The overall goal of our research program is to investigate the role of activity-dependent processes, and the requisite gene programs, involved in synaptic plasticity and how these processes go awry in neurological disorders.

  • Beagan JA, Pastuzyn ED, Fernandez LR, Guo MH, Feng K, Titus KR, Chandrashekar H, Shepherd JD, Phillips-Cremins JE. Three-dimensional genome restructuring across timescales of activity-induced neuronal gene expression. Nature Neuroscience. 2020 May 25; Read article»

  • Kyrke-Smith M, Volk LJ, Cooke SF, Bear MF, Huganir RL, Shepherd JD. The immediate early gene Arc is not required for hippocampal long-term potentiation. Read bioRxiv preprint »
  • Regier MJShepherd JD. Expanding the AtLAS of non-coding RNA functions in the brain. Cell Res. 2020 Feb 28; Read article»

  • Jenks K, Shepherd JD. Experience-dependent development and maintenance of binocular neurons in the mouse visual cortex. Read article »
  • Guo R, Pan Z, Taibi A, Shepherd JD, Menon R. Computational Cannula Microscopy of Neurons Using Neural Networks. Optics Letters. 2020 Jan 4. Read article»

  • Erlendsson S, Morado DR, Cullen HB, Feschotte C, Shepherd JS, Briggs, JAG. Structures of virus-like capsids formed by the Drosophila neuronal Arc proteins. Nature Neuroscience. 2020 Jan 06. Read article »
  • Eavri R, Shepherd JD, Welsh C, Flanders G, Bear M, Nedivi E. Interneuron Simplification and Loss of Structural Plasticity As Markers of Aging-Related Functional Decline. J Neuro. 2018 Sep 26; 38; 8421-8432. Read article »
  • Shepherd JD. Deconstructing the synapse. Nat Neuro. 2018 Sep 24; 21; 1294–1295. Read article »
  • Wall. M, Collins D, Chery S, Allen Z, Pastuzyn E.D, George A, Nikolova V, Moy S, Philpot B, Shepherd JD, Müller J, Ehlers M, Mabb A, Corrêa S. The Temporal Dynamics of Arc Expression Regulate Cognitive Flexibility. Neuron. 2018 Jun 27; 6; 124-1132.e7. Read article »
  • Pastuzyn E.D, Day C.E, Kearns R.B, Kyrke-Smith M, Taibi A.V, McCormick J, Yoder N, Belnap D.M, Erlendsson S, Morado D.R, Briggs J.A.G, Feschotte C, Shepherd J.D. The Neuronal Gene Arc Encodes a Repurposed Retrotransposon Gag Protein that Mediates Intercellular RNA Transfer. Cell. 2018 Jan 11; 172; 1-2. Read article »
  • Jenks K.R*, Kim T*, Pastuzyn E.D*, Okuno H, Taibi A.V, Bito H, Bear M.F, Shepherd J.D. Arc restores juvenile plasticity in adult mouse visual cortex. PNAS. 2017 Jul 17; Read article »
  • Pastuzyn E.D, Shepherd J.D. Activity-Dependent Arc Expression and Homeostatic Synaptic Plasticity Are Altered in Neurons from a Mouse Model of Angelman Syndrome. Frontiers in Mol. Neuro. 2017 Jul 28; Read article »
  • Kim G, Nagarajan N, Pastuzyn E, Jenks K.R, Capecchi M, Shepherd J, Menon R. Deep-brain imaging via epi-fluorescence computational cannula microscopy. Scientific Reports. 2017 Mar 20; 7, 44791. Read article »
  • Day C, Shepherd J.D. Arc: building a bridge from viruses to memory. Biochem J. 2015 Jul 1;469(1):e1-3. doi: 10.1042/BJ20150487. PMID: 26173260 Read article »
  • Gee J.M., Smith N.A., Fernandez F.R., Economo M.N., Brunert D., Rothermel M., Morris S.C., Talbot A., Palumbos S., Ichida J.M., Shepherd J.D., West P.J., Wachowiak M., Capecchi M.R., Wilcox K.S., White J.A., Tvrdik P. Imaging activity in neurons and glia with a Polr2a-based and cre-dependent GCaMP5G-IRES-tdTomato reporter mouse. Neuron. 2014 Sep 3;83(5):1058-72. Read article »

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  • Uzunova G, Hollander E, Shepherd J.D. The role of ionotropic glutamate receptors in childhood neurodevelopmental disorders: autism spectrum disorders and fragile x syndrome. Curr Neuropharmacol. 2014 Jan;12(1):71-98.  Read article »
  • Shepherd J.D. Memory, plasticity and sleep – A role for calcium permeable AMPA receptors? Front Mol Neurosci. (2012);5:49. Read article »
  • Wu J., Petralia R.S., Kurushima H., Patel H., Jung M., Volk L., Chowdhury S., Shepherd J.D., Dehoff M., Li Y., Kuhl D., Huganir R.L., Price D.L., Scannevin R., Troncoso J.C., Wong P.C., Worley P.F. Arc/Arg3.1 Regulates an Endosomal Pathway Essential for Activity-Dependent β-Amyloid Generation. Cell (2011) Oct 27;147(3):615-628. Read article »
  • Shepherd J.D. and Bear M.F. New views of Arc, a master regulator of synaptic plasticity. Nature Neuroscience (2011) March; 14(3): 279–284. Read article »
  • Smith-Hicks C, Xiao B, Deng R, Ji Y, Zhao X, Shepherd J.D., Posern G, Kuhl D, Huganir R.L, Ginty D.D, Worley P.F, Linden D.J. SRF binding to SRE 6.9 in the arc promoter Is essential for the late phase of LTD in cultured cerebellar purkinje cells. Nature Neuroscience (2010) Sep;13(9):1082-9. Read article »
  • McCurry C*. Shepherd J.D.*, Tropea D., Wang K., Bear M.F., Sur M. Loss of Arc renders the visual cortex impervious to the effects of sensory experience or deprivation. Nature Neuroscience (2010) Apr;13(4):450-7. Read article »
  • Park S., Park J.M., Kim S., Kim J.A., Shepherd J.D., Smith-Hicks C.L., Chowdhury S., Kaufmann W., Kuhl D., Ryazanov A.G., Huganir R.L., Linden D.J., Worley P.F. (2008). Eukaryotic elongation factor 2 and fragile X mental retardation protein control the dynamic translation of Arc essential for mGluR-LTD. Neuron (2008) Jul 10;59(1):70-83. Read article »
  • Shepherd J.D., Huganir R.L. The cell biology of synaptic plasticity: AMPA receptor trafficking. Annual Review of Cell and Developmental Biology (2007) Nov Vol. 23: 613-643. Read article »
  • Shepherd J.D.*, Rumbaugh G.*, Wu J. Chowdhury S., Plath N., Kuhl D., Huganir R.L., Worley P.F. Arc/Arg3.1 Mediates homeostatic synaptic scaling of AMPA receptors. Neuron (2006) Nov 9;52(3):475-84. Read article »


  • Chowdhury S.* Shepherd J.D.*, Ojuno H., Lyford G.,Petralia R., Plath N., Kuhl D., Huganir R.L., Worley P.F. Arc/Arg3.1 interacts with the endocytic machinery to regulate AMPA receptor trafficking. Neuron(2006) Nov 9;52(3):445-59. Read article »
  • Oddo S, Caccamo A*, Shepherd J.D.*, Murphy M.P, Golde T.E, Kayed R, Metherate R, Mattson M.P, Akbari Y, LaFerla F.M. Triple-transgenic model of Alzheimer’s disease with plaques and tangles: intracellular Abeta and synaptic dysfunction. Neuron (2003) Jul 31;39(3):409-21. Read article »