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People
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Principal Investigator
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Mark Bathe
Assistant Professor
Department of Biological Engineering
Massachusetts Institute of Technology |
Administrative Assistant
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Darlene Ray
Administrative Assistant
Department of Biological Engineering
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Postdoctoral Researchers
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Dr. Etienne Boulais
PhD Engineering Physics, Ecole Polytechnique de Montreal
Computer-aided Engineering of DNA-based Light-harvesting Antennas
Programmed self-assembly of DNA enables the precise construction of nanometer-scale light-harvesting antennas to replicate photosynthesis. I am using computational modeling to design optimal DNA-based scaffolds for efficient photon capture and energy transfer to biomimetic reaction centers.
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Dr. Aprotim Mazumder
PhD Biology, National Centre for Biological Sciences TIFR
Single Cell DNA Damage Response
Corrective responses to DNA damage are essential to the healthy propagation of all cells. I am performing a genome-wide screen and single-cell mRNA and protein measurement using fluorescence imaging to investigate gene regulation in response to DNA-damage.
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Dr. Keyao Pan
PhD Bioengineering, Rice University
Bayesian Inference of Chromosome Structure and DNA Nanotechnology
Local and global chromosome structure play central roles in gene regulation and copy number variations leading to cancer. I am developing a Bayesian computational approach to infer the molecular-level structure of chromosomes from fluorescence in situ hybridization and chromosome conformation capture datasets. I am additionally developing computer algorithms for molecular-level modeling and control of structural nucleic acid nanotechnology.
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Dr. Lun Yang
PhD Civil & Environmental Engineering, Carnegie Mellon University
Computational Nucleic Acid Nanotechnology
Recent advances in nucleic acid nanotechnology enable the synthesis of complex three-dimensional structures at the nanometer scale. I am developing a computational framework to enable the rational design of DNA- and RNA-based nanostructures based on primary sequence for light-harvesting and enzyme catalysis applications.
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Graduate Students
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Matthew Adendorff
PhD Candidate in Biological Engineering
MSc Chemistry, Rhodes University
BSc Chemistry, Rhodes University
Nucleic Acid Nanostructure Optimization for Molecular Cascades
The highly programmable nature of nucleic acids allows for the synthesis of complex three-dimensional structures at the nanometer-scale. I am applying computational optimization to automate the nanostructure design process with application to maximize the light-harvesting capacity of DNA-based nanoscale antennas.
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Zachary Barry
PhD Candidate in Biological Engineering
BSc Biomedical Engineering, Georgia Institute of Technology
Bayesian Analysis of Receptor Dynamics
Epidermal Growth Factor Receptor (EGFR) is a central target for cancer therapy. I am applying highly parallel single-particle trajectory analysis to characterize and infer the mode of activation of EGFR.
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Jeremy Bigness
PhD Candidate in Biological Engineering
MA Quantitative and Computational Biology, Princeton University
BSc Physics and Biomedical Engineering, Rensselaer Polytechnic Institute
Inferring Collective Cellular Dynamics from Particle Tracking
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Syuan-Ming Guo
PhD Candidate in Chemistry
Bayesian Inference of EGFR Dynamics from Imaging FCS
Epidermal Growth Factor Receptor (EGFR) is a central target for cancer therapy. I am developing highly parallel fluorescence correlation spectroscopy (FCS) analysis approach to enable the characterization of spatiotemporal EGFR dynamics in normal and cancer cells to understand its mode of activation and inhibition by various therapies.
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Nilah Monnier
PhD Candidate in Harvard Biophysics
MPhil Chemistry, University of Cambridge
BA Biochemical Sciences, Harvard University
Quantitative analysis of intracellular transport
I am developing Bayesian and Hidden Markov Model approaches to study the dynamics of intracellular particles during transport. In particular, I am analyzing the motion of chromosomes to characterize a novel mechanism of intracellular actin-based transport in oocytes.
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Benjamin Steele
PhD Candidate in Biology
BA Biology, Caltech
Thermodynamic modeling of DNA nanostructures
I am developing a thermodynamic model for the formation of DNA nanostructures programmed to self-assemble by complementary nucleic acid base-pairing. This model will be used to enable the rational design of DNA-based scaffolds for diverse applications in biomolecular science and technology.
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Undergraduate & Visiting Students
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Nikita Kodali
Senior at Middlesex High School
Automated Epithelial Cell Tracking
I am developing automated image analysis procedures for tracking the motion of epithelial cells during embryogenesis.
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Alumni
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