-
1
-
-
34447295350
-
Characterization of human embryonic stem cell lines by the International Stem Cell Initiative
-
Adewumi, O., Aflatoonian, B., and Ahrlund-Richter, L. (2007). Characterization of human embryonic stem cell lines by the International Stem Cell Initiative. Nature 25, 803-816.
-
(2007)
Nature
, vol.25
, pp. 803-816
-
-
Adewumi, O.1
Aflatoonian, B.2
Ahrlund-Richter, L.3
-
2
-
-
80955179571
-
Stem cells and reprogramming: breaking the epigenetic barrier?
-
Ang, Y. -S., Gaspar-Maia, A., Lemischka, I. R., and Bernstein, E. (2011). Stem cells and reprogramming: breaking the epigenetic barrier? Trends Pharmacol. Sci. 32, 394-401.
-
(2011)
Trends Pharmacol. Sci.
, vol.32
, pp. 394-401
-
-
Ang, Y.-S.1
Gaspar-Maia, A.2
Lemischka, I.R.3
Bernstein, E.4
-
3
-
-
77954647251
-
A model for genetic and epigenetic regulatory networks identifies rare pathways for transcription factor induced pluripotency
-
doi:10.1371/journal.pcbi.1000785
-
Artyomov, M., Meissner, A., and Chakraborty, A. (2010). A model for genetic and epigenetic regulatory networks identifies rare pathways for transcription factor induced pluripotency. PLoS Comput. Biol. 6, e1000785. doi:10.1371/journal.pcbi.1000785
-
(2010)
PLoS Comput. Biol.
, vol.6
-
-
Artyomov, M.1
Meissner, A.2
Chakraborty, A.3
-
4
-
-
79957461243
-
A deterministic map of Waddington's epigenetic landscape for cell fate specification
-
doi:10.1186/1752-0509-5-85
-
Bhattacharya, S., Zhang, Q., and Andersen, M. E. (2011). A deterministic map of Waddington's epigenetic landscape for cell fate specification. BMC Syst. Biol. 5, 85. doi:10.1186/1752-0509-5-85
-
(2011)
BMC Syst. Biol.
, vol.5
, pp. 85
-
-
Bhattacharya, S.1
Zhang, Q.2
Andersen, M.E.3
-
5
-
-
80052933429
-
DNA Demethylation dynamics
-
Bhutani, N., Burns, D., and Blau, H. (2011). DNA Demethylation dynamics. Cell 146, 866-872.
-
(2011)
Cell
, vol.146
, pp. 866-872
-
-
Bhutani, N.1
Burns, D.2
Blau, H.3
-
6
-
-
25144525014
-
Core transcriptional regulatory circuitry in human embryonic stem cells
-
Boyer, L. A., Lee, T. I., Cole, M. F., Johnstone, S. E., Levine, S. S., Zucker, J. P., Guenther, M. G., Kumar, R. M., Murray, H. L., Jenner, R. G., Gifford, D. K., Melton, D. A., Jaenisch, R., and Young, R. A. (2005). Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 122, 947-956.
-
(2005)
Cell
, vol.122
, pp. 947-956
-
-
Boyer, L.A.1
Lee, T.I.2
Cole, M.F.3
Johnstone, S.E.4
Levine, S.S.5
Zucker, J.P.6
Guenther, M.G.7
Kumar, R.M.8
Murray, H.L.9
Jenner, R.G.10
Gifford, D.K.11
Melton, D.A.12
Jaenisch, R.13
Young, R.A.14
-
7
-
-
67349190247
-
Linking DNA methylation and histone modification: patterns and paradigms
-
Cedar, H., and Bergman, Y. (2009). Linking DNA methylation and histone modification: patterns and paradigms. Nat. Rev. Genet. 10, 295-304.
-
(2009)
Nat. Rev. Genet.
, vol.10
, pp. 295-304
-
-
Cedar, H.1
Bergman, Y.2
-
8
-
-
84855274655
-
Systematic search for recipes to generate induced pluripotent stem cells
-
doi:10.1371/journal.pcbi.1002300
-
Chang, R., Shoemaker, R., and Wang, W. (2011). Systematic search for recipes to generate induced pluripotent stem cells. PLoS Comput. Biol. 7, e1002300. doi:10.1371/journal.pcbi.1002300
-
(2011)
PLoS Comput. Biol.
, vol.7
-
-
Chang, R.1
Shoemaker, R.2
Wang, W.3
-
9
-
-
67949100470
-
In silico identification of a core regulatory network of OCT4 in human embryonic stem cells using an integrated approach
-
doi:10.1186/1471-2164-10-314
-
Chavez, L., Bais, A., Vingron, M., Lehrach, H., Adjaye, J., and Herwig, R. (2009). In silico identification of a core regulatory network of OCT4 in human embryonic stem cells using an integrated approach. BMC Genomics 10, 314. doi:10.1186/1471-2164-10-314
-
(2009)
BMC Genomics
, vol.10
, pp. 314
-
-
Chavez, L.1
Bais, A.2
Vingron, M.3
Lehrach, H.4
Adjaye, J.5
Herwig, R.6
-
10
-
-
55649104699
-
A computational model for understanding stem cell, trophectoderm and endoderm lineage determination
-
doi:10.1371/journal.pone.0003478
-
Chickarmane, V., and Peterson, C. (2008). A computational model for understanding stem cell, trophectoderm and endoderm lineage determination. PLoS ONE 3, e3478. doi:10.1371/journal.pone.0003478
-
(2008)
PLoS ONE
, vol.3
-
-
Chickarmane, V.1
Peterson, C.2
-
11
-
-
33749350211
-
Transcriptional dynamics of the embryonic stem cell switch
-
doi:10.1371/journal.pcbi.0020123
-
Chickarmane, V., Troein, C., and Nuber, U. (2006). Transcriptional dynamics of the embryonic stem cell switch. PLoS Comput. Biol. 2, e123. doi:10.1371/journal.pcbi.0020123
-
(2006)
PLoS Comput. Biol.
, vol.2
-
-
Chickarmane, V.1
Troein, C.2
Nuber, U.3
-
12
-
-
79951859664
-
Epigenetics of induced pluripotency, the seven-headed dragon
-
Djuric, U., and Ellis, J. (2010). Epigenetics of induced pluripotency, the seven-headed dragon. Stem Cell Res. Ther. 1, 3.
-
(2010)
Stem Cell Res. Ther.
, vol.1
, pp. 3
-
-
Djuric, U.1
Ellis, J.2
-
13
-
-
34249080596
-
Theoretical analysis of epigenetic cell memory by nucleosome modification
-
Dodd, I. B., Micheelsen, M. A., Sneppen, K., and Thon, G. (2007). Theoretical analysis of epigenetic cell memory by nucleosome modification. Cell 129, 813-822.
-
(2007)
Cell
, vol.129
, pp. 813-822
-
-
Dodd, I.B.1
Micheelsen, M.A.2
Sneppen, K.3
Thon, G.4
-
14
-
-
84855644327
-
Mathematical modelling of stem cell differentiation: the PU. 1-GATA-1 interaction
-
Duff, C., Smith-Miles, K., Lopes, L., and Tian, T. (2012). Mathematical modelling of stem cell differentiation: the PU. 1-GATA-1 interaction. J. Math. Biol. 64, 449-468.
-
(2012)
J. Math. Biol.
, vol.64
, pp. 449-468
-
-
Duff, C.1
Smith-Miles, K.2
Lopes, L.3
Tian, T.4
-
15
-
-
55549145072
-
De novo DNA methylation promoted by G9a prevents reprogramming of embryonically silenced genes
-
Epsztejn-Litman, S., Feldman, N., Abu-Remaileh, M., Shufaro, Y., Gerson, A., Ueda, J., Deplus, R., Fuks, F., Shinkai, Y., Cedar, H., and Bergman, Y (2008). De novo DNA methylation promoted by G9a prevents reprogramming of embryonically silenced genes. Nat. Struct. Mol. Biol. 15, 1176-1183.
-
(2008)
Nat. Struct. Mol. Biol.
, vol.15
, pp. 1176-1183
-
-
Epsztejn-Litman, S.1
Feldman, N.2
Abu-Remaileh, M.3
Shufaro, Y.4
Gerson, A.5
Ueda, J.6
Deplus, R.7
Fuks, F.8
Shinkai, Y.9
Cedar, H.10
Bergman, Y.11
-
16
-
-
0034330420
-
Nuclear compartmentalization and gene activity
-
Francastel, C., Schuebeler, D., Martin, D. I., and Groudine, M. (2000). Nuclear compartmentalization and gene activity. Nat. Rev. Mol. Cell Biol. 1, 137-143.
-
(2000)
Nat. Rev. Mol. Cell Biol.
, vol.1
, pp. 137-143
-
-
Francastel, C.1
Schuebeler, D.2
Martin, D.I.3
Groudine, M.4
-
17
-
-
0033988813
-
DNA methyltransferase Dnmt1 associates with histone deacetylase activity
-
Fuks, F., Burgers, W. A., Brehm, A., Hughes-Davies, L., and Kouzarides, T. (2000). DNA methyltransferase Dnmt1 associates with histone deacetylase activity. Nat. Genet. 24, 88-91.
-
(2000)
Nat. Genet.
, vol.24
, pp. 88-91
-
-
Fuks, F.1
Burgers, W.A.2
Brehm, A.3
Hughes-Davies, L.4
Kouzarides, T.5
-
18
-
-
66349086263
-
Modeling stochasticity and robustness in gene regulatory networks
-
Garg, A., Mohanram, K., Di Cara, A., De Micheli, G., and Xenarios, I. (2009). Modeling stochasticity and robustness in gene regulatory networks. Bioinformatics 25, i101-i109.
-
(2009)
Bioinformatics
, vol.25
-
-
Garg, A.1
Mohanram, K.2
Di Cara, A.3
De Micheli, G.4
Xenarios, I.5
-
19
-
-
67349092536
-
Stem cell decision making and critical-like exploratory networks
-
Halley, J. D., Burden, E R., and Winkler, D. A. (2009). Stem cell decision making and critical-like exploratory networks. Stem Cell Res. 2, 165-177.
-
(2009)
Stem Cell Res.
, vol.2
, pp. 165-177
-
-
Halley, J.D.1
Burden, E.R.2
Winkler, D.A.3
-
20
-
-
71449109765
-
Direct cell reprogramming is a stochastic process amenable to acceleration
-
Hanna, J., Saha, K., Pando, B., van Zon, J., Lengner, C. J., Creyghton, M. P., van Oudenaarden, A., and Jaenisch, R. (2009). Direct cell reprogramming is a stochastic process amenable to acceleration. Nature 462, 595-601.
-
(2009)
Nature
, vol.462
, pp. 595-601
-
-
Hanna, J.1
Saha, K.2
Pando, B.3
van Zon, J.4
Lengner, C.J.5
Creyghton, M.P.6
van Oudenaarden, A.7
Jaenisch, R.8
-
21
-
-
0038243168
-
The role of DNA methylation in setting up chromatin structure during development
-
Hashimshony, T., Zhang, J., Keshet, I., Bustin, M., and Cedar, H. (2003). The role of DNA methylation in setting up chromatin structure during development. Nat. Genet. 34, 187-192.
-
(2003)
Nat. Genet.
, vol.34
, pp. 187-192
-
-
Hashimshony, T.1
Zhang, J.2
Keshet, I.3
Bustin, M.4
Cedar, H.5
-
22
-
-
77953809032
-
Distinct epigenomic landscapes of pluripotent and lineage-committed human cells
-
Hawkins, R. D., Hon, G. C., Lee, L. K., Ngo, Q., Lister, R., Pelizzola, M., Edsall, L. E., Kuan, S., Luu, Y., and Klugman, S. (2010). Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell 6, 479-491.
-
(2010)
Cell Stem Cell
, vol.6
, pp. 479-491
-
-
Hawkins, R.D.1
Hon, G.C.2
Lee, L.K.3
Ngo, Q.4
Lister, R.5
Pelizzola, M.6
Edsall, L.E.7
Kuan, S.8
Luu, Y.9
Klugman, S.10
-
23
-
-
69349100179
-
Suppression of induced pluripotent stem cell generation by the p53-p21 pathway
-
Hong, H., Takahashi, K., Ichisaka, T., Aoi, T., Kanagawa, O., Nakagawa, M., Okita, K., and Yamanaka, S. (2009). Suppression of induced pluripotent stem cell generation by the p53-p21 pathway. Nature 460, 1132-1135.
-
(2009)
Nature
, vol.460
, pp. 1132-1135
-
-
Hong, H.1
Takahashi, K.2
Ichisaka, T.3
Aoi, T.4
Kanagawa, O.5
Nakagawa, M.6
Okita, K.7
Yamanaka, S.8
-
24
-
-
55549127205
-
Retroviral vector silencing during iPS cell induction: an epigenetic beacon that signals distinct pluripotent states
-
Hotta, A., and Ellis, J. (2008). Retroviral vector silencing during iPS cell induction: an epigenetic beacon that signals distinct pluripotent states. J. Cell. Biochem. 105, 940-948.
-
(2008)
J. Cell. Biochem.
, vol.105
, pp. 940-948
-
-
Hotta, A.1
Ellis, J.2
-
25
-
-
34248199004
-
Bifurcation dynamics in lineage-commitment in bipotent progenitor cells
-
Huang, S., Guo, Y. -P., May, G., and Enver, T. (2007). Bifurcation dynamics in lineage-commitment in bipotent progenitor cells. Dev. Biol. 305, 695-713.
-
(2007)
Dev. Biol.
, vol.305
, pp. 695-713
-
-
Huang, S.1
Guo, Y.-P.2
May, G.3
Enver, T.4
-
26
-
-
46949085597
-
Induction of pluripotent stem cells by defined factors is greatly improved by small-molecule compounds
-
Huangfu, D., Maehr, R., Guo, W., Eijkelenboom, A., Snitow, M., Chen, A. E., and Melton, D. A. (2008). Induction of pluripotent stem cells by defined factors is greatly improved by small-molecule compounds. Nat. Biotechnol. 26, 795-797.
-
(2008)
Nat. Biotechnol.
, vol.26
, pp. 795-797
-
-
Huangfu, D.1
Maehr, R.2
Guo, W.3
Eijkelenboom, A.4
Snitow, M.5
Chen, A.E.6
Melton, D.A.7
-
27
-
-
70350536767
-
A small-molecule inhibitor of Tgf-[beta] signaling replaces Sox2 in reprogramming by inducing NANOG
-
Ichida, J. K., Blanchard, J., Lam, K., Son, E. Y., Chung, J. E., Egli, D., Loh, K. M., Carter, A. C., Di Giorgio, F. P., Koszka, K., Huangfu, D., Akutsu, H., Liu, D. R., Rubin, L. L., and Eggan, K. (2009). A small-molecule inhibitor of Tgf-[beta] signaling replaces Sox2 in reprogramming by inducing NANOG. Cell Stem Cell 5, 491-503.
-
(2009)
Cell Stem Cell
, vol.5
, pp. 491-503
-
-
Ichida, J.K.1
Blanchard, J.2
Lam, K.3
Son, E.Y.4
Chung, J.E.5
Egli, D.6
Loh, K.M.7
Carter, A.C.8
Di Giorgio, F.P.9
Koszka, K.10
Huangfu, D.11
Akutsu, H.12
Liu, D.R.13
Rubin, L.L.14
Eggan, K.15
-
28
-
-
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
-
29
-
-
68049139696
-
Regulated fluctuations in NANOG expression mediate cell fate decisions in embryonic stem cells
-
doi:10.1371/journal.pbio.1000149
-
Kalmar, T., Lim, C., Hayward, P., Muñoz-Descalzo, S., Nichols, J., Garcia-Ojalvo, J., and Arias, A. M. (2009). Regulated fluctuations in NANOG expression mediate cell fate decisions in embryonic stem cells. PLoS Biol. 7, e1000149. doi:10.1371/journal.pbio.1000149
-
(2009)
PLoS Biol.
, vol.7
-
-
Kalmar, T.1
Lim, C.2
Hayward, P.3
Muñoz-Descalzo, S.4
Nichols, J.5
Garcia-Ojalvo, J.6
Arias, A.M.7
-
30
-
-
4444311806
-
A proposal for using the ensemble approach to understand genetic regulatory networks
-
Kauffman, S. (2004). A proposal for using the ensemble approach to understand genetic regulatory networks. J. Theor. Biol. 230, 581-590.
-
(2004)
J. Theor. Biol.
, vol.230
, pp. 581-590
-
-
Kauffman, S.1
-
31
-
-
69349100455
-
Linking the p53 tumour suppressor pathway to somatic cell reprogramming
-
Kawamura, T., Suzuki, J., Wang, Y. V., Menendez, S., Morera, L. B., Raya, A., Wahl, G. M., and Belmonte, J. C. I. (2009). Linking the p53 tumour suppressor pathway to somatic cell reprogramming. Nature 460, 1140-1144.
-
(2009)
Nature
, vol.460
, pp. 1140-1144
-
-
Kawamura, T.1
Suzuki, J.2
Wang, Y.V.3
Menendez, S.4
Morera, L.B.5
Raya, A.6
Wahl, G.M.7
Belmonte, J.C.I.8
-
32
-
-
77649267695
-
Dynamic changes in the human methylome during differentiation
-
Laurent, L., Wong, E., Li, G., Huynh, T., Tsirigos, A., Ong, C. T., Low, H. M., Kin Sung, K. W., Rigoutsos, I., Loring, J., and Wei, C. -L. (2010). Dynamic changes in the human methylome during differentiation. Genome Res. 20, 320-331.
-
(2010)
Genome Res.
, vol.20
, pp. 320-331
-
-
Laurent, L.1
Wong, E.2
Li, G.3
Huynh, T.4
Tsirigos, A.5
Ong, C.T.6
Low, H.M.7
Kin Sung, K.W.8
Rigoutsos, I.9
Loring, J.10
Wei, C.-L.11
-
33
-
-
0026708177
-
Targeted mutation of the DNA methyltransferase gene results in embryonic lethality
-
Li, E., Bestor, T. H., and Jaenisch, R. (1992). Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 69, 915-926.
-
(1992)
Cell
, vol.69
, pp. 915-926
-
-
Li, E.1
Bestor, T.H.2
Jaenisch, R.3
-
34
-
-
44649086468
-
NANOG and oct4 associate with unique transcriptional repression complexes in embryonic stem cells
-
Liang, J., Wan, M., Zhang, Y., Gu, P., Xin, H., Jung, S. Y., Qin, J., Wong, J., Cooney, A. J., Liu, D., and Songyang, Z. (2008). NANOG and oct4 associate with unique transcriptional repression complexes in embryonic stem cells. Nat. Cell Biol. 10, 731-739.
-
(2008)
Nat. Cell Biol.
, vol.10
, pp. 731-739
-
-
Liang, J.1
Wan, M.2
Zhang, Y.3
Gu, P.4
Xin, H.5
Jung, S.Y.6
Qin, J.7
Wong, J.8
Cooney, A.J.9
Liu, D.10
Songyang, Z.11
-
35
-
-
70450217879
-
Human DNA methylomes at base resolution show widespread epigenomic differences
-
Lister, R., Pelizzola, M., Dowen, R. H., Hawkins, R. D., Hon, G., Tonti-Filippini, J., Nery, J. R., Lee, L., Ye, Z., Ngo, Q. -M., Edsall, L., Antosiewicz-Bourget, J., Stewart, R., Ruotti, V., Millar, A. H., Thomson, J. A., Ren, B., and Ecker, J. R. (2009). Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462, 315-322.
-
(2009)
Nature
, vol.462
, pp. 315-322
-
-
Lister, R.1
Pelizzola, M.2
Dowen, R.H.3
Hawkins, R.D.4
Hon, G.5
Tonti-Filippini, J.6
Nery, J.R.7
Lee, L.8
Ye, Z.9
Ngo, Q.-M.10
Edsall, L.11
Antosiewicz-Bourget, J.12
Stewart, R.13
Ruotti, V.14
Millar, A.H.15
Thomson, J.A.16
Ren, B.17
Ecker, J.R.18
-
36
-
-
79952264847
-
Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells
-
Lister, R., Pelizzola, M., Kida, Y. S., Hawkins, R. D., Nery, J. R., Hon, G., Antosiewicz-Bourget, J., O'Malley, R., Castanon, R., Klugman, S., Downes, M., Yu, R., Stewart, R., Ren, B., Thomson, J. A., Evans, R. M., and Ecker, J. R. (2011). Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature 471, 68-73.
-
(2011)
Nature
, vol.471
, pp. 68-73
-
-
Lister, R.1
Pelizzola, M.2
Kida, Y.S.3
Hawkins, R.D.4
Nery, J.R.5
Hon, G.6
Antosiewicz-Bourget, J.7
O'Malley, R.8
Castanon, R.9
Klugman, S.10
Downes, M.11
Yu, R.12
Stewart, R.13
Ren, B.14
Thomson, J.A.15
Evans, R.M.16
Ecker, J.R.17
-
37
-
-
33645381936
-
The Oct4 and NANOG transcription network regulates pluripotency in mouse embryonic stem cells
-
Loh, Y. -H., Wu, Q., Chew, J. -L., Vega, V. B., Zhang, W., Chen, X., Bourque, G., George, J., Leong, B., Liu, J., Wong, K. -Y., Sung, K. W., Lee, C. W H., Zhao, X. -D., Chiu, K. -P., Lipovich, L., Kuznetsov, V. A., Robson, P., Stanton, L. W., Wei, C. -L., Ruan, Y., Lim, B., and Ng, H. -H. (2006). The Oct4 and NANOG transcription network regulates pluripotency in mouse embryonic stem cells. Nat. Genet. 38, 431-440.
-
(2006)
Nat. Genet.
, vol.38
, pp. 431-440
-
-
Loh, Y.-H.1
Wu, Q.2
Chew, J.-L.3
Vega, V.B.4
Zhang, W.5
Chen, X.6
Bourque, G.7
George, J.8
Leong, B.9
Liu, J.10
Wong, K.-Y.11
Sung, K.W.12
Lee, C.W.H.13
Zhao, X.-D.14
Chiu, K.-P.15
Lipovich, L.16
Kuznetsov, V.A.17
Robson, P.18
Stanton, L.W.19
Wei, C.-L.20
Ruan, Y.21
Lim, B.22
Ng, H.-H.23
more..
-
38
-
-
52649162487
-
Stochasticity and the molecular mechanisms of induced pluripotency
-
doi:10.1371/journal.pone.0003086
-
MacArthur, B., and Please, C. (2008). Stochasticity and the molecular mechanisms of induced pluripotency. PLoS ONE 3, e3086. doi:10.1371/journal.pone.0003086
-
(2008)
PLoS ONE
, vol.3
-
-
MacArthur, B.1
Please, C.2
-
39
-
-
52649162487
-
Stochasticity and the molecular mechanisms of induced pluripotency
-
doi:10.1371/journal.pone.0003086
-
MacArthur, B. D., Please, C. P., and Oreffo, R. O. C. (2008). Stochasticity and the molecular mechanisms of induced pluripotency. PLoS ONE 3, e3086. doi:10.1371/journal.pone.0003086
-
(2008)
PLoS ONE
, vol.3
-
-
MacArthur, B.D.1
Please, C.P.2
Oreffo, R.O.C.3
-
40
-
-
70349559776
-
Why are cellular switches Boolean? General conditions for multistable genetic circuits
-
Macía, J., Widder, S., andSolé, R. (2009). Why are cellular switches Boolean? General conditions for multistable genetic circuits. J. Theor. Biol. 261, 126-135.
-
(2009)
J. Theor. Biol.
, vol.261
, pp. 126-135
-
-
Macía, J.1
Widder, S.2
Solé, R.3
-
41
-
-
80052314331
-
Molecular insights into reprogramming-initiation events mediated by the OSKM gene regulatory network
-
doi:10.1371/journal.pone.0024351
-
Mah, N., Wang, Y., Liao, M. -C., Prigione, A., Jozefczuk, J., Lichtner, B., Wolfrum, K., Haltmeier, M., Flöttmann, M., Schaefer, M., Hahn, A., Mrowka, R., Klipp, E., Andrade-Navarro, M. A., and Adjaye, J. (2011). Molecular insights into reprogramming-initiation events mediated by the OSKM gene regulatory network. PLoS ONE 6, e24351. doi:10.1371/journal.pone.0024351
-
(2011)
PLoS ONE
, vol.6
-
-
Mah, N.1
Wang, Y.2
Liao, M.-C.3
Prigione, A.4
Jozefczuk, J.5
Lichtner, B.6
Wolfrum, K.7
Haltmeier, M.8
Flöttmann, M.9
Schaefer, M.10
Hahn, A.11
Mrowka, R.12
Klipp, E.13
Andrade-Navarro, M.A.14
Adjaye, J.15
-
42
-
-
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
-
43
-
-
29744447772
-
Hyperdynamic plasticity of chromatin proteins in pluripotent embryonic stem cells
-
Meshorer, E., Yellajoshula, D., George, E., Scambler, P. J., Brown, D. T., and Misteli, T. (2006). Hyperdynamic plasticity of chromatin proteins in pluripotent embryonic stem cells. Dev. Cell 10, 105-116.
-
(2006)
Dev. Cell
, vol.10
, pp. 105-116
-
-
Meshorer, E.1
Yellajoshula, D.2
George, E.3
Scambler, P.J.4
Brown, D.T.5
Misteli, T.6
-
44
-
-
46449094276
-
Dissecting direct reprogramming through integrative genomic analysis
-
Mikkelsen, T. S., Hanna, J., Zhang, X., Ku, M., Wernig, M., Schorderet, P., Bernstein, B. E., Jaenisch, R., Lander, E. S., and Meissner, A. (2008). Dissecting direct reprogramming through integrative genomic analysis. Nature 454, 49-55.
-
(2008)
Nature
, vol.454
, pp. 49-55
-
-
Mikkelsen, T.S.1
Hanna, J.2
Zhang, X.3
Ku, M.4
Wernig, M.5
Schorderet, P.6
Bernstein, B.E.7
Jaenisch, R.8
Lander, E.S.9
Meissner, A.10
-
45
-
-
0025802792
-
Decrease in DNA methylase activity during preimplantation development in the mouse
-
Monk, M., Adams, R. L., and Rinaldi, A. (1991). Decrease in DNA methylase activity during preimplantation development in the mouse. Development 112, 189-192.
-
(1991)
Development
, vol.112
, pp. 189-192
-
-
Monk, M.1
Adams, R.L.2
Rinaldi, A.3
-
46
-
-
77952851181
-
BoolNet - an R package for generation, reconstruction, and analysis of Boolean networks
-
Müssel, C., Hopfensitz, M., and Kestler, H. A. (2010). BoolNet - an R package for generation, reconstruction, and analysis of Boolean networks. Bioinformatics 26, 1378-1380.
-
(2010)
Bioinformatics
, vol.26
, pp. 1378-1380
-
-
Müssel, C.1
Hopfensitz, M.2
Kestler, H.A.3
-
47
-
-
0033983960
-
A GATA box in the GATA-1 gene hematopoietic enhancer is a critical element in the network of GATA factors and sites that regulate this gene
-
Nishimura, S., Takahashi, S., Kuroha, T., Suwabe, N., Nagasawa, T., and Trainor, C. (2000). A GATA box in the GATA-1 gene hematopoietic enhancer is a critical element in the network of GATA factors and sites that regulate this gene. Mol. Cell. Biol. 20, 713-723.
-
(2000)
Mol. Cell. Biol.
, vol.20
, pp. 713-723
-
-
Nishimura, S.1
Takahashi, S.2
Kuroha, T.3
Suwabe, N.4
Nagasawa, T.5
Trainor, C.6
-
48
-
-
79957998057
-
DNA Methylation Dynamics in Human Induced Pluripotent Stem Cells over Time
-
doi:10.1371/journal.pgen.1002085
-
Nishino, K., Toyoda, M., Yamazaki-Inoue, M., Fukawatase, Y., Chikazawa, E., Sakaguchi, H., Akutsu, H., and Umezawa, A. (2011). DNA Methylation Dynamics in Human Induced Pluripotent Stem Cells over Time. PLoS Genet. 7, e1002085. doi:10.1371/journal.pgen.1002085
-
(2011)
PLoS Genet.
, vol.7
-
-
Nishino, K.1
Toyoda, M.2
Yamazaki-Inoue, M.3
Fukawatase, Y.4
Chikazawa, E.5
Sakaguchi, H.6
Akutsu, H.7
Umezawa, A.8
-
49
-
-
33947308285
-
How is pluripotency determined and maintained?
-
Niwa, H. (2007). How is pluripotency determined and maintained? Development 134, 635-646.
-
(2007)
Development
, vol.134
, pp. 635-646
-
-
Niwa, H.1
-
50
-
-
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
-
51
-
-
55849117368
-
Generation of mouse induced pluripotent stem cells without viral vectors
-
Okita, K., Nakagawa, M., Hyenjong, H., Ichisaka, T., and Yamanaka, S. (2008). Generation of mouse induced pluripotent stem cells without viral vectors. Science 322, 949-953.
-
(2008)
Science
, vol.322
, pp. 949-953
-
-
Okita, K.1
Nakagawa, M.2
Hyenjong, H.3
Ichisaka, T.4
Yamanaka, S.5
-
52
-
-
20144368117
-
Potential autoregulation of transcription factor PU. 1 by an upstream regulatory element
-
Okuno, Y., Huang, G., Rosenbauer, F., Erica, K., Radomska, H. S., Iwasaki, H., Akashi, K., Moreau-Gachelin, F., Li, Y., Zhang, P., Tenen, D. G., Okuno, Y., Huang, G., Rosenbauer, F., Evans, E. K., Radomska, H. S., Iwasaki, H., Akashi, K., Moreau-Gachelin, F., and Li, Y (2005). Potential autoregulation of transcription factor PU. 1 by an upstream regulatory element. Mol. Cell. Biol. 25, 2832-2845.
-
(2005)
Mol. Cell. Biol.
, vol.25
, pp. 2832-2845
-
-
Okuno, Y.1
Huang, G.2
Rosenbauer, F.3
Erica, K.4
Radomska, H.S.5
Iwasaki, H.6
Akashi, K.7
Moreau-Gachelin, F.8
Li, Y.9
Zhang, P.10
Tenen, D.G.11
Okuno, Y.12
Huang, G.13
Rosenbauer, F.14
Evans, E.K.15
Radomska, H.S.16
Iwasaki, H.17
Akashi, K.18
Moreau-Gachelin, F.19
Li, Y.20
more..
-
53
-
-
33947368681
-
Histone deacetylase inhibitor trichostatin a induces global and gene-specific DNA demethylation in human cancer cell lines
-
Ou, J. -N., Torrisani, J., Unterberger, A., Provençal, N., Shikimi, K., Karimi, M., Ekström, T. J., and Szyf, M. (2007). Histone deacetylase inhibitor trichostatin a induces global and gene-specific DNA demethylation in human cancer cell lines. Biochem. Pharmacol. 73, 1297-1307.
-
(2007)
Biochem. Pharmacol.
, vol.73
, pp. 1297-1307
-
-
Ou, J.-N.1
Torrisani, J.2
Unterberger, A.3
Provençal, N.4
Shikimi, K.5
Karimi, M.6
Ekström, T.J.7
Szyf, M.8
-
54
-
-
0034329445
-
Retrovirus vector silencing is de novo methylase independent and marked by a repressive histone code
-
Pannell, D., Osborne, C. S., Yao, S., Sukonnik, T., Pasceri, P., Karaiskakis, A., Okano, M., Li, E., Lipshitz, H. D., and Ellis, J. (2000). Retrovirus vector silencing is de novo methylase independent and marked by a repressive histone code. EMBO J. 19, 5884-5894.
-
(2000)
EMBO J.
, vol.19
, pp. 5884-5894
-
-
Pannell, D.1
Osborne, C.S.2
Yao, S.3
Sukonnik, T.4
Pasceri, P.5
Karaiskakis, A.6
Okano, M.7
Li, E.8
Lipshitz, H.D.9
Ellis, J.10
-
55
-
-
79952538234
-
Reprogramming to pluripotency: stepwise resetting of the epigenetic landscape
-
Papp, B., and Plath, K. (2011). Reprogramming to pluripotency: stepwise resetting of the epigenetic landscape. Cell Res. 21, 486-501.
-
(2011)
Cell Res.
, vol.21
, pp. 486-501
-
-
Papp, B.1
Plath, K.2
-
56
-
-
38649104138
-
Understanding stem cell differentiation through self-organization theory
-
Qu, K., and Ortoleva, P. (2008). Understanding stem cell differentiation through self-organization theory. J. Theor. Biol. 250, 606-620.
-
(2008)
J. Theor. Biol.
, vol.250
, pp. 606-620
-
-
Qu, K.1
Ortoleva, P.2
-
57
-
-
22244487659
-
Genetic regulation of stem cell origins in the mouse embryo
-
Ralston, A., and Rossant, J. (2005). Genetic regulation of stem cell origins in the mouse embryo. Clin. Genet. 68, 106-112.
-
(2005)
Clin. Genet.
, vol.68
, pp. 106-112
-
-
Ralston, A.1
Rossant, J.2
-
58
-
-
0033151624
-
Direct interaction of hematopoietic transcription factors PU. 1 and GATA-1: functional antagonism in erythroid cells
-
Rekhtman, N., Radparvar, F., Evans, T., Rekhtman, N., Radparvar, F., Evans, T., andSkoultchi, A. I. (1999). Direct interaction of hematopoietic transcription factors PU. 1 and GATA-1: functional antagonism in erythroid cells. Genes Dev. 13, 1398-1411.
-
(1999)
Genes Dev.
, vol.13
, pp. 1398-1411
-
-
Rekhtman, N.1
Radparvar, F.2
Evans, T.3
Rekhtman, N.4
Radparvar, F.5
Evans, T.6
Skoultchi, A.I.7
-
59
-
-
33746040437
-
Towards an understanding of lineage specification in hematopoietic stem cells: a mathematical model for the interaction of transcription factors GATA-1 and PU. 1
-
Roeder, I., and Glauche, I. (2006). Towards an understanding of lineage specification in hematopoietic stem cells: a mathematical model for the interaction of transcription factors GATA-1 and PU. 1. J. Theor. Biol. 241, 852-865.
-
(2006)
J. Theor. Biol.
, vol.241
, pp. 852-865
-
-
Roeder, I.1
Glauche, I.2
-
60
-
-
0036184629
-
Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks
-
Shmulevich, I. (2002). Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks. Bioinformatics 18, 261-274.
-
(2002)
Bioinformatics
, vol.18
, pp. 261-274
-
-
Shmulevich, I.1
-
61
-
-
33747195353
-
Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors
-
Takahashi, K. (2006). Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126, 663-676.
-
(2006)
Cell
, vol.126
, pp. 663-676
-
-
Takahashi, K.1
-
62
-
-
36248966518
-
Induction of pluripotent stem cells from adult human fibroblasts by defined factors
-
Takahashi, K., Tanabe, K., Ohnuki, M., and Narita, M. (2007). Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell 131, 861-872.
-
(2007)
Cell
, vol.131
, pp. 861-872
-
-
Takahashi, K.1
Tanabe, K.2
Ohnuki, M.3
Narita, M.4
-
63
-
-
77951116072
-
CpG islands influence chromatin structure via the CpG-binding protein Cfp1
-
Thomson, J. P., Skene, P. J., Selfridge, J., Clouaire, T., Guy, J., Webb, S., Kerr, A. R. W., Deaton, A., Andrews, R., James, K. D., Turner, D. J., Illingworth, R., and Bird, A. (2010). CpG islands influence chromatin structure via the CpG-binding protein Cfp1. Nature 464, 1082-1086.
-
(2010)
Nature
, vol.464
, pp. 1082-1086
-
-
Thomson, J.P.1
Skene, P.J.2
Selfridge, J.3
Clouaire, T.4
Guy, J.5
Webb, S.6
Kerr, A.R.W.7
Deaton, A.8
Andrews, R.9
James, K.D.10
Turner, D.J.11
Illingworth, R.12
Bird, A.13
-
64
-
-
4444237490
-
Demethylating agent, 5-azacytidine, reverses differentiation of embryonic stem cells
-
Tsuji-Takayama, K., Inoue, T., Ijiri, Y., Otani, T., Motoda, R., Nakamura, S., and Orita, K. (2004). Demethylating agent, 5-azacytidine, reverses differentiation of embryonic stem cells. Biochem. Biophys. Res. Commun. 323, 86-90.
-
(2004)
Biochem. Biophys. Res. Commun.
, vol.323
, pp. 86-90
-
-
Tsuji-Takayama, K.1
Inoue, T.2
Ijiri, Y.3
Otani, T.4
Motoda, R.5
Nakamura, S.6
Orita, K.7
-
65
-
-
78649879265
-
Stochasticity in reactions: a probabilistic boolean modeling approach
-
(Trento: ACM)
-
Twardziok, S., Siebert, H., and Heyl, A. (2010). "Stochasticity in reactions: a probabilistic boolean modeling approach," in Computational Methods in Systems Biology (Trento: ACM), 76-85.
-
(2010)
Computational Methods in Systems Biology
, pp. 76-85
-
-
Twardziok, S.1
Siebert, H.2
Heyl, A.3
-
66
-
-
77649162059
-
Direct conversion of fibroblasts to functional neurons by defined factors
-
Vierbuchen, T., Ostermeier, A., Pang, Z. P., Kokubu, Y., Südhof, T. C., and Wernig, M. (2010). Direct conversion of fibroblasts to functional neurons by defined factors. Nature 463, 1035-1041.
-
(2010)
Nature
, vol.463
, pp. 1035-1041
-
-
Vierbuchen, T.1
Ostermeier, A.2
Pang, Z.P.3
Kokubu, Y.4
Südhof, T.C.5
Wernig, M.6
-
67
-
-
77952914558
-
The potential landscape of genetic circuits imposes the arrow of time in stem cell differentiation
-
Wang, J., Xu, L., Wang, E., and Huang, S. (2010). The potential landscape of genetic circuits imposes the arrow of time in stem cell differentiation. Biophys. J. 99, 29-39.
-
(2010)
Biophys. J.
, vol.99
, pp. 29-39
-
-
Wang, J.1
Xu, L.2
Wang, E.3
Huang, S.4
-
68
-
-
79954989303
-
A cyclic AMP analog, 8-Br-cAMP, enhances the induction of pluripotency in human fibroblast cells
-
Wang, Y., and Adjaye, J. (2010). A cyclic AMP analog, 8-Br-cAMP, enhances the induction of pluripotency in human fibroblast cells. Stem Cell Rev. 7, 331-341.
-
(2010)
Stem Cell Rev.
, vol.7
, pp. 331-341
-
-
Wang, Y.1
Adjaye, J.2
-
69
-
-
34249908901
-
In vitro reprogramming of fibroblasts into a pluripotent es-cell-like state
-
Wernig, M., Meissner, A., Foreman, R., Brambrink, T., Ku, M., Hochedlinger, K., Bernstein, B. E., and Jaenisch, R. (2007). In vitro reprogramming of fibroblasts into a pluripotent es-cell-like state. Nature 448, 318-324.
-
(2007)
Nature
, vol.448
, pp. 318-324
-
-
Wernig, M.1
Meissner, A.2
Foreman, R.3
Brambrink, T.4
Ku, M.5
Hochedlinger, K.6
Bernstein, B.E.7
Jaenisch, R.8
-
70
-
-
0033083803
-
Cross-regulation of C/EBP alpha and PPAR gamma controls the transcriptional pathway of adipogenesis and insulin sensitivity
-
Wu, Z., Rosen, E. D., Brun, R., Hauser, S., Adelmant, G., Troy, A. E., McKeon, C., Darlington, G. J., and Spiegelman, B. M. (1999). Cross-regulation of C/EBP alpha and PPAR gamma controls the transcriptional pathway of adipogenesis and insulin sensitivity. Mol. Cell 3, 151-158.
-
(1999)
Mol. Cell
, vol.3
, pp. 151-158
-
-
Wu, Z.1
Rosen, E.D.2
Brun, R.3
Hauser, S.4
Adelmant, G.5
Troy, A.E.6
McKeon, C.7
Darlington, G.J.8
Spiegelman, B.M.9
-
71
-
-
66049135249
-
Generation of induced pluripotent stem cells using recombinant proteins
-
Zhou, H., Wu, S., Joo, J. Y., Zhu, S., Han, D. W., Lin, T., Trauger, S., Bien, G., Yao, S., Zhu, Y., Siuzdak, G., Schöler, H. R., Duan, L., and Ding, S. (2009). Generation of induced pluripotent stem cells using recombinant proteins. Cell Stem Cell 4, 381-384.
-
(2009)
Cell Stem Cell
, vol.4
, pp. 381-384
-
-
Zhou, H.1
Wu, S.2
Joo, J.Y.3
Zhu, S.4
Han, D.W.5
Lin, T.6
Trauger, S.7
Bien, G.8
Yao, S.9
Zhu, Y.10
Siuzdak, G.11
Schöler, H.R.12
Duan, L.13
Ding, S.14
-
72
-
-
36749083429
-
A gene regulatory network in mouse embryonic stem cells
-
Zhou, Q., Chipperfield, H., and Melton, D. (2007). A gene regulatory network in mouse embryonic stem cells. Proc. Natl. Acad. Sci. U. S. A. 104, 16438-16443.
-
(2007)
Proc. Natl. Acad. Sci. U. S. A.
, vol.104
, pp. 16438-16443
-
-
Zhou, Q.1
Chipperfield, H.2
Melton, D.3
|