Project List

Full Shepherd bibliography with chapters, reviews and books available here.

Brain Microcircuits

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We carry out research on nerve cells as complex integrative systems.  The current experimental approaches with our colleagues include in vitro and in vivo electrophysiology, optogenetics, and high-resolution functional brain imaging.  In this work we use the olfactory pathway as a model system.

Computational Modeling

Our lab has pioneered applying realistic computational modeling methods to experimental data, to reveal mechanisms of information processing in dendritic spines, dendritic trees, and cortical microcircuits.  Our methods include 3D models and the first 3D printer neurons.

Computational Modeling Video

Cortical evolution

The earliest mammalian brains were dominated by olfactory cortex.  We are developing evidence that the basic functional principles are embedded in neocortex.

The Olfactory System

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Main Connections of the Olfactory System

Odorant molecules bind to receptors on olfactory sensory neurons (OSNs) in the olfactory epithelium (OE), initiating an action potential. OSN populations that express a single receptor type (the segregated information represented as magenta, dark green, or orange cell somas) converge onto glomeruli (GL) in the olfactory bulb (OB). Periglomerular (PG) cells act in a mainly inhibitory manner at the glomerular level. Tufted cells (TC) and mitral cells (MC) innervate single glomeruli and project information to the pyramidal cells (PC) in the olfactory cortex. Granule cells (GC) inhibit MCs and TCs at synapses on their lateral dendrites and cell somas. PCs send centrifugal fibers to the GCs. Small arrows indicate the direction of postsynaptic potential and action potential propagation.


Recognition of odor images, and the importance of retronasal smell, are giving us a new understanding of how the brain creates the perception of food flavor.  This is contributing to the current intense interest in brain mechanisms underlying healthy eating and disorders such as obesity.


How the Brain Creates Flavor from Food

Neuroenology (Neuro-oenology)

The neurogastronomical approach is also giving rise to a new scientific understanding of how the brain creates the taste of wine.


How the Brain Creates the Taste of Wine


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Through our integrative approach our lab is pioneering in the development of neuroinformatics.  The SenseLab Project contains 9 databases to facilitate the integration of multidisciplinary data, including over 14,000 olfactory receptor-like genes and 900 computational models.  We are building tools to organize and navigate functional connectomes.   CellPropDB, NeuronDB, ModelDB, MicrocircuitDB, 3DModelDB, ORDB, OdorDB, OdorMapDB, ORModelDB, BrainPharm

The SenseLab Project

Neuroscience History

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We stand on the shoulders of giants.  This perspective has been explored in studies of the founding of the neuron doctrine, the rise of modern neuroscience in the 1950s, the origins of brain imaging and cognitive neuroscience, and a biography in preparation of John Farquhar Fulton.