-
1
-
-
0037109192
-
Additivity in protein-DNA interactions: How good an approximation is it?
-
Benos,P.V., Bulyk,M.L. and Stormo,G.D. (2002) Additivity in protein-DNA interactions: How good an approximation is it? Nucleic Acids Res., 30, 4442-4451.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 4442-4451
-
-
Benos, P.V.1
Bulyk, M.L.2
Stormo, G.D.3
-
2
-
-
0023147228
-
Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters
-
Berg,O.G. and von Hippel,P.H. (1987) Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. J. Mol. Biol., 193, 723-750.
-
(1987)
J. Mol. Biol.
, vol.193
, pp. 723-750
-
-
Berg, O.G.1
von Hippel, P.H.2
-
3
-
-
0032561246
-
The transcriptional program of sporulation in budding yeast
-
Chu,S., DeRisi,J., Eisen,M., Mulholland,J., Botstein,D., Brown,P.O. and Herskowitz,I. (1998) The transcriptional program of sporulation in budding yeast. Science, 282, 699-705.
-
(1998)
Science
, vol.282
, pp. 699-705
-
-
Chu, S.1
DeRisi, J.2
Eisen, M.3
Mulholland, J.4
Botstein, D.5
Brown, P.O.6
Herskowitz, I.7
-
4
-
-
0242574990
-
A biophysical approach to transcription factor binding site discovery
-
Djordjevic,M., Sengupta,A.M. and Shraiman,B.I. (2003) A biophysical approach to transcription factor binding site discovery. Genome Res., 13, 2381-2390.
-
(2003)
Genome Res.
, vol.13
, pp. 2381-2390
-
-
Djordjevic, M.1
Sengupta, A.M.2
Shraiman, B.I.3
-
5
-
-
33645542019
-
Quantitative modeling and data analysis of SELEX experiments
-
Djordjevic,M. and Sengupta,A.M. (2006) Quantitative modeling and data analysis of SELEX experiments. Phys. Biol., 3, 13-28.
-
(2006)
Phys. Biol.
, vol.3
, pp. 13-28
-
-
Djordjevic, M.1
Sengupta, A.M.2
-
6
-
-
0027049805
-
The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted alpha helices: Crystal structure of the protein-DNA complex
-
Ellenberger,T.E., Brandl,C.J., Struhl,K. and Harrison,S.C. (1992) The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted alpha helices: Crystal structure of the protein-DNA complex. Cell, 71, 1223-1237.
-
(1992)
Cell
, vol.71
, pp. 1223-1237
-
-
Ellenberger, T.E.1
Brandl, C.J.2
Struhl, K.3
Harrison, S.C.4
-
7
-
-
4544293652
-
Toward an atomistic model for predicting transcription-factor binding sites
-
Endres,R.G., Schulthess,T.C. and Wingreen,N.S. (2004) Toward an atomistic model for predicting transcription-factor binding sites. Proteins, 57, 262-268.
-
(2004)
Proteins
, vol.57
, pp. 262-268
-
-
Endres, R.G.1
Schulthess, T.C.2
Wingreen, N.S.3
-
8
-
-
29144500327
-
Profiling condition-specific, genome-wide regulation of mRNA stability in yeast
-
Foat,B.C., Houshmandi,S.S., Olivas,W.M. and Bussemaker,H.J. (2005) Profiling condition-specific, genome-wide regulation of mRNA stability in yeast. Proc. Natl. Acad. Sci. USA, 102, 17675-17680.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 17675-17680
-
-
Foat, B.C.1
Houshmandi, S.S.2
Olivas, W.M.3
Bussemaker, H.J.4
-
9
-
-
0019878376
-
Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide gel electrophoresis
-
Fried,M. and Crothers,D.M. (1981) Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide gel electrophoresis. Nucleic Acids Res., 9, 6505-6525.
-
(1981)
Nucleic Acids Res.
, vol.9
, pp. 6505-6525
-
-
Fried, M.1
Crothers, D.M.2
-
10
-
-
0029973652
-
Participation of the yeast activator Abf1 in meiosis-specific expression of the HOP1 gene
-
Gailus-Durner,V., Xie,J., Chintamaneni,C. and Vershon,A.K. (1996) Participation of the yeast activator Abf1 in meiosis-specific expression of the HOP1 gene. Mol. Cell. Biol., 16, 2777-2786.
-
(1996)
Mol. Cell. Biol.
, vol.16
, pp. 2777-2786
-
-
Gailus-Durner, V.1
Xie, J.2
Chintamaneni, C.3
Vershon, A.K.4
-
11
-
-
34548087820
-
Explicit equilibrium modeling of transcription-factor binding and gene regulation
-
Granek,J.A. and Clarke,N.D. (2005) Explicit equilibrium modeling of transcription-factor binding and gene regulation. Genome Biol., 6, R87.
-
(2005)
Genome Biol.
, vol.6
-
-
Granek, J.A.1
Clarke, N.D.2
-
12
-
-
84946031884
-
Procedures for detecting outlying observations in samples
-
Grubbs,F. (1969) Procedures for detecting outlying observations in samples. Technometrics, 11, 1-21.
-
(1969)
Technometrics
, vol.11
, pp. 1-21
-
-
Grubbs, F.1
-
13
-
-
4544352942
-
Transcriptional regulatory code of a eukaryotic genome
-
Harbison,C.T., Gordon,D.B., Lee,T.I., Rinaldi,N.J., Macisaac,K.D., Danford,T.W., Hannett,N.M., Tagne,J.B., Reynolds,D.B., Yoo,J., Jennings,E.G., Zeitlinger,J., Pokholok,D.K., Kellis,M., Rolfe,P.A., Takusagawa,K.T., Lander,E.S., Gifford,D.K., Fraenkel,E. and Young,R.A. (2004) Transcriptional regulatory code of a eukaryotic genome. Nature, 431, 99-104.
-
(2004)
Nature
, vol.431
, 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
Hannett, N.M.7
Tagne, J.B.8
Reynolds, D.B.9
Yoo, J.10
Jennings, E.G.11
Zeitlinger, J.12
Pokholok, D.K.13
Kellis, M.14
Rolfe, P.A.15
Takusagawa, K.T.16
Lander, E.S.17
Gifford, D.K.18
Fraenkel, E.19
Young, R.A.20
more..
-
14
-
-
7044239239
-
A simple physical model for the prediction and design of protein-DNA interactions
-
Havranek,J.J., Duarte,C.M. and Baker,D. (2004) A simple physical model for the prediction and design of protein-DNA interactions. J. Mol. Biol., 344,59-70.
-
(2004)
J. Mol. Biol.
, vol.344
, pp. 59-70
-
-
Havranek, J.J.1
Duarte, C.M.2
Baker, D.3
-
15
-
-
18444386817
-
Saccharomyces Genome Database
-
Issel-Tarver,L., Christie,K.R., Dolinski,K., Andrada,R., Balakrishnan,R., Ball,C.A., Binkley,G., Dong,S., Dwight,S.S., Fisk,D.G., Harris,M., Schroeder,M., Sethuraman,A., Tse,K., Weng,S., Botstein,D. and Cherry,J.M. (2002) Saccharomyces Genome Database. Methods Enzymol., 350, 329-346.
-
(2002)
Methods Enzymol.
, vol.350
, pp. 329-346
-
-
Issel-Tarver, L.1
Christie, K.R.2
Dolinski, K.3
Andrada, R.4
Balakrishnan, R.5
Ball, C.A.6
Binkley, G.7
Dong, S.8
Dwight, S.S.9
Fisk, D.G.10
Harris, M.11
Schroeder, M.12
Sethuraman, A.13
Tse, K.14
Weng, S.15
Botstein, D.16
Cherry, J.M.17
-
16
-
-
0035945567
-
Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF
-
Iyer,V.R., Horak,C.E., Scafe,C.S., Botstein,D., Snyder,M. and Brown,P.O. (2001) Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature, 409, 533-538.
-
(2001)
Nature
, vol.409
, pp. 533-538
-
-
Iyer, V.R.1
Horak, C.E.2
Scafe, C.S.3
Botstein, D.4
Snyder, M.5
Brown, P.O.6
-
17
-
-
0029963828
-
The crystal structure of the DNA-binding domain of yeast RAP1 in complex with telomeric DNA
-
Konig,P., Giraldo,R., Chapman,L. and Rhodes,D. (1996) The crystal structure of the DNA-binding domain of yeast RAP1 in complex with telomeric DNA. Cell, 85, 125-136.
-
(1996)
Cell
, vol.85
, pp. 125-136
-
-
Konig, P.1
Giraldo, R.2
Chapman, L.3
Rhodes, D.4
-
18
-
-
0037470581
-
An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes
-
Kortemme,T., Morozov,A.V. and Baker,D. (2003) An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. J. Mol. Biol., 326, 1239-1259.
-
(2003)
J. Mol. Biol.
, vol.326
, pp. 1239-1259
-
-
Kortemme, T.1
Morozov, A.V.2
Baker, D.3
-
19
-
-
0036835785
-
Structure of the sporulation-specific transcription factor Ndt80 bound to DNA
-
Lamoureux,J.S., Stuart,D., Tsang,R., Wu,C. and Glover,J.N.M. (2002) Structure of the sporulation-specific transcription factor Ndt80 bound to DNA. EMBO J., 21, 5721-5732.
-
(2002)
EMBO J.
, vol.21
, pp. 5721-5732
-
-
Lamoureux, J.S.1
Stuart, D.2
Tsang, R.3
Wu, C.4
Glover, J.N.M.5
-
20
-
-
0037174671
-
Transcriptional regulatory networks in Saccharomyces cerevisiae
-
Lee,T.I., Rinaldi,N.J., Robert,F., Odom,D.T., Bar-Joseph,Z., Gerber,G.K., Hannett,N.M., Harbison,C.T., Thompson,C.M., Simon,I., Zeitlinger,J., Jennings,E.G., Murray,H.L., Gordon,D.B., Ren,B., Wyrick,J.J., Tagne,J.B., Volkert,T.L., Fraenkel,E., Gifford,D.K. and Young,R.A. (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science, 298, 799-804.
-
(2002)
Science
, vol.298
, pp. 799-804
-
-
Lee, T.I.1
Rinaldi, N.J.2
Robert, F.3
Odom, D.T.4
Bar-Joseph, Z.5
Gerber, G.K.6
Hannett, N.M.7
Harbison, C.T.8
Thompson, C.M.9
Simon, I.10
Zeitlinger, J.11
Jennings, E.G.12
Murray, H.L.13
Gordon, D.B.14
Ren, B.15
Wyrick, J.J.16
Tagne, J.B.17
Volkert, T.L.18
Fraenkel, E.19
Gifford, D.K.20
Young, R.A.21
more..
-
21
-
-
0034934774
-
Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association
-
Lieb,J.D., Liu,X., Botstein,D. and Brown,P.O. (2001) Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat. Genet., 28, 327-334.
-
(2001)
Nat. Genet.
, vol.28
, pp. 327-334
-
-
Lieb, J.D.1
Liu, X.2
Botstein, D.3
Brown, P.O.4
-
22
-
-
0036324753
-
An algorithm for finding protein-dna binding sites with applications to chromatin-immunoprecipitation microarray experiments
-
Liu,X.S., Brutlag,D.L. and Liu,J.S. (2002) An algorithm for finding protein-dna binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nat. Biotechnol., 20, 835-839.
-
(2002)
Nat. Biotechnol.
, vol.20
, pp. 835-839
-
-
Liu, X.S.1
Brutlag, D.L.2
Liu, J.S.3
-
23
-
-
0035228215
-
Bioprospector: Discovering conserved dna motifs in upstream regulatory regions of co-expressed genes
-
Liu,X., Brutlag,D.L. and Liu,J.S. (2001) Bioprospector: Discovering conserved dna motifs in upstream regulatory regions of co-expressed genes. Pac. Symp. Biocomput. 127-138.
-
(2001)
Pac. Symp. Biocomput.
, pp. 127-138
-
-
Liu, X.1
Brutlag, D.L.2
Liu, J.S.3
-
24
-
-
0036396542
-
Rationalization of gene regulation by a eukaryotic transcription factor: Calculation of regulatory region occupancy from predicted binding affinities
-
Liu,X. and Clarke,N.D. (2002) Rationalization of gene regulation by a eukaryotic transcription factor: Calculation of regulatory region occupancy from predicted binding affinities. J. Mol. Biol., 323, 1-8.
-
(2002)
J. Mol. Biol.
, vol.323
, pp. 1-8
-
-
Liu, X.1
Clarke, N.D.2
-
25
-
-
15544375816
-
DIP-chip: Rapid and accurate determination of DNA-binding specificity
-
Liu,X., Noll,D.M., Lieb,J.D. and Clarke,N.D. (2005) DIP-chip: Rapid and accurate determination of DNA-binding specificity. Genome Res., 15, 421-427.
-
(2005)
Genome Res.
, vol.15
, pp. 421-427
-
-
Liu, X.1
Noll, D.M.2
Lieb, J.D.3
Clarke, N.D.4
-
26
-
-
0242396923
-
3DNA: A software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures
-
Lu,X.J. and Olson,W.K. (2003) 3DNA: A software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res., 31, 5108-5121.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 5108-5121
-
-
Lu, X.J.1
Olson, W.K.2
-
27
-
-
27244460904
-
Protein-DNA binding specificity predictions with structural models
-
Morozov,A.V., Havranek,J.J., Baker,D. and Siggia,E.D. (2005) Protein-DNA binding specificity predictions with structural models. Nucleic Acids Res., 33, 5781-5798.
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 5781-5798
-
-
Morozov, A.V.1
Havranek, J.J.2
Baker, D.3
Siggia, E.D.4
-
28
-
-
9644268153
-
Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays
-
Mukherjee,S., Berger,M.F., Jona,G., Wang,X.S., Muzzey,D., Snyder,M., Young,R.A. and Bulyk,M.L. (2004) Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays. Nat. Genet., 36, 1331-1339.
-
(2004)
Nat. Genet.
, vol.36
, pp. 1331-1339
-
-
Mukherjee, S.1
Berger, M.F.2
Jona, G.3
Wang, X.S.4
Muzzey, D.5
Snyder, M.6
Young, R.A.7
Bulyk, M.L.8
-
29
-
-
0032530555
-
DNA sequence-dependent deformability deduced from protein-DNA crystal complexes
-
Olson,W.K., Gorin,A.A., Lu,X.J., Hock,L.M. and Zhurkin,V.B. (1998) DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proc. Natl. Acad. Sci. USA, 95, 11163-11168.
-
(1998)
Proc. Natl. Acad. Sci. USA
, vol.95
, pp. 11163-11168
-
-
Olson, W.K.1
Gorin, A.A.2
Lu, X.J.3
Hock, L.M.4
Zhurkin, V.B.5
-
30
-
-
1842479952
-
Exploring protein native states and large-scale conformational changes with a modified Generalized Born model
-
Onufriev,A., Bashford,D. and Case,D.A. (2004) Exploring protein native states and large-scale conformational changes with a modified Generalized Born model. Proteins, 55, 383-394.
-
(2004)
Proteins
, vol.55
, pp. 383-394
-
-
Onufriev, A.1
Bashford, D.2
Case, D.A.3
-
31
-
-
0026331267
-
X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil
-
O'Shea,E.K., Klemm,J.D., Kim,P.S. and Alber,T. (1991) X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil. Science, 254, 539-544.
-
(1991)
Science
, vol.254
, pp. 539-544
-
-
O'Shea, E.K.1
Klemm, J.D.2
Kim, P.S.3
Alber, T.4
-
32
-
-
1642452665
-
Analyzing protein-DNA recognition mechanisms
-
Paillard,G. and Lavery,R. (2004) Analyzing protein-DNA recognition mechanisms. Structure, 12, 113- 122.
-
(2004)
Structure
, vol.12
, pp. 113-122
-
-
Paillard, G.1
Lavery, R.2
-
33
-
-
0037774598
-
Sum1 and Ndt80 proteins compete for binding to middle sporulation element sequences that control meiotic gene expression
-
Pierce,M., Benjamin,K.R., Montano,S.P., Georgiadis,M.M., Winter,E. and Vershon,A.K. (2003) Sum1 and Ndt80 proteins compete for binding to middle sporulation element sequences that control meiotic gene expression. Mol. Cell. Biol., 23, 4814-4825.
-
(2003)
Mol. Cell. Biol.
, vol.23
, pp. 4814-4825
-
-
Pierce, M.1
Benjamin, K.R.2
Montano, S.P.3
Georgiadis, M.M.4
Winter, E.5
Vershon, A.K.6
-
34
-
-
0034704248
-
Genome-wide location and function of DNA binding proteins
-
Ren,B., Robert,F., Wyrick,J.J., Aparicio,O., Jennings,E.G., Simon,I., Zeitlinger,J., Schreiber,J., Hannett,N., Kanin,E., Volkert,T.L., Wilson,C.J., Bell,S.P. and Young,R.A. (2000) Genome-wide location and function of DNA binding proteins. Science, 290, 2306-2309.
-
(2000)
Science
, vol.290
, pp. 2306-2309
-
-
Ren, B.1
Robert, F.2
Wyrick, J.J.3
Aparicio, O.4
Jennings, E.G.5
Simon, I.6
Zeitlinger, J.7
Schreiber, J.8
Hannett, N.9
Kanin, E.10
Volkert, T.L.11
Wilson, C.J.12
Bell, S.P.13
Young, R.A.14
-
35
-
-
0025008168
-
Sequence logos: A new way to display consensus sequences
-
Schneider,T.D. and Stephens,R.M. (1990) Sequence logos: A new way to display consensus sequences. Nucleic Acids Res., 18, 6097-6100.
-
(1990)
Nucleic Acids Res.
, vol.18
, pp. 6097-6100
-
-
Schneider, T.D.1
Stephens, R.M.2
-
36
-
-
17944372930
-
Serial regulation of transcriptional regulators in the yeast cell cycle
-
Simon,I., Barnett,J., Hannett,N., Harbison,C.T., Rinaldi,N.J., Volkert,T.L., Wyrick,J.J., Zeitlinger,J., Gifford,D.K., Jaakkola,T.S. and Young,R.A. (2001) Serial regulation of transcriptional regulators in the yeast cell cycle. Cell, 106, 697-708.
-
(2001)
Cell
, vol.106
, pp. 697-708
-
-
Simon, I.1
Barnett, J.2
Hannett, N.3
Harbison, C.T.4
Rinaldi, N.J.5
Volkert, T.L.6
Wyrick, J.J.7
Zeitlinger, J.8
Gifford, D.K.9
Jaakkola, T.S.10
Young, R.A.11
-
37
-
-
0032032780
-
Specificity, free energy and information content in protein-DNA interactions
-
Stormo,G.D. and Fields,D.S. (1998) Specificity, free energy and information content in protein-DNA interactions. Trends Biochem. Sci., 23, 109-113.
-
(1998)
Trends Biochem. Sci.
, vol.23
, pp. 109-113
-
-
Stormo, G.D.1
Fields, D.S.2
-
38
-
-
0023057575
-
Quantitative analysis of the relationship between nucleotide sequence and functional activity
-
Stormo,G.D., Schneider,T.D. and Gold,L. (1986) Quantitative analysis of the relationship between nucleotide sequence and functional activity. Nucleic Acids Res., 14, 6661-6679.
-
(1986)
Nucleic Acids Res.
, vol.14
, pp. 6661-6679
-
-
Stormo, G.D.1
Schneider, T.D.2
Gold, L.3
-
39
-
-
0034072450
-
DNA binding sites: Representation and discovery
-
Stormo,G.D. (2000) DNA binding sites: Representation and discovery. Bioinformatics, 16, 16-23.
-
(2000)
Bioinformatics
, vol.16
, pp. 16-23
-
-
Stormo, G.D.1
|