-
1
-
-
46249106990
-
Mapping and quantifying mammalian transcriptomes by RNA-Seq
-
Mortazavi A, et al. (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5:621-628.
-
(2008)
Nat Methods
, vol.5
, pp. 621-628
-
-
Mortazavi, A.1
-
2
-
-
46249103973
-
Stem cell transcriptome profiling via massive-scale mRNA sequencing
-
Cloonan N, et al. (2008) Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat Methods 5:613-619.
-
(2008)
Nat Methods
, vol.5
, pp. 613-619
-
-
Cloonan, N.1
-
3
-
-
25144525014
-
Core transcriptional regulatory circuitry in human embryonic stem cells
-
Boyer LA, et al. (2005) Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 122:947-956.
-
(2005)
Cell
, vol.122
, pp. 947-956
-
-
Boyer, L.A.1
-
4
-
-
34250159524
-
Genome-wide mapping of in vivo protein-DNA interactions
-
Johnson DS, Mortazavi A, Myers RM, Wold B (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
Mortazavi, A.2
Myers, R.M.3
Wold, B.4
-
5
-
-
0035135420
-
Regulatory element detection using correlation with expression
-
Bussemaker HJ, Li H, Siggia ED (2001) Regulatory element detection using correlation with expression. Nat Genet 27:167-171.
-
(2001)
Nat Genet
, vol.27
, pp. 167-171
-
-
Bussemaker, H.J.1
Li, H.2
Siggia, E.D.3
-
6
-
-
0036740483
-
Identification of regulatory elements using a feature selection method
-
Keles S, van der Laan M, Eisen MB (2002) Identification of regulatory elements using a feature selection method. Bioinformatics 18:1167-1175.
-
(2002)
Bioinformatics
, vol.18
, pp. 1167-1175
-
-
Keles, S.1
van der Laan, M.2
Eisen, M.B.3
-
7
-
-
0037453009
-
Integrating regulatory motif discovery and genome-wide expression analysis
-
Conlon EM, Liu XS, Lieb JD, Liu JS (2003) Integrating regulatory motif discovery and genome-wide expression analysis. Proc Natl Acad Sci USA 100:3339-3344.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 3339-3344
-
-
Conlon, E.M.1
Liu, X.S.2
Lieb, J.D.3
Liu, J.S.4
-
8
-
-
2942582468
-
Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data
-
Gao F, Foat BC, Bussemaker HJ (2004) Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data. BMC Bioinformatics 5:31.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 31
-
-
Gao, F.1
Foat, B.C.2
Bussemaker, H.J.3
-
9
-
-
0345824737
-
Network component analysis: Reconstruction of regulatory signals in biological systems
-
Liao JC, et al. (2003) Network component analysis: Reconstruction of regulatory signals in biological systems. Proc Natl Acad Sci USA 100:15522-15527.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 15522-15527
-
-
Liao, J.C.1
-
10
-
-
9244257298
-
Interacting models of cooperative gene regulation
-
Das D, Banerjee N, Zhang MQ (2004) Interacting models of cooperative gene regulation. Proc Natl Acad Sci USA 101:16234-16239.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 16234-16239
-
-
Das, D.1
Banerjee, N.2
Zhang, M.Q.3
-
11
-
-
33745440791
-
-
Das D, Nahl Z, Zhang MQ (2006) Adaptively inferring human transcriptional subnetworks. Mol Syst Biol 2:msb4100067.
-
Das D, Nahl Z, Zhang MQ (2006) Adaptively inferring human transcriptional subnetworks. Mol Syst Biol 2:msb4100067.
-
-
-
-
12
-
-
33744501241
-
Bayesian error analysis model for reconstructing transcriptional regulatory networks
-
Sun N, Carroll RJ, Zhao H (2006) Bayesian error analysis model for reconstructing transcriptional regulatory networks. Proc Natl Acad Sci USA 103:7988-7993.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 7988-7993
-
-
Sun, N.1
Carroll, R.J.2
Zhao, H.3
-
13
-
-
47249118465
-
Extracting sequence features to predict protein-DNA interactions: A comparative study
-
Zhou Q, Liu JS (2008) Extracting sequence features to predict protein-DNA interactions: a comparative study. Nucleic Acids Res 36:4137-4148.
-
(2008)
Nucleic Acids Res
, vol.36
, pp. 4137-4148
-
-
Zhou, Q.1
Liu, J.S.2
-
14
-
-
23744491001
-
Predicting transcription factor activities from combined analysis of microarray and ChIP data:Apartial least squares approach
-
Boulesteix AL, Strimmer K (2005) Predicting transcription factor activities from combined analysis of microarray and ChIP data:Apartial least squares approach. Theor Biol Med Model 2:23.
-
(2005)
Theor Biol Med Model
, vol.2
, pp. 23
-
-
Boulesteix, A.L.1
Strimmer, K.2
-
15
-
-
33745431808
-
-
Nguyen DH, D'Haeseleer P (2006) Deciphering principles of transcription regulation in eukaryotic genomes. Mol Syst Biol 2:msb4100054.
-
Nguyen DH, D'Haeseleer P (2006) Deciphering principles of transcription regulation in eukaryotic genomes. Mol Syst Biol 2:msb4100054.
-
-
-
-
16
-
-
67149141513
-
Learning global models of transcriptional regulatory networks from data
-
Madar A, Bonneau R (2009) Learning global models of transcriptional regulatory networks from data. Methods Mol Biol 541:1-30.
-
(2009)
Methods Mol Biol
, vol.541
, pp. 1-30
-
-
Madar, A.1
Bonneau, R.2
-
17
-
-
6044269157
-
Self-renewal of teratocarcinoma and embryonic stem cells
-
Chambers I, Smith A (2004) Self-renewal of teratocarcinoma and embryonic stem cells. Oncogene 23:7150-7160.
-
(2004)
Oncogene
, vol.23
, pp. 7150-7160
-
-
Chambers, I.1
Smith, A.2
-
18
-
-
33746773659
-
Dissecting self-renewal in stem cells with RNA interference
-
Ivanova N, et al. (2006) Dissecting self-renewal in stem cells with RNA interference. Nature 442:533-538.
-
(2006)
Nature
, vol.442
, pp. 533-538
-
-
Ivanova, N.1
-
19
-
-
33751092246
-
Aprotein interaction network for pluripotency of embryonic stem cells
-
WangJ, et al. (2006)Aprotein interaction network for pluripotency of embryonic stem cells. Nature 444:364-368.
-
(2006)
Nature
, vol.444
, pp. 364-368
-
-
WangJ1
-
20
-
-
44649117905
-
Integration of external signaling pathways with the core transcriptional network in embryonic stem cells
-
Chen X, et al. (2008) Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 133:1106-1117.
-
(2008)
Cell
, vol.133
, pp. 1106-1117
-
-
Chen, X.1
-
22
-
-
18244384210
-
Multiple-laboratory comparison of microarray platforms
-
Irizarry RA, et al. (2005) Multiple-laboratory comparison of microarray platforms. Nat Methods 2:345-350.
-
(2005)
Nat Methods
, vol.2
, pp. 345-350
-
-
Irizarry, R.A.1
-
23
-
-
33748491517
-
The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements
-
Shi L, et al. (2006) The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 24:1151-1161.
-
(2006)
Nat Biotechnol
, vol.24
, pp. 1151-1161
-
-
Shi, L.1
-
24
-
-
33746108159
-
A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies
-
Kuo WP, et al. (2006) A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies. Nat Biotechnol 24:832-840.
-
(2006)
Nat Biotechnol
, vol.24
, pp. 832-840
-
-
Kuo, W.P.1
-
25
-
-
0038005018
-
DAVID: Database for Annotation, Visualization, and Integrated Discovery
-
Dennis G, Jr, et al. (2003) DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol 4:P3.
-
(2003)
Genome Biol
, vol.4
-
-
Dennis Jr, G.1
-
27
-
-
33745140886
-
Unbiased location analysis of E2F1-binding sites suggests awidespread role for E2F1 in the human genome
-
Bieda M, Xu X, Singer MA, Green R, Farnham PJ (2006) Unbiased location analysis of E2F1-binding sites suggests awidespread role for E2F1 in the human genome. Genome Res 16:595-605.
-
(2006)
Genome Res
, vol.16
, pp. 595-605
-
-
Bieda, M.1
Xu, X.2
Singer, M.A.3
Green, R.4
Farnham, P.J.5
-
28
-
-
33745737494
-
Myc-binding-site recognition in the human genome is determined by chromatin context
-
Guccione E, et al. (2006) Myc-binding-site recognition in the human genome is determined by chromatin context. Nat Cell Biol 8:764-770.
-
(2006)
Nat Cell Biol
, vol.8
, pp. 764-770
-
-
Guccione, E.1
-
29
-
-
40749104852
-
An extended transcriptional network for pluripotency of embryonic stem cells
-
Kim J, Chu J, Shen X, Wang J, Orkin SH (2008) An extended transcriptional network for pluripotency of embryonic stem cells. Cell 132:1049-1061.
-
(2008)
Cell
, vol.132
, pp. 1049-1061
-
-
Kim, J.1
Chu, J.2
Shen, X.3
Wang, J.4
Orkin, S.H.5
-
30
-
-
33646882068
-
Polycomb complexes repress developmental regulators in murine embryonic stem cells
-
Boyer LA, et al. (2006) Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature 441:349-353.
-
(2006)
Nature
, vol.441
, pp. 349-353
-
-
Boyer, L.A.1
-
31
-
-
33646865180
-
Control of developmental regulators by Polycomb in human embryonic stem cells
-
Lee TI, et al. (2006) Control of developmental regulators by Polycomb in human embryonic stem cells. Cell 125:301-313.
-
(2006)
Cell
, vol.125
, pp. 301-313
-
-
Lee, T.I.1
-
32
-
-
44649086468
-
Nanog and Oct4 associate with unique transcriptional repression complexes in embryonic stem cells
-
Liang J, et al. (2008) Nanog and Oct4 associate with unique transcriptional repression complexes in embryonic stem cells. Nat Cell Biol 10:731-739.
-
(2008)
Nat Cell Biol
, vol.10
, pp. 731-739
-
-
Liang, J.1
-
33
-
-
33747072322
-
Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster
-
Moorman C, et al. (2006) Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster. Proc Natl Acad Sci USA 103:12027-12032.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 12027-12032
-
-
Moorman, C.1
-
34
-
-
40149095913
-
Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm
-
Li XY, et al. (2008) Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biol 6:e27.
-
(2008)
PLoS Biol
, vol.6
-
-
Li, X.Y.1
-
35
-
-
55749094855
-
An integrated software system for analyzing ChIP-chip and ChIP-seq data
-
Ji H, et al. (2008) An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat Biotechnol 26:1293-1300.
-
(2008)
Nat Biotechnol
, vol.26
, pp. 1293-1300
-
-
Ji, H.1
-
36
-
-
0034682504
-
Fundamental patterns underlying gene expression profiles: Simplicity from complexity
-
Holter NS, et al. (2000) Fundamental patterns underlying gene expression profiles: simplicity from complexity. Proc Natl Acad Sci USA 97:8409-8414.
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, pp. 8409-8414
-
-
Holter, N.S.1
-
37
-
-
0034730140
-
Singular value decomposition for genome-wide expression data processing and modeling
-
Alter O, Brown PO, Botstein D (2000) Singular value decomposition for genome-wide expression data processing and modeling. Proc Natl Acad Sci USA 97:10101-10106.
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, pp. 10101-10106
-
-
Alter, O.1
Brown, P.O.2
Botstein, D.3
-
38
-
-
34250366235
-
Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions
-
Zhang ZD, et al. (2007) Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions. Genome Res 17:787-797.
-
(2007)
Genome Res
, vol.17
, pp. 787-797
-
-
Zhang, Z.D.1
|