-
1
-
-
25144525014
-
Core transcriptional regulatory circuitry in human embryonic stem cells
-
DOI 10.1016/j.cell.2005.08.020, PII S0092867405008251
-
Boyer LA, Lee TI, Cole MF et al (2005) Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 122:947-956. (Pubitemid 41345211)
-
(2005)
Cell
, vol.122
, Issue.6
, pp. 947-956
-
-
Boyer, L.A.1
Tong, I.L.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
-
2
-
-
44649117905
-
Integration of external signaling pathways with the core transcriptional network in embryonic stem cells
-
DOI 10.1016/j.cell.2008.04.043, PII S009286740800617X
-
Chen X, Xu H, Yuan P et al (2008) Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 133:1106-1117. (Pubitemid 351787745)
-
(2008)
Cell
, vol.133
, Issue.6
, pp. 1106-1117
-
-
Chen, X.1
Xu, H.2
Yuan, P.3
Fang, F.4
Huss, M.5
Vega, V.B.6
Wong, E.7
Orlov, Y.L.8
Zhang, W.9
Jiang, J.10
Loh, Y.-H.11
Yeo, H.C.12
Yeo, Z.X.13
Narang, V.14
Govindarajan, K.R.15
Leong, B.16
Shahab, A.17
Ruan, Y.18
Bourque, G.19
Sung, W.-K.20
Clarke, N.D.21
Wei, C.-L.22
Ng, H.-H.23
more..
-
3
-
-
65249173999
-
An embryonic stem cell chromatin remodeling complex, esBAF, is an essential component of the core pluripotency transcriptional network
-
Ho L, Jothi R, Ronan JL et al (2009) An embryonic stem cell chromatin remodeling complex, esBAF, is an essential component of the core pluripotency transcriptional network. Proceedings of the National Academy of Sciences of the United States of America 106:5187-5191.
-
(2009)
Proceedings of the National Academy of Sciences of the United States of America
, vol.106
, pp. 5187-5191
-
-
Ho, L.1
Jothi, R.2
Ronan, J.L.3
-
4
-
-
0034671733
-
The zinc finger-containing transcription factors GATA-4, -5, and -6: Ubiquitously expressed regulators of tissue-specific gene expression
-
DOI 10.1074/jbc.R000029200
-
Molkentin JD (2000) The zinc finger-containing transcription factors GATA-4,-5, and-6. Ubiquitously expressed regulators of tissuespecific gene expression. J Biol Chem 275:38949-38952. (Pubitemid 32058903)
-
(2000)
Journal of Biological Chemistry
, vol.275
, Issue.50
, pp. 38949-38952
-
-
Molkentin, J.D.1
-
6
-
-
77951744473
-
Replication initiation and DNA topology: The twisted life of the origin
-
Rampakakis E, Gkogkas C, Di Paola D et al (2010) Replication initiation and DNA topology: The twisted life of the origin. J Cell Biochem 110:35-43.
-
(2010)
J Cell Biochem
, vol.110
, pp. 35-43
-
-
Rampakakis, E.1
Gkogkas, C.2
Di Paola, D.3
-
7
-
-
55249090457
-
Chromatin recruitment of DNA repair proteins: Lessons from the fanconi anemia and double-strand break repair pathways
-
Cohn MA, D'Andrea AD (2008) Chromatin recruitment of DNA repair proteins: lessons from the fanconi anemia and double-strand break repair pathways. Mol Cell 32:306-312.
-
(2008)
Mol Cell
, vol.32
, pp. 306-312
-
-
Cohn, M.A.1
D'andrea, A.D.2
-
8
-
-
3242878504
-
DNA recombination, chromosomal stability and carcinogenesis: Insights into the role of BRCA2
-
DOI 10.1016/j.dnarep.2004.03.008, PII S1568786404000679
-
Shivji MK, Venkitaraman AR (2004) DNA recombination, chromosomal stability and carcinogenesis: insights into the role of BRCA2. DNA Repair (Amst) 3:835-843. (Pubitemid 38997925)
-
(2004)
DNA Repair
, vol.3
, Issue.8-9
, pp. 835-843
-
-
Shivji, M.K.K.1
Venkitaraman, A.R.2
-
9
-
-
0023948705
-
Mapping protein-DNA interactions in vivo with formaldehyde: Evidence that histone H4 is retained on a highly transcribed gene
-
Solomon MJ, Larsen PL, Varshavsky A (1988) Mapping protein-DNA interactions in vivo with formaldehyde: evidence that histone H4 is retained on a highly transcribed gene. Cell 53:937-947.
-
(1988)
Cell
, vol.53
, pp. 937-947
-
-
Solomon, M.J.1
Larsen, P.L.2
Varshavsky, A.3
-
10
-
-
0034704248
-
Genome-wide location and function of DNA binding proteins
-
DOI 10.1126/science.290.5500.2306
-
Ren B, Robert F, Wyrick JJ et al (2000) Genome-wide location and function of DNA binding proteins. Science 290:2306-2309. (Pubitemid 32041573)
-
(2000)
Science
, vol.290
, Issue.5500
, pp. 2306-2309
-
-
Ren, B.1
Robert, F.2
Wyrick, J.J.3
Aparicio, O.4
Jennings, E.G.5
Simon, I.6
Zeitlinger, J.7
Schreiber, J.8
Hannett, N.9
Kanin, E.10
Volkert, T.L.11
Wilson, C.J.12
Bell, S.P.13
Young, R.A.14
-
11
-
-
34547630151
-
ChIP-seq: Welcome to the new frontier
-
DOI 10.1038/nmeth0807-613, PII NMETH0807-613
-
Mardis ER (2007) ChIP-seq: welcome to the new frontier. Nat Methods 4:613-614. (Pubitemid 47202468)
-
(2007)
Nature Methods
, vol.4
, Issue.8
, pp. 613-614
-
-
Mardis, E.R.1
-
12
-
-
70349312354
-
ChIP-seq: Advantages and challenges of a maturing technology
-
Park PJ (2009) ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet 10:669-680.
-
(2009)
Nat Rev Genet
, vol.10
, pp. 669-680
-
-
Park, P.J.1
-
13
-
-
34249026300
-
High-resolution profiling of histone methylations in the human genome
-
DOI 10.1016/j.cell.2007.05.009, PII S0092867407006009
-
Barski A, Cuddapah S, Cui K et al (2007) High-resolution profiling of histone methylations in the human genome. Cell 129:823-837. (Pubitemid 46802390)
-
(2007)
Cell
, vol.129
, Issue.4
, pp. 823-837
-
-
Barski, A.1
Cuddapah, S.2
Cui, K.3
Roh, T.-Y.4
Schones, D.E.5
Wang, Z.6
Wei, G.7
Chepelev, I.8
Zhao, K.9
-
14
-
-
34250159524
-
Genome-wide mapping of in vivo protein-DNA interactions
-
DOI 10.1126/science.1141319
-
Johnson DS, Mortazavi A, Myers RM et al (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science 316:1497-1502. (Pubitemid 46906620)
-
(2007)
Science
, vol.316
, Issue.5830
, pp. 1497-1502
-
-
Johnson, D.S.1
Mortazavi, A.2
Myers, R.M.3
Wold, B.4
-
15
-
-
34547633677
-
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing
-
DOI 10.1038/nmeth1068, PII NMETH1068
-
Robertson G, Hirst M, Bainbridge M et al (2007) Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. NatMethods 4:651-657. (Pubitemid 47202477)
-
(2007)
Nature Methods
, vol.4
, Issue.8
, pp. 651-657
-
-
Robertson, G.1
Hirst, M.2
Bainbridge, M.3
Bilenky, M.4
Zhao, Y.5
Zeng, T.6
Euskirchen, G.7
Bernier, B.8
Varhol, R.9
Delaney, A.10
Thiessen, N.11
Griffith, O.L.12
He, A.13
Marra, M.14
Snyder, M.15
Jones, S.16
-
16
-
-
70349643725
-
Chromatin poises miRNA-and protein-coding genes for expression
-
Barski A, Jothi R, Cuddapah S et al (2009) Chromatin poises miRNA-and protein-coding genes for expression. Genome Research 19:1742-1751.
-
(2009)
Genome Research
, vol.19
, pp. 1742-1751
-
-
Barski, A.1
Jothi, R.2
Cuddapah, S.3
-
17
-
-
60149095014
-
Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains
-
Cuddapah S, Jothi R, Schones DE et al (2009) Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains. Genome Research 19:24-32.
-
(2009)
Genome Research
, vol.19
, pp. 24-32
-
-
Cuddapah, S.1
Jothi, R.2
Schones, D.E.3
-
18
-
-
66149186985
-
Genomic location analysis by ChIP-Seq
-
Barski A, Zhao K (2009) Genomic location analysis by ChIP-Seq. J Cell Biochem 107:11-18.
-
(2009)
J Cell Biochem
, vol.107
, pp. 11-18
-
-
Barski, A.1
Zhao, K.2
-
19
-
-
68349122404
-
Native chromatin preparation and Illumina/Solexa library construction
-
pdb prot5237
-
Cuddapah S, Barski A, Cui K et al (2009) Native chromatin preparation and Illumina/Solexa library construction. Cold Spring Harb Protoc 2009:pdb prot5237.
-
(2009)
Cold Spring Harb Protoc
, vol.2009
-
-
Cuddapah, S.1
Barski, A.2
Cui, K.3
-
20
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead B, Trapnell C, Pop M et al (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25.
-
(2009)
Genome Biol
, vol.10
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
-
21
-
-
55549097836
-
Mapping short DNA sequencing reads and calling variants using mapping quality scores
-
Li H, Ruan J, Durbin R (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Research 18:1851-1858.
-
(2008)
Genome Research
, vol.18
, pp. 1851-1858
-
-
Li, H.1
Ruan, J.2
Durbin, R.3
-
22
-
-
52649132425
-
Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data
-
Jothi R, Cuddapah S, Barski A et al (2008) Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acids Research 36:5221-5231.
-
(2008)
Nucleic Acids Research
, vol.36
, pp. 5221-5231
-
-
Jothi, R.1
Cuddapah, S.2
Barski, A.3
-
23
-
-
84860886879
-
-
http://www.rajajothi.com.
-
-
-
-
24
-
-
84860884224
-
-
http://dir.nhlbi.nih.gov/papers/lmi/epigenomes/sissrs/
-
-
-
-
25
-
-
84860886878
-
-
http://www.perl.org
-
-
-
-
26
-
-
84860881409
-
-
http://genome.ucsc.edu/FAQ/FAQformat#format1
-
-
-
-
27
-
-
36949023082
-
A nucleosome-guided map of transcription factor binding sites in yeast
-
Narlikar L, Gordan R, Hartemink AJ (2007) A nucleosome-guided map of transcription factor binding sites in yeast. PLoS Comput Biol 3:e215.
-
(2007)
PLoS Comput Biol
, vol.3
-
-
Narlikar, L.1
Gordan, R.2
Hartemink, A.J.3
-
28
-
-
0028685490
-
Fitting a mixture model by expectation maximization to discover motifs in biopolymers
-
Bailey TL, Elkan C (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 2:28-36.
-
(1994)
Proc Int Conf Intell Syst Mol Biol
, vol.2
, pp. 28-36
-
-
Bailey, T.L.1
Elkan, C.2
-
29
-
-
59649113226
-
GADEM: A genetic algorithm guided formation of spaced dyads coupled with an em algorithm for motif discovery
-
Li L (2009) GADEM: a genetic algorithm guided formation of spaced dyads coupled with an EM algorithm for motif discovery. J Comput Biol 16:317-329.
-
(2009)
J Comput Biol
, vol.16
, pp. 317-329
-
-
Li, L.1
|