An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer’s disease

Fast gapped-read alignment with Bowtie 2

Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400 · see citing works

Cytoscape: A software Environment for integrated models of biomolecular interaction networks

Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003) · Genome Research · doi:10.1101/gr.1239303 · Cited by 51,888 · see citing works

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

Huang, D. W., Sherman, B. T., & Lempicki, R. A. (2009) · Nature Protocols · doi:10.1038/nprot.2008.211 · Cited by 35,890 · see citing works

BEDTools: a flexible suite of utilities for comparing genomic features

Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437 · see citing works

An integrated encyclopedia of DNA elements in the human genome

The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072 · see citing works

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

Szklarczyk, D., Gable, A. L., Lyon, D., Junge, A., Wyder, S., Huerta-Cepas, J., Simonovic, M., Doncheva, N. T., Morris, J. H., Bork, P., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky1131 · Cited by 17,749 · see citing works

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

Heinz, S., Benner, C., Spann, N., Bertolino, E., Lin, Y. C., Laslo, P., Cheng, J. X., Murre, C., Singh, H., & Glass, C. K. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.05.004 · Cited by 13,382 · see citing works

The Human Genome Browser at UCSC

Kent, W. J., Sugnet, C. W., Furey, T. S., Roskin, K. M., Pringle, T. H., Zahler, A. M., & Haussler, A. D. (2002) · Genome Research · doi:10.1101/gr.229102 · Cited by 10,400 · see citing works

Epigenetic Regulations of GABAergic Neurotransmission: Relevance for Neurological Disorders and Epigenetic Therapy

Shrestha, S., & Offer, S. M. (2016) · Medical Epigenetics · doi:10.1159/000444713 · Cited by 8,949 · see citing works

GREAT improves functional interpretation of cis-regulatory regions

McLean, C. Y., Bristor, D., Hiller, M., Clarke, S. L., Schaar, B. T., Lowe, C. B., Wenger, A. M., & Bejerano, G. (2010) · Nature Biotechnology · doi:10.1038/nbt.1630 · Cited by 4,502 · see citing works

Meta-Analysis of 74,046 Individuals Identifies 11 New Susceptibility Loci for Alzheimer’s Disease

(EADI), E. A. D. I., Lambert, J.-C., (GERAD), G. A. E. R. I. A. D., Alzheimer's Disease Genetic Consortium (ADGC), (CHARGE), C. F. H. A. A. R. I. G. E., Ibrahim-Verbaas, C. A., Harold, D., Naj, A. C., Sims, R., Bellenguez, C., et al. (2013) · Nature Genetics · doi:10.1038/ng.2802 · Cited by 4,336 · see citing works

Histone H3K27ac separates active from poised enhancers and predicts developmental state

Creyghton, M. P., Cheng, A. W., Welstead, G. G., Kooistra, T., Carey, B. W., Steine, E. J., Hanna, J., Lodato, M. A., Frampton, G. M., Sharp, P. A., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1016071107 · Cited by 4,302 · see citing works

Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome

Heintzman, N. D., Stuart, R. K., Hon, G., Fu, Y., Ching, C. W., Hawkins, R. D., Barrera, L. O., Van Calcar, S., Qu, C., Ching, K. A., et al. (2007) · Nature Genetics · doi:10.1038/ng1966 · Cited by 3,398 · see citing works

Staging of Alzheimer disease-associated neurofibrillary pathology using paraffin sections and immunocytochemistry

Braak, H., Alafuzoff, I., Arzberger, T., Kretzschmar, H., & Del Tredici, K. (2006) · Acta Neuropathologica · doi:10.1007/s00401-006-0127-z · Cited by 3,172 · see citing works

Genetic meta-analysis of diagnosed Alzheimer’s disease identifies new risk loci and implicates Aβ, tau, immunity and lipid processing

Alzheimer Disease Genetics Consortium (ADGC), Kunkle, B. W., The European Alzheimer’s Disease Initiative (EADI), Cohorts for Heart and Aging Research in Genomic Epidemiology Consortium (CHARGE), Genetic and Environmental Risk in AD/Defining Genetic, P. A. E. R. F. A. D. C. (., Grenier-Boley, B., Sims, R., Bis, J. C., Damotte, V., Naj, A. C., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0358-2 · Cited by 2,946 · see citing works

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

Chen, X., Han, X., Yuan, P., Fang, F., Huss, M., Vega, V. B., Wong, E., Orlov, Y. L., Zhang, W., Jiang, J., et al. (2008) · Cell · doi:10.1016/j.cell.2008.04.043 · Cited by 2,474 · see citing works

Combinatorial patterns of histone acetylations and methylations in the human genome

Wang, Z., Zang, C., Rosenfeld, J. A., Schones, D. E., Barski, A., Cuddapah, S., Cui, K., Roh, T.-Y., Peng, W., Zhang, M. Q., et al. (2008) · Nature Genetics · doi:10.1038/ng.154 · Cited by 2,331 · see citing works

Normalization of RNA-seq data using factor analysis of control genes or samples

Risso, D., Ngai, J., Speed, T. P., & Dudoit, S. (2014) · Nature Biotechnology · doi:10.1038/nbt.2931 · Cited by 2,169 · see citing works

Spatio-temporal transcriptome of the human brain

Kang, H. J., Kawasawa, Y. I., Cheng, F., Zhu, Y., Xu, X., Li, M., Sousa, A. M. M., Pletikos, M., Meyer, K. A., Sedmak, G., et al. (2011) · Nature · doi:10.1038/nature10523 · Cited by 2,084 · see citing works

The diverse functions of histone lysine methylation

Martin, C., & Zhang, Y. (2005) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1761 · Cited by 2,066 · see citing works

Adult hippocampal neurogenesis is abundant in neurologically healthy subjects and drops sharply in patients with Alzheimer’s disease

Moreno-Jiménez, E. P., Flor-García, M., Terreros-Roncal, J., Rábano, A., Cafini, F., Pallas-Bazarra, N., Ávila, J., & Llorens-Martín, M. (2019) · Nature Medicine · doi:10.1038/s41591-019-0375-9 · Cited by 1,577 · see citing works

CTCF: Master Weaver of the Genome

Phillips‐Cremins, J. E., & Corces, V. G. (2009) · Cell · doi:10.1016/j.cell.2009.06.001 · Cited by 1,540 · see citing works

Modification of Enhancer Chromatin: What, How, and Why?

Calo, E., & Wysocka, J. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.01.038 · Cited by 1,457 · see citing works

Untitled work

Wyss-Coray (2006) · doi:10.1038/nm1484 · Cited by 1,284 · see citing works

Rubinstein-Taybi syndrome caused by mutations in the transcriptional co-activator CBP

Petrif, F., Giles, R. H., Dauwerse, H. G., Saris, J. J., Hennekam, R. C. M., Masuno, M., Tommerup, N., van Ommen, G.-J. B., Goodman, R. H., Peters, D. J. M., et al. (1995) · Nature · doi:10.1038/376348a0 · Cited by 1,217 · see citing works

Sibling rivalry in the E2F family

Trimarchi, J. M., & Lees, J. A. (2002) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm714 · Cited by 1,158 · see citing works

Acetylation: a regulatory modification to rival phosphorylation?

Kouzarides, T. (2000) · The EMBO Journal · doi:10.1093/emboj/19.6.1176 · Cited by 1,155 · see citing works

Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci

De Jager, P. L., Srivastava, G., Lunnon, K., Burgess, J., Schalkwyk, L. C., Yu, L., Eaton, M. L., Keenan, B. T., Ernst, J., McCabe, C., et al. (2014) · Nature Neuroscience · doi:10.1038/nn.3786 · Cited by 956 · see citing works

Epigenetic mechanisms of longevity and aging

Sen, P., Shah, P. P., Nativio, R., & Berger, S. L. (2016) · Cell · doi:10.1016/j.cell.2016.07.050 · Cited by 956 · see citing works

Acetylation of Tau Inhibits Its Degradation and Contributes to Tauopathy

Min, S.-W., Cho, S.-H., Zhou, Y., Schroeder, S., Haroutunian, V., Seeley, W. W., Huang, E. J., Shen, Y., Masliah, E., Mukherjee, C., et al. (2010) · Neuron · doi:10.1016/j.neuron.2010.08.044 · Cited by 949 · see citing works

Understanding the language of Lys36 methylation at histone H3

Wagner, E. J., & Carpenter, P. B. (2012) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3274 · Cited by 933 · see citing works

Distinct roles of GCN5/PCAF‐mediated H3K9ac and CBP/p300‐mediated H3K18/27ac in nuclear receptor transactivation

Jin, Q., Yu, L., Wang, L., Zhang, Z., Kasper, L. H., Lee, J., Wang, C., Brindle, P. K., Dent, S. Y. R., & Ge, K. (2011) · The EMBO Journal · doi:10.1038/emboj.2010.318 · Cited by 877 · see citing works

The genetic landscape of Alzheimer disease: clinical implications and perspectives

Van Cauwenberghe, C., Van Broeckhoven, C., & Sleegers, K. (2016) · Genetics in Medicine · doi:10.1038/gim.2015.117 · Cited by 863 · see citing works

An epigenetic blockade of cognitive functions in the neurodegenerating brain

Gräff, J., Rei, D., Guan, J.-S., Wang, W.-Y., Seo, J., Hennig, K. M., Nieland, T. J. F., Fass, D. M., Kao, P. F., Kahn, M., et al. (2012) · Nature · doi:10.1038/nature10849 · Cited by 853 · see citing works

Mitochondria and Mitochondrial Cascades in Alzheimer’s disease

Swerdlow, R. H. (2018) · Journal of Alzheimer’s Disease · doi:10.3233/jad-170585 · Cited by 850 · see citing works

Daxx, a Novel Fas-Binding Protein That Activates JNK and Apoptosis

Yang, X., Khosravi‐Far, R., Chang, H. Y., & Baltimore, D. (1997) · Cell · doi:10.1016/s0092-8674(00)80294-9 · Cited by 830 · see citing works

CBP Histone Acetyltransferase Activity Is a Critical Component of Memory Consolidation

Korzus, E., Rosenfeld, M. G., & Mayford, M. (2004) · Neuron · doi:10.1016/j.neuron.2004.06.002 · Cited by 823 · see citing works

REST and stress resistance in ageing and Alzheimer’s disease

Lu, T., Aron, L., Zullo, J., Pan, Y., Kim, H., Chen, Y., Yang, T.-H., Kim, H., Drake, D., Liu, X., et al. (2014) · Nature · doi:10.1038/nature13163 · Cited by 760 · see citing works

Deregulated transcription factor E2F-1 expression leads to S-phase entry and p53-mediated apoptosis.

Qin, X. Q., Livingston, D. M., Kaelin, W. G., & Adams, P. D. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.23.10918 · Cited by 753 · see citing works

Therapeutics of Alzheimer's disease: Past, present and future

Anand, R., Gill, K. D., & Mahdi, A. A. (2013) · Neuropharmacology · doi:10.1016/j.neuropharm.2013.07.004 · Cited by 748 · see citing works

JMJD6 Is a Histone Arginine Demethylase

Chang, B., Chen, Y., Zhao, Y., & Bruick, R. K. (2007) · Science · doi:10.1126/science.1145801 · Cited by 746 · see citing works

Histone acetylation: molecular mnemonics on the chromatin

Gräff, J., & Tsai, L.-H. (2013) · Nature Reviews Neuroscience · doi:10.1038/nrn3427 · Cited by 680 · see citing works

Epigenetic regulation of ageing: linking environmental inputs to genomic stability

Benayoun, B. A., Pollina, E. A., & Brunet, A. (2015) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm4048 · Cited by 610 · see citing works

Why do trials for Alzheimer’s disease drugs keep failing? A discontinued drug perspective for 2010-2015

Mehta, D. G., Jackson, R., Paul, G., Shi, J., & Sabbagh, M. N. (2017) · Expert Opinion on Investigational Drugs · doi:10.1080/13543784.2017.1323868 · Cited by 603 · see citing works

Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer's disease

Gjoneska, E., Pfenning, A. R., Mathys, H., Quon, G., Kundaje, A., Tsai, L.-H., & Kellis, M. (2015) · Nature · doi:10.1038/nature14252 · Cited by 576 · see citing works

CBP-mediated acetylation of histone H3 lysine 27 antagonizesDrosophilaPolycomb silencing

Tie, F., Banerjee, R., Stratton, C. A., Prasad-Sinha, J., Stepanik, V. A., Zlobin, A., Dı́az, M. O., Scacheri, P. C., & Harte, P. J. (2009) · Development · doi:10.1242/dev.037127 · Cited by 575 · see citing works

Methylomic profiling implicates cortical deregulation of ANK1 in Alzheimer's disease

Lunnon, K., Smith, R., Hannon, E., De Jager, P. L., Srivastava, G., Volta, M., Troakes, C., Al-Sarraj, S., Burrage, J., Macdonald, R., et al. (2014) · Nature Neuroscience · doi:10.1038/nn.3782 · Cited by 574 · see citing works

Deregulated Expression of E2F-1 Induces S-Phase Entry and Leads to Apoptosis

Shan, B., & Lee, W. (1994) · Molecular and Cellular Biology · doi:10.1128/mcb.14.12.8166 · Cited by 529 · see citing works

Tau promotes neurodegeneration through global chromatin relaxation

Frost, B., Hemberg, M., Lewis, J., & Feany, M. B. (2014) · Nature Neuroscience · doi:10.1038/nn.3639 · Cited by 519 · see citing works

Time-Resolved Analysis Reveals Rapid Dynamics and Broad Scope of the CBP/p300 Acetylome

Weinert, B. T., Narita, T., Satpathy, S., Srinivasan, B., Hansen, B. K., Scholz, C. W., Hamilton, W. B., Zucconi, B. E., Wang, W., Liu, W. R., et al. (2018) · Cell · doi:10.1016/j.cell.2018.04.033 · Cited by 514 · see citing works

The Mount Sinai cohort of large-scale genomic, transcriptomic and proteomic data in Alzheimer’s disease

Wang, M., Beckmann, N. D., Roussos, P., Wang, E., Zhou, X., Wang, Q., Ming, C., Neff, R., Ma, W., Fullard, J. F., et al. (2018) · Scientific Data · doi:10.1038/sdata.2018.185 · Cited by 502 · see citing works

Expression quantitative trait loci: present and future

Nica, A. C., & Dermitzakis, E. T. (2013) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2012.0362 · Cited by 498 · see citing works

Genetic Heterogeneity in Rubinstein-Taybi Syndrome: Mutations in Both the CBP and EP300 Genes Cause Disease

Roelfsema, J. H., White, S. J., Ariyürek, Y., Bartholdi, D., Niedrist, D., Papadia, F., Bacino, C. A., den Dunnen, J. T., van Ommen, G. B., Breuning, M. H., et al. (2005) · The American Journal of Human Genetics · doi:10.1086/429130 · Cited by 481 · see citing works

Alteration of the microRNA network during the progression of Alzheimer's disease

Lau, P., Bossers, K., Janky, R., Salta, E., Frigerio, C. S., Barbash, S., Rothman, R., Sierksma, A. S. R., Thathiah, A., Greenberg, D., et al. (2013) · EMBO Molecular Medicine · doi:10.1002/emmm.201201974 · Cited by 474 · see citing works

5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells

Stroud, H., Feng, S., Kinney, S. R. M., Pradhan, S., & Jacobsen, S. E. (2011) · Genome biology · doi:10.1186/gb-2011-12-6-r54 · Cited by 466 · see citing works

Human whole genome genotype and transcriptome data for Alzheimer’s and other neurodegenerative diseases

Allen, M., Carrasquillo, M. M., Funk, C., Heavner, B. D., Zou, F., Younkin, C. S., Burgess, J. D., Chai, H.-S., Crook, J., Eddy, J. A., et al. (2016) · Scientific Data · doi:10.1038/sdata.2016.89 · Cited by 439 · see citing works

Mitochondrial dysfunction in Alzheimer's disease: role in pathogenesis and novel therapeutic opportunities

Perez Ortiz, J. M., & Swerdlow, R. H. (2019) · British Journal of Pharmacology · doi:10.1111/bph.14585 · Cited by 426 · see citing works

Apoptosis and the cell cycle

Meikrantz, W., & Schlegel, R. (1995) · Journal of Cellular Biochemistry · doi:10.1002/jcb.240580205 · Cited by 421 · see citing works

Sox2, a key factor in the regulation of pluripotency and neural differentiation

Zhang, S. (2014) · World Journal of Stem Cells · doi:10.4252/wjsc.v6.i3.305 · Cited by 399 · see citing works

Epigenetic Regulation in Neurodegenerative Diseases

Berson, A., Nativio, R., Berger, S. L., & Bonini, N. M. (2018) · Trends in Neurosciences · doi:10.1016/j.tins.2018.05.005 · Cited by 386 · see citing works

Dysregulation of the epigenetic landscape of normal aging in Alzheimer’s disease

Nativio, R., Donahue, G., Berson, A., Lan, Y., Amlie-Wolf, A., Tuzer, F., Toledo, J. B., Gosai, S. J., Gregory, B. D., Torres, C., et al. (2018) · Nature Neuroscience · doi:10.1038/s41593-018-0101-9 · Cited by 363 · see citing works

Separation of basal histone synthesis from S-phase histone synthesis in dividing cells

Wu, R. S., & Bonner, W. M. (1981) · Cell · doi:10.1016/0092-8674(81)90415-3 · Cited by 360 · see citing works

The BAH domain of ORC1 links H4K20me2 to DNA replication licensing and Meier–Gorlin syndrome

Kuo, A. J., Song, J., Cheung, P., Ishibe-Murakami, S., Yamazoe, S., Chen, J., Patel, D. J., & Gozani, O. (2012) · Nature · doi:10.1038/nature10956 · Cited by 349 · see citing works

MicroRNA-125b induces tau hyperphosphorylation and cognitive deficits in Alzheimer’s disease

Banzhaf‐Strathmann, J., Benito, E., May, S., Arzberger, T., Tahirovic, S., Kretzschmar, H., Fischer, A., & Edbauer, D. (2014) · The EMBO Journal · doi:10.15252/embj.201387576 · Cited by 326 · see citing works

Cohesin Is Required for Higher-Order Chromatin Conformation at the Imprinted IGF2-H19 Locus

Nativio, R., Wendt, K. S., Ito, Y., Huddleston, J. E., Uribe‐Lewis, S., Woodfine, K., Krueger, C., Reik, W., Peters, J., & Murrell, A. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000739 · Cited by 325 · see citing works

Lessons Learned from Alzheimer Disease: Clinical Trials with Negative Outcomes

Cummings, J. (2018) · Clinical and Translational Science · doi:10.1111/cts.12491 · Cited by 298 · see citing works

The ER stress factor XBP1s prevents amyloid-β neurotoxicity

Casas-Tinto, S., Zhang, Y., Sanchez-Garcia, J., Gomez-Velazquez, M., Rincon-Limas, D. E., & Fernandez-Funez, P. (2011) · Human Molecular Genetics · doi:10.1093/hmg/ddr100 · Cited by 275 · see citing works

Regulation of Transcription through Acetylation of H3K122 on the Lateral Surface of the Histone Octamer

Tropberger, P., Pott, S., Keller, C., Kamieniarz-Gdula, K., Caron, M. J., Richter, F. M., Li, G., Mittler, G., Liu, E. T., Bühler, M., et al. (2013) · Cell · doi:10.1016/j.cell.2013.01.032 · Cited by 272 · see citing works

Epigenome-wide study uncovers large-scale changes in histone acetylation driven by tau pathology in aging and Alzheimer’s human brains

Klein, H., Aubin, C., Gjoneska, E., Sullivan, S. E., Kaskow, B. J., Tang, A. Y., Smith, R. V., Xu, J., Pfenning, A. R., Bernstein, B., et al. (2018) · Nature Neuroscience · doi:10.1038/s41593-018-0291-1 · Cited by 267 · see citing works

Multiple faces of the SAGA complex

Koutelou, E., Hirsch, C. L., & Dent, S. (2010) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2010.03.005 · Cited by 258 · see citing works

CBP gene transfer increases BDNF levels and ameliorates learning and memory deficits in a mouse model of Alzheimer's disease

Caccamo, A., Maldonado, M. A., Bokov, A. F., Majumder, S., & Oddo, S. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1012851108 · Cited by 249 · see citing works

Histone H3 globular domain acetylation identifies a new class of enhancers

Pradeepa, M. M., Grimes, G. R., Kumar, Y., Olley, G., Taylor, G. C. A., Schneider, R., & Bickmore, W. A. (2016) · Nature Genetics · doi:10.1038/ng.3550 · Cited by 240 · see citing works

INRICH: interval-based enrichment analysis for genome-wide association studies

Lee, P. H., O'Dushlaine, C., Thomas, B., & Purcell, S. M. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts191 · Cited by 238 · see citing works

The CERAD Neuropathology Protocol and Consensus Recommendations for the Postmortem Diagnosis of Alzheimer’s Disease: A Commentary

Mirra, S. S. (1997) · Neurobiology of Aging · doi:10.1016/s0197-4580(97)00058-4 · Cited by 236 · see citing works

A platform for discovery: The University of Pennsylvania Integrated Neurodegenerative Disease Biobank

Toledo, J. B., Van Deerlin, V. M., Lee, E. B., Suh, E., Baek, Y., Robinson, J. L., Xie, S. X., McBride, J., Wood, E. M., Schuck, T., et al. (2014) · Alzheimer's & Dementia · doi:10.1016/j.jalz.2013.06.003 · Cited by 234 · see citing works

A histone acetylome-wide association study of Alzheimer’s disease identifies disease-associated H3K27ac differences in the entorhinal cortex

Marzi, S. J., Leung, S. K., Ribarska, T., Hannon, E., Smith, A. R., Pishva, E., Poschmann, J., Moore, K., Troakes, C., Al-Sarraj, S., et al. (2018) · Nature Neuroscience · doi:10.1038/s41593-018-0253-7 · Cited by 232 · see citing works

Hypoxia-Inducible Factor 3 Is an Oxygen-Dependent Transcription Activator and Regulates a Distinct Transcriptional Response to Hypoxia

Zhang, P., Yao, Q., Lu, L., Li, Y., Chen, P.-J., & Duan, C. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.02.011 · Cited by 232 · see citing works

Probing Nucleosome Function: A Highly Versatile Library of Synthetic Histone H3 and H4 Mutants

Dai, J., Hyland, E. M., Yuan, D., Huang, H., Bader, J. S., & Boeke, J. D. (2008) · Cell · doi:10.1016/j.cell.2008.07.019 · Cited by 229 · see citing works

Patterns of histone variant synthesis can distinguish go from G1 cells

Wu, R. S., Tsai, S., & Bonner, W. M. (1982) · Cell · doi:10.1016/0092-8674(82)90130-1 · Cited by 228 · see citing works

Identification and Characterization of E2F7, a Novel Mammalian E2F Family Member Capable of Blocking Cellular Proliferation

de Bruin, A., Maiti, B., Jakoi, L., Timmers, C., Buerki, R., & Leone, G. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m308105200 · Cited by 221 · see citing works

Brain Expression Genome-Wide Association Study (eGWAS) Identifies Human Disease-Associated Variants

Zou, F., Chai, H. S., Younkin, C. S., Allen, M., Crook, J. E., Pankratz, V. S., Carrasquillo, M. M., Rowley, C. N., Nair, A., Middha, S., et al. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002707 · Cited by 216 · see citing works

Complete Workflow for Analysis of Histone Post-translational Modifications Using Bottom-up Mass Spectrometry: From Histone Extraction to Data Analysis

Sidoli, S., Bhanu, N. V., Karch, K. R., Wang, X., & Garcia, B. A. (2016) · Journal of Visualized Experiments · doi:10.3791/54112 · Cited by 215 · see citing works

Microarray analyses of laser-captured hippocampus reveal distinct gray and white matter signatures associated with incipient Alzheimer's disease

Blalock, E. M., Buechel, H. M., Popovic, J., Geddes, J. W., & Landfield, P. W. (2011) · Journal of Chemical Neuroanatomy · doi:10.1016/j.jchemneu.2011.06.007 · Cited by 211 · see citing works

Targeting HDACs: A Promising Therapy for Alzheimer's Disease

Xu, K., Dai, X., Huang, H., & Jiang, Z.-F. (2011) · Oxidative Medicine and Cellular Longevity · doi:10.1155/2011/143269 · Cited by 206 · see citing works

Histone H3 lysine-to-methionine mutants as a paradigm to study chromatin signaling

Herz, H.-M., Morgan, M., Gao, X., Jackson, J., Rickels, R., Swanson, S. K., Florens, L., Washburn, M. P., Eissenberg, J. C., & Shilatifard, A. (2014) · Science · doi:10.1126/science.1255104 · Cited by 199 · see citing works

H3 Lysine 4 Is Acetylated at Active Gene Promoters and Is Regulated by H3 Lysine 4 Methylation

Guillemette, B., Drogaris, P., Lin, H.-H. S., Armstrong, H., Hiragami-Hamada, K., Imhof, A., Bonneil, É., Thibault, P., Verreault, A., & Festenstein, R. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1001354 · Cited by 199 · see citing works

NFAT control of immune function: New Frontiers for an Abiding Trooper

Vaeth, M., & Feske, S. (2018) · F1000Research · doi:10.12688/f1000research.13426.1 · Cited by 191 · see citing works

EpiProfile 2.0: A Computational Platform for Processing Epi-Proteomics Mass Spectrometry Data

Yuan, Z., Sidoli, S., Marchione, D. M., Simithy, J., Janssen, K. A., Szurgot, M. R., & Garcia, B. A. (2018) · Journal of Proteome Research · doi:10.1021/acs.jproteome.8b00133 · Cited by 187 · see citing works

ATAC-king the complexity of SAGA during evolutionPreprint

Spedale, G., Timmers, H. T. M., & Pijnappel, W. W. M. P. (2012) · Genes & Development · doi:10.1101/gad.184705.111 · Cited by 180 · see citing works

A Highly Sensitive and Robust Method for Genome-wide 5hmC Profiling of Rare Cell Populations

Han, D., Lu, X., Shih, A. H., Nie, J., You, Q., Xu, M. M., Melnick, A. M., Levine, R. L., & He, C. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.06.028 · Cited by 167 · see citing works

Loss of nuclear factor E2-related factor 1 in the brain leads to dysregulation of proteasome gene expression and neurodegeneration

Lee, C. S., Lee, C., Hu, T., Nguyen, J. M., Zhang, J., Martin, M. V., Vawter, M. P., Huang, E. J., & Chan, J. Y. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1019209108 · Cited by 164 · see citing works

Discussion

Nagy, Z., Esiri, M. M., & Smith, A. D. (1998) · Neuroscience · doi:10.1016/s0306-4522(98)00293-0 · Cited by 157 · see citing works

Wnt signaling in Alzheimer's disease: Up or down, that is the question

Boonen, R. A. C. M., van Tijn, P., & Živković, D. (2008) · Ageing Research Reviews · doi:10.1016/j.arr.2008.11.003 · Cited by 143 · see citing works

Pathway Analysis of ChIP-Seq-Based NRF1 Target Genes Suggests a Logical Hypothesis of their Involvement in the Pathogenesis of Neurodegenerative Diseases

Satoh, J., Kawana, N., & Yamamoto, Y. (2013) · Gene Regulation and Systems Biology · doi:10.4137/grsb.s13204 · Cited by 141 · see citing works

Neurons in Vulnerable Regions of the Alzheimer’s Disease Brain Display Reduced ATM Signaling

Shen, X., Chen, J., Li, J., Kofler, J., & Herrup, K. (2016) · eNeuro · doi:10.1523/eneuro.0124-15.2016 · Cited by 118 · see citing works

Role of CBP and SATB-1 in Aging, Dietary Restriction, and Insulin-Like Signaling

Zhang, M., Poplawski, M. M., Yen, K., Cheng, H., Bloss, E. B., Zhu, X., Patel, H., & Mobbs, C. V. (2009) · PLoS Biology · doi:10.1371/journal.pbio.1000245 · Cited by 113 · see citing works

A chromodomain switch mediated by histone H3 Lys 4 acetylation regulates heterochromatin assemblyPreprint

Xhemalçe, B., & Kouzarides, T. (2010) · Genes & Development · doi:10.1101/gad.1881710 · Cited by 101 · see citing works

Wnt/β-Catenin Signaling in Alzheimer’s Disease

Ferrari, G., Avila, M., Medina, M., Perez-Palma, E., Bustos, B., & Alarcon, M. (2014) · CNS & Neurological Disorders - Drug Targets · doi:10.2174/1871527312666131223113900 · Cited by 95 · see citing works

From development to diseases: The role of 5hmC in brain

Sun, W., Zang, L., Shu, Q., & Li, X. (2014) · Genomics · doi:10.1016/j.ygeno.2014.08.021 · Cited by 90 · see citing works

CXXC finger protein 1 restricts the Setd1A histone H3K4 methyltransferase complex to euchromatin

Tate, C. M., Lee, J., & Skalnik, D. G. (2009) · FEBS Journal · doi:10.1111/j.1742-4658.2009.07475.x · Cited by 73 · see citing works

Quantification of Histone Deacetylase Isoforms in Human Frontal Cortex, Human Retina, and Mouse Brain

Anderson, K. W., Chen, J., Wang, M., Mast, N., Pikuleva, I. A., & Turko, I. V. (2015) · PLoS ONE · doi:10.1371/journal.pone.0126592 · Cited by 69 · see citing works

Drosophila Eye Model to Study Neuroprotective Role of CREB Binding Protein (CBP) in Alzheimer’s Disease

Cutler, T., Sarkar, A., Moran, M. T., Steffensmeier, A. M., Puli, O. R., Mancini, G., Tare, M., Gogia, N., & Singh, A. (2015) · PLoS ONE · doi:10.1371/journal.pone.0137691 · Cited by 65 · see citing works

Low Resolution Data-Independent Acquisition in an LTQ-Orbitrap Allows for Simplified and Fully Untargeted Analysis of Histone Modifications

Sidoli, S., Simithy, J., Karch, K. R., Kulej, K., & Garcia, B. A. (2015) · Analytical Chemistry · doi:10.1021/acs.analchem.5b03009 · Cited by 61 · see citing works

AP-1 Repressor Protein JDP-2: Inhibition of UV-Mediated Apoptosis through p53 Down-Regulation

Piu, F., Aronheim, A., Katz, S., & Karin, M. (2001) · Molecular and Cellular Biology · doi:10.1128/mcb.21.9.3012-3024.2001 · Cited by 61 · see citing works

Methylation of single CpG dinucleotides within a promoter element of the Herpes simplex virus tk gene reduces its transcription in vivo

Benhattar, J., & Jiricny, J. (1988) · Gene · doi:10.1016/0378-1119(88)90458-1 · Cited by 60 · see citing works

An E2F7-dependent transcriptional program modulates DNA damage repair and genomic stability

Mitxelena, J., Apraiz, A., Vallejo-Rodríguez, J., García‐Santisteban, I., Fullaondo, A., Álvarez‐Fernández, M., Malumbres, M., & Zubiaga, A. M. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky218 · Cited by 59 · see citing works

Histone H4 lysine 20 acetylation is associated with gene repression in human cells

Kaimori, J.-Y., Maehara, K., Hayashi‐Takanaka, Y., Harada, A., Fukuda, M., Yamamoto, S., Ichimaru, N., Umehara, T., Yokoyama, S., Matsuda, R., et al. (2016) · Scientific Reports · doi:10.1038/srep24318 · Cited by 56 · see citing works

Aberrant Expression of Histone Deacetylases 4 in Cognitive Disorders: Molecular Mechanisms and a Potential Target

Wu, Y., Hou, F., Wang, X., Kong, Q., Han, X., & Bai, B. (2016) · Frontiers in Molecular Neuroscience · doi:10.3389/fnmol.2016.00114 · Cited by 52 · see citing works

Premature aging with impaired oxidative stress defense in mice lacking TR4

Lee, Y., Liu, S., Liu, N.-C., Wang, R.-S., Chen, L., Lin, W., Ting, H., Ho, H.-C., Li, G., Puzas, E. J., et al. (2011) · American Journal of Physiology-Endocrinology and Metabolism · doi:10.1152/ajpendo.00701.2010 · Cited by 40 · see citing works

Interaction of E2F7 Transcription Factor with E2F1 and C-terminal-binding Protein (CtBP) Provides a Mechanism for E2F7-dependent Transcription Repression*

Liu, B.-Y., Shats, I., Angus, S. P., Gatza, M., & Nevins, J. (2013) · Journal of Biological Chemistry · doi:10.1074/jbc.m113.467506 · Cited by 36 · see citing works

PLZF mutation alters mouse hematopoietic stem cell function and cell cycle progression

Vincent‐Fabert, C., Platet, N., Vandevelde, A., Poplineau, M., Koubi, M., Finetti, P., Tibéri, G., Imbert, A., Bertucci, F., & Duprez, E. (2016) · Blood · doi:10.1182/blood-2015-09-666974 · Cited by 34 · see citing works

Daxx Is a Transcriptional Repressor of CCAAT/Enhancer-binding Protein β

Wethkamp, N., & Klempnauer, K. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m109.041186 · Cited by 31 · see citing works

Histone complements of human tissues, carcinomas, and carcinoma-derived cell lines

Gabriellia, F., Aden, D. P., Carrele, S. C., von Bahrd, C., Raned, A., Angelettie, C. A., & Hancockf, R. (1984) · Molecular and Cellular Biochemistry · doi:10.1007/bf00226019 · Cited by 26 · see citing works

Targeted Disruption in Mice of a Neural Stem Cell-Maintaining, KRAB-Zn Finger-Encoding Gene That Has Rapidly Evolved in the Human Lineage

Chien, H., Wang, H., Su, Y.-N., Lai, K.-Y., Lu, L.-C., Chen, P., Tsai, S., Wu, C., Hsieh, W., & Shen, C.-K. J. (2012) · PLoS ONE · doi:10.1371/journal.pone.0047481 · Cited by 14 · see citing works

Modulation of cellular processes by histone and non-histone protein acetylation

Shvedunova, M., & Akhtar, A. (2022) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-021-00441-y · Cited by 975 · see citing works

Biological aging processes underlying cognitive decline and neurodegenerative disease

Gonzales, M. M., Garbarino, V. R., Pollet, E., Palavicini, J. P., Kellogg, D. L., Kraig, E., & Orr, M. E. (2022) · Journal of Clinical Investigation · doi:10.1172/jci158453 · Cited by 394 · see citing works

The role of histone modifications: from neurodevelopment to neurodiseases

Park, J., Lee, K., Kim, K., & Yi, S.-J. (2022) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-022-01078-9 · Cited by 321 · see citing works

The human connectome in Alzheimer disease — relationship to biomarkers and genetics

Yu, M., Sporns, O., & Saykin, A. J. (2021) · Nature Reviews Neurology · doi:10.1038/s41582-021-00529-1 · Cited by 265 · see citing works

Deep learning-based approaches for multi-omics data integration and analysis

Ballard, J. L., Wang, Z., Li, W., Shen, L., & Long, Q. (2024) · BioData Mining · doi:10.1186/s13040-024-00391-z · Cited by 287 · see citing works

Gene–environment interactions in Alzheimer disease: the emerging role of epigenetics

Migliore, L., & Coppedè, F. (2022) · Nature Reviews Neurology · doi:10.1038/s41582-022-00714-w · Cited by 217 · see citing works

Dementia in Africa: current evidence, knowledge gaps, and future directions

Akinyemi, R. O., Yaria, J., Ojagbemi, A., Guerchet, M., Okubadejo, N., Njamnshi, A. K., Sarfo, F. S., Akpalu, A., Ogbole, G., Ayantayo, T., et al. (2022) · Alzheimer's & Dementia · doi:10.1002/alz.12432 · Cited by 184 · see citing works

Acetyl-CoA Metabolism and Histone Acetylation in the Regulation of Aging and Lifespan

Bradshaw, P. C. (2021) · Antioxidants · doi:10.3390/antiox10040572 · Cited by 185 · see citing works

A benchmark study of deep learning-based multi-omics data fusion methods for cancer

Leng, D., Zheng, L., Wen, Y., Zhang, Y., Wu, L., Wang, J., Wang, M., Zhang, Z., He, S., & Bo, X. (2022) · Genome biology · doi:10.1186/s13059-022-02739-2 · Cited by 163 · see citing works

Insights from multi-omics integration in complex disease primary tissues

Kreitmaier, P., Katsoula, G., & Zeggini, E. (2022) · Trends in Genetics · doi:10.1016/j.tig.2022.08.005 · Cited by 160 · see citing works

Multi-Omics Integration for the Design of Novel Therapies and the Identification of Novel Biomarkers

Ivanisevic, T., & Sewduth, R. (2023) · Proteomes · doi:10.3390/proteomes11040034 · Cited by 118 · see citing works

The interaction between ageing and Alzheimer's disease: insights from the hallmarks of ageing

Liu, Y., Tan, Y., Zhang, Z., Yi, M., Zhu, L., & Peng, W. (2024) · Translational Neurodegeneration · doi:10.1186/s40035-024-00397-x · Cited by 144 · see citing works

Stress, epigenetics, and aging: Unraveling the intricate crosstalk

Wu, Z., Qu, J. T., Zhang, W., & Liu, G. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.10.006 · Cited by 142 · see citing works

Histone Modifications in Alzheimer’s Disease

Santana, D. A., Smith, M. D. A. C., & Chen, E. (2023) · Genes · doi:10.3390/genes14020347 · Cited by 109 · see citing works

Role of Histone Post-Translational Modifications in Inflammatory Diseases

Lin, Y., Qiu, T., Wei, G., Que, Y., Wang, W., Kong, Y., Xie, T., & Chen, X. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.852272 · Cited by 95 · see citing works

Multiomics technologies: role in disease biomarker discoveries and therapeutics

Dar, M. A., Arafah, A. M., Bhat, K. A., Khan, A., Khan, M. S., Ali, A., Ahmad, S. M., Rashid, S. M., & Rehman, M. U. (2022) · Briefings in Functional Genomics · doi:10.1093/bfgp/elac017 · Cited by 96 · see citing works

Linking environmental risk factors with epigenetic mechanisms in Parkinson’s disease

Tsalenchuk, M., Gentleman, S., & Marzi, S. J. (2023) · npj Parkinson s Disease · doi:10.1038/s41531-023-00568-z · Cited by 90 · see citing works

Artificial intelligence-driven multi-omics approaches in Alzheimer's disease: Progress, challenges, and future directions

Ren, F., Wei, J., Chen, Q., Hu, M., Yu, L., Mi, J., Zhou, X., Qin, D., Wu, J., & Wu, A. (2025) · Acta Pharmaceutica Sinica B · doi:10.1016/j.apsb.2025.07.030 · Cited by 97 · see citing works

Machine Intelligence in Single-Cell Data Analysis: Advances and New Challenges

Liu, J., Fan, Z., Zhao, W., & Zhou, X. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.655536 · Cited by 84 · see citing works

Nuclei isolation of multiple brain cell types for omics interrogation

Nott, A., Schlachetzki, J. C. M., Fixsen, B. R., & Glass, C. K. (2021) · Nature Protocols · doi:10.1038/s41596-020-00472-3 · Cited by 79 · see citing works

The transcriptional coactivator CBP/p300 is an evolutionarily conserved node that promotes longevity in response to mitochondrial stress

Li, T. Y., Sleiman, M. B., Li, H., Gao, A. W., Mottis, A., Bachmann, A. M., Alam, G. E., Li, X., Goeminne, L. J. E., Schoonjans, K., et al. (2021) · Nature Aging · doi:10.1038/s43587-020-00025-z · Cited by 78 · see citing works

Multi Omics Applications in Biological Systems

Reyes, C. D. G., Alejo‐Jacuinde, G., Sanchez, B. P., Chávez‐Reyes, J., Onigbinde, S. B., Mogut, D., Hernández‐Jasso, I., Calderón-Vallejo, D., Quintanar, J. L., & Mechref, Y. S. (2024) · Current Issues in Molecular Biology · doi:10.3390/cimb46060345 · Cited by 85 · see citing works

Modeling late-onset Alzheimer’s disease neuropathology via direct neuronal reprogramming

Sun, Z., Kwon, J.-S., Ren, Y., Chen, S., Walker, C. K., Lu, X., Cates, K., Karahan, H., Sviben, S., Fitzpatrick, J. A. J., et al. (2024) · Science · doi:10.1126/science.adl2992 · Cited by 77 · see citing works

Emerging epigenetic insights into aging mechanisms and interventions

Wu, Z., Zhang, W., Qu, J. T., & Liu, G. (2024) · Trends in Pharmacological Sciences · doi:10.1016/j.tips.2023.12.002 · Cited by 74 · see citing works

Transcriptomic analysis of human brains with Alzheimer’s disease reveals the altered expression of synaptic genes linked to cognitive deficits

Williams, J. B., Cao, Q., & Yan, Z. (2021) · Brain Communications · doi:10.1093/braincomms/fcab123 · Cited by 72 · see citing works

The exposome of healthy and accelerated aging across 40 countries

Hernandez, H., Santamaria-Garcia, H., Moguilner, S., Farina, F. R., Legaz, A., Prado, P., Cuadros, J., Gonzalez, L., Gonzalez-Gomez, R., Migeot, J., et al. (2025) · Nature Medicine · doi:10.1038/s41591-025-03808-2 · Cited by 71 · see citing works

Applied machine learning in Alzheimer's disease research: omics, imaging, and clinical data

Li, Z., Jiang, X., Wang, Y., & Kim, Y. (2021) · Emerging Topics in Life Sciences · doi:10.1042/etls20210249 · Cited by 67 · see citing works

A hyper-quiescent chromatin state formed during aging is reversed by regeneration

Yang, N., Occean, J. R., Melters, D. P., Shi, C., Wang, L., Stransky, S., Doyle, M. E., Cui, C., Delannoy, M. R., Fan, J., et al. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.04.005 · Cited by 71 · see citing works

Brain high-throughput multi-omics data reveal molecular heterogeneity in Alzheimer’s disease

Eteleeb, A. M., Novotny, B. C., Tarraga, C. S., Sohn, C., Dhungel, E., Brase, L., Nallapu, A., Buss, J., Farias, F., Bergmann, K., et al. (2024) · PLOS Biology · doi:10.1371/journal.pbio.3002607 · Cited by 64 · see citing works

Gut microbiota-host lipid crosstalk in Alzheimer’s disease: implications for disease progression and therapeutics

Luo, Y., Yang, L.-L., & Yao, X. (2024) · Molecular Neurodegeneration · doi:10.1186/s13024-024-00720-0 · Cited by 70 · see citing works

Single-cell multiregion epigenomic rewiring in Alzheimer’s disease progression and cognitive resilience

Liu, Z., Zhang, S., James, B. T., Galani, K., Mangan, R. J., Fass, S. B., Liang, C., Wagle, M. M., Boix, C. A., Tanigawa, Y., et al. (2025) · Cell · doi:10.1016/j.cell.2025.06.031 · Cited by 65 · see citing works

Phase separation of phospho-HDAC6 drives aberrant chromatin architecture in triple-negative breast cancer

Lu, B., Qiu, R., Wei, J., Wang, L., Zhang, Q., Li, M., Zhan, X., Chen, J., Hsieh, I.-Y., Yang, C., et al. (2024) · Nature Cancer · doi:10.1038/s43018-024-00816-y · Cited by 62 · see citing works

Role of histone modifications in neurogenesis and neurodegenerative disease development

Zhao, A., Xu, W., Han, R., Wei, J., Qi, Y., Wang, M., Li, H., Li, M., & Chi, G. (2024) · Ageing Research Reviews · doi:10.1016/j.arr.2024.102324 · Cited by 59 · see citing works

Biomarkers for Alzheimer’s Disease: Context of Use, Qualification, and Roadmap for Clinical Implementation

Cummings, J. L., & Kinney, J. W. (2022) · Medicina · doi:10.3390/medicina58070952 · Cited by 58 · see citing works

Epigenetic Regulation of Neuroinflammation in Alzheimer’s Disease

Ma, Y., Wang, W., Liu, S., Qiao, X., Xing, Y., Zhou, Q., & Zhang, Z. (2023) · Cells · doi:10.3390/cells13010079 · Cited by 57 · see citing works

Role of Epigenetic Modulation in Neurodegenerative Diseases: Implications of Phytochemical Interventions

Prasanth, M. I., Sivamaruthi, B. S., Cheong, C. S. Y., Verma, K., Tencomnao, T., Brimson, J. M., & Prasansuklab, A. (2024) · Antioxidants · doi:10.3390/antiox13050606 · Cited by 57 · see citing works

Omics Data and Their Integrative Analysis to Support Stratified Medicine in Neurodegenerative Diseases

Cognata, V. L., Morello, G., & Cavallaro, S. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22094820 · Cited by 56 · see citing works

Trace elements and Alzheimer dementia in population-based studies: A bibliometric and meta-analysis

Li, K., Li, A., Mei, Y., Zhao, J., Zhou, Q., Li, Y., Yang, M., & Xu, Q. (2022) · Environmental Pollution · doi:10.1016/j.envpol.2022.120782 · Cited by 54 · see citing works

Omics-based biomarkers discovery for Alzheimer's disease

Aerqin, Q., Wang, Z.-T., Wu, K., He, X., Dong, Q., & Yu, J. (2022) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-022-04614-6 · Cited by 55 · see citing works

Neurodegeneration cell per cell

Balusu, S., Praschberger, R., Lauwers, E., Strooper, B. D., & Verstreken, P. (2023) · Neuron · doi:10.1016/j.neuron.2023.01.016 · Cited by 51 · see citing works

Promoting Alzheimer’s disease research and therapy with stem cell technology

Cao, Z., Kong, F., Ding, J., Chen, C., He, F., & Deng, W. (2024) · Stem Cell Research & Therapy · doi:10.1186/s13287-024-03737-w · Cited by 59 · see citing works

TRAPT: a multi-stage fused deep learning framework for predicting transcriptional regulators based on large-scale epigenomic data

Zhang, G., Song, C., Yin, M., Liu, L., Zhang, Y., Li, Y., Zhang, J., Guo, M., & Li, C. (2025) · Nature Communications · doi:10.1038/s41467-025-58921-0 · Cited by 55 · see citing works

Role of primary aging hallmarks in Alzheimer´s disease

Zhao, J., & Huai, J. (2022) · Theranostics · doi:10.7150/thno.79535 · Cited by 53 · see citing works

Relieving Cellular Energy Stress in Aging, Neurodegenerative, and Metabolic Diseases, SIRT1 as a Therapeutic and Promising Node

Yang, F., Wang, X., Yang, D., Lu, Y., Wei, G., Yu, W., Liu, X., Zheng, Q., Ying, J., & Hua, F. (2021) · Frontiers in Aging Neuroscience · doi:10.3389/fnagi.2021.738686 · Cited by 50 · see citing works

A Review of the Recent Advances in Alzheimer’s Disease Research and the Utilization of Network Biology Approaches for Prioritizing Diagnostics and Therapeutics

Hajjo, R., Sabbah, D. A., Abusara, O. H., & Bawab, A. Q. A. (2022) · Diagnostics · doi:10.3390/diagnostics12122975 · Cited by 55 · see citing works

The role of epigenetic modifications for the pathogenesis of Crohn's disease

Hornschuh, M., Wirthgen, E., Wolfien, M., Singh, K. P., Wolkenhauer, O., & Däbritz, J. (2021) · Clinical Epigenetics · doi:10.1186/s13148-021-01089-3 · Cited by 51 · see citing works

Multi-omics analysis reveals the key factors involved in the severity of the Alzheimer’s disease

Meng, L., Jin, H., Yulug, B., Altay, O., Li, X., Hanoglu, L., Cankaya, S., Coskun, E., Idil, E., Nogaylar, R., et al. (2024) · Alzheimer's Research & Therapy · doi:10.1186/s13195-024-01578-6 · Cited by 49 · see citing works

Nutritional metabolism and cerebral bioenergetics in Alzheimer's disease and related dementias

Yassine, H. N., Self, W. K., Kerman, B. E., Santoni, G., Shanmugam, N. K. N., Abdullah, L. I., Golden, L. R., Fonteh, A. N., Harrington, M. G., Gräff, J., et al. (2022) · Alzheimer s & Dementia · doi:10.1002/alz.12845 · Cited by 49 · see citing works

A machine learning and deep learning-based integrated multi-omics technique for leukemia prediction

Abbasi, E. Y., Deng, Z., Arain, Q. A., Khan, A., Shaikh, A., Reshan, M. S. A., Sulaiman, A. A., & Alshahrani, H. M. (2024) · Heliyon · doi:10.1016/j.heliyon.2024.e25369 · Cited by 49 · see citing works

The hitchhikers’ guide to RNA sequencing and functional analysis

Chen, J.-W., Shrestha, L., Green, G. A., Leier, A., & Marquez‐Lago, T. T. (2023) · Briefings in Bioinformatics · doi:10.1093/bib/bbac529 · Cited by 47 · see citing works

Restoring the epigenome in Alzheimer's disease: advancing HDAC inhibitors as therapeutic agents

Pereira, M. S., Cruz, M. T., Fortuna, A. C., & Bicker, J. (2024) · Drug Discovery Today · doi:10.1016/j.drudis.2024.104052 · Cited by 44 · see citing works

Targeting acetyl-CoA metabolism attenuates the formation of fear memories through reduced activity-dependent histone acetylation

Alexander, D. C., Corman, T. S., Mendoza, M. R., Glass, A., Belity, T., Wu, R., Campbell, R. R., Han, J., Keiser, A. A., Winkler, J. D., et al. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2114758119 · Cited by 40 · see citing works

The microglial lysosomal system in Alzheimer’s disease: Guardian against proteinopathy

Acker, Z. P. V., Perdok, A., Bretou, M., & Annaert, W. G. (2021) · Ageing Research Reviews · doi:10.1016/j.arr.2021.101444 · Cited by 45 · see citing works

Clearance Systems in the Brain, From Structure to Function

Liu, J., Guo, Y., Zhang, C., Zeng, Y., Luo, Y., & Wang, G. (2022) · Frontiers in Cellular Neuroscience · doi:10.3389/fncel.2021.729706 · Cited by 42 · see citing works

The promise of multi-omics approaches to discover biological alterations with clinical relevance in Alzheimer’s disease

Clark, C., Rabl, M., Dayon, L., & Popp, J. (2022) · Frontiers in Aging Neuroscience · doi:10.3389/fnagi.2022.1065904 · Cited by 40 · see citing works

The reverse transcriptase inhibitor <scp>3TC</scp> protects against age‐related cognitive dysfunction

Wahl, D., Smith, M. E., McEntee, C. M., Cavalier, A. N., Osburn, S. C., Burke, S. D., Grant, R. A., Nerguizian, D., Lark, D. S., Link, C. D., et al. (2023) · Aging Cell · doi:10.1111/acel.13798 · Cited by 40 · see citing works

A novel missense variant in ACAA1 contributes to early-onset Alzheimer’s disease, impairs lysosomal function, and facilitates amyloid-β pathology and cognitive decline

Luo, R., Fan, Y., Yang, J., Ye, M., Zhang, D., Guo, K., Li, X., Bi, R., Xu, M., Yang, L.-X., et al. (2021) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-021-00748-4 · Cited by 41 · see citing works

Global and cross-modal feature aggregation for multi-omics data classification and application on drug response prediction

Zheng, X., Wang, M., Huang, K., & Zhu, E. (2023) · Information Fusion · doi:10.1016/j.inffus.2023.102077 · Cited by 39 · see citing works

Integrative approach of omics and imaging data to discover new insights for understanding brain diseases

Yoon, J. H., Lee, H., Kwon, D., Lee, D., Lee, S., Cho, E., Kim, J., & Kim, D. (2024) · Brain Communications · doi:10.1093/braincomms/fcae265 · Cited by 39 · see citing works

Epigenetic Regulation of Aging and its Rejuvenation

An, Y., Wang, Q., Gao, K., Zhang, C., Ouyang, Y., Li, R., Zhou, M., Wu, T., Zhou, L., Xie, Z., et al. (2025) · MedComm · doi:10.1002/mco2.70369 · Cited by 44 · see citing works

AI-DrugNet: A network-based deep learning model for drug repurposing and combination therapy in neurological disorders

Pan, X., Yun, J., Coban‐Akdemir, Z., Jiang, X., Wu, E., Huang, J. H., Sahni, N., & Yi, S. S. (2023) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2023.02.004 · Cited by 36 · see citing works

Aging the brain: multi-region methylation principal component based clock in the context of Alzheimer’s disease

Thrush, K., Bennett, D. A., Gaiteri, C., Horvath, S., van Dyck, C. H., Higgins‐Chen, A., & Levine, M. E. (2022) · Aging · doi:10.18632/aging.204196 · Cited by 38 · see citing works

SMGR: a joint statistical method for integrative analysis of single-cell multi-omics data

Song, Q., Zhu, X., Jin, L., Chen, M., Zhang, W., & Su, J. (2022) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqac056 · Cited by 37 · see citing works

Comprehensive analyses of brain cell communications based on multiple scRNA‐seq and snRNA‐seq datasets for revealing novel mechanism in neurodegenerative diseases

Zhang, C., Tan, G., Zhang, Y., Zhong, X., Zhao, Z., Peng, Y., Cheng, Q., Xue, K., Xu, Y., Li, X., et al. (2023) · CNS Neuroscience & Therapeutics · doi:10.1111/cns.14280 · Cited by 35 · see citing works

Epigenetic control of microglial immune responses

Scholz, R., Brösamle, D., Yuan, X., Beyer, M., & Neher, J. J. (2024) · Immunological Reviews · doi:10.1111/imr.13317 · Cited by 39 · see citing works

Curcumin protects against manganese-induced neurotoxicity in rat by regulating oxidative stress-related gene expression via H3K27 acetylation

Yang, Y., Liu, Y., Zhang, A.-L., Tang, S., Ming, Q., Ao, C.-Y., Liu, Y., Li, C.-Z., Yu, C. W., Zhao, H. Y., et al. (2022) · Ecotoxicology and Environmental Safety · doi:10.1016/j.ecoenv.2022.113469 · Cited by 36 · see citing works

Dissecting the brain with spatially resolved multi-omics

Fangma, Y., Liu, M., Liao, J., Chen, Z., & Zheng, Y. (2023) · Journal of Pharmaceutical Analysis · doi:10.1016/j.jpha.2023.04.003 · Cited by 37 · see citing works

Targeting epigenetics: A novel promise for Alzheimer’s disease treatment

Jeremic, D., Jiménez‐Díaz, L., & Navarro‐López, J. D. (2023) · Ageing Research Reviews · doi:10.1016/j.arr.2023.102003 · Cited by 36 · see citing works

Challenges and Approaches of Drugs Such as Memantine, Donepezil, Rivastigmine, and Aducanumab in the Treatment, Control and Management of Alzheimer's Disease

Saeedi, M., & Mehranfar, F. (2022) · Recent Patents on Biotechnology · doi:10.2174/1872208316666220302115901 · Cited by 35 · see citing works

Multi-omic integration via similarity network fusion to detect molecular subtypes of ageing

Yang, M., Matan-Lithwick, S., Wang, Y., De Jager, P. L., Bennett, D. A., & Felsky, D. (2023) · Brain Communications · doi:10.1093/braincomms/fcad110 · Cited by 35 · see citing works

CUT&Tag recovers up to half of ENCODE ChIP-seq histone acetylation peaks

Abbasova, L., Urbanaviciute, P., Hu, D., Ismail, J. N., Schilder, B. M., Nott, A., Skene, N., & Marzi, S. J. (2025) · Nature Communications · doi:10.1038/s41467-025-58137-2 · Cited by 32 · see citing works

Histone H3 Lysine 4 and 27 Trimethylation Landscape of Human Alzheimer’s Disease

Persico, G., Casciaro, F., Amatori, S., Rusin, M., Cantatore, F., Perna, A., Alberi, L. A., Fanelli, M., & Giorgio, M. (2022) · Cells · doi:10.3390/cells11040734 · Cited by 35 · see citing works

Structure, Function, and Allosteric Regulation of the 20S Proteasome by the 11S/PA28 Family of Proteasome Activators

Thomas, T. A., Salcedo-Tacuma, D., & Smith, D. M. (2023) · Biomolecules · doi:10.3390/biom13091326 · Cited by 33 · see citing works

Epigenomic analysis of Alzheimer's disease brains reveals diminished CTCF binding on genes involved in synaptic organization

Patel, P. J., Ren, Y., & Yan, Z. (2023) · Neurobiology of Disease · doi:10.1016/j.nbd.2023.106192 · Cited by 32 · see citing works

HAT and HDAC: Enzyme with Contradictory Action in Neurodegenerative Diseases

Singh, R., Rathore, A. S., Dilnashin, H., Keshri, P. K., Gupta, N. K., Satyaprakash, S. A., Zahra, W., Singh, S., & Singh, S. P. (2024) · Molecular Neurobiology · doi:10.1007/s12035-024-04115-6 · Cited by 32 · see citing works

Alzheimer’s disease and progressive supranuclear palsy share similar transcriptomic changes in distinct brain regions

Wang, X., Allen, M., İş, Ö., Reddy, J. S., Tutor‐New, F. Q., Casey, M. C., Carrasquillo, M. M., Oatman, S. R., Min, Y., Asmann, Y. W., et al. (2021) · Journal of Clinical Investigation · doi:10.1172/jci149904 · Cited by 30 · see citing works

Genetic insights into immune mechanisms of Alzheimer’s and Parkinson’s disease

Nott, A., & Holtman, I. R. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1168539 · Cited by 31 · see citing works

Inhibition of histone methyltransferase Smyd3 rescues NMDAR and cognitive deficits in a tauopathy mouse model

Williams, J. B., Cao, Q., Wang, W., Lee, Y., Qin, L., Zhong, P., Ren, Y., Ma, K., & Yan, Z. (2023) · Nature Communications · doi:10.1038/s41467-022-35749-6 · Cited by 29 · see citing works

Epigenomics and Lipidomics Integration in Alzheimer Disease: Pathways Involved in Early Stages

Peña‐Bautista, C., Álvarez‐Sánchez, L., Martínez, A. J. C., Baquero, M., & Cháfer‐Pericás, C. (2021) · Biomedicines · doi:10.3390/biomedicines9121812 · Cited by 28 · see citing works

Transcriptomic and epigenomic landscapes of Alzheimer's disease evidence mitochondrial-related pathways

Marmolejo-Garza, A., Medeiros-Furquim, T., Rao, R. G., Eggen, B. J. L., Boddeke, E., & Dolga, A. M. (2022) · Biochimica et Biophysica Acta (BBA) - Molecular Cell Research · doi:10.1016/j.bbamcr.2022.119326 · Cited by 28 · see citing works

Targeting epigenetics as a promising therapeutic strategy for treatment of neurodegenerative diseases

Zhang, L., Liu, Y., Lu, Y., & Wang, G. (2022) · Biochemical Pharmacology · doi:10.1016/j.bcp.2022.115295 · Cited by 27 · see citing works

Neuroepigenetics of ageing and neurodegeneration-associated dementia: An updated review

Mir, F. A., Amanullah, A., Jain, B. P., Hyderi, Z., & Gautam, A. (2023) · Ageing Research Reviews · doi:10.1016/j.arr.2023.102067 · Cited by 28 · see citing works

Histone acetylation in an Alzheimer’s disease cell model promotes homeostatic amyloid-reducing pathways

Xu, D. C., Sas‐Nowosielska, H., Donahue, G., Huang, H., Pourshafie, N., Good, C. R., & Berger, S. L. (2024) · Acta Neuropathologica Communications · doi:10.1186/s40478-023-01696-6 · Cited by 30 · see citing works

Gene body DNA hydroxymethylation restricts the magnitude of transcriptional changes during aging

Occean, J. R., Yang, N., Sun, Y., Dawkins, M. S., Munk, R. B., Belair, C., Dar, S. A., Anerillas, C., Wang, L., Shi, C., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-50725-y · Cited by 27 · see citing works

DNA methylation, histone acetylation in the regulation of memory and its modulation during aging

Singh, P., & Paramanik, V. (2025) · Frontiers in Aging · doi:10.3389/fragi.2024.1480932 · Cited by 27 · see citing works

Epigenetic regulation in Alzheimer’s disease: is it a potential therapeutic target?

Coppedè, F. (2021) · Expert Opinion on Therapeutic Targets · doi:10.1080/14728222.2021.1916469 · Cited by 27 · see citing works

Disease‐specific interactome alterations via epichaperomics: the case for Alzheimer’s disease

Ginsberg, S. D., Neubert, T. A., Sharma, S., Digwal, C. S., Yan, P., Timbus, C., Wang, T., & Chiosis, G. (2021) · FEBS Journal · doi:10.1111/febs.16031 · Cited by 27 · see citing works

Upregulation of HDAC9 in hippocampal neurons mediates depression-like behaviours by inhibiting ANXA2 degradation

Dai, Y., Wei, T., Huang, Y., Bei, Y., Lin, H., Shen, Z., Yu, L., Yang, M., Xu, H., He, W., et al. (2023) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-023-04945-y · Cited by 22 · see citing works

A Review of the Application of Spatial Transcriptomics in Neuroscience

Zhang, L., Xiong, Z., & Xiao, M. (2024) · Interdisciplinary Sciences: Computational Life Sciences · doi:10.1007/s12539-024-00603-4 · Cited by 29 · see citing works

Using blood transcriptome analysis for Alzheimer's disease diagnosis and patient stratification

Zhong, H., Zhou, X., Uhm, H., Jiang, Y., Cao, H., Chen, Y., Mak, T. T. W., Lo, R. M. N., Wong, B. W. Y., Cheng, E. Y. L., et al. (2024) · Alzheimer's &amp; Dementia · doi:10.1002/alz.13691 · Cited by 25 · see citing works

Distinct regional vulnerability to Aβ and iron accumulation in post mortem AD brains

Yao, J., Li, Z., Zhou, Z., Bao, A., Wang, Z., Wei, H., & He, H. (2024) · Alzheimer s & Dementia · doi:10.1002/alz.14188 · Cited by 24 · see citing works

Epigenetic biomarkers in Alzheimer's disease: Diagnostic and prognostic relevance

Behl, T., Kyada, A., Roopashree, R., Nathiya, D., Arya, R., Kumar, M., Khalid, M., Gulati, M., Sachdeva, M., Fareed, M., et al. (2024) · Ageing Research Reviews · doi:10.1016/j.arr.2024.102556 · Cited by 25 · see citing works

Senescent brain cell types in Alzheimer's disease: Pathological mechanisms and therapeutic opportunities

Hudson, H. R., Sun, X., & Orr, M. E. (2025) · Neurotherapeutics · doi:10.1016/j.neurot.2024.e00519 · Cited by 26 · see citing works

SIRT6 Through the Brain Evolution, Development, and Aging

García-Venzor, A., & Toiber, D. (2021) · Frontiers in Aging Neuroscience · doi:10.3389/fnagi.2021.747989 · Cited by 26 · see citing works

Application of Optogenetics in Neurodegenerative Diseases

Zhang, Q., Li, T., Xu, M., Islam, B., & Wang, J. (2024) · Cellular and Molecular Neurobiology · doi:10.1007/s10571-024-01486-1 · Cited by 25 · see citing works

Human amyloid beta and α-synuclein co-expression in neurons impair behavior and recapitulate features for Lewy body dementia in Caenorhabditis elegans

Huang, X., Wang, C., Chen, L., Zhang, T., Leung, K. L., & Wong, G. (2021) · Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease · doi:10.1016/j.bbadis.2021.166203 · Cited by 24 · see citing works

Gut microbes influence the development of central nervous system disorders through epigenetic inheritance

Liu, T., Du, D., Zhao, R., Xie, Q., & Dong, Z. (2023) · Microbiological Research · doi:10.1016/j.micres.2023.127440 · Cited by 24 · see citing works

CCPA: cloud-based, self-learning modules for consensus pathway analysis using GO, KEGG and Reactome

Nguyen, H., Pham, V.-D., Nguyen, H., Tran, B., Petereit, J., & Nguyen, T. (2024) · Briefings in Bioinformatics · doi:10.1093/bib/bbae222 · Cited by 24 · see citing works

Mechanism of KAT2A regulation of H3K36ac in manganese-induced oxidative damage to mitochondria in the nervous system and intervention by curcumin

Liu, Y., Zeng, J.-M., Zhao, H. Y., Ao, C.-Y., Ao, L.-H., Ban, J.-Q., & Li, J. (2024) · Ecotoxicology and Environmental Safety · doi:10.1016/j.ecoenv.2024.116155 · Cited by 23 · see citing works

Novel histone post-translational modifications in Alzheimer’s disease: current advances and implications

Qin, Y., Yang, P. C., He, W., Li, D., Zeng, L., Li, J., Zhou, T., Peng, J., Cao, L., & Huang, W. G. (2024) · Clinical Epigenetics · doi:10.1186/s13148-024-01650-w · Cited by 26 · see citing works

Epigenomic aberrations of histone methylation in prefrontal cortex of humans with mild cognitive impairment and Alzheimer's disease

Patel, P. J., & Yan, Z. (2026) · Journal of Alzheimer s Disease · doi:10.1177/13872877251414887 · Cited by 1 · see citing works

A histone acetylome-wide association study of Alzheimer’s disease identifies disease-associated H3K27ac differences in the entorhinal cortex

Marzi, S. J., Leung, S. K., Ribarska, T., Hannon, E., Smith, A. R., Pishva, E., Poschmann, J., Moore, K., Troakes, C., Al-Sarraj, S., et al. (2018) · Nature Neuroscience · doi:10.1038/s41593-018-0253-7 · Cited by 232 · see citing works

Histone H3 Lysine 4 and 27 Trimethylation Landscape of Human Alzheimer’s Disease

Persico, G., Casciaro, F., Amatori, S., Rusin, M., Cantatore, F., Perna, A., Alberi, L. A., Fanelli, M., & Giorgio, M. (2022) · Cells · doi:10.3390/cells11040734 · Cited by 35 · see citing works

Histone acetylation in an Alzheimer’s disease cell model promotes homeostatic amyloid-reducing pathways

Xu, D. C., Sas‐Nowosielska, H., Donahue, G., Huang, H., Pourshafie, N., Good, C. R., & Berger, S. L. (2024) · Acta Neuropathologica Communications · doi:10.1186/s40478-023-01696-6 · Cited by 30 · see citing works

The epigenetic dimension of Alzheimer's disease: causal, consequence, or curiosity?

Millan, M. J. (2014) · Dialogues in Clinical Neuroscience · doi:10.31887/dcns.2014.16.3/mmillan · Cited by 63 · see citing works