-
1
-
-
0034704248
-
Genome-wide location and function of DNA binding proteins
-
Ren, B., Robert, F., Wyrick, J.J., et al.: Genome-wide location and function of DNA binding proteins. Science 290, 2306-2309 (2000)
-
(2000)
Science
, vol.290
, pp. 2306-2309
-
-
Ren, B.1
Robert, F.2
Wyrick, J.J.3
-
2
-
-
34250159524
-
Genome-wide mapping of in vivo protein-DNA interactions
-
Johnson, D.S., Mortazavi, A., Myers, R.M., Wold, B.: Genome-wide mapping of in vivo protein-DNA interactions. Science 316, 1497-1502 (2007)
-
(2007)
Science
, vol.316
, pp. 1497-1502
-
-
Johnson, D.S.1
Mortazavi, A.2
Myers, R.M.3
Wold, B.4
-
3
-
-
33750882505
-
Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities
-
Berger, M.F., Philippakis, A.A., Qureshi, A.M., et al.: Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nat. Biotech. 24, 1429-1435 (2006)
-
(2006)
Nat. Biotech.
, vol.24
, pp. 1429-1435
-
-
Berger, M.F.1
Philippakis, A.A.2
Qureshi, A.M.3
-
4
-
-
78651303899
-
UniPROBE, update 2011: Expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions
-
Robasky, K., Bulyk, M.L.: UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions. Nucleic Acids Research 39, D124-D128 (2011)
-
(2011)
Nucleic Acids Research
, vol.39
-
-
Robasky, K.1
Bulyk, M.L.2
-
5
-
-
33644876958
-
TRANSFAC and its module TRANSCompel: Transcriptional gene regulation in eukaryotes
-
Matys, V., Kel-Margoulis, O.V., Fricke, E., et al.: TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Research 34, D108-D110 (2006)
-
(2006)
Nucleic Acids Research
, vol.34
-
-
Matys, V.1
Kel-Margoulis, O.V.2
Fricke, E.3
-
6
-
-
75549083247
-
JASPAR 2010: The greatly expanded open-access database of transcription factor binding profiles
-
Portales-Casamar, E., Thongjuea, S., Kwon, A.T., et al.: JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Research 38, D105-D110 (2010)
-
(2010)
Nucleic Acids Research
, vol.38
-
-
Portales-Casamar, E.1
Thongjuea, S.2
Kwon, A.T.3
-
7
-
-
67649982744
-
Diversity and complexity in DNA recognition by transcription factors
-
Badis, G., Berger, M.F., Philippakis, A.A., et al.: Diversity and complexity in DNA recognition by transcription factors. Science 324, 1720-1723 (2009)
-
(2009)
Science
, vol.324
, pp. 1720-1723
-
-
Badis, G.1
Berger, M.F.2
Philippakis, A.A.3
-
8
-
-
0037133707
-
The identification of E2F1-specific target genes
-
Wells, J., Graveel, C.R., Bartley, S.M., et al.: The identification of E2F1-specific target genes. Proc. Natl. Acad. Sci. U S A 99, 3890-3895 (2002)
-
(2002)
Proc. Natl. Acad. Sci. U S A
, vol.99
, pp. 3890-3895
-
-
Wells, J.1
Graveel, C.R.2
Bartley, S.M.3
-
9
-
-
70350270053
-
The E2F family and the role of E2F1 in apoptosis
-
Wu, Z., Zheng, S., Yu, Q.: The E2F family and the role of E2F1 in apoptosis. Int. J. Biochem. Cell Biol. 41, 2389-2397 (2009)
-
(2009)
Int. J. Biochem. Cell Biol.
, vol.41
, pp. 2389-2397
-
-
Wu, Z.1
Zheng, S.2
Yu, Q.3
-
10
-
-
0030688065
-
Subunit composition determines E2F DNA-binding site specificity
-
Tao, Y., Kassatly, R., Cress, W., Horowitz, J.: Subunit composition determines E2F DNA-binding site specificity. Mol. Cell Biol. 17, 6994-7007 (1997)
-
(1997)
Mol. Cell Biol.
, vol.17
, pp. 6994-7007
-
-
Tao, Y.1
Kassatly, R.2
Cress, W.3
Horowitz, J.4
-
11
-
-
34547641224
-
Genome-wide analyses reveal properties of redundant and specific promoter occupancy within the ETS gene family
-
Hollenhorst, P.C., Shah, A.A., Hopkins, C., Graves, B.J.: Genome-wide analyses reveal properties of redundant and specific promoter occupancy within the ETS gene family. Genes Dev. 21, 1882-1894 (2007)
-
(2007)
Genes Dev.
, vol.21
, pp. 1882-1894
-
-
Hollenhorst, P.C.1
Shah, A.A.2
Hopkins, C.3
Graves, B.J.4
-
12
-
-
77954954652
-
Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo
-
Wei, G.H., Badis, G., Berger, M.F., et al.: Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo. EMBO J. 29, 2147-2160 (2010)
-
(2010)
EMBO J.
, vol.29
, pp. 2147-2160
-
-
Wei, G.H.1
Badis, G.2
Berger, M.F.3
-
13
-
-
84862139720
-
Transcriptional dominance of Pax7 in adult myogenesis is due to high-affinity recognition of homeodomain motifs
-
Soleimani, V.D., Punch, V.G., Kawabe, Y.I., et al.: Transcriptional dominance of Pax7 in adult myogenesis is due to high-affinity recognition of homeodomain motifs. Dev. Cell 22, 1208-1220 (2012)
-
(2012)
Dev. Cell
, vol.22
, pp. 1208-1220
-
-
Soleimani, V.D.1
Punch, V.G.2
Kawabe, Y.I.3
-
14
-
-
35949000033
-
A comprehensive ChIP-chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals interchangeable roles of E2F family members
-
Xu, X., Bieda, M., Jin, V.X., et al.: A comprehensive ChIP-chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals interchangeable roles of E2F family members. Genome Research 17, 1550-1561 (2007)
-
(2007)
Genome Research
, vol.17
, pp. 1550-1561
-
-
Xu, X.1
Bieda, M.2
Jin, V.X.3
-
15
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
ENCODE Project Consortium
-
ENCODE Project Consortium, Bernstein, B., Birney, E., Dunham, I., Green, E., Gunter, C., Snyder,M.: An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012)
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
Bernstein, B.1
Birney, E.2
Dunham, I.3
Green, E.4
Gunter, C.5
Snyder, M.6
-
16
-
-
68949213578
-
Insights from genomic profiling of transcription factors
-
Farnham, P.J.: Insights from genomic profiling of transcription factors. Nat. Rev. Genet. 10, 605-616 (2009)
-
(2009)
Nat. Rev. Genet.
, vol.10
, pp. 605-616
-
-
Farnham, P.J.1
-
17
-
-
0034524132
-
The Myc/Max/Mad network and the transcriptional control of cell behavior
-
Grandori, C., Cowley, S.M., James, L.P., Eisenman, R.N.: The Myc/Max/Mad network and the transcriptional control of cell behavior. Annu. Rev. Cell Dev. Biol. 16, 653-699 (2000)
-
(2000)
Annu. Rev. Cell Dev. Biol.
, vol.16
, pp. 653-699
-
-
Grandori, C.1
Cowley, S.M.2
James, L.P.3
Eisenman, R.N.4
-
18
-
-
34249753618
-
Support-vector networks
-
Cortes, C., Vapnik, V.: Support-vector networks. Machine Learning 20, 273-297 (1995)
-
(1995)
Machine Learning
, vol.20
, pp. 273-297
-
-
Cortes, C.1
Vapnik, V.2
-
19
-
-
0035478854
-
Random forests
-
Breiman, L.: Random forests. Machine Learning 45, 5-32 (2001)
-
(2001)
Machine Learning
, vol.45
, pp. 5-32
-
-
Breiman, L.1
-
20
-
-
84861859517
-
ENCODE whole-genome data in the UCSC Genome Browser: Update
-
Rosenbloom, K.R., Dreszer, T.R., Long, J.C., et al.: ENCODE whole-genome data in the UCSC Genome Browser: update, Nucleic Acids Research 40, D912-D917 (2012)
-
(2012)
Nucleic Acids Research
, vol.40
-
-
Rosenbloom, K.R.1
Dreszer, T.R.2
Long, J.C.3
-
21
-
-
22344457014
-
EnoLOGOS: A versatile web tool for energy normalized sequence logos
-
Workman, C.T., Yin, Y., Corcoran, D., et al.: enoLOGOS: a versatile web tool for energy normalized sequence logos. Nucl. Acids Res. 33, W389 (2005)
-
(2005)
Nucl. Acids Res.
, vol.33
-
-
Workman, C.T.1
Yin, Y.2
Corcoran, D.3
-
22
-
-
0034072450
-
DNA binding sites: Representation and discovery
-
Stormo, G.D.: DNA binding sites: representation and discovery. Bioinformatics 16, 16-23 (2000)
-
(2000)
Bioinformatics
, vol.16
, pp. 16-23
-
-
Stormo, G.D.1
-
23
-
-
70350731108
-
Distinguishing direct versus indirect transcription factor-DNA interactions
-
Gordân, R., Hartemink, A., Bulyk, M.: Distinguishing direct versus indirect transcription factor-DNA interactions. Genome Res. 19, 2090-2100 (2009)
-
(2009)
Genome Res.
, vol.19
, pp. 2090-2100
-
-
Gordân, R.1
Hartemink, A.2
Bulyk, M.3
-
24
-
-
77956276383
-
DNase-seq: A high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells
-
pdb.prot5384
-
Song, L., Crawford, G.E.: DNase-seq: A high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells. Cold Spring Harbor Protocols 2010, pdb.prot5384 (2010)
-
(2010)
Cold Spring Harbor Protocols
, vol.2010
-
-
Song, L.1
Crawford, G.E.2
-
26
-
-
77954485448
-
On safari to random jungle: A fast implementation of random forests for high-dimensional data
-
Schwarz, D.F., König, I.R., Ziegler, A.: On safari to random jungle: a fast implementation of random forests for high-dimensional data. Bioinformatics 26, 1752-1758 (2010)
-
(2010)
Bioinformatics
, vol.26
, pp. 1752-1758
-
-
Schwarz, D.F.1
König, I.R.2
Ziegler, A.3
-
27
-
-
30644464444
-
Gene selection and classification of microarray data using random forest
-
Díaz-Uriarte, R., Alvarez de Andrés, S.: Gene selection and classification of microarray data using random forest. BMC Bioinformatics 7, 3 (2006)
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 3
-
-
Díaz-Uriarte, R.1
Alvarez De Andrés, S.2
-
28
-
-
1442303228
-
Autorepression of c-myc requires both initiator and E2F-binding site elements and cooperation with the p107 gene product
-
Luo, Q., Li, J., Cenkci, B., Kretzner, L.: Autorepression of c-myc requires both initiator and E2F-binding site elements and cooperation with the p107 gene product. Oncogene 23, 1088-1097 (2004)
-
(2004)
Oncogene
, vol.23
, pp. 1088-1097
-
-
Luo, Q.1
Li, J.2
Cenkci, B.3
Kretzner, L.4
-
29
-
-
78649938792
-
Sp100 as a potent tumor suppressor: Accelerated senescence and rapid malignant transformation of human fibroblasts through modulation of an embryonic stem cell program
-
Negorev, D.G., Vladimirova, O.V., Kossenkov, A.V., et al.: Sp100 as a potent tumor suppressor: accelerated senescence and rapid malignant transformation of human fibroblasts through modulation of an embryonic stem cell program. Cancer Research 70, 9991-10001 (2010)
-
(2010)
Cancer Research
, vol.70
, pp. 9991-10001
-
-
Negorev, D.G.1
Vladimirova, O.V.2
Kossenkov, A.V.3
-
30
-
-
0031571164
-
The human gene ZFP161 on 18p11.21-pter encodes a putative c-myc repressor and is homologous to murine Zfp161 (Chr 17) and Zfp161-rs1 (X Chr)
-
Sobek-Klocke, I., Disque-Kochem, C., Ronsiek, M., Klocke, R., et al.: The human gene ZFP161 on 18p11.21-pter encodes a putative c-myc repressor and is homologous to murine Zfp161 (Chr 17) and Zfp161-rs1 (X Chr). Genomics 43, 156-164 (1997)
-
(1997)
Genomics
, vol.43
, pp. 156-164
-
-
Sobek-Klocke, I.1
Disque-Kochem, C.2
Ronsiek, M.3
Klocke, R.4
-
31
-
-
80054122132
-
Searching ChIP-seq genomic islands for combinatorial regulatory codes in mouse ES cells
-
Chen, G., Zhou, Q.: Searching ChIP-seq genomic islands for combinatorial regulatory codes in mouse ES cells. BMC Genomics 12, 515 (2011)
-
(2011)
BMC Genomics
, vol.12
, pp. 515
-
-
Chen, G.1
Zhou, Q.2
-
32
-
-
79958117256
-
MEME-ChIP: Motif analysis of large DNA datasets
-
Machanick, P., Bailey, T.L.: MEME-ChIP: motif analysis of large DNA datasets. Bioinformatics 27, 1696-1697 (2011)
-
(2011)
Bioinformatics
, vol.27
, pp. 1696-1697
-
-
Machanick, P.1
Bailey, T.L.2
-
33
-
-
84857859359
-
RSAT peak-motifs: Motif analysis in full-size ChIP-seq datasets
-
Thomas-Chollier, M., Herrmann, C., Defrance, M., et al.: RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets. NAR 40, e31 (2012)
-
(2012)
NAR
, vol.40
-
-
Thomas-Chollier, M.1
Herrmann, C.2
Defrance, M.3
-
34
-
-
80055092183
-
Inferring transcription factor complexes from ChIP-seq data
-
Whitington, T., Frith, M.C., Johnson, J., Bailey, T.L.: Inferring transcription factor complexes from ChIP-seq data. NAR 39, e98 (2011)
-
(2011)
NAR
, vol.39
-
-
Whitington, T.1
Frith, M.C.2
Johnson, J.3
Bailey, T.L.4
-
35
-
-
84865739425
-
Architecture of the human regulatory network derived from ENCODE data
-
Gerstein, M.B., Kundaje, A., Hariharan, M., 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
Kundaje, A.2
Hariharan, M.3
|