Integrative single-nucleus multi-omics analysis prioritizes candidate cis and trans regulatory networks and their target genes in Alzheimer’s disease brains

Model-based Analysis of ChIP-Seq (MACS)

Zhang, Y., Liu, T., Meyer, C. A., Eeckhoute, J., Johnson, D. S., Bernstein, B. E., Nusbaum, C., Myers, R. M., Brown, M., Li, W., et al. (2008) · Genome Biology · doi:10.1186/gb-2008-9-9-r137 · Cited by 18,386 · see citing works

Integrated analysis of multimodal single-cell data

Hao, Y., Hao, S., Andersen-Nissen, E., Mauck, W. M., Zheng, S., Butler, A., Lee, M. J., Wilk, A. J., Darby, C., Zagar, M., et al. (2020) · doi:10.1101/2020.10.12.335331 · Cited by 15,508 · see citing works

Comprehensive Integration of Single-Cell Data

Stuart, T., Butler, A., Hoffman, P., Hafemeister, C., Papalexi, E., Mauck, W. M., Hao, Y., Stoeckius, M., Smibert, P., & Satija, R. (2019) · Cell · doi:10.1016/j.cell.2019.05.031 · Cited by 15,453 · 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

Fast, sensitive and accurate integration of single-cell data with Harmony

Korsunsky, I., Millard, N., Fan, J., Slowikowski, K., Zhang, F., Wei, K., Baglaenko, Y., Brenner, M., Loh, P.-R., & Raychaudhuri, S. (2019) · Nature Methods · doi:10.1038/s41592-019-0619-0 · Cited by 10,488 · see citing works

Gene Dose of Apolipoprotein E Type 4 Allele and the Risk of Alzheimer's Disease in Late Onset Families

Corder, E. H., Saunders, A. M., Strittmatter, W. J., Schmechel, D. E., Gaskell, P. C., Small, G. W., Roses, A. D., Haines, J. L., & Pericak-Vance, M. A. (1993) · Science · doi:10.1126/science.8346443 · Cited by 9,429 · see citing works

Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression

Hafemeister, C., & Satija, R. (2019) · Genome Biology · doi:10.1186/s13059-019-1874-1 · Cited by 4,479 · cited 1× · 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

Association of apolipoprotein E allele ϵ4 with late‐onset familial and sporadic Alzheimer's disease

Saunders, A. M., Strittmatter, W. J., Schmechel, D., St. George-Hyslop, P. H., Pericak-Vance, M. A., Joo, S. H., Rosi, B. L., Gusella, J. F., Crapper-MacLachlan, D. R., Alberts, M. J., et al. (1993) · Neurology · doi:10.1212/wnl.43.8.1467 · Cited by 3,786 · see citing works

Genome-wide association study identifies variants at CLU and PICALM associated with Alzheimer's disease

Harold, D., Abraham, R., Hollingworth, P., Sims, R., Gerrish, A., Hamshere, M. L., Pahwa, J. S., Moskvina, V., Dowzell, K., Williams, A., et al. (2009) · Nature Genetics · doi:10.1038/ng.440 · Cited by 3,326 · see citing works

MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data

Finak, G., McDavid, A., Yajima, M., Deng, J., Gersuk, V., Shalek, A. K., Slichter, C. K., Miller, H. W., McElrath, M. J., Prlic, M., et al. (2015) · Genome Biology · doi:10.1186/s13059-015-0844-5 · Cited by 3,159 · see citing works

The TREM2-APOE Pathway Drives the Transcriptional Phenotype of Dysfunctional Microglia in Neurodegenerative Diseases

Krasemann, S., Madore, C., Cialic, R., Baufeld, C., Calcagno, N., El Fatimy, R., Beckers, L., O’Loughlin, E., Xu, Y., Fanek, Z., et al. (2017) · Immunity · doi:10.1016/j.immuni.2017.08.008 · Cited by 2,979 · 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

GENCODE reference annotation for the human and mouse genomes

Frankish, A., Diekhans, M., Ferreira, A.-M., Johnson, R., Jungreis, I., Loveland, J. E., Mudge, J. M., Sisu, C., Wright, J. C., Armstrong, J. C., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky955 · Cited by 2,929 · see citing works

Single-cell transcriptomic analysis of Alzheimer’s disease

Mathys, H., Davila-Velderrain, J., Peng, Z., Gao, F., Mohammadi, S., Young, J. Z., Menon, M., He, L., Abdurrob, F., Jiang, X., et al. (2019) · Nature · doi:10.1038/s41586-019-1195-2 · Cited by 2,568 · see citing works

New insights on the genetic etiology of Alzheimer’s and related dementia

(2020) · doi:10.1101/2020.10.01.20200659 · Cited by 2,499 · see citing works

New insights into the genetic etiology of Alzheimer’s disease and related dementias

Bellenguez, C., Küçükali, F., Jansen, I. E., Kleineidam, L., Moreno-Grau, S., Amin, N., Naj, A. C., Campos-Martin, R., Grenier-Boley, B., Andrade, V., et al. (2022) · Nature Genetics · doi:10.1038/s41588-022-01024-z · Cited by 2,498 · see citing works

Purification and Characterization of Progenitor and Mature Human Astrocytes Reveals Transcriptional and Functional Differences with Mouse

Zhang, Y., Sloan, S. A., Clarke, L. E., Caneda, C., Plaza, C. A., Blumenthal, P. D., Vogel, H., Steinberg, G. K., Edwards, M. S. B., Li, G., et al. (2016) · Neuron · doi:10.1016/j.neuron.2015.11.013 · Cited by 2,295 · see citing works

Genome-wide meta-analysis identifies new loci and functional pathways influencing Alzheimer’s disease risk

Jansen, I. E., Savage, J. E., Watanabe, K., Bryois, J., Williams, D. M., Steinberg, S., Sealock, J., Karlsson, I. K., Hägg, S., Athanasiu, L., et al. (2019) · Nature Genetics · doi:10.1038/s41588-018-0311-9 · Cited by 2,277 · see citing works

Genome-wide association study identifies variants at CLU and CR1 associated with Alzheimer's disease

the European Alzheimer's Disease Initiative Investigators, Lambert, J.-C., Heath, S., Even, G., Campion, D., Sleegers, K., Hiltunen, M., Combarros, O., Zelenika, D., Bullido, M. J., et al. (2009) · Nature Genetics · doi:10.1038/ng.439 · Cited by 2,234 · see citing works

Common variants at ABCA7, MS4A6A/MS4A4E, EPHA1, CD33 and CD2AP are associated with Alzheimer's disease

Initiative, T. A. D. N., Hollingworth, P., CHARGE consortium, EADI1 consortium, Harold, D., Sims, R., Gerrish, A., Lambert, J.-C., Carrasquillo, M. M., Abraham, R., et al. (2011) · Nature Genetics · doi:10.1038/ng.803 · Cited by 1,997 · see citing works

Microglia in Alzheimer’s disease

Hansen, D. V., Hanson, J. E., & Sheng, M. (2018) · Journal of Cell Biology · doi:10.1083/jcb.201709069 · Cited by 1,935 · cited 1× · see citing works

Common variants at MS4A4/MS4A6E, CD2AP, CD33 and EPHA1 are associated with late-onset Alzheimer's disease

Naj, A. C., Jun, G., Beecham, G. W., Wang, L.-S., Vardarajan, B. N., Buros, J., Gallins, P. J., Buxbaum, J. D., Jarvik, G. P., Crane, P. K., et al. (2011) · Nature Genetics · doi:10.1038/ng.801 · Cited by 1,901 · see citing works

The ENCODE Blacklist: Identification of Problematic Regions of the Genome

Amemiya, H. M., Kundaje, A., & Boyle, A. P. (2019) · Scientific Reports · doi:10.1038/s41598-019-45839-z · Cited by 1,831 · see citing works

Single-cell chromatin state analysis with Signac

Stuart, T., Srivastava, A., Madad, S., Lareau, C. A., & Satija, R. (2021) · Nature Methods · doi:10.1038/s41592-021-01282-5 · Cited by 1,769 · see citing works

JASPAR 2020: update of the open-access database of transcription factor binding profiles

Fornes, O., Castro-Mondragon, J. A., Khan, A., van der Lee, R., Zhang, X., Richmond, P. A., Modi, B. P., Correard, S., Gheorghe, M., Baranašić, D., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz1001 · Cited by 1,763 · see citing works

Depletion of microglia and inhibition of exosome synthesis halt tau propagation

Asai, H., Ikezu, S., Tsunoda, S., Medalla, M., Luebke, J., Haydar, T., Wolozin, B., Butovsky, O., Kügler, S., & Ikezu, T. (2015) · Nature Neuroscience · doi:10.1038/nn.4132 · Cited by 1,591 · see citing works

Increased amyloid beta-peptide deposition in cerebral cortex as a consequence of apolipoprotein E genotype in late-onset Alzheimer disease.

Schmechel, D. E., Saunders, A. M., Strittmatter, W. J., Crain, B. J., Hulette, C. M., Joo, S. H., Pericak-Vance, M. A., Goldgaber, D., & Roses, A. D. (1993) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.90.20.9649 · Cited by 1,525 · see citing works

Assessing computational tools for the discovery of transcription factor binding sites

Tompa, M., Li, N., Bailey, T. L., Church, G. M., De Moor, B., Eskin, E., Favorov, A. V., Frith, M. C., Fu, Y., Kent, W. J., et al. (2005) · Nature Biotechnology · doi:10.1038/nbt1053 · Cited by 1,268 · see citing works

ApoE4 markedly exacerbates tau-mediated neurodegeneration in a mouse model of tauopathy

Initiative, A. D. N., Shi, Y., Yamada, K., Liddelow, S. A., Smith, S. T., Zhao, L., Luo, W., Tsai, R. M., Spina, S., Grinberg, L. T., et al. (2017) · Nature · doi:10.1038/nature24016 · Cited by 1,220 · see citing works

Applied bioinformatics for the identification of regulatory elements

Wasserman, W. W., & Sandelin, A. (2004) · Nature Reviews Genetics · doi:10.1038/nrg1315 · Cited by 1,206 · see citing works

Human and mouse single-nucleus transcriptomics reveal TREM2-dependent and TREM2-independent cellular responses in Alzheimer’s disease

Zhou, Y., Song, W. M., Andhey, P. S., Swain, A., Levy, T., Miller, K. R., Poliani, P. L., Cominelli, M., Grover, S., Gilfillan, S., et al. (2020) · Nature Medicine · doi:10.1038/s41591-019-0695-9 · Cited by 1,150 · 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

A single-cell atlas of entorhinal cortex from individuals with Alzheimer’s disease reveals cell-type-specific gene expression regulation

Grubman, A., Chew, G., Ouyang, J. F., Sun, G., Choo, X. Y., McLean, C., Simmons, R. K., Buckberry, S., Vargas-Landin, D. B., Poppe, D., et al. (2019) · Nature Neuroscience · doi:10.1038/s41593-019-0539-4 · Cited by 956 · see citing works

Brain cell type–specific enhancer–promoter interactome maps and disease <b>-</b> risk association

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., et al. (2019) · Science · doi:10.1126/science.aay0793 · Cited by 823 · see citing works

Comparative cellular analysis of motor cortex in human, marmoset and mouse

Bakken, T. E., Jorstad, N. L., Hu, Q., Lake, B. B., Tian, W., Kalmbach, B. E., Crow, M., Hodge, R. D., Krienen, F. M., Sorensen, S. A., et al. (2021) · Nature · doi:10.1038/s41586-021-03465-8 · Cited by 812 · see citing works

Evolution of cellular diversity in primary motor cortex of human, marmoset monkey, and mouse

Bakken, T. E., Jorstad, N. L., Hu, Q., Lake, B. B., Tian, W., Kalmbach, B. E., Crow, M., Hodge, R. D., Krienen, F. M., Sorensen, S. A., et al. (2020) · doi:10.1101/2020.03.31.016972 · Cited by 809 · cited 3× · see citing works

A human brain vascular atlas reveals diverse mediators of Alzheimer’s risk

Yang, A. C., Vest, R. T., Kern, F., Lee, D. P., Agam, M., Maat, C. A., Losada, P. M., Chen, M. B., Schaum, N., Khoury, N., et al. (2022) · Nature · doi:10.1038/s41586-021-04369-3 · Cited by 797 · see citing works

Cicero predicts cis-regulatory DNA interactions from single-cell chromatin accessibility data

Pliner, H. A., Packer, J. S., McFaline-Figueroa, J. L., Cusanovich, D. A., Daza, R. M., Aghamirzaie, D., Srivatsan, S., Qiu, X., Jackson, D., Minkina, A., et al. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.06.044 · Cited by 789 · see citing works

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

Cusanovich, D. A., Hill, A. J., Aghamirzaie, D., Daza, R. M., Pliner, H. A., Berletch, J. B., Filippova, G. N., Huang, X., Christiansen, L., DeWitt, W. S., et al. (2018) · Cell · doi:10.1016/j.cell.2018.06.052 · Cited by 759 · see citing works

A sensitive assay for dNTPs based on long synthetic oligonucleotides, EvaGreen dye and inhibitor-resistant high-fidelity DNA polymerase

Purhonen, J., Banerjee, R., McDonald, A. E., Fellman, V., & Kallijärvi, J. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa516 · Cited by 657 · see citing works

Single-nucleus chromatin accessibility and transcriptomic characterization of Alzheimer’s disease

Morabito, S., Miyoshi, E., Michael, N., Shahin, S., Martini, A. C., Head, E., Silva, J., Leavy, K., Perez-Rosendahl, M., & Swarup, V. (2021) · Nature Genetics · doi:10.1038/s41588-021-00894-z · Cited by 643 · see citing works

A High-Density Whole-Genome Association Study Reveals That APOE Is the Major Susceptibility Gene for Sporadic Late-Onset Alzheimer's Disease

Coon, K. D., Myers, A. J., Craig, D. W., Webster, J. A., Pearson, J. V., Lince, D. H., Zismann, V. L., Beach, T. G., Leung, D., Bryden, L., et al. (2007) · The Journal of Clinical Psychiatry · doi:10.4088/jcp.v68n0419 · Cited by 569 · see citing works

GWAS on family history of Alzheimer’s disease

Marioni, R. E., Harris, S. E., Zhang, Q., McRae, A. F., Hagenaars, S. P., Hill, W. D., Davies, G., Ritchie, C. W., Gale, C. R., Starr, J. M., et al. (2018) · Translational Psychiatry · doi:10.1038/s41398-018-0150-6 · Cited by 564 · see citing works

GWAS on family history of Alzheimer’s disease

(2018) · doi:10.1101/246223 · Cited by 564 · see citing works

Dynamics of the Microglial/Amyloid Interaction Indicate a Role in Plaque Maintenance

Bolmont, T., Haiss, F., Eicke, D., Radde, R., Mathis, C. A., Klunk, W. E., Kohsaka, S., Jucker, M., & Calhoun, M. E. (2008) · The Journal of Neuroscience · doi:10.1523/jneurosci.4814-07.2008 · Cited by 526 · see citing works

Molecular characterization of selectively vulnerable neurons in Alzheimer’s disease

Leng, K., Li, E., Eser, R., Piergies, A., Sit, R., Tan, M., Neff, N., Li, S. H., Rodriguez, R. D., Suemoto, C. K., et al. (2021) · Nature Neuroscience · doi:10.1038/s41593-020-00764-7 · Cited by 485 · see citing works

Anti-Inflammatory Drug Therapy Alters β-Amyloid Processing and Deposition in an Animal Model of Alzheimer's Disease

Yan, Q., Zhang, J., Liu, H., Babu-Khan, S., Vassar, R., Biere, A. L., Citron, M., & Landreth, G. (2003) · The Journal of Neuroscience · doi:10.1523/jneurosci.23-20-07504.2003 · Cited by 469 · see citing works

Distinct amyloid-β and tau-associated microglia profiles in Alzheimer’s disease

Gerrits, E., Brouwer, N., Kooistra, S. M., Woodbury, M. E., Vermeiren, Y., Lambourne, M., Mulder, J., Kummer, M., Möller, T., Biber, K., et al. (2021) · Acta Neuropathologica · doi:10.1007/s00401-021-02263-w · Cited by 441 · see citing works

Identification and therapeutic modulation of a pro-inflammatory subset of disease-associated-microglia in Alzheimer’s disease

Rangaraju, S., Dammer, E. B., Raza, S. A., Rathakrishnan, P., Xiao, H., Gao, T., Duong, D. M., Pennington, M. W., Lah, J. J., Seyfried, N. T., et al. (2018) · Molecular Neurodegeneration · doi:10.1186/s13024-018-0254-8 · Cited by 430 · see citing works

Alzheimer’s Patient Microglia Exhibit Enhanced Aging and Unique Transcriptional Activation

Srinivasan, K., Friedman, B. A., Etxeberria, A., Huntley, M. A., van der Brug, M. P., Foreman, O., Paw, J. S., Modrusan, Z., Beach, T. G., Serrano, G. E., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.107843 · Cited by 427 · see citing works

Glial contributions to neurodegeneration in tauopathies

Leyns, C. E. G., & Holtzman, D. M. (2017) · Molecular Neurodegeneration · doi:10.1186/s13024-017-0192-x · Cited by 409 · see citing works

Mutations Affecting G-Protein Subunit α 11 in Hypercalcemia and Hypocalcemia

Nesbit, M. A., Hannan, F. M., Howles, S., Babinsky, V. N., Head, R. A., Cranston, T., Rust, N. A., Hobbs, M. R., Heath, H., & Thakker, R. V. (2013) · New England Journal of Medicine · doi:10.1056/nejmoa1300253 · Cited by 402 · see citing works

Neuronal Diversity in GABAergic Long-Range Projections from the Hippocampus

Jinno, S., Klausberger, T., Marton, L. F., Dalezios, Y., Roberts, J. D. B., Fuentealba, P., Bushong, E. A., Henze, D., Buzsáki, G., & Somogyi, P. (2007) · The Journal of Neuroscience · doi:10.1523/jneurosci.1847-07.2007 · Cited by 369 · 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

The cis-regulatory dynamics of embryonic development at single-cell resolution

Cusanovich, D. A., Reddington, J. P., Garfield, D. A., Daza, R. M., Aghamirzaie, D., Marco-Ferreres, R., Pliner, H. A., Christiansen, L., Qiu, X., Steemers, F. J., et al. (2018) · Nature · doi:10.1038/nature25981 · Cited by 363 · see citing works

A practical solution to pseudoreplication bias in single-cell studies

Zimmerman, K. D., Espeland, M. A., & Langefeld, C. D. (2021) · Nature Communications · doi:10.1038/s41467-021-21038-1 · Cited by 362 · cited 2× · see citing works

Nonsteroidal Anti-Inflammatory Drugs and Peroxisome Proliferator-Activated Receptor-γ Agonists Modulate Immunostimulated Processing of Amyloid Precursor Protein through Regulation of β-Secretase

Sastre, M., Dewachter, I., Landreth, G. E., Willson, T. M., Klockgether, T., LEUVEN, F. V., & Heneka, M. T. (2003) · Journal of Neuroscience · doi:10.1523/jneurosci.23-30-09796.2003 · Cited by 359 · see citing works

Inflammation in Alzheimer’s disease: Lessons learned from microglia-depletion models

Spangenberg, E. E., & Green, K. N. (2017) · Brain, Behavior, and Immunity · doi:10.1016/j.bbi.2016.07.003 · Cited by 352 · see citing works

Expression of Novel Alzheimer’s Disease Risk Genes in Control and Alzheimer’s Disease Brains

Karch, C. M., Jeng, A. T., Nowotny, P., Cady, J., Cruchaga, C., & Goate, A. M. (2012) · PLoS ONE · doi:10.1371/journal.pone.0050976 · Cited by 328 · see citing works

Association of Brain DNA Methylation in<i>SORL1</i>,<i>ABCA7</i>,<i>HLA-DRB5</i>,<i>SLC24A4</i>, and<i>BIN1</i>With Pathological Diagnosis of Alzheimer Disease

Yu, L., Chibnik, L. B., Srivastava, G. P., Pochet, N., Yang, J., Xu, J., Kozubek, J., Obholzer, N., Leurgans, S. E., Schneider, J. A., et al. (2015) · JAMA Neurology · doi:10.1001/jamaneurol.2014.3049 · Cited by 290 · see citing works

Genetic analysis of the human microglial transcriptome across brain regions, aging and disease pathologies

Lopes, K. D. P., Snijders, G. J. L., Humphrey, J., Allan, A., Sneeboer, M. A. M., Navarro, E., Schilder, B. M., Vialle, R. A., Parks, M., Missall, R., et al. (2022) · Nature Genetics · doi:10.1038/s41588-021-00976-y · Cited by 273 · see citing works

Ribosomal Protein s15 Phosphorylation Mediates LRRK2 Neurodegeneration in Parkinson’s Disease

Martin, I., Kim, J. W., Lee, B. D., Kang, H. C., Xu, J.-C., Jia, H., Stankowski, J., Kim, M.-S., Zhong, J., Kumar, M., et al. (2014) · Cell · doi:10.1016/j.cell.2014.01.064 · Cited by 265 · see citing works

Genome-wide association study of Alzheimer's disease

Kamboh, M. I., Demirci, F. Y., Wang, X., Minster, R. L., Carrasquillo, M. M., Pankratz, V. S., Younkin, S. G., Saykin, A. J., Initiative, A. D. N., Jun, G., et al. (2012) · Translational Psychiatry · doi:10.1038/tp.2012.45 · Cited by 242 · see citing works

Epigenetic dysregulation of enhancers in neurons is associated with Alzheimer’s disease pathology and cognitive symptoms

Li, P., Marshall, L., Oh, G., Jakubowski, J. L., Groot, D., He, Y., Wang, T., Petronis, A., & Labrie, V. (2019) · Nature Communications · doi:10.1038/s41467-019-10101-7 · Cited by 234 · see citing works

DNA methylation analysis on purified neurons and glia dissects age and Alzheimer’s disease-specific changes in the human cortex

Gasparoni, G., Bultmann, S., Lutsik, P., Kraus, T. F. J., Sordon, S., Vlcek, J., Dietinger, V., Steinmaurer, M., Haider, M., Mulholland, C. B., et al. (2018) · Epigenetics &amp; Chromatin · doi:10.1186/s13072-018-0211-3 · Cited by 229 · see citing works

TREM2, microglia, and Alzheimer’s disease.

Qin, Q., Teng, Z., Liu, C., Li, Q., Yin, Y., & Tang, Y. (2021) · Mechanisms of Ageing and Development · doi:10.1016/j.mad.2021.111438 · Cited by 219 · 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

Age-Dependent Effects of apoE Reduction Using Antisense Oligonucleotides in a Model of β-amyloidosis

Huynh, T.-P. V., Liao, F., Francis, C. M., Robinson, G. O., Serrano, J. R., Jiang, H., Roh, J., Finn, M. B., Sullivan, P. M., Esparza, T. J., et al. (2017) · Neuron · doi:10.1016/j.neuron.2017.11.014 · Cited by 209 · see citing works

Genome-wide DNA methylation profiling in the superior temporal gyrus reveals epigenetic signatures associated with Alzheimer’s disease

Watson, C. T., Roussos, P., Garg, P., Ho, D. J., Azam, N., Katsel, P. L., Haroutunian, V., & Sharp, A. J. (2016) · Genome Medicine · doi:10.1186/s13073-015-0258-8 · Cited by 201 · see citing works

Haploinsufficiency of Human APOE Reduces Amyloid Deposition in a Mouse Model of Amyloid-β Amyloidosis

Kim, J., Jiang, H., Park, S., Eltorai, A. E. M., Stewart, F. R., Yoon, H., Basak, J. M., Finn, M. B., & Holtzman, D. M. (2011) · The Journal of Neuroscience · doi:10.1523/jneurosci.3773-11.2011 · Cited by 199 · see citing works

TFEB dysregulation as a driver of autophagy dysfunction in neurodegenerative disease: Molecular mechanisms, cellular processes, and emerging therapeutic opportunities

Cortés, C. J., & Spada, A. R. L. (2018) · Neurobiology of Disease · doi:10.1016/j.nbd.2018.05.012 · Cited by 197 · see citing works

Analytic Pearson residuals for normalization of single-cell RNA-seq UMI data

Lause, J., Berens, P., & Kobak, D. (2021) · Genome Biology · doi:10.1186/s13059-021-02451-7 · Cited by 195 · see citing works

Isolation of neuronal chromatin from brain tissue

Jiang, Y., Matevossian, A., Huang, H.-S., Straubhaar, J., & Akbarian, S. (2008) · BMC Neuroscience · doi:10.1186/1471-2202-9-42 · Cited by 193 · see citing works

Expression of APP pathway mRNAs and proteins in Alzheimer’s disease

Matsui, T., Ingelsson, M., Fukumoto, H., Ramasamy, K., Kowa, H., Frosch, M. P., Irizarry, M. C., & Hyman, B. T. (2007) · Brain Research · doi:10.1016/j.brainres.2007.05.050 · Cited by 187 · see citing works

A single-nuclei RNA sequencing study of Mendelian and sporadic AD in the human brain

Del-Aguila, J. L., Li, Z., Dube, U., Mihindukulasuriya, K. A., Budde, J. P., Fernandez, M. V., Ibanez, L., Bradley, J., Wang, F., Bergmann, K., et al. (2019) · Alzheimer's Research &amp; Therapy · doi:10.1186/s13195-019-0524-x · Cited by 183 · see citing works

Single-nucleus multiregion transcriptomic analysis of brain vasculature in Alzheimer’s disease

Sun, N., Akay, L. A., Murdock, M. H., Park, Y., Galiana-Melendez, F., Bubnys, A., Galani, K., Mathys, H., Jiang, X., Ng, A. P., et al. (2023) · Nature Neuroscience · doi:10.1038/s41593-023-01334-3 · Cited by 177 · see citing works

Transcriptional Regulation by Fos and Jun In Vitro: Interaction among Multiple Activator and Regulatory Domains

Abate, C., Luk, D. C., & Curran, T. (1991) · Molecular and Cellular Biology · doi:10.1128/mcb.11.7.3624 · Cited by 176 · see citing works

Mechanisms of microglia accumulation in Alzheimer’s disease: therapeutic implications

Khoury, J. E., & Luster, A. D. (2008) · Trends in Pharmacological Sciences · doi:10.1016/j.tips.2008.08.004 · Cited by 171 · see citing works

Reducing Human Apolipoprotein E Levels Attenuates Age-Dependent Aβ Accumulation in Mutant Human Amyloid Precursor Protein Transgenic Mice

Bien-Ly, N., Gillespie, A. K., Walker, D., Yoon, S. Y., & Huang, Y. (2012) · The Journal of Neuroscience · doi:10.1523/jneurosci.0033-12.2012 · Cited by 170 · see citing works

Lathosterolosis: an inborn error of human and murine cholesterol synthesis due to lathosterol 5-desaturase deficiency

Krakowiak, P. A. (2003) · Human Molecular Genetics · doi:10.1093/hmg/ddg172 · Cited by 161 · see citing works

The APOE Gene is Differentially Methylated in Alzheimer’s Disease

Foraker, J. E., Millard, S. P., Leong, L., Thomson, Z., Chen, S., Keene, C. D., Bekris, L. M., & Yu, C. (2015) · Journal of Alzheimer s Disease · doi:10.3233/jad-143060 · Cited by 145 · see citing works

Haplotype‐Association Analysis

Liu, N., Zhang, K., & Zhao, H. (2008) · Advances in genetics · doi:10.1016/s0065-2660(07)00414-2 · Cited by 141 · see citing works

Genome-Wide Scan of Copy Number Variation in Late-Onset Alzheimer's Disease

Heinzen, E. L., Need, A. C., Hayden, K. M., Chiba‐Falek, O., Roses, A. D., Strittmatter, W. J., Burke, J. R., Hulette, C. M., Welsh-Bohmer, K. A., & Goldstein, D. B. (2010) · Journal of Alzheimer s Disease · doi:10.3233/jad-2010-1212 · Cited by 129 · see citing works

Tau exon 10, whose missplicing causes frontotemporal dementia, is regulated by an intricate interplay of cis elements and trans factors

Wang, J., Gao, Q., Wang, Y., Lafyatis, R., Stamm, S., & Andreadis, A. (2004) · Journal of Neurochemistry · doi:10.1046/j.1471-4159.2003.02232.x · Cited by 125 · see citing works

Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) sequencing technology and application

Li, G., Cai, L., Chang, H., Hong, P., Zhou, Q., Kulakova, E. V., Kolchanov, N. A., & Ruan, Y. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-s12-s11 · Cited by 125 · see citing works

Microglial cells are the driving force in fibrillar plaque formation, whereas astrocytes are a leading factor in plaque degradation

Wegiel, J., Wang, K. C., Tarnawski, M., & Lach, B. (2000) · Acta Neuropathologica · doi:10.1007/s004010000199 · Cited by 124 · see citing works

The role of hnRNPs in frontotemporal dementia and amyotrophic lateral sclerosis

Bampton, A., Gittings, L. M., Fratta, P., Lashley, T., & Gatt, A. P. (2020) · Acta Neuropathologica · doi:10.1007/s00401-020-02203-0 · Cited by 118 · see citing works

Alzheimer’s disease risk polymorphisms regulate gene expression in the ZCWPW1 and the CELF1 loci

Karch, C. M., Ezerskiy, L. A., Bertelsen, S., Alzheimer’s Disease Genetics Consortium (ADGC), & Goate, A. M. (2016) · PLoS ONE · doi:10.1371/journal.pone.0148717 · Cited by 111 · see citing works

A genome‐wide profiling of brain DNA hydroxymethylation in Alzheimer's disease

Zhao, J., Zhu, Y., Yang, J., Lin, L., Wu, H., Jager, P. L. D., Jin, P., & Bennett, D. A. (2017) · Alzheimer s & Dementia · doi:10.1016/j.jalz.2016.10.004 · Cited by 111 · see citing works

Microglial efferocytosis: Diving into the Alzheimer’s disease gene pool

Romero-Molina, C., Garretti, F., Andrews, S. J., Marcora, E., & Goate, A. M. (2022) · Neuron · doi:10.1016/j.neuron.2022.10.015 · Cited by 111 · cited 1× · see citing works

atSNP: transcription factor binding affinity testing for regulatory SNP detection

Zuo, C., Shin, S., & Keleş, S. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv328 · Cited by 101 · see citing works

Genome-wide association analysis of age-at-onset in Alzheimer's disease

Kamboh, M. I., Barmada, M. M., Demirci, F. Y., Minster, R. L., Carrasquillo, M. M., Pankratz, V. S., Younkin, S. G., Saykin, A. J., Initiative, T. A. D. N., Sweet, R. A., et al. (2012) · Molecular Psychiatry · doi:10.1038/mp.2011.135 · Cited by 100 · see citing works

Using combined evidence from replicates to evaluate ChIP-seq peaks

Jalili, V., Matteucci, M., Masseroli, M., & Morelli, M. J. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv293 · Cited by 99 · see citing works

Somatostatin-positive interneurons in the dentate gyrus of mice provide local- and long-range septal synaptic inhibition

Yuan, M., Meyer, T., Benkowitz, C., Savanthrapadian, S., Ansel-Bollepalli, L., Foggetti, A., Wulff, P., Alcami, P., Elgueta, C., & Bartos, M. (2017) · eLife · doi:10.7554/elife.21105 · Cited by 93 · see citing works

Forebrain microglia from wild-type but not adult 5xFAD mice prevent amyloid-β plaque formation in organotypic hippocampal slice cultures

Hellwig, S., Masuch, A., Nestel, S., Katzmarski, N., Meyer-Luehmann, M., & Biber, K. (2015) · Scientific Reports · doi:10.1038/srep14624 · Cited by 91 · see citing works

The cis ‐regulatory effect of an Alzheimer's disease‐associated poly‐T locus on expression of TOMM40 and apolipoprotein E genes

Linnertz, C. L., Anderson, L., Gottschalk, W. K., Crenshaw, D. G., Lutz, M. W., Allen, J., Saith, S., Mihovilovic, M., Burke, J. R., Welsh-Bohmer, K. A., et al. (2014) · Alzheimer s & Dementia · doi:10.1016/j.jalz.2013.08.280 · Cited by 90 · see citing works

Step by step: towards a better understanding of the genetic architecture of Alzheimer’s disease

Lambert, J.-C., Ramirez, A., Grenier-Boley, B., & Bellenguez, C. (2023) · Molecular Psychiatry · doi:10.1038/s41380-023-02076-1 · Cited by 87 · see citing works

DNA methylation of TOMM40-APOE-APOC2 in Alzheimer’s disease

Shao, Y. Y., Shaw, M. L., Todd, K. W., Khrestian, M., D’Aleo, G., Barnard, P. J., Zahratka, J. A., Pillai, J. A., Yu, C., Keene, C. D., et al. (2018) · Journal of Human Genetics · doi:10.1038/s10038-017-0393-8 · Cited by 84 · see citing works

Single nucleus multiomics identifies ZEB1 and MAFB as candidate regulators of Alzheimer’s disease-specific cis-regulatory elements

Anderson, A. G., Rogers, B. B., Loupe, J. M., Rodriguez-Nunez, I., Roberts, S. C., White, L. M., Brazell, J. N., Bunney, W. E., Bunney, B. G., Watson, S. J., et al. (2023) · Cell Genomics · doi:10.1016/j.xgen.2023.100263 · Cited by 82 · cited 7× · see citing works

RNA-Seq analysis of the parietal cortex in Alzheimer's disease reveals alternatively spliced isoforms related to lipid metabolism

Mills, J. D., Nalpathamkalam, T., Jacobs, H. I. L., Janitz, C., Merico, D., Hu, P., & Janitz, M. (2013) · Neuroscience Letters · doi:10.1016/j.neulet.2012.12.042 · Cited by 82 · see citing works

Microglia heterogeneity and neurodegeneration: The emerging paradigm of the role of immunity in Alzheimer's disease

Hashemiaghdam, A., & Mroczek, M. (2020) · Journal of Neuroimmunology · doi:10.1016/j.jneuroim.2020.577185 · Cited by 77 · see citing works

Enhancer variants associated with Alzheimer’s disease affect gene expression via chromatin looping

Kikuchi, M., Hara, N., Hasegawa, M., Miyashita, A., Kuwano, R., Ikeuchi, T., & Nakaya, A. (2019) · BMC Medical Genomics · doi:10.1186/s12920-019-0574-8 · Cited by 74 · cited 1× · see citing works

A novel role for the late-onset Alzheimer’s disease (LOAD)-associated protein Bin1 in regulating postsynaptic trafficking and glutamatergic signaling

Schürmann, B., Bermingham, D. P., Kopeikina, K. J., Myczek, K., Yoon, S., Horan, K. E., Kelly, C. J., Martin-de-Saavedra, M. D., Forrest, M. P., Fawcett-Patel, J. M., et al. (2020) · Molecular Psychiatry · doi:10.1038/s41380-019-0407-3 · Cited by 72 · see citing works

Transcriptomic profiling of the human brain reveals that altered synaptic gene expression is associated with chronological aging

Dillman, A., Majounie, E., Ding, J., Gibbs, J. R., Hernandez, D. G., Arepalli, S., Traynor, B. J., Singleton, A., Galter, D., & Cookson, M. R. (2017) · Scientific Reports · doi:10.1038/s41598-017-17322-0 · Cited by 65 · see citing works

The Alzheimer susceptibility gene BIN1 induces isoform-dependent neurotoxicity through early endosome defects

Lambert, E., Saha, O., Landeira, B. S., de Farias, A. R. M., Hermant, X., Carrier, A., Pelletier, A., Gadaut, J., Davoine, L., Dupont, C., et al. (2022) · Acta Neuropathologica Communications · doi:10.1186/s40478-021-01285-5 · Cited by 64 · see citing works

Glia-specific APOE epigenetic changes in the Alzheimer’s disease brain

Tulloch, J., Leong, L., Thomson, Z., Chen, S., Lee, E.-G., Keene, C. D., Millard, S. P., & Yu, C. (2018) · Brain Research · doi:10.1016/j.brainres.2018.08.006 · Cited by 58 · see citing works

Increased Apolipoprotein E mRNA in the Hippocampus in Alzheimer Disease and in Rats after Entorhinal Cortex Lesioning

Zarow, C., & Victoroff, J. (1998) · Experimental Neurology · doi:10.1006/exnr.1997.6709 · Cited by 55 · see citing works

The BIN1 rs744373 Alzheimer's disease risk SNP is associated with faster Aβ‐associated tau accumulation and cognitive decline

Franzmeier, N., Ossenkoppele, R., Brendel, M., Rubinski, A., Smith, R. A., Kumar, A., Mattsson, N., Strandberg, O. T., Duering, M., Büerger, K., et al. (2021) · Alzheimer s & Dementia · doi:10.1002/alz.12371 · Cited by 55 · see citing works

A novel method for improved accuracy of transcription factor binding site prediction

Khamis, A. M., Motwalli, O., Oliva, R., Janković, B. R., Medvedeva, Y. A., Ashoor, H., Essack, M., Gao, X., & Bajić, V. B. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky237 · Cited by 55 · see citing works

Selective deletion of apolipoprotein E in astrocytes ameliorates the spatial learning and memory deficits in Alzheimer's disease (APP/PS1) mice by inhibiting TGF-β/Smad2/STAT3 signaling

Zheng, J., Sun, J., Ji, C.-M., Shen, L., Chen, Z.-J., Xie, P., Sun, Y.-Z., & Yu, R. (2017) · Neurobiology of Aging · doi:10.1016/j.neurobiolaging.2017.03.002 · Cited by 54 · see citing works

Identification of genetic heterogeneity of Alzheimer's disease across age

Lo, M., Kauppi, K., Fan, C.-C., Sanyal, N., Reas, E. T., Sundar, V. S., Lee, W., Desikan, R. S., McEvoy, L. K., & Chen, C. (2019) · Neurobiology of Aging · doi:10.1016/j.neurobiolaging.2019.02.022 · Cited by 52 · see citing works

A novel mutation of the NDUFS7 gene leads to activation of a cryptic exon and impaired assembly of mitochondrial complex I in a patient with Leigh syndrome

Lebon, S., Minai, L., Chrétien, D., Corcos, J., Serre, V., Kadhom, N., Steffann, J., Pauchard, J.-Y., Münnich, A., Bonnefont, J., et al. (2007) · Molecular Genetics and Metabolism · doi:10.1016/j.ymgme.2007.05.010 · Cited by 49 · see citing works

Haplotype analysis of APOE intragenic SNPs

Babenko, V. N., Afonnikov, D. A., Ignatieva, E. V., Klimov, A. V., Gusev, F. E., & Rogaev, E. I. (2018) · BMC Neuroscience · doi:10.1186/s12868-018-0413-4 · Cited by 47 · see citing works

APOE: The New Frontier in the Development of a Therapeutic Target towards Precision Medicine in Late-Onset Alzheimer’s

Yang, A., Kantor, B., & Chiba‐Falek, O. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22031244 · Cited by 47 · see citing works

Association of ApoE and LRP mRNA levels with dementia and AD neuropathology

Akram, A. M., Schmeidler, J., Katsel, P., Hof, P. R., & Haroutunian, V. H. (2011) · Neurobiology of Aging · doi:10.1016/j.neurobiolaging.2011.04.010 · Cited by 37 · see citing works

Alzheimer's disease BIN1 coding variants increase intracellular Aβ levels by interfering with BACE1 recycling

Perdigão, C., Barata, M. A., Burrinha, T., & Almeida, C. G. (2021) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2021.101056 · Cited by 33 · see citing works

Preparation of active nuclei

Marzluff, W. F. (1990) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/0076-6879(90)81109-8 · Cited by 33 · see citing works

Genetic meta-analysis identifies 9 novel loci and functional pathways for Alzheimer’s disease riskPreprint

Jansen, I. E., Savage, J. E., Watanabe, K., Bryois, J., Williams, D. M., Steinberg, S., Sealock, J., Karlsson, I., Hägg, S., Athanasiu, L., et al. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/258533 · Cited by 33 · see citing works

The role of copper and the copper-related protein CUTA in mediating APP processing and Aβ generation

Hou, P., Liu, G., Zhao, Y., Shi, Z., Zheng, Q., Bu, G., Xu, H., & Zhang, Y.-W. (2015) · Neurobiology of Aging · doi:10.1016/j.neurobiolaging.2014.12.005 · Cited by 32 · cited 1× · see citing works

A Neurotoxic Phosphoform of Elk-1 Associates with Inclusions from Multiple Neurodegenerative Diseases

Sharma, A. K., Callahan, L. M., Sul, J., Kim, T. K., Barrett, L. E., Kim, M., Powers, J. M., Federoff, H. J., & Eberwine, J. H. (2010) · PLoS ONE · doi:10.1371/journal.pone.0009002 · Cited by 32 · see citing works

The Role of Upregulated APOE in Alzheimer's Disease Etiology

Gottschalk, W. K., & Mihovilovic, M. (2016) · Journal of Alzheimer’s Disease & Parkinsonism · doi:10.4172/2161-0460.1000209 · Cited by 31 · see citing works

Tree-Based Position Weight Matrix Approach to Model Transcription Factor Binding Site Profiles

Bi, Y., Kim, H., Gupta, R., & Davuluri, R. V. (2011) · PLoS ONE · doi:10.1371/journal.pone.0024210 · Cited by 31 · see citing works

Analytic Pearson residuals for normalization of single-cell RNA-seq UMI dataPreprint

Lause, J., Berens, P., & Kobak, D. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.12.01.405886 · Cited by 28 · see citing works

Lessons from Microglia Aging for the Link between Inflammatory Bone Disorders and Alzheimer’s Disease

Wu, Z., & Nakanishi, H. (2015) · Journal of Immunology Research · doi:10.1155/2015/471342 · Cited by 27 · see citing works

Bioinformatics strategy to advance the interpretation of Alzheimer's disease GWAS discoveries: The roads from association to causation

Lutz, M. W., Sprague, D., & Chiba‐Falek, O. (2019) · Alzheimer s & Dementia · doi:10.1016/j.jalz.2019.04.014 · Cited by 27 · see citing works

Combinatorial analyses reveal cellular composition changes have different impacts on transcriptomic changes of cell type specific genes in Alzheimer’s Disease

Johnson, T. S., Xiang, S., Dong, T., Huang, Z., Cheng, M., Wang, T., Yang, K., Ni, D., Huang, K., & Zhang, J. (2021) · Scientific Reports · doi:10.1038/s41598-020-79740-x · Cited by 26 · see citing works

FZR1 loss increases sensitivity to DNA damage and consequently promotes murine and human B-cell acute leukemia

Ishizawa, J., Sugihara, E., Kuninaka, S., Mogushi, K., Kojima, K., Benton, C. B., Zhao, R., Chachad, D., Hashimoto, N., Jacamo, R. O., et al. (2017) · Blood · doi:10.1182/blood-2016-07-726216 · Cited by 25 · see citing works

Atlas of genetic effects in human microglia transcriptome across brain regions, aging and disease pathologiesPreprint

Lopes, K. D. P., Snijders, G. J. L., Humphrey, J., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.10.27.356113 · Cited by 23 · see citing works

Somatostatin-Expressing Interneurons Form Axonal Projections to the Contralateral Hippocampus

Eyre, M. D., & Bartos, M. (2019) · Frontiers in Neural Circuits · doi:10.3389/fncir.2019.00056 · Cited by 22 · see citing works

Differential Methylation in APOE (Chr19; Exon Four; from 44,909,188 to 44,909,373/hg38) and Increased Apolipoprotein E Plasma Levels in Subjects with Mild Cognitive Impairment

Páez, O. M., Estrada-Orozco, K., Mahecha, M. F., Sanabria, F. C., Bonilla-Vargas, K. J., Sandoval, N., Guerrero, E., Salcedo-Tacuma, D., Melgarejo, J. D., Vega, E., et al. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20061394 · Cited by 20 · see citing works

Genetic Heterogeneity of Alzheimer’s Disease: Embracing Research Partnerships

Nacmias, B., Bagnoli, S., Piaceri, I., & Sorbi, S. (2017) · Journal of Alzheimer s Disease · doi:10.3233/jad-170570 · Cited by 15 · see citing works

Identification of transcriptional signatures for cell types from single-cell RNA-SeqPreprint

Ntranos, V., Yi, L., Melsted, P., & Pachter, L. S. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/258566 · Cited by 15 · see citing works

Sex dependent glial-specific changes in the chromatin accessibility landscape in late-onset Alzheimer’s disease brains

Barrera, J., Song, L., Safi, A., Yun, Y., Garrett, M. E., Gamache, J., Premasinghe, I., Sprague, D., Chipman, D., Li, J., et al. (2021) · Molecular Neurodegeneration · doi:10.1186/s13024-021-00481-0 · Cited by 12 · see citing works

Methyl-CpG binding domain protein 3: a new diagnostic marker and potential therapeutic target of melanoma

Ishibashi, T., Kajihara, I., Mizuhashi, S., Kuriyama, H., Kimura, T., Kanemaru, H., Makino, K., Miyashita, A., Aoi, J., Makino, T., et al. (2020) · BioScience Trends · doi:10.5582/bst.2020.01048 · Cited by 4 · 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

Advancements in APOE and dementia research: Highlights from the 2023 AAIC Advancements: APOE conference

Kloske, C. M., Belloy, M. E., Blue, E. E., Bowman, G. R., Carrillo, M. C., Chen, X., Chiba‐Falek, O., Davis, A. A., Paolo, G. D., Garretti, F., et al. (2024) · Alzheimer's &amp; Dementia · doi:10.1002/alz.13877 · Cited by 33 · see citing works

Single-nucleus multi-omics of Parkinson’s disease reveals a glutamatergic neuronal subtype susceptible to gene dysregulation via alteration of transcriptional networks

Shwab, E. K., Gingerich, D. C., Man, Z., Gamache, J., Garrett, M. E., Crawford, G. E., Ashley‐Koch, A. E., Serrano, G. E., Beach, T. G., Lutz, M. W., et al. (2024) · Acta Neuropathologica Communications · doi:10.1186/s40478-024-01803-1 · Cited by 27 · see citing works

Alzheimer’s Disease: Models and Molecular Mechanisms Informing Disease and Treatments

Nystuen, K., McNamee, S. M., Akula, M., Holton, K. M., DeAngelis, M. M., & Haider, N. B. (2024) · Bioengineering · doi:10.3390/bioengineering11010045 · Cited by 27 · see citing works

APOE-Targeted Therapeutics for Alzheimer's Disease

Yassine, H. N., Hugo, C., O’Donovan, B., Stephens, I. O., Johnson, L. A., Cole, G. M., Julia, T. C. W., Johansson, J. O., Kisler, K., & Chiba‐Falek, O. (2025) · Journal of Neuroscience · doi:10.1523/jneurosci.1388-25.2025 · Cited by 16 · see citing works

Leveraging multiomic approaches to elucidate mechanisms of heterogeneity in Alzheimer's disease: Neuropsychiatric symptoms, co‐pathologies, and sex differences

Shwab, E. K., Pathak, G. A., Harvey, J., Belloy, M. E., Fischer, C. E., Lutz, M. W., Scholz, S. W., Cook, N., Reid, D. M., Chen, J., et al. (2025) · Alzheimer s & Dementia · doi:10.1002/alz.70549 · Cited by 11 · see citing works

Chromatin accessibility provides a window into the genetic etiology of human brain disease

Bendl, J. M., Fullard, J. F., Girdhar, K., Dong, P., Kosoy, R., Zeng, B., Hoffman, G. E., & Roussos, P. (2025) · Trends in Genetics · doi:10.1016/j.tig.2025.01.001 · Cited by 9 · see citing works

Limitations and opportunities in multi-omics integration for neurodevelopmental, neurodegenerative and psychiatric disorders: A systematic review

Behrens, L. M. P., Fernandes, G. D. S., Gonçalves, G. F., Nunes, F. V. M., Weimer, R. D., Moreira, J. C. F., & Dorn, M. (2026) · Neuroscience · doi:10.1016/j.neuroscience.2026.01.019 · Cited by 8 · see citing works

Integrative epigenomic landscape of Alzheimer’s Disease brains reveals oligodendrocyte molecular perturbations associated with tau

Oatman, S. R., Reddy, J. S., Atashgaran, A., Wang, X., Min, Y., Quicksall, Z., Vanelderen, F., Carrasquillo, M. M., Liu, C.-C., Yamazaki, Y., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-68864-9 · Cited by 6 · see citing works

Application of computational algorithms for single-cell RNA-seq and ATAC-seq in neurodegenerative diseases

Choi, H. K., Kim, H., Chung, H., Lee, D.-S., & Kim, J. (2024) · Briefings in Functional Genomics · doi:10.1093/bfgp/elae044 · Cited by 5 · see citing works

Comparative mapping of single‐cell transcriptomic landscapes in neurodegenerative diseases

Shwab, E. K., Man, Z., Gingerich, D. C., Gamache, J., Garrett, M. E., Serrano, G. E., Beach, T. G., Crawford, G. E., Ashley‐Koch, A. E., & Chiba‐Falek, O. (2025) · Alzheimer s & Dementia · doi:10.1002/alz.70012 · Cited by 5 · see citing works

Frontal cortex pyramidal neuron expression profiles differentiate the prodromal stage from progressive degeneration across the Alzheimer's disease spectrum

Labuza, A., Alldred, M. J., Pidikiti, H., Malek‐Ahmadi, M. H., Lee, S. H., Heguy, A., Coleman, P. D., Chakrabarty, S., Chiosis, G., Mufson, E. J., et al. (2025) · Alzheimer s & Dementia · doi:10.1002/alz.70395 · Cited by 3 · see citing works

From correlation to causation: cell‐type‐specific gene regulatory networks in Alzheimer's disease

Liu, D., Jiang, Z., Kim, H., Tukker, A. M., Dalvi, A., Xie, J., Li, Y., Yuan, C., Bowman, A. B., Zhang, D., et al. (2026) · Alzheimer s & Dementia · doi:10.1002/alz.71053 · Cited by 1 · see citing works

Personalized single-cell transcriptomics reveals molecular diversity in Alzheimer’s disease

Chandrashekar, P. B., Alatkar, S. A., Kalafut, N. C., Jin, T., Gupta, C., Burczak, R. C., Xiang, H., Liu, S., Li, A. Z., Hong, A., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-72310-1 · Cited by 2 · see citing works

Personalized Single-cell Transcriptomics Reveals Molecular Diversity in Alzheimer’s DiseasePreprint

Chandrashekar, P. B., Alatkar, S. A., Kalafut, N. C., Jin, T., Gupta, C., Burzak, R., Huang, X., Liu, S., Li, A. Z., Girdhar, K., et al. (2024) · medRxiv · doi:10.1101/2024.11.01.24316589 · Cited by 1 · see citing works

KOLF2.1J iTF-Microglia: A standardized platform to study microglial transcriptional regulatory networks in CNS diseasePreprint

Rodríguez-Nunez, I., Bartley, S. C., Taylor, J. W., Johnston, S. Q., Rogers, B. B., Meadows, S. K., Newberry, K. M., Cochran, J. N., & Myers, R. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.05.30.657077 · Cited by 1 · see citing works

Additional file 2 of Single-nucleus multi-omics of Parkinson’s disease reveals a glutamatergic neuronal subtype susceptible to gene dysregulation via alteration of transcriptional networks

Shwab, E. K., Gingerich, D. C., Man, Z., Gamache, J., Garrett, M. E., Crawford, G. E., Ashley‐Koch, A. E., Serrano, G. E., Beach, T. G., Lutz, M. W., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26157557

Additional file 1 of Single-nucleus multi-omics of Parkinson’s disease reveals a glutamatergic neuronal subtype susceptible to gene dysregulation via alteration of transcriptional networks

Shwab, E. K., Gingerich, D. C., Man, Z., Gamache, J., Garrett, M. E., Crawford, G. E., Ashley‐Koch, A. E., Serrano, G. E., Beach, T. G., Lutz, M. W., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26157254

MOSAIC: A Spectral Framework for Integrative Phenotypic Characterization Using Population-Level Single-Cell Multi-OmicsPreprint

Lu, C., Kluger, Y., & Ma, R. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.02.10.705077

KOLF2.1J iTF-Microglia: A standardized platform to study microglial transcriptional regulatory networks in CNS disease

Rogers, B. B., Anderson, A. G., Rodríguez-Nunez, I., Bartley, S. C., Johnston, S. Q., Taylor, J. W., Meadows, S. K., Newberry, K. M., Myers, R., & Cochran, J. N. (2026) · iScience · doi:10.1016/j.isci.2026.116412 · Cited by 1 · see citing works

A diagnostic plasma omics‐biomarker for Alzheimer's disease informed by microglial single‐cell transcriptomics: A pilot study

Lutz, M. W., Man, Z., Zheng, Y., Venkatesan, S., & Chiba‐Falek, O. (2026) · Alzheimer s & Dementia Translational Research & Clinical Interventions · doi:10.1002/trc2.70273

Dissecting cell‐subtype specific regulatory variants and their target genes underpinning the pathogenesis of late onset Alzheimer’s disease

Gamache, J., Gingerich, D. C., Garrett, M. E., Barrera, J., Ashley‐Koch, A. E., Crawford, G. E., & Chiba‐Falek, O. (2022) · Alzheimer s & Dementia · doi:10.1002/alz.066324 · Cited by 1 · see citing works

Single-nucleus chromatin accessibility and transcriptomic characterization of Alzheimer’s disease

Morabito, S., Miyoshi, E., Michael, N., Shahin, S., Martini, A. C., Head, E., Silva, J., Leavy, K., Perez-Rosendahl, M., & Swarup, V. (2021) · Nature Genetics · doi:10.1038/s41588-021-00894-z · Cited by 643 · see citing works

Additional file 1 of Integrative single-nucleus multi-omics analysis prioritizes candidate cis and trans regulatory networks and their target genes in Alzheimer’s disease brains

Gamache, J., Gingerich, D. C., Shwab, E. K., Barrera, J., Garrett, M. E., Hume, C., Crawford, G. E., Ashley‐Koch, A. E., & Chiba‐Falek, O. (2024) · Figshare · doi:10.6084/m9.figshare.26622151

Unraveling the genetic complexity of Alzheimer's disease across diverse populations via integrative single‐cell multi‐omics

Shwab, E. K., Gingerich, D., Hodgson, D., Man, Z., Garrett, M. E., Crawford, G. E., Ashley‐Koch, A. E., & Chiba‐Falek, O. (2025) · Alzheimer s & Dementia · doi:10.1002/alz70855_099090

Genomic and epigenomic insights into purkinje and granule cells in Alzheimer's disease‐related dementia using single‐nucleus multiome analysis

Cheng, F., Feng, Y., Flanagan, M. E., Bonakdarpour, B., & Cummings, J. L. (2025) · Alzheimer s & Dementia · doi:10.1002/alz70855_105855