-
1
-
-
33646070846
-
A bivalent chromatin structure marks key developmental genes in embryonic stem cells
-
Bernstein, B. E. et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125, 315-326 (2006).
-
(2006)
Cell
, vol.125
, pp. 315-326
-
-
Bernstein, B.E.1
-
2
-
-
84867073340
-
Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage
-
Wamstad, J. A. et al. Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage. Cell 151, 206-220 (2012).
-
(2012)
Cell
, vol.151
, pp. 206-220
-
-
Wamstad, J.A.1
-
3
-
-
84868484735
-
Epigenomic annotation of enhancers predicts transcriptional regulators of human neural crest
-
Rada-Iglesias, A. et al. Epigenomic annotation of enhancers predicts transcriptional regulators of human neural crest. Cell Stem Cell 11, 633-648 (2012).
-
(2012)
Cell Stem Cell
, vol.11
, pp. 633-648
-
-
Rada-Iglesias, A.1
-
4
-
-
84878282421
-
Epigenomic analysis of multilineage differentiation of human embryonic stem cells
-
Xie, W. et al. Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell 153, 1134-1148 (2013).
-
(2013)
Cell
, vol.153
, pp. 1134-1148
-
-
Xie, W.1
-
5
-
-
80455144479
-
Pioneer transcription factors: Establishing competence for gene expression
-
Zaret, K. S. & Carroll, J. S. Pioneer transcription factors: establishing competence for gene expression. Genes Dev. 25, 2227-2241 (2011).
-
(2011)
Genes Dev.
, vol.25
, pp. 2227-2241
-
-
Zaret, K.S.1
Carroll, J.S.2
-
6
-
-
0033617522
-
Notch signaling: Cell fate control and signal integration in development
-
Artavanis-Tsakonas, S., Rand, M. D. & Lake, R. J. Notch signaling: cell fate control and signal integration in development. Science 284, 770-776 (1999).
-
(1999)
Science
, vol.284
, pp. 770-776
-
-
Artavanis-Tsakonas, S.1
Rand, M.D.2
Lake, R.J.3
-
7
-
-
20544460148
-
Notch/c-secretase inhibition turns proliferative cells in intestinal crypts and adenomas into goblet cells
-
van Es, J. H. et al. Notch/c-secretase inhibition turns proliferative cells in intestinal crypts and adenomas into goblet cells. Nature 435, 959-963 (2005).
-
(2005)
Nature
, vol.435
, pp. 959-963
-
-
Van Es, J.H.1
-
8
-
-
79953204955
-
Dll1-and dll4-mediated notch signaling are required for homeostasis of intestinal stem cells
-
Pellegrinet, L. et al. Dll1-and dll4-mediated notch signaling are required for homeostasis of intestinal stem cells. Gastroenterology 140, 1230-1240 (2011).
-
(2011)
Gastroenterology
, vol.140
, pp. 1230-1240
-
-
Pellegrinet, L.1
-
9
-
-
80052526022
-
Delta1 expression, cell cycle exit, and commitment to a specific secretory fate coincide within a few hours in themouse intestinal stemcell system
-
Stamataki, D. et al. Delta1 expression, cell cycle exit, and commitment to a specific secretory fate coincide within a few hours in themouse intestinal stemcell system. PLoS ONE 6, e24484 (2011).
-
(2011)
PLoS ONE
, vol.6
-
-
Stamataki, D.1
-
10
-
-
35548974423
-
Identification of stem cells in small intestine and colon by marker gene Lgr5
-
Barker, N. et al. Identification of stem cells in small intestine and colon by marker gene Lgr5. Nature 449, 1003-1007 (2007).
-
(2007)
Nature
, vol.449
, pp. 1003-1007
-
-
Barker, N.1
-
11
-
-
0035824487
-
Requirement of Math1 for secretory cell lineage commitment in the mouse intestine
-
Yang, Q., Bermingham, N. A., Finegold, M. J. & Zoghbi, H. Y. Requirement of Math1 for secretory cell lineage commitment in the mouse intestine. Science 294, 2155-2158 (2001).
-
(2001)
Science
, vol.294
, pp. 2155-2158
-
-
Yang, Q.1
Bermingham, N.A.2
Finegold, M.J.3
Zoghbi, H.Y.4
-
12
-
-
79953176341
-
Genetic evidence that intestinal Notch functions vary regionally andoperate througha commonmechanismofMath1repression
-
Kim, T. H. & Shivdasani, R. A. Genetic evidence that intestinal Notch functions vary regionally andoperate througha commonmechanismofMath1repression. J. Biol. Chem. 286, 11427-11433 (2011).
-
(2011)
J. Biol. Chem.
, vol.286
, pp. 11427-11433
-
-
Kim, T.H.1
Shivdasani, R.A.2
-
13
-
-
77956883150
-
Mouse atonal homolog 1 directs intestinal progenitors to secretory cell rather than absorptive cell fate
-
VanDussen, K. L. & Samuelson, L. C. Mouse atonal homolog 1 directs intestinal progenitors to secretory cell rather than absorptive cell fate. Dev. Biol. 346, 215-223 (2010).
-
(2010)
Dev. Biol.
, vol.346
, pp. 215-223
-
-
Vandussen, K.L.1
Samuelson, L.C.2
-
14
-
-
34249987090
-
Intestine-specific ablation of mouse atonal homolog 1 (Math1) reveals a role in cellular homeostasis
-
Shroyer, N. F. et al. Intestine-specific ablation of mouse atonal homolog 1 (Math1) reveals a role in cellular homeostasis. Gastroenterology 132, 2478-2488 (2007).
-
(2007)
Gastroenterology
, vol.132
, pp. 2478-2488
-
-
Shroyer, N.F.1
-
15
-
-
8444247084
-
Modulation of notch processing by c-secretase inhibitors causes intestinal goblet cell metaplasia and induction of genes known to specify gut secretory lineage differentiation
-
Milano, J. et al. Modulation of notch processing by c-secretase inhibitors causes intestinal goblet cell metaplasia and induction of genes known to specify gut secretory lineage differentiation. Toxicol. Sci. 82, 341-358 (2004).
-
(2004)
Toxicol. Sci.
, vol.82
, pp. 341-358
-
-
Milano, J.1
-
16
-
-
77956144348
-
Atonal homolog 1 is required for growth and differentiation effects of notch/c-secretase inhibitors on normal and cancerous intestinal epithelial cells
-
Kazanjian, A., Noah, T., Brown, D., Burkart, J. & Shroyer, N. F. Atonal homolog 1 is required for growth and differentiation effects of notch/c-secretase inhibitors on normal and cancerous intestinal epithelial cells. Gastroenterology 139, 918-928 (2010).
-
(2010)
Gastroenterology
, vol.139
, pp. 918-928
-
-
Kazanjian, A.1
Noah, T.2
Brown, D.3
Burkart, J.4
Shroyer, N.F.5
-
17
-
-
84867097416
-
Dll11 secretory progenitor cells revert to stem cells upon crypt damage
-
van Es, J. H. et al. Dll11 secretory progenitor cells revert to stem cells upon crypt damage. Nature Cell Biol. 14, 1099-1104 (2012).
-
(2012)
Nature Cell Biol.
, vol.14
, pp. 1099-1104
-
-
Van Es, J.H.1
-
18
-
-
34249026300
-
High-resolution profiling of histone methylations in the human genome
-
Barski, A. et al. High-resolution profiling of histone methylations in the human genome. Cell 129, 823-837 (2007).
-
(2007)
Cell
, vol.129
, pp. 823-837
-
-
Barski, A.1
-
19
-
-
78149485097
-
Differentiation-specific histone modifications reveal dynamic chromatin interactions and partners for the intestinal transcription factor CDX2
-
Verzi, M. P. et al. Differentiation-specific histone modifications reveal dynamic chromatin interactions and partners for the intestinal transcription factor CDX2. Dev. Cell 19, 713-726 (2010).
-
(2010)
Dev. Cell
, vol.19
, pp. 713-726
-
-
Verzi, M.P.1
-
20
-
-
33847334699
-
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the humangenome
-
Heintzman, N. D. et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the humangenome. NatureGenet.39, 311-318 (2007).
-
(2007)
NatureGenet.
, vol.39
, pp. 311-318
-
-
Heintzman, N.D.1
-
21
-
-
84865739425
-
Architecture of the human regulatory network derived from ENCODE data
-
Gerstein, M. B. et al. Architecture of the human regulatory network derived from ENCODE data. Nature 489, 91-100 (2012).
-
(2012)
Nature
, vol.489
, pp. 91-100
-
-
Gerstein, M.B.1
-
22
-
-
79951516056
-
Auniquechromatin signature uncovers early developmental enhancers in humans
-
Rada-Iglesias, A. et al.Auniquechromatin signature uncovers early developmental enhancers in humans. Nature 470, 279-283 (2011).
-
(2011)
Nature
, vol.470
, pp. 279-283
-
-
Rada-Iglesias, A.1
-
23
-
-
78650758676
-
Histone H3K27ac separates active from poised enhancers and predicts developmental state
-
Creyghton, M. P. et al. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc. Natl Acad. Sci. USA 107, 21931-21936 (2010).
-
(2010)
Proc. Natl Acad. Sci. USA
, vol.107
, pp. 21931-21936
-
-
Creyghton, M.P.1
-
24
-
-
38649099445
-
High-resolutionmapping and characterization of open chromatin across the genome
-
Boyle, A. P. et al. High-resolutionmapping and characterization of open chromatin across the genome. Cell 132, 311-322 (2008).
-
(2008)
Cell
, vol.132
, pp. 311-322
-
-
Boyle, A.P.1
-
25
-
-
79952769989
-
In vivo Atoh1 targetome reveals how a proneural transcription factor regulates cerebellar development
-
Klisch, T. J. et al. In vivo Atoh1 targetome reveals how a proneural transcription factor regulates cerebellar development. Proc. Natl Acad. Sci. USA 108, 3288-3293 (2011).
-
(2011)
Proc. Natl Acad. Sci. USA
, vol.108
, pp. 3288-3293
-
-
Klisch, T.J.1
-
26
-
-
84861865440
-
Bistability bifurcations, and Waddington's epigenetic landscape
-
Ferrell, J. E. Jr. Bistability, bifurcations, and Waddington's epigenetic landscape. Curr. Biol. 22, R458-R466 (2012).
-
(2012)
Curr. Biol.
, vol.22
-
-
Ferrell Jr., J.E.1
-
27
-
-
84872600554
-
Intestinal tumorigenesis initiated by dedifferentiation and acquisition of stem-cell-like properties
-
Schwitalla, S. et al. Intestinal tumorigenesis initiated by dedifferentiation and acquisition of stem-cell-like properties. Cell 152, 25-38 (2013).
-
(2013)
Cell
, vol.152
, pp. 25-38
-
-
Schwitalla, S.1
-
28
-
-
84874730918
-
Intestinal label-retaining cells are secretory precursors expressing Lgr5
-
Buczacki, S. J. et al. Intestinal label-retaining cells are secretory precursors expressing Lgr5. Nature 495, 65-69 (2013).
-
(2013)
Nature
, vol.495
, pp. 65-69
-
-
Buczacki, S.J.1
-
29
-
-
70350758680
-
Excitatory neurons of the proprioceptive, interoceptive, and arousal hindbrain networks share a developmental requirement for Math1
-
Rose, M. F., Ahmad, K. A., Thaller, C. & Zoghbi, H. Y. Excitatory neurons of the proprioceptive, interoceptive, and arousal hindbrain networks share a developmental requirement for Math1. Proc. Natl Acad. Sci. USA 106, 22462-22467 (2009).
-
(2009)
Proc. Natl Acad. Sci. USA
, vol.106
, pp. 22462-22467
-
-
Rose, M.F.1
Ahmad, K.A.2
Thaller, C.3
Zoghbi, H.Y.4
-
30
-
-
84878248139
-
DNA methylation dynamics during intestinal stem cell differentiation reveals enhancers driving gene expression in the villus
-
Kaaij, L. T. et al. DNA methylation dynamics during intestinal stem cell differentiation reveals enhancers driving gene expression in the villus. Genome Biol. 14, R50 (2013).
-
(2013)
Genome Biol.
, vol.14
-
-
Kaaij, L.T.1
-
31
-
-
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
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
32
-
-
67650711619
-
A clustering approach for identification of enriched domains from histone modification ChIP-Seq data
-
Zang, C. et al. A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics 25, 1952-1958 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 1952-1958
-
-
Zang, C.1
-
33
-
-
53849146020
-
Model-based analysis of ChIP-Seq (MACS)
-
Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).
-
(2008)
Genome Biol.
, vol.9
-
-
Zhang, Y.1
-
34
-
-
84866127830
-
Identifying ChIP-seq enrichment using MACS
-
Feng, J., Liu, T., Qin, B., Zhang, Y. & Liu, X. S. Identifying ChIP-seq enrichment using MACS. Nature Protocols 7, 1728-1740 (2012).
-
(2012)
Nature Protocols
, vol.7
, pp. 1728-1740
-
-
Feng, J.1
Liu, T.2
Qin, B.3
Zhang, Y.4
Liu, X.S.5
-
35
-
-
80052022462
-
Cistrome: An integrative platform for transcriptional regulation studies
-
Liu, T. et al. Cistrome: an integrative platform for transcriptional regulation studies. Genome Biol. 12, R83 (2011).
-
(2011)
Genome Biol.
, vol.12
-
-
Liu, T.1
-
36
-
-
0142121516
-
Exploration, normalization, and summaries of high density oligonucleotide array probe level data
-
Irizarry, R. A. et al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4, 249-264 (2003).
-
(2003)
Biostatistics
, vol.4
, pp. 249-264
-
-
Irizarry, R.A.1
-
37
-
-
4544341015
-
Linearmodels and empirical bayesmethods for assessing differential expression in microarray experiments
-
Smyth, G. K. Linearmodels and empirical bayesmethods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 3, http://dx.doi.org/10.2202/1544-6115.1027 (2004).
-
(2004)
Stat. Appl. Genet. Mol. Biol.
, pp. 3
-
-
Smyth, G.K.1
-
38
-
-
0035988246
-
Inducible gene knockout of transcription factor recombination signal binding protein-J reveals its essential role in T versus B lineage decision
-
Han, H. et al. Inducible gene knockout of transcription factor recombination signal binding protein-J reveals its essential role in T versus B lineage decision. Int. Immunol. 14, 637-645 (2002).
-
(2002)
Int. Immunol.
, vol.14
, pp. 637-645
-
-
Han, H.1
-
39
-
-
4043059169
-
Tissue-specific and inducible Cre-mediated recombination in the gut epithelium
-
El Marjou, F. et al. Tissue-specific and inducible Cre-mediated recombination in the gut epithelium. Genesis 39, 186-193 (2004).
-
(2004)
Genesis
, vol.39
, pp. 186-193
-
-
El Marjou, F.1
-
40
-
-
3042856262
-
Cre reporter strains produced by targeted insertion of EYFP and ECFP into the ROSA26 locus
-
Srinivas, S. et al. Cre reporter strains produced by targeted insertion of EYFP and ECFP into the ROSA26 locus. BMC Dev. Biol. 1, 4 (2001).
-
(2001)
BMC Dev. Biol.
, vol.1
, pp. 4
-
-
Srinivas, S.1
-
41
-
-
79955550445
-
A user's guide to the Encyclopedia ofDNA Elements (ENCODE)
-
ENCODE Project Consortium.
-
ENCODE Project Consortium. A user's guide to the Encyclopedia ofDNA Elements (ENCODE). PLoS Biol. 9, e1001046 (2011).
-
(2011)
PLoS Biol.
, vol.9
-
-
|