a new field of Transcriptomic Physics, where an interpretable and mathematically well-founded framework guides the analysis of high-dimensional and dynamical gene expression data.
Representative studies:
A dynamical systems viewpoint of cellular differentiation
A Neural ODE approach to inferring trajectories in single-cell RNA sequencing data
A statistical approach to a more robust dimensionality reduction
The Ecology of Life
Working closely with the Kuehn Lab at UChicago we have been pursuing statistical relations between the structure of natural microbial ecosystems to their collective metabolic functions. While the work started in the context of synthetic communities of natural isolates we are now studying natural communities directly.
Representative studies:
Predicting microbial metabolic function from genetic structure (Diane Newman and Avi Flamholz's opinion piece on the work)
Exploring the ecological origins of global taxonomic trends with environmental
The Adaptability of Life
Working closely with the Pincus Lab at UChicago we are beginning to study how cell's adapt and allocate resources during development and cancer.
The Algorithms of Life
We envision building AI models for whole genome regulation.