Publications

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bioRxiv preprints
  1. Tharp, M.E., Han, C.Z., Balak, C.D., Fitzpatrick, C., O’Connor, C., Preissl, S., Buchanan, J., NOTT, A., Escoubet, L., Mavrommatis, K., Gupta, M., Schwartz, M.S., Sang, U.H., Jones, P.S., Levy, M.L., Gonda, D.D., Ben-Haim, S., Ciacci, J., Barba, D., Khalessi, A., Coufal, N.G., Chen, C.C., Glass, C.K., Page D.C.  The inactive X chromosome drives sex differences in microglial inflammatory activity in human glioblastoma  (2024) bioRxiv doi: https://doi.org/10.1101/2022.11.28.517913
2026
  1. Ziegler*, K.C., Askarova*, A., Gergian, C., Yaa, R.M., van Dalen, J., Transfeld, J., Zoppi, F., Du, J., Clode, D., Rahbar, P., Graham, R.E., Sargurupremraj, M., Debette, S., Gonda, D.D., Levy, M.L., Chandran, S., Falk, S., Karow, M., Matthews, P., Coufal, N., NOTT, A.  The brain neurovascular epigenome and its association with dementia. (2025) Neuron doi: 10.1016/j.neuron.2025.10.001  
     Open access article
2025
  1. Askarova, A., Yaa, R.M., Marzi, S.J., NOTT, A.  Genetic risk for neurodegenerative conditions is linked to disease-specific microglial pathways. (2025) PLOS Genetics doi: 10.1371/journal.pgen.1011407  
     Open access article   bioRxiv preprint
  2. Murphy, K.B., Ye, Y., Tsalenchuk, M., NOTT, A., Marzi, S.J.  CHAS infers cell type-specific signatures in bulk brain histone acetylation studies of neurological and psychiatric disorders. (2025) Cell Rep Methods doi: 10.1016/j.crmeth.2025.101032  
     Open access article   bioRxiv preprint
  3. Cho, J., Bae, S., Jeon, J., Transfeld, J., Lee, C., NOTT, A., Gao, F., Seo, J.  Enhanced differentiation of neural progenitor cells in Alzheimer’s disease into vulnerable immature neurons. (2025) iScience doi: 10.1016/j.isci.2025.112446  
     Open access article
  4. Abbasova*, L., Urbanaviciute*, P., Hu*, D., Ismail, J.N., Schilder, B.M., NOTT, A., Skene, N.G., Marzi S.J.  CUTTag recovers up to half of ENCODE ChIP-seq histone acetylation peaks. (2025) Nat. Commun. doi: 10.1038/s41467-025-58137-2  
     Open access article   bioRxiv preprint
  5. Haglund, A., Zuber, V., Yang, Y., Abouzeid, M., Feleke, R., Ko, J.H., NOTT, A., Babtie, A.C., Mills, J.D., Muhammed, L., Laaniste, L., Gveric, D.O., Clode, D., Pagni, S., Bellampalli, R., Somani, A., McDade, K., Anink, J.J., Mesarosova, L., Aronica, E., Thom, M., Sisodiya, S.M., Srivastava, P.K., Malhotra, D., Bryois, J., Bottolo, L., Johnson M.R.  Cell state-dependent allelic effects and contextual Mendelian randomisation analysis for human brain phenotypes. (2025) Nat. Genetics doi: 10.1038/s41588-024-02050-9  
     Open access article   bioRxiv preprint
2024
  1. Bedwell, L., Mavrotas, M., Demchenko, N., Yaa, R.M, Willis, B., Demianova, Z., Syed, N., Whitwell§, H.J., NOTT,§, A.  FANS Unfixed: Isolation and Proteomic Analysis of Mouse Cell Type-Specific Brain Nuclei. (2024) J. Proteome Res. doi: 10.1021/acs.jproteome.4c00161  
     Open access article
2023
  1. NOTT*,§, A., Holtman§, I.R.  Genetic insights into immune mechanisms of Alzheimer’s and Parkinson’s disease. (2023) Front Immunol. 14.   §corresponding authors
     Open access article
  2. Marzi, S.J., Schilder, B.M., NOTT, A., Sala Frigerio, C., Willaime-Morawek, S., Bucholc, M., Hanger, D.P., James, C., Lourida, I, Noble, W., Rodriguez-Algarra, F., Sharif, J.-A., Tsalenchuk, M., Winchester, L.M., Yaman, U., Yao, Z., Ranson, J.M., Llewllyn, D.J.  Artificial intelligence for neurodegenerative experimental models. (2023) Alzheimers Dement. 19(12):5970-5987.  
     Open access article
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.  Somatic mosaicism reveals clonal distributions of neocortical development. (2022) Nature (7907):689-696.  
     View-only version   bioRxiv preprint
  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 for tracking early events in brain development and deficits in Rett syndrome. (2022) Elife 11:e78079.  
     Open access article   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.