-
1
-
-
84901838628
-
Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts
-
Ay,F. et al. (2014) Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts. Genome Res., 24, 999-1011.
-
(2014)
Genome Res.
, vol.24
, pp. 999-1011
-
-
Ay, F.1
-
2
-
-
33750882505
-
Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities
-
Berger,M.F. et al. (2006) Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nat. Biotechnol., 24, 1429-1435.
-
(2006)
Nat. Biotechnol.
, vol.24
, pp. 1429-1435
-
-
Berger, M.F.1
-
3
-
-
84874947727
-
The BioGRID interaction database: 2013 update
-
Chatr-Aryamontri,A. et al. (2013) The BioGRID interaction database: 2013 update. Nucleic Acids Res., 41, D816-D823.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D816-D823
-
-
Chatr-Aryamontri, A.1
-
4
-
-
79351469446
-
MM-ChIP enables integrative analysis of cross-platform and between-laboratory ChIP-ChIP or ChIP-seq data
-
Chen,Y. et al. (2011) MM-ChIP enables integrative analysis of cross-platform and between-laboratory ChIP-ChIP or ChIP-seq data. Genome Biol, 12, R11.
-
(2011)
Genome Biol.
, vol.12
, pp. R11
-
-
Chen, Y.1
-
5
-
-
84865712383
-
Understanding transcriptional regulation by integrative analysis of transcription factor binding data
-
Cheng,C. et al. (2012) Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Res., 22, 1658-1667.
-
(2012)
Genome Res.
, vol.22
, pp. 1658-1667
-
-
Cheng, C.1
-
6
-
-
80053908619
-
Resveratrol, through NF-Y/p53/Sin3/HDAC1 complex phosphorylation, inhibits estrogen receptor alpha gene expression via p38MAPK/CK2 signaling in human breast cancer cells
-
De Amicis,F. et al. (2011) Resveratrol, through NF-Y/p53/Sin3/HDAC1 complex phosphorylation, inhibits estrogen receptor alpha gene expression via p38MAPK/CK2 signaling in human breast cancer cells. FASEB J., 25, 3695-3707.
-
(2011)
FASEB J.
, vol.25
, pp. 3695-3707
-
-
De Amicis, F.1
-
7
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
Encode
-
ENCODE. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature, 489, 57-74.
-
(2012)
Nature.
, vol.489
, pp. 57-74
-
-
-
8
-
-
84857707318
-
ChromHMM: Automating chromatin-state discovery and characterization
-
Ernst,J. and Kellis,M. (2012) ChromHMM: automating chromatin-state discovery and characterization. Nat. Methods, 9, 215-216.
-
(2012)
Nat. Methods.
, vol.9
, pp. 215-216
-
-
Ernst, J.1
Kellis, M.2
-
9
-
-
77956654773
-
De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis
-
Fordyce,P.M. et al. (2010) De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis. Nat. Biotechnol., 28, 970-975.
-
(2010)
Nat. Biotechnol.
, vol.28
, pp. 970-975
-
-
Fordyce, P.M.1
-
10
-
-
84865739425
-
Architecture of the human regulatory network derived from ENCODE data
-
Gerstein,M.B. et al. (2012) Architecture of the human regulatory network derived from ENCODE data. Nature, 489, 91-100.
-
(2012)
Nature.
, vol.489
, pp. 91-100
-
-
Gerstein, M.B.1
-
11
-
-
84881171276
-
Inferring chromatin-bound protein complexes from genome-wide binding assays
-
Giannopoulou,E.G. and Elemento,O. (2013) Inferring chromatin-bound protein complexes from genome-wide binding assays. Genome Res., 23, 1295-1306.
-
(2013)
Genome Res.
, vol.23
, pp. 1295-1306
-
-
Giannopoulou, E.G.1
Elemento, O.2
-
12
-
-
84866086842
-
High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints
-
Guo,Y. et al. (2012) High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints. PLoS Comput. Biol., 8, e1002638.
-
(2012)
PLoS Comput. Biol.
, vol.8
, pp. e1002638
-
-
Guo, Y.1
-
13
-
-
0035676057
-
On clustering validation techniques
-
Halkidi,M. et al. (2001) On clustering validation techniques. J. Intell. Inf. Syst., 17, 107-145.
-
(2001)
J. Intell. Inf. Syst.
, vol.17
, pp. 107-145
-
-
Halkidi, M.1
-
14
-
-
0033553541
-
Ras regulates the association of serum response factor and CCAAT/enhancer-binding protein beta
-
Hanlon,M. and Sealy,L. (1999) Ras regulates the association of serum response factor and CCAAT/enhancer-binding protein beta. J. Biol. Chem., 274, 14224-14228.
-
(1999)
J. Biol. Chem.
, vol.274
, pp. 14224-14228
-
-
Hanlon, M.1
Sealy, L.2
-
15
-
-
12344252237
-
AP-1 subunits: Quarrel and harmony among siblings
-
Hess,J. et al. (2004) AP-1 subunits: quarrel and harmony among siblings. J. Cell. Sci., 117 (Pt 25), 5965-5973.
-
(2004)
J. Cell. Sci.
, vol.117
, pp. 5965-5973
-
-
Hess, J.1
-
16
-
-
33745614618
-
Linking DNA-binding proteins to their recognition sequences by using protein microarrays
-
Ho,S.W. et al. (2006) Linking DNA-binding proteins to their recognition sequences by using protein microarrays. Proc. Natl Acad. Sci. USA, 103, 9940-9945.
-
(2006)
Proc. Natl Acad. Sci. USA.
, vol.103
, pp. 9940-9945
-
-
Ho, S.W.1
-
17
-
-
84862785201
-
Unsupervised pattern discovery in human chromatin structure through genomic segmentation
-
Hoffman,M.M. et al. (2012) Unsupervised pattern discovery in human chromatin structure through genomic segmentation. Nat. Methods, 9, 473-476.
-
(2012)
Nat. Methods.
, vol.9
, pp. 473-476
-
-
Hoffman, M.M.1
-
18
-
-
84875448918
-
Integrative annotation of chromatin elements from ENCODE data
-
Hoffman,M.M. et al. (2013) Integrative annotation of chromatin elements from ENCODE data. Nucleic Acids Res., 41, 827-841.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. 827-841
-
-
Hoffman, M.M.1
-
19
-
-
70350340058
-
Profiling the human protein-DNA interactome reveals ERK2 as a transcriptional repressor of interferon signaling
-
Hu,S. et al. (2009) Profiling the human protein-DNA interactome reveals ERK2 as a transcriptional repressor of interferon signaling. Cell, 139, 610-622.
-
(2009)
Cell.
, vol.139
, pp. 610-622
-
-
Hu, S.1
-
20
-
-
36048976921
-
USF1 recruits histone modification complexes and is critical for maintenance of a chromatin barrier
-
Huang,S. et al. (2007) USF1 recruits histone modification complexes and is critical for maintenance of a chromatin barrier. Mol. Cell. Biol., 27, 7991-8002.
-
(2007)
Mol. Cell. Biol.
, vol.27
, pp. 7991-8002
-
-
Huang, S.1
-
21
-
-
84876855559
-
Differential principal component analysis of ChIP-seq
-
Ji,H. et al. (2013) Differential principal component analysis of ChIP-seq. Proc. Natl Acad. Sci. USA, 110, 6789-6794.
-
(2013)
Proc. Natl Acad. Sci. USA.
, vol.110
, pp. 6789-6794
-
-
Ji, H.1
-
22
-
-
34250159524
-
Genome-wide mapping of in vivo protein-DNA interactions
-
Johnson,D.S. et al. (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science, 316, 1497-1502.
-
(2007)
Science.
, vol.316
, pp. 1497-1502
-
-
Johnson, D.S.1
-
23
-
-
74549114755
-
A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments
-
Laajala,T.D. et al. (2009) A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments. BMC Genomics, 10, 618.
-
(2009)
BMC Genomics.
, vol.10
, pp. 618
-
-
Laajala, T.D.1
-
24
-
-
84859582058
-
Genome-wide protein-DNA binding dynamics suggest a molecular clutch for transcription factor function
-
Lickwar,C.R. et al. (2012) Genome-wide protein-DNA binding dynamics suggest a molecular clutch for transcription factor function. Nature, 484, 251-255.
-
(2012)
Nature.
, vol.484
, pp. 251-255
-
-
Lickwar, C.R.1
-
25
-
-
39149109887
-
The structural basis of protein acetylation by the p300/CBP transcriptional coactivator
-
Liu,X. et al. (2008) The structural basis of protein acetylation by the p300/CBP transcriptional coactivator. Nature, 451, 846-850.
-
(2008)
Nature.
, vol.451
, pp. 846-850
-
-
Liu, X.1
-
26
-
-
84897436870
-
An integrated model of multiple-condition ChIP-Seq data reveals predeterminants of Cdx2 binding
-
Mahony,S. et al. (2014) An integrated model of multiple-condition ChIP-Seq data reveals predeterminants of Cdx2 binding. PLoS Comput. Biol., 10, e1003501.
-
(2014)
PLoS Comput. Biol.
, vol.10
, pp. e1003501
-
-
Mahony, S.1
-
27
-
-
0037370029
-
Cascade of distinct histone modifications during collagenase gene activation
-
Martens,J.H. et al. (2003) Cascade of distinct histone modifications during collagenase gene activation. Mol. Cell. Biol., 23, 1808-1816.
-
(2003)
Mol. Cell. Biol.
, vol.23
, pp. 1808-1816
-
-
Martens, J.H.1
-
28
-
-
84884516365
-
Architecture of an RNA polymerase II transcription preinitiation complex
-
Murakami,K. et al. (2013) Architecture of an RNA polymerase II transcription preinitiation complex. Science, 342, 1238724.
-
(2013)
Science.
, vol.342
, pp. 1238724
-
-
Murakami, K.1
-
29
-
-
0033201447
-
Bcl3, an IkappaB protein, stimulates activating protein-1 transactivation and cellular proliferation
-
Na,S.Y. et al. (1999) Bcl3, an IkappaB protein, stimulates activating protein-1 transactivation and cellular proliferation. J. Biol. Chem., 274, 28491-28496.
-
(1999)
J. Biol. Chem.
, vol.274
, pp. 28491-28496
-
-
Na, S.Y.1
-
30
-
-
20444504323
-
Uncovering the overlapping community structure of complex networks in nature and society
-
Palla,G. et al. (2005) Uncovering the overlapping community structure of complex networks in nature and society. Nature, 435, 814-818.
-
(2005)
Nature.
, vol.435
, pp. 814-818
-
-
Palla, G.1
-
31
-
-
0034704248
-
Genome-wide location and function of DNA binding proteins
-
Ren,B. et al. (2000) Genome-wide location and function of DNA binding proteins. Science, 290, 2306-2309.
-
(2000)
Science.
, vol.290
, pp. 2306-2309
-
-
Ren, B.1
-
32
-
-
0028971290
-
Human TAFII250 interacts with RAP74: Implications for RNA polymerase II initiation
-
Ruppert,S. and Tjian,R. (1995) Human TAFII250 interacts with RAP74: implications for RNA polymerase II initiation. Genes Dev., 9, 2747-2755.
-
(1995)
Genes Dev.
, vol.9
, pp. 2747-2755
-
-
Ruppert, S.1
Tjian, R.2
-
33
-
-
23744458086
-
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
-
Siepel,A. et al. (2005) Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res., 15, 1034-1050.
-
(2005)
Genome Res.
, vol.15
, pp. 1034-1050
-
-
Siepel, A.1
-
34
-
-
34250376736
-
Synergistic activation of the tumor suppressor, HLJ1, by the transcription factors YY1 and activator protein 1
-
Wang,C.C. et al. (2007) Synergistic activation of the tumor suppressor, HLJ1, by the transcription factors YY1 and activator protein 1 Cancer Res., 67, 4816-4826.
-
(2007)
Cancer Res.
, vol.67
, pp. 4816-4826
-
-
Wang, C.C.1
-
36
-
-
84870063111
-
Iaseq: Integrative analysis of allele-specificity of protein-DNA interactions in multiple ChIP-seq datasets
-
Wei,Y. et al. (2012) iaseq: integrative analysis of allele-specificity of protein-DNA interactions in multiple ChIP-seq datasets. BMC Genomics, 13, 681.
-
(2012)
BMC Genomics.
, vol.13
, pp. 681
-
-
Wei, Y.1
-
37
-
-
77955368935
-
Evaluation of algorithm performance in ChIP-seq peak detection
-
Wilbanks,E.G. and Facciotti,M.T. (2010) Evaluation of algorithm performance in ChIP-seq peak detection. PLoS One, 5, e11471.
-
(2010)
PLoS One.
, vol.5
, pp. e11471
-
-
Wilbanks, E.G.1
Facciotti, M.T.2
-
38
-
-
84887011782
-
DNA motif elucidation using belief propagation
-
Wong,K.C. et al. (2013) DNA Motif Elucidation using Belief Propagation. Nucleic Acids Research, 41, e153.
-
(2013)
Nucleic Acids Research.
, vol.41
, pp. e153
-
-
Wong, K.C.1
-
39
-
-
84886780296
-
Dynamic trans-acting factor colocalization in human cells
-
Xie,D. et al. (2013) Dynamic trans-acting factor colocalization in human cells. Cell, 155, 713-724.
-
(2013)
Cell.
, vol.155
, pp. 713-724
-
-
Xie, D.1
-
40
-
-
34447527890
-
Extracellular matrix-regulated gene expression requires cooperation of SWI/SNF and transcription factors
-
Xu,R. et al. (2007) Extracellular matrix-regulated gene expression requires cooperation of SWI/SNF and transcription factors. J. Biol. Chem., 282, 14992-14999.
-
(2007)
J. Biol. Chem.
, vol.282
, pp. 14992-14999
-
-
Xu, R.1
-
41
-
-
33846214719
-
Prevalence of the initiator over the TATA box in human and yeast genes and identification of DNA motifs enriched in human TATA-less core promoters
-
Yang,C. et al. (2007) Prevalence of the initiator over the TATA box in human and yeast genes and identification of DNA motifs enriched in human TATA-less core promoters. Gene, 389, 52-65.
-
(2007)
Gene.
, vol.389
, pp. 52-65
-
-
Yang, C.1
-
42
-
-
84879357102
-
JMOSAiCS: Joint analysis of multiple ChIP-seq datasets
-
Zeng,X. et al. (2013) jMOSAiCS: joint analysis of multiple ChIP-seq datasets. Genome Biol., 14, R38.
-
(2013)
Genome Biol.
, vol.14
, pp. R38
-
-
Zeng, X.1
-
43
-
-
34548504321
-
A novel role of Brg1 in the regulation of SRF/MRTFAdependent smooth muscle-specific gene expression
-
Zhang,M. et al. (2007) A novel role of Brg1 in the regulation of SRF/MRTFAdependent smooth muscle-specific gene expression. J. Biol. Chem., 282, 25708-25716.
-
(2007)
J. Biol. Chem.
, vol.282
, pp. 25708-25716
-
-
Zhang, M.1
-
44
-
-
0037869164
-
Criterion functions for document clustering: Experiments and analysis
-
In: Technical report. University of Minnesota
-
Zhao,Y. and Karypis,G. (2002) Criterion functions for document clustering: experiments and analysis. In: Technical report. Department of Computer Science, University of Minnesota.
-
(2002)
Department of Computer Science.
-
-
Zhao, Y.1
Karypis, G.2
|