Publications

Full list of publications can be found here
bioRxiv preprints
  1. Hu, D., Abbasova, L., Schilder, B.M., NOTT, A., Skene, N.G., Marzi S.J.  CUT&Tag recovers up to half of ENCODE ChIP-seq peaks  (2022) bioRxiv doi: https://doi.org/10.1101/2022.03.30.486382
  2. Yildirim, M., Delepine, C., Feldman, D., Pham, V., Chou, S., Ip, J.P.K., NOTT, A., Tsai, L.-H., Ming, G.-L., So, P.T.C., Sur, M.  Label-free three-photon imaging of intact human cerebral organoids: tracking early events in brain development and deficits in Rett Syndrome. (2022) bioRxiv doi: https://doi.org/10.1101/2022.02.28.482282
  3. Murphy, K.B., NOTT, A., Marzi, S.J.  CHAS, a deconvolution tool, infers cell type-specific signatures in bulk brain histone acetylation studies of brain disorders. (2021) bioRxiv doi: https://doi.org/10.1101/2021.09.06.459142
2022
  1. Breuss*, M.W., Yang*, X., Schlachetzki*, J.C.M., Antaki*, D., Lana, A.J., Xu, X., Chung, C., Chai, G., Stanley, V., Song, Q., Newmeyer, T.F., Nguyen, A., O'Brien, S., Hoeksema, M.A., Cao, B., NOTT, A., McEvoy-Venneri, J., Pasillas, M.P., Barton, S.T., Copeland, B.R., Nahas, S., Van Der Kraan, L., Ding, Y., NIMH Brain Somatic Mosaicism Network, Glass, C.K., Gleeson, J.G. Nature  Somatic mosaicism reveals clonal distributions of neocortical development. (2022) Nature doi: 10.1038/s41586-022-04602-7.  
     View-only version   bioRxiv preprint
2021
  1. NOTT*,§, A., Schlachetzki*,§, J.C.M., Fixsen, B.R., Glass§, C.K.  Nuclei isolation protocol for omics interrogation of multiple brain cell types. (2021) Nat Protoc. doi: 10.1038/s41596-020-00472-3.   *Authors contributed equally   §Corresponding author
      NIH open access     View-only version
2020
  1. Morshed, N., Ralvenius, R.T., NOTT, A., Watson, A., Rodriguez F.H., Akay, L.A., Joughin, B.A., Pao, P.-C., Penney, J., LaRocque, L., Mastroeni, D., Tsai, L.-H., White, F.M.  Phosphoproteomics identifies microglial Siglec-F inflammatory response during neurodegeneration. (2020) Mol Syst Biol. 16:e9819.  
     Open access article   bioRxiv preprint
  2. Pao, P.-C., Patnaik, D., Watson, L.A., Gao, F., Pan, L., Wang, J., Adaikkan, C., Penney, J., Cam, H., Huang, W.-C., Rubino, L.P., Lee, A., NOTT, A., Phan, T.X., Gjoneska, E., Elmsaouri, S., Haggarty, S.J., Tsai, L.-H.  HDAC1 modulates OGG1-initiated oxidative DNA damage repair in the aging brain and Alzheimer’s disease. (2020) Nat Commun. 11(1):2484.
     Open access article
2019
  1. NOTT*, A., Holtman*, I.R., Coufal*, N.G., Schlachetzki, J.C.M., Yu, M., Hu, R., Han, C.Z., Pena, M., Xiao, J., Wu, Y., Keulen, Z., Pasillas, M.P., O’Connor, C., Nickl, C.K., Schafer, S.T., Shen, Z., Rissman, R.A., Brewer, J.B., Gosselin, D., Gonda, D.D., Levy, M.L., Rosenfeld, M.G., McVicker, G., Gage, F.H., Ren, B., Glass, C.K.  Brain cell type-specific enhancer-promoter interactome maps and disease-risk association. (2019) Science 366(6469):1134-1139.   *Authors contributed equally  
      NIH open access    bioRxiv preprint
  2. Sakai*, M., Troutman*, T.D., Seidman*, J.S., Ouyang, Z., Spann, N.J., Abe, Y., Ego, K.M., Bruni, C.M., Deng, Z., Schlachetzki, J.C.M., NOTT, A., Bennett, H., Chang, J., Vu, B.T., Pasillas, M.P., Link, V.M., Texari, L., Heinz, S., Thompson, B.M., McDonald, J.G., Geissmann, F., Glass, C.K.  Liver-Derived Signals Sequentially Reprogram Myeloid Enhancers to Initiate and Maintain Kupffer Cell Identity. (2019) Immunity. 51(4):655-670.
      Open access article
2018
  1.   NOTT, A., Glass C.K. Immune memory in the brain. (2018) Nature. 556(7701):312-313.
2016
  1. NOTT§, A., Cheng, J., Gao, F., Lin, Y.-T., Gjoneska, E., Ko, T., Minhas, P., Zamudio, A.V., Meng, J., Zhang, F., Jin, P., Tsai, L.-H.  Histone deacetylase 3 associates with MeCP2 to regulate FOXO and social behavior. (2016) Nat Neurosci. 19(11):1497-1505.   §Corresponding author
      NIH open access
  2. Seneviratne*, U., NOTT*, A., Bhat, V., Kodihalli, R., Wishnok, J., Tsai, L.-H., Tannenbaum, S.R.  S-nitrosation of proteins relevant to Alzheimer’s disease during early stages of neurodegeneration. (2016) Proc Natl Acad Sci USA. 113(15):4152-7.   *Authors contributed equally
      Open access article
  3. Nitarska, J., Smith, J.G., Sherlock, W.T., Hillege, M.H.H., NOTT, A., Barshop, W.D., Vashisht, A.A., Wohlschlegel, J.A., Mitter, R., Riccio, A. A functional switch of the NuRD chromatin remodeling complex subunits regulates mouse cortical development. (2016) Cell Reports. 17:1683-98.
      Open access article
  4. Durak, O., Gao, F., Kaeser-Woo, Y.J., Rueda, R., Martorell, A., NOTT, A., Liu, C.Y., Watson, L.A., Tsai, L.-H. The chromatin remodeler Chd8 transcriptionally regulates cell cycle and neurogenesis in the developing mouse cortex. (2016) Nat Neurosci. 19(11):1477-1488.
      NIH open access
2015
  1. Madabhushi, R., Gao, F., Pfenning, A.R., Pan, L., Yamakawa, S., Seo, J., Rueda, R., Phan, T.X., Yamakawa, H., Pao, P.C., Stott, R.T., Gjoneska, E., NOTT, A., Cho, S., Kellis, M., Tsai, L.-H. Activity-induced DNA breaks govern the expression of neuronal early-response genes. (2015) Cell. 161(7):1592-605.
     Open access article
  2. NOTT*, A., Cho*, S., Seo, J., Tsai, L.-H. HDAC2 expression in parvalbumin interneurons regulates synaptic plasticity in the mouse visual cortex. (2015) Neuroepigenetics. 1(1):34-40.   *Authors contributed equally
      Open access article
2013
  1. NOTT, A., Nitarska, J., Veenvliet, J.V., Schacke, S., Derijck, A.A., Sirko, P., Muchardt, C., Pasterkamp, J., Smidt, M.P., Riccio, A. S-Nitrosylation of HDAC2 regulates the expression of the chromatin remodeling factor Brm during radial neuron migration. (2013) Proc Natl Acad Sci USA. 110(8):3113-8.
      Open access article
  2. NOTT, A., Tsai, L.-H. The Top3β way to untangle RNA. (2013) Nat. Neurosci. 16(9):1163-4.
2012
  1. NOTT, A., Fass, D.M., Haggarty, S.J., Tsai, L.-H. HDAC inhibitors as novel therapeutics in aging, and alzheimer’s disease. (2012) In: Epigenetic Regulation in the Nervous System. (Sweatt, J.D., Meaney, M., Nestler, E., Akbarian, S. ed’s) Oxford: Academic Press. Pp. 224-49.
2009
  1. NOTT, A., Riccio, A. Nitric oxide-mediated epigenetic mechanisms in developing neurons. (2009) Cell Cycle. 8:725-30.
      Open access article
  2. NOTT, A., Riccio, A. Regulation of Histone Deacetylases: the Role of Nitric Oxide. (2009) In: Epigenetic Control and Neuronal Function. (Sassone-Corsi, P. ed) Washington, DC: Society for Neuroscience. pp. 35-43.
2008
  1. NOTT, A., Watson, P.M., Robinson, J.D., Crepaldi, L., Riccio, A. S-nitrosylation of histone deacetylase 2 induces chromatin remodeling in neurons. (2008) Nature. 455(7211):411-5.
  2. NOTT, A., Robinson, J.D., Riccio, A. DAF-FM detection of nitric oxide in embryonic cortical neurons. (2008) Protocol Exchange | Nature Research. DOI: 10.1038/nprot.2008.235
2006
  1. NOTT, A., Levin, E.D. Dorsal hippocampal alpha7 and alpha4beta2 nicotinic receptors and memory. (2006) Brain Research. 1081(1):72-8.