Multiscale Analysis of Independent Alzheimer’s Cohorts Finds Disruption of Molecular, Genetic, and Clinical Networks by Human Herpesvirus

Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

Benjamini, Y., & Hochberg, Y. (1995) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.2517-6161.1995.tb02031.x · Cited by 109,482 · see citing works

Basic local alignment search tool

Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669 · see citing works

The Sequence Alignment/Map format and SAMtools

Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041 · see citing works

Fast and accurate short read alignment with Burrows-Wheeler transform

Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607 · see citing works

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

Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles

Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506580102 · Cited by 53,625 · see citing works

STAR: ultrafast universal RNA-seq aligner

Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., & Gingeras, T. R. (2013) · Bioinformatics · doi:10.1093/bioinformatics/bts635 · Cited by 51,709 · see citing works

<tt>edgeR</tt> : a Bioconductor package for differential expression analysis of digital gene expression data

Robinson, M. D., McCarthy, D. J., & Smyth, G. K. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp616 · Cited by 41,364 · see citing works

limma powers differential expression analyses for RNA-sequencing and microarray studies

Ritchie, M. E., Phipson, B., Wu, D., Hu, Y., Law, C. W., Shi, W., & Smyth, G. K. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv007 · Cited by 40,458 · see citing works

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

Liao, Y., Smyth, G. K., & Shi, W. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btt656 · Cited by 27,219 · see citing works

Initial sequencing and analysis of the human genome

International Human Genome Sequencing Consortium, Whitehead Institute for Biomedical Research, C. F. G. R., Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., et al. (2001) · Nature · doi:10.1038/35057062 · Cited by 24,216 · see citing works

A global reference for human genetic variation

The 1000 Genomes Project Consortium, authors, C., Auton, A., Abecasis, G. R., Steering committee, Altshuler, D. M., Durbin, R. M., Abecasis, G. R., Bentley, D. R., Chakravarti, A., et al. (2015) · Nature · doi:10.1038/nature15393 · Cited by 18,247 · see citing works

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

Cox, J., & Mann, M. (2008) · Nature Biotechnology · doi:10.1038/nbt.1511 · Cited by 14,855 · see citing works

Robust enumeration of cell subsets from tissue expression profiles

Newman, A. M., Liu, C. L., Green, M. R., Gentles, A. J., Feng, W., Xu, Y., Hoang, C. D., Diehn, M., & Alizadeh, A. A. (2015) · Nature Methods · doi:10.1038/nmeth.3337 · Cited by 12,116 · see citing works

Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments

Smyth, G. K. (2004) · Statistical Applications in Genetics and Molecular Biology · doi:10.2202/1544-6115.1027 · Cited by 11,829 · see citing works

Toward defining the preclinical stages of Alzheimer’s disease: Recommendations from the National Institute on Aging-Alzheimer’s Association workgroups on diagnostic guidelines for Alzheimer’s disease

Sperling, R. A., Aisen, P. S., Beckett, L. A., Bennett, D. A., Craft, S., Fagan, A. M., Iwatsubo, T., Jack, C. R., Kaye, J., Montine, T. J., et al. (2011) · Alzheimer's &amp; Dementia · doi:10.1016/j.jalz.2011.03.003 · Cited by 7,155 · see citing works

From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline

Van der Auwera, G. A., Carneiro, M. O., Hartl, C., Poplin, R., del Angel, G., Levy‐Moonshine, A., Jordan, T., Shakir, K., Roazen, D., Thibault, J., et al. (2013) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi1110s43 · Cited by 6,687 · see citing works

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

Law, C. W., Chen, Y., Shi, W., & Smyth, G. K. (2014) · Genome Biology · doi:10.1186/gb-2014-15-2-r29 · Cited by 6,155 · see citing works

A fast, lock-free approach for efficient parallel counting of occurrences of <i>k</i> -mers

Marçais, G., & Kingsford, C. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr011 · Cited by 4,661 · see citing works

xCell: digitally portraying the tissue cellular heterogeneity landscape

Aran, D., Hu, Z., & Butte, A. J. (2017) · Genome Biology · doi:10.1186/s13059-017-1349-1 · Cited by 4,397 · 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

A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies

Howie, B. N., Donnelly, P., & Marchini, J. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000529 · Cited by 3,928 · 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

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

Liao, Y., Smyth, G. K., & Shi, W. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt214 · Cited by 3,064 · 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

Alzheimer's disease: cell-specific pathology isolates the hippocampal formation.

Hyman, B. T., Van Hoesen, G. W., Damasio, A. R., & Barnes, C. L. (1984) · Science · doi:10.1126/science.6474172 · Cited by 2,268 · cited 1× · see citing works

MatInspector and beyond: promoter analysis based on transcription factor binding sites

Cartharius, K., Frech, K., Grote, K., Klocke, B., Haltmeier, M., Klingenhoff, A., Frisch, M., Bayerlein, M., & Werner, T. (2005) · Computer applications in the biosciences · doi:10.1093/bioinformatics/bti473 · Cited by 1,962 · see citing works

Profound Loss of Layer II Entorhinal Cortex Neurons Occurs in Very Mild Alzheimer’s Disease

Gómez-Isla, T., Price, J. L., McKeel Jr., D. W., Morris, J. C., Growdon, J. H., & Hyman, B. T. (1996) · The Journal of Neuroscience · doi:10.1523/jneurosci.16-14-04491.1996 · Cited by 1,796 · cited 1× · see citing works

Matrix eQTL: ultra fast eQTL analysis via large matrix operations

Shabalin, A. A. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts163 · Cited by 1,694 · see citing works

Integrated Systems Approach Identifies Genetic Nodes and Networks in Late-Onset Alzheimer’s Disease

Zhang, B., Gaiteri, C., Bodea, L.-G., Wang, Z., McElwee, J., Podtelezhnikov, A. A., Zhang, C., Xie, T., Tran, L., Dobrin, R., et al. (2013) · Cell · doi:10.1016/j.cell.2013.03.030 · Cited by 1,657 · see citing works

Extensive Involvement of Autophagy in Alzheimer Disease: An Immuno-Electron Microscopy Study

Nixon, R. A., Wegiel, J., Kumar, A., Yu, W. H., Peterhoff, C., Cataldo, A., & Cuervo, A. M. (2005) · Journal of Neuropathology &amp; Experimental Neurology · doi:10.1093/jnen/64.2.113 · Cited by 1,588 · see citing works

Mutant presenilins specifically elevate the levels of the 42 residue β-amyloid peptide in vivo: evidence for augmentation of a 42-specific γ secretase

Jankowsky, J. L., Fadale, D. J., Anderson, J., Xu, G. M., Gonzales, V., Jenkins, N. A., Copeland, N. G., Lee, M. K., Younkin, L. H., Wagner, S. L., et al. (2004) · Human Molecular Genetics · doi:10.1093/hmg/ddh019 · Cited by 1,575 · see citing works

The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins

Rouillard, A. D., Gundersen, G. W., Fernandez, N. F., Wang, Z., Monteiro, C. D., McDermott, M. G., & Ma’ayan, A. (2016) · Database · doi:10.1093/database/baw100 · Cited by 1,515 · see citing works

G-quadruplexes and their regulatory roles in biology

Rhodes, D., & Lipps, H. J. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv862 · Cited by 1,494 · see citing works

Regulation of the Germinal Center Response by MicroRNA-155

Thai, T., Calado, D. P., Casola, S. S., Ansel, K. M., Xiao, C., Xue, Y., Murphy, A. J., Frendewey, D. A., Valenzuela, D. M., Kutok, J. L., et al. (2007) · Science · doi:10.1126/science.1141229 · Cited by 1,477 · see citing works

A survey of human brain transcriptome diversity at the single cell level

Darmanis, S., Sloan, S. A., Zhang, Y., Enge, M., Caneda, C., Shuer, L. M., Hayden Gephart, M. G., Barres, B. A., & Quake, S. R. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1507125112 · Cited by 1,401 · see citing works

miRTarBase: a database curates experimentally validated microRNA–target interactions

Hsu, S.-D., Lin, F., Wu, W.-Y., Liang, C., Huang, W.-C., Chan, W.-L., Tsai, W.-T., Chen, G.-Z., Lee, C.-J., Chiu, C.-M., et al. (2010) · Nucleic Acids Res. · doi:10.1093/nar/gkq1107 · Cited by 1,387 · see citing works

The Alzheimer's Disease-Associated Amyloid β-Protein Is an Antimicrobial Peptide

Soscia, S. J., Kirby, J. E., Washicosky, K. J., Tucker, S. M., Ingelsson, M., Hyman, B., Burton, M. A., Goldstein, L. E., Duong, S., Tanzi, R. E., et al. (2010) · PLoS ONE · doi:10.1371/journal.pone.0009505 · Cited by 1,060 · see citing works

ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments

Lachmann, A., Xu, H., Krishnan, J., Berger, S., Mazloom, A. R., & Ma’ayan, A. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq466 · Cited by 997 · see citing works

Amyloid-β peptide protects against microbial infection in mouse and worm models of Alzheimer’s disease

Kumar, D. K. V., Choi, S. H., Washicosky, K. J., Eimer, W. A., Tucker, S., Ghofrani, J., Lefkowitz, A., McColl, G., Goldstein, L. E., Tanzi, R. E., et al. (2016) · Science Translational Medicine · doi:10.1126/scitranslmed.aaf1059 · Cited by 971 · see citing works

Genotype Imputation with Thousands of Genomes

Howie, B., Marchini, J., & Stephens, M. (2011) · G3 Genes|Genomes|Genetics · doi:10.1534/g3.111.001198 · Cited by 966 · see citing works

Preliminary NINDS neuropathologic criteria for Steele‐Richardson‐Olszewski syndrome (progressive supranuclear palsy)

Hauw, J., Daniel, S. E., Dickson, D. W., Horoupian, D. S., Jellinger, K. A., Lantos, P. L., McKee, A. C., Tabaton, M., & Litvan, I. (1994) · Neurology · doi:10.1212/wnl.44.11.2015 · Cited by 854 · see citing works

Overview and Findings from the Rush Memory and Aging Project

Bennett, D. A., Schneider, J. A., Buchman, A. S., Barnes, L. L., Boyle, P. A., & Wilson, R. S. (2012) · Current Alzheimer Research · doi:10.2174/156720512801322663 · Cited by 837 · see citing works

A Versatile Gene-Based Test for Genome-wide Association Studies

Liu, J. Z., McRae, A. F., Nyholt, D. R., Medland, S. E., Wray, N. R., Brown, K. M., Hayward, N. K., Montgomery, G. W., Visscher, P. M., Martin, N. G., et al. (2010) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2010.06.009 · Cited by 791 · see citing works

Massive mining of publicly available RNA-seq data from human and mouse

Lachmann, A., Torre, D., Keenan, A. B., Jagodnik, K. M., Lee, H. J., Wang, L., Silverstein, M. C., & Ma’ayan, A. (2018) · Nature Communications · doi:10.1038/s41467-018-03751-6 · Cited by 701 · see citing works

Optimal tests for rare variant effects in sequencing association studies

Lee, S., Wu, M. C., & Lin, X. (2012) · Biostatistics · doi:10.1093/biostatistics/kxs014 · Cited by 683 · see citing works

NCBI Viral Genomes Resource

Brister, J. R., Ako-adjei, D., Bào, Y., & Blinkova, O. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku1207 · Cited by 648 · see citing works

Overview and Findings from the Religious Orders Study

Bennett, D. A., Schneider, J. A., Arvanitakis, Z., & Wilson, R. S. (2012) · Current Alzheimer Research · doi:10.2174/156720512801322573 · Cited by 647 · see citing works

Identification of normal and pathological aging in prospectively studied nondemented elderly humans

Dickson, D. W., Crystal, H. A., Mattiace, L. A., Masur, D. M., Blau, A. D., Davies, P., Yen, S.-H., & Aronson, M. K. (1992) · Neurobiology of Aging · doi:10.1016/0197-4580(92)90027-u · Cited by 643 · see citing works

Immunohistochemical evidence for apoptosis in Alzheimer's disease.

Su, J., Anderson, A., Cummings, B. J., & Cotman, C. (1994) · NeuroReport · doi:10.1097/00001756-199412000-00031 · Cited by 607 · see citing works

A viral microRNA functions as an orthologue of cellular miR-155

Gottwein, E., Mukherjee, N., Sachse, C., Frenzel, C., Majoros, W. H., Chi, J., Braich, R. S., Manoharan, M., Soutschek, J., Ohler, U., et al. (2007) · Nature · doi:10.1038/nature05992 · Cited by 566 · see citing works

Microbes and Alzheimer’s Disease

Itzhaki, R. F., Lathe, R., Balin, B. J., Ball, M. J., Bearer, E. L., Braak, H., Bullido, M. J., Carter, C., Clerici, M., Cosby, S. L., et al. (2016) · Journal of Alzheimer’s Disease · doi:10.3233/jad-160152 · Cited by 532 · see citing works

Ensembl Genomes 2016: more genomes, more complexity

Kersey, P. J., Allen, J. E., Armean, I. M., Boddu, S., Bolt, B. J., Carvalho‐Silva, D., Christensen, M. B., Davis, P. A., Falin, L. J., Grabmüller, C., et al. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1209 · Cited by 503 · see citing works

Necroptosis activation in Alzheimer's disease

Caccamo, A., Branca, C., Piras, I. S., Ferreira, E., Huentelman, M. J., Liang, W. S., Readhead, B., Dudley, J. T., Spangenberg, E. E., Green, K. N., et al. (2017) · Nature Neuroscience · doi:10.1038/nn.4608 · Cited by 482 · see citing works

A stop-codon mutation in the BRI gene associated with familial British dementia

Vidal, R., Frangione, B., Rostagno, A., Mead, S., Révész, T., Plant, G., & Ghiso, J. (1999) · Nature · doi:10.1038/21637 · 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

Human gastric mucin. Identification of a unique species by expression cloning.

Toribara, N. W., Roberton, A. M., Ho, S. B., Kuo, W.-L., Gum, E. T., Hicks, J. W., Gum, J. R., Byrd, J. C., Siddiki, B., & Kim, Y. S. (1993) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)53402-5 · Cited by 366 · see citing works

F-Seq: a feature density estimator for high-throughput sequence tags

Boyle, A. P., Guinney, J., Crawford, G. E., & Furey, T. S. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn480 · Cited by 363 · see citing works

The latent human herpesvirus-6A genome specifically integrates in telomeres of human chromosomes in vivo and in vitro

Arbuckle, J. H., Medveczky, M. M., Luka, J., Hadley, S. H., Luegmayr, A., Ablashi, D. V., Lund, T. C., Tolar, J., Meirleir, K. D., Montoya, J. G., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0913586107 · Cited by 357 · see citing works

Gene expression profiles in anatomically and functionally distinct regions of the normal aged human brain

Liang, W. S., Dunckley, T. L., Beach, T. G., Grover, A., Mastroeni, D., Walker, D. G., Caselli, R. J., Kukull, W. A., McKeel, D. W., Morris, J. C., et al. (2006) · Physiological Genomics · doi:10.1152/physiolgenomics.00208.2006 · Cited by 342 · see citing works

Altered neuronal gene expression in brain regions differentially affected by Alzheimer's disease: a reference data set

Liang, W. S., Dunckley, T., Beach, T. G., Grover, A., Mastroeni, D., Ramsey, K., Caselli, R. J., Kukull, W. A., McKeel, D., Morris, J. C., et al. (2008) · Physiological Genomics · doi:10.1152/physiolgenomics.00242.2007 · Cited by 309 · see citing works

Strategies for aggregating gene expression data: The collapseRows R function

Miller, J. A., Cai, C., Langfelder, P., Geschwind, D. H., Kurian, S. M., Salomon, D. R., & Horvath, S. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-322 · Cited by 300 · see citing works

A decamer duplication in the 3′ region of the <i>BRI</i> gene originates an amyloid peptide that is associated with dementia in a Danish kindred

Vidal, R., Révész, T., Rostagno, A., Kim, E., Holton, J. L., Bek, T., Bojsen-Møller, M., Braendgaard, H., Plant, G., Ghiso, J., et al. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.080076097 · Cited by 300 · see citing works

Regional distribution of neuritic plaques in the nondemented elderly and subjects with very mild Alzheimer disease

Haroutunian, V. (1998) · Archives of Neurology · doi:10.1001/archneur.55.9.1185 · Cited by 289 · see citing works

Cardiometabolic risk loci share downstream cis- and trans-gene regulation across tissues and diseases

Franzén, O., Ermel, R., Cohain, A., Akers, N. K., Di Narzo, A., Talukdar, H. A., Foroughi-Asl, H., Giambartolomei, C., Fullard, J. F., Sukhavasi, K., et al. (2016) · Science · doi:10.1126/science.aad6970 · Cited by 288 · see citing works

G-quadruplexes regulate Epstein-Barr virus–encoded nuclear antigen 1 mRNA translation

Murat, P., Zhong, J., Lekieffre, L., Cowieson, N. P., Clancy, J. L., Preiß, T., Balasubramanian, S., Khanna, R., & Tellam, J. (2014) · Nature Chemical Biology · doi:10.1038/nchembio.1479 · Cited by 272 · see citing works

VEGAS2: Software for More Flexible Gene-Based Testing

Mishra, A., & Macgregor, S. (2015) · Twin Research and Human Genetics · doi:10.1017/thg.2014.79 · Cited by 257 · see citing works

Epstein–Barr virus latent membrane protein 1 trans-activates miR-155 transcription through the NF-κB pathway

Gatto, G., Rossi, A., Rossi, D. P., Kroening, S., Bonatti, S., & Mallardo, M. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn666 · Cited by 254 · see citing works

d-serine levels in Alzheimer’s disease: implications for novel biomarker development

Madeira, C., Lourenco, M. V., Vargas-Lopes, C., Suemoto, C. K., Brandão, C. O., Reis, T., Leite, R. E. P., Laks, J., Jacob-Filho, W., Pasqualucci, C. A., et al. (2015) · Translational Psychiatry · doi:10.1038/tp.2015.52 · Cited by 233 · see citing works

Disentangling molecular relationships with a causal inference test

Millstein, J., Zhang, B., Zhu, J. W., & Schadt, E. E. (2009) · BMC Genetics · doi:10.1186/1471-2156-10-23 · Cited by 230 · see citing works

Primer tRNAs for reverse transcription

Mak, J., & Kleiman, L. (1997) · Journal of Virology · doi:10.1128/jvi.71.11.8087-8095.1997 · Cited by 226 · see citing works

Human herpesvirus 6 (HHV‐6) is transmitted from parent to child in an integrated form and characterization of cases with chromosomally integrated HHV‐6 DNA

Tanaka‐Taya, K., Sashihara, J., Kurahashi, H., Amo, K., Miyagawa, H., Kondo, K., Okada, S., & Yamanishi, K. (2004) · Journal of Medical Virology · doi:10.1002/jmv.20113 · Cited by 219 · see citing works

Faster and More Accurate Sequence Alignment with SNAPPreprint

Zaharia, M., Bolosky, W. J., Curtis, K., Fox, A., Patterson, D. A., Shenker, S. J., Stoica, I. G., Karp, R. M., & Sittler, T. (2011) · arXiv (Cornell University) · doi:10.48550/arxiv.1111.5572 · Cited by 219 · see citing works

Herpes virus in Alzheimer's disease: relation to progression of the disease

Carbone, I., Lazzarotto, T., Ianni, M., Porcellini, E., Forti, P., Masliah, E., Gabrielli, L., & Licastro, F. (2013) · Neurobiology of Aging · doi:10.1016/j.neurobiolaging.2013.06.024 · Cited by 208 · see citing works

Morbus Alzheimer and Morbus Pick: A Genetic, Clinical and Patho-anatomical Study

SJOGREN, T., Sjögren, H., & Lindgren, A. (1953) · AIBS Bulletin · doi:10.1093/aibsbulletin/3.2.16-c · Cited by 208 · see citing works

Alterations in metabolic pathways and networks in Alzheimer’s disease

Kaddurah‐Daouk, R., Zhu, H., Sharma, S., Bogdanov, M. B., Rozen, S., Matson, W. R., Oki, N. O., Motsinger‐Reif, A. A., Churchill, E., Lei, Z., et al. (2013) · Translational Psychiatry · doi:10.1038/tp.2013.18 · Cited by 205 · see citing works

Reactivated herpes simplex infection increases the risk of Alzheimer's disease

Lövheim, H., Gilthorpe, J. D., Adolfsson, R., Nilsson, L., & Elgh, F. (2014) · Alzheimer s & Dementia · doi:10.1016/j.jalz.2014.04.522 · Cited by 202 · see citing works

Herpes simplex virus type 1 and Alzheimer’s disease: increasing evidence for a major role of the virus

Itzhaki, R. F. (2014) · Frontiers in Aging Neuroscience · doi:10.3389/fnagi.2014.00202 · Cited by 199 · see citing works

Wellington: a novel method for the accurate identification of digital genomic footprints from DNase-seq data

Piper, J., Elze, M. C., Cauchy, P., Cockerill, P. N., Bonifer, C., & Ott, S. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt850 · Cited by 194 · see citing works

Role of SP1-binding domains in in vivo transcriptional regulation of the human immunodeficiency virus type 1 long terminal repeat

Harrich, D., Garcia, J. A., Wu, F. K., Mitsuyasu, R. T., Gonazalez, J., & Gaynor, R. B. (1989) · Journal of Virology · doi:10.1128/jvi.63.6.2585-2591.1989 · Cited by 189 · see citing works

Herpesviruses in brain and Alzheimer's disease

Lin, W., Wozniak, M. A., Cooper, R. J., Wilcock, G. K., & Itzhaki, R. F. (2002) · The Journal of Pathology · doi:10.1002/path.1127 · Cited by 187 · see citing works

Expression2Kinases: mRNA profiling linked to multiple upstream regulatory layers

Chen, E. Y., Xu, H., Gordonov, S., Lim, M. P., Perkins, M. H., & Ma’ayan, A. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr625 · Cited by 175 · see citing works

Exploring mRNA 3′-UTR G-quadruplexes: evidence of roles in both alternative polyadenylation and mRNA shortening

Beaudoin, J.-D., & Perreault, J. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt265 · Cited by 169 · see citing works

Targeting Fyn Kinase in Alzheimer’s Disease

Nygaard, H. B. (2018) · Biological Psychiatry · doi:10.1016/j.biopsych.2017.06.004 · Cited by 162 · see citing works

Staying Alive: Cell Death in Antiviral Immunity

Upton, J. W., & Chan, F. K.-M. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.01.027 · Cited by 156 · see citing works

Analysis of computational footprinting methods for DNase sequencing experiments

Gusmao, E. G., Allhoff, M., Zenke, M., & Costa, I. G. (2016) · Nature Methods · doi:10.1038/nmeth.3772 · Cited by 152 · see citing works

ViromeScan: a new tool for metagenomic viral community profiling

Rampelli, S., Soverini, M., Turroni, S., Quercia, S., Biagi, E., Brigidi, P., & Candela, M. (2016) · BMC Genomics · doi:10.1186/s12864-016-2446-3 · Cited by 146 · see citing works

Metabolomic changes in autopsy‐confirmed Alzheimer's disease

Kaddurah-Daouk, R. F., Rozen, S., Matson, W. R., Han, X., Hulette, C. M., Burke, J. R., Doraiswamy, P. M., & Welsh-Bohmer, K. A. (2010) · Alzheimer s & Dementia · doi:10.1016/j.jalz.2010.06.001 · Cited by 145 · see citing works

A Functional MicroRNA-155 Ortholog Encoded by the Oncogenic Marek's Disease Virus

Zhao, Y., Yao, Y., Xu, H., Lambeth, L. S., Smith, L. P., Kgosana, L. B., Wang, X., & Nair, V. (2008) · Journal of Virology · doi:10.1128/jvi.01166-08 · Cited by 142 · see citing works

Herpes simplex infection and the risk of Alzheimer’s disease: A nested case-control study

Lövheim, H., Gilthorpe, J., Johansson, A., Eriksson, S., Hallmans, G., & Elgh, F. (2015) · Alzheimer's &amp; Dementia · doi:10.1016/j.jalz.2014.07.157 · Cited by 136 · see citing works

Incorporation of lysyl-tRNA synthetase into human immunodeficiency virus type 1

Cen, S., Khorchid, A., Javanbakht, H., Gabor, J., Stello, T., Shiba, K., Musier-Forsyth, K., & Kleiman, L. (2001) · Journal of Virology · doi:10.1128/jvi.75.11.5043-5048.2001 · Cited by 134 · see citing works

Meditation and vacation effects have an impact on disease-associated molecular phenotypes

Epel, E. S., Puterman, E., Lin, J., Blackburn, E. H., Lum, P. Y., Beckmann, N. D., Zhu, J., Lee, E., Gilbert, A., Rissman, R. A., et al. (2016) · Translational Psychiatry · doi:10.1038/tp.2016.164 · Cited by 105 · see citing works

Integrative Analysis of DNA Methylation and Gene Expression Data Identifies EPAS1 as a Key Regulator of COPD

Yoo, S., Takikawa, S., Geraghty, P. M., Argmann, C., Campbell, J. D., Lin, L., Huang, T., Tu, Z., Feronjy, R., Spira, A. E., et al. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1004898 · Cited by 100 · see citing works

Poly(ADP-ribose) polymerase-1 is required for efficient HIV-1 integration

Ha, H. C., Juluri, K. R., Zhou, Y., Leung, S., Hermankova, M., & Snyder, S. H. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.051633498 · Cited by 97 · see citing works

miR-155 Is Essential for Inflammation-Induced Hippocampal Neurogenic Dysfunction

Woodbury, M. E., Freilich, R. W., Cheng, C. J., Asai, H., Ikezu, S., Boucher, J. D., Slack, F. J., & Ikezu, T. (2015) · Journal of Neuroscience · doi:10.1523/jneurosci.4790-14.2015 · Cited by 94 · see citing works

miR-155 is involved in Alzheimer’s disease by regulating T lymphocyte function

Song, J., & Lee, J. E. (2015) · Frontiers in Aging Neuroscience · doi:10.3389/fnagi.2015.00061 · Cited by 91 · see citing works

The Effect of Human Herpesvirus-6 (HHV-6) on Cultured Human Neural Cells: Oligodendrocytes and Microglia

Albright, A. V., Lavi, E., Black, J. B., Goldberg, S. H., O’Connor, M. J., & González‐Scarano, F. (1998) · Journal of NeuroVirology · doi:10.3109/13550289809113493 · Cited by 90 · see citing works

Visualization of DNA G-quadruplexes in herpes simplex virus 1-infected cells

Artusi, S., Perrone, R., Lago, S., Raffa, P., Iorio, E. D., Palù, G., & Richter, S. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw968 · Cited by 85 · see citing works

Activation of Sp1-mediated transcription by Rta of Epstein-Barr virus via an interaction with MCAF1

Li, C. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki956 · Cited by 72 · see citing works

Nucleotide Pool Depletion Induces G-Quadruplex-Dependent Perturbation of Gene Expression

Papadopoulou, C., Guilbaud, G., Schiavone, D., & Sale, J. E. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.11.039 · Cited by 71 · see citing works

Herpes Simplex Virus 1 Infection Activates Poly(ADP-Ribose) Polymerase and Triggers the Degradation of Poly(ADP-Ribose) Glycohydrolase

Grady, S. L., Hwang, J., Vastag, L., Rabinowitz, J. D., & Shenk, T. E. (2012) · Journal of Virology · doi:10.1128/jvi.00495-12 · Cited by 71 · see citing works

Genetic Association of Neurotrophic Tyrosine Kinase Receptor Type 2 (NTRK2) With Alzheimer's Disease

Chen, Z., Simmons, M. S., Perry, R. T., Wiener, H. W., Harrell, L. E., & Go, R. C. P. (2007) · American Journal of Medical Genetics Part B Neuropsychiatric Genetics · doi:10.1002/ajmg.b.30607 · Cited by 71 · see citing works

SRp40 and SRp55 Promote the Translation of Unspliced Human Immunodeficiency Virus Type 1 RNA

Swanson, C. M., Sherer, N. M., & Malim, M. H. (2010) · Journal of Virology · doi:10.1128/jvi.02526-09 · Cited by 68 · see citing works

Laser-captured microglia in the Alzheimer's and Parkinson's brain reveal unique regional expression profiles and suggest a potential role for hepatitis B in the Alzheimer's brain

Mastroeni, D., Nolz, J., Sekar, S., Delvaux, E., Serrano, G. E., Cuyugan, L., Liang, W. S., Beach, T. G., Rogers, J., & Coleman, P. D. (2017) · Neurobiology of Aging · doi:10.1016/j.neurobiolaging.2017.10.019 · Cited by 65 · see citing works

Elevation of the level and activity of acid ceramidase in Alzheimer's disease brain

Huang, Y., Tanimukai, H., Liu, F., Iqbal, K., Grundke, I., & Gong, C. (2004) · European Journal of Neuroscience · doi:10.1111/j.1460-9568.2004.03852.x · Cited by 60 · see citing works

Reactivation of Chromosomally Integrated Human Herpesvirus-6 by Telomeric Circle Formation

Prusty, B. K., Krohne, G., & Rudel, T. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1004033 · Cited by 58 · see citing works

Evaluation of the poly(ADP‐ribose) polymerase‐1 gene variants in Alzheimer's disease

Liu, H., Lin, W., Wu, B., Liu, S. R., Wang, W., Tsai, C., Lee, C., & Tsai, F. (2010) · Journal of Clinical Laboratory Analysis · doi:10.1002/jcla.20379 · Cited by 54 · see citing works

Sequence Kernel Association Test of Multiple Continuous Phenotypes

Wu, B., & Pankow, J. S. (2016) · Genetic Epidemiology · doi:10.1002/gepi.21945 · Cited by 53 · see citing works

Encephalopathy following measles infection in children with chronic illness

Murphy, J. V., & Yunis, E. J. (1976) · The Journal of Pediatrics · doi:10.1016/s0022-3476(76)81045-1 · Cited by 53 · see citing works

G4RNA: an RNA G-quadruplex database

Garant, J., Luce, M.-J., Scott, M. S., et al. (2015) · Database · doi:10.1093/database/bav059 · Cited by 52 · see citing works

HERPES-SIMPLEX VIRAL GENOME AND SENILE AND PRESENILE DEMENTIAS OF ALZHEIMER AND PICK

Middleton, P. J., Petrić, M., Kozak, M., Rewcastle, N. B., & McLachlan, D. R. C. (1980) · The Lancet · doi:10.1016/s0140-6736(80)91490-7 · Cited by 51 · see citing works

HHV-6A in vitro infection of thyrocytes and T cells alters the expression of miRNA associated to autoimmune thyroiditis

Caselli, E., D’Accolti, M., Soffritti, I., Zatelli, M. C., Rossi, R., Uberti, E. C. D., & Luca, D. D. (2017) · Virology Journal · doi:10.1186/s12985-016-0672-6 · Cited by 49 · see citing works

Transcriptional profiling reveals molecular signatures associated with HIV permissiveness in Th1Th17 cells and identifies Peroxisome Proliferator-Activated Receptor Gammaas an intrinsic negative regulator of viral replication

Bernier, A., Cleret‐Buhot, A., Zhang, Y., Goulet, J.-P., Monteiro, P., Gosselin, A., DaFonseca, S., Wacleche, V. S., Jenabian, M.-A., Routy, J., et al. (2013) · Retrovirology · doi:10.1186/1742-4690-10-160 · Cited by 49 · see citing works

Possible chromosomal and germline integration of human herpesvirus 7

Prusty, B. K., Gulve, N., Rasa, S., Murovska, M., Hernández, P. C., & Ablashi, D. V. (2016) · Journal of General Virology · doi:10.1099/jgv.0.000692 · Cited by 42 · see citing works

Viral and Host-Cell Protein KinasesEnticing Antiviral Targets and Relevance of Nucleoside, and Viral Thymidine, Kinases

Shugar, D. (1999) · Pharmacology & Therapeutics · doi:10.1016/s0163-7258(99)00004-2 · Cited by 40 · see citing works

Lack of Evidence for a Role of HHV-6 in the Pathogenesis of Alzheimer’s Disease

Agostini, S., Mancuso, R., Baglio, F., Cabinio, M., Hernis, A., Guerini, F. R., Calabrese, E., Nemni, R., & Clerici, M. (2015) · Journal of Alzheimer s Disease · doi:10.3233/jad-150464 · Cited by 39 · see citing works

Amyloid beta selectively modulates neuronal TrkB alternative transcript expression with implications for Alzheimer's disease

Wong, J., Higgins, M. J., Halliday, G. M., & Garner, B. (2012) · Neuroscience · doi:10.1016/j.neuroscience.2012.02.037 · Cited by 38 · see citing works

tRNA Shifts the G‐quadruplex–Hairpin Conformational Equilibrium in RNA towards the Hairpin Conformer

Rode, A. B., Endoh, T., & Sugimoto, N. (2016) · Angewandte Chemie International Edition · doi:10.1002/anie.201605431 · Cited by 33 · see citing works

Decreased HHV-6 IgG in Alzheimer’s Disease

Westman, G., Blomberg, J., Yun, Z., Lannfelt, L., Ingelsson, M., & Eriksson, B. (2017) · Frontiers in Neurology · doi:10.3389/fneur.2017.00040 · Cited by 31 · see citing works

Aminoacylation of tRNAs Encoded by Chlorella Virus CVK2

Nishida, K., Kawasaki, T., Fujie, M., et al. (1999) · Virology · doi:10.1006/viro.1999.9949 · Cited by 30 · see citing works

Analysis of Human Herpesvirus 6 U3 Gene, which Is a Positional Homolog of Human Cytomegalovirus UL 24 Gene

Mori, Y., Yagi, H., Shimamoto, T., et al. (1998) · Virology · doi:10.1006/viro.1998.9305 · Cited by 28 · see citing works

Inhibition of Poly(ADP-ribose)polymerase impairs Epstein Barr Virus lytic cycle progression

Mattiussi, S., Tempera, I., Matusali, G., Mearini, G., Lenti, L., Fratarcangeli, S., Mosca, L., D’Erme, M., & Mattia, E. D. (2007) · Infectious Agents and Cancer · doi:10.1186/1750-9378-2-18 · Cited by 26 · see citing works

EXPLORING THE REPRODUCIBILITY OF PROBABILISTIC CAUSAL MOLECULAR NETWORK MODELS

Cohain, A. T., Divaraniya, A. A., Zhu, K., Scarpa, J. R., Kasarskis, A., Zhu, J., Chang, R. R., Dudley, J. T., & Schadt, E. E. (2016) · Pacific Symposium on Biocomputing (PSB) · doi:10.1142/9789813207813_0013 · Cited by 21 · see citing works

Human kinome analysis reveals novel kinases contributing to virus infection and retinoic-acid inducible gene I-induced type I and type III IFN gene expression

Nousiainen, L., Sillanpää, M., Jiang, M., et al. (2013) · Innate Immunity · doi:10.1177/1753425912473345 · Cited by 18 · see citing works

Productive Infection of Primary Macrophages with Human Herpesvirus 7

Zhang, Y., Bolle, L. D., Aquaro, S., et al. (2001) · Journal of Virology · doi:10.1128/jvi.75.21.10511-10514.2001 · Cited by 17 · see citing works

Molecular systems evaluation of oligomerogenic APPE693Q and fibrillogenic APPKM670/671NL/PSEN1Δexon9 mouse models identifies shared features with human Alzheimer’s brain molecular pathology

Readhead, B., Haure‐Mirande, J., Zhang, B., Haroutunian, V. H., Gandy, S., Schadt, E. E., Dudley, J. T., & Ehrlich, M. E. (2015) · Molecular Psychiatry · doi:10.1038/mp.2015.167 · Cited by 14 · see citing works

Thrombin induces Sp1-mediated antiviral effects in cytomegalovirus-infected human retinal pigment epithelial cells

Scholz, M., Vogel, J., Höver, G., et al. (2003) · Medical Microbiology and Immunology · doi:10.1007/s00430-003-0194-x · Cited by 9 · see citing works

Probing the Interaction between U24 and the SH3 Domain of Fyn Tyrosine Kinase

Sang, Y., Tait, A. R., Scott, W. R. P., et al. (2014) · Biochemistry · doi:10.1021/bi500945x · Cited by 7 · see citing works

Alzheimer Disease: An Update on Pathobiology and Treatment Strategies

Long, J. M., & Holtzman, D. M. (2019) · Cell · doi:10.1016/j.cell.2019.09.001 · Cited by 3,204 · see citing works

Molecular and cellular mechanisms underlying the pathogenesis of Alzheimer’s disease

Guo, T., Zhang, D., Zeng, Y., Huang, T. Y., Xu, H., & Zhao, Y. (2020) · Molecular Neurodegeneration · doi:10.1186/s13024-020-00391-7 · Cited by 994 · see citing works

History and progress of hypotheses and clinical trials for Alzheimer’s disease

Liu, P.-P., Xie, Y., Meng, X.-Y., & Kang, J.-S. (2019) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-019-0063-8 · Cited by 723 · see citing works

Alzheimer’s Disease-Associated β-Amyloid Is Rapidly Seeded by Herpesviridae to Protect against Brain Infection

Eimer, W. A., Vijaya Kumar, D. K., Navalpur Shanmugam, N. K., Rodriguez, A. S., Mitchell, T., Washicosky, K. J., György, B., Breakefield, X. O., Tanzi, R. E., & Moir, R. D. (2018) · Neuron · doi:10.1016/j.neuron.2018.06.030 · Cited by 674 · see citing works

Alzheimer’s disease drug development pipeline: 2020

Cummings, J., Lee, G., Ritter, A., Sabbagh, M., & Zhong, K. (2020) · Alzheimer's &amp; Dementia: Translational Research &amp; Clinical Interventions · doi:10.1002/trc2.12050 · Cited by 557 · see citing works

The innate immunity protein IFITM3 modulates γ-secretase in Alzheimer’s disease

Hur, J.-Y., Frost, G. R., Wu, X., Crump, C., Pan, S. J., Wong, E., Barros, M., Li, T., Nie, P., Zhai, Y., et al. (2020) · Nature · doi:10.1038/s41586-020-2681-2 · Cited by 382 · see citing works

The amyloid hypothesis on trial

Makin, S. (2018) · Nature · doi:10.1038/d41586-018-05719-4 · Cited by 360 · see citing works

Herpes Simplex Virus-1 in the Brain: The Dark Side of a Sneaky Infection

Marcocci, M. E., Napoletani, G., Protto, V., Kolesova, O., Piacentini, R., Li Puma, D. D., Lomonte, P., Grassi, C., Palamara, A. T., & De Chiara, G. (2020) · Trends in Microbiology · doi:10.1016/j.tim.2020.03.003 · Cited by 303 · see citing works

T cells promote microglia-mediated synaptic elimination and cognitive dysfunction during recovery from neuropathogenic flaviviruses

Garber, C., Soung, A., Vollmer, L. L., Kanmogne, M., Last, A., Brown, J., & Klein, R. S. (2019) · Nature Neuroscience · doi:10.1038/s41593-019-0427-y · Cited by 272 · see citing works

COVID‐19 and dementia: Analyses of risk, disparity, and outcomes from electronic health records in the US

Wang, Q., Davis, P. B., Gurney, M. E., & Xu, R. (2021) · Alzheimer's &amp; Dementia · doi:10.1002/alz.12296 · Cited by 257 · see citing works

Corroboration of a Major Role for Herpes Simplex Virus Type 1 in Alzheimer’s Disease

Itzhaki, R. F. (2018) · Frontiers in Aging Neuroscience · doi:10.3389/fnagi.2018.00324 · Cited by 256 · see citing works

A 3D human brain–like tissue model of herpes-induced Alzheimer’s disease

Cairns, D. M., Rouleau, N., Parker, R. N., Walsh, K. G., Gehrke, L., & Kaplan, D. L. (2020) · Science Advances · doi:10.1126/sciadv.aay8828 · Cited by 247 · see citing works

The Microbiome as a Modifier of Neurodegenerative Disease Risk

Fang, P., Kazmi, S. A., Jameson, K. G., & Hsiao, E. Y. (2020) · Cell Host &amp; Microbe · doi:10.1016/j.chom.2020.06.008 · Cited by 226 · see citing works

Early neuronal accumulation of DNA double strand breaks in Alzheimer’s disease

Shanbhag, N. M., Evans, M. D., Mao, W., Nana, A. L., Seeley, W. W., Adame, A., Rissman, R. A., Masliah, E., & Mucke, L. (2019) · Acta Neuropathologica Communications · doi:10.1186/s40478-019-0723-5 · Cited by 214 · see citing works

Questions concerning the role of amyloid-β in the definition, aetiology and diagnosis of Alzheimer’s disease

Morris, G. P., Clark, I. A., & Vissel, B. (2018) · Acta Neuropathologica · doi:10.1007/s00401-018-1918-8 · Cited by 212 · see citing works

The viral protein corona directs viral pathogenesis and amyloid aggregation

Ezzat, K., Pernemalm, M., Pålsson, S., Roberts, T. C., Järver, P., Dondalska, A., Bestas, B., Sobkowiak, M. J., Levänen, B., Sköld, M., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-10192-2 · Cited by 209 · see citing works

Hospital-treated infectious diseases and the risk of dementia: a large, multicohort, observational study with a replication cohort

Sipilä, P. N., Heikkilä, N., Lindbohm, J. V., Hakulinen, C., Vahtera, J., Elovainio, M., Suominen, S., Väänänen, A., Koskinen, A., Nyberg, S. T., et al. (2021) · The Lancet Infectious Diseases · doi:10.1016/s1473-3099(21)00144-4 · Cited by 197 · see citing works

Multiscale causal networks identify VGF as a key regulator of Alzheimer’s disease

Beckmann, N. D., Lin, W.-J., Wang, M., Cohain, A. T., Charney, A. W., Wang, P., Ma, W., Wang, Y.-C., Jiang, C., Audrain, M., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-17405-z · Cited by 172 · see citing works

New Approaches for the Treatment of Alzheimer’s Disease

Fish, P. V., Steadman, D., Bayle, E. D., & Whiting, P. (2019) · Bioorganic &amp; Medicinal Chemistry Letters · doi:10.1016/j.bmcl.2018.11.034 · Cited by 189 · see citing works

Time to test antibacterial therapy in Alzheimer’s disease

Panza, F., Lozupone, M., Solfrizzi, V., Watling, M., & Imbimbo, B. P. (2019) · Brain · doi:10.1093/brain/awz244 · Cited by 161 · see citing works

Infectious agents and Alzheimer's disease

Piekut, T., Hurła, M., Banaszek, N., Szejn, P., Dorszewska, J., Kozubski, W., & Prendecki, M. (2022) · Journal of Integrative Neuroscience · doi:10.31083/j.jin2102073 · Cited by 123 · see citing works

Non-coding variability at the APOE locus contributes to the Alzheimer’s risk

Zhou, X., Chen, Y., Mok, K. Y., Kwok, T. C. Y., Mok, V. C. T., Guo, Q., Ip, F. C., Chen, Y., Mullapudi, N., Initiative, A. D. N., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-10945-z · Cited by 120 · see citing works

Detecting Microglial Density With Quantitative Multi-Compartment Diffusion MRI

Yi, S. Y., Barnett, B. R., Torres-Velázquez, M., Zhang, Y., Hurley, S. A., Rowley, P. A., Hernando, D., & Yu, J.-P. J. (2019) · Frontiers in Neuroscience · doi:10.3389/fnins.2019.00081 · Cited by 104 · see citing works

Amyloid, tau, pathogen infection and antimicrobial protection in Alzheimer’s disease –conformist, nonconformist, and realistic prospects for AD pathogenesis

Li, H., Liu, C.-C., Zheng, H., & Huang, T. Y. (2018) · Translational Neurodegeneration · doi:10.1186/s40035-018-0139-3 · Cited by 103 · see citing works

Blockade of STING Activation Alleviates Microglial Dysfunction and a Broad Spectrum of Alzheimer's Disease Pathologies

Chung, S., Jeong, J.-H., Park, J.-C., Han, J. W., Lee, Y., Kim, J.-I., & Mook-Jung, I. (2024) · Experimental &amp; Molecular Medicine · doi:10.1038/s12276-024-01295-y · Cited by 103 · see citing works

Microbial functional amyloids serve diverse purposes for structure, adhesion and defence

Shanmugam, N., Baker, M. O. D. G., Ball, S. R., Steain, M., Pham, C. L. L., & Sunde, M. (2019) · Biophysical Reviews · doi:10.1007/s12551-019-00526-1 · Cited by 75 · see citing works

Identification of Conserved Proteomic Networks in Neurodegenerative Dementia

Swarup, V., Chang, T. S., Duong, D. M., Dammer, E. B., Dai, J., Lah, J. J., Johnson, E. C. B., Seyfried, N. T., Levey, A. I., & Geschwind, D. H. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.107807 · Cited by 78 · see citing works

Identification of conserved proteomic networks in neurodegenerative dementia

Swarup, V., Chang, T. S., Duong, D. M., Dammer, E. B., Lah, J. J., Johnson, E. E. C. B., Seyfried, N. T., Levey, A. I., & Geschwind, D. H. (2019) · doi:10.1101/825802 · Cited by 78 · see citing works

The viral hypothesis: how herpesviruses may contribute to Alzheimer’s disease

Wainberg, M., Luquez, T., Koelle, D. M., Readhead, B., Johnston, C., Darvas, M., & Funk, C. C. (2021) · Molecular Psychiatry · doi:10.1038/s41380-021-01138-6 · Cited by 74 · see citing works

Highly efficient intercellular spreading of protein misfolding mediated by viral ligand-receptor interactions

Liu, S., Hossinger, A., Heumüller, S.-E., Hornberger, A., Buravlova, O., Konstantoulea, K., Müller, S. A., Paulsen, L., Rousseau, F., Schymkowitz, J., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-25855-2 · Cited by 72 · see citing works

Plasma proteins, cognitive decline, and 20-year risk of dementia in the Whitehall II and Atherosclerosis Risk in Communities studies

Lindbohm, J. V., Mars, N., Walker, K. A., Singh‐Manoux, A., Livingston, G., Brunner, E. J., Sipilä, P. N., Saksela, K., Ferrie, J. E., Lovering, R. C., et al. (2022) · Alzheimer's &amp; Dementia · doi:10.1002/alz.12419 · Cited by 70 · see citing works

Modulation of β-Amyloid Fibril Formation in Alzheimer’s Disease by Microglia and Infection

Brown, M. R., Radford, S. E., & Hewitt, E. W. (2020) · Frontiers in Molecular Neuroscience · doi:10.3389/fnmol.2020.609073 · Cited by 67 · see citing works

Viral pathogens increase risk of neurodegenerative disease

Blackhurst, B. M., & Funk, K. E. (2023) · Nature Reviews Neurology · doi:10.1038/s41582-023-00790-6 · Cited by 57 · see citing works

The modulatory effects of gut microbes and metabolites on blood-brain barrier integrity and brain function in sepsis-associated encephalopathy

Li, Z., Zhang, F., Sun, M., Liu, J., Zhao, L., Liu, S., Li, S., & Wang, B. (2023) · PeerJ · doi:10.7717/peerj.15122 · Cited by 43 · see citing works

Roles of HSV-1 infection-induced microglial immune responses in CNS diseases: friends or foes?

Wang, Y., Jia, J., Wang, Y., Li, F., Song, X., Qin, S., Wang, Z., Kitazato, K., & Wang, Y. (2019) · Critical Reviews in Microbiology · doi:10.1080/1040841x.2019.1660615 · Cited by 40 · see citing works

Testing the amyloid cascade hypothesis: Prevention trials in autosomal dominant Alzheimer disease

Levin, J., Vöglein, J., Quiroz, Y. T., Bateman, R. J., Ghisays, V., Lopera, F., McDade, E., Reiman, E., Tariot, P. N., & Morris, J. C. (2022) · Alzheimer's &amp; Dementia · doi:10.1002/alz.12624 · Cited by 40 · see citing works

Inherited Chromosomally Integrated Human Herpesvirus 6 Demonstrates Tissue-Specific RNA Expression <i>In Vivo</i> That Correlates with an Increased Antibody Immune Response

Peddu, V., Dubuc, I., Gravel, A., Xie, H., Huang, M.-L., Tenenbaum, D., Jerome, K. R., Tardif, J.-C., Dubé, M.-P., Flamand, L., et al. (2019) · Journal of Virology · doi:10.1128/jvi.01418-19 · Cited by 39 · see citing works

Herpes viruses and Alzheimer's disease: new evidence in the debate

Balin, B. J., & Hudson, A. P. (2018) · The Lancet Neurology · doi:10.1016/s1474-4422(18)30316-8 · Cited by 38 · see citing works

Can Infections Cause Alzheimer Disease?

Komaroff, A. L. (2020) · JAMA · doi:10.1001/jama.2020.4085 · Cited by 36 · see citing works

Activation of Endogenous Retrovirus, Brain Infections and Environmental Insults in Neurodegeneration and Alzheimer’s Disease

Licastro, F., & Porcellini, E. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22147263 · Cited by 33 · see citing works

Alzheimer’s Disease (AD) Therapeutics—2: Beyond Amyloid—Re-Defining AD and Its Causality to Discover Effective Therapeutics

Mullane, K., & Williams, M. (2018) · Biochemical Pharmacology · doi:10.1016/j.bcp.2018.09.027 · Cited by 32 · see citing works

Deep Profiling of the Aggregated Proteome in Alzheimer’s Disease: From Pathology to Disease Mechanisms

Lutz, B. M., & Peng, J. (2018) · Proteomes · doi:10.3390/proteomes6040046 · Cited by 27 · see citing works

Herpes Viruses in the Baltimore Longitudinal Study of Aging: Associations With Brain Volumes, Cognitive Performance, and Plasma Biomarkers

Duggan, M. R., Peng, Z., An, Y., Kitner Triolo, M. H., Shafer, A. T., Davatzikos, C., Erus, G., Karikkineth, A., Lewis, A., Moghekar, A., et al. (2022) · Neurology · doi:10.1212/wnl.0000000000201036 · Cited by 24 · see citing works

Identification of viral-mediated pathogenic mechanisms in neurodegenerative diseases using network-based approaches

Onisiforou, A., & Spyrou, G. M. (2021) · Briefings in Bioinformatics · doi:10.1093/bib/bbab141 · Cited by 23 · see citing works

Microbial infection promotes amyloid pathology in a mouse model of Alzheimer’s disease via modulating γ-secretase

Zhao, M., Ma, G., Yan, X., Li, X., Wang, E., Xu, X.-X., Zhao, J.-B., Ma, X., & Zeng, J. (2024) · Molecular Psychiatry · doi:10.1038/s41380-024-02428-5 · Cited by 21 · see citing works

Potential Role for Herpesviruses in Alzheimer’s Disease

Duggan, M. R., Torkzaban, B., Ahooyi, T. M., & Khalili, K. (2020) · Journal of Alzheimer's Disease · doi:10.3233/jad-200814 · Cited by 13 · see citing works

The Brief Case: Inherited Chromosomally Integrated Human Herpesvirus 6 (HHV-6) in the Age of Multiplex HHV-6 Testing

Greninger, A. L., Naccache, S. N., Pannaraj, P., Jerome, K. R., Dien Bard, J., & Ruderman, J. W. (2019) · Journal of Clinical Microbiology · doi:10.1128/jcm.02016-18 · Cited by 13 · see citing works

Herpes simplex virus and rates of cognitive decline or whole brain atrophy in the Dominantly Inherited Alzheimer Network

Warren‐Gash, C., Cadogan, S. L., Nicholas, J. M., Breuer, J. M., Shah, D., Pearce, N., Shiekh, S., Smeeth, L., Farlow, M. R., Mori, H., et al. (2022) · Annals of Clinical and Translational Neurology · doi:10.1002/acn3.51669 · Cited by 11 · see citing works

What would it take to prove that a chronic infection is a causal agent in Alzheimer’s disease?

Brutkiewicz, R. R., Cao, W., Morgan, D., Reis, R. S. D., Suryadevara, V., Willette, A. A., Willette, S. A., Wyatt-Johnson, S. K., & Duggan, M. R. (2025) · Trends in Neurosciences · doi:10.1016/j.tins.2025.05.009 · Cited by 3 · see citing works