Neuronal brain-region-specific DNA methylation and chromatin accessibility are associated with neuropsychiatric trait heritability

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

<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

A Simple Sequentially Rejective Multiple Test Procedure

(1979) · Scandinavian Journal of Statistics · doi:10.2307/4615733 · Cited by 21,526 · see citing works

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

ggplot2: Elegant Graphics for Data Analysis

Wickham, H. (2009) · doi:10.1007/978-0-387-98141-3 · Cited by 14,447 · see citing works

Bioconductor: open software development for computational biology and bioinformatics

Gentleman, R., Carey, V., Bates, D., Bolstad, B., Dettling, M., Dudoit, S., Ellis, B., Gautier, L., Ge, Y., Gentry, J., et al. (2004) · Genome Biology · doi:10.1186/gb-2004-5-10-r80 · Cited by 13,133 · see citing works

Salmon provides fast and bias-aware quantification of transcript expression

Patro, R., Duggal, G., Love, M. I., Irizarry, R. A., & Kingsford, C. (2017) · Nature Methods · doi:10.1038/nmeth.4197 · Cited by 12,700 · see citing works

Data Analysis

Wickham, H. (2016) · Use R! · doi:10.1007/978-3-319-24277-4_9 · Cited by 12,675 · see citing works

A scaling normalization method for differential expression analysis of RNA-seq data

Robinson, M. D., & Oshlack, A. (2010) · Genome Biology · doi:10.1186/gb-2010-11-3-r25 · Cited by 7,876 · see citing works

Biological insights from 108 schizophrenia-associated genetic loci

Schizophrenia Working Group of the Psychiatric Genomics Consortium (2014) · Nature · doi:10.1038/nature13595 · Cited by 7,577 · see citing works

Fast Stable Restricted Maximum Likelihood and Marginal Likelihood Estimation of Semiparametric Generalized Linear Models

Wood, S. N. (2010) · Journal of the Royal Statistical Society Series B (Statistical Methodology) · doi:10.1111/j.1467-9868.2010.00749.x · Cited by 7,538 · see citing works

Integrative analysis of 111 reference human epigenomes

Roadmap Epigenomics Consortium, Kundaje, A., Meuleman, W., Ernst, J., Bilenky, M., Yen, A., Heravi-Moussavi, A., Kheradpour, P., Zhang, Z., Wang, J., et al. (2015) · Nature · doi:10.1038/nature14248 · Cited by 6,368 · cited 4× · 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

LD Score regression distinguishes confounding from polygenicity in genome-wide association studies

Schizophrenia Working Group of the Psychiatric Genomics Consortium, Bulik-Sullivan, B. K., Loh, P.-R., Finucane, H. K., Ripke, S., Yang, J., Patterson, N., Daly, M. J., Price, A. L., & Neale, B. M. (2015) · Nature Genetics · doi:10.1038/ng.3211 · Cited by 5,559 · see citing works

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

Krueger, F., & Andrews, S. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr167 · Cited by 5,161 · see citing works

GENCODE: The reference human genome annotation for The ENCODE Project

Harrow, J., Frankish, A., Gonzalez, J. M., Tapanari, E., Diekhans, M., Kokocinski, F., Aken, B. L., Barrell, D., Zadissa, A., Searle, S., et al. (2012) · Genome Research · doi:10.1101/gr.135350.111 · Cited by 4,585 · see citing works

GREAT improves functional interpretation of cis-regulatory regions

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

Software for Computing and Annotating Genomic Ranges

Lawrence, M. F., Huber, W. K., Pagès, H., Aboyoun, P., Carlson, M. R. J., Gentleman, R. C., Morgan, M. T., & Carey, V. J. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003118 · Cited by 4,284 · see citing works

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

Durinck, S., Spellman, P. T., Birney, E., & Huber, W. K. (2009) · Nature Protocols · doi:10.1038/nprot.2009.97 · Cited by 4,081 · see citing works

Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences

Soneson, C., Love, M. I., & Robinson, M. D. (2015) · F1000Research · doi:10.12688/f1000research.7563.1 · Cited by 3,929 · see citing works

Orchestrating high-throughput genomic analysis with Bioconductor

Huber, W. K., Carey, V. J., Gentleman, R. C., Anders, S., Carlson, M. R. J., Carvalho, B. S., Bravo, H. C., Davis, S. R., Gatto, L., Girke, T., et al. (2015) · Nature Methods · doi:10.1038/nmeth.3252 · Cited by 3,499 · see citing works

Biological, clinical and population relevance of 95 loci for blood lipids

Teslovich, T. M., Musunuru, K., Smith, A. V., Edmondson, A. C., Stylianou, I. M., Koseki, M., Pirruccello, J. P., Ripatti, S., Chasman, D. I., Willer, C. J., et al. (2010) · Nature · doi:10.1038/nature09270 · Cited by 3,487 · see citing works

CpG islands in vertebrate genomes.

Gardiner-Garden, M., & Frommer, M. (1987) · Journal of Molecular Biology · doi:10.1016/0022-2836(87)90689-9 · Cited by 3,462 · see citing works

ATAC-seq: a method for assaying chromatin accessibility genome-wide

Buenrostro, J. D., Wu, B., Chang, H. Y., & Greenleaf, W. J. (2015) · Current Protocols in Molecular Biology · doi:10.1002/0471142727.mb2129s109 · Cited by 3,289 · see citing works

Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq

Zeisel, A., Muñoz-Manchado, A. B., Codeluppi, S., Lönnerberg, P., La Manno, G., Juréus, A., Marques, S., Munguba, H., He, L., Betsholtz, C., et al. (2015) · Science · doi:10.1126/science.aaa1934 · Cited by 3,124 · see citing works

Partitioning heritability by functional annotation using genome-wide association summary statistics

ReproGen Consortium, Finucane, H. K., Schizophrenia Working Group of the Psychiatric Genomics Consortium, The RACI Consortium, Bulik-Sullivan, B., Gusev, A., Trynka, G., Reshef, Y., Loh, P.-R., Anttila, V., et al. (2015) · Nature Genetics · doi:10.1038/ng.3404 · Cited by 2,604 · see citing works

An atlas of active enhancers across human cell types and tissues

The FANTOM Consortium, Andersson, R., Gebhard, C., Miguel-Escalada, I., Hoof, I., Bornholdt, J., Boyd, M., Chen, Y., Zhao, X., Schmidl, C., et al. (2014) · Nature · doi:10.1038/nature12787 · Cited by 2,550 · see citing works

BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis

Durinck, S., Moreau, Y., Kasprzyk, A., Davis, S. R., Moor, B. D., Brāzma, A., & Huber, W. K. (2005) · Computer applications in the biosciences · doi:10.1093/bioinformatics/bti525 · Cited by 2,327 · see citing works

Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences

Soneson, C., Love, M. I., & Robinson, M. D. (2016) · F1000Research · doi:10.12688/f1000research.7563.2 · Cited by 1,936 · see citing works

Capturing Heterogeneity in Gene Expression Studies by Surrogate Variable Analysis

Leek, J. T., & Storey, J. D. (2007) · PLoS Genetics · doi:10.1371/journal.pgen.0030161 · Cited by 1,930 · see citing works

Global epigenomic reconfiguration during mammalian brain development

Lister, R., Mukamel, E. A., Nery, J. R., Urich, M., Puddifoot, C. A., Johnson, N. D., Lucero, J., Huang, Y., Dwork, A. J., Schultz, M. D., et al. (2013) · Science · doi:10.1126/science.1237905 · Cited by 1,830 · see citing works

Adult mouse cortical cell taxonomy revealed by single cell transcriptomics

Tasic, B., Menon, V., Nguyen, T. N., Kim, T. K., Jarsky, T., Yao, Z., Levi, B., Gray, L. T., Sorensen, S. A., Dolbeare, T., et al. (2016) · Nature Neuroscience · doi:10.1038/nn.4216 · Cited by 1,714 · see citing works

Phenotypic plasticity and the epigenetics of human disease

Feinberg, A. P. (2007) · Nature · doi:10.1038/nature05919 · Cited by 1,613 · see citing works

Impact of cytosine methylation on DNA binding specificities of human transcription factors

Yin, Y., Morgunova, E., Jolma, A., Kaasinen, E., Sahu, B., Khund-Sayeed, S., Das, P. K., Kivioja, T., Dave, K., Zhong, F., et al. (2017) · Science · doi:10.1126/science.aaj2239 · Cited by 1,257 · see citing works

Oligodendrocyte heterogeneity in the mouse juvenile and adult central nervous system

Marques, S., Zeisel, A., Codeluppi, S., van Bruggen, D., Mendanha Falcão, A., Xiao, L., Li, H., Häring, M., Hochgerner, H., Romanov, R. A., et al. (2016) · Science · doi:10.1126/science.aaf6463 · Cited by 1,246 · see citing works

The search for true numbers of neurons and glial cells in the human brain: A review of 150 years of cell counting

von Bartheld, C. S., Bahney, J., & Herculano‐Houzel, S. (2016) · Journal of Comparative Neurology · doi:10.1002/cne.24040 · Cited by 1,063 · see citing works

Increased methylation variation in epigenetic domains across cancer types

Hansen, K. D., Timp, W., Bravo, H. C., Sabunciyan, S., Langmead, B., McDonald, O. G., Wen, B., Wu, H., Liu, Y., Diep, D. H., et al. (2011) · Nature Genetics · doi:10.1038/ng.865 · Cited by 1,053 · see citing works

The UCSC Genome Browser database: 2015 update

Rosenbloom, K., Armstrong, J., Barber, G. P., Casper, J., Clawson, H., Diekhans, M., Dreszer, T. R., Fujita, P. A., Guruvadoo, L., Haeussler, M., et al. (2014) · Nucleic Acids Res. · doi:10.1093/nar/gku1177 · Cited by 1,011 · see citing works

rtracklayer: an R package for interfacing with genome browsers

Lawrence, M. F., Gentleman, R. C., & Carey, V. J. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp328 · Cited by 971 · see citing works

Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain

Lake, B. B., Ai, R., Kaeser, G. E., Salathia, N. S., Yung, Y. C., Liu, R., Wildberg, A., Gao, D., Fung, H.-L., Chen, S., et al. (2016) · Science · doi:10.1126/science.aaf1204 · Cited by 957 · see citing works

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

Mathelier, A., Fornes, O., Arenillas, D. J., Chen, C.-Y., Denay, G., Lee, J., Shi, W., Shyr, C., Tan, G., Worsley-Hunt, R., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1176 · Cited by 937 · see citing works

The UCSC genome browser and associated tools

Kuhn, R. M., Haussler, D., & Kent, W. J. (2013) · Briefings in Bioinformatics · doi:10.1093/bib/bbs038 · Cited by 883 · see citing works

Meta- and Orthogonal Integration of Influenza “OMICs” Data Defines a Role for UBR4 in Virus Budding

Tripathi, S., Pohl, M. O., Zhou, Y., Rodríguez-Frandsen, A., Wang, G., Stein, D. A., Moulton, H. M., DeJesus, P., Che, J., Mulder, L. C. F., et al. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2015.11.002 · Cited by 846 · see citing works

BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions

Hansen, K. D., Langmead, B., & Irizarry, R. A. (2012) · Genome biology · doi:10.1186/gb-2012-13-10-r83 · Cited by 780 · see citing works

Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain

Mo, A., Mukamel, E. A., Davis, F. P., Luo, C., Henry, G. L., Picard, S., Urich, M. A., Nery, J. R., Sejnowski, T. J., Lister, R., et al. (2015) · Neuron · doi:10.1016/j.neuron.2015.05.018 · Cited by 739 · see citing works

Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain

Guo, J. U., Su, Y., Shin, J. H., Shin, J., Li, H., Xie, B., Zhong, C., Hu, S., Le, T., Fan, G., et al. (2014) · Nature Neuroscience · doi:10.1038/nn.3607 · Cited by 714 · see citing works

Functional annotation of the human brain methylome identifies tissue-specific epigenetic variation across brain and blood

Davies, M. N., Volta, M., Pidsley, R., Lunnon, K., Dixit, A., Lovestone, S., Coarfa, C., Harris, R. A., Milosavljevic, A., Troakes, C., et al. (2012) · Genome Biology · doi:10.1186/gb-2012-13-6-r43 · Cited by 630 · see citing works

Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche

Study, A. O. C., Perry, J. R. B., The GENICA Network, kConFab, Study, T. L. C., The InterAct Consortium, Early Growth Genetics (EGG) Consortium, Day, F., Elks, C. E., Sulem, P., et al. (2014) · Nature · doi:10.1038/nature13545 · Cited by 604 · see citing works

Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex

Luo, C., Keown, C. L., Kurihara, L., Zhou, J., He, Y., Li, J., Castanon, R., Lucero, J., Nery, J. R., Sandoval, J. P., et al. (2017) · Science · doi:10.1126/science.aan3351 · Cited by 545 · see citing works

Mapping DNA methylation across development, genotype and schizophrenia in the human frontal cortex

Jaffe, A. E., Gao, Y., Deep-Soboslay, A., Tao, R., Hyde, T. M., Weinberger, D. R., & Kleinman, J. E. (2016) · Nature Neuroscience · doi:10.1038/nn.4181 · Cited by 511 · see citing works

Genomic Distribution and Inter-Sample Variation of Non-CpG Methylation across Human Cell Types

Ziller, M. J., Müller, F., Liao, J., Zhang, Y., Gu, H., Bock, C., Boyle, P. J., Epstein, C. B., Bernstein, B., Lengauer, T., et al. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002389 · Cited by 398 · see citing works

Developmental and genetic regulation of the human cortex transcriptome illuminate schizophrenia pathogenesis

The BrainSeq Consortium, Jaffe, A. E., Straub, R. E., Shin, J. H., Tao, R., Gao, Y., Collado-Torres, L., Kam-Thong, T., Xi, H. S., Quan, J., et al. (2018) · Nature Neuroscience · doi:10.1038/s41593-018-0197-y · Cited by 364 · see citing works

Epigenetic Modifications in Stress Response Genes Associated With Childhood Trauma

Jiang, S., Postovit, L., Cattaneo, A., Binder, E. B., & Aitchison, K. J. (2019) · Frontiers in Psychiatry · doi:10.3389/fpsyt.2019.00808 · Cited by 288 · see citing works

DNA Methylation Signatures within the Human Brain

Ladd‐Acosta, C., Pevsner, J., Sabunciyan, S., Yolken, R. H., Webster, M. J., Dinkins, T., Callinan, P. A., Fan, J., Potash, J. B., & Feinberg, A. P. (2007) · The American Journal of Human Genetics · doi:10.1086/524110 · Cited by 277 · see citing works

Regulation and function of immediate-early genes in the brain: Beyond neuronal activity markers

Okuno, H. (2010) · Neuroscience Research · doi:10.1016/j.neures.2010.12.007 · Cited by 276 · see citing works

Molecular and Functional Properties of Regional Astrocytes in the Adult Brain

Morel, L., Chiang, M. S. R., Higashimori, H., Shoneye, T., Iyer, L. K., Yelick, J., Tai, A., & Yang, Y. (2017) · The Journal of Neuroscience · doi:10.1523/jneurosci.3956-16.2017 · Cited by 243 · 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

Epigenomic Profiling of Human CD4+ T Cells Supports a Linear Differentiation Model and Highlights Molecular Regulators of Memory Development

Durek, P., Nordström, K. J. V., Gasparoni, G., Salhab, A., Kressler, C., de Almeida, M., Bassler, K. E., Ulas, T., Schmidt, F., Xiong, J., et al. (2016) · Immunity · doi:10.1016/j.immuni.2016.10.022 · Cited by 197 · see citing works

Early-Life Gene Expression in Neurons Modulates Lasting Epigenetic States

Stroud, H., Su, S. C., Hrvatin, S., Greben, A. W., Renthal, W. R., Boxer, L. D., Nagy, M. A., Hochbaum, D. R., Kinde, B., Gabel, H. W., et al. (2017) · Cell · doi:10.1016/j.cell.2017.09.047 · Cited by 186 · see citing works

Epigenomic landscapes of retinal rods and cones

Mo, A., Luo, C., Davis, F. P., Mukamel, E. A., Henry, G. L., Nery, J. R., Urich, M. A., Picard, S., Lister, R., Eddy, S. R., et al. (2016) · eLife · doi:10.7554/elife.11613 · Cited by 158 · see citing works

Human DNA methylomes of neurodegenerative diseases show common epigenomic patterns

Sanchez-Mut, J. V., Heyn, H., Vidal, E., Morán, S., Sayols, S., Delgado‐Morales, R., Schultz, M. D., Ansoleaga, B., Garcia‐Esparcia, P., Pons‐Espinal, M., et al. (2016) · Translational Psychiatry · doi:10.1038/tp.2015.214 · Cited by 157 · see citing works

Differences in DNA methylation between human neuronal and glial cells are concentrated in enhancers and non-CpG sites

Kozlenkov, A., Roussos, P., Timashpolsky, A., Barbu, M., Rudchenko, S., Bibikova, M. V., Klotzle, B., Byne, W. M., Lyddon, R., Narzo, A. F. D., et al. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt838 · Cited by 154 · see citing works

Large-scale hypomethylated blocks associated with Epstein-Barr virus–induced B-cell immortalizationPreprint

Hansen, K. D., Sabunciyan, S., Langmead, B., Nagy, N., Curley, R., Klein, G., Klein, E., Salamon, D., & Feinberg, A. P. (2013) · Genome Research · doi:10.1101/gr.157743.113 · Cited by 127 · see citing works

Substantial DNA methylation differences between two major neuronal subtypes in human brain

Kozlenkov, A., Wang, M., Roussos, P., Rudchenko, S., Barbu, M., Bibikova, M. V., Klotzle, B., Dwork, A. J., Zhang, B., Hurd, Y. L., et al. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1304 · Cited by 125 · see citing works

Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction

Schmidt, F., Gasparoni, N., Gasparoni, G., Gianmoena, K., Cadenas, C., Polansky, J. K., Ebert, P., Nordström, K. J. V., Barann, M., Sinha, A. N., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw1061 · Cited by 118 · see citing works

Measuring cell-type specific differential methylation in human brain tissue

Montaño, C., Irizarry, R. A., Kaufmann, W. E., Talbot, K., Gur, R. E., Feinberg, A. P., & Taub, M. A. (2013) · Genome biology · doi:10.1186/gb-2013-14-8-r94 · Cited by 110 · see citing works

Schizophrenia-associated methylomic variation: molecular signatures of disease and polygenic risk burden across multiple brain regions

Viana, J., Hannon, E., Dempster, E., Pidsley, R., Macdonald, R., Knox, O., Spiers, H., Troakes, C., Al-Saraj, S., Turecki, G., et al. (2016) · Human Molecular Genetics · doi:10.1093/hmg/ddw373 · Cited by 105 · see citing works

Associations Among Monoamine Neurotransmitter Pathways, Personality Traits, and Major Depressive Disorder

Shao, X., & Zhu, G. (2020) · Frontiers in Psychiatry · doi:10.3389/fpsyt.2020.00381 · Cited by 87 · see citing works

Large-Scale Identification of Coregulated Enhancer Networks in the Adult Human Brain

Vermunt, M. W., Reinink, P., Korving, J., de Bruijn, E., Creyghton, P. M., Başak, O., Geeven, G., Toonen, P. W., Lansu, N. R., Meunier, C., et al. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.09.023 · Cited by 85 · see citing works

Striatal regulation of ΔFosB, FosB, and cFos during cocaine self‐administration and withdrawal

Larson, E. B., Akkentli, F., Edwards, S., Graham, D. L., Simmons, D. L., Alibhai, I. N., Nestler, E. J., & Self, D. W. (2010) · Journal of Neurochemistry · doi:10.1111/j.1471-4159.2010.06907.x · Cited by 83 · see citing works

Global gene expression profiling of healthy human brain and its application in studying neurological disorders

Negi, S., & Guda, C. (2017) · Scientific Reports · doi:10.1038/s41598-017-00952-9 · Cited by 76 · see citing works

Open chromatin profiling of human postmortem brain infers functional roles for non-coding schizophrenia loci

Fullard, J. F., Giambartolomei, C., Hauberg, M. E., Xu, K., Voloudakis, G., Shao, Z., Bare, C., Dudley, J. T., Mattheisen, M., Robakis, N. K. R. K., et al. (2017) · Human Molecular Genetics · doi:10.1093/hmg/ddx103 · Cited by 75 · see citing works

Aberrant NMDA receptor DNA methylation detected by epigenome-wide analysis of hippocampus and prefrontal cortex in major depression

Kaut, O., Schmitt, I., Hofmann, A., Hoffmann, P., Schlaepfer, T. E., Wüllner, U., & Hurlemann, R. (2015) · European Archives of Psychiatry and Clinical Neuroscience · doi:10.1007/s00406-014-0572-y · Cited by 68 · see citing works

Hemispheric asymmetry in the human brain and in Parkinson’s disease is linked to divergent epigenetic patterns in neurons

Li, P., Ensink, E., Lang, S., Marshall, L. L., Schilthuis, M., Lamp, J. A., Vega, I. E., & Labrie, V. (2020) · Genome biology · doi:10.1186/s13059-020-01960-1 · Cited by 65 · see citing works

Epigenomics of Major Depressive Disorders and Schizophrenia: Early Life Decides

Hoffmann, A., Sportelli, V., Ziller, M. J., & Spengler, D. (2017) · International Journal of Molecular Sciences · doi:10.3390/ijms18081711 · Cited by 61 · see citing works

Inter-individual variability contrasts with regional homogeneity in the human brain DNA methylome

Illingworth, R. S., Gruenewald-Schneider, U., Sousa, D. D., Webb, S., Merusi, C., Kerr, A. R. W., James, K., Smith, C., WALKER, R. E., Andrews, R., et al. (2015) · Nucleic Acids Research · doi:10.1093/nar/gku1305 · Cited by 41 · see citing works

Integration of gene expression and GWAS results supports involvement of calcium signaling in Schizophrenia

Hertzberg, L., Katsel, P., Roussos, P., Haroutunian, V. H., & Domany, E. (2015) · Schizophrenia Research · doi:10.1016/j.schres.2015.02.001 · Cited by 39 · see citing works

Exaggerated CpH methylation in the autism-affected brain

Ellis, S., Gupta, S., Moes, A., West, A. B., & Arking, D. E. (2017) · Molecular Autism · doi:10.1186/s13229-017-0119-y · Cited by 39 · see citing works

Neuronal and glial DNA methylation and gene expression changes in early epileptogenesis

Berger, T. C., Vigeland, M. D., Hjorthaug, H. S., Etholm, L., Nome, C. G., Taubøll, E., Heuser, K., & Selmer, K. K. (2019) · PLoS ONE · doi:10.1371/journal.pone.0226575 · Cited by 36 · see citing works

Differential expression of transcriptional regulatory units in the prefrontal cortex of patients with bipolar disorder: potential role of early growth response gene 3

Pfaffenseller, B., Magalhães, P. V. D. S., Bastiani, M. A. D., Castro, M. A. A., Gallitano, A. L., Kapczinski, F. P., & Klamt, F. (2016) · Translational Psychiatry · doi:10.1038/tp.2016.78 · Cited by 31 · see citing works

Haystack: systematic analysis of the variation of epigenetic states and cell-type specific regulatory elements

Pinello, L., Farouni, R., & Yuan, G. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty031 · Cited by 19 · see citing works

Convergence of neurotransmissions at synapse on IEG regulation in nucleus

Fukuchi, M. (2017) · Frontiers in bioscience · doi:10.2741/4533 · Cited by 13 · see citing works

Resequencing of early growth response 2 (EGR2) gene revealed a recurrent patient-specific mutation in schizophrenia

Hu, T., Chen, C., Chuang, Y.-A., Hsu, S.-H., & Cheng, M.-C. (2015) · Psychiatry Research · doi:10.1016/j.psychres.2015.05.035 · Cited by 10 · see citing works

Profiling haplotype specific CpG and CpH methylation within a schizophrenia GWAS locus on chromosome 14 in schizophrenia and healthy subjects

Алфимова, М. В., Kondratyev, N. V., Golov, A. K., & Голимбет, В. Е. (2020) · Scientific Reports · doi:10.1038/s41598-020-61671-2 · Cited by 6 · see citing works

Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex

Maynard, K. R., Collado-Torres, L., Weber, L. M., Uytingco, C., Barry, B. K., Williams, S. R., Catallini, J. L., Tran, M. N., Besich, Z., Tippani, M., et al. (2021) · Nature Neuroscience · doi:10.1038/s41593-020-00787-0 · Cited by 1,222 · see citing works

Epigenetic Modifications in Stress Response Genes Associated With Childhood Trauma

Jiang, S., Postovit, L., Cattaneo, A., Binder, E. B., & Aitchison, K. J. (2019) · Frontiers in Psychiatry · doi:10.3389/fpsyt.2019.00808 · Cited by 288 · see citing works

Biological embedding of experience: a primer on epigenetics

Aristizabal, M. J., Anreiter, I., Halldorsdottir, T., Odgers, C. L., McDade, T. W., Goldenberg, A., Mostafavi, S., Kobor, M. S., Binder, E. B., Sokolowski, M. B., et al. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1820838116 · Cited by 268 · 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

Single-nucleus transcriptome analysis reveals cell-type-specific molecular signatures across reward circuitry in the human brain

Tran, M. N., Maynard, K. R., Spangler, A., Huuki, L. A., Montgomery, K. D., Sadashivaiah, V., Tippani, M., Barry, B. K., Hancock, D. B., Hicks, S. C., et al. (2021) · Neuron · doi:10.1016/j.neuron.2021.09.001 · Cited by 219 · see citing works

Integrated DNA methylation and gene expression profiling across multiple brain regions implicate novel genes in Alzheimer’s disease

Semick, S. A., Bharadwaj, R. A., Collado‐Torres, L., Tao, R., Shin, J. H., Deep‐Soboslay, A., Weiss, J. R., Weinberger, D. R., Hyde, T. M., Kleinman, J. E., et al. (2019) · Acta Neuropathologica · doi:10.1007/s00401-019-01966-5 · Cited by 113 · see citing works

Cell type-specific epigenetic links to schizophrenia risk in the brain

Mendizabal, I., Berto, S., Usui, N., Toriumi, K., Chatterjee, P., Douglas, C., Huh, I., Jeong, H., Layman, T. S., Tamminga, C. A., et al. (2019) · Genome biology · doi:10.1186/s13059-019-1747-7 · Cited by 106 · see citing works

Evolution of DNA methylation in the human brain

Jeong, H., Mendizabal, I., Berto, S., Chatterjee, P., Layman, T. S., Usui, N., Toriumi, K., Douglas, C., Singh, D., Huh, I., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-21917-7 · Cited by 112 · see citing works

Developmental dynamics of RNA translation in the human brain

Duffy, E. E., Finander, B., Choi, G., Carter, A. C., Pritišanac, I., Alam, A., Luria, V., Karger, A., Phu, W., Sherman, M. A., et al. (2022) · Nature Neuroscience · doi:10.1038/s41593-022-01164-9 · Cited by 92 · see citing works

Epigenetics, Development, and Psychopathology

O'Donnell, K. J., & Meaney, M. J. (2020) · Annual Review of Clinical Psychology · doi:10.1146/annurev-clinpsy-050718-095530 · Cited by 94 · see citing works

A Meta-Analysis of Brain DNA Methylation Across Sex, Age, and Alzheimer's Disease Points for Accelerated Epigenetic Aging in Neurodegeneration

Pellegrini, C., Pirazzini, C., Sala, C., Sambati, L., Yusipov, I., Kalyakulina, A., Ravaioli, F., Kwiatkowska, K. M., Durso, D. F., Ivanchenko, M., et al. (2021) · Frontiers in Aging Neuroscience · doi:10.3389/fnagi.2021.639428 · Cited by 88 · see citing works

Divergent neuronal DNA methylation patterns across human cortical development reveal critical periods and a unique role of CpH methylation

Price, A. J., Collado‐Torres, L., Ivanov, N. A., Xia, W. T., Burke, E. E., Shin, J. H., Tao, R., Ma, L., Jia, Y., Hyde, T. M., et al. (2019) · Genome biology · doi:10.1186/s13059-019-1805-1 · Cited by 85 · see citing works

Associations Among Monoamine Neurotransmitter Pathways, Personality Traits, and Major Depressive Disorder

Shao, X., & Zhu, G. (2020) · Frontiers in Psychiatry · doi:10.3389/fpsyt.2020.00381 · Cited by 87 · see citing works

PCA outperforms popular hidden variable inference methods for molecular QTL mapping

Zhou, H. J., Li, L., Li, Y., Li, W., & Li, J. J. (2022) · Genome biology · doi:10.1186/s13059-022-02761-4 · Cited by 83 · see citing works

Common schizophrenia risk variants are enriched in open chromatin regions of human glutamatergic neurons

Hauberg, M. E., Creus‐Muncunill, J., Bendl, J. M., Kozlenkov, A., Zeng, B., Corwin, C., Chowdhury, S., Kranz, H. D., Hurd, Y. L., Wegner, M., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-19319-2 · Cited by 75 · see citing works

An Activity-Mediated Transition in Transcription in Early Postnatal Neurons

Stroud, H., Yang, M. G., Tsitohay, Y. N., Davis, C. P., Sherman, M. A., Hrvatin, S., Ling, E., & Greenberg, M. E. (2020) · Neuron · doi:10.1016/j.neuron.2020.06.008 · Cited by 76 · see citing works

Modeling epigenetic lesions that cause gliomas

Rahme, G. J., Javed, N. M., Puorro, K. L., Xin, S., Hovestadt, V., Johnstone, S. E., & Bernstein, B. (2023) · Cell · doi:10.1016/j.cell.2023.06.022 · Cited by 73 · see citing works

Epigenomic landscape study reveals molecular subtypes and EBV-associated regulatory epigenome reprogramming in nasopharyngeal carcinoma

Chow, L. K.-Y., Chung, D. L., Tao, L., Chan, K. F., Tung, S. Y., Ngan, R. K., Ng, W. T., Lee, A. W. M., Yau, C. C., Kwong, D. L., et al. (2022) · EBioMedicine · doi:10.1016/j.ebiom.2022.104357 · Cited by 71 · see citing works

Hemispheric asymmetry in the human brain and in Parkinson’s disease is linked to divergent epigenetic patterns in neurons

Li, P., Ensink, E., Lang, S., Marshall, L. L., Schilthuis, M., Lamp, J. A., Vega, I. E., & Labrie, V. (2020) · Genome biology · doi:10.1186/s13059-020-01960-1 · Cited by 65 · see citing works

ATACdb: a comprehensive human chromatin accessibility database

Wang, F., Bai, X., Wang, Y., Jiang, Y., Ai, B., Zhang, Y., Liu, Y., Xu, M., Wang, Q., Han, X., et al. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa943 · Cited by 66 · see citing works

Genome-wide sequencing-based identification of methylation quantitative trait loci and their role in schizophrenia risk

Mandell, K. A. P., Eagles, N. J., Wilton, R. N., Price, A. J., Semick, S. A., Collado‐Torres, L., Ulrich, W. S., Tao, R., Han, S., Szalay, A. S., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-25517-3 · Cited by 66 · see citing works

Activity-dependent regulome of human GABAergic neurons reveals new patterns of gene regulation and neurological disease heritability

Boulting, G. L., Durresi, E., Ataman, B., Sherman, M. A., Mei, K., Harmin, D. A., Carter, A. C., Hochbaum, D. R., Granger, A. J., Engreitz, J., et al. (2021) · Nature Neuroscience · doi:10.1038/s41593-020-00786-1 · Cited by 61 · see citing works

MicroRNA-29 is an essential regulator of brain maturation through regulation of CH methylation

Swahari, V., Nakamura, A., Hollville, É., Stroud, H., Simon, J. M., Ptacek, T., Beck, M. V., Flowers, C., Guo, J., Plestant, C., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.108946 · Cited by 61 · see citing works

Non-CG methylation and multiple histone profiles associate child abuse with immune and small GTPase dysregulation

Lutz, P.-É., Chay, M.-A., Pacis, A., Chen, G. G., Aouabed, Z., Maffioletti, E., Théroux, J., Grenier, J., Yang, J., Aguirre, M., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-21365-3 · Cited by 57 · see citing works

Precocious neuronal differentiation and disrupted oxygen responses in Kabuki syndrome

Carosso, G. A., Boukas, L., Augustin, J. J., Nguyen, H. N., Winer, B. L., Cannon, G. H., Robertson, J. D., Zhang, L., Hansen, K. D., Goff, L. A., et al. (2019) · JCI Insight · doi:10.1172/jci.insight.129375 · Cited by 57 · see citing works

Potential Role of DNA Methylation as a Driver of Plastic Responses to the Environment Across Cells, Organisms, and Populations

Bogan, S. N., & Yi, S. V. (2024) · Genome Biology and Evolution · doi:10.1093/gbe/evae022 · Cited by 57 · see citing works

Gene regulatory mechanisms underlying sex differences in brain development and psychiatric disease

Manoli, D. S., & Tollkühn, J. (2018) · Annals of the New York Academy of Sciences · doi:10.1111/nyas.13564 · Cited by 54 · see citing works

Hippocampal and cortical tissue-specific epigenetic clocks indicate an increased epigenetic age in a mouse model for Alzheimer’s disease

Coninx, E., Chew, Y. C., Yang, X., Guo, W., Coolkens, A., Baatout, S., Moons, L., Verslegers, M., & Quintens, R. (2020) · Aging · doi:10.18632/aging.104056 · Cited by 45 · see citing works

DNA methylation signature as a biomarker of major neuropsychiatric disorders

Shirvani-Farsani, Z., Maloum, Z., Bagheri‐Hosseinabadi, Z., Vilor‐Tejedor, N., & Sadeghi, I. (2021) · Journal of Psychiatric Research · doi:10.1016/j.jpsychires.2021.06.013 · Cited by 47 · see citing works

The fusiform gyrus exhibits an epigenetic signature for Alzheimer’s disease

Ma, D., Fetahu, I. S., Wang, M., Fang, R., Li, J., Liu, H., Gramyk, T., Iwanicki, I. J., Gu, S., Xu, W., et al. (2020) · Clinical Epigenetics · doi:10.1186/s13148-020-00916-3 · Cited by 43 · see citing works

Identification of cell type-specific methylation signals in bulk whole genome bisulfite sequencing data

Scott, C. A., Duryea, J., MacKay, H., Baker, M. S., Laritsky, E., Gunasekara, C., Coarfa, C., & Waterland, R. A. (2020) · Genome biology · doi:10.1186/s13059-020-02065-5 · Cited by 40 · see citing works

Drug addiction and treatment: An epigenetic perspective

Koijam, A. S., Singh, K. D., Singh, N. B., Haobam, R., & Rajashekar, Y. (2023) · Biomedicine & Pharmacotherapy · doi:10.1016/j.biopha.2023.115951 · Cited by 43 · see citing works

Decreased DNA methylation at promoters and gene-specific neuronal hypermethylation in the prefrontal cortex of patients with bipolar disorder

Bundo, M., Ueda, J., Nakachi, Y., Kasai, K., Kato, T., & Iwamoto, K. (2021) · Molecular Psychiatry · doi:10.1038/s41380-021-01079-0 · Cited by 40 · see citing works

CpG and Non-CpG Methylation in the Diet–Epigenetics–Neurodegeneration Connection

Fuso, A., & Lucarelli, M. (2019) · Current Nutrition Reports · doi:10.1007/s13668-019-0266-1 · Cited by 38 · see citing works

Differential DNA Methylation of the Genes for Amyloid Precursor Protein, Tau, and Neurofilaments in Human Traumatic Brain Injury

Hamdeh, S. A., Ciuculete, D. M., Sarkisyan, D., Bakalkin, G. Y., Ingelsson, M., Schiöth, H. B., & Marklund, N. (2020) · Journal of Neurotrauma · doi:10.1089/neu.2020.7283 · Cited by 35 · see citing works

Neuronal and glial DNA methylation and gene expression changes in early epileptogenesis

Berger, T. C., Vigeland, M. D., Hjorthaug, H. S., Etholm, L., Nome, C. G., Taubøll, E., Heuser, K., & Selmer, K. K. (2019) · PLoS ONE · doi:10.1371/journal.pone.0226575 · Cited by 36 · see citing works

Associations between DNA methylation and gene regulation depend on chromatin accessibility during transgenerational plasticity

Bogan, S. N., Strader, M. E., & Hofmann, G. E. (2023) · BMC Biology · doi:10.1186/s12915-023-01645-8 · Cited by 35 · see citing works

DNA Epigenetics in Addiction Susceptibility

Kaplan, G., Xu, H., Abreu, K., & Feng, J. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.806685 · Cited by 34 · see citing works

Epigenetics applied to child and adolescent mental health: Progress, challenges and opportunities

Cecil, C. A. M., Neumann, A., & Walton, E. (2022) · JCPP Advances · doi:10.1002/jcv2.12133 · Cited by 33 · see citing works

Profiling neuronal methylome and hydroxymethylome of opioid use disorder in the human orbitofrontal cortex

Rompala, G. R., Nagamatsu, S. T., Martínez‐Magaña, J. J., Núñez-Ríos, D. L., Wang, J., Girgenti, M. J., Krystal, J. H., Gelernter, J. E., Alvarez, V. E., Benedek, D. M., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-40285-y · Cited by 33 · see citing works

Human brain region-specific variably methylated regions are enriched for heritability of distinct neuropsychiatric traits

Rizzardi, L. F., Hickey, P. F., Idrizi, A., Tryggvadóttir, R., Callahan, C. M., Stephens, K., Taverna, S. D., Zhang, H., Ramazanoglu, S., Hansen, K. D., et al. (2021) · Genome biology · doi:10.1186/s13059-021-02335-w · Cited by 31 · see citing works

Dnmt3a knockout in excitatory neurons impairs postnatal synapse maturation and increases the repressive histone modification H3K27me3

Li, J., Pinto‐Duarte, A., Zander, M., Cuoco, M. S., Lai, C.-Y., Osteen, J. K., Fang, L., Luo, C., Lucero, J. D., Castanon, R., et al. (2022) · eLife · doi:10.7554/elife.66909 · Cited by 37 · see citing works

HIV-1 Tat and cocaine impact mitochondrial epigenetics: effects on DNA methylation

Doke, M., Jeganathan, V., McLaughlin, J. P., & Samikkannu, T. (2020) · Epigenetics · doi:10.1080/15592294.2020.1834919 · Cited by 30 · see citing works

DNA methylation variation in the brain of laying hens in relation to differential behavioral patterns

Guerrero‐Bosagna, C., Pértille, F., Gómez, Y., Rezaei, S., Gebhardt‐Henrich, S. G., Vögeli, S., Stratmann, A., Voelkl, B., & Toscano, M. J. (2020) · Comparative Biochemistry and Physiology Part D Genomics and Proteomics · doi:10.1016/j.cbd.2020.100700 · Cited by 29 · see citing works

Cocaine-related DNA methylation in caudate neurons alters 3D chromatin structure of the IRXA gene cluster

Vaillancourt, K., Yang, J., Chen, G. G., Yerko, V., Théroux, J., Aouabed, Z., López, A. J., Thibeault, K. C., Calipari, E. S., Labonté, B., et al. (2020) · Molecular Psychiatry · doi:10.1038/s41380-020-00909-x · Cited by 29 · see citing works

Methylation differences in Alzheimer’s disease neuropathologic change in the aged human brain

Lang, A.-L., Eulalio, T. Y., Fox, E., Yakabi, K., Bukhari, S. A., Kawas, C. H., Corrada, M. M., Montgomery, S. B., Heppner, F. L., Capper, D., et al. (2022) · Acta Neuropathologica Communications · doi:10.1186/s40478-022-01470-0 · Cited by 24 · see citing works

Contribution of Age, Brain Region, Mood Disorder Pathology, and Interindividual Factors on the Methylome of Human Microglia

de Witte, L. D., Wang, Z., Snijders, G. J. L., Mendelev, N., Liu, Q., Sneeboer, M. A. M., Boks, M. P., Ge, Y., & Haghighi, F. G. (2021) · Biological Psychiatry · doi:10.1016/j.biopsych.2021.10.020 · Cited by 25 · see citing works

Epigenetic changes in sperm are associated with paternal and child quantitative autistic traits in an autism-enriched cohort

Feinberg, J. I., Schrott, R., Ladd‐Acosta, C., Newschaffer, C. J., Hertz‐Picciotto, I., Croen, L., Fallin, M. D., Feinberg, A. P., & Volk, H. E. (2023) · Molecular Psychiatry · doi:10.1038/s41380-023-02046-7 · Cited by 26 · see citing works

Rich Chromatin Structure Prediction from Hi-C Data

Malik, L. I., & Patro, R. (2018) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2018.2851200 · Cited by 26 · see citing works

Fetal Programming by Methyl Donors Modulates Central Inflammation and Prevents Food Addiction-Like Behavior in Rats

Cruz-Carrillo, G., Montalvo-Martínez, L., Cárdenas‐Tueme, M., Bernal‐Vega, S., Maldonado‐Ruiz, R., Reséndez‐Pérez, D., Rodríguez‐Ríos, D., Lund, G., Garza‐Ocañas, L., & Camacho‐Morales, A. (2020) · Frontiers in Neuroscience · doi:10.3389/fnins.2020.00452 · Cited by 25 · see citing works

The role of Gadd45b in neurologic and neuropsychiatric disorders: An overview

Shen, X., Shi, S.-H., Li, H., Wang, C., Zhang, Y., Yu, H., Li, Y., & Liu, B. (2022) · Frontiers in Molecular Neuroscience · doi:10.3389/fnmol.2022.1021207 · Cited by 24 · see citing works

Using Openly Accessible Resources to Strengthen Causal Inference in Epigenetic Epidemiology of Neurodevelopment and Mental Health

Walton, E., Relton, C. L., & Caramaschi, D. (2019) · Genes · doi:10.3390/genes10030193 · Cited by 20 · see citing works

Epigenetic regulation in the pathophysiology of Lewy body dementia

Chouliaras, L., Kumar, G. S., Thomas, A. J., Lunnon, K., Chinnery, P. F., & O'Brien, J. T. (2020) · Progress in Neurobiology · doi:10.1016/j.pneurobio.2020.101822 · Cited by 23 · see citing works

Epigenetics of neural differentiation: Spotlight on enhancers

Giacoman-Lozano, M., Meléndez-Ramírez, C., Martínez-Ledesma, E., Durán, R. C., & Velasco, I. (2022) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2022.1001701 · Cited by 22 · see citing works

Hierarchical deconvolution for extensive cell type resolution in the human brain using DNA methylation

Zhang, Z., Wiencke, J. K., Kelsey, K. T., Koestler, D. C., Molinaro, A. M., Pike, S. C., Karra, P., Christensen, B. C., & Salas, L. A. (2023) · Frontiers in Neuroscience · doi:10.3389/fnins.2023.1198243 · Cited by 22 · see citing works

Neuronal MAPT expression is mediated by long-range interactions with cis-regulatory elements

Rogers, B. B., Anderson, A. G., Lauzon, S. N., Davis, M. N., Hauser, R. M., Roberts, S. C., Rodríguez-Nunez, I., Trausch‐Lowther, K., Barinaga, E. A., Hall, P. I., et al. (2024) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2023.12.015 · Cited by 21 · see citing works

Characterizing the dynamic and functional DNA methylation landscape in the developing human cortex

Perzel Mandell, K. A., Price, A. J., Wilton, R., Collado-Torres, L., Tao, R., Eagles, N. J., Szalay, A. S., Hyde, T. M., Weinberger, D. R., Kleinman, J. E., et al. (2021) · Epigenetics · doi:10.1080/15592294.2020.1786304 · Cited by 21 · see citing works

Melatonin enhances nitrogen metabolism and haustorium development in hemiparasite Santalum album Linn.

Meng, S., Wang, X., Bian, Z., Li, Z., Yang, F., Wang, S., Yoder, J. I., & Lu, J. (2021) · Environmental and Experimental Botany · doi:10.1016/j.envexpbot.2021.104460 · Cited by 21 · see citing works

Sex-specific epigenetic development in the mouse hypothalamic arcuate nucleus pinpoints human genomic regions associated with body mass index

MacKay, H., Gunasekara, C., Yam, K., Srisai, D., Yalamanchili, H. K., Li, Y., Chen, R., Coarfa, C., & Waterland, R. A. (2022) · Science Advances · doi:10.1126/sciadv.abo3991 · Cited by 20 · see citing works

Normalization benchmark of ATAC-seq datasets shows the importance of accounting for GC-content effects

den Berge, K. V., Chou, H.-J., de Bézieux, H. R., Street, K., Risso, D., Ngai, J., & Dudoit, S. (2022) · Cell Reports Methods · doi:10.1016/j.crmeth.2022.100321 · Cited by 19 · see citing works

Cortical cellular diversity and development in schizophrenia

Price, A. J., Jaffe, A. E., & Weinberger, D. R. (2020) · Molecular Psychiatry · doi:10.1038/s41380-020-0775-8 · Cited by 20 · see citing works

Extensive long-range polycomb interactions and weak compartmentalization are hallmarks of human neuronal 3D genome

Pletenev, I. A., Bazarevich, M., Zagirova, D., Kononkova, A. D., Cherkasov, A. V., Efimova, O., Tiukacheva, E. A., Morozov, K. V., Ulianov, K. A., Komkov, D., et al. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae271 · Cited by 18 · see citing works

Cell type-specific chromatin accessibility analysis in the mouse and human brain

Rocks, D., Jarić, I., Tesfa, L., Greally, J. M., Suzuki, M., & Kundaković, M. (2021) · Epigenetics · doi:10.1080/15592294.2021.1896983 · Cited by 18 · see citing works

Mitochondrial DNA methylation profiling of the human prefrontal cortex and nucleus accumbens: correlations with aging and drug use

Huang, C.-H., Chang, M., Lai, Y., Lin, C., Hsu, C., Tseng, B., Hsiao, C. K., Lu, T., Yu, S., Hsieh, S., et al. (2022) · Clinical Epigenetics · doi:10.1186/s13148-022-01300-z · Cited by 18 · see citing works

Traversing the epigenetic landscape: DNA methylation from retina to brain in development and disease

Xu, C., Fu, X.-Y., Qin, H., & Yao, K. (2024) · Frontiers in Cellular Neuroscience · doi:10.3389/fncel.2024.1499719 · Cited by 17 · see citing works

The potential roles of genetic factors in predicting ageing-related cognitive change and Alzheimer’s disease

Pan, G., King, A. E., Wu, F., Simpson, S., Woodhouse, A., Phipps, A., & Vickers, J. C. (2021) · Ageing Research Reviews · doi:10.1016/j.arr.2021.101402 · Cited by 17 · see citing works

Changes in DNA methylation hallmark alterations in chromatin accessibility and gene expression for eye lens differentiation

Disatham, J., Brennan, L., Jiao, X., Ma, Z., Hejtmancik, J. F., & Kantorow, M. (2022) · Epigenetics & Chromatin · doi:10.1186/s13072-022-00440-z · Cited by 16 · see citing works

Cell type-specific DNA methylome signatures reveal epigenetic mechanisms for neuronal diversity and neurodevelopmental disorder

Jin, Y., Su, K., Kong, H. E., Ma, W., Wang, Z., Li, Y., Li, R., Allen, E. G., Wu, H., & Jin, P. (2022) · Human Molecular Genetics · doi:10.1093/hmg/ddac189 · Cited by 15 · see citing works

Differential usage of DNA modifications in neurons, astrocytes, and microglia

Tooley, K. B., Chucair‐Elliott, A. J., Ocañas, S. R., Machalinski, A. H., Pham, K. D., Hoolehan, W., Kulpa, A. M., Stanford, D. R., & Freeman, W. M. (2023) · Epigenetics & Chromatin · doi:10.1186/s13072-023-00522-6 · Cited by 13 · see citing works

Existence and possible roles of independent non-CpG methylation in the mammalian brain

Lee, J. H., Saitō, Y., Park, S., & Nakai, K. (2020) · DNA Research · doi:10.1093/dnares/dsaa020 · Cited by 14 · see citing works

Targeting neuronal epigenomes for brain rejuvenation

Zocher, S. (2024) · The EMBO Journal · doi:10.1038/s44318-024-00148-8 · Cited by 12 · see citing works

Cord blood DNA methylation modifications in infants are associated with white matter microstructure in the context of prenatal maternal depression and anxiety

Dean, D., Madrid, A., Planalp, E. M., Moody, J. F., Papale, L. A., Knobel, K. M., Wood, E. K., McAdams, R. M., Coe, C. L., Goldsmith, H. H., et al. (2021) · Scientific Reports · doi:10.1038/s41598-021-91642-0 · Cited by 12 · see citing works

Brain-derived cell-free DNA

Southwood, D., Singh, S., & Chatterton, Z. (2022) · Neural Regeneration Research · doi:10.4103/1673-5374.335794 · Cited by 11 · see citing works

β-Hexachlorocyclohexane triggers neuroinflammatory activity, epigenetic histone post-translational modifications and cognitive dysfunction

Grieco, M., Giorgi, A., Giacovazzo, G., Maggiore, A., Ficchì, S., D’Erme, M., Mosca, L., Mignogna, G., Maras, B., & Coccurello, R. (2024) · Ecotoxicology and Environmental Safety · doi:10.1016/j.ecoenv.2024.116487 · Cited by 11 · see citing works

Evolution of genome-wide methylation profiling technologiesPreprint

Montaño, C., & Timp, W. (2025) · Genome Research · doi:10.1101/gr.278407.123 · Cited by 12 · see citing works

DNA methylation and hydroxymethylation characterize the identity of D1 and D2 striatal projection neurons

Marion‐Poll, L., Roussarie, J.-P., Taing, L., Dard-Dascot, C., Servant, N., Jaszczyszyn, Y., Jordi, E., Mulugeta, E., Hervé, D., Bourc’his, D., et al. (2022) · Communications Biology · doi:10.1038/s42003-022-04269-w · Cited by 10 · see citing works

Alcohol Use Disorder–Associated DNA Methylation in the Nucleus Accumbens and Dorsolateral Prefrontal Cortex

White, J. D., Minto, M. S., Willis, C., Quach, B. C., Han, S., Tao, R., Deep‐Soboslay, A., Zillich, L., Witt, S. H., Spanagel, R., et al. (2024) · Biological Psychiatry Global Open Science · doi:10.1016/j.bpsgos.2024.100375 · Cited by 9 · see citing works

Genome-wide DNA methylation sequencing reveals the involvement of ferroptosis in hepatotoxicity induced by dietary exposure to food-grade titanium dioxide

Shang, J., Yan, J., Lou, H., Shou, R., Zhan, Y., Lu, X., & Fan, X. (2024) · Particle and Fibre Toxicology · doi:10.1186/s12989-024-00598-2 · Cited by 10 · see citing works

DNA methylation of the promoter region at the CREB1 binding site is a mechanism for the epigenetic regulation of brain-specific PKMζ

Pramio, D. T., Vieceli, F. M., Branco, E. V., Goes, C. P., Kobayashi, G. S., Pellegrina, D. V. D. S., de Moraes, B. C., Allam, A. E., Kumar, B. D., Jara, G. E., et al. (2023) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2023.194909 · Cited by 10 · see citing works

An integrative understanding of comparative cognition: lessons from human brain evolution

Liu, Y., & Konopka, G. (2020) · Integrative and Comparative Biology · doi:10.1093/icb/icaa109 · Cited by 10 · see citing works

Deciphering the Role of Rapidly Evolving Conserved Elements in Primate Brain Development and Exploring Their Potential Involvement in Alzheimer's Disease

Hu, B., Zhuang, X.-L., Zhou, L., Zhang, G., Cooper, D. N., & Wu, D. (2024) · Molecular Biology and Evolution · doi:10.1093/molbev/msae001 · Cited by 8 · 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

The Neuroepigenome: Implications of Chemical and Physical Modifications of Genomic DNA in Schizophrenia

Girdhar, K., Rahman, S., Dong, P., Fullard, J. F., & Roussos, P. (2022) · Biological Psychiatry · doi:10.1016/j.biopsych.2022.04.018 · Cited by 9 · see citing works

Differential Glial Activation in Early Epileptogenesis—Insights From Cell-Specific Analysis of DNA Methylation and Gene Expression in the Contralateral Hippocampus

Berger, T. C., Vigeland, M. D., Hjorthaug, H. S., Nome, C. G., Taubøll, E., Selmer, K. K., & Heuser, K. (2020) · Frontiers in Neurology · doi:10.3389/fneur.2020.573575 · Cited by 9 · see citing works

Mendelian Randomization Reveals Causalities Between DNA Methylation and Schizophrenia

Wang, D., Li, D., Dang, X., Mu, C., Liu, C., Zeng, Y., Yuan, Y., Teng, Z., Li, Y., & Luo, X. (2025) · Biological Psychiatry · doi:10.1016/j.biopsych.2025.03.012 · Cited by 8 · see citing works

Evaluation of Illumina and Oxford Nanopore Sequencing for the Study of DNA Methylation in Alzheimer’s Disease and Frontotemporal Dementia

Pagano, L., Lagrotteria, D., Facconi, A., Saraceno, C., Longobardi, A., Bellini, S., Ingannato, A., Bagnoli, S., Ducci, T., Mingrino, A., et al. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26094198 · Cited by 8 · see citing works

Transcriptomic and epigenomic consequences of heterozygous loss-of-function mutations in AKAP11, a shared risk gene for bipolar disorder and schizophrenia

Farhangdoost, N., Liao, C., Liu, Y., Rochefort, D. L., Aboasali, F., Pietrantonio, A., Alda, M., Dion, P. A., Chaumette, B., Khayachi, A., et al. (2025) · Molecular Psychiatry · doi:10.1038/s41380-025-03040-x · Cited by 9 · see citing works

Methods for Dealing With Missing Covariate Data in Epigenome-Wide Association Studies

Mills, H. L., Heron, J., Relton, C. L., Suderman, M. J., & Tilling, K. M. (2019) · American Journal of Epidemiology · doi:10.1093/aje/kwz186 · Cited by 8 · see citing works

DNA Hypermethylation Induced by L-Methionine Leads to Oligodendroglial and Myelin Deficits and Schizophrenia-Like Behaviors in Adolescent Mice

Chen, X., Huang, N.-X., Cheng, Y.-J., Cai, Q., Tian, Y., Chen, X.-S., & Xiao, L. (2021) · Frontiers in Neuroscience · doi:10.3389/fnins.2021.659853 · Cited by 8 · see citing works

Maternal high fat and high sugar diet impacts on key DNA methylation enzymes in offspring brain in a sex‐specific manner

Hor, K., Dearden, L., Herzstein, E., Ozanne, S. E., Hardingham, G. E., & Drake, A. J. (2025) · Journal of Neuroendocrinology · doi:10.1111/jne.70046 · Cited by 7 · see citing works

Informing disease modelling with brain-relevant functional genomic annotations

Reynolds, R. H., Hardy, J., Ryten, M., & Taliun, S. A. G. (2019) · Brain · doi:10.1093/brain/awz295 · Cited by 8 · see citing works

Using Two- and Three-Dimensional Human iPSC Culture Systems to Model Psychiatric Disorders

Christian, K. M., Song, H., & Ming, G. (2020) · Advances in neurobiology · doi:10.1007/978-3-030-45493-7_9 · Cited by 7 · see citing works

BMAP: a comprehensive and reproducible biomedical data analysis platformPreprint

Ren, Y., Cheng, Z., Li, L., Zhang, Y., Dai, F., Deng, L., Wu, Y., Gu, J., Lin, Q., Wang, X., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.07.15.603507 · Cited by 7 · see citing works

CRISPRi screening in cultured human astrocytes uncovers distal enhancers controlling genes dysregulated in Alzheimer’s disease

Green, N. F. O., Sutton, G. J., Pérez‐Burillo, J., Wang, J., Bagot, S., Danon, H. G., Walsh, K., Gokoolparsadh, A., Miles, S. A., Yang, G., et al. (2025) · Nature Neuroscience · doi:10.1038/s41593-025-02154-3 · Cited by 6 · see citing works

Profiling haplotype specific CpG and CpH methylation within a schizophrenia GWAS locus on chromosome 14 in schizophrenia and healthy subjects

Алфимова, М. В., Kondratyev, N. V., Golov, A. K., & Голимбет, В. Е. (2020) · Scientific Reports · doi:10.1038/s41598-020-61671-2 · Cited by 6 · see citing works

Functional annotation of the human PTSD methylome identifies tissue-specific epigenetic variation across subcortical brain regionsPreprint

Li, H., Wang, J., Cruz, D. A., Modliszewski, J. L., Corcoran, D. L., Martínez‐Magaña, J. J., Montalvo‐Ortiz, J. L., Roache, J. D., Averill, L. A., Young‐McCaughan, S., et al. (2023) · medRxiv · doi:10.1101/2023.04.18.23288704 · Cited by 6 · see citing works

Epigenomic profiling of mouse nucleus accumbens at single-cell resolution

Bhatia, P., Yang, L., Luo, J. X. J., Xu, M., & Renthal, W. (2023) · Molecular and Cellular Neuroscience · doi:10.1016/j.mcn.2023.103857 · Cited by 5 · see citing works

Detection of Brain-Derived Cell-Free DNA in Plasma

Pellegrini, C., Ravaioli, F., Fanti, S. D., Pirazzini, C., D’Silva, C., Garagnani, P., Franceschi, C., Bonifazi, F., Zinzani, P. L., Bonafè, M., et al. (2024) · Diagnostics · doi:10.3390/diagnostics14222541 · Cited by 5 · see citing works

Epigenome‐wide association study on methamphetamine dependence

Shirai, T., Okazaki, S., Tanifuji, T., Otsuka, I., Horai, T., Mouri, K., Takemura, Y., Aso, K., Yamamoto, N., & Hishimoto, A. (2024) · Addiction Biology · doi:10.1111/adb.13383 · Cited by 5 · see citing works

Self and the Brain. The Immune Metaphor

Sánchez‐Ramón, S., & Faure, F. (2020) · Frontiers in Psychiatry · doi:10.3389/fpsyt.2020.540676 · Cited by 4 · see citing works

Neuronal brain region-specific DNA methylation and chromatin accessibility are associated with neuropsychiatric disease heritabilityPreprint

Rizzardi, L. F., Hickey, P. F., DiBlasi, V. R., Tryggvadóttir, R., Callahan, C. M., Idrizi, A., Hansen, K. D., & Feinberg, A. P. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/120386 · Cited by 5 · see citing works

Human brain region-specific variably methylated regions are enriched for heritability of distinct neuropsychiatric traits

Rizzardi, L. F., Hickey, P. F., Idrizi, A., Tryggvadóttir, R., Callahan, C. M., Stephens, K., Taverna, S. D., Zhang, H., Ramazanoglu, S., Hansen, K. D., et al. (2021) · Genome biology · doi:10.1186/s13059-021-02335-w · Cited by 31 · see citing works

Additional file 1 of Human brain region-specific variably methylated regions are enriched for heritability of distinct neuropsychiatric traits

Rizzardi, L. F., Hickey, P. F., Idrizi, A., Tryggvadóttir, R., Callahan, C. M., Stephens, K. E., Taverna, S. D., Zhang, H., Ramazanoglu, S., Hansen, K. D., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14471439

Additional file 19 of Human brain region-specific variably methylated regions are enriched for heritability of distinct neuropsychiatric traits

Rizzardi, L. F., Hickey, P. F., Idrizi, A., Tryggvadóttir, R., Callahan, C. M., Stephens, K. E., Taverna, S. D., Zhang, H., Ramazanoglu, S., Hansen, K. D., et al. (2021) · Figshare · doi:10.6084/m9.figshare.14471436

Chromatin accessibility in neuropsychiatric disorders

Egervári, G. (2021) · Neurobiology of Learning and Memory · doi:10.1016/j.nlm.2021.107438 · Cited by 3 · see citing works