Thierry Emonet
Associate Professor of Molecular, Cellular, and Developmental Biology and of Physics
Research Interests
Computational Biology chemotaxis, olfaction, immunology
Research Summary
We are interested in biological sensing and decision making. We study how bacteria sense and explore their environment, how flies smell, and how T cells decide to mount or not an immune response. We use experiments and mathematical modeling to study the dynamical properties of biological systems and uncover the molecular origin of behavior. Our lab employs a mixture of biologists, physicists, computer scientists and mathematicians.
Extensive Research Description
Digital assays and multiscale agent-based modeling: The goal of this project is to build a modular,
parallel-ready simulator capable of replicating the modular, multi-scalar
architecture of complex biological systems, from individual molecular events to
cellular populations and organ behavior. By reproducing biological design in
silico, the aim of this effort is to produce a useful tool for systems biology,
and in the process, to discover important design principles relevant to
information processing systems in general. Our emphasis is to connect
in a computer, molecular mechanisms to behavior (http://emonet.biology.yale.edu/nfsim/
).
Dynamical encoding of odors by the fly: We are interested in the role of time in
the encoding of odor identity and intensity in the primary layer of the fly
olfactory system. In collaboration with John Carlson (MCDB) we perform in vivo electrophysiological recordings
to assay the dynamical properties of olfactory receptor neurons. In
collaboration with Steve Zucker (applied mathematics) we are analyzing the
geometry of the odor space.
The role of phenotypic variability in bacterial sensing: The question is how molecular noise might control a biological
function at the population level by tuning the distribution of single cell
behaviors. As
model system we use a canonical sensory system in biology, bacterial chemotaxis
in E. coli. For this project, we use direct comparison
between in vivo and in silico experiments.
Spatial
localization in signal processing:We are interested in the effect of spatial localization on signaling pathway
and in understanding the interplay between physical forces, enzymatic reactions
and spatial control in bacteria. We have developed CellTracker,
an automated cell detection and lineage analysis software that enable us to
quantify the spatio-temporal localization of fluorescently labeled proteins
inside single cells within a genealogy. In collaboration with the Jacobs-Wagner
lab we are looking at the localization of mRNA in bacteria and we study the
relationship between cell shape and bacterial cell wall synthesis.
Modeling the dynamical interaction between T
regulatory cells and T effector cells during an immune response: Together
with the Altan-Bonnet lab at the Memorial Sloan-Kettering Cancer Center we are
studying the highly dynamical interactions between effector and regulatory T
cells and the role of this dynamics in decision making.
Selected Publications
