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Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells
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Cites
Takahashi, K., & Yamanaka, S. (2006) · Cell · doi:10.1016/j.cell.2006.07.024 · Cited by 26,673
High-Resolution Profiling of Histone Methylations in the Human Genome
Barski, A., Cuddapah, S., Cui, K., Roh, T.-Y., Schones, D. E., Wang, Z., Wei, G., Chepelev, I., & Zhao, K. (2007) · Cell · doi:10.1016/j.cell.2007.05.009 · Cited by 6,845
The ENCODE Project Consortium (2007) · Nature · doi:10.1038/nature05874 · Cited by 5,223
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
Mikkelsen, T. S., Ku, M., Jaffe, D. B., Issac, B., Lieberman, E., Giannoukos, G., Alvarez, P., Brockman, W., Kim, T.-K., Koche, R. P., et al. (2007) · Nature · doi:10.1038/nature06008 · Cited by 4,129
Heintzman, N. D., Stuart, R. K., Hon, G., Fu, Y., Ching, C. W., Hawkins, R. D., Barrera, L. O., Van Calcar, S., Qu, C., Ching, K. A., et al. (2007) · Nature Genetics · doi:10.1038/ng1966 · Cited by 3,398 · cited 9×
“p300 is a histone acetyltransferase commonly found at enhancer regions (Heintzman et al., 2007; Ogryzko et al., 1996).”
BackgroundMethodInfluentialRobertson, G., Hirst, M., Bainbridge, M., Bilenky, M., Zhao, Y., Zeng, T., Euskirchen, G., Bernier, B., Varhol, R., Delaney, A., et al. (2007) · Nature Methods · doi:10.1038/nmeth1068 · Cited by 1,454
Cawley, S., Bekiranov, S., Ng, H. H., Kapranov, P., Sekinger, E. A., Kampa, D., Piccolboni, A., Sementchenko, V., Cheng, J., Williams, A. J., et al. (2004) · Cell · doi:10.1016/s0092-8674(04)00127-8 · Cited by 1,095
Self-citationWathelet, M. G., Lin, C. H., Parekh, B. S., Ronco, L. V., Howley, P. M., & Maniatis, T. (1998) · Molecular Cell · doi:10.1016/s1097-2765(00)80051-9 · Cited by 730
DNA Binding Specificity of Different STAT Proteins
Ehret, G. B., Reichenbach, P., Schindler, U., Horvath, C. M., Fritz, S., Nabholz, M., & Bucher, P. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m001748200 · Cited by 369
Transcriptional enhancers: Intelligent enhanceosomes or flexible billboards?
Arnosti, D. N., & Kulkarni, M. M. (2005) · Journal of Cellular Biochemistry · doi:10.1002/jcb.20352 · Cited by 309
Cited by
Heinz, S., Benner, C., Spann, N., Bertolino, E., Lin, Y. C., Laslo, P., Cheng, J. X., Murre, C., Singh, H., & Glass, C. K. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.05.004 · Cited by 13,382
Immunity, Inflammation, and Cancer
Grivennikov, S. I., Greten, F. R., & Karin, M. (2010) · Cell · doi:10.1016/j.cell.2010.01.025 · Cited by 10,755
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
Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes
Whyte, W. A., Orlando, D. A., Hnisz, D., Abraham, B. J., Lin, C. Y., Kagey, M. H., Rahl, P. B., Lee, T. I., & Young, R. A. (2013) · Cell · doi:10.1016/j.cell.2013.03.035 · Cited by 4,143
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
Super-enhancers in the control of cell identity and disease
Hnisz, D., Abraham, B. J., Lee, T. I., Lau, A., Saint-André, V., Sigova, A. A., Hoke, H. A., & Young, R. A. (2013) · Cell · doi:10.1016/j.cell.2013.09.053 · Cited by 3,662
Transcriptional regulation of macrophage polarization: enabling diversity with identity
Lawrence, T., & Natoli, G. (2011) · Nature Reviews Immunology · doi:10.1038/nri3088 · Cited by 2,284
ChIP-seq accurately predicts tissue-specific activity of enhancers
Visel, A., Blow, M. J., Li, Z., Zhang, T., Akiyama, J. A., Holt, A., Plajzer-Frick, I., Shoukry, M., Wright, C., Chen, F., et al. (2009) · Nature · doi:10.1038/nature07730 · Cited by 1,639
Reflecting on 25 years with MYC
Meyer, N., & Penn, L. Z. (2008) · Nature Reviews Cancer · doi:10.1038/nrc2231 · Cited by 1,575
DNA-binding factors shape the mouse methylome at distal regulatory regions
Stadler, M. B., Murr, R., Burger, L., Ivanek, R., Lienert, F., Schöler, A., Nimwegen, E. V., Wirbelauer, C., Oakeley, E. J., Gaidatzis, D., et al. (2011) · Nature · doi:10.1038/nature10716 · Cited by 1,383
A map of the cis-regulatory sequences in the mouse genome
Shen, Y., Yue, F., McCleary, D. F., Ye, Z., Edsall, L., Kuan, S., Wagner, U., Dixon, J., Lee, L., Lobanenkov, V. V., et al. (2012) · Nature · doi:10.1038/nature11243 · Cited by 1,361
TGF-β and the TGF-β family: context-dependent roles in cell and tissue physiology
Morikawa, M., Derynck, R., & Miyazono, K. (2016) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a021873 · Cited by 1,321
c-Myc Regulates Transcriptional Pause Release
Rahl, P. B., Lin, C. Y., Seila, A. C., Flynn, R. A., McCuine, S., Burge, C. B., Sharp, P. A., & Young, R. A. (2010) · Cell · doi:10.1016/j.cell.2010.03.030 · Cited by 1,279
Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations
Fulco, C. P., Nasser, J., Jones, T. R., Munson, G., Bergman, D. T., Subramanian, V., Grossman, S. R., Anyoha, R., Doughty, B. R., Patwardhan, T. A., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0538-0 · Cited by 1,111
Mechanisms and consequences of Jak–STAT signaling in the immune system
Villarino, A. V., Kanno, Y., & O'Shea, J. J. (2017) · Nature Immunology · doi:10.1038/ni.3691 · Cited by 1,221
HnRNP proteins controlled by c-Myc deregulate pyruvate kinase mRNA splicing in cancer
David, C. J., Chen, M., Assanah, M., Canoll, P., & Manley, J. L. (2010) · Nature · doi:10.1038/nature08697 · Cited by 1,179
A Validated Regulatory Network for Th17 Cell Specification
Ciofani, M., Madar, A., Galan, C., Sellars, M., Mace, K., Pauli, F., Agarwal, A., Huang, W., Parkurst, C. N., Muratet, M., et al. (2012) · Cell · doi:10.1016/j.cell.2012.09.016 · Cited by 1,160
Nanog Is the Gateway to the Pluripotent Ground State
Silva, J., Nichols, J., Theunissen, T. W., Guo, G., van Oosten, A. L., Barrandon, O., Wray, J., Yamanaka, S., Chambers, I., & Smith, A. (2009) · Cell · doi:10.1016/j.cell.2009.07.039 · Cited by 1,031
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
The epigenetic landscape of T cell exhaustion
Sen, D. R., Kaminski, J., Barnitz, R. A., Kurachi, M., Gerdemann, U., Yates, K. B., Tsao, H.-W., Godec, J., LaFleur, M. W., Brown, F. D., et al. (2016) · Science · doi:10.1126/science.aae0491 · Cited by 986
Samavarchi-Tehrani, P., Golipour, A., David, L., Sung, H.-K., Beyer, T. A., Datti, A., Woltjen, K., Nagy, A., & Wrana, J. L. (2010) · Cell Stem Cell · doi:10.1016/j.stem.2010.04.015 · Cited by 943
Soufi, A., Donahue, G., & Zaret, K. S. (2012) · Cell · doi:10.1016/j.cell.2012.09.045 · Cited by 933
Latent Enhancers Activated by Stimulation in Differentiated Cells
Ostuni, R., Piccolo, V., Barozzi, I., Polletti, S., Termanini, A., Bonifacio, S., Curina, A., Prosperini, E., Ghisletti, S., & Natoli, G. (2013) · Cell · doi:10.1016/j.cell.2012.12.018 · Cited by 867
Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state
Rotem, A., Ram, O., Shoresh, N., Sperling, R. A., Goren, A., Weitz, D. A., & Bernstein, B. E. (2015) · Nature Biotechnology · doi:10.1038/nbt.3383 · Cited by 854
Koh, K. P., Yabuuchi, A., Rao, S., Huang, Y., Cunniff, K., Nardone, J., Laiho, A., Tahiliani, M., Sommer, C. A., Mostoslavsky, G., et al. (2011) · Cell Stem Cell · doi:10.1016/j.stem.2011.01.008 · Cited by 776
Wilson, N. K., Foster, S. D., Wang, X., Knezevic, K., Schütte, J., Kaimakis, P., Chilarska, P. M., Kinston, S., Ouwehand, W. H., Dzierzak, E., et al. (2010) · Cell stem cell · doi:10.1016/j.stem.2010.07.016 · Cited by 728
Transcription factors as readers and effectors of DNA methylation
Zhu, H., Wang, G., & Qian, J. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.83 · Cited by 649
Enhancers as non-coding RNA transcription units: recent insights and future perspectives
Li, W., Notani, D., & Rosenfeld, M. G. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.4 · Cited by 710
Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation
Kolodziejczyk, A. A., Kim, J. K., Tsang, J. C. H., Ilicic, T., Henriksson, J., Natarajan, K. N., Tuck, A. C., Gao, X., Bühler, M., Liu, P., et al. (2015) · Cell Stem Cell · doi:10.1016/j.stem.2015.09.011 · Cited by 570
Cooperative Binding of Transcription Factors Orchestrates Reprogramming
Chronis, C., Fiziev, P., Papp, B., Butz, S., Bonora, G., Sabri, S., Ernst, J., & Plath, K. (2017) · Cell · doi:10.1016/j.cell.2016.12.016 · Cited by 555
Base-resolution models of transcription-factor binding reveal soft motif syntax
Avsec, Ž., Weilert, M., Shrikumar, A., Krueger, S., Alexandari, A., Dalal, K., Fropf, R., McAnany, C., Gagneur, J., Kundaje, A., et al. (2021) · Nature Genetics · doi:10.1038/s41588-021-00782-6 · Cited by 610
Genomic views of distant-acting enhancers
Visel, A., Rubin, E. M., & Pennacchio, L. A. (2009) · Nature · doi:10.1038/nature08451 · Cited by 610
Enhancer decommissioning by LSD1 during embryonic stem cell differentiation
Whyte, W. A., Bilodeau, S., Orlando, D. A., Hoke, H. A., Frampton, G. M., Foster, C. T., Cowley, S. M., & Young, R. A. (2012) · Nature · doi:10.1038/nature10805 · Cited by 602
Single-Molecule Dynamics of Enhanceosome Assembly in Embryonic Stem Cells
Chen, J., Zhang, Z., Li, L., Chen, B.-C., Revyakin, A., Hajj, B., Legant, W., Dahan, M., Lionnet, T., Betzig, E., et al. (2014) · Cell · doi:10.1016/j.cell.2014.01.062 · Cited by 602
An Oct4-Centered Protein Interaction Network in Embryonic Stem Cells
van den Berg, D. L. C., Snoek, T., Mullin, N. P., Yates, A., Bezstarosti, K., Demmers, J., Chambers, I., & Poot, R. A. (2010) · Cell Stem Cell · doi:10.1016/j.stem.2010.02.014 · Cited by 542
Insights from genomic profiling of transcription factors
Farnham, P. J. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2636 · Cited by 519
Competition between DNA methylation and transcription factors determines binding of NRF1
Domcke, S., Bardet, A. F., Adrian Ginno, P., Hartl, D., Burger, L., & Schübeler, D. (2015) · Nature · doi:10.1038/nature16462 · Cited by 508
Reorganization of enhancer patterns in transition from naive to primed pluripotency
Buecker, C., Srinivasan, R., Wu, Z., Calo, E., Acampora, D., Faial, T., Simeone, A., Tan, M., Swigut, T., & Wysocka, J. (2014) · Cell Stem Cell · doi:10.1016/j.stem.2014.04.003 · Cited by 507
Genome-wide Analysis Reveals TET- and TDG-Dependent 5-Methylcytosine Oxidation Dynamics
Shen, L., Wu, H., Diep, D., Yamaguchi, S., D’Alessio, A. C., Fung, H.-L., Zhang, K., & Zhang, Y. (2013) · Cell · doi:10.1016/j.cell.2013.04.002 · Cited by 497
Convergence of Developmental and Oncogenic Signaling Pathways at Transcriptional Super-Enhancers
Hnisz, D., Schuijers, J., Lin, C. Y., Weintraub, A. S., Abraham, B. J., Lee, T. I., Bradner, J. E., & Young, R. A. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.02.014 · Cited by 476
The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements
Schoenfelder, S., Furlan-Magaril, M., Mifsud, B., Tavares-Cadete, F., Sugar, R., Javierre, B.-M., Nagano, T., Katsman, Y., Sakthidevi, M., Wingett, S. W., et al. (2015) · Genome Research · doi:10.1101/gr.185272.114 · Cited by 460
The 3D genome in transcriptional regulation and pluripotency
Gorkin, D. U., Leung, D., & Ren, B. (2014) · Cell Stem Cell · doi:10.1016/j.stem.2014.05.017 · Cited by 391
The FANTOM Consortium, & Riken Omics Science Center (2009) · Nature Genetics · doi:10.1038/ng.375 · Cited by 427
Transforming growth factor‐β in stem cells and tissue homeostasis
Xu, X., Zheng, L., Yuan, Q., Zhen, G., Crane, J. L., Zhou, X., & Cao, X. (2018) · Bone Research · doi:10.1038/s41413-017-0005-4 · Cited by 414
Polycomb repressive complex PRC1 spatially constrains the mouse embryonic stem cell genome
Schoenfelder, S., Sugar, R., Dimond, A., Javierre, B.-M., Armstrong, H., Mifsud, B., Dimitrova, E., Matheson, L., Tavares-Cadete, F., Furlan-Magaril, M., et al. (2015) · Nature Genetics · doi:10.1038/ng.3393 · Cited by 398
ChIP-Seq identification of weakly conserved heart enhancers
Blow, M. J., McCulley, D. J., Li, Z., Zhang, T., Akiyama, J. A., Holt, A., Plajzer-Frick, I., Shoukry, M., Wright, C., Chen, F., et al. (2010) · Nature Genetics · doi:10.1038/ng.650 · Cited by 392
Nativio, R., Lan, Y., Donahue, G., Sidoli, S., Berson, A., Srinivasan, A. R., Shcherbakova, O., Amlie-Wolf, A., Nie, J., Cui, X., et al. (2020) · Nature Genetics · doi:10.1038/s41588-020-0696-0 · Cited by 380
Defining an essential transcription factor program for naïve pluripotency
Dunn, S.-J., Martello, G., Yordanov, B., Emmott, S., & Smith, A. G. (2014) · Science · doi:10.1126/science.1248882 · Cited by 370
Methylation-Dependent and -Independent Genomic Targeting Principles of the MBD Protein Family
Baubec, T., Ivánek, R., Lienert, F., & Schübeler, D. (2013) · Cell · doi:10.1016/j.cell.2013.03.011 · Cited by 365
Dysregulation of the epigenetic landscape of normal aging in Alzheimer’s disease
Nativio, R., Donahue, G., Berson, A., Lan, Y., Amlie-Wolf, A., Tuzer, F., Toledo, J. B., Gosai, S. J., Gregory, B. D., Torres, C., et al. (2018) · Nature Neuroscience · doi:10.1038/s41593-018-0101-9 · Cited by 363
DNA methylation presents distinct binding sites for human transcription factors
Hu, S., Wan, J., Su, Y., Song, Q., Zeng, Y., Nguyen, H. N., Shin, J., Cox, E., Rho, H. S., Woodard, C., et al. (2013) · eLife · doi:10.7554/elife.00726 · Cited by 349
Bonetto, A., Aydogdu, T., Kunzevitzky, N., Guttridge, D. C., Khuri, S., Koniaris, L. G., & Zimmers, T. A. (2011) · PLoS ONE · doi:10.1371/journal.pone.0022538 · Cited by 348
Live-cell imaging reveals enhancer-dependent Sox2 transcription in the absence of enhancer proximity
Alexander, J. M., Guan, J., Li, B., Maliskova, L., Song, M., Shen, Y., Huang, B., Lomvardas, S., & Weiner, O. D. (2019) · eLife · doi:10.7554/elife.41769 · Cited by 346
Hon, G. C., Song, C.-X., Du, T., Jin, F., Selvaraj, S., Lee, A. Y., Yen, C.-A., Ye, Z., Mao, S.-Q., Wang, B.-A., et al. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.08.026 · Cited by 344
Interaction with WDR5 Promotes Target Gene Recognition and Tumorigenesis by MYC
Thomas, L. R., Wang, Q., Grieb, B. C., Phan, J., Foshage, A. M., Sun, Q., Olejniczak, E. T., Clark, T., Dey, S., Lorey, S., et al. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.02.028 · Cited by 310
Animal Transcription Networks as Highly Connected, Quantitative Continua
Biggin, M. D. (2011) · Developmental Cell · doi:10.1016/j.devcel.2011.09.008 · Cited by 308
Epigenetics of Reprogramming to Induced Pluripotency
Papp, B., & Plath, K. (2013) · Cell · doi:10.1016/j.cell.2013.02.043 · Cited by 307
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
Mitotic and mitogenic Wnt signalling
Niehrs, C., & Acebron, S. P. (2012) · The EMBO Journal · doi:10.1038/emboj.2012.124 · Cited by 305
YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment
Beagan, J. A., Duong, M. T., Titus, K. R., Zhou, L., Cao, Z., Ma, J., Lachanski, C. V., Gillis, D. R., & Phillips-Cremins, J. E. (2017) · Genome Research · doi:10.1101/gr.215160.116 · Cited by 299
“across more than 100 mammalian cell types (Kim et al. 2007; Chen et al. 2008; Cuddapah et al. 2009; Wang et al. 2012; Maurano et al. 2015).”
Genomic views of STAT function in CD4+ T helper cell differentiation
O'Shea, J. J., Lahesmaa, R., Vahedi, G., Laurence, A., & Kanno, Y. (2011) · Nature Reviews Immunology · doi:10.1038/nri2958 · Cited by 295
Lin, Y. C., Benner, C., Mansson, R., Heinz, S., Miyazaki, K., Miyazaki, M., Chandra, V., Bossen, C., Glass, C. K., & Murre, C. (2012) · Nature Immunology · doi:10.1038/ni.2432 · Cited by 281
Tbx3 improves the germ-line competency of induced pluripotent stem cells
Han, J., Yuan, P., Yang, H., Zhang, J., Soh, B. S., Li, P., Lim, S. L., Cao, S., Tay, J., Orlov, Y. L., et al. (2010) · Nature · doi:10.1038/nature08735 · Cited by 285
Self-citationMason, M. J., Fan, G., Plath, K., Zhou, Q., & Horvath, S. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-327 · Cited by 243
“Binding data from Chen et al (2008), Boyer et al (2006), and Loh et al (2006), are marked in blue (bound) and beige (unbound).”
BackgroundMethodInfluentialDistinct Classes of Chromatin Loops Revealed by Deletion of an RNA-Binding Region in CTCF
Hansen, A. S., Hsieh, T.-H. S., Cattoglio, C., Pustova, I., Saldaña-Meyer, R., Reinberg, D., Darzacq, X., & Tjian, R. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.07.039 · Cited by 279
Li, M., He, Y., Dubois, W., Wu, X., Shi, J., & Huang, J. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.01.020 · Cited by 264
King, H. W., & Klose, R. J. (2017) · eLife · doi:10.7554/elife.22631 · Cited by 270
DNA methylation status predicts cell type‐specific enhancer activity
Wiench, M., John, S., Baek, S., Johnson, T. A., Sung, M., Escobar, T., Simmons, C. A., Pearce, K. H., Biddie, S. C., Sabo, P. J., et al. (2011) · The EMBO Journal · doi:10.1038/emboj.2011.210 · Cited by 245
Chromatin Accessibility Dynamics during iPSC Reprogramming
Li, D., Liu, J., Yang, X., Zhou, C., Guo, J., Wu, C., Qin, Y., Guo, L., He, J., Yu, S., et al. (2017) · Cell Stem Cell · doi:10.1016/j.stem.2017.10.012 · Cited by 251
Reynolds, N., Latos, P., Hynes-Allen, A., Loos, R., Leaford, D., O'Shaughnessy, A., Mosaku, O., Signolet, J., Brennecke, P., Kalkan, T., et al. (2012) · Cell Stem Cell · doi:10.1016/j.stem.2012.02.020 · Cited by 236
“Both Zfp57 and Esrrb are implicated in cell fate decisions during development (Chen et al., 2008; Li et al., 2008).”
BackgroundCruz-Molina, S., Respuela, P., Tebartz, C., Kolovos, P., Nikolic, M., Fueyo, R., van Ijcken, W. F. J., Grosveld, F., Frommolt, P., Bazzi, H., et al. (2017) · Cell Stem Cell · doi:10.1016/j.stem.2017.02.004 · Cited by 240
Transcription Factor Cooperativity in Early Adipogenic Hotspots and Super-Enhancers
Siersbæk, R., Rabiee, A., Nielsen, R., Sidoli, S., Traynor, S., Loft, A., Poulsen, L. L. C., Rogowska-Wrzesinska, A., Jensen, O. N., & Mandrup, S. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.04.042 · Cited by 234
Lim, C. Y., Tam, W.-L., Zhang, J., Ang, H. S., Jia, H., Lipovich, L., Ng, H.-H., Wei, C.-L., Sung, W. K., Robson, P., et al. (2008) · Cell Stem Cell · doi:10.1016/j.stem.2008.08.004 · Cited by 224
Self-citationCiiiDER: A tool for predicting and analysing transcription factor binding sites
Gearing, L. J., Cumming, H. E., Chapman, R., Finkel, A. M., Woodhouse, I. B., Luu, K., Gould, J. A., Forster, S. C., & Hertzog, P. J. (2019) · PLOS ONE · doi:10.1371/journal.pone.0215495 · Cited by 221
Complex architecture and regulated expression of the Sox2ot locus during vertebrate development
Amaral, P. P., Neyt, C., Wilkins, S. J., Askarian-Amiri, M. E., Sunkin, S. M., Perkins, A. C., & Mattick, J. S. (2009) · RNA · doi:10.1261/rna.1705309 · Cited by 209
Li, X.-Y., Thomas, S., Sabo, P. J., Eisen, M. B., Stamatoyannopoulos, J. A., & Biggin, M. D. (2011) · Genome Biology · doi:10.1186/gb-2011-12-4-r34 · Cited by 217
Wei, Z., Gao, F., Kim, S., Yang, H., Lyu, J., An, W., Wang, K., & Lu, W. (2013) · Cell Stem Cell · doi:10.1016/j.stem.2013.05.010 · Cited by 214
CRISPR Reveals a Distal Super-Enhancer Required for Sox2 Expression in Mouse Embryonic Stem Cells
Li, Y., Rivera, C. M., Ishii, H., Jin, F., Selvaraj, S., Lee, A. Y., Dixon, J. R., & Ren, B. (2014) · PLoS ONE · doi:10.1371/journal.pone.0114485 · Cited by 212
Psat1-Dependent Fluctuations in α-Ketoglutarate Affect the Timing of ESC Differentiation
Hwang, I.-Y., Kwak, S., Lee, S., Kim, H., Lee, S. E., Kim, J.-H., Kim, Y. A., Jeon, Y. K., Chung, D. H., Jin, X., et al. (2016) · Cell Metabolism · doi:10.1016/j.cmet.2016.06.014 · Cited by 180
Xie, W., Song, C., Young, N. L., Sperling, A. S., Xu, F., Sridharan, R., Conway, A. E., Garcia, B. A., Plath, K., Clark, A. T., et al. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.02.004 · Cited by 197
Activin/nodal signalling in stem cells
Pauklin, S., & Vallier, L. (2015) · Development · doi:10.1242/dev.091769 · Cited by 195
A Sox2 distal enhancer cluster regulates embryonic stem cell differentiation potential
Zhou, H. Y., Katsman, Y., Dhaliwal, N. K., Davidson, S., Macpherson, N. N., Sakthidevi, M., Collura, F., & Mitchell, J. A. (2014) · Genes & Development · doi:10.1101/gad.248526.114 · Cited by 192
Neri, F., Incarnato, D., Krepelova, A., Rapelli, S., Pagnani, A., Zecchina, R., Parlato, C., & Oliviero, S. (2013) · Genome Biology · doi:10.1186/gb-2013-14-8-r91 · Cited by 179
Stat3 and c-Myc genome-wide promoter occupancy in embryonic stem cells
Kidder, B. L., Yang, J., & Palmer, S. (2008) · PLoS ONE · doi:10.1371/journal.pone.0003932 · Cited by 184
Robertson, A. G., Bilenky, M., Tam, A., Zhao, Y., Zeng, T., Thiessen, N., Cezard, T., Fejes, A. P., Wederell, E. D., Cullum, R., et al. (2008) · Genome Research · doi:10.1101/gr.078519.108 · Cited by 182
LRP8-Reelin-regulated neuronal enhancer signature underlying learning and memory formation
Telese, F., Ma, Q., Perez, P. M., Notani, D., Oh, S., Li, W., Comoletti, D., Ohgi, K. A., Taylor, H., & Rosenfeld, M. G. (2015) · Neuron · doi:10.1016/j.neuron.2015.03.033 · Cited by 166
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Festuccia, N., Dubois, A., Vandormael-Pournin, S., Gallego Tejeda, E., Mouren, A., Bessonnard, S., Mueller, F., Proux, C., Cohen-Tannoudji, M., & Navarro, P. (2016) · Nature Cell Biology · doi:10.1038/ncb3418 · Cited by 158
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Rao, S., Zhen, S., Roumiantsev, S., McDonald, L. T., Yuan, G.-C., & Orkin, S. H. (2010) · Molecular and Cellular Biology · doi:10.1128/mcb.00419-10 · Cited by 173
Control of embryonic stem cell lineage commitment by core promoter factor, TAF3
Liu, Z., Scannell, D. R., Eisen, M. B., & Tjian, R. (2011) · Cell · doi:10.1016/j.cell.2011.08.005 · Cited by 167
Integrative genomic analysis of human ribosomal DNA
Zentner, G. E., Saiakhova, A., Manaenkov, P., Adams, M. D., & Scacheri, P. C. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq1326 · Cited by 165
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Baksh, S. C., & Finley, L. W. S. (2021) · Trends in Cell Biology · doi:10.1016/j.tcb.2020.09.010 · Cited by 165
Oct4 links multiple epigenetic pathways to the pluripotency network
Ding, J., Xu, H., Faiola, F., Ma'ayan, A., & Wang, J. (2012) · Cell Research · doi:10.1038/cr.2011.179 · Cited by 162
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
Occupancy maps of 208 chromatin-associated proteins in one human cell type
Partridge, E. C., Chhetri, S. B., Prokop, J. W., Ramaker, R. C., Jansen, C. S., Goh, S.-T., Mackiewicz, M., Newberry, K. M., Brandsmeier, L. A., Meadows, S. K., et al. (2020) · Nature · doi:10.1038/s41586-020-2023-4 · Cited by 154
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Guan, Y., Enejder, A., Wang, M., Fang, Z., Cui, L., Chen, S.-Y., Wang, J., Tan, Y., Wu, M., Chen, X., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-26410-9 · Cited by 149
Self-citationBoxer, L. D., Barajas, B., Tao, S., Zhang, J., & Khavari, P. A. (2014) · Genes & Development · doi:10.1101/gad.246579.114 · Cited by 147
Feng, C., Song, C., Liu, Y., Qian, F., Gao, Y., Ning, Z., Wang, Q., Jiang, Y., Li, Y., Li, M., et al. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkz881 · Cited by 147
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Sandberg, M., Flandin, P., Silberberg, S., Su-Feher, L., Price, J. D., Hu, J. S., Kim, C., Visel, A., Nord, A. S., & Rubenstein, J. L. R. (2016) · Neuron · doi:10.1016/j.neuron.2016.08.020 · Cited by 129
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Ngan, C. Y., Wong, C. H., Tjong, H., Wang, W., Goldfeder, R. L., Choi, C., He, H., Gong, L., Lin, J., Urban, B., et al. (2020) · Nature Genetics · doi:10.1038/s41588-020-0581-x · Cited by 140
Self-citationLigand-dependent dynamics of retinoic acid receptor binding during early neurogenesis
Mahony, S., Mazzoni, E. O., McCuine, S., Young, R. A., Wichterle, H., & Gifford, D. K. (2011) · Genome Biology · doi:10.1186/gb-2011-12-1-r2 · Cited by 142
Metadata
- Authors
- Chen, X., Xu, H., Yuan, P., Fang, F., Huss, M., Vega, V. B., Wong, E., Orlov, Y. L., Zhang, W., Jiang, J., Loh, Y.-H., Yeo, H. C., Yeo, Z. X., Narang, V., Govindarajan, K. R., Leong, B., Shahab, A., Ruan, Y., Bourque, G., Sung, W.-K., Clarke, N. D., Wei, C.-L., & Ng, H.-H.
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2008-06
- Volume
- 133
- Issue
- 6
- Pages
- 1106-1117
- ISSN
- 0092-8674 (ISSN-L)
- OpenAlex
- W1988294855
- Cited by
- 2,501
- References
- 10
- FWCI
- 74.70
- Type
- journal article
- Language
- en
- Open access
- bronze
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.