-
1
-
-
1542563409
-
Initial sequencing and comparative analysis of the mouse genome
-
Waterston, R. H. et al. Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520-562 (2002).
-
(2002)
Nature
, vol.420
, pp. 520-562
-
-
Waterston, R.H.1
-
2
-
-
69049086389
-
Distinct retroelement classes define evolutionary breakpoints demarcating sites of evolutionary novelty
-
Longo, M. S. , Carone, D. M. , Green, E. D. , O'Neill, M. J. & O'Neill, R. J. Distinct retroelement classes define evolutionary breakpoints demarcating sites of evolutionary novelty. BMC Genomics 10, 334 (2009).
-
(2009)
BMC Genomics
, vol.10
, pp. 334
-
-
Longo, M.S.1
Carone, D.M.2
Green, E.D.3
O'Neill, M.J.4
O'Neill, R.J.5
-
3
-
-
58149191245
-
Chromosomal inversions betweenhumanand chimpanzee lineages caused by retrotransposons
-
Lee, J. , Han, K. , Meyer, T. J. , Kim, H. S. & Batzer, M. A. Chromosomal inversions betweenhumanand chimpanzee lineages caused by retrotransposons. PLoSONE 3, e4047 (2008).
-
(2008)
PloS ONE
, vol.3
, pp. e4047
-
-
Lee, J.1
Han, K.2
Meyer, T.J.3
Kim, H.S.4
Batzer, M.A.5
-
4
-
-
84858429240
-
Endogenous viruses: Insights into viral evolution and impact on host biology
-
Feschotte, C. & Gilbert, C. Endogenous viruses: insights into viral evolution and impact on host biology. Nature Rev. Genet. 13, 283-296 (2012).
-
(2012)
Nature Rev. Genet.
, vol.13
, pp. 283-296
-
-
Feschotte, C.1
Gilbert, C.2
-
5
-
-
79957844585
-
DNA methylation and SETDB1/H3K9me3 regulate predominantly distinct sets of genes, retroelements, and chimeric transcripts in mESCs
-
Karimi, M. M. et al. DNA methylation and SETDB1/H3K9me3 regulate predominantly distinct sets of genes, retroelements, and chimeric transcripts in mESCs. Cell Stem Cell 8, 676-687 (2011).
-
(2011)
Cell Stem Cell
, vol.8
, pp. 676-687
-
-
Karimi, M.M.1
-
6
-
-
84874626481
-
TRIM28 repression of retrotransposon-based enhancers is necessary to preserve transcriptional dynamics in embryonic stem cells
-
Rowe, H. M. et al. TRIM28 repression of retrotransposon-based enhancers is necessary to preserve transcriptional dynamics in embryonic stem cells. Genome Res. 23, 452-461 (2013).
-
(2013)
Genome Res.
, vol.23
, pp. 452-461
-
-
Rowe, H.M.1
-
7
-
-
84874608346
-
Nonallelic homologous recombination between retrotransposable elements is a driver of de novo unbalanced translocations
-
Robberecht, C. , Voet, T. , Zamani Esteki, M. , Nowakowska, B. A. & Vermeesch, J. R. Nonallelic homologous recombination between retrotransposable elements is a driver of de novo unbalanced translocations. Genome Res. 23, 411-418 (2013).
-
(2013)
Genome Res.
, vol.23
, pp. 411-418
-
-
Robberecht, C.1
Voet, T.2
Esteki, Z.M.3
Nowakowska, B.A.4
Vermeesch, J.R.5
-
8
-
-
55549102967
-
Keeping active endogenous retroviral-like elements in check: The epigenetic perspective
-
Maksakova, I. A. , Mager, D. L. & Reiss, D. Keeping active endogenous retroviral-like elements in check: the epigenetic perspective. Cell. Mol. Life Sci. 65, 3329-3347 (2008).
-
(2008)
Cell. Mol. Life Sci.
, vol.65
, pp. 3329-3347
-
-
Maksakova, I.A.1
Mager, D.L.2
Reiss, D.3
-
9
-
-
84876799419
-
Transposable elements as genetic regulatory substrates in early development
-
Gifford, W. D. , Pfaff, S. L. & Macfarlan, T. S. Transposable elements as genetic regulatory substrates in early development. Trends Cell Biol. 23, 218-226 (2013).
-
(2013)
Trends Cell Biol.
, vol.23
, pp. 218-226
-
-
Gifford, W.D.1
Pfaff, S.L.2
MacFarlan, T.S.3
-
10
-
-
77950862656
-
Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET
-
Matsui, T. et al. Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET. Nature 464, 927-931 (2010).
-
(2010)
Nature
, vol.464
, pp. 927-931
-
-
Matsui, T.1
-
11
-
-
74549116659
-
KAP1 controls endogenous retroviruses in embryonic stemcells
-
Rowe, H. M. et al. KAP1 controls endogenous retroviruses in embryonic stemcells. Nature 463, 237-240 (2010).
-
(2010)
Nature
, vol.463
, pp. 237-240
-
-
Rowe, H.M.1
-
12
-
-
77649099092
-
Distinct factors control histone variant H3. 3 localization at specific genomic regions
-
Goldberg, A. D. et al. Distinct factors control histone variant H3. 3 localization at specific genomic regions. Cell 140, 678-691 (2010).
-
(2010)
Cell
, vol.140
, pp. 678-691
-
-
Goldberg, A.D.1
-
13
-
-
77956282773
-
Daxx is an H3. 3-specific histone chaperone and cooperates with ATRX in replicationindependent chromatin assembly at telomeres
-
Lewis, P. W. , Elsaesser, S. J. , Noh, K. M. , Stadler, S. C. & Allis, C. D. Daxx is an H3. 3-specific histone chaperone and cooperates with ATRX in replicationindependent chromatin assembly at telomeres. Proc. Natl Acad. Sci. USA 107, 14075-14080 (2010).
-
(2010)
Proc. Natl Acad. Sci. USA
, vol.107
, pp. 14075-14080
-
-
Lewis, P.W.1
Elsaesser, S.J.2
Noh, K.M.3
Stadler, S.C.4
Allis, C.D.5
-
14
-
-
77953955724
-
The death-associated proteinDAXXis a novel histone chaperone involved inthe replication-independent deposition of H3. 3
-
Drané, P. , Ouararhni, K. , Depaux, A. , Shuaib, M. &Hamiche, A. The death-associated proteinDAXXis a novel histone chaperone involved inthe replication-independent deposition of H3. 3. Genes Dev. 24, 1253-1265 (2010).
-
(2010)
Genes Dev
, vol.24
, pp. 1253-1265
-
-
Drané, P.1
Ouararhni, K.2
Depaux, A.3
Shuaib, M.4
Hamiche, A.5
-
15
-
-
61849118594
-
Histone H3. 3 incorporation provides a unique and functionally essential telomeric chromatin inembryonic stemcells
-
Wong, L. H. et al. Histone H3. 3 incorporation provides a unique and functionally essential telomeric chromatin inembryonic stemcells. GenomeRes. 19, 404-414 (2009).
-
(2009)
Genome Res
, vol.19
, pp. 404-414
-
-
Wong, L.H.1
-
16
-
-
84884865693
-
Hira-dependent histone H3. 3 deposition facilitates PRC2 recruitment at developmental loci in ES cells
-
Banaszynski, L. A. et al. Hira-dependent histone H3. 3 deposition facilitates PRC2 recruitment at developmental loci in ES cells. Cell 155, 107-120 (2013).
-
(2013)
Cell
, vol.155
, pp. 107-120
-
-
Banaszynski, L.A.1
-
17
-
-
34547624303
-
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
-
Mikkelsen, T. S. et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448, 553-560 (2007).
-
(2007)
Nature
, vol.448
, pp. 553-560
-
-
Mikkelsen, T.S.1
-
18
-
-
77953935308
-
Estimating enrichment of repetitive elements from high-throughput sequence data
-
Day, D. S. , Luquette, L. J. , Park, P. J. & Kharchenko, P. V. Estimating enrichment of repetitive elements from high-throughput sequence data. Genome Biol. 11, R69 (2010).
-
(2010)
Genome Biol.
, vol.11
, pp. R69
-
-
Day, D.S.1
Luquette, L.J.2
Park, P.J.3
Kharchenko, P.V.4
-
19
-
-
8644284670
-
Clustering, duplication and chromosomal distribution of mouse SINE retrotransposons
-
Jurka, J. , Kohany, O. , Pavlicek, A. , Kapitonov, V. V. & Jurka, M. V. Clustering, duplication and chromosomal distribution of mouse SINE retrotransposons. Cytogenet. Genome Res. 110, 117-123 (2005).
-
(2005)
Cytogenet. Genome Res.
, vol.110
, pp. 117-123
-
-
Jurka, J.1
Kohany, O.2
Pavlicek, A.3
Kapitonov, V.V.4
Jurka, M.V.5
-
20
-
-
84866852810
-
Epigenetic interplay betweenmouse endogenous retroviruses and host genes
-
Rebollo, R. et al. Epigenetic interplay betweenmouse endogenous retroviruses and host genes. Genome Biol. 13, R89 (2012).
-
(2012)
Genome Biol.
, vol.13
, pp. R89
-
-
Rebollo, R.1
-
21
-
-
41649117808
-
An infectious progenitor for the murine IAP retrotransposon: Emergence of an intracellular genetic parasite froman ancient retrovirus
-
Ribet, D. et al. An infectious progenitor for the murine IAP retrotransposon: emergence of an intracellular genetic parasite froman ancient retrovirus. Genome Res. 18, 597-609 (2008).
-
(2008)
Genome Res.
, vol.18
, pp. 597-609
-
-
Ribet, D.1
-
22
-
-
2442554169
-
Identification of autonomous IAP LTR retrotransposons mobile in mammalian cells
-
Dewannieux, M. , Dupressoir, A. , Harper, F. , Pierron, G. &Heidmann, T. Identification of autonomous IAP LTR retrotransposons mobile in mammalian cells. Nature Genet. 36, 534-539 (2004).
-
(2004)
Nature Genet.
, vol.36
, pp. 534-539
-
-
Dewannieux, M.1
Dupressoir, A.2
Harper, F.3
Pierron, G.4
Heidmann, T.5
-
23
-
-
40149098109
-
Genome-wide assessments reveal extremely high levels of polymorphism of two active families of mouse endogenous retroviral elements
-
Zhang, Y. , Maksakova, I. A. , Gagnier, L. , van de Lagemaat, L. N. & Mager, D. L. Genome-wide assessments reveal extremely high levels of polymorphism of two active families of mouse endogenous retroviral elements. PLoS Genet. 4, e1000007 (2008).
-
(2008)
PLoS Genet.
, vol.4
, pp. e1000007
-
-
Zhang, Y.1
Maksakova, I.A.2
Gagnier, L.3
Van De Lagemaat, L.N.4
Mager, D.L.5
-
24
-
-
83855165105
-
Repetitive DNA and next-generation sequencing: Computational challenges and solutions
-
Treangen, T. J. & Salzberg, S. L. Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nature Rev. Genet. 13, 36-46 (2012).
-
(2012)
Nature Rev. Genet.
, vol.13
, pp. 36-46
-
-
Treangen, T.J.1
Salzberg, S.L.2
-
25
-
-
84885353806
-
H3. 3 actively marks enhancers and primes gene transcription via opening higher-ordered chromatin
-
Chen, P. et al. H3. 3 actively marks enhancers and primes gene transcription via opening higher-ordered chromatin. Genes Dev. 27, 2109-2124 (2013).
-
(2013)
Genes Dev.
, vol.27
, pp. 2109-2124
-
-
Chen, P.1
-
26
-
-
84930962818
-
A system for genome-wide histone variant dynamics in ES cells reveals dynamic MacroH2A2 replacement at promoters
-
Yildirim, O. et al. A system for genome-wide histone variant dynamics in ES cells reveals dynamic MacroH2A2 replacement at promoters. PLoS Genet. 10, e1004515 (2014).
-
(2014)
PLoS Genet.
, vol.10
, pp. e1004515
-
-
Yildirim, O.1
-
27
-
-
84904537943
-
Suv39h-dependent H3K9me3 marks intact retrotransposons and silences LINE elements inmouse embryonic stemcells
-
Bulut-Karslioglu, A. et al. Suv39h-dependent H3K9me3 marks intact retrotransposons and silences LINE elements inmouse embryonic stemcells. Mol. Cell 55, 277-290 (2014).
-
(2014)
Mol. Cell
, vol.55
, pp. 277-290
-
-
Bulut-Karslioglu, A.1
-
28
-
-
84898946550
-
DAXX co-folds with H3. 3/H4 using high local stability conferred by the H3. 3 variant recognition residues
-
DeNizio, J. E. , Elsasser, S. J. & Black, B. E. DAXX co-folds with H3. 3/H4 using high local stability conferred by the H3. 3 variant recognition residues. Nucleic Acids Res. 42, 4318-4331 (2014).
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. 4318-4331
-
-
Denizio, J.E.1
Elsasser, S.J.2
Black, B.E.3
-
29
-
-
84884889017
-
Transcription recovery after DNA damage requires chromatin priming by the H3, 3 histone chaperone HIRA
-
Adam, S. , Polo, S. E. & Almouzni, G. Transcription recovery after DNA damage requires chromatin priming by the H3. 3 histone chaperone HIRA. Cell 155, 94-106 (2013).
-
(2013)
Cell
, vol.155
, pp. 94-106
-
-
Adam, S.1
Polo, S.E.2
Almouzni, G.3
-
30
-
-
84908207503
-
Histone H3. 3 is required to maintain replication fork progression after UV damage
-
Frey, A. , Listovsky, T. , Guilbaud, G. , Sarkies, P. & Sale, J. E. Histone H3. 3 is required to maintain replication fork progression after UV damage. Curr. Biol. 24, 2195-2201 (2014).
-
(2014)
Curr. Biol.
, vol.24
, pp. 2195-2201
-
-
Frey, A.1
Listovsky, T.2
Guilbaud, G.3
Sarkies, P.4
Sale, J.E.5
-
31
-
-
84910088832
-
ATRX directs binding of PRC2 to Xist RNA and Polycomb targets
-
Sarma, K. et al. ATRX directs binding of PRC2 to Xist RNA and Polycomb targets. Cell 159, 869-883 (2014).
-
(2014)
Cell
, vol.159
, pp. 869-883
-
-
Sarma, K.1
-
32
-
-
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. & Young, R. A. SetDB1 contributes to repression of genes encoding developmental regulators and maintenance of ES cell state. Genes Dev. 23, 2484-2489 (2009).
-
(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
-
33
-
-
84892369527
-
Distinct and combinatorial functions of Jmjd2b/Kdm4b and Jmjd2c/Kdm4c in mouse embryonic stem cell identity
-
Das, P. P. et al. Distinct and combinatorial functions of Jmjd2b/Kdm4b and Jmjd2c/Kdm4c in mouse embryonic stem cell identity. Mol. Cell 53, 32-48 (2014).
-
(2014)
Mol. Cell
, vol.53
, pp. 32-48
-
-
Das, P.P.1
-
34
-
-
62349130698
-
Ultrafast andmemory-efficient alignment of short DNA sequences to the human genome
-
Langmead, B. , Trapnell, C. , Pop, M. &Salzberg, S. L. Ultrafast andmemory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
-
(2009)
Genome Biol.
, vol.10
, pp. R25
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
35
-
-
68549104404
-
The sequence alignment/map format and SAM tools
-
Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
-
36
-
-
84919692480
-
Use model-based analysis of ChIP-Seq (MACS) to analyze short reads generated by sequencing protein-DNA interactions in embryonic stem cells
-
Liu, T. Use model-based analysis of ChIP-Seq (MACS) to analyze short reads generated by sequencing protein-DNA interactions in embryonic stem cells. Methods Mol. Biol. 1150, 81-95 (2014).
-
(2014)
Methods Mol. Biol.
, vol.1150
, pp. 81-95
-
-
Liu, T.1
-
37
-
-
84899493057
-
Ngs. Plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases
-
Shen, L. , Shao, N. , Liu, X. & Nestler, E. ngs. plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases. BMC Genomics 15, 284 (2014).
-
(2014)
BMC Genomics
, vol.15
, pp. 284
-
-
Shen, L.1
Shao, N.2
Liu, X.3
Nestler, E.4
-
38
-
-
70349871718
-
CEAS: Cis-regulatory element annotation system
-
Shin, H. , Liu, T. , Manrai, A. K. & Liu, X. S. CEAS: cis-regulatory element annotation system. Bioinformatics 25, 2605-2606 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 2605-2606
-
-
Shin, H.1
Liu, T.2
Manrai, A.K.3
Liu, X.S.4
-
39
-
-
65449136284
-
TopHat: Discovering splice junctions with RNA-Seq
-
Trapnell, C. , Pachter, L. & Salzberg, S. L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105-1111 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 1105-1111
-
-
Trapnell, C.1
Pachter, L.2
Salzberg, S.L.3
-
40
-
-
84872198346
-
Differential analysis of gene regulation at transcript resolution with RNA-seq
-
Trapnell, C. et al. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nature Biotechnol. 31, 46-53 (2013).
-
(2013)
Nature Biotechnol.
, vol.31
, pp. 46-53
-
-
Trapnell, C.1
|