Here is a broad overview of my current work, I'll try to keep these projects updated as we make progress.
Cells as Attractors in a Dynamical System
Stem cells offer great therapeutical potential and have garnered lots of research interest. Recent experiments have successfully reprogrammed skin cells to embryonic stem cell-like cells, dubbed induced pluripotent stem cells (iPSCs). This has rekindled interest in an old idea of the Waddington landscape (modern image of the landscape above), in which cells are viewed as attractors in a dynamical system. We are currently working on using ideas from physics, such as spin glasses, to mathematically model the Waddington Landscape. This should allow us to give experimental predictions for novel reprogramming experiments.
Flux Balance Analysis and Bacterial Communication
Systems biology is a broad research area that encompasses diverse ideas from flux balance analysis (FBA) to bacterial communication. FBA is a technique for prediction of the growth rate of individual bacteria under different nutrient conditions by detailed reconstruction of the underlying metabolic network, while bacterial communication research focuses on collective behaviors such as quorum sensing and biofilm production. Statistical physics techniques have proved useful separately in FBA and bacterial communication, so we are trying to use statistical physics ideas as one coherent framework to study the trade off between individuality and collective behavior of bacteria, initially focusing on E. coli and their use of AI-2.
MicroRNAs are short sequences of RNA that can regulate gene regulation by binding to messenger RNA. They have recently been suggested to provide a novel gene regulation method. The ceRNA hypothesis recently proposed that messenger RNAs can indirectly regulate each by competing for the same pool of microRNAs. Our group is working on mathematically modeling this ceRNA hypothesis to see what parametric conditions are necessary for cross-talk between messenger RNAs.