Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells

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

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

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

Trapnell, C., Roberts, A., Goff, L. A., Pertea, G. M., Kim, D., Kelley, D. R., Pimentel, H., Salzberg, S. L., Rinn, J. L., & Pachter, L. S. (2012) · Nature Protocols · doi:10.1038/nprot.2012.016 · Cited by 12,145

TopHat: discovering splice junctions with RNA-Seq

Trapnell, C., Pachter, L. S., & Salzberg, S. L. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp120 · Cited by 11,682

Numerical Recipes, The Art of Scientific Computing

Press, W. H., Flannery, B. P., Teukolsky, S. A., Vetterling, W. T., & Gould, H. (1987) · American Journal of Physics · doi:10.1119/1.14981 · Cited by 10,032

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

Thorvaldsdottir, H., Robinson, J. T., & Mesirov, J. P. (2013) · Briefings in Bioinformatics · doi:10.1093/bib/bbs017 · Cited by 9,049

Numerical Recipes: The Art of Scientific Computing

Ziegel, E. R., Press, W. H., Flannery, B. P., Teukolsky, S. A., & Vetterling, W. T. (1987) · Technometrics · doi:10.2307/1269484 · Cited by 6,704

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

Histone H3K27ac separates active from poised enhancers and predicts developmental state

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

FIMO: scanning for occurrences of a given motif

Grant, C. E., Bailey, T. L., & Noble, W. S. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr064 · Cited by 4,247

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

Genetic and epigenetic fine mapping of causal autoimmune disease variants

Farh, K. K.-H., Marson, A., Zhu, J., Kleinewietfeld, M., Housley, W. J., Beik, S., Shoresh, N., Whitton, H., Ryan, R. J. H., Shishkin, A. A., et al. (2015) · Nature · doi:10.1038/nature13835 · Cited by 1,956

The DNA methyltransferase family: a versatile toolkit for epigenetic regulation

Lyko, F. (2017) · Nature Reviews Genetics · doi:10.1038/nrg.2017.80 · Cited by 1,510

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

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

The DNA methylation landscape of human early embryos

Guo, H., Zhu, P., Yan, L., Li, R., Hu, B., Lian, Y., Yan, J., Ren, X., Lin, S., Li, J., et al. (2014) · Nature · doi:10.1038/nature13544 · Cited by 942

Epigenomic Analysis of Multilineage Differentiation of Human Embryonic Stem Cells

Xie, W., Schultz, M. D., Lister, R., Hou, Z., Rajagopal, N., Ray, P. R., Whitaker, J. W., Tian, S., Hawkins, R. D., Leung, D., et al. (2013) · Cell · doi:10.1016/j.cell.2013.04.022 · Cited by 739

Library construction for next-generation sequencing: Overviews and challenges

Head, S. R., Komori, H. K., LaMere, S. A., Whisenant, T. C., Nieuwerburgh, F. V., Salomon, D. R., & Ordoukhanian, P. T. (2014) · BioTechniques · doi:10.2144/000114133 · Cited by 716

Chromatin modifiers and remodellers: regulators of cellular differentiation

Chen, T., & Dent, S. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3607 · Cited by 636

Mapping Human Epigenomes

Rivera, C. M., & Ren, B. (2013) · Cell · doi:10.1016/j.cell.2013.09.011 · Cited by 550

A Dual Program for Translation Regulation in Cellular Proliferation and Differentiation

Gingold, H., Tehler, D., Christoffersen, N. R., Nielsen, M. M., Asmar, F., Kooistra, S. M., Christophersen, N. S., Christensen, L. L., Borre, M., Sørensen, K. D., et al. (2014) · Cell · doi:10.1016/j.cell.2014.08.011 · Cited by 513

Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells

Liao, J., Karnik, R., Gu, H., Ziller, M. J., Clement, K., Tsankov, A. M., Akopian, V., Gifford, C. A., Donaghey, J., Galonska, C., et al. (2015) · Nature Genetics · doi:10.1038/ng.3258 · Cited by 497

Efficient endoderm induction from human pluripotent stem cells by logically directing signals controlling lineage bifurcations

Loh, K. M., Ang, L. T., Zhang, J., Kumar, V., Ang, J., Auyeong, J. Q., Lee, K. L., Choo, S. H., Lim, C. Y. Y., Nichane, M., et al. (2014) · Cell Stem Cell · doi:10.1016/j.stem.2013.12.007 · Cited by 418

Chromatin dynamics during cellular reprogramming

Apostolou, E., & Hochedlinger, K. (2013) · Nature · doi:10.1038/nature12749 · Cited by 414

Breaking bad: R-loops and genome integrity

Sollier, J., & Cimprich, K. A. (2015) · Trends in Cell Biology · doi:10.1016/j.tcb.2015.05.003 · Cited by 393

Rapid and Pervasive Changes in Genome-wide Enhancer Usage during Mammalian Development

Nord, A. S., Blow, M. J., Attanasio, C., Akiyama, J. A., Holt, A., Hosseini, R., Phouanenavong, S., Plajzer-Frick, I., Shoukry, M., Afzal, V., et al. (2013) · Cell · doi:10.1016/j.cell.2013.11.033 · Cited by 375

Transcription factor binding dynamics during human ES cell differentiation

Tsankov, A. M., Gu, H., Akopian, V., Ziller, M. J., Donaghey, J., Amit, I., Gnirke, A., & Meissner, A. (2015) · Nature · doi:10.1038/nature14233 · Cited by 358

Epigenetic regulatory functions of DNA modifications: 5-methylcytosine and beyond

Breiling, A., & Lyko, F. (2015) · Epigenetics & Chromatin · doi:10.1186/s13072-015-0016-6 · Cited by 379

LKB1 loss links serine metabolism to DNA methylation and tumorigenesis

Kottakis, F., Nicolay, B. N., Roumane, A., Karnik, R., Gu, H., Nagle, J. M., Boukhali, M., Hayward, M. C., Li, Y. Y., Chen, T., et al. (2016) · Nature · doi:10.1038/nature20132 · Cited by 348

LIN28 Regulates Stem Cell Metabolism and Conversion to Primed Pluripotency

Zhang, J., Ratanasirintrawoot, S., Chandrasekaran, S., Wu, Z., Ficarro, S. B., Yu, C., Ross, C. A., Cacchiarelli, D., Xia, Q., Seligson, M. T., et al. (2016) · Cell stem cell · doi:10.1016/j.stem.2016.05.009 · Cited by 345

Loss of Tet Enzymes Compromises Proper Differentiation of Embryonic Stem Cells

Dawlaty, M. M., Breiling, A., Le, T., Barrasa, M. I., Raddatz, G., Gao, Q., Powell, B. E., Cheng, A. W., Faull, K. F., Lyko, F., et al. (2014) · Developmental Cell · doi:10.1016/j.devcel.2014.03.003 · Cited by 338

Whole-genome fingerprint of the DNA methylome during human B cell differentiation

Kulis, M., Merkel, A., Heath, S. C., Queirós, A. C., Schuyler, R. P., Castellano, G., Beekman, R., Raineri, E., Esteve‐Codina, A., Clot, G., et al. (2015) · Nature Genetics · doi:10.1038/ng.3291 · Cited by 336

Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing

Ziller, M. J., Hansen, K. D., Meissner, A., & Aryee, M. J. (2014) · Nature Methods · doi:10.1038/nmeth.3152 · Cited by 314

CRISPR/Cas9-based engineering of the epigenome

Pulecio, J., Verma, N., Mejía-Ramírez, E., Huangfu, D., & Raya, A. (2017) · Cell Stem Cell · doi:10.1016/j.stem.2017.09.006 · Cited by 300

Models of human core transcriptional regulatory circuitriesPreprint

Saint‐André, V., Alexander Joel Federation, Lin, C. Y., Abraham, B. J., Reddy, J., Lee, T. I., Bradner, J. E., & Young, R. A. (2016) · Genome Research · doi:10.1101/gr.197590.115 · Cited by 303

Chromatin and Single-Cell RNA-Seq Profiling Reveal Dynamic Signaling and Metabolic Transitions during Human Spermatogonial Stem Cell Development

Guo, J., Grow, E. J., Yi, C., Mlčochová, H., Maher, G. J., Lindskog, C., Murphy, P. J., Wike, C. L., Carrell, D. T., Goriely, A., et al. (2017) · Cell stem cell · doi:10.1016/j.stem.2017.09.003 · Cited by 297

Human-Chimpanzee Differences in a FZD8 Enhancer Alter Cell-Cycle Dynamics in the Developing Neocortex

Boyd, J. L., Skove, S. L., Rouanet, J. P., Pilaz, L., Bepler, T., Gordân, R., Wray, G. A., & Silver, D. L. (2015) · Current Biology · doi:10.1016/j.cub.2015.01.041 · Cited by 289

Biology and Mechanisms of Action of the Vitamin D Hormone

Pike, J. W., & Christakos, S. (2017) · Endocrinology and Metabolism Clinics of North America · doi:10.1016/j.ecl.2017.07.001 · Cited by 292

Epigenetic Regulation of Pluripotency and Differentiation

Boland, M. J., Nazor, K. L., & Loring, J. F. (2014) · Circulation Research · doi:10.1161/circresaha.115.301517 · Cited by 284

Non-CG Methylation in the Human Genome

He, Y., & Ecker, J. R. (2015) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-090413-025437 · Cited by 280

DNA methylation in mammalian development and disease

Smith, Z. D., Hetzel, S., & Meissner, A. (2024) · Nature Reviews Genetics · doi:10.1038/s41576-024-00760-8 · Cited by 310

Plant and animal stem cells: similar yet different

Heidstra, R., & Sabatini, S. (2014) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3790 · Cited by 273

Enhancer Function: Mechanistic and Genome-Wide Insights Come Together

Plank, J. L., & Dean, A. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.06.015 · Cited by 263

LncPRESS1 Is a p53-Regulated LncRNA that Safeguards Pluripotency by Disrupting SIRT6-Mediated De-acetylation of Histone H3K56

Jain, A. K., Xi, Y., McCarthy, R. L., Allton, K. L., Akdemir, K. C., Patel, L. R., Aronow, B. J., Lin, C., Li, W., Yang, L., et al. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.10.039 · Cited by 249

Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency

Cacchiarelli, D., Trapnell, C., Ziller, M. J., Soumillon, M., Cesana, M., Karnik, R., Donaghey, J., Smith, Z. D., Ratanasirintrawoot, S., Zhang, X., et al. (2015) · Cell · doi:10.1016/j.cell.2015.06.016 · Cited by 240

Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells

Barakat, T. S., Halbritter, F., Zhang, M., Rendeiro, A. F., Perenthaler, E., Bock, C., & Chambers, I. (2018) · Cell stem cell · doi:10.1016/j.stem.2018.06.014 · Cited by 227

Epigenetic plasticity cooperates with cell-cell interactions to direct pancreatic tumorigenesis

Burdziak, C., Alonso‐Curbelo, D., Walle, T., Reyes, J. S., Barriga, F. M., Haviv, D., Xie, Y., Zhao, Z., Zhao, C. J., Chen, H.-A., et al. (2023) · Science · doi:10.1126/science.add5327 · Cited by 213

Myc Regulates Chromatin Decompaction and Nuclear Architecture during B Cell Activation

Kieffer-Kwon, K.-R., Nimura, K., Rao, S. S. P., Xu, J., Jung, S., Pękowska, A., Dose, M., Stevens, E., Mathé, E. A., Dong, P., et al. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.07.013 · Cited by 210

The head and neck cancer cell oncogenome: a platform for the development of precision molecular therapies

Martı́n, D., Abba, M. C., Molinolo, A., Vitale-Cross, L. A., Wang, Z., Zaida, M., Delic, N. C., Samuels, Y., Lyons, J. G., & Gutkind, J. S. (2014) · Oncotarget · doi:10.18632/oncotarget.2417 · Cited by 206

Dissecting neural differentiation regulatory networks through epigenetic footprinting

Ziller, M. J., Edri, R., Yaffe, Y., Donaghey, J., Pop, R., Mallard, W., Issner, R., Gifford, C. A., Goren, A., Xing, J. C., et al. (2014) · Nature · doi:10.1038/nature13990 · Cited by 203

Identification of Novel Long Noncoding RNAs Underlying Vertebrate Cardiovascular Development

Kurian, L., Aguirre, A., Sancho-Martinez, I., Benner, C., Hishida, T., Nguyen, T. B., Reddy, P., Nivet, E., Krause, M. N., Nelles, D. A., et al. (2015) · Circulation · doi:10.1161/circulationaha.114.013303 · Cited by 189

Circadian Entrainment Triggers Maturation of Human In Vitro Islets

Alvarez-Dominguez, J. R., Donaghey, J., Rasouli, N., Kenty, J. H. R., Helman, A., Charlton, J., Straubhaar, J. R., Meissner, A., & Melton, D. A. (2020) · Cell Stem Cell · doi:10.1016/j.stem.2019.11.011 · Cited by 189

Regulation, functions and transmission of bivalent chromatin during mammalian development

Macrae, T. A., Fothergill-Robinson, J., & Ramalho‐Santos, M. (2022) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-022-00518-2 · Cited by 196

Profiling DNA methylome landscapes of mammalian cells with single-cell reduced-representation bisulfite sequencing

Guo, H., Zhu, P., Guo, F., Li, X., Wu, X., Fan, X., Wen, L., & Tang, F. (2015) · Nature Protocols · doi:10.1038/nprot.2015.039 · Cited by 188

Reprogramming of cell fate: epigenetic memory and the erasure of memories past

Nashun, B., Hill, P. W. S., & Hájková, P. (2015) · The EMBO Journal · doi:10.15252/embj.201490649 · Cited by 184

Dynamic changes in replication timing and gene expression during lineage specification of human pluripotent stem cellsPreprint

Rivera‐Mulia, J. C., Buckley, Q., Sasaki, T., Zimmerman, J., Didier, R., Nazor, K. L., Loring, J. F., Lian, Z., Weissman, S. M., Robins, A. J., et al. (2015) · Genome Research · doi:10.1101/gr.187989.114 · Cited by 166

Genetic determinants and epigenetic effects of pioneer-factor occupancy

Donaghey, J., Thakurela, S., Charlton, J., Chen, J., Smith, Z. D., Gu, H., Pop, R., Clement, K., Stamenova, E. K., Karnik, R., et al. (2018) · Nature Genetics · doi:10.1038/s41588-017-0034-3 · Cited by 166

GATA2/3-TFAP2A/C transcription factor network couples human pluripotent stem cell differentiation to trophectoderm with repression of pluripotency

Krendl, C., Shaposhnikov, D., Rishko, V. M., Ori, C., Ziegenhain, C., Sass, S., Simon, L. M., Müller, N. S., Straub, T., Brooks, K. E., et al. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1708341114 · Cited by 169

Genetic sources of population epigenomic variation

Taudt, A., Colomé‐Tatché, M., & Johannes, F. M. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.45 · Cited by 166

lncRNA DIGIT and BRD3 protein form phase-separated condensates to regulate endoderm differentiation

Daneshvar, K., Ardehali, M. B., Klein, I. A., Hsieh, F., Kratkiewicz, A. J., Mahpour, A., Cancelliere, S., Zhou, C., Cook, B. M., Li, W., et al. (2020) · Nature Cell Biology · doi:10.1038/s41556-020-0572-2 · Cited by 164

A qPCR ScoreCard quantifies the differentiation potential of human pluripotent stem cells

Tsankov, A. M., Akopian, V., Pop, R., Chetty, S., Gifford, C. A., Daheron, L. M., Tsankova, N. M., & Meissner, A. (2015) · Nature Biotechnology · doi:10.1038/nbt.3387 · Cited by 163

Genome-wide tracking of dCas9-methyltransferase footprints

Galonska, C., Charlton, J., Mattei, A. L., Donaghey, J., Clement, K., Gu, H., Mohammad, A. W., Stamenova, E. K., Cacchiarelli, D., Klages, S., et al. (2018) · Nature Communications · doi:10.1038/s41467-017-02708-5 · Cited by 160

Positively selected enhancer elements endow osteosarcoma cells with metastatic competence

Morrow, J. J., Bayles, I., Funnell, A. P. W., Miller, T. E., Saiakhova, A., Lizardo, M. M., Bartels, C. F., Kapteijn, M. Y., Hung, S., Mendoza, A., et al. (2018) · Nature Medicine · doi:10.1038/nm.4475 · Cited by 161

Global reorganisation of cis-regulatory units upon lineage commitment of human embryonic stem cells

Freire-Pritchett, P., Schoenfelder, S., Várnai, C., Wingett, S. W., Cairns, J., Collier, A. J., García-Vílchez, R., Furlan-Magaril, M., Osborne, C. S., Fraser, P., et al. (2017) · eLife · doi:10.7554/elife.21926 · Cited by 161

Dynamic and static maintenance of epigenetic memory in pluripotent and somatic cells

Shipony, Z., Mukamel, Z., Cohen, N. M., Landan, G., Chomsky, E., Zeliger, S. R., Fried, Y. C., Ainbinder, E., Friedman, N., & Tanay, A. (2014) · Nature · doi:10.1038/nature13458 · Cited by 159

Molecular features of cellular reprogramming and development

Smith, Z. D., Sindhu, C., & Meissner, A. (2016) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2016.6 · Cited by 155

Deletion of the Polycomb-Group Protein EZH2 Leads to Compromised Self-Renewal and Differentiation Defects in Human Embryonic Stem Cells

Collinson, A., Collier, A. J., Morgan, N. P., Sienerth, A. R., Chandra, T., Andrews, S., & Rugg‐Gunn, P. J. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.11.032 · Cited by 146

Decoding the function of bivalent chromatin in development and cancerPreprint

Kumar, D., Cinghu, S., Oldfield, A., Yang, P., & Jothi, R. (2021) · Genome Research · doi:10.1101/gr.275736.121 · Cited by 139

DNA methylation and gene expression dynamics during spermatogonial stem cell differentiation in the early postnatal mouse testis

Kubo, N., Toh, H., Shirane, K., Shirakawa, T., Kobayashi, H., Sato, T., Sone, H., Sato, Y., Tomizawa, S.-I., Tsurusaki, Y., et al. (2015) · BMC Genomics · doi:10.1186/s12864-015-1833-5 · Cited by 145

Cross-Regulation between TDP-43 and Paraspeckles Promotes Pluripotency-Differentiation Transition

Modic, M., Grosch, M., Rot, G., Schirge, S., Lepko, T., Yamazaki, T., Lee, F. C. Y., Rusha, E., Shaposhnikov, D., Palo, M., et al. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.03.041 · Cited by 136

Otx2 and Oct4 Drive Early Enhancer Activation during Embryonic Stem Cell Transition from Naive Pluripotency

Yang, S., Kalkan, T., Morrisroe, C., Marks, H., Stunnenberg, H. G., Smith, A. G., & Sharrocks, A. D. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.05.037 · Cited by 134

Joint-specific DNA methylation and transcriptome signatures in rheumatoid arthritis identify distinct pathogenic processes

Ai, R., Hammaker, D. R., Boyle, D. L., Morgan, R. L., Walsh, A. M., Fan, S., Firestein, G. S., & Wang, W. (2016) · Nature Communications · doi:10.1038/ncomms11849 · Cited by 135

An integrated chromatin accessibility and transcriptome landscape of human pre-implantation embryos

Liu, L., Leng, L., Liu, C., Lu, C., Yuan, Y., Wu, L. L., Gong, F., Zhang, S., Wei, X., Wang, M., et al. (2019) · Nature Communications · doi:10.1038/s41467-018-08244-0 · Cited by 133

3D culture increases pluripotent gene expression in mesenchymal stem cells through relaxation of cytoskeleton tension

Zhou, B. Y., Chen, H., Li, H., & Wu, Y. (2017) · Journal of Cellular and Molecular Medicine · doi:10.1111/jcmm.12946 · Cited by 130

Initiation of stem cell differentiation involves cell cycle-dependent regulation of developmental genes by Cyclin DPreprint

Pauklin, S., Madrigal, P., Bertero, A., & Vallier, L. (2016) · Genes & Development · doi:10.1101/gad.271452.115 · Cited by 134

DNMT3A-dependent DNA methylation is required for spermatogonial stem cells to commit to spermatogenesis

Dura, M., Teissandier, A., Armand, M., Barau, J., Lapoujade, C., Fouchet, P., Bonneville, L., Schulz, M., Weber, M., Baudrin, L. G., et al. (2022) · Nature Genetics · doi:10.1038/s41588-022-01040-z · Cited by 135

DNA methylation regulates discrimination of enhancers from promoters through a H3K4me1-H3K4me3 seesaw mechanism

Sharifi‐Zarchi, A., Daniela Gerovska, D., Adachi, K., Totonchi, M., Pezeshk, H., Taft, R. J., Schöler, H. R., Chitsaz, H., Sadeghi, M., Baharvand, H., et al. (2017) · BMC Genomics · doi:10.1186/s12864-017-4353-7 · Cited by 133

KeyGenes, a Tool to Probe Tissue Differentiation Using a Human Fetal Transcriptional Atlas

Roost, M. S., van Iperen, L., Ariyürek, Y., Buermans, H. P. J., Arindrarto, W., Devalla, H. D., Passier, R. C., Mummery, C. L., Carlotti, F., de Koning, E. J. P., et al. (2015) · Stem Cell Reports · doi:10.1016/j.stemcr.2015.05.002 · Cited by 128

KDM6 Demethylase Independent Loss of Histone H3 Lysine 27 Trimethylation during Early Embryonic Development

Shpargel, K. B., Starmer, J., Yee, D., Pohlers, M., & Magnuson, T. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004507 · Cited by 127

G-quadruplex DNA structures in human stem cells and differentiation

Zyner, K. G., Simeone, A., Flynn, S. M., Doyle, C., Marsico, G., Adhikari, S., Portella, G., Tannahill, D., & Balasubramanian, S. (2022) · Nature Communications · doi:10.1038/s41467-021-27719-1 · Cited by 124

Epigenetic Control of Smooth Muscle Cell Identity and Lineage Memory

Gomez, D. A., Swiatlowska, P., & Owens, G. K. (2015) · Arteriosclerosis Thrombosis and Vascular Biology · doi:10.1161/atvbaha.115.305044 · Cited by 131

PRC2 specifies ectoderm lineages and maintains pluripotency in primed but not naïve ESCs

Shan, Y., Liang, Z., Qi, X., Zhang, T., Wang, B., Tian, S., Huang, W., Zhang, Y., Jiao, Y., Zhu, Y., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-00668-4 · Cited by 124

p53: emerging roles in stem cells, development and beyond

Jain, A. K., & Barton, M. C. (2018) · Development · doi:10.1242/dev.158360 · Cited by 130

Ground State Conditions Induce Rapid Reorganization of Core Pluripotency Factor Binding before Global Epigenetic Reprogramming

Galonska, C., Ziller, M. J., Karnik, R., & Meissner, A. (2015) · Cell stem cell · doi:10.1016/j.stem.2015.07.005 · Cited by 118

Transcriptional and epigenetic regulation of T‐helper lineage specification

Tripathi, S. K., & Lahesmaa, R. (2014) · Immunological Reviews · doi:10.1111/imr.12204 · Cited by 118

Alternative Splicing of MBD2 Supports Self-Renewal in Human Pluripotent Stem Cells

Lu, Y., Loh, Y., Li, H., Cesana, M., Ficarro, S. B., Parikh, J. R., Salomonis, N., Toh, C.-X. D., Andreadis, S. T., Luckey, C. J., et al. (2014) · Cell stem cell · doi:10.1016/j.stem.2014.04.002 · Cited by 115

DNA methylation dynamics in cellular commitment and differentiation

Suelves, M., Carrió, E., Núñez‐Álvarez, Y., & Peinado, M. A. (2016) · Briefings in Functional Genomics · doi:10.1093/bfgp/elw017 · Cited by 120

Stepwise Clearance of Repressive Roadblocks Drives Cardiac Induction in Human ESCs

Rao, J., Pfeiffer, M. J., Frank, S., Adachi, K., Piccini, I., Quaranta, R., Araúzo-Bravo, M. J., Schwarz, J., Schade, D., Leidel, S. A., et al. (2015) · Cell stem cell · doi:10.1016/j.stem.2015.11.019 · Cited by 112

Genome-wide DNA methylation patterns in LSH mutant reveals de-repression of repeat elements and redundant epigenetic silencing pathwaysPreprint

Yu, W., MCINTOSH, C. E., Lister, R., Zhu, I., Han, Y., Ren, J., Landsman, D., Lee, E. Y., Briones, V. R., Terashima, M., et al. (2014) · Genome Research · doi:10.1101/gr.172015.114 · Cited by 115

A Multi-step Transcriptional and Chromatin State Cascade Underlies Motor Neuron Programming from Embryonic Stem Cells

Velasco, S., Ibrahim, M. M., Kakumanu, A., Garipler, G., Aydin, B., Al-Sayegh, M. A., Hirsekorn, A., Abdul-Rahman, F., Satija, R., Ohler, U., et al. (2017) · Cell Stem Cell · doi:10.1016/j.stem.2016.11.006 · Cited by 111

Identification and Massively Parallel Characterization of Regulatory Elements Driving Neural Induction

Inoue, F., Kreimer, A., Ashuach, T., Ahituv, N., & Yosef, N. (2019) · Cell stem cell · doi:10.1016/j.stem.2019.09.010 · Cited by 109

The role of DNA methylation in directing the functional organization of the cancer epigenomePreprint

Lay, F. D., Liu, Y., Kelly, T. K., Witt, H. N., Farnham, P., Jones, P. A., & Berman, B. P. (2015) · Genome Research · doi:10.1101/gr.183368.114 · Cited by 111

Multifactorial profiling of epigenetic landscapes at single-cell resolution using MulTI-Tag

Meers, M. P., Llagas, G., Janssens, D. H., Codomo, C. A., & Henikoff, S. (2022) · Nature Biotechnology · doi:10.1038/s41587-022-01522-9 · Cited by 105

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 130

MPRAnalyze: statistical framework for massively parallel reporter assays

Ashuach, T., Fischer, D. S., Kreimer, A., Ahituv, N., Theis, F. J., & Yosef, N. (2019) · Genome biology · doi:10.1186/s13059-019-1787-z · Cited by 105

Chronic Inflammation Induces a Novel Epigenetic Program That Is Conserved in Intestinal Adenomas and in Colorectal Cancer

Abu-Remaileh, M., Bender, S., Raddatz, G., Ansari, I., Cohen, D., Gutekunst, J., Musch, T., Linhart, H., Breiling, A., Pikarsky, E., et al. (2015) · Cancer Research · doi:10.1158/0008-5472.can-14-3295 · Cited by 102

DNA Methylation Landscapes of Human Fetal Development

Slieker, R. C., Roost, M. S., van Iperen, L., Suchiman, H. E. D., Tobi, E. W., Carlotti, F., de Koning, E. J. P., Slagboom, P. E., Heijmans, B. T., & Lopes, S. M. C. D. S. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1005583 · Cited by 101

Chromatin features and the epigenetic regulation of pluripotency states in ESCs

Tee, W., & Reinberg, D. (2014) · Development · doi:10.1242/dev.096982 · Cited by 98

Single-Cell RNA-Sequencing-Based CRISPRi Screening Resolves Molecular Drivers of Early Human Endoderm Development

Genga, R. M. J., Kernfeld, E. M., Parsi, K. M., Parsons, T. J., Ziller, M. J., & Maehr, R. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.03.076 · Cited by 92

Aging is associated with highly defined epigenetic changes in the human epidermis

Raddatz, G., Hagemann, S., Aran, D., Söhle, J., Kulkarni, P. P., Kaderali, L., Hellman, A., Winnefeld, M., & Lyko, F. (2013) · Epigenetics & Chromatin · doi:10.1186/1756-8935-6-36 · Cited by 95

Global delay in nascent strand DNA methylation

Charlton, J., Downing, T. L., Smith, Z. D., Gu, H., Clement, K., Pop, R., Akopian, V., Klages, S., Santos, D. P., Tsankov, A. M., et al. (2018) · Nature Structural & Molecular Biology · doi:10.1038/s41594-018-0046-4 · Cited by 96

ADAR1 is required for differentiation and neural induction by regulating microRNA processing in a catalytically independent manner

Chen, T. X., Xiang, J., Zhu, S., Chen, S., Yin, Q.-F., Zhang, X.-O., Zhang, J., Feng, H., Dong, R., Li, X.-J., et al. (2015) · Cell Research · doi:10.1038/cr.2015.24 · Cited by 91

Developmental enhancers revealed by extensive DNA methylome maps of zebrafish early embryos

Lee, H. J., Lowdon, R. F., Maricque, B. B., Zhang, B., Stevens, M. W., Li, D., Johnson, S. L., & Wang, T. (2015) · Nature Communications · doi:10.1038/ncomms7315 · Cited by 92

Engineering of a Histone-Recognition Domain in Dnmt3a Alters the Epigenetic Landscape and Phenotypic Features of Mouse ESCs

Noh, K., Wang, H., Kim, H. R., Wenderski, W., Fang, F., Li, C. H., Dewell, S. B., Hughes, S. H., Melnick, A. M., Patel, D. J., et al. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.05.017 · Cited by 93

Pre-marked chromatin and transcription factor co-binding shape the pioneering activity of Foxa2

Cernilogar, F. M., Hasenöder, S., Wang, Z., Scheibner, K., Burtscher, I., Sterr, M., Smialowski, P., Groh, S., Evenroed, I. M., Gilfillan, G. D., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz627 · Cited by 86

DNMTs and Impact of CpG Content, Transcription Factors, Consensus Motifs, lncRNAs, and Histone Marks on DNA Methylation

Loaeza‐Loaeza, J., Beltrán, A. S., & Hernández‐Sotelo, D. (2020) · Genes · doi:10.3390/genes11111336 · Cited by 93

Cell-of-Origin DNA Methylation Signatures Are Maintained during Colorectal Carcinogenesis

Bormann, F., Rodríguez‐Paredes, M., Lasitschka, F., Edelmann, D., Musch, T., Benner, A., Bergman, Y., Dieter, S. M., Ball, C. R., Glimm, H., et al. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.05.045 · Cited by 86

Understanding the Relevance of DNA Methylation Changes in Immune Differentiation and Disease

de la Calle‐Fabregat, C., Morante-Palacios, O., & Ballestar, E. (2020) · Genes · doi:10.3390/genes11010110 · Cited by 89

Mutations in the noncoding genome

Scacheri, C., & Scacheri, P. C. (2015) · Current Opinion in Pediatrics · doi:10.1097/mop.0000000000000283 · Cited by 103

Epigenetic regulation of cancer stem cell formation and maintenance

French, R., & Pauklin, S. (2020) · International Journal of Cancer · doi:10.1002/ijc.33398 · Cited by 87

Calibrating ChIP-Seq with Nucleosomal Internal Standards to Measure Histone Modification Density Genome Wide

Grzybowski, A. T., Chen, Z., & Ruthenburg, A. J. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.04.022 · Cited by 84

Transcriptional and Epigenetic Dynamics Observed During Lineage Specification of Human Embryonic Stem Cells

Gifford, C. A. (2014) · Digital Access to Scholarship at Harvard (DASH) (Harvard University)

Transcription factor binding dynamics during human ES cell differentiation

Tsankov, A. M., Gu, H., Akopian, V., Ziller, M. J., Donaghey, J., Amit, I., Gnirke, A., & Meissner, A. (2015) · Nature · doi:10.1038/nature14233 · Cited by 358

Epigenetic signatures and temporal expression of lineage-specific genes in hESCs during differentiation to hepatocytes in vitro

Kim, H., Jang, M.-J., Kang, M., & Han, Y. (2010) · Human Molecular Genetics · doi:10.1093/hmg/ddq476 · Cited by 24

Epigenetic changes in differentiation of human pluripotent stem cells

Golebiewska, A. (2008) · OpenGrey (Institut de l'Information Scientifique et Technique)

Epigenetic modifications of histone H3 lysine methylation in embryonic stem cell pluripotency

Otani, M., Amano, K., & Furukawa, O. (2025) · International Journal of Biology Sciences · doi:10.33545/26649926.2025.v7.i9b.626