-
1
-
-
84887167528
-
Context-dependent wiring of Sox2 regulatory networks for self-renewal of embryonic and trophoblast stem cells
-
Adachi, K., Nikaido, I., Ohta, H., Ohtsuka, S., Ura, H., Kadota, M., Wakayama, T., Ueda, H.R., and Niwa, H. (2013). Context-dependent wiring of Sox2 regulatory networks for self-renewal of embryonic and trophoblast stem cells. Mol. Cell 52, 380-392.
-
(2013)
Mol. Cell
, vol.52
, pp. 380-392
-
-
Adachi, K.1
Nikaido, I.2
Ohta, H.3
Ohtsuka, S.4
Ura, H.5
Kadota, M.6
Wakayama, T.7
Ueda, H.R.8
Niwa, H.9
-
2
-
-
78149492548
-
Histone variants in metazoan development
-
Banaszynski, L.A., Allis, C.D., and Lewis, P.W. (2010). Histone variants in metazoan development. Dev. Cell 19, 662-674.
-
(2010)
Dev. Cell
, vol.19
, pp. 662-674
-
-
Banaszynski, L.A.1
Allis, C.D.2
Lewis, P.W.3
-
3
-
-
0037062492
-
Increased ionizing radiation sensitivity and genomic instability in the absence of histone H2AX
-
Bassing, C.H., Chua, K.F., Sekiguchi, J., Suh, H., Whitlow, S.R., Fleming, J.C., Monroe, B.C., Ciccone, D.N., Yan, C., Vlasakova, K., et al. (2002). Increased ionizing radiation sensitivity and genomic instability in the absence of histone H2AX. Proc. Natl. Acad. Sci. USA 99, 8173-8178.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 8173-8178
-
-
Bassing, C.H.1
Chua, K.F.2
Sekiguchi, J.3
Suh, H.4
Whitlow, S.R.5
Fleming, J.C.6
Monroe, B.C.7
Ciccone, D.N.8
Yan, C.9
Vlasakova, K.10
-
4
-
-
70350686180
-
SetDB1 contributes to repression of genes encoding developmental regulators and maintenance of ES cell state
-
Bilodeau, S., Kagey, M.H., Frampton, G.M., Rahl, P.B., and Young, R.A. (2009). SetDB1 contributes to repression of genes encoding developmental regulators and maintenance of ES cell state. Genes Dev. 23, 2484-2489.
-
(2009)
Genes Dev
, vol.23
, pp. 2484-2489
-
-
Bilodeau, S.1
Kagey, M.H.2
Frampton, G.M.3
Rahl, P.B.4
Young, R.A.5
-
5
-
-
33646870495
-
Genome-wide mapping of Polycomb target genes unravels their roles in cell fate transitions
-
Bracken, A.P., Dietrich, N., Pasini, D., Hansen, K.H., and Helin, K. (2006). Genome-wide mapping of Polycomb target genes unravels their roles in cell fate transitions. Genes Dev. 20, 1123-1136.
-
(2006)
Genes Dev
, vol.20
, pp. 1123-1136
-
-
Bracken, A.P.1
Dietrich, N.2
Pasini, D.3
Hansen, K.H.4
Helin, K.5
-
6
-
-
84861883921
-
Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk
-
Brinkman, A.B., Gu, H., Bartels, S.J.J., Zhang, Y., Matarese, F., Simmer, F., Marks, H., Bock, C., Gnirke, A., Meissner, A., and Stunnenberg, H.G. (2012). Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk. Genome Res. 22, 1128-1138.
-
(2012)
Genome Res
, vol.22
, pp. 1128-1138
-
-
Brinkman, A.B.1
Gu, H.2
Bartels, S.J.J.3
Zhang, Y.4
Matarese, F.5
Simmer, F.6
Marks, H.7
Bock, C.8
Gnirke, A.9
Meissner, A.10
Stunnenberg, H.G.11
-
7
-
-
84877978530
-
Mechanisms and models of somatic cell reprogramming
-
Buganim, Y., Faddah, D.A., and Jaenisch, R. (2013). Mechanisms and models of somatic cell reprogramming. Nat. Rev. Genet. 14, 427-439.
-
(2013)
Nat. Rev. Genet
, vol.14
, pp. 427-439
-
-
Buganim, Y.1
Faddah, D.A.2
Jaenisch, R.3
-
8
-
-
84878226536
-
Origins and implications of pluripotent stem cell variability and heterogeneity
-
Cahan, P., and Daley, G.Q. (2013). Origins and implications of pluripotent stem cell variability and heterogeneity. Nat. Rev. Mol. Cell Biol. 14, 357-368.
-
(2013)
Nat. Rev. Mol. Cell Biol
, vol.14
, pp. 357-368
-
-
Cahan, P.1
Daley, G.Q.2
-
9
-
-
0037012845
-
Genomic instability in mice lacking histone H2AX
-
Celeste, A., Petersen, S., Romanienko, P.J., Fernandez-Capetillo, O., Chen, H.T., Sedelnikova, O.A., Reina-San-Martin, B., Coppola, V., Meffre, E., Difilippantonio, M.J., et al. (2002). Genomic instability in mice lacking histone H2AX. Science 296, 922-927.
-
(2002)
Science
, vol.296
, pp. 922-927
-
-
Celeste, A.1
Petersen, S.2
Romanienko, P.J.3
Fernandez-Capetillo, O.4
Chen, H.T.5
Sedelnikova, O.A.6
Reina-San-Martin, B.7
Coppola, V.8
Meffre, E.9
Difilippantonio, M.J.10
-
10
-
-
84874781927
-
Cell reprogramming requires silencing of a core subset of polycomb targets
-
Fragola, G., Germain, P.-L., Laise, P., Cuomo, A., Blasimme, A., Gross, F., Signaroldi, E., Bucci, G., Sommer, C., Pruneri, G., et al. (2013). Cell reprogramming requires silencing of a core subset of polycomb targets. PLoS Genet. 9, e1003292.
-
(2013)
PLoS Genet
, vol.9
, pp. e1003292
-
-
Fragola, G.1
Germain, P.-L.2
Laise, P.3
Cuomo, A.4
Blasimme, A.5
Gross, F.6
Signaroldi, E.7
Bucci, G.8
Sommer, C.9
Pruneri, G.10
-
11
-
-
84875805512
-
Homologous recombination DNA repair genes play a critical role in reprogramming to a pluripotent state
-
González, F., Georgieva, D., Vanoli, F., Shi, Z.-D., Stadtfeld, M., Ludwig, T., Jasin, M., and Huangfu, D. (2013). Homologous recombination DNA repair genes play a critical role in reprogramming to a pluripotent state. Cell Reports 3, 651-660.
-
(2013)
Cell Reports
, vol.3
, pp. 651-660
-
-
González, F.1
Georgieva, D.2
Vanoli, F.3
Shi, Z.-D.4
Stadtfeld, M.5
Ludwig, T.6
Jasin, M.7
Huangfu, D.8
-
12
-
-
0033167121
-
Expression of Fgfr2 in the early mouse embryo indicates its involvement in preimplantation development
-
Haffner-Krausz, R., Gorivodsky, M., Chen, Y., and Lonai, P. (1999). Expression of Fgfr2 in the early mouse embryo indicates its involvement in preimplantation development. Mech. Dev. 85, 167-172.
-
(1999)
Mech. Dev
, vol.85
, pp. 167-172
-
-
Haffner-Krausz, R.1
Gorivodsky, M.2
Chen, Y.3
Lonai, P.4
-
13
-
-
77952567987
-
Simple combinations of lineagedetermining transcription factors prime cis-regulatory elements required for macrophage and B cell identities
-
Heinz, S., Benner, C., Spann, N., Bertolino, E., Lin, Y.C., Laslo, P., Cheng, J.X., Murre, C., Singh, H., and Glass, C.K. (2010). Simple combinations of lineagedetermining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576-589.
-
(2010)
Mol. Cell
, vol.38
, pp. 576-589
-
-
Heinz, S.1
Benner, C.2
Spann, N.3
Bertolino, E.4
Lin, Y.C.5
Laslo, P.6
Cheng, J.X.7
Murre, C.8
Singh, H.9
Glass, C.K.10
-
14
-
-
33746773659
-
Dissecting self-renewal in stem cells with RNA interference
-
Ivanova, N., Dobrin, R., Lu, R., Kotenko, I., Levorse, J., DeCoste, C., Schafer, X., Lun, Y., and Lemischka, I.R. (2006). Dissecting self-renewal in stem cells with RNA interference. Nature 442, 533-538.
-
(2006)
Nature
, vol.442
, pp. 533-538
-
-
Ivanova, N.1
Dobrin, R.2
Lu, R.3
Kotenko, I.4
Levorse, J.5
Decoste, C.6
Schafer, X.7
Lun, Y.8
Lemischka, I.R.9
-
15
-
-
79551587102
-
Tet1 and Tet2 regulate 5-hydroxymethylcytosine production and cell lineage specification in mouse embryonic stem cells
-
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). Tet1 and Tet2 regulate 5-hydroxymethylcytosine production and cell lineage specification in mouse embryonic stem cells. Cell Stem Cell 8, 200-213.
-
(2011)
Cell Stem Cell
, vol.8
, pp. 200-213
-
-
Koh, K.P.1
Yabuuchi, A.2
Rao, S.3
Huang, Y.4
Cunniff, K.5
Nardone, J.6
Laiho, A.7
Tahiliani, M.8
Sommer, C.A.9
Mostoslavsky, G.10
-
16
-
-
77953532417
-
Activation of the imprinted Dlk1-Dio3 region correlates with pluripotency levels of mouse stem cells
-
Liu, L., Luo, G.-Z., Yang, W., Zhao, X., Zheng, Q., Lv, Z., Li, W., Wu, H.-J., Wang, L., Wang, X.-J., and Zhou, Q. (2010). Activation of the imprinted Dlk1-Dio3 region correlates with pluripotency levels of mouse stem cells. J. Biol. Chem. 285, 19483-19490.
-
(2010)
J. Biol. Chem
, vol.285
, pp. 19483-19490
-
-
Liu, L.1
Luo, G.-Z.2
Yang, W.3
Zhao, X.4
Zheng, Q.5
Lv, Z.6
Li, W.7
Wu, H.-J.8
Wang, L.9
Wang, X.-J.10
Zhou, Q.11
-
17
-
-
0037381174
-
Genome imprinting regulated by the mouse Polycomb group protein Eed
-
Mager, J., Montgomery, N.D., de Villena, F.P.-M., and Magnuson, T. (2003). Genome imprinting regulated by the mouse Polycomb group protein Eed. Nat. Genet. 33, 502-507.
-
(2003)
Nat. Genet
, vol.33
, pp. 502-507
-
-
Mager, J.1
Montgomery, N.D.2
De Villena, F.P.-M.3
Magnuson, T.4
-
18
-
-
34547569191
-
STAMP: A web tool for exploring DNAbinding motif similarities
-
Mahony, S., and Benos, P.V. (2007). STAMP: a web tool for exploring DNAbinding motif similarities. Nucleic Acids Res. 35, W253-W258.
-
(2007)
Nucleic Acids Res
, vol.35
, pp. W253-W258
-
-
Mahony, S.1
Benos, P.V.2
-
19
-
-
69349094006
-
A p53-mediated DNA damage response limits reprogramming to ensure iPS cell genomic integrity
-
Marión, R.M., Strati, K., Li, H., Murga, M., Blanco, R., Ortega, S., Fernandez-Capetillo, O., Serrano, M., and Blasco, M.A. (2009). A p53-mediated DNA damage response limits reprogramming to ensure iPS cell genomic integrity. Nature 460, 1149-1153.
-
(2009)
Nature
, vol.460
, pp. 1149-1153
-
-
Marión, R.M.1
Strati, K.2
Li, H.3
Murga, M.4
Blanco, R.5
Ortega, S.6
Fernandez-Capetillo, O.7
Serrano, M.8
Blasco, M.A.9
-
20
-
-
77950862656
-
Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET
-
Matsui, T., Leung, D., Miyashita, H., Maksakova, I.A., Miyachi, H., Kimura, H., Tachibana, M., Lorincz, M.C., and Shinkai, Y. (2010). Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET. Nature 464, 927-931.
-
(2010)
Nature
, vol.464
, pp. 927-931
-
-
Matsui, T.1
Leung, D.2
Miyashita, H.3
Maksakova, I.A.4
Miyachi, H.5
Kimura, H.6
Tachibana, M.7
Lorincz, M.C.8
Shinkai, Y.9
-
21
-
-
84861397707
-
Picking ChIP-seq peak detectors for analyzing chromatin modification experiments
-
Micsinai, M., Parisi, F., Strino, F., Asp, P., Dynlacht, B.D., and Kluger, Y. (2012). Picking ChIP-seq peak detectors for analyzing chromatin modification experiments. Nucleic Acids Res. 40, e70.
-
(2012)
Nucleic Acids Res
, Issue.40
, pp. e70
-
-
Micsinai, M.1
Parisi, F.2
Strino, F.3
Asp, P.4
Dynlacht, B.D.5
Kluger, Y.6
-
22
-
-
84861912972
-
Overcoming reprogramming resistance of Fanconi anemia cells
-
Müller, L.U.W., Milsom, M.D., Harris, C.E., Vyas, R., Brumme, K.M., Parmar, K., Moreau, L.A., Schambach, A., Park, I.-H., London, W.B., et al. (2012). Overcoming reprogramming resistance of Fanconi anemia cells. Blood 119, 5449-5457.
-
(2012)
Blood
, vol.119
, pp. 5449-5457
-
-
Müller, L.U.W.1
Milsom, M.D.2
Harris, C.E.3
Vyas, R.4
Brumme, K.M.5
Parmar, K.6
Moreau, L.A.7
Schambach, A.8
Park, I.-H.9
London, W.B.10
-
23
-
-
79952219919
-
Single cell transcriptional profiling reveals heterogeneity of human induced pluripotent stem cells
-
Narsinh, K.H., Sun, N., Sanchez-Freire, V., Lee, A.S., Almeida, P., Hu, S., Jan, T., Wilson, K.D., Leong, D., Rosenberg, J., et al. (2011). Single cell transcriptional profiling reveals heterogeneity of human induced pluripotent stem cells. J. Clin. Invest. 121, 1217-1221.
-
(2011)
J. Clin. Invest
, vol.121
, pp. 1217-1221
-
-
Narsinh, K.H.1
Sun, N.2
Sanchez-Freire, V.3
Lee, A.S.4
Almeida, P.5
Hu, S.6
Jan, T.7
Wilson, K.D.8
Leong, D.9
Rosenberg, J.10
-
24
-
-
55549119925
-
Epigenetic restriction of embryonic cell lineage fate by methylation of Elf5
-
Ng, R.K., Dean, W., Dawson, C., Lucifero, D., Madeja, Z., Reik, W., and Hemberger, M. (2008). Epigenetic restriction of embryonic cell lineage fate by methylation of Elf5. Nat. Cell Biol. 10, 1280-1290.
-
(2008)
Nat. Cell Biol
, vol.10
, pp. 1280-1290
-
-
Ng, R.K.1
Dean, W.2
Dawson, C.3
Lucifero, D.4
Madeja, Z.5
Reik, W.6
Hemberger, M.7
-
25
-
-
70349325798
-
Uncovering early response of gene regulatory networks in ESCs by systematic induction of transcription factors
-
Nishiyama, A., Xin, L., Sharov, A.A., Thomas, M., Mowrer, G., Meyers, E., Piao, Y., Mehta, S., Yee, S., Nakatake, Y., et al. (2009). Uncovering early response of gene regulatory networks in ESCs by systematic induction of transcription factors. Cell Stem Cell 5, 420-433.
-
(2009)
Cell Stem Cell
, vol.5
, pp. 420-433
-
-
Nishiyama, A.1
Xin, L.2
Sharov, A.A.3
Thomas, M.4
Mowrer, G.5
Meyers, E.6
Piao, Y.7
Mehta, S.8
Yee, S.9
Nakatake, Y.10
-
26
-
-
0034028901
-
Quantitative expression of Oct-3/4 defines differentiation, dedifferentiation or self-renewal of ES cells
-
Niwa, H., Miyazaki, J., and Smith, A.G. (2000). Quantitative expression of Oct-3/4 defines differentiation, dedifferentiation or self-renewal of ES cells. Nat. Genet. 24, 372-376.
-
(2000)
Nat. Genet
, vol.24
, pp. 372-376
-
-
Niwa, H.1
Miyazaki, J.2
Smith, A.G.3
-
27
-
-
28344436489
-
Interaction between Oct3/4 and Cdx2 determines trophectoderm differentiation
-
Niwa, H., Toyooka, Y., Shimosato, D., Strumpf, D., Takahashi, K., Yagi, R., and Rossant, J. (2005). Interaction between Oct3/4 and Cdx2 determines trophectoderm differentiation. Cell 123, 917-929.
-
(2005)
Cell
, vol.123
, pp. 917-929
-
-
Niwa, H.1
Toyooka, Y.2
Shimosato, D.3
Strumpf, D.4
Takahashi, K.5
Yagi, R.6
Rossant, J.7
-
28
-
-
33751407923
-
Trophoblast stem cells
-
Oda, M., Shiota, K., and Tanaka, S. (2006). Trophoblast stem cells. Methods Enzymol. 419, 387-400.
-
(2006)
Methods Enzymol
, vol.419
, pp. 387-400
-
-
Oda, M.1
Shiota, K.2
Tanaka, S.3
-
29
-
-
79958252915
-
Chromatin connections to pluripotency and cellular reprogramming
-
Orkin, S.H., and Hochedlinger, K. (2011). Chromatin connections to pluripotency and cellular reprogramming. Cell 145, 835-850.
-
(2011)
Cell
, vol.145
, pp. 835-850
-
-
Orkin, S.H.1
Hochedlinger, K.2
-
30
-
-
79951516056
-
A unique chromatin signature uncovers early developmental enhancers in humans
-
Rada-Iglesias, A., Bajpai, R., Swigut, T., Brugmann, S.A., Flynn, R.A., and Wysocka, J. (2011). A unique chromatin signature uncovers early developmental enhancers in humans. Nature 470, 279-283.
-
(2011)
Nature
, vol.470
, pp. 279-283
-
-
Rada-Iglesias, A.1
Bajpai, R.2
Swigut, T.3
Brugmann, S.A.4
Flynn, R.A.5
Wysocka, J.6
-
31
-
-
74349118193
-
Gata3 regulates trophoblast development downstream of Tead4 and in parallel to Cdx2
-
Ralston, A., Cox, B.J., Nishioka, N., Sasaki, H., Chea, E., Rugg-Gunn, P., Guo, G., Robson, P., Draper, J.S., and Rossant, J. (2010). Gata3 regulates trophoblast development downstream of Tead4 and in parallel to Cdx2. Development 137, 395-403.
-
(2010)
Development
, vol.137
, pp. 395-403
-
-
Ralston, A.1
Cox, B.J.2
Nishioka, N.3
Sasaki, H.4
Chea, E.5
Rugg-Gunn, P.6
Guo, G.7
Robson, P.8
Draper, J.S.9
Rossant, J.10
-
32
-
-
0036531895
-
Histone H2A variants H2AX and H2AZ
-
Redon, C., Pilch, D., Rogakou, E., Sedelnikova, O., Newrock, K., and Bonner, W. (2002). Histone H2A variants H2AX and H2AZ. Curr. Opin. Genet. Dev. 12, 162-169.
-
(2002)
Curr. Opin. Genet. Dev
, vol.12
, pp. 162-169
-
-
Redon, C.1
Pilch, D.2
Rogakou, E.3
Sedelnikova, O.4
Newrock, K.5
Bonner, W.6
-
33
-
-
33845985573
-
Stem cells and lineage development in the mammalian blastocyst
-
Rossant, J. (2007). Stem cells and lineage development in the mammalian blastocyst. Reprod. Fertil. Dev. 19, 111-118.
-
(2007)
Reprod. Fertil. Dev
, vol.19
, pp. 111-118
-
-
Rossant, J.1
-
34
-
-
79952598545
-
Identifying dispersed epigenomic domains from ChIP-Seq data
-
Song, Q., and Smith, A.D. (2011). Identifying dispersed epigenomic domains from ChIP-Seq data. Bioinformatics 27, 870-871.
-
(2011)
Bioinformatics
, vol.27
, pp. 870-871
-
-
Song, Q.1
Smith, A.D.2
-
35
-
-
77952425747
-
Aberrant silencing of imprinted genes on chromosome 12qF1 in mouse induced pluripotent stem cells
-
Stadtfeld, M., Apostolou, E., Akutsu, H., Fukuda, A., Follett, P., Natesan, S., Kono, T., Shioda, T., and Hochedlinger, K. (2010a). Aberrant silencing of imprinted genes on chromosome 12qF1 in mouse induced pluripotent stem cells. Nature 465, 175-181.
-
(2010)
Nature
, vol.465
, pp. 175-181
-
-
Stadtfeld, M.1
Apostolou, E.2
Akutsu, H.3
Fukuda, A.4
Follett, P.5
Natesan, S.6
Kono, T.7
Shioda, T.8
Hochedlinger, K.9
-
36
-
-
74049138336
-
A reprogrammable mouse strain from gene-targeted embryonic stem cells
-
Stadtfeld, M., Maherali, N., Borkent, M., and Hochedlinger, K. (2010b). A reprogrammable mouse strain from gene-targeted embryonic stem cells. Nat. Methods 7, 53-55.
-
(2010)
Nat. Methods
, vol.7
, pp. 53-55
-
-
Stadtfeld, M.1
Maherali, N.2
Borkent, M.3
Hochedlinger, K.4
-
37
-
-
19744365010
-
Cdx2 is required for correct cell fate specification and differentiation of trophectoderm in the mouse blastocyst
-
Strumpf, D., Mao, C.-A., Yamanaka, Y., Ralston, A., Chawengsaksophak, K., Beck, F., and Rossant, J. (2005). Cdx2 is required for correct cell fate specification and differentiation of trophectoderm in the mouse blastocyst. Development 132, 2093-2102.
-
(2005)
Development
, vol.132
, pp. 2093-2102
-
-
Strumpf, D.1
Mao, C.-A.2
Yamanaka, Y.3
Ralston, A.4
Chawengsaksophak, K.5
Beck, F.6
Rossant, J.7
-
38
-
-
70350686165
-
Eset partners with Oct4 to restrict extraembryonic trophoblast lineage potential in embryonic stem cells
-
Yuan, P., Han, J., Guo, G., Orlov, Y.L., Huss, M., Loh, Y.-H., Yaw, L.-P., Robson, P., Lim, B., and Ng, H.-H. (2009). Eset partners with Oct4 to restrict extraembryonic trophoblast lineage potential in embryonic stem cells. Genes Dev. 23, 2507-2520.
-
(2009)
Genes Dev
, vol.23
, pp. 2507-2520
-
-
Yuan, P.1
Han, J.2
Guo, G.3
Orlov, Y.L.4
Huss, M.5
Loh, Y.-H.6
Yaw, L.-P.7
Robson, P.8
Lim, B.9
Ng, H.-H.10
|