-
1
-
-
84923362619
-
Integrative analysis of 111 reference human epigenomes
-
Roadmap Epigenomics Consortium Integrative analysis of 111 reference human epigenomes. Nature 2015, 518:317-330.
-
(2015)
Nature
, vol.518
, pp. 317-330
-
-
-
2
-
-
84878682420
-
The genotype-tissue expression (GTEx) project
-
GTEx Consortium The genotype-tissue expression (GTEx) project. Nat Genet 2013, 45:580-585.
-
(2013)
Nat Genet
, vol.45
, pp. 580-585
-
-
-
3
-
-
84934922563
-
The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge
-
Tomczak K., Czerwinska P., Wiznerowicz M. The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge. Contemp Oncol (Pozn) 2015, 19:A68-A77.
-
(2015)
Contemp Oncol (Pozn)
, vol.19
, pp. A68-A77
-
-
Tomczak, K.1
Czerwinska, P.2
Wiznerowicz, M.3
-
4
-
-
0034072450
-
DNA binding sites: representation and discovery
-
Stormo G.D. DNA binding sites: representation and discovery. Bioinformatics 2000, 16:16-23.
-
(2000)
Bioinformatics
, vol.16
, pp. 16-23
-
-
Stormo, G.D.1
-
5
-
-
33750882505
-
Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities
-
Berger M.F., et al. Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nat Biotechnol 2006, 24:1429-1435.
-
(2006)
Nat Biotechnol
, vol.24
, pp. 1429-1435
-
-
Berger, M.F.1
-
6
-
-
32244448130
-
Defining the sequence-recognition profile of DNA-binding molecules
-
Warren C.L., et al. Defining the sequence-recognition profile of DNA-binding molecules. Proc Natl Acad Sci USA 2006, 103:867-872.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 867-872
-
-
Warren, C.L.1
-
7
-
-
77958096076
-
Determining the specificity of protein-DNA interactions
-
Stormo G.D., Zhao Y. Determining the specificity of protein-DNA interactions. Nat Rev Genet 2010, 11:751-760.
-
(2010)
Nat Rev Genet
, vol.11
, pp. 751-760
-
-
Stormo, G.D.1
Zhao, Y.2
-
8
-
-
77953006022
-
Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities
-
Jolma A., et al. Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities. Genome Res 2010, 20:861-873.
-
(2010)
Genome Res
, vol.20
, pp. 861-873
-
-
Jolma, A.1
-
9
-
-
83255188878
-
Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins
-
Slattery M., et al. Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins. Cell 2011, 147:1270-1282.
-
(2011)
Cell
, vol.147
, pp. 1270-1282
-
-
Slattery, M.1
-
10
-
-
85045330440
-
SMiLE-seq identifies binding motifs of single and dimeric transcription factors
-
Isakova A., et al. SMiLE-seq identifies binding motifs of single and dimeric transcription factors. Nat Methods 2017, 351:1450-1454.
-
(2017)
Nat Methods
, vol.351
, pp. 1450-1454
-
-
Isakova, A.1
-
11
-
-
84873594686
-
Evaluation of methods for modeling transcription factor sequence specificity
-
Weirauch M.T., et al. Evaluation of methods for modeling transcription factor sequence specificity. Nat Biotechnol 2013, 31:126-134.
-
(2013)
Nat Biotechnol
, vol.31
, pp. 126-134
-
-
Weirauch, M.T.1
-
12
-
-
34347237542
-
Predictive modeling of genome-wide mRNA expression: from modules to molecules
-
Bussemaker H.J., Foat B.C., Ward L.D. Predictive modeling of genome-wide mRNA expression: from modules to molecules. Annu Rev Biophys Biomol Struct 2007, 36:329-347.
-
(2007)
Annu Rev Biophys Biomol Struct
, vol.36
, pp. 329-347
-
-
Bussemaker, H.J.1
Foat, B.C.2
Ward, L.D.3
-
13
-
-
23144463134
-
T-profiler: scoring the activity of predefined groups of genes using gene expression data
-
Boorsma A., et al. T-profiler: scoring the activity of predefined groups of genes using gene expression data. Nucleic Acids Res 2005, 33(Web Server issue):W592-W595.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. W592-W595
-
-
Boorsma, A.1
-
14
-
-
27344435774
-
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles
-
Subramanian A., et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 2005, 102:15545-15550.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 15545-15550
-
-
Subramanian, A.1
-
15
-
-
52349095482
-
Inferring condition-specific modulation of transcription factor activity in yeast through regulon-based analysis of genomewide expression
-
Boorsma A., et al. Inferring condition-specific modulation of transcription factor activity in yeast through regulon-based analysis of genomewide expression. PLoS One 2008, 3:e3112.
-
(2008)
PLoS One
, vol.3
-
-
Boorsma, A.1
-
16
-
-
16844376909
-
Reverse engineering of regulatory networks in human B cells
-
Basso K., et al. Reverse engineering of regulatory networks in human B cells. Nat Genet 2005, 37:382-390.
-
(2005)
Nat Genet
, vol.37
, pp. 382-390
-
-
Basso, K.1
-
17
-
-
84975246805
-
Functional characterization of somatic mutations in cancer using network-based inference of protein activity
-
Alvarez M.J., et al. Functional characterization of somatic mutations in cancer using network-based inference of protein activity. Nat Genet 2016, 48:838-847.
-
(2016)
Nat Genet
, vol.48
, pp. 838-847
-
-
Alvarez, M.J.1
-
18
-
-
35348955882
-
A universal framework for regulatory element discovery across all genomes and data types
-
Elemento O., Slonim N., Tavazoie S. A universal framework for regulatory element discovery across all genomes and data types. Mol Cell 2007, 28:337-350.
-
(2007)
Mol Cell
, vol.28
, pp. 337-350
-
-
Elemento, O.1
Slonim, N.2
Tavazoie, S.3
-
19
-
-
0035135420
-
Regulatory element detection using correlation with expression
-
Bussemaker H.J., Li H., Siggia E.D. Regulatory element detection using correlation with expression. Nat Genet 2001, 27:167-171.
-
(2001)
Nat Genet
, vol.27
, pp. 167-171
-
-
Bussemaker, H.J.1
Li, H.2
Siggia, E.D.3
-
20
-
-
0037168519
-
A systematic approach to reconstructing transcription networks in Saccharomyces cerevisiae
-
Wang W., et al. A systematic approach to reconstructing transcription networks in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 2002, 99:16893-16898.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 16893-16898
-
-
Wang, W.1
-
21
-
-
33748191291
-
Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE
-
Foat B.C., Morozov A.V., Bussemaker H.J. Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE. Bioinformatics 2006, 22:e141-e149.
-
(2006)
Bioinformatics
, vol.22
-
-
Foat, B.C.1
Morozov, A.V.2
Bussemaker, H.J.3
-
22
-
-
46249089455
-
Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences
-
Ward L.D., Bussemaker H.J. Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences. Bioinformatics 2008, 24:i165-i171.
-
(2008)
Bioinformatics
, vol.24
-
-
Ward, L.D.1
Bussemaker, H.J.2
-
23
-
-
84899806626
-
ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs
-
Balwierz P.J., et al. ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs. Genome Res 2014, 24:869-884.
-
(2014)
Genome Res
, vol.24
, pp. 869-884
-
-
Balwierz, P.J.1
-
24
-
-
84929456295
-
Linking signaling pathways to transcriptional programs in breast cancer
-
Osmanbeyoglu H.U., et al. Linking signaling pathways to transcriptional programs in breast cancer. Genome Res 2014, 24:1869-1880.
-
(2014)
Genome Res
, vol.24
, pp. 1869-1880
-
-
Osmanbeyoglu, H.U.1
-
25
-
-
77957273682
-
Identifying the genetic determinants of transcription factor activity
-
Lee E., Bussemaker H.J. Identifying the genetic determinants of transcription factor activity. Mol Syst Biol 2010, 6:412.
-
(2010)
Mol Syst Biol
, vol.6
, pp. 412
-
-
Lee, E.1
Bussemaker, H.J.2
-
26
-
-
0037177625
-
Genetic dissection of transcriptional regulation in budding yeast
-
Brem R.B., et al. Genetic dissection of transcriptional regulation in budding yeast. Science 2002, 296:752-755.
-
(2002)
Science
, vol.296
, pp. 752-755
-
-
Brem, R.B.1
-
27
-
-
84898787688
-
Identifying regulatory mechanisms underlying tumorigenesis using locus expression signature analysis
-
Lee E., et al. Identifying regulatory mechanisms underlying tumorigenesis using locus expression signature analysis. Proc Natl Acad Sci USA 2014, 111:5747-5752.
-
(2014)
Proc Natl Acad Sci USA
, vol.111
, pp. 5747-5752
-
-
Lee, E.1
-
28
-
-
84915815121
-
Identification of causal genetic drivers of human disease through systems-level analysis of regulatory networks
-
Chen J.C., et al. Identification of causal genetic drivers of human disease through systems-level analysis of regulatory networks. Cell 2014, 159:402-414.
-
(2014)
Cell
, vol.159
, pp. 402-414
-
-
Chen, J.C.1
-
29
-
-
34250735674
-
RNA regulons: coordination of post-transcriptional events
-
Keene J.D. RNA regulons: coordination of post-transcriptional events. Nat Rev Genet 2007, 8:533-543.
-
(2007)
Nat Rev Genet
, vol.8
, pp. 533-543
-
-
Keene, J.D.1
-
30
-
-
19344365947
-
Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast
-
Gerber A.P., Herschlag D., Brown P.O. Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast. PLoS Biol 2004, 2:E79.
-
(2004)
PLoS Biol
, vol.2
, pp. E79
-
-
Gerber, A.P.1
Herschlag, D.2
Brown, P.O.3
-
31
-
-
29144500327
-
Profiling condition-specific, genome-wide regulation of mRNA stability in yeast
-
Foat B.C., et al. Profiling condition-specific, genome-wide regulation of mRNA stability in yeast. Proc Natl Acad Sci USA 2005, 102:17675-17680.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 17675-17680
-
-
Foat, B.C.1
-
32
-
-
84959926512
-
Inferred miRNA activity identifies miRNA-mediated regulatory networks underlying multiple cancers
-
Lee E., et al. Inferred miRNA activity identifies miRNA-mediated regulatory networks underlying multiple cancers. Bioinformatics 2016, 32:96-105.
-
(2016)
Bioinformatics
, vol.32
, pp. 96-105
-
-
Lee, E.1
-
33
-
-
33749037129
-
Identifying regulatory mechanisms using individual variation reveals key role for chromatin modification
-
Lee S.I., et al. Identifying regulatory mechanisms using individual variation reveals key role for chromatin modification. Proc Natl Acad Sci USA 2006, 103:14062-14067.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 14062-14067
-
-
Lee, S.I.1
-
34
-
-
84906222360
-
Harnessing natural sequence variation to dissect posttranscriptional regulatory networks in yeast
-
Fazlollahi M., et al. Harnessing natural sequence variation to dissect posttranscriptional regulatory networks in yeast. G3 (Bethesda) 2014, 4:1539-1553.
-
(2014)
G3 (Bethesda)
, vol.4
, pp. 1539-1553
-
-
Fazlollahi, M.1
-
35
-
-
34547874585
-
Divergence of transcription factor binding sites across related yeast species
-
Borneman A.R., et al. Divergence of transcription factor binding sites across related yeast species. Science 2007, 317:815-819.
-
(2007)
Science
, vol.317
, pp. 815-819
-
-
Borneman, A.R.1
-
36
-
-
84979608897
-
The genetics of transcription factor DNA binding variation
-
Deplancke B., Alpern D., Gardeux V. The genetics of transcription factor DNA binding variation. Cell 2016, 166:538-554.
-
(2016)
Cell
, vol.166
, pp. 538-554
-
-
Deplancke, B.1
Alpern, D.2
Gardeux, V.3
-
37
-
-
84859916280
-
Effects of sequence variation on differential allelic transcription factor occupancy and gene expression
-
Reddy T.E., et al. Effects of sequence variation on differential allelic transcription factor occupancy and gene expression. Genome Res 2012, 22:860-869.
-
(2012)
Genome Res
, vol.22
, pp. 860-869
-
-
Reddy, T.E.1
-
38
-
-
84976908652
-
Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks
-
Kelley D.R., Snoek J., Rinn J.L. Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks. Genome Res 2016, 26:990-999.
-
(2016)
Genome Res
, vol.26
, pp. 990-999
-
-
Kelley, D.R.1
Snoek, J.2
Rinn, J.L.3
-
39
-
-
84958257565
-
Predicting effects of noncoding variants with deep learning-based sequence model
-
Zhou J., Troyanskaya O.G. Predicting effects of noncoding variants with deep learning-based sequence model. Nat Methods 2015, 12:931-934.
-
(2015)
Nat Methods
, vol.12
, pp. 931-934
-
-
Zhou, J.1
Troyanskaya, O.G.2
-
40
-
-
84938276507
-
A method to predict the impact of regulatory variants from DNA sequence
-
Lee D., et al. A method to predict the impact of regulatory variants from DNA sequence. Nat Genet 2015, 47:955-961.
-
(2015)
Nat Genet
, vol.47
, pp. 955-961
-
-
Lee, D.1
-
41
-
-
85014164610
-
Genetic regulatory signatures underlying islet gene expression and type 2 diabetes
-
Varshney A., et al. Genetic regulatory signatures underlying islet gene expression and type 2 diabetes. Proc Natl Acad Sci USA 2017, 114:2301-2306.
-
(2017)
Proc Natl Acad Sci USA
, vol.114
, pp. 2301-2306
-
-
Varshney, A.1
-
42
-
-
84962217539
-
Survey of variation in human transcription factors reveals prevalent DNA binding changes
-
Barrera L.A., et al. Survey of variation in human transcription factors reveals prevalent DNA binding changes. Science 2016, 351:1450-1454.
-
(2016)
Science
, vol.351
, pp. 1450-1454
-
-
Barrera, L.A.1
-
43
-
-
85012297184
-
Promoter shape varies across populations and affects promoter evolution and expression noise
-
Schor I.E., et al. Promoter shape varies across populations and affects promoter evolution and expression noise. Nat Genet 2017, 49:550-558.
-
(2017)
Nat Genet
, vol.49
, pp. 550-558
-
-
Schor, I.E.1
-
44
-
-
0036699526
-
Revealing modular organization in the yeast transcriptional network
-
Ihmels J., et al. Revealing modular organization in the yeast transcriptional network. Nat Genet 2002, 31:370-377.
-
(2002)
Nat Genet
, vol.31
, pp. 370-377
-
-
Ihmels, J.1
-
45
-
-
0345824737
-
Network component analysis: reconstruction of regulatory signals in biological systems
-
Liao J.C., et al. Network component analysis: reconstruction of regulatory signals in biological systems. Proc Natl Acad Sci USA 2003, 100:15522-15527.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 15522-15527
-
-
Liao, J.C.1
-
46
-
-
2942582468
-
Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data
-
Gao F., Foat B.C., Bussemaker H.J. Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data. BMC Bioinformatics 2004, 5:31.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 31
-
-
Gao, F.1
Foat, B.C.2
Bussemaker, H.J.3
-
47
-
-
84897394513
-
The functional consequences of variation in transcription factor binding
-
Cusanovich D.A., et al. The functional consequences of variation in transcription factor binding. PLoS Genet 2014, 10:e1004226.
-
(2014)
PLoS Genet
, vol.10
-
-
Cusanovich, D.A.1
-
48
-
-
70249108504
-
Genome-wide identification of post-translational modulators of transcription factor activity in human B cells
-
Wang K., et al. Genome-wide identification of post-translational modulators of transcription factor activity in human B cells. Nat Biotechnol 2009, 27:829-839.
-
(2009)
Nat Biotechnol
, vol.27
, pp. 829-839
-
-
Wang, K.1
-
49
-
-
84962034216
-
Identifying genetic modulators of the connectivity between transcription factors and their transcriptional targets
-
Fazlollahi M., et al. Identifying genetic modulators of the connectivity between transcription factors and their transcriptional targets. Proc Natl Acad Sci USA 2016, 113:E1835-E1843.
-
(2016)
Proc Natl Acad Sci USA
, vol.113
, pp. E1835-E1843
-
-
Fazlollahi, M.1
|