-
1
-
-
27944508215
-
CLIP: A method for identifying protein-RNA interaction sites in living cells
-
DOI 10.1016/j.ymeth.2005.07.018, PII S1046202305001787, Post-transcriptional Regulation of Gene Expression
-
Ule,J., Jensen,K., Mele,A. and Darnell,R.B. (2005) CLIP: a method for identifying protein-RNA interaction sites in living cells. Methods, 37, 376-386. (Pubitemid 41682508)
-
(2005)
Methods
, vol.37
, Issue.4
, pp. 376-386
-
-
Ule, J.1
Jensen, K.2
Mele, A.3
Darnell, R.B.4
-
2
-
-
1242316281
-
ChIP-chip: Considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments
-
Buck,M.J. and Lieb,J.D. (2004) ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics, 83, 349.
-
(2004)
Genomics
, vol.83
, pp. 349
-
-
Buck, M.J.1
Lieb, J.D.2
-
3
-
-
0023948705
-
Mapping protein-DNA interactions in vivo with formaldehyde: Evidence that histone H4 is retained on a highly transcribed gene
-
Solomon,M.J., Larsen,P.L. and Varshavsky,A. (1988) Mapping protein-DNA interactions in vivo with formaldehyde: evidence that histone H4 is retained on a highly transcribed gene. Cell, 53, 937-947.
-
(1988)
Cell
, vol.53
, pp. 937-947
-
-
Solomon, M.J.1
Larsen, P.L.2
Varshavsky, A.3
-
4
-
-
67649982744
-
Diversity and complexity in DNA recognition by transcription factors
-
Badis,G., Berger,M.F., Philippakis,A.A., Talukder,S., Gehrke,A.R., Jaeger,S.A., Chan,E.T., Metzler,G., Vedenko,A., Chen,X. et al. (2009) Diversity and complexity in DNA recognition by transcription factors. Science, 324, 1720-1723.
-
(2009)
Science
, vol.324
, 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
Chan, E.T.7
Metzler, G.8
Vedenko, A.9
Chen, X.10
-
5
-
-
58149200952
-
UniPROBE: An online database of protein binding microarray data on protein-DNA interactions
-
Newburger,D.E. and Bulyk,M.L. (2009) UniPROBE: an online database of protein binding microarray data on protein-DNA interactions. Nucleic Acids Res., 37, D77-D82.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Newburger, D.E.1
Bulyk, M.L.2
-
6
-
-
0025194307
-
Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase
-
Tuerk,C. and Gold,L. (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science, 249, 505-510.
-
(1990)
Science
, vol.249
, pp. 505-510
-
-
Tuerk, C.1
Gold, L.2
-
7
-
-
41649086194
-
High-throughput biochemical analysis of in vivo location data reveals novel distinct classes of POU5F1(Oct4)/DNA complexes
-
DOI 10.1101/gr.072942.107
-
Tantin,D., Gemberling,M., Callister,C. and Fairbrother,W. (2008) High-throughput biochemical analysis of in vivo location data reveals novel distinct classes of POU5F1(Oct4)/DNA complexes. Genome Res., 18, 631-639. (Pubitemid 351482787)
-
(2008)
Genome Research
, vol.18
, Issue.4
, pp. 631-639
-
-
Tantin, D.1
Gemberling, M.2
Callister, C.3
Fairbrother, W.4
-
8
-
-
85047656664
-
A rapid high-throughput method for mapping ribonucleoproteins (RNPs) on human pre-mRNA
-
Watkins,K.H., Stewart,A. and Fairbrother,W. (2009) A rapid high-throughput method for mapping ribonucleoproteins (RNPs) on human pre-mRNA. J. Vis. Exp, 2, 34.
-
(2009)
J. Vis. Exp.
, vol.2
, pp. 34
-
-
Watkins, K.H.1
Stewart, A.2
Fairbrother, W.3
-
9
-
-
17044396348
-
Logic functions of the genomic cis-regulatory code
-
Istrail,S. and Davidson,E.H. (2005) Logic functions of the genomic cis-regulatory code. Proc. Natl Acad. Sci. USA, 102, 4954-4959.
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 4954-4959
-
-
Istrail, S.1
Davidson, E.H.2
-
10
-
-
34347232364
-
Combinatorial transcriptional control of the lactose operon of Escherichia coli
-
Kuhlman,T., Zhang,Z., Saier,M.H. Jr and Hwa,T. (2007) Combinatorial transcriptional control of the lactose operon of Escherichia coli. Proc. Natl Acad. Sci. USA, 104, 6043-6048.
-
(2007)
Proc. Natl Acad. Sci. USA
, vol.104
, pp. 6043-6048
-
-
Kuhlman, T.1
Zhang, Z.2
Saier Jr., M.H.3
Hwa, T.4
-
11
-
-
0032128171
-
New POU dimer configuration mediates antagonistic control of an osteopontin preimplantation enhancer by Oct-4 and Sox-2
-
Botquin,V., Hess,H., Fuhrmann,G., Anastassiadis,C., Gross,M.K., Vriend,G. and Scholer,H.R. (1998) New POU dimer configuration mediates antagonistic control of an osteopontin preimplantation enhancer by Oct-4 and Sox-2. Genes Dev., 12, 2073-2090. (Pubitemid 28323880)
-
(1998)
Genes and Development
, vol.12
, Issue.13
, pp. 2073-2090
-
-
Botquin, V.1
Hess, H.2
Fuhrmann, G.3
Anastassiadis, C.4
Gross, M.K.5
Vriend, G.6
Scholer, H.R.7
-
12
-
-
13144260704
-
Crossing the line between activation and repression
-
Ma,J. (2005) Crossing the line between activation and repression. Trends Genet., 21, 54-59.
-
(2005)
Trends Genet.
, vol.21
, pp. 54-59
-
-
Ma, J.1
-
13
-
-
0034656243
-
Analysis of p53-regulated gene expression patterns using oligonucleotide arrays
-
Zhao,R., Gish,K., Murphy,M., Yin,Y., Notterman,D., Hoffman,W.H., Tom,E., Mack,D.H. and Levine,A.J. (2000) Analysis of p53-regulated gene expression patterns using oligonucleotide arrays. Genes Dev., 14, 981-993. (Pubitemid 30253006)
-
(2000)
Genes and Development
, vol.14
, Issue.8
, pp. 981-993
-
-
Zhao, R.1
Gish, K.2
Murphy, M.3
Yin, Y.4
Notterman, D.5
Hoffman, W.H.6
Tom, E.7
Mack, D.H.8
Levine, A.J.9
-
14
-
-
0032549745
-
Genomic cis-regulatory logic: Experimental and computational analysis of a sea urchin gene
-
DOI 10.1126/science.279.5358.1896
-
Yuh,C.H., Bolouri,H. and Davidson,E.H. (1998) Genomic cis-regulatory logic: experimental and computational analysis of a sea urchin gene. Science, 279, 1896-1902. (Pubitemid 28168638)
-
(1998)
Science
, vol.279
, Issue.5358
, pp. 1896-1902
-
-
Yuh, C.-H.1
Bolouri, H.2
Davidson, E.H.3
-
15
-
-
25144525014
-
Core transcriptional regulatory circuitry in human embryonic stem cells
-
DOI 10.1016/j.cell.2005.08.020, PII S0092867405008251
-
Boyer,L.A., Lee,T.I., Cole,M.F., Johnstone,S.E., Levine,S.S., Zucker,J.P., Guenther,M.G., Kumar,R.M., Murray,H.L., Jenner,R.G. et al. (2005) Core transcriptional regulatory circuitry in human embryonic stem cells. Cell, 122, 947-956. (Pubitemid 41345211)
-
(2005)
Cell
, vol.122
, Issue.6
, pp. 947-956
-
-
Boyer, L.A.1
Tong, I.L.2
Cole, M.F.3
Johnstone, S.E.4
Levine, S.S.5
Zucker, J.P.6
Guenther, M.G.7
Kumar, R.M.8
Murray, H.L.9
Jenner, R.G.10
Gifford, D.K.11
Melton, D.A.12
Jaenisch, R.13
Young, R.A.14
-
16
-
-
34548755108
-
Correlation between binding rate constants and individual information of E. coli Fis binding sites
-
DOI 10.1093/nar/gkm471
-
Shultzaberger,R.K., Roberts,L.R., Lyakhov,I.G., Sidorov,I.A., Stephen,A.G., Fisher,R.J. and Schneider,T.D. (2007) Correlation between binding rate constants and individual information of E. coli Fis binding sites. Nucleic Acids Res., 35, 5275-5283. (Pubitemid 47430456)
-
(2007)
Nucleic Acids Research
, vol.35
, Issue.16
, pp. 5275-5283
-
-
Shultzaberger, R.K.1
Roberts, L.R.2
Lyakhov, I.G.3
Sidorov, I.A.4
Stephen, A.G.5
Fisher, R.J.6
Schneider, T.D.7
-
17
-
-
58149182724
-
NCBI GEO: Archive for high-throughput functional genomic data
-
Barrett,T., Troup,D.B., Wilhite,S.E., Ledoux,P., Rudnev,D., Evangelista,C., Kim,I.F., Soboleva,A., Tomashevsky,M., Marshall,K.A. et al. (2009) NCBI GEO: archive for high-throughput functional genomic data. Nucleic Acids Res., 37, D885-D890.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Barrett, T.1
Troup, D.B.2
Wilhite, S.E.3
Ledoux, P.4
Rudnev, D.5
Evangelista, C.6
Kim, I.F.7
Soboleva, A.8
Tomashevsky, M.9
Marshall, K.A.10
-
18
-
-
27344435774
-
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
-
Subramanian,A., Tamayo,P., Mootha,V.K., Mukherjee,S., Ebert,B.L., Gillette,M.A., Paulovich,A., Pomeroy,S.L., Golub,T.R., Lander,E.S. et al. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA, 102, 15545-15550.
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 15545-15550
-
-
Subramanian, A.1
Tamayo, P.2
Mootha, V.K.3
Mukherjee, S.4
Ebert, B.L.5
Gillette, M.A.6
Paulovich, A.7
Pomeroy, S.L.8
Golub, T.R.9
Lander, E.S.10
-
19
-
-
0347125328
-
JASPAR: An open-access database for eukaryotic transcription factor binding profiles
-
Sandelin,A., Alkema,W., Engstrom,P., Wasserman,W.W. and Lenhard,B. (2004) JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res., 32, D91-D94. (Pubitemid 38081611)
-
(2004)
Nucleic Acids Research
, vol.32
, Issue.DATABASE ISS.
-
-
Sandelin, A.1
Alkema, W.2
Engstrom, P.3
Wasserman, W.W.4
Lenhard, B.5
-
20
-
-
0032826179
-
Identifying DNA and protein patterns with statistically significant alignments of multiple sequences
-
Hertz,G.Z. and Stormo,G.D. (1999) Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics, 15, 563-577. (Pubitemid 29462105)
-
(1999)
Bioinformatics
, vol.15
, Issue.7-8
, pp. 563-577
-
-
Hertz, G.Z.1
Stormo, G.D.2
-
21
-
-
43449100341
-
REST maintains self-renewal and pluripotency of embryonic stem cells
-
DOI 10.1038/nature06863, PII NATURE06863
-
Singh,S.K., Kagalwala,M.N., Parker-Thornburg,J., Adams,H. and Majumder,S. (2008) REST maintains self-renewal and pluripotency of embryonic stem cells. Nature, 453, 223-227. (Pubitemid 351667975)
-
(2008)
Nature
, vol.453
, Issue.7192
, pp. 223-227
-
-
Singh, S.K.1
Kagalwala, M.N.2
Parker-Thornburg, J.3
Adams, H.4
Majumder, S.5
-
22
-
-
61349200079
-
Is REST required for ESC pluripotency?
-
discussion E7
-
Jorgensen,H.F., Chen,Z.F., Merkenschlager,M. and Fisher,A.G. (2009) Is REST required for ESC pluripotency? Nature, 457, E4-5; discussion E7.
-
(2009)
Nature
, vol.457
-
-
Jorgensen, H.F.1
Chen, Z.F.2
Merkenschlager, M.3
Fisher, A.G.4
-
23
-
-
1842584947
-
Applied bioinformatics for the identification of regulatory elements
-
DOI 10.1038/nrg1315
-
Wasserman,W.W. and Sandelin,A. (2004) Applied bioinformatics for the identification of regulatory elements. Nature Rev., 5, 276-287. (Pubitemid 38435623)
-
(2004)
Nature Reviews Genetics
, vol.5
, Issue.4
, pp. 276-287
-
-
Wasserman, W.W.1
Sandelin, A.2
-
24
-
-
77949796916
-
High-throughput binding analysis determines the binding specificity of ASF/SF2 on alternatively spliced human pre-mRNAs
-
Chang,B., Levin,J., Thompson,W.A. and Fairbrother,W.G. (2009) High-throughput binding analysis determines the binding specificity of ASF/SF2 on alternatively spliced human pre-mRNAs. Com. Chem. High T. Scr, 13, 242-252.
-
(2009)
Com. Chem. High T. Scr.
, vol.13
, pp. 242-252
-
-
Chang, B.1
Levin, J.2
Thompson, W.A.3
Fairbrother, W.G.4
-
25
-
-
8844278362
-
A single nucleotide polymorphism in the MDM2 promoter attenuates the p53 tumor suppressor pathway and accelerates tumor formation in humans
-
DOI 10.1016/j.cell.2004.11.022, PII S0092867404010517
-
Bond,G.L., Hu,W., Bond,E.E., Robins,H., Lutzker,S.G., Arva,N.C., Bargonetti,J., Bartel,F., Taubert,H., Wuerl,P. et al. (2004) A single nucleotide polymorphism in the MDM2 promoter attenuates the p53 tumor suppressor pathway and accelerates tumor formation in humans. Cell, 119, 591-602. (Pubitemid 39535748)
-
(2004)
Cell
, vol.119
, Issue.5
, pp. 591-602
-
-
Bond, G.L.1
Hu, W.2
Bond, E.E.3
Robins, H.4
Lutzker, S.G.5
Arva, N.C.6
Bargonetti, J.7
Bartel, F.8
Taubert, H.9
Wuerl, P.10
Onel, K.11
Yip, L.12
Hwang, S.-J.13
Strong, L.C.14
Lozano, G.15
Levine, A.J.16
-
26
-
-
67649524640
-
Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (formaldehyde assisted isolation of regulatory elements)
-
Giresi,P.G. and Lieb,J.D. (2009) Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (formaldehyde assisted isolation of regulatory elements). Methods, 48, 233-239.
-
(2009)
Methods
, vol.48
, pp. 233-239
-
-
Giresi, P.G.1
Lieb, J.D.2
-
27
-
-
34250369627
-
FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin
-
DOI 10.1101/gr.5533506
-
Giresi,P.G., Kim,J., McDaniell,R.M., Iyer,V.R. and Lieb,J.D. (2007) FAIRE (formaldehyde-assisted isolation of regulatory elements) isolates active regulatory elements from human chromatin. Genome Res., 17, 877-885. (Pubitemid 46919722)
-
(2007)
Genome Research
, vol.17
, Issue.6
, pp. 877-885
-
-
Giresi, P.G.1
Kim, J.2
McDaniell, R.M.3
Iyer, V.R.4
Lieb, J.D.5
-
28
-
-
38649090044
-
Genome-wide analysis of transcript isoform variation in humans
-
Kwan,T., Benovoy,D., Dias,C., Gurd,S., Provencher,C., Beaulieu,P., Hudson,T.J., Sladek,R. and Majewski,J. (2008) Genome-wide analysis of transcript isoform variation in humans. Nat. Genet., 40, 225-231.
-
(2008)
Nat. Genet.
, vol.40
, pp. 225-231
-
-
Kwan, T.1
Benovoy, D.2
Dias, C.3
Gurd, S.4
Provencher, C.5
Beaulieu, P.6
Hudson, T.J.7
Sladek, R.8
Majewski, J.9
-
29
-
-
0037903275
-
Human Gene Mutation Database (HGMD): 2003 update
-
Stenson,P.D., Ball,E.V., Mort,M., Phillips,A.D., Shiel,J.A., Thomas,N.S., Abeysinghe,S., Krawczak,M. and Cooper,D.N. (2003) Human Gene Mutation Database (HGMD): 2003 update. Hum. Mutat., 21, 577-581.
-
(2003)
Hum. Mutat.
, vol.21
, pp. 577-581
-
-
Stenson, P.D.1
Ball, E.V.2
Mort, M.3
Phillips, A.D.4
Shiel, J.A.5
Thomas, N.S.6
Abeysinghe, S.7
Krawczak, M.8
Cooper, D.N.9
-
30
-
-
15544379277
-
Are splicing mutations the most frequent cause of hereditary disease?
-
Lopez-Bigas,N., Audit,B., Ouzounis,C., Parra,G. and Guigo,R. (2005) Are splicing mutations the most frequent cause of hereditary disease? FEBS Lett., 579, 1900-1903.
-
(2005)
FEBS Lett.
, vol.579
, pp. 1900-1903
-
-
Lopez-Bigas, N.1
Audit, B.2
Ouzounis, C.3
Parra, G.4
Guigo, R.5
|