Boyden's research encompasses
optogenetics,
expansion microscopy,
deep brain stimulation,
multiplexed imaging,
machine learning, and more. He has authored or co-authored over 275 scientific papers, with a
h-index of 124.
Optogenetics In optogenetics, a light-sensitive ion channel or pump such as
channelrhodopsin-2 is genetically expressed in neurons, allowing neuronal activity to be controlled by light. There were early efforts to achieve targeted optical control dating back to 2002 that did not involve a directly light-activated ion channel, but it was the method based on directly light-activated channels from microbes, such as channelrhodopsin, emerging in 2005 that turned out to be broadly useful. Optogenetics in this way has been widely adopted by neuroscientists as a research tool, and it is also thought to have potential therapeutic applications. Boyden reported in 2007 that targeting the codon-optimized light-driven
halorhodopsin chloride pump (Halo) from
Natronomas pharaonis allowed for optogenetic silencing with yellow light. Later in 2010, he reported that
archaerhodopsin-3 (Arch) from
Halorubrum sodomense facilitated near-complete silencing of neurons using yellow light. Arch is also capable of spontaneously recovering from inactivation unlike Halo, which goes into lengthy inactive states. Its high performance enabled many new neuroscientific investigations using brain engineering. In 2014, Boyden reported how the channelrhodopsin Chronos could respond extremely fast to light, and how the channelrhodopsin Chrimson responded to red light. Chronos's
kinetics is quicker than previous channelrhodopsins but is more sensitive to light. This discovery enabled two-color activation of neurons without significant cross-talk. This led to the first optogenetics in people in 2021, where a blind patient was injected with an
adeno-associated viral vector encoding ChrimsonR coupled with goggle-enabled light stimulation. The patient successfully perceived, located, counted, and touched objects using the vector-treated eye with the goggles. This case reports the greatest partial functional recovery to date, for such forms of blindness. The cruxhalorhodopsin (Jaws) from Haloarcula salinarum was engineered to induce inhibition in response to red light in 2014. In 2017, Boyden designed a high-efficacy soma-targeted
opsin through combining the
N-terminal 150 residues of kainate receptor subunit 2 (KA2) to the high-photocurrent channelrhodopsin CoChR. This restricts its expression to neural somas, responding to
holographic stimulation with temporal precision.
Expansion microscopy Expansion microscopy (ExM) was developed as an alternative to the
light microscope, which is limited in resolution. In 2015, Boyden was able to expand a specimen by synthesizing a swellable
polymer network within it. By attaching specific label on the network, its swelling allows for the isotropic separation and
optical resolution. This allows for
superresolution microscopy using diffraction-limited microscopes. ExM has been optimized for
proteins,
nucleic acids, clinical tissues, decrowding,
in situ sequencing, and has developed a larger expansion factor. In 2018, Boyden developed a method of shrinking
3D printed materials to achieve
nanoscale feature sizes. By using
hydrogel scaffolds, Implosion Fabrication (ImpFab) creates
conductive 3D silver
nanostructures with complex geometries and resolutions in the tens of nanometers.
Deep brain stimulation In 2017, Boyden reported a
noninvasive method of deep electrical stimulation of neurons. By delivering
electric fields at frequencies higher than that able to recruit neural firing but within its
dynamic range, neurons within a region enveloped by the electric field can be modulated. This temporal interference (TI) successfully altered motor patterns in living mice. TI was validated in humans in 2023 where it modulated
hippocampal activity and increased the accuracy of
episodic memories in healthy subjects.
Multiplexed imaging Multiplexed imaging is the simultaneous measurement of the dynamics of many signals within a
signal transduction network. In 2020, Boyden fused a
fluorescent reporter to a pair of a
self-assembling peptides to create signaling reporter islands (SiRIs), which can be modularly designed. SiRIs can thus be adapted for simultaneous measurement of multiple signals in a network within single cells distant enough to be resolved under a microscope but close enough to spatially sample the biology (spatial multiplexing). Temporally multiplexed imaging (TMI), reported in 2023, uses genetically encoded fluorescent proteins with temporal properties to represent different signals. This is used to examine relationships between
kinase activities within single cells in addition to
cell-cycle activities. In 2018, Boyden reported a novel method of engineering complex proteins toward multidimensional specification through robotically picking identified cells as expressing proteins simultaneously exhibiting several properties. This enables the screening of hundreds of thousands of proteins in a few hours while evaluating each for multiple performance properties. The robot was applied to develop a fluorescent voltage indicator, Archon. Voltage imaging, using Archon as well as indicators made by other groups, was applied in areas of the mouse brain in 2019 and later across the entire brains of larval zebrafish in 2023. == Entrepreneurship ==