-
1
-
-
84923872716
-
Temporal analysis of genome alterations induced by single-cell passaging in human embryonic stem cells
-
Bai Q, J-M Ramirez, F. Becker, V. Pantesco, T. Lavabre-Bertrand, O. Hovatta, J-M Lemaître, F. Pellestor, and J. De Vos. (2015). Temporal analysis of genome alterations induced by single-cell passaging in human embryonic stem cells. Stem Cells Dev 24: 653-662
-
(2015)
Stem Cells Dev
, vol.24
, pp. 653-662
-
-
Bai, Q.1
Ramirez, J.-M.2
Becker, F.3
Pantesco, V.4
Lavabre-Bertrand, T.5
Hovatta, O.6
Lemaître, J.-M.7
Pellestor, F.8
De Vos, J.9
-
2
-
-
84875805512
-
Homologous recombination DNA repair genes play a critical role in reprogramming to a pluripotent state
-
González F, D. Georgieva, F. Vanoli, Z-D Shi, M. Stadtfeld, T. Ludwig, M. Jasin, and D. Huangfu. (2013). Homologous recombination DNA repair genes play a critical role in reprogramming to a pluripotent state. Cell Rep 3: 651-660
-
(2013)
Cell Rep
, 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
-
3
-
-
79952258224
-
Somatic coding mutations in human induced pluripotent stem cells
-
Gore A, Z. Li, H-L Fung, J.E. Young, S. Agarwal, J. Antosiewicz-Bourget, I. Canto, A. Giorgetti, M.A. Israel, et al. (2011). Somatic coding mutations in human induced pluripotent stem cells. Nature 471: 63-67
-
(2011)
Nature
, vol.471
, pp. 63-67
-
-
Gore, A.1
Li, Z.2
Fung, H.-L.3
Young, J.E.4
Agarwal, S.5
Antosiewicz-Bourget, J.6
Canto, I.7
Giorgetti, A.8
Israel, M.A.9
-
4
-
-
79952126043
-
Copy number variation, and selection during reprogramming to pluripotency
-
Hussein SM, N.N. Batada, S. Vuoristo, R.W. Ching, R. Autio, E. Närvä, S. Ng, M. Sourour, R. Hämäläinen, et al. (2011). Copy number variation, and selection during reprogramming to pluripotency. Nature 471: 58-62
-
(2011)
Nature
, vol.471
, pp. 58-62
-
-
Hussein, S.M.1
Batada, N.N.2
Vuoristo, S.3
Ching, R.W.4
Autio, R.5
Närvä, E.6
Ng, S.7
Sourour, M.8
Hämäläinen, R.9
-
5
-
-
78650971216
-
Dynamic changes in the copy number of pluripotency, and cell proliferation genes in human ESCs, and iPSCs during reprogramming, and time in culture
-
Laurent LC, I. Ulitsky, I. Slavin, H. Tran, A. Schork, R. Morey, C. Lynch, J.V. Harness, S. Lee, et al. (2011). Dynamic changes in the copy number of pluripotency, and cell proliferation genes in human ESCs, and iPSCs during reprogramming, and time in culture. Cell Stem Cell 8: 106-118
-
(2011)
Cell Stem Cell
, vol.8
, pp. 106-118
-
-
Laurent, L.C.1
Ulitsky, I.2
Slavin, I.3
Tran, H.4
Schork, A.5
Morey, R.6
Lynch, C.7
Harness, J.V.8
Lee, S.9
-
6
-
-
84898041397
-
The distribution of genomic variations in human iPSCs is related to replicationtiming reorganization during reprogramming
-
Lu J, H. Li, M. Hu, T. Sasaki, A. Baccei, D.M. Gilbert, J.S. Liu, J.J. Collins, and P.H. Lerou. (2014). The distribution of genomic variations in human iPSCs is related to replicationtiming reorganization during reprogramming. Cell Rep 7: 70-78
-
(2014)
Cell Rep
, vol.7
, pp. 70-78
-
-
Lu, J.1
Li, H.2
Hu, M.3
Sasaki, T.4
Baccei, A.5
Gilbert, D.M.6
Liu, J.S.7
Collins, J.J.8
Lerou, P.H.9
-
7
-
-
84929190623
-
Factor-induced reprogramming, and zinc finger nuclease-Aided gene targeting cause different genome instability in b-Thalassemia induced pluripotent stem cells (iPSCs
-
Ma N, Y. Shan, B. Liao, G. Kong, C. Wang, K. Huang, H. Zhang, X. Cai, S. Chen, et al. (2015). Factor-induced reprogramming, and zinc finger nuclease-Aided gene targeting cause different genome instability in b-Thalassemia induced pluripotent stem cells (iPSCs). J Biol Chem 290: 12079-12089
-
(2015)
J Biol Chem
, vol.290
, pp. 12079-12089
-
-
Ma, N.1
Shan, Y.2
Liao, B.3
Kong, G.4
Wang, C.5
Huang, K.6
Zhang, H.7
Cai, X.8
Chen, S.9
-
8
-
-
79958109873
-
Recurrent copy number variations in human induced pluripotent stem cells
-
Martins-Taylor K, B.S. Nisler, S.M. Taapken, T. Compton, L. Crandall, K.D. Montgomery, M. Lalande, and R-H Xu. (2011). Recurrent copy number variations in human induced pluripotent stem cells. Nat Biotechnol 29: 488-491
-
(2011)
Nat Biotechnol
, vol.29
, pp. 488-491
-
-
Martins-Taylor, K.1
Nisler, B.S.2
Taapken, S.M.3
Compton, T.4
Crandall, L.5
Montgomery, K.D.6
Lalande, M.7
Xu, R.-H.8
-
9
-
-
77957334627
-
Identification, and classification of chromosomal aberrations in human induced pluripotent stem cells
-
Mayshar Y, U. Ben-David, N. Lavon, J-C Biancotti, B. Yakir, A.T. Clark, K. Plath, W.E. Lowry, and N. Benvenisty. (2010). Identification, and classification of chromosomal aberrations in human induced pluripotent stem cells. Cell Stem Cell 7: 521-531
-
(2010)
Cell Stem Cell
, vol.7
, pp. 521-531
-
-
Mayshar, Y.1
Ben-David, U.2
Lavon, N.3
Biancotti, J.-C.4
Yakir, B.5
Clark, A.T.6
Plath, K.7
Lowry, W.E.8
Benvenisty, N.9
-
10
-
-
84925341709
-
A comparison of non-integrating reprogramming methods
-
Schlaeger TM, L. Daheron, T.R. Brickler, S. Entwisle, K. Chan, A. Cianci, A. DeVine, A. Ettenger, K. Fitzgerald, et al. (2015). A comparison of non-integrating reprogramming methods. Nat Biotechnol 33: 58-63
-
(2015)
Nat Biotechnol
, vol.33
, pp. 58-63
-
-
Schlaeger, T.M.1
Daheron, L.2
Brickler, T.R.3
Entwisle, S.4
Chan, K.5
Cianci, A.6
DeVine, A.7
Ettenger, A.8
Fitzgerald, K.9
-
11
-
-
48649099481
-
Copy number variant analysis of human embryonic stem cells
-
Wu H, K.J. Kim, K. Mehta, S. Paxia, A. Sundstrom, T. Anantharaman, A.I. Kuraishy, T. Doan, J. Ghosh, et al. (2008). Copy number variant analysis of human embryonic stem cells. Stem Cells 26: 1484-1489
-
(2008)
Stem Cells
, vol.26
, pp. 1484-1489
-
-
Wu, H.1
Kim, K.J.2
Mehta, K.3
Paxia, S.4
Sundstrom, A.5
Anantharaman, T.6
Kuraishy, A.I.7
Doan, T.8
Ghosh, J.9
-
12
-
-
84959016909
-
Whole-genome mutational burden analysis of three pluripotency induction methods
-
Bhutani K, K.L. Nazor, R. Williams, H. Tran, H. Dai, Z Dzakula, E.H. Cho, AWC Pang, M. Rao, et al. (2016). Whole-genome mutational burden analysis of three pluripotency induction methods. Nat Commun 7: 10536
-
(2016)
Nat Commun
, vol.7
, pp. 10536
-
-
Bhutani, K.1
Nazor, K.L.2
Williams, R.3
Tran, H.4
Dai, H.5
Dzakula, Z.6
Cho, E.H.7
Pang, A.W.C.8
Rao, M.9
-
13
-
-
84965092064
-
RIKEN suspends first clinical trial involving induced pluripotent stem cells
-
Garber K. (2015). RIKEN suspends first clinical trial involving induced pluripotent stem cells. Nat Biotechnol 33: 890-891
-
(2015)
Nat Biotechnol
, vol.33
, pp. 890-891
-
-
Garber, K.1
-
14
-
-
84928534190
-
Concise review: Induced pluripotency by defined factors: Prey of oxidative stress
-
Qi S, Z. Fang, D. Wang, P. Menendez, K. Yao, and J. Ji. (2015). Concise review: induced pluripotency by defined factors: prey of oxidative stress. Stem Cells 33: 1371-1376
-
(2015)
Stem Cells
, vol.33
, pp. 1371-1376
-
-
Qi, S.1
Fang, Z.2
Wang, D.3
Menendez, P.4
Yao, K.5
Ji, J.6
-
15
-
-
84870955253
-
Differential relation-ship of DNA replication timing to different forms of human mutation, and variation
-
Koren A, P. Polak, J. Nemesh, J.J. Michaelson, J. Sebat, S.R. Sunyaev, and S.A. McCarroll. (2012). Differential relation-ship of DNA replication timing to different forms of human mutation, and variation. Am J Hum Genet 91: 1033-1040
-
(2012)
Am J Hum Genet
, vol.91
, pp. 1033-1040
-
-
Koren, A.1
Polak, P.2
Nemesh, J.3
Michaelson, J.J.4
Sebat, J.5
Sunyaev, S.R.6
McCarroll, S.A.7
-
16
-
-
84923358817
-
Cell-of-origin chromatin organization shapes the mutational landscape of cancer
-
Polak P, R. Karlić, A. Koren, R. Thurman, R. Sandstrom, M.S. Lawrence, A. Reynolds, E. Rynes, K. Vlahoviček, J.A. Stamatoyannopoulos, and S.R. Sunyaev. (2015). Cell-of-origin chromatin organization shapes the mutational landscape of cancer. Nature 518: 360-364
-
(2015)
Nature
, vol.518
, pp. 360-364
-
-
Polak, P.1
Karlić, R.2
Koren, A.3
Thurman, R.4
Sandstrom, R.5
Lawrence, M.S.6
Reynolds, A.7
Rynes, E.8
Vlahoviček, K.9
Stamatoyannopoulos, J.A.10
Sunyaev, S.R.11
-
17
-
-
84911478490
-
Topologically associating domains are stable units of replication-Timing regulation
-
Pope BD, T. Ryba, V. Dileep, F. Yue, W. Wu, O. Denas, D.L. Vera, Y. Wang, R.S. Hansen, et al. (2014). Topologically associating domains are stable units of replication-Timing regulation. Nature 515: 402-405
-
(2014)
Nature
, vol.515
, pp. 402-405
-
-
Pope, B.D.1
Ryba, T.2
Dileep, V.3
Yue, F.4
Wu, W.5
Denas, O.6
Vera, D.L.7
Wang, Y.8
Hansen, R.S.9
-
18
-
-
0034612926
-
Proximity matters
-
Savage JRK. (2000). Proximity matters. Science 290: 62-63
-
(2000)
Science
, vol.290
, pp. 62-63
-
-
Savage, J.R.K.1
-
19
-
-
78349288865
-
Higher-order genome organization in human disease
-
Misteli T. (2010). Higher-order genome organization in human disease. Cold Spring Harb Perspect Biol 2: a000794
-
(2010)
Cold Spring Harb Perspect Biol
, vol.2
, pp. a000794
-
-
Misteli, T.1
-
20
-
-
79953685437
-
Ataxia-Telangiectasia mutated (ATM) deficiency decreases reprogramming efficiency, and leads to genomic instability in iPS cells
-
Kinoshita T, G. Nagamatsu, T. Kosaka, K. Takubo, A. Hotta, J. Ellis, and T. Suda. (2011). Ataxia-Telangiectasia mutated (ATM) deficiency decreases reprogramming efficiency, and leads to genomic instability in iPS cells. Biochem Biophys Res Commun 407: 321-326
-
(2011)
Biochem Biophys Res Commun
, vol.407
, pp. 321-326
-
-
Kinoshita, T.1
Nagamatsu, G.2
Kosaka, T.3
Takubo, K.4
Hotta, A.5
Ellis, J.6
Suda, T.7
-
21
-
-
84873745182
-
Induced pluripotent stem cells from ataxia-Telangiectasia recapitulate the cellular phenotype
-
Nayler S, M. Gatei, S. Kozlov, R. Gatti, J.C. Mar, C.A. Wells, M. Lavin, and E. Wolvetang. (2012). Induced pluripotent stem cells from ataxia-Telangiectasia recapitulate the cellular phenotype. Stem Cells Transl Med 1: 523-535
-
(2012)
Stem Cells Transl Med
, vol.1
, pp. 523-535
-
-
Nayler, S.1
Gatei, M.2
Kozlov, S.3
Gatti, R.4
Mar, J.C.5
Wells, C.A.6
Lavin, M.7
Wolvetang, E.8
-
22
-
-
84903649929
-
Ataxia telangiectasia derived iPS cells show preserved x-ray sensitivity, and decreased chromosomal instability
-
Fukawatase Y, M. Toyoda, K. Okamura, K. Nakamura, K. Nakabayashi, S. Takada, M. Yamazaki-Inoue, A. Masuda, M. Nasu, et al. (2014). Ataxia telangiectasia derived iPS cells show preserved x-ray sensitivity, and decreased chromosomal instability. Sci Rep 4: 5421
-
(2014)
Sci Rep
, vol.4
, pp. 5421
-
-
Fukawatase, Y.1
Toyoda, M.2
Okamura, K.3
Nakamura, K.4
Nakabayashi, K.5
Takada, S.6
Yamazaki-Inoue, M.7
Masuda, A.8
Nasu, M.9
-
23
-
-
84878545143
-
SMRT compounds abrogate cellular phenotypes of ataxia telangiectasia in neural derivatives of patient-specific hiPSCs
-
Lee P, N.T. Martin, K. Nakamura, S. Azghadi, M. Amiri, U. Ben-David, S. Perlman, R.A. Gatti, H. Hu, and W.E. Lowry. (2013). SMRT compounds abrogate cellular phenotypes of ataxia telangiectasia in neural derivatives of patient-specific hiPSCs. Nat Commun 4: 1824
-
(2013)
Nat Commun
, vol.4
, pp. 1824
-
-
Lee, P.1
Martin, N.T.2
Nakamura, K.3
Azghadi, S.4
Amiri, M.5
Ben-David, U.6
Perlman, S.7
Gatti, R.A.8
Hu, H.9
Lowry, W.E.10
-
24
-
-
84949533058
-
Spontaneous ATM gene reversion in A-T iPSC to produce an isogenic cell line
-
Lin L, MR Swerdel, MP Lazaropoulos, GSHoffman, A.J. Toro-Ramos, J. Wright, H. Lederman, J. Chen, J.C. Moore, and R.P. Hart. (2015). Spontaneous ATM gene reversion in A-T iPSC to produce an isogenic cell line. Stem Cell Rep 5: 1097-1108
-
(2015)
Stem Cell Rep
, vol.5
, pp. 1097-1108
-
-
Lin, L.1
Swerdel, M.R.2
Lazaropoulos, M.P.3
Hoffman, G.S.4
Toro-Ramos, A.J.5
Wright, J.6
Lederman, H.7
Chen, J.8
Moore, J.C.9
Hart, R.P.10
-
25
-
-
50249098740
-
Generation of human-induced pluripotent stem cells
-
Park I, P. Lerou, R. Zhao, H. Huo, and G. Daley. (2008). Generation of human-induced pluripotent stem cells. Nat Protoc 3: 1180-1186
-
(2008)
Nat Protoc
, vol.3
, pp. 1180-1186
-
-
Park, I.1
Lerou, P.2
Zhao, R.3
Huo, H.4
Daley, G.5
-
26
-
-
84908092597
-
Passage number is a major contributor to genomic structural variations in mouse iPSCs
-
Liu P, A. Kaplan, B. Yuan, J.H. Hanna, J.R. Lupski, and O. Reiner. (2014). Passage number is a major contributor to genomic structural variations in mouse iPSCs. Stem Cells 32: 2657-2667
-
(2014)
Stem Cells
, vol.32
, pp. 2657-2667
-
-
Liu, P.1
Kaplan, A.2
Yuan, B.3
Hanna, J.H.4
Lupski, J.R.5
Reiner, O.6
-
27
-
-
0034576494
-
The many substrates, and functions of ATM
-
Kastan MB, and D.S. Lim. (2000). The many substrates, and functions of ATM. Nat Rev Mol Cell Biol 1: 179-186
-
(2000)
Nat Rev Mol Cell Biol
, vol.1
, pp. 179-186
-
-
Kastan, M.B.1
Lim, D.S.2
-
28
-
-
84892878347
-
Quality control: Genome maintenance in pluripotent stem cells
-
Weissbein U, N. Benvenisty, and U. Ben-David. (2014). Quality control: genome maintenance in pluripotent stem cells. J Cell Biol 204: 153-163
-
(2014)
J Cell Biol
, vol.204
, pp. 153-163
-
-
Weissbein, U.1
Benvenisty, N.2
Ben-David, U.3
-
29
-
-
84862778059
-
Spatial organization of the mouse genome, and its role in recurrent chromosomal translocations
-
Zhang Y, R.P. McCord, Y-J Ho, B.R. Lajoie, D.G. Hildebrand, A.C. Simon, M.S. Becker, F.W. Alt, and J. Dekker. (2012). Spatial organization of the mouse genome, and its role in recurrent chromosomal translocations. Cell 148: 908-921
-
(2012)
Cell
, vol.148
, pp. 908-921
-
-
Zhang, Y.1
McCord, R.P.2
Ho, Y.-J.3
Lajoie, B.R.4
Hildebrand, D.G.5
Simon, A.C.6
Becker, M.S.7
Alt, F.W.8
Dekker, J.9
-
30
-
-
84978655886
-
Large-scale chromatin structure-function relationships during the cell cycle, and development: Insights from replication timing
-
Epub ahead of print]
-
Dileep V, J.C. Rivera-Mulia, J. Sima, and D.M. Gilbert. (2015). Large-scale chromatin structure-function relationships during the cell cycle, and development: Insights from replication timing. Cold Spring Harb Symp Quant Biol [Epub ahead of print]; DOI: 10.1101/sqb.2015.80.027284
-
(2015)
Cold Spring Harb Symp Quant Biol
-
-
Dileep, V.1
Rivera-Mulia, J.C.2
Sima, J.3
Gilbert, D.M.4
-
31
-
-
54949085778
-
Global reorganization of replication domains during embryonic stem cell differentiation
-
Hiratani I, T. Ryba, M. Itoh, T. Yokochi, M. Schwaiger, C.W. Chang, Y. Lyou, T.M. Townes, D. Schübeler, and D.M. Gilbert. (2008). Global reorganization of replication domains during embryonic stem cell differentiation. PLoS Biol 6: e245
-
(2008)
PLoS Biol
, vol.6
, pp. e245
-
-
Hiratani, I.1
Ryba, T.2
Itoh, M.3
Yokochi, T.4
Schwaiger, M.5
Chang, C.W.6
Lyou, Y.7
Townes, T.M.8
Schübeler, D.9
Gilbert, D.M.10
-
32
-
-
77952994784
-
Evolutionarily conserved replication timing profiles predict long-range chromatin interactions, and distinguish closely related cell types
-
Ryba T, I. Hiratani, J. Lu, M. Itoh, M. Kulik, J. Zhang, T.C. Schulz, A.J. Robins, S. Dalton, and D.M. Gilbert. (2010). Evolutionarily conserved replication timing profiles predict long-range chromatin interactions, and distinguish closely related cell types. Genome Res 20: 761-770
-
(2010)
Genome Res
, vol.20
, pp. 761-770
-
-
Ryba, T.1
Hiratani, I.2
Lu, J.3
Itoh, M.4
Kulik, M.5
Zhang, J.6
Schulz, T.C.7
Robins, A.J.8
Dalton, S.9
Gilbert, D.M.10
-
33
-
-
0027490716
-
Evidence that retroviruses integrate into post-replication host DNA
-
Hajihosseini M, L. Iavachev, and J. Price. (1993). Evidence that retroviruses integrate into post-replication host DNA. EMBO J 12: 4969-4974
-
(1993)
EMBO J
, vol.12
, pp. 4969-4974
-
-
Hajihosseini, M.1
Iavachev, L.2
Price, J.3
-
34
-
-
0019406879
-
Rous sarcoma virus infection of synchronized cells establishes provirus integration during S-phase DNA synthesis prior to cellular division
-
Humphries EH, C. Glover, and M.E. Reichmann. (1981). Rous sarcoma virus infection of synchronized cells establishes provirus integration during S-phase DNA synthesis prior to cellular division. Proc Natl Acad Sci U S A 78: 2601-2605
-
(1981)
Proc Natl Acad Sci U S A
, vol.78
, pp. 2601-2605
-
-
Humphries, E.H.1
Glover, C.2
Reichmann, M.E.3
-
35
-
-
14844355218
-
High-resolution genome-wide mapping of transposon integration in mammals
-
Yant SR, X. Wu, Y. Huang, B. Garrison, S.M. Burgess, and M.A. Kay. (2005). High-resolution genome-wide mapping of transposon integration in mammals. Mol Cell Biol 25: 2085-2094
-
(2005)
Mol Cell Biol
, vol.25
, pp. 2085-2094
-
-
Yant, S.R.1
Wu, X.2
Huang, Y.3
Garrison, B.4
Burgess, S.M.5
Kay, M.A.6
-
36
-
-
84939780353
-
Limiting replication stress during somatic cell reprogramming reduces genomic instability in induced pluripotent stem cells
-
Ruiz S, A.J. Lopez-Contreras, M. Gabut, R.M. Marion, P. Gutierrez-Martinez, S. Bua, O. Ramirez, I. Olalde, S. Rodrigo-Perez, et al. (2015). Limiting replication stress during somatic cell reprogramming reduces genomic instability in induced pluripotent stem cells. Nat Commun 6: 8036
-
(2015)
Nat Commun
, vol.6
, pp. 8036
-
-
Ruiz, S.1
Lopez-Contreras, A.J.2
Gabut, M.3
Marion, R.M.4
Gutierrez-Martinez, P.5
Bua, S.6
Ramirez, O.7
Olalde, I.8
Rodrigo-Perez, S.9
-
37
-
-
79451474060
-
Protecting the heritable genome: DNA damage response mechanisms in spermatogonial stem cells
-
Rübe CE, S. Zhang, N. Miebach, A. Fricke, and C. Rübe. (2011). Protecting the heritable genome: DNA damage response mechanisms in spermatogonial stem cells. DNA Repair 10: 159-168
-
(2011)
DNA Repair
, vol.10
, pp. 159-168
-
-
Rübe, C.E.1
Zhang, S.2
Miebach, N.3
Fricke, A.4
Rübe, C.5
-
38
-
-
47349107760
-
ATM signaling facilitates repair of DNA double-strand breaks associated with heterochromatin
-
Goodarzi AA, A.T. Noon, D. Deckbar, Y. Ziv, Y. Shiloh, M. Löbrich, and P.A. Jeggo. (2008). ATM signaling facilitates repair of DNA double-strand breaks associated with heterochromatin. Mol Cell 31: 167-177
-
(2008)
Mol Cell
, vol.31
, pp. 167-177
-
-
Goodarzi, A.A.1
Noon, A.T.2
Deckbar, D.3
Ziv, Y.4
Shiloh, Y.5
Löbrich, M.6
Jeggo, P.A.7
-
39
-
-
84925615834
-
Differential DNA mismatch repair underlies mutation rate variation across the human genome
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Supek F, and B. Lehner. (2015). Differential DNA mismatch repair underlies mutation rate variation across the human genome. Nature 521: 81-84
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(2015)
Nature
, vol.521
, pp. 81-84
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Supek, F.1
Lehner, B.2
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