Dynamic changes in DNA methylation and hydroxymethylation when hES cells undergo differentiation toward a neuronal lineage

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

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

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

Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by MLL Partner TET1

Tahiliani, M., Koh, K. P., Shen, Y., Pastor, W. A., Bandukwala, H., Brudno, Y., Agarwal, S., Iyer, L. M., Liu, D. R., Aravind, L., et al. (2009) · Science · doi:10.1126/science.1170116 · Cited by 5,836 · see citing works

The Nuclear DNA Base 5-Hydroxymethylcytosine Is Present in Purkinje Neurons and the Brain

Kriaucionis, S., & Heintz, N. (2009) · Science · doi:10.1126/science.1169786 · Cited by 2,700 · see citing works

Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification

Ito, S., D’Alessio, A. C., Taranova, O., Hong, K., Sowers, L. C., & Zhang, Y. (2010) · Nature · doi:10.1038/nature09303 · Cited by 2,542 · see citing works

A unique chromatin signature uncovers early developmental enhancers in humans

Rada-Iglesias, A., Bajpai, R., Swigut, T., Brugmann, S. A., Flynn, R. A., & Wysocka, J. (2011) · Nature · doi:10.1038/nature09692 · Cited by 2,233 · see citing works

Stability and flexibility of epigenetic gene regulation in mammalian development

Reik, W. (2007) · Nature · doi:10.1038/nature05918 · Cited by 1,963 · cited 1× · see citing works

Cloning and characterization of a family of novel mammalian DNA (cytosine-5) methyltransferases

Okano, M., Xie, S., & Li, E. (1998) · Nature Genetics · doi:10.1038/890 · Cited by 1,643 · see citing works

Hydroxylation of 5-Methylcytosine by TET1 Promotes Active DNA Demethylation in the Adult Brain

Guo, J. U., Su, Y., Zhong, C., Ming, G., & Song, H. (2011) · Cell · doi:10.1016/j.cell.2011.03.022 · Cited by 1,355 · see citing works

Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation

Ficz, G., Branco, M. R., Seisenberger, S., Santos, F., Krueger, F., Hore, T. A., Marques, C. J., Andrews, S., & Reik, W. (2011) · Nature · doi:10.1038/nature10008 · Cited by 1,123 · see citing works

Transcription of IAP endogenous retroviruses is constrained by cytosine methylation

Walsh, C. P., Chaillet, J. R., & Bestor, T. H. (1998) · Nature Genetics · doi:10.1038/2413 · Cited by 1,105 · see citing works

Active DNA demethylation: many roads lead to Rome

Wu, S. C., & Zhang, Y. (2010) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2950 · Cited by 1,054 · see citing works

Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome

Yu, M., Hon, G. C., Szulwach, K. E., Song, C., Zhang, L., Kim, A., Li, X., Dai, Q., Shen, Y., Park, B., et al. (2012) · Cell · doi:10.1016/j.cell.2012.04.027 · Cited by 1,022 · see citing works

TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity

Williams, K., Christensen, J., Pedersen, M. T., Johansen, J. V., Cloos, P. A. C., Rappsilber, J., & Helin, K. (2011) · Nature · doi:10.1038/nature10066 · Cited by 1,021 · see citing works

Genomewide Analysis of PRC1 and PRC2 Occupancy Identifies Two Classes of Bivalent Domains

Ku, M., Koche, R. P., Rheinbay, E., Mendenhall, E. M., Endoh, M., Mikkelsen, T. S., Aiden, A. P., Nusbaum, C., Xie, X. S., Chi, A. S., et al. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000242 · Cited by 996 · see citing works

Derivation of midbrain dopamine neurons from human embryonic stem cells

Perrier, A. L., Tabar, V. S., Barberi, T., Rubio, M. E., Brusés, J. L., Topf, N., Harrison, N. L., & Studer, L. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0404700101 · Cited by 981 · see citing works

Dynamic Readers for 5-(Hydroxy)Methylcytosine and Its Oxidized Derivatives

Spruijt, C. G., Gnerlich, F., Smits, A. H., Pfaffeneder, T., Jansen, P. W. T. C., Bauer, C., Münzel, M., Wagner, M., Müller, M., Khan, F., et al. (2013) · Cell · doi:10.1016/j.cell.2013.02.004 · Cited by 973 · see citing works

MeCP2 binds to 5hmC enriched within active genes and accessible chromatin in the nervous system

Mellén, M., Ayata, P., Dewell, S., Kriaucionis, S., & Heintz, N. (2012) · Cell · doi:10.1016/j.cell.2012.11.022 · Cited by 943 · see citing works

Forkhead Transcription Factors: Key Players in Development and Metabolism

Carlsson, P., & Mahlapuu, M. (2002) · Developmental Biology · doi:10.1006/dbio.2002.0780 · Cited by 842 · see citing works

The PARP Side of the Nucleus: Molecular Actions, Physiological Outcomes, and Clinical Targets

Krishnakumar, R., & Kraus, W. L. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.06.017 · Cited by 836 · see citing works

5-hmC–mediated epigenetic dynamics during postnatal neurodevelopment and aging

Szulwach, K. E., Li, X., Li, Y., Song, C., Wu, H., Dai, Q., Irier, H. A., Upadhyay, A. K., Gearing, M., Levey, A. I., et al. (2011) · Nature Neuroscience · doi:10.1038/nn.2959 · Cited by 819 · see citing works

Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells

Pastor, W. A., Pape, U. J., Huang, Y., Henderson, H. R., Lister, R., Ko, M., McLoughlin, E. M., Brudno, Y., Mahapatra, S., Kapranov, P., et al. (2011) · Nature · doi:10.1038/nature10102 · Cited by 804 · see citing works

Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells

Wu, H., D’Alessio, A. C., Ito, S., Xia, K., Wang, Z., Cui, K., Zhao, K., Eve Sun, Y., & Zhang, Y. (2011) · Nature · doi:10.1038/nature09934 · Cited by 646 · see citing works

Genome-wide Regulation of 5hmC, 5mC, and Gene Expression by Tet1 Hydroxylase in Mouse Embryonic Stem Cells

Xu, Y., Wu, F., Tan, L., Kong, L., Xiong, L., Deng, J., Barbera, A. J., Zheng, L., Zhang, H., Huang, S., et al. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.04.005 · Cited by 634 · see citing works

Targets and dynamics of promoter DNA methylation during early mouse development

Borgel, J., Guibert, S., Li, Y., Chiba, H., Schübeler, D., Sasaki, H., Forné, T., & Weber, M. (2010) · Nature Genetics · doi:10.1038/ng.708 · Cited by 602 · see citing works

Quantitative comparison of genome-wide DNA methylation mapping technologies

Bock, C., Tomazou, E. M., Brinkman, A. B., Müller, F., Simmer, F., Gu, H., Jäger, N., Gnirke, A., Stunnenberg, H. G., & Meissner, A. (2010) · Nature Biotechnology · doi:10.1038/nbt.1681 · Cited by 587 · see citing works

Genome-wide analysis of 5-hydroxymethylcytosine distribution reveals its dual function in transcriptional regulation in mouse embryonic stem cellsPreprint

Wu, H., D’Alessio, A. C., Ito, S., Wang, Z., 崔凯荣, Zhao, K., Sun, Y. E., & Zhang, Y. (2011) · Genes & Development · doi:10.1101/gad.2036011 · Cited by 585 · see citing works

Pluripotency Factors in Embryonic Stem Cells Regulate Differentiation into Germ Layers

Thomson, M. W., Liu, S. J., Zou, L.-N., Smith, Z., Meissner, A., & Ramanathan, S. (2011) · Cell · doi:10.1016/j.cell.2011.05.017 · Cited by 533 · see citing works

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

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

Dynamics of 5-Hydroxymethylcytosine and Chromatin Marks in Mammalian Neurogenesis

Hahn, M. A., Qiu, R., Wu, X., Li, A. X., Zhang, H., Wang, J., Jui, J., Jin, S., Jiang, Y., Pfeifer, G. P., et al. (2013) · Cell Reports · doi:10.1016/j.celrep.2013.01.011 · Cited by 457 · see citing works

Promoter CpG Methylation Contributes to ES Cell Gene Regulation in Parallel with Oct4/Nanog, PcG Complex, and Histone H3 K4/K27 Trimethylation

Fouse, S. D., Shen, Y., Pellegrini, M. A., Cole, S. W., Meissner, A., Neste, L. V., Jaenisch, R., & Fan, G. (2008) · Cell stem cell · doi:10.1016/j.stem.2007.12.011 · Cited by 452 · see citing works

Early-stage epigenetic modification during somatic cell reprogramming by Parp1 and Tet2

Doege, C. A., Inoue, K., Yamashita, T., Rhee, D. B., Travis, S. N., Fujita, R., Guarnieri, P., Bhagat, G., Vanti, W. B., Shih, A. H., et al. (2012) · Nature · doi:10.1038/nature11333 · Cited by 382 · see citing works

Epigenetic modifications in pluripotent and differentiated cells

Meissner, A. (2010) · Nature Biotechnology · doi:10.1038/nbt.1684 · Cited by 373 · see citing works

Human embryonic stem cells have a unique epigenetic signaturePreprint

Bibikova, M. V., Chudin, E., Wu, B., Zhou, L., Wickham‐Garcia, E., Liu, Y., Shin, S., Plaia, T. W., Auerbach, J. M., Arking, D. E., et al. (2006) · Genome Research · doi:10.1101/gr.5319906 · Cited by 272 · see citing works

In vitroandin vivoanalyses of human embryonic stem cell‐derived dopamine neurons

Park, C., Minn, Y., Lee, J., et al. (2005) · Journal of Neurochemistry · doi:10.1111/j.1471-4159.2004.03006.x · Cited by 268 · see citing works

RGM and its receptor neogenin regulate neuronal survival

Matsunaga, E., Tauszig-Delamasure, S., Monnier, P. P., Mueller, B. K., Strittmatter, S. M., Mehlen, P., & Chédotal, A. (2004) · Nature Cell Biology · doi:10.1038/ncb1157 · Cited by 267 · see citing works

Dynamic hydroxymethylation of deoxyribonucleic acid marks differentiation-associated enhancers

Sérandour, A. A., Avner, S., Oger, F., Bizot, M., Percevault, F., Lucchetti-Miganeh, C., Palierne, G., Gheeraert, C., Barloy-Hubler, F., Péron, C. L., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks595 · Cited by 186 · see citing works

Defining the nature of human pluripotent stem cell progeny

Patterson, M., Chan, D. N., Ha, I., Case, D., Cui, Y., Handel, B. V., Mikkola, H. K., & Lowry, W. E. (2012) · Cell Research · doi:10.1038/cr.2011.133 · Cited by 145 · see citing works

LIG Family Receptor Tyrosine Kinase-Associated Proteins Modulate Growth Factor Signals during Neural Development

Mandai, K., Guo, T., Hillaire, C. S., Meabon, J. S., Kanning, K. C., Bothwell, M. A., & Ginty, D. D. (2009) · Neuron · doi:10.1016/j.neuron.2009.07.031 · Cited by 92 · see citing works

Conserved DNA methylation patterns in healthy blood cells and extensive changes in leukemia measured by a new quantitative technique

Jelı́nek, J., Liang, S., Lu, Y., He, R. L., Ramagli, L. S., Shpall, E. J., Estecio, M. R., & Issa, J. J. (2012) · Epigenetics · doi:10.4161/epi.22552 · Cited by 71 · see citing works

Human embryonic stem cell‐derived neural precursors as a continuous, stable, and on‐demand source for human dopamine neurons

Ko, J., Park, C., Koh, H.-C., Cho, Y., Kyhm, J. H., Kim, Y. S., Lee, I., Lee, Y., & Lee, S. (2007) · Journal of Neurochemistry · doi:10.1111/j.1471-4159.2007.04898.x · Cited by 67 · see citing works

LRRC3B , Encoding a Leucine-Rich Repeat-Containing Protein, Is a Putative Tumor Suppressor Gene in Gastric Cancer

Kim, M., Kim, J., Jang, H.-R., Kim, H., Lee, C., Noh, S., Song, K., Cho, J.-S., Jeong, H. Y., Hahn, Y., et al. (2008) · Cancer Research · doi:10.1158/0008-5472.can-08-0667 · Cited by 49 · see citing works

Regulation of α-Fetoprotein Expression by Nkx2.8

Kajiyama, Y., Tian, J., & Locker, J. D. (2002) · Molecular and Cellular Biology · doi:10.1128/mcb.22.17.6122-6130.2002 · Cited by 30 · see citing works

Identification of DNA methylation markers for lineage commitment of in vitro hepatogenesis

Kim, M., Kang, T.-W., Lee, H., Han, Y., Kim, H. M., Shin, H. D., Cheong, H. S., Lee, D., Kim, S., & Kim, Y. S. (2011) · Human Molecular Genetics · doi:10.1093/hmg/ddr171 · Cited by 12 · 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

Addressing variability in iPSC-derived models of human disease: guidelines to promote reproducibility

Volpato, V., & Webber, C. (2020) · Disease Models & Mechanisms · doi:10.1242/dmm.042317 · Cited by 379 · see citing works

Age-dependent instability of mature neuronal fate in induced neurons from Alzheimer’s patients

Mertens, J., Herdy, J. R., Traxler, L., Schafer, S. T., Schlachetzki, J. C. M., Böhnke, L., Reid, D. A., Lee, H., Zangwill, D., Fernandes, D. P., et al. (2021) · Cell Stem Cell · doi:10.1016/j.stem.2021.04.004 · Cited by 240 · see citing works

Developmental regulation of human cortex transcription and its clinical relevance at single base resolution

Jaffe, A. E., Shin, J., Collado-Torres, L., Leek, J. T., Tao, R., Li, C., Gao, Y., Jia, Y., Maher, B. J., Hyde, T. M., et al. (2015) · Nature Neuroscience · doi:10.1038/nn.3898 · Cited by 156 · see citing works

Structural basis for Klf4 recognition of methylated DNA

Liu, Y., Olanrewaju, Y. O., Zheng, Y., Hashimoto, H., Blumenthal, R. M., Zhang, X., & Cheng, X. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku134 · Cited by 99 · see citing works

DNA methylation alterations in iPSC- and hESC-derived neurons: Potential implications for neurological disease modeling

de Boni, L., Gasparoni, G., Haubenreich, C., Tierling, S., Schmitt, I., Peitz, M., Koch, P., Walter, J., Wüllner, U., & Brüstle, O. (2018) · Clinical Epigenetics · doi:10.1186/s13148-018-0440-0 · Cited by 47 · see citing works

Decoding the role of TET family dioxygenases in lineage specification

Wu, X., Li, G., & Xie, R. (2018) · Epigenetics & Chromatin · doi:10.1186/s13072-018-0228-7 · Cited by 43 · see citing works

[The function of fatty acid signals in neurogenesis].

Sakayori, N., & Osumi, N. (2011) · PubMed

Factors influencing adult neurogenesis

Liu, Y. M., Li, Y., & Li, J. (2006) · Junshi Yixue Kexueyuan yuankan

Differentiation of human pluripotent stem cells into airway epithelial cells

Ulrich, S., Weinreich, S., Haller, R., et al. (2015) · Pneumologie · doi:10.1055/s-0035-1556638

A Small Molecule that Promotes Cardiac Differentiation of Human Pluripotent Stem Cells under Defined, Cytokine- and Xeno-free Conditions

Minami, I., Yamada, K., Otsuji, T. G., Yamamoto, T., Shen, Y., Otsuka, S., Kadota, S., Morone, N., Barve, M. P., Asai, Y., et al. (2012) · Cell Reports · doi:10.1016/j.celrep.2012.09.015 · Cited by 248 · see citing works

Differentiation and Transplantation of Functional Pancreatic Beta Cells Generated from Induced Pluripotent Stem Cells Derived from a Type 1 Diabetes Mouse Model

Jeon, K., Lim, H., Kim, J.-H., Nguyen, T., Park, S.-H., Lim, Y., Choi, H., Lee, E.-R., Kim, J.-H., Lee, M.-S., et al. (2012) · Stem Cells and Development · doi:10.1089/scd.2011.0665 · Cited by 111 · see citing works