Mark Bathe

Associate Professor of Biological Engineering


  • Biological Engineering (BE)


(617) 324-5685

Research Areas: 

Research Summary: 

The Bathe lab’s philosophy is to apply principles and approaches from physics, chemistry, computer science and inference to solve leading-edge problems in quantitative biology and biophysics. Principal applications are focused on diverse aspects of membrane biology and biophysics including the in situ characterization of neuronal synapse proteomic composition, amyloid aggregation, bacterial cell wall synthesis, and bacterial toxin transport. Tools developed and applied by the lab include quantitative fluorescence imaging and spectroscopy together with synthetic nucleic acid architectures that act as nanometer-scale 3D scaffolds for dyes, proteins, RNAs, and plasmonic nanoparticles.

Together, the group bring these tools to bear on leading biological questions using highly data- driven, quantitative approaches to inferring the molecular structure and dynamics of complex biological systems that can be used together with precise nucleic acid architectures to interrogate and control biological systems from a molecular perspective.

The lab’s day-to-day work spans computational and experimental platforms encompassing physics-based inference and high resolution fluorescence imaging in a highly collaborative context where the group works closely with leading biologists in diverse application areas of interest. Major current thrusts of our group's current and constantly evolving work include the use of DNA probes for highly multiplexed super-resolution imaging to map single-molecule protein levels and localizations in neuronal synapses, using targeted fluorescence imaging to infer the mechanism of bacterial cell wall synthesis and growth, using live-cell fluorescence imaging of cancer cells to infer mechanisms of growth factor signaling and response, and mapping complex intracellular transport dynamics of mRNAs controlling spatial regulation of protein expression. The lab is also very active in the rational design of functional nucleic acid architectures to probe and program basic biological processes ranging from bacterial light harvesting to bacterial toxin assembly and trans-membrane transport.

Research Interest: 

Computational Biology; Quantitative Imaging and Microscopy; Cell Division