Publications

Citations per year. Data from Google Scholar.

publications

Twa, G.M., Phillips III, R.A., Robinson, N.J., & Day, J.J. (2024). Accurate sample deconvolution of pooled snRNA-seq using sex-dependent gene expression patterns. bioRxiv, doi: https://doi.org/10.1101/2024.11.29.626066
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Brida, K.L., Jorgensen, E.T., Phillips III, R.A., Newman, C.E., Tuscher, J.J., Morring, E.K., Zipperly, M.E., Ianov, L., Montgomery, K.D., Tippani, M., Hyde, T. M., Maynard, K.R., Martinowich, K., and Day, J.J. (2024). Reelin marks cocaine-activated striatal ensembles, promotes neuronal excitability, and regulates cocaine reward. bioRxiv. doi: https://doi.org/10.1101/2024.06.17.599348
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Fitzgerald, N.D. & Day, J.J. (2024). Neuronal heterogeneity in the ventral tegmental area: distinct contributions to reward circuitry and motivated behavior. Addiction Neuroscience, In press. doi: https://doi.org/10.1016/j.addicn.2024.100191.

Tuscher, J.J., Phillips, R.A. III., & Day, J.J. (2024). Genome editing technologies for investigation of activity-dependent transcription. In: Transcriptional Regulation by Neuronal Activity: To the Nucleus and Back. Edited by: Ramendra Saha & Serena Dudek. Springer/Nature Press (2024). doi: https://doi.org/10.1007/978-3-031-68550-7
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Andraka, E., Phillips III, R.A., Brida, K.L., & Day, J.J. (2024). Chst9 marks a spatially and transcriptionally unique population of Oprm1-expressing neurons in the nucleus accumbens. Addiction Neuroscience. doi: https://doi.org/10.1016/j.addicn.2024.100153
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Bach, S.V., Bauman, A.J., Hosein, D., Tuscher, J.J., Ianov, L., Greathouse, K.M., Henderson, B.W., Herskowitz, J.H., Martinowich, K., & Day, J.J. (2024). Distinct roles of Bdnf I and Bdnf IV transcript variant expression in hippocampal neurons. Hippocampus, doi: https://doi.org/10.1101/2023.04.05.535694
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Roth J.R., Rush, T., Thompson, S.J., Aldaher, A.R., Dunn, T.B., Mesina, J.S., Cochran, J.N., Boyle, N.R., Dean, H.B., Yang, Z., Pathak, V., Ruiz, P., Wu, M., Day, J.J., Bostwick, J.R., Suto, M.J., Augelli-Szafran, C.E., & Roberson, E.D. Development of small-molecule Tau-SH3 interaction inhibitors that prevent amyloid-β toxicity and network hyperexcitability. Neurotherapeutics, available online 19 December 2023, e00291. doi: https://doi.org/10.1016/j.neurot.2023.10.001
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West, A.E. & Day, J.J. (2023). Genetics and epigenetics approaches as a path to the future of addiction science. Molecular and Cellular Neuroscience. doi: 10.1016/j.mcn.2023.103898
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Phillips III, R.A., Wan, E., Tuscher, J.J., Reid, D., Ianov, L., & Day, J.J. (2023). Temporally specific gene expression and chromatin remodeling programs regulate a conserved Pdyn enhancer. eLife. doi: https://doi.org/10.7554/eLife.89993.1
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Reynolds, L.M., Hernandez, G., Popescu, C., MacGowan, D., Nouel, D., Cuesta, S., Burke, S., Savell, K.E., Zhao, J., Restrepo-Lozano, J.M., Pokinko, M., Giroux, M., Israel, S., Orsini, T., He, S., Wodzinski, M., Epelbaum, J.G., Trudeau, L.E., Kolb, B., Day, J.J., & Flores, C. (2023). Amphetamine disrupts dopamine axon growth in adolescence by a sex-specific mechanism. Nature Communications. 14(1):4035. doi: 10.1038/s41467-023-39665-1.
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Walker, C., Greathouse, K., Tuscher, J.J., Dammer, E., Weber, A., Liu, E., Curtis, K., Boros, B., Freeman, C., Vin Seo, J., Ramdas, R., Hurst, C., Duong, D., Gearing, M., Murchison, C., Day, J.J., Seyfried, N., & Herskowitz, J. (2023). Cross-Platform Synaptic Network Analysis of Human Entorhinal Cortex Identifies TWF2 as a Modulator of Dendritic Spine Length. The Journal of Neuroscience, Apr 13;JN-RM-2102-22. doi: 10.1523/JNEUROSCI.2102-22.2023.
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Phillips, R.A. III., Tuscher, J.J., Wan, E., Fitzgerald, N.D., Zipperly, M.E., Duke, C.G., Ianov, L.I., & Day, J.J. (2023). Distinct subpopulations of D1 medium spiny neurons exhibit unique transcriptional responsiveness to cocaine. Molecular and Cellular Neuroscience, Mar 24;125:103849. doi: 10.1016/j.mcn.2023.103849
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Day, J.J. & Martinowich, K. (2023). Single-cell transcriptional profiling in brain reward structures. Neuropsychopharmacology, Jan;48(1):243-244. doi: 10.1038/s41386-022-01394-2.
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Phillips, R.A. III*, Tuscher, J.J.*, Black, S.L., Andraka, E., Fitzgerald, N.D., Ianov, L., & Day, J.J. (2022). An atlas of transcriptionally defined cell populations in the rat ventral tegmental area. Cell Reports, 39(1): 116016. doi: https://doi.org/10.1016/j.celrep.2022.110616
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Carullo, N.V.N., Hinds, J.E., Revanna, J.S., Tuscher, J.J., Bauman, A.J., & Day, J.J. (2021). A Cre-dependent CRISPR/dCas9 system for gene expression regulation in neurons. eNeuro. doi: https://doi.org/10.1523/ENEURO.0188-21.2021
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Tuscher, J.J., & Day, J.J. (2021). Morphine, the microbiome, and fatty acids: short chains make a big link in opioid reward. Neuropsychopharmacology, Nov;46(12):2039-2040. doi: 10.1038/s41386-021-01093-4.
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Davis, S.E., Roth, J.R., Aljabi, Q., Hakim, A.R., Savell, K.E., Day, J.J., & Arrant, A.E. (2021). Delivering progranulin to neuronal lysosomes protects against excitotoxicity. Journal of Biological Chemistry. DOI:https://doi.org/10.1016/j.jbc.2021.100993
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Mews, P., Calipari, E.S., Day, J.J., Lobo, M.K., Bredy, T., & Abel, T. (2021). From circuits to chromatin: The emerging role of epigenetics in mental health. The Journal of Neuroscience, JN-SY-1649-20; DOI: https://doi.org/10.1523/JNEUROSCI.1649-20.2020.
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Zipperly, M.E., Sultan, F.A., Graham, G.E., Brane, A.C., Simpkins, N.A., Carullo, N.V.N., Ianov, L., & Day, J.J. (2020). Regulation of dopamine-dependent transcription and cocaine action by Gadd45b. Neuropsychopharmacology. https://doi.org/10.1038/s41386-020-00828-z
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Duke, C.G., Bach, S.V., Revanna, J.S., Sultan, F.A., Southern, N.T., Davis, M.N., Carullo, N.V.N., Bauman, A.J., Phillips III, R.A., & Day, J.J. (2020). An improved CRISPR/dCas9 interference tool for neuronal gene suppression. Frontiers in Genome Editing, DOI: 10.3389/fgeed.2020.00009.
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Carullo, N.V.N., Phillips III, R.A., Simon, R.C., Roman Soto, S.A., Hinds, J.E., Salisbury, A.J., Revanna, J.S., Bunner, K.D., Ianov, L., Sultan, F.A., Savell, K.E., Gersbach, C.A., Day, J.J. (2020). Enhancer RNAs predict enhancer-gene regulatory links and are critical for enhancer function in neuronal systems. Nucleic Acids Research, 18:gkaa671.
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Voskobiynyk, Y., Roth, J.R., Cochran, J.N., Rush, T., Carullo, N.V.N., Mesina, J.S., Waqas, M., Vollmer, R.M., Day, J.J., McMahon, L.L., & Roberson, E.D. (2020). Alzheimer’s disease risk gene BIN1 induces Tau-dependent network hyperexcitability. eLife, 9:e57354.
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Savell, K.E.*, Tuscher, J.J.*, Zipperly, M.E.*, Duke, C.G.*, Phillips III, R.A.*, Bauman, A.J., Thukral, S., Sultan, F.A., Goska, N.A., Ianov, L., & Day, J.J. (2020). A dopamine-induced gene expression signature regulates neuronal function and cocaine response. Science Advances 6(26): eaba4221.
*These authors contributed equally.
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Day, J.J. (2019). Genetic and epigenetic editing in the nervous system. Dialogues in Clinical Neuroscience, 21 (4): 359-368.
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Duke, C.G., Savell, K.E., Tuscher, J.T., Phillips III, R.A., & Day, J.J. (2019). Blue light-induced gene expression alterations in cultured neurons are the result of phototoxic interactions with neuronal culture media. eNeuro. ENEURO.0386-19.2019; DOI: https://doi.org/10.1523/ENEURO.0386-19.2019.
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Savell, K.E., Sultan, F.A., & Day, J.J. (2019). A Novel Dual Lentiviral CRISPR-based Transcriptional Activation System for Gene Expression Regulation in Neurons. Bio-protocol, 9(17): e3348. DOI: 10.21769/BioProtoc.3348.
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Tuscher, J.J. & Day, J.J. (2019). Multigenerational epigenetic inheritance: One step forward, two generations back. Neurobiology of Disease. DOI: https://doi.org/10.1016/j.nbd.2019.104591
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Savell, K.E., Bach, S.V., Zipperly, M.E., Revanna, J.S., Goska, N.A., Tuscher, J.J., Duke, C.G., Sultan, F.A., Burke, J.N., Williams, D.M., Ianov, L., & Day, J.J. (2019). A neuron-optimized CRISPR/dCas9 activation system for robust and specific gene regulation. eNeuro. DOI: https://doi.org/10.1523/ENEURO.0495-18.2019.
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Carullo, N.V.N. & Day, J.J. (2019). Genomic enhancers in brain health and disease. Genes. DOI: https://doi.org/10.3390/genes10010043
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Stefanelli, G., Azam, A.B., Walters, B.J., Brimble, M.A., Gettens, C.P., Bouchard-Cannon, P., Cheng, H-Y.M., Davidoff, A.M., Narkaj, K., Day, J.J., Kennedy, A.J., & Zovkic, I.B. (2018). Learning and age-related changes in genome-wide H2A.Z binding in the hippocampus. Cell Reports 2(5):1124-1131.
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Ianov, L., DeBoth, M., Chawla, M.K., Rani, A., Kennedy, A.J., Piras, I., Day, J.J., Siniard, A., Kumar, A., Sweatt, J.D., Barnes, C.A., Huentelman, M.J., & Foster, T.C. (2017) Hippocampal Transcriptomic Profiles: Subfield Vulnerability to Age and Cognitive Impairment. Frontiers in Aging Neuroscience 9:383.
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Savell, K.E., & Day, J.J. (2017) Applications of CRISPR/Cas9 in the mammalian central nervous system. Yale Journal of Biology and Medicine 90(4):567-581.
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Duke, C.G., Kennedy, A.J., Gavin, C., Day, J.J.*, & Sweatt, J.D.* (2017) Experience-dependent epigenomic reorganization in the hippocampus. Learning & Memory 24: 278-288. *corresponding authors
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Kennedy, A.J., Rahn, E.J., Paulukaitis, B.S., Wang, J., Lewis, J.W., Watson, J.P., Strange, S.K., Barnard, B.A., Guzman-Karlsson, M.C., Phillips, S.E., Day, J.J., & Sweatt, J.D. (2016) Tcf4 regulates synaptic plasticity, DNA methylation, and memory function. Cell Reports 16(10): 2666–2685.
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Resendez, S.L., Keyes, P.C., Day, J.J., Hambro, C., Austin, C.J., Maina, F.K., Eidson, L., Porter-Stransky, K.A., Nevarez, N., McLean, J.W., Kuhnmeunch, M.A., Murphy, A.Z., Mathews, T.A., & Aragona, B.J. (2016) Dopamine and opioid systems interact within the nucleus accumbens to maintain monogamous pair bonds. eLife 2016;10.7554/eLife.15325.
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Savell, K. E., Gallus, N.V.N., Simon, R., Brown J., Revanna, J.S., Osborn, M.K., Song, E.Y., O’Malley, J.J., Stackhouse, C.T., Norvil, A., Gowher, H., Sweatt, J.D., & Day, J.J. (2016). Extra-coding RNAs regulate neuronal DNA methylation dynamics. Nature Communications 7: 12091.
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Press: Nature, BioTechniques, Epigenie

Meadows, J.P., Guzman-Karlsson, M., Phillips, S., Holleman, C., Posey, J.L., Day, J.J., Hablitz, J.J., & Sweatt, J.D. (2015). DNA methylation regulates cell-wide glutamatergic synaptic scaling. Science Signaling 8(382): ra61.
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Day, J.J., & Roberson, E.D. (2015) An epigenetic brake on genetic inheritance: DNA methylation slows effects of C9ORF72 mutations. Neurology 84(16): 1616-1617.
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Day, J.J., Kennedy, A., & Sweatt, J.D. (2015). DNA methylation and its implication and accessibility for pharmacological treatments in learning and memory. Annual Reviews in Pharmacology and Toxicology 6(55):591-611.
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Zovkic, I.B., Paulukaitis, B.S., Day, J.J., Etikala, D.M., & Sweatt, J.D. (2014). Histone H2A.Z subunit exchange controls transcription-dependent consolidation of recent and remote memory. Nature. 515(7528):582-586.
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Press: Epigenie, Science Daily

Day, J.J. (2014). New approaches to manipulating the epigenome. Dialogues in Clinical Neuroscience 16(3):345-357.
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Day, J.J., Childs, D., Guzman-Karlsson, M.C., Kibe, M., Moulden, J., Song, E., Tahir, A., & Sweatt, J.D. (2013). DNA methylation regulates associative reward learning. Nature Neuroscience 16(10), 1445-1452.
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Press: Science Daily, AL.com, UAB press

Porter-Stransky, K., Seiler, J., Day, J.J., & Aragona, B.J. (2013). Development of behavioral preferences for the optimal choice following unexpected reward omission is mediated by a reduction of D2-like receptor tone in the nucleus accumbens. The European Journal of Neuroscience 38(4):2572-88.
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Parrish, R., Day, J.J., & Lubin, F. (2012) Direct bisulfite sequencing for examination of DNA methylation patterns with gene and nucleotide resolution from brain tissues. Current Protocols in Neuroscience Jul;Chapter 7:Unit 7.24.
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Sugam, J.A., Day, J.J., Wightman, R.M., & Carelli, R.M. (2012) Phasic nucleus accumbens dopamine encodes risk-based decision-making behavior. Biological Psychiatry 71(3):199-205.
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Day, J.J., & Sweatt, J.D. (2011). Epigenetic mechanisms in cognition. Neuron 70(5): 813-29.
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Day, J.J., & Sweatt, J.D. (2011). Epigenetic treatments for cognitive impairments. Neuropsychopharmacology 37(1): 247-260.
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Wheeler, R.A., Aragona, B.J., Fuhrmann, K.A., Jones, J.L., Day, J.J., Cacciapaglia, F., Wightman, R.M., & Carelli, R.M. (2011). Cocaine cues drive opposing context-dependent shifts in reward processing and emotional state. Biological Psychiatry 69(11): 1067-74.
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Day, J.J., & Sweatt, J.D. (2011). Cognitive neuroepigenetics: A role for epigenetic mechanisms in learning and memory. Neurobiology of Learning and Memory 96(1):2-12.
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Sultan, F. & Day, J.J. (2011). Epigenetic mechanisms in memory and synaptic function. Epigenomics 3(2) 157-81.
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Day, J.J., Jones, J.L., & Carelli, R.M. (2011) Nucleus accumbens neurons encode predicted and ongoing reward costs. The European Journal of Neuroscience 33(2): 308-21.
Link Commentary by John Salamone

Day, J.J., & Sweatt, J.D. (2011). Epigenetic modifications in neurons are essential for formation and storage of behavioral memory. Neuropsychopharmacology 36(1): 357-58.
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Day, J.J., & Sweatt, J.D. (2010). DNA methylation and memory formation. Nature Neuroscience 13(11):1319-1323.
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Jones, J.L., Day, J.J., Wheeler, R.A., & Carelli, R.M. (2010). The basolateral amygdala differentially regulates conditioned neural responses within the nucleus accumbens core and shell. Neuroscience 169(3):1186-1198.
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Day, J.J., Jones, J.L., Wightman, R.M., & Carelli, R.M. (2010). Phasic nucleus accumbens dopamine release encodes effort and delay related costs. Biological Psychiatry 68(3):306-309.
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Jones, J.L., Day, J.J., Aragona, B.J., Wheeler, R.A., Wightman, R.M., & Carelli, R.M. (2010). Basolateral amygdala modulates terminal dopamine release in the nucleus accumbens and conditioned responding. Biological Psychiatry 67(8):737-744.
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Aragona, B.J., Day, J.J., Roitman, M.F., Cleaveland, N.A., Wightman, R.M., & Carelli, R.M. (2009). Opposite directionality in real-time dopamine transmission within the nucleus accumbens core and shell during the development of a cue-cocaine association. The European Journal of Neuroscience 30(10):1889-1899.
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Aragona, B.J., Cleaveland, N.A., Stuber, G.D., Day, J.J., Carelli, R.M., & Wightman, R.M. (2008). Preferential enhancement of dopamine transmission within the nucleus accumbens shell by cocaine is due to a direct increase in phasic dopamine release events. The Journal of Neuroscience 28(35): 8821-8831.
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Day, J.J. (2008). ERK activation during natural reward learning: A physiological role for phasic nucleus accumbens dopamine? The Journal of Neuroscience 28(17): 4295-4297.
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Day, J.J., & Carelli, R.M. (2008). Methamphetamine induces chronic corticostriatal depression: Too much of a bad thing. Neuron 58(1): 6-7.
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Day, J.J., Roitman, M.F., Wightman, R.M., & Carelli, R.M. (2007). Associative learning mediates dynamic shifts in dopamine signaling in the nucleus accumbens. Nature Neuroscience 10(8): 1020-1028.
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Paletz, E.M., Day, J.J., Craig-Schmidt, M.C., & Newland, M.C. (2007). Spatial and visual discrimination reversals in adult and geriatric rats exposed during gestation to methylmercury and n-3 polyunsaturated fatty acids. Neurotoxicology 28(4):707-719.
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Day, J.J. & Carelli, R.M. (2007). The nucleus accumbens and Pavlovian reward learning. The Neuroscientist 13(2): 148-159.
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Day, J.J., Wheeler, R.A., Roitman, M.F., & Carelli R.M. (2006). Nucleus accumbens neurons encode Pavlovian approach behaviors: Evidence from an autoshaping paradigm. The European Journal of Neuroscience 23(5): 1341-1351.
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Day, J.J., Reed, M.N., & Newland, M.C. (2005). Neuromotor deficits in aging rats exposed to methylmercury and n-3 fatty acids. Neurotoxicology and Teratology 27(4): 629-641.
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Preprints

Andraka, E., Phillips III, R.A., Brida, K.L., & Day, J.J. (2023). Chst9 marks a spatially and transcriptionally unique population of Oprm1-expressing neurons in the nucleus accumbens. bioRxiv. doi: https://doi.org/10.1101/2023.10.16.562623
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Published version

Phillips III, R.A., Wan, E., Tuscher, J.J., Reid, D., Ianov, L., & Day, J.J. (2023). Temporally specific gene expression and chromatin remodeling programs regulate a conserved Pdyn enhancer. bioRxiv. doi: https://doi.org/10.1101/2023.06.02.543489
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Published version

Bach, S.V., Bauman, A.J., Hosein, D., Tuscher, J.J., Ianov, L., Greathouse, K.M., Henderson, B.W., Herskowitz, J.H., Martinowich, K., & Day, J.J. (2023). Distinct roles of Bdnf I and Bdnf IV transcript variant expression in hippocampal neurons. bioRxiv, doi: https://doi.org/10.1101/2023.04.05.535694
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Published version

Phillips, R.A. III., Tuscher, J.J., Wan, E., Fitzgerald, N.D., Zipperly, M.E., Duke, C.G., Ianov, L.I., & Day, J.J. (2023). Distinct subpopulations of D1 medium spiny neurons exhibit unique transcriptional responsiveness to cocaine. bioRxiv, doi: https://doi.org/10.1101/2023.01.12.523845
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Published version

Phillips, R.A. III, Tuscher, J.J.*, Black, S.L., Ianov, L., & Day, J.J. (2021). An atlas of transcriptionally defined cell populations in the rat ventral tegmental area. bioRxiv. doi: https://doi.org/10.1101/2021.06.02.446737
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Published version

Carullo, N.V.N., Hinds, J.E., Revanna, J.S., Tuscher, J.J., Bauman, A.J., & Day, J.J. (2021). A Cre-dependent CRISPR/dCas9 system for gene expression regulation in neurons. bioRxiv. doi: https://doi.org/10.1101/2020.11.20.391987
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Published version

Duke, C.G., Bach, S.V., Revanna, J.S., Sultan, F.A., Southern, N.T., Davis, M.N., Carullo, N.V.N., Bauman, A.J., Phillips III, R.A., & Day, J.J. (2020). An improved CRISPR/dCas9 interference tool for neuronal gene suppression. bioRxiv. doi: https://doi.org/10.1101/2020.05.26.116822
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Published version

Zipperly, M.E., Sultan, F.A., Graham, G.E., Brane, A.C., Simpkins, N.A., Ianov, L., & Day, J.J. (2020). Regulation of dopamine-dependent transcription and cocaine action by Gadd45b. bioRxiv. doi: https://doi.org/10.1101/2020.05.01.072926
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Published version

Duke, C.G., Savell, K.E., Phillips III, R.A., & Day, J.J. (2019). Blue light-induced gene expression alterations in cultured neurons are the result of phototoxic interactions with neuronal culture media. bioRxiv. doi: https://doi.org/10.1101/783084
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Published version

Savell, K.E.*, Zipperly, M.E.*, Tuscher, J.J.*, Duke, C.G.*, Phillips III, R.A.*, Bauman, A.J., Thukral, S., Sultan, F.A., Goska, N.A., Ianov, L., & Day, J.J. (2019). A dopamine-induced gene expression signature regulates neuronal function and cocaine response. bioRxiv. doi: https://doi.org/10.1101/781872
*These authors contributed equally.
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Published version

Carullo, N.V.N., Phillips III, R.A., Simon, R.C., Roman Soto, S.A., Hinds, J.E., Salisbury, A.J., Revanna, J.S., Bunner, K.D., Ianov, L., Sultan, F.A., Savell, K.E., Gersbach, C.A., Day, J.J. (2018, updated 2020). Enhancer RNAs predict enhancer-gene regulatory links and are critical for enhancer function in neuronal systems. bioRxiv. doi: https://doi.org/10.1101/270967
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Published version