Mark Bathe, PhD

Photo of Professor Bathe.



Associate Professor of Biological Engineering


Nucleic acid nanotechnology
Synthetic structural biology
Quantitative fluorescence imaging and spectroscopy
Complex data analysis and Bayesian inference
Membrane biophysics, synapse structure and dynamics, mRNA transport, cell division, cell migration
Neurobiology, microbiology, cancer biology


Broad Institute of MIT & Harvard
Center for Environmental Health Sciences
Center for Excitonics
Center for Neurobiological Engineering
Department of Mechanical Engineering


Prof. Bathe obtained his Bachelor's, Master's and Doctoral Degrees at MIT working in the Departments of Mechanical Engineering, Chemical Engineering, Chemistry, and Biological Engineering before moving to Munich to carry out his postdoctoral research in Biological Physics. Bathe returned to MIT in 2009 to join the faculty in the Department of Biological Engineering, where he runs an interdisciplinary research group consisting of Biologists, Chemists, Physicists, and Engineers focused on quantitative physical approaches to understanding complex biological processes from a molecular perspective.


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 Areas: 

Selected Publications:

Monnier, Nilah, Zachary Barry, Hye Yoon Park, Kuan-Chung Su, Zachary Katz, Brian P. English, Arkajit Dey, Keyao Pan, Iain M. Cheeseman, Robert H. Singer et al. "Inferring transient particle transport dynamics in live cells." Nat Methods 12, no. 9 (2015): 838-40.
Sun, Wei, Etienne Boulais, Yera Hakobyan, Wei Li Wang, Amy Guan, Mark Bathe, and Peng Yin. "Casting inorganic structures with DNA molds." Science 346, no. 6210 (2014): 1258361.
Guo, Syuan-Ming, Nirmalya Bag, Aseem Mishra, Thorsten Wohland, and Mark Bathe. "Bayesian total internal reflection fluorescence correlation spectroscopy reveals hIAPP-induced plasma membrane domain organization in live cells." Biophys J 106, no. 1 (2014): 190-200.
Pan, Keyao, Do-Nyun Kim, Fei Zhang, Matthew R. Adendorff, Hao Yan, and Mark Bathe. "Lattice-free prediction of three-dimensional structure of programmed DNA assemblies." Nat Commun 5 (2014): 5578.
Castro, Carlos Ernesto, Fabian Kilchherr, Do-Nyun Kim, Enrique Lin Shiao, Tobias Wauer, Philipp Wortmann, Mark Bathe, and Hendrik Dietz. "A primer to scaffolded DNA origami." Nat Methods 8, no. 3 (2011): 221-9.