-
1
-
-
68949213578
-
Insights from genomic profiling of transcription factors
-
Farnham PJ: Insights from genomic profiling of transcription factors. Nat Rev Genet. 2009, 10 (9): 605-616. 10.1038/nrg2636.
-
(2009)
Nat Rev Genet
, vol.10
, Issue.9
, pp. 605-616
-
-
Farnham, P.J.1
-
2
-
-
33746691336
-
Extensive low-affinity transcriptional interactions in the yeast genome
-
Tanay A: Extensive low-affinity transcriptional interactions in the yeast genome. Genome Research. 2006, 16 (8): 962-972. 10.1101/gr.5113606.
-
(2006)
Genome Research
, vol.16
, Issue.8
, pp. 962-972
-
-
Tanay, A.1
-
3
-
-
70350731108
-
Distinguishing direct versus indirect transcription factor-DNA interactions
-
Gordan R, Hartemink AJ, Bulyk ML: Distinguishing direct versus indirect transcription factor-DNA interactions. Genome Research. 2009, 19 (11): 2090-2100. 10.1101/gr.094144.109.
-
(2009)
Genome Research
, vol.19
, Issue.11
, pp. 2090-2100
-
-
Gordan, R.1
Hartemink, A.J.2
Bulyk, M.L.3
-
4
-
-
70349312354
-
ChIP-seq: advantages and challenges of a maturing technology
-
Park PJ: ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet. 2009, 10 (10): 669-680. 10.1038/nrg2641.
-
(2009)
Nat Rev Genet
, vol.10
, Issue.10
, pp. 669-680
-
-
Park, P.J.1
-
5
-
-
84873594686
-
Evaluation of methods for modeling transcription factor sequence specificity
-
Weirauch MT, Cote A, Norel R, Annala M, Zhao Y, Riley TR, et al: Evaluation of methods for modeling transcription factor sequence specificity. Nature Biotechnology. 31 (2): 126-134.
-
Nature Biotechnology
, vol.31
, Issue.2
, pp. 126-134
-
-
Weirauch, M.T.1
Cote, A.2
Norel, R.3
Annala, M.4
Zhao, Y.5
Riley, T.R.6
-
6
-
-
65249131241
-
Genome-wide discovery of functional transcription factor binding sites by comparative genomics: the case of Stat3
-
Vallania F, Schiavone D, Dewilde S, Pupo E, Garbay S, Calogero R, et al: Genome-wide discovery of functional transcription factor binding sites by comparative genomics: the case of Stat3. Proc Natl Acad Sci U S A. 2009, 106 (13): 5117-5122. 10.1073/pnas.0900473106.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, Issue.13
, pp. 5117-5122
-
-
Vallania, F.1
Schiavone, D.2
Dewilde, S.3
Pupo, E.4
Garbay, S.5
Calogero, R.6
-
7
-
-
84866937220
-
Machanick P: Inferring direct DNA binding from ChIP-seq
-
Bailey TL, Machanick P: Inferring direct DNA binding from ChIP-seq. Nucleic Acids Res. 40 (17): e128-
-
Nucleic Acids Res.
, vol.40
, Issue.17
, pp. e128
-
-
Bailey, T.L.1
-
8
-
-
70450265377
-
BayesPI - a new model to study protein-DNA interactions: a case study of condition-specific protein binding parameters for Yeast transcription factors
-
Wang J Morigen: BayesPI - a new model to study protein-DNA interactions: a case study of condition-specific protein binding parameters for Yeast transcription factors. BMC bioinformatics. 2009, 10: 345-10.1186/1471-2105-10-345.
-
(2009)
BMC bioinformatics
, vol.10
, pp. 345
-
-
Wang, M.J.1
-
9
-
-
84908138119
-
Quality versus accuracy: result of a reanalysis of protein-binding microarrays from the DREAM5 challenge by using BayesPI2 including dinucleotide interdependence.
-
Wang J: Quality versus accuracy: result of a reanalysis of protein-binding microarrays from the DREAM5 challenge by using BayesPI2 including dinucleotide interdependence. BMC bioinformatics. 15 (1): 289-
-
BMC bioinformatics
, vol.15
, Issue.1
, pp. 289
-
-
-
10
-
-
67649982744
-
Diversity and complexity in DNA recognition by transcription factors
-
Badis G, Berger MF, Philippakis AA, Talukder S, Gehrke AR, Jaeger SA, et al: Diversity and complexity in DNA recognition by transcription factors. Science. 2009, 324 (5935): 1720-1723. 10.1126/science.1162327.
-
(2009)
Science
, vol.324
, Issue.5935
, pp. 1720-1723
-
-
Badis, G.1
Berger, M.F.2
Philippakis, A.A.3
Talukder, S.4
Gehrke, A.R.5
Jaeger, S.A.6
-
11
-
-
77952062004
-
Estrogen receptor alpha controls a gene network in luminal-like breast cancer cells comprising multiple transcription factors and microRNAs
-
Cicatiello L, Mutarelli M, Grober OM, Paris O, Ferraro L, Ravo M, et al: Estrogen receptor alpha controls a gene network in luminal-like breast cancer cells comprising multiple transcription factors and microRNAs. Am J Pathol. 2010, 176 (5): 2113-2130. 10.2353/ajpath.2010.090837.
-
(2010)
Am J Pathol
, vol.176
, Issue.5
, pp. 2113-2130
-
-
Cicatiello, L.1
Mutarelli, M.2
Grober, O.M.3
Paris, O.4
Ferraro, L.5
Ravo, M.6
-
12
-
-
84862152044
-
Exploiting synthetic lethality for the therapy of ABC diffuse large B cell lymphoma
-
Yang Y, Shaffer AL, Emre NC, Ceribelli M, Zhang M, Wright G, et al: Exploiting synthetic lethality for the therapy of ABC diffuse large B cell lymphoma. Cancer Cell. 21 (6): 723-737.
-
Cancer Cell
, vol.21
, Issue.6
, pp. 723-737
-
-
-
13
-
-
52649132425
-
Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data
-
Jothi R, Cuddapah S, Barski A, Cui K, Zhao K: Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acids Res. 2008, 36 (16): 5221-5231. 10.1093/nar/gkn488.
-
(2008)
Nucleic Acids Res
, vol.36
, Issue.16
, pp. 5221-5231
-
-
Jothi, R.1
Cuddapah, S.2
Barski, A.3
Cui, K.4
Zhao, K.5
-
14
-
-
66549085342
-
ChIP-Seq of ERalpha and RNA polymerase II defines genes differentially responding to ligands
-
Welboren WJ, van Driel MA, Janssen-Megens EM, van Heeringen SJ, Sweep FC, Span PN, Stunnenberg HG: ChIP-Seq of ERalpha and RNA polymerase II defines genes differentially responding to ligands. EMBO J. 2009, 28 (10): 1418-1428. 10.1038/emboj.2009.88.
-
(2009)
EMBO J
, vol.28
, Issue.10
, pp. 1418-1428
-
-
Welboren, W.J.1
van Driel, M.A.2
Janssen-Megens, E.M.3
van Heeringen, S.J.4
Sweep, F.C.5
Span, P.N.6
Stunnenberg, H.G.7
-
15
-
-
33747072322
-
Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster
-
Moorman C, Sun LV, Wang J, de Wit E, Talhout W, Ward LD, et al: Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster. Proc Natl Acad Sci U S A. 2006, 103 (32): 12027-12032. 10.1073/pnas.0605003103.
-
(2006)
Proc Natl Acad Sci U S A
, vol.103
, Issue.32
, pp. 12027-12032
-
-
Moorman, C.1
Sun, L.V.2
Wang, J.3
de Wit, E.4
Talhout, W.5
Ward, L.D.6
-
16
-
-
4544352942
-
Transcriptional regulatory code of a eukaryotic genome
-
Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW, et al: Transcriptional regulatory code of a eukaryotic genome. Nature. 2004, 431 (7004): 99-104. 10.1038/nature02800.
-
(2004)
Nature
, vol.431
, Issue.7004
, pp. 99-104
-
-
Harbison, C.T.1
Gordon, D.B.2
Lee, T.I.3
Rinaldi, N.J.4
Macisaac, K.D.5
Danford, T.W.6
-
17
-
-
40649107189
-
Discovering gapped binding sites of yeast transcription factors
-
Chen CY, Tsai HK, Hsu CM, May Chen MJ, Hung HG, Huang GT, Li WH: Discovering gapped binding sites of yeast transcription factors. Proc Natl Acad Sci U S A. 2008, 105 (7): 2527-2532. 10.1073/pnas.0712188105.
-
(2008)
Proc Natl Acad Sci U S A
, vol.105
, Issue.7
, pp. 2527-2532
-
-
Chen, C.Y.1
Tsai, H.K.2
Hsu, C.M.3
May Chen, M.J.4
Hung, H.G.5
Huang, G.T.6
Li, W.H.7
-
18
-
-
33644873683
-
The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae
-
Teixeira MC, Monteiro P, Jain P, Tenreiro S, Fernandes AR, Mira NP, et al: The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae. Nucleic Acids Res. 2006, 34 (Database): D446-D451.
-
(2006)
Nucleic Acids Res
, vol.34
, Issue.DATABASE
, pp. D446-D451
-
-
Teixeira, M.C.1
Monteiro, P.2
Jain, P.3
Tenreiro, S.4
Fernandes, A.R.5
Mira, N.P.6
-
19
-
-
77956643239
-
Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers
-
Vermeulen M, Eberl HC, Matarese F, Marks H, Denissov S, Butter F, et al: Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers. Cell. 2010, 142 (6): 967-980. 10.1016/j.cell.2010.08.020.
-
(2010)
Cell
, vol.142
, Issue.6
, pp. 967-980
-
-
Vermeulen, M.1
Eberl, H.C.2
Matarese, F.3
Marks, H.4
Denissov, S.5
Butter, F.6
-
20
-
-
78650638953
-
Integrative model of genomic factors for determining binding site selection by estrogen receptor-alpha
-
Joseph R, Orlov YL, Huss M, Sun W, Kong SL, Ukil L, et al: Integrative model of genomic factors for determining binding site selection by estrogen receptor-alpha. Molecular Syst Biol. 2010, 6: 456-
-
(2010)
Molecular Syst Biol
, vol.6
, pp. 456
-
-
Joseph, R.1
Orlov, Y.L.2
Huss, M.3
Sun, W.4
Kong, S.L.5
Ukil, L.6
-
21
-
-
79958115193
-
Quantitative analysis demonstrates most transcription factors require only simple models of specificity
-
Zhao Y, Stormo GD: Quantitative analysis demonstrates most transcription factors require only simple models of specificity. Nature Biotechnology. 2011, 29 (6): 480-483.
-
(2011)
Nature Biotechnology
, vol.29
, Issue.6
, pp. 480-483
-
-
Zhao, Y.1
Stormo, G.D.2
-
22
-
-
79958153978
-
Jury remains out on simple models of transcription factor specificity
-
Morris Q, Bulyk ML, Hughes TR: Jury remains out on simple models of transcription factor specificity. Nature Biotechnology. 2011, 29 (6): 483-484. 10.1038/nbt.1892.
-
(2011)
Nature Biotechnology
, vol.29
, Issue.6
, pp. 483-484
-
-
Morris, Q.1
Bulyk, M.L.2
Hughes, T.R.3
-
23
-
-
4844223097
-
Detecting DNA regulatory motifs by incorporating positional trends in information content
-
Kechris KJ, van Zwet E, Bickel PJ, Eisen MB: Detecting DNA regulatory motifs by incorporating positional trends in information content. Genome Biology. 2004, 5 (7): R50-10.1186/gb-2004-5-7-r50.
-
(2004)
Genome Biology
, vol.5
, Issue.7
, pp. R50
-
-
Kechris, K.J.1
van Zwet, E.2
Bickel, P.J.3
Eisen, M.B.4
-
24
-
-
0642368358
-
Position specific variation in the rate of evolution in transcription factor binding sites
-
Moses AM, Chiang DY, Kellis M, Lander ES, Eisen MB: Position specific variation in the rate of evolution in transcription factor binding sites. BMC Evolutionary Biology. 2003, 3: 19-10.1186/1471-2148-3-19.
-
(2003)
BMC Evolutionary Biology
, vol.3
, pp. 19
-
-
Moses, A.M.1
Chiang, D.Y.2
Kellis, M.3
Lander, E.S.4
Eisen, M.B.5
-
25
-
-
79953233745
-
Computational study of associations between histone modification and protein-DNA binding in yeast genome by integrating diverse information
-
Wang J: Computational study of associations between histone modification and protein-DNA binding in yeast genome by integrating diverse information. BMC Genomics. 2011, 12: 172-10.1186/1471-2164-12-172.
-
(2011)
BMC Genomics
, vol.12
, pp. 172
-
-
Wang, J.1
-
26
-
-
84873027803
-
Genome-wide analysis uncovers high frequency, strong differential chromosomal interactions and their associated epigenetic patterns in E2-mediated gene regulation
-
Wang J, Lan X, Hsu PY, Hsu HK, Huang K, Parvin J, et al: Genome-wide analysis uncovers high frequency, strong differential chromosomal interactions and their associated epigenetic patterns in E2-mediated gene regulation. BMC Genomics. 2011, 14: 70-10.1186/1471-2164-14-70.
-
(2011)
BMC Genomics
, vol.14
, pp. 70
-
-
Wang, J.1
Lan, X.2
Hsu, P.Y.3
Hsu, H.K.4
Huang, K.5
Parvin, J.6
-
27
-
-
84865280797
-
H3K9 and H3K14 acetylation co-occur at many gene regulatory elements, while H3K14ac marks a subset of inactive inducible promoters in mouse embryonic stem cells
-
Karmodiya K, Krebs AR, Oulad-Abdelghani M, Kimura H, Tora L: H3K9 and H3K14 acetylation co-occur at many gene regulatory elements, while H3K14ac marks a subset of inactive inducible promoters in mouse embryonic stem cells. BMC Genomics. 2011, 13: 424-
-
(2011)
BMC Genomics
, vol.13
, pp. 424
-
-
Karmodiya, K.1
Krebs, A.R.2
Oulad-Abdelghani, M.3
Kimura, H.4
Tora, L.5
-
28
-
-
84873161936
-
High throughput kinase inhibitor screens reveal TRB3 and MAPK-ERK/TGFβ pathways as fundamental Notch regulators in breast cancer
-
Izrailit J, Berman HK, Datti A, Wrana JL, Reedijk M: High throughput kinase inhibitor screens reveal TRB3 and MAPK-ERK/TGFβ pathways as fundamental Notch regulators in breast cancer. Proc Natl Acad Sci U S A. 2013, 110 (5): 1714-1719. 10.1073/pnas.1214014110.
-
(2013)
Proc Natl Acad Sci U S A
, vol.110
, Issue.5
, pp. 1714-1719
-
-
Izrailit, J.1
Berman, H.K.2
Datti, A.3
Wrana, J.L.4
Reedijk, M.5
-
29
-
-
84869213410
-
Quantitative immunofluorescence reveals the signature of active B-cell receptor signaling in diffuse large B-cell lymphoma
-
Bogusz AM, Baxter RH, Currie T, Sinha P, Sohani AR, Kutok JL, Rodig SJ: Quantitative immunofluorescence reveals the signature of active B-cell receptor signaling in diffuse large B-cell lymphoma. Clin Cancer Res. 2012, 18 (22): 6122-6135. 10.1158/1078-0432.CCR-12-0397.
-
(2012)
Clin Cancer Res
, vol.18
, Issue.22
, pp. 6122-6135
-
-
Bogusz, A.M.1
Baxter, R.H.2
Currie, T.3
Sinha, P.4
Sohani, A.R.5
Kutok, J.L.6
Rodig, S.J.7
-
30
-
-
0141630791
-
On the specificity of DNA-protein interactions
-
von Hippel PH, Berg OG: On the specificity of DNA-protein interactions. Proc Natl Acad Sci U S A. 1986, 83 (6): 1608-1612. 10.1073/pnas.83.6.1608.
-
(1986)
Proc Natl Acad Sci U S A
, vol.83
, Issue.6
, pp. 1608-1612
-
-
von Hippel, P.H.1
Berg, O.G.2
-
31
-
-
36049002205
-
A new framework for identifying combinatorial regulation of transcription factors: a case study of the yeast cell cycle
-
Wang J: A new framework for identifying combinatorial regulation of transcription factors: a case study of the yeast cell cycle. J Biomed Inform. 2007, 40 (6): 707-725. 10.1016/j.jbi.2007.02.003.
-
(2007)
J Biomed Inform
, vol.40
, Issue.6
, pp. 707-725
-
-
Wang, J.1
-
32
-
-
67649884743
-
Fast and accurate short read alignment with Burrows-Wheeler transform
-
Li H, Durbin R: Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009, 25 (14): 1754-1760. 10.1093/bioinformatics/btp324.
-
(2009)
Bioinformatics
, vol.25
, Issue.14
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
33
-
-
77952214662
-
GREAT improves functional interpretation of cis-regulatory regions
-
McLean CY, Bristor D, Hiller M, Clarke SL, Schaar BT, Lowe CB, et al: GREAT improves functional interpretation of cis-regulatory regions. Nature Biotechnology. 2010, 28 (5): 495-501. 10.1038/nbt.1630.
-
(2010)
Nature Biotechnology
, vol.28
, Issue.5
, pp. 495-501
-
-
McLean, C.Y.1
Bristor, D.2
Hiller, M.3
Clarke, S.L.4
Schaar, B.T.5
Lowe, C.B.6
-
34
-
-
44649117905
-
Integration of external signaling pathways with the core transcriptional network in embryonic stem cells
-
Chen X, Xu H, Yuan P, Fang F, Huss M, Vega VB, et al: Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell. 2008, 133 (6): 1106-1117. 10.1016/j.cell.2008.04.043.
-
(2008)
Cell
, vol.133
, Issue.6
, pp. 1106-1117
-
-
Chen, X.1
Xu, H.2
Yuan, P.3
Fang, F.4
Huss, M.5
Vega, V.B.6
-
35
-
-
34547589578
-
DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists
-
Huang da W, Sherman BT, Tan Q, Kir J, Liu D, Bryant D, et al: DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Research. 2007, 35 (Web Server issue): W169-W175.
-
(2007)
Nucleic Acids Research
, vol.35
, Issue.WEB SERVER ISSUE
, pp. W169-W175
-
-
Huang da, W.1
Sherman, B.T.2
Tan, Q.3
Kir, J.4
Liu, D.5
Bryant, D.6
-
36
-
-
0023147228
-
Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters
-
Berg OG, von Hippel PH: Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. Journal of Molecular Biology. 1987, 193 (4): 723-750. 10.1016/0022-2836(87)90354-8.
-
(1987)
Journal of Molecular Biology
, vol.193
, Issue.4
, pp. 723-750
-
-
Berg, O.G.1
von Hippel, P.H.2
-
37
-
-
0038359359
-
Identification and characterization of a PU.1/Spi-B binding site in the bovine leukemia virus long terminal repeat
-
Dekoninck A, Calomme C, Nizet S, de Launoit Y, Burny A, Ghysdael J, Van Lint C: Identification and characterization of a PU.1/Spi-B binding site in the bovine leukemia virus long terminal repeat. Oncogene. 2003, 22 (19): 2882-2896. 10.1038/sj.onc.1206392.
-
(2003)
Oncogene
, vol.22
, Issue.19
, pp. 2882-2896
-
-
Dekoninck, A.1
Calomme, C.2
Nizet, S.3
de Launoit, Y.4
Burny, A.5
Ghysdael, J.6
Van Lint, C.7
-
38
-
-
33748191291
-
Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE
-
Foat BC, Morozov AV, Bussemaker HJ: Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE. Bioinformatics. 2006, 22 (14): e141-e149. 10.1093/bioinformatics/btl223.
-
(2006)
Bioinformatics
, vol.22
, Issue.14
, pp. e141-e149
-
-
Foat, B.C.1
Morozov, A.V.2
Bussemaker, H.J.3
-
39
-
-
77955120332
-
The effect of prior assumptions over the weights in BayesPI with application to study protein-DNA interactions from ChIP-based high-throughput data
-
Wang J: The effect of prior assumptions over the weights in BayesPI with application to study protein-DNA interactions from ChIP-based high-throughput data. BMC Bioinformatics. 2010, 11: 412-10.1186/1471-2105-11-412.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 412
-
-
Wang, J.1
-
40
-
-
46249089455
-
Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences
-
Ward LD, Bussemaker HJ: Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences. Bioinformatics. 2008, 24 (13): i165-i171. 10.1093/bioinformatics/btn154.
-
(2008)
Bioinformatics
, vol.24
, Issue.13
, pp. i165-i171
-
-
Ward, L.D.1
Bussemaker, H.J.2
-
41
-
-
0347125328
-
JASPAR: an open-access database for eukaryotic transcription factor binding profiles
-
Sandelin A, Alkema W, Engstrom P, Wasserman WW, Lenhard B: JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Research. 2004, 32 (Database issue): D91-D94.
-
(2004)
Nucleic Acids Research
, vol.32
, Issue.DATABASE ISSUE
, pp. D91-D94
-
-
Sandelin, A.1
Alkema, W.2
Engstrom, P.3
Wasserman, W.W.4
Lenhard, B.5
-
42
-
-
0029960055
-
TRANSFAC: a database on transcription factors and their DNA binding sites
-
Wingender E, Dietze P, Karas H, Knuppel R: TRANSFAC: a database on transcription factors and their DNA binding sites. Nucleic Acids Research. 1996, 24 (1): 238-241. 10.1093/nar/24.1.238.
-
(1996)
Nucleic Acids Research
, vol.24
, Issue.1
, pp. 238-241
-
-
Wingender, E.1
Dietze, P.2
Karas, H.3
Knuppel, R.4
-
43
-
-
2942601439
-
Tumor classification and marker gene prediction by feature selection and fuzzy c-means clustering using microarray data
-
Wang J, Bo TH, Jonassen I, Myklebost O, Hovig E: Tumor classification and marker gene prediction by feature selection and fuzzy c-means clustering using microarray data. BMC Bioinformatics. 2003, 4: 60-10.1186/1471-2105-4-60.
-
(2003)
BMC Bioinformatics
, vol.4
, pp. 60
-
-
Wang, J.1
Bo, T.H.2
Jonassen, I.3
Myklebost, O.4
Hovig, E.5
|