-
2
-
-
0032575756
-
DNA structure in human RNA polymerase II promoters
-
Pedersen,A.G., Baldi,P., Chauvin,Y. and Brunak,S. (1998) DNA structure in human RNA polymerase II promoters. J. Mol. Biol., 281, 663-673.
-
(1998)
J. Mol. Biol.
, vol.281
, pp. 663-673
-
-
Pedersen, A.G.1
Baldi, P.2
Chauvin, Y.3
Brunak, S.4
-
3
-
-
0030798605
-
Clues and consequences of DNA bending in transcription
-
Perez-Martin,J. and de Lorenzo,V. (1997) Clues and consequences of DNA bending in transcription. Annu. Rev. Microbiol., 51, 593-628.
-
(1997)
Annu. Rev. Microbiol.
, vol.51
, pp. 593-628
-
-
Perez-Martin, J.1
de Lorenzo, V.2
-
4
-
-
0034724393
-
Insertion site preferences of the P transposable element in Drosophila melanogaster
-
Liao,G.C., Rehm,E.J. and Rubin,G.M. (2000) Insertion site preferences of the P transposable element in Drosophila melanogaster. Proc. Natl Acad. Sci. USA, 97, 3347-3351.
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 3347-3351
-
-
Liao, G.C.1
Rehm, E.J.2
Rubin, G.M.3
-
5
-
-
0034698001
-
A-form conformational motifs in ligand-bound DNA structures
-
Lu,X.J., Shakked,Z. and Olson,W.K. (2000) A-form conformational motifs in ligand-bound DNA structures. J. Mol. Biol., 300, 819-840.
-
(2000)
J. Mol. Biol.
, vol.300
, pp. 819-840
-
-
Lu, X.J.1
Shakked, Z.2
Olson, W.K.3
-
6
-
-
0034674176
-
A DNA structural atlas for Escherichia coli
-
Pedersen,A.G., Jensen,L.J., Brunak,S., Staerfeldt,H.H. and Ussery,D.W. (2000) A DNA structural atlas for Escherichia coli. J. Mol. Biol., 299, 907-930.
-
(2000)
J. Mol. Biol.
, vol.299
, pp. 907-930
-
-
Pedersen, A.G.1
Jensen, L.J.2
Brunak, S.3
Staerfeldt, H.H.4
Ussery, D.W.5
-
7
-
-
0034667792
-
Orchestrated response: A symphony of transcription factors for gene control
-
Lemon,B. and Tjian,R. (2000) Orchestrated response: A symphony of transcription factors for gene control. Genes Dev., 14, 2551-2569.
-
(2000)
Genes Dev.
, vol.14
, pp. 2551-2569
-
-
Lemon, B.1
Tjian, R.2
-
8
-
-
0030248496
-
Core promoters and transcriptional control
-
Novina,C.D. and Roy,A.L. (1996) Core promoters and transcriptional control. Trends Genet., 12, 351-355.
-
(1996)
Trends Genet.
, vol.12
, pp. 351-355
-
-
Novina, C.D.1
Roy, A.L.2
-
9
-
-
1542328272
-
The RNA polymerase II transcription cycle: Cycling through chromatin
-
Svejstrup,J.Q. (2004) The RNA polymerase II transcription cycle: Cycling through chromatin. Biochim. Biophys. Acta, 1677, 64-73.
-
(2004)
Biochim. Biophys. Acta
, vol.1677
, pp. 64-73
-
-
Svejstrup, J.Q.1
-
10
-
-
0033032415
-
DNA bending and wrapping around RNA polymerase: A revolutionary model describing transcriptional mechanisms
-
Coulombe,B. and Burton,Z.F. (1999) DNA bending and wrapping around RNA polymerase: A revolutionary model describing transcriptional mechanisms. Microbiol. Mol. Biol. Rev., 63, 457-478.
-
(1999)
Microbiol. Mol. Biol. Rev.
, vol.63
, pp. 457-478
-
-
Coulombe, B.1
Burton, Z.F.2
-
11
-
-
0028826669
-
Trinucleotide models for DNA bending propensity: Comparison of models based on DNaseI digestion and nucleosome packaging data
-
Brukner,I., Sanchez,R., Suck,D. and Pongor,S. (1995) Trinucleotide models for DNA bending propensity: Comparison of models based on DNaseI digestion and nucleosome packaging data. J. Biomol. Struct. Dyn., 13, 309-317.
-
(1995)
J. Biomol. Struct. Dyn.
, vol.13
, pp. 309-317
-
-
Brukner, I.1
Sanchez, R.2
Suck, D.3
Pongor, S.4
-
12
-
-
2542609960
-
Helix bending as a factor in protein/DNA recognition
-
Dickerson,R.E. and Chiu,T.K. (1997) Helix bending as a factor in protein/ DNA recognition. Biopolymers, 44, 361-403.
-
(1997)
Biopolymers
, vol.44
, pp. 361-403
-
-
Dickerson, R.E.1
Chiu, T.K.2
-
13
-
-
0032522139
-
DNA bending: The prevalence of kinkiness and the virtues of normality
-
Dickerson,R.E. (1998) DNA bending: The prevalence of kinkiness and the virtues of normality. Nucleic Acids Res., 26, 1906-1926.
-
(1998)
Nucleic Acids Res.
, vol.26
, pp. 1906-1926
-
-
Dickerson, R.E.1
-
14
-
-
0032168436
-
Rod models of DNA: Sequence-dependent anisotropic elastic modelling of local bending phenomena
-
Munteanu,M.G., Vlahovicek,K., Parthasarathy,S., Simon,I. and Pongor,S. (1998) Rod models of DNA: Sequence-dependent anisotropic elastic modelling of local bending phenomena. Trends Biochem. Sci., 23, 341-347.
-
(1998)
Trends Biochem. Sci.
, vol.23
, pp. 341-347
-
-
Munteanu, M.G.1
Vlahovicek, K.2
Parthasarathy, S.3
Simon, I.4
Pongor, S.5
-
15
-
-
0034682870
-
A-tract bending: Insights into experimental structures by computational models
-
Strahs,D. and Schlick,T. (2000) A-tract bending: Insights into experimental structures by computational models. J. Mol. Biol., 301, 643-663.
-
(2000)
J. Mol. Biol.
, vol.301
, pp. 643-663
-
-
Strahs, D.1
Schlick, T.2
-
16
-
-
0037126028
-
Physical constraints and functional characteristics of transcription factor-DNA interaction
-
Gerland,U., Moroz,J.D. and Hwa,T. (2002) Physical constraints and functional characteristics of transcription factor-DNA interaction. Proc. Natl Acad. Sci. USA, 99, 12015-12020.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 12015-12020
-
-
Gerland, U.1
Moroz, J.D.2
Hwa, T.3
-
17
-
-
0642374383
-
The role of DNA deformation energy at individual base steps for the identification of DNA protein binding sites
-
Steffen,N.R., Murphy,S.D., Lathrop,R.H., Opel,M.L., Tolleri,L. and Hatfield,G.W. (2002) The role of DNA deformation energy at individual base steps for the identification of DNA protein binding sites. Genome Inform. Ser. Workshop Genome Inform., 13, 153-162.
-
(2002)
Genome Inform. Ser. Workshop Genome Inform.
, vol.13
, pp. 153-162
-
-
Steffen, N.R.1
Murphy, S.D.2
Lathrop, R.H.3
Opel, M.L.4
Tolleri, L.5
Hatfield, G.W.6
-
18
-
-
0038226895
-
DNA sequence and structure: Direct and indirect recognition in protein-DNA binding
-
Steffen,N.R., Murphy,S.D., Tolleri,L., Hatfield,G.W. and Lathrop,R.H. (2002) DNA sequence and structure: Direct and indirect recognition in protein-DNA binding. Bioinformatics, 18 (Suppl. 1), S22-S30.
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 1
-
-
Steffen, N.R.1
Murphy, S.D.2
Tolleri, L.3
Hatfield, G.W.4
Lathrop, R.H.5
-
19
-
-
0038013991
-
RNA polymerase holoenzyme: Structure, function and biological implications
-
Borukhov,S. and Nudler,E. (2003) RNA polymerase holoenzyme: Structure, function and biological implications. Curr. Opin. Microbiol., 6, 93-100.
-
(2003)
Curr. Opin. Microbiol.
, vol.6
, pp. 93-100
-
-
Borukhov, S.1
Nudler, E.2
-
20
-
-
0030738183
-
Distal enhancer regulation by promoter derepression in topologically constrained DNA in vitro
-
Barton,M.C., Madani,N. and Emerson,B.M. (1997) Distal enhancer regulation by promoter derepression in topologically constrained DNA in vitro. Proc. Natl Acad. Sci. USA, 94, 7257-7262.
-
(1997)
Proc. Natl. Acad. Sci. USA
, vol.94
, pp. 7257-7262
-
-
Barton, M.C.1
Madani, N.2
Emerson, B.M.3
-
21
-
-
0034235931
-
HMG I/Y regulates long-range enhancer-dependent transcription on DNA and chromatin by changes in DNA topology
-
Bagga,R., Michalowski,S., Sabnis,R., Griffith,J.D. and Emerson,B.M. (2000) HMG I/Y regulates long-range enhancer-dependent transcription on DNA and chromatin by changes in DNA topology. Nucleic Acids Res., 28, 2541-2550.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 2541-2550
-
-
Bagga, R.1
Michalowski, S.2
Sabnis, R.3
Griffith, J.D.4
Emerson, B.M.5
-
22
-
-
0036289102
-
Long-range correlations between DNA bending sites: Relation to the structure and dynamics of nucleosomes
-
Audit,B., Vaillant,C., Arneodo,A., d'Aubenton-Carafa,Y. and Thermes,C. (2002) Long-range correlations between DNA bending sites: Relation to the structure and dynamics of nucleosomes. J. Mol. Biol., 316, 903-918.
-
(2002)
J. Mol. Biol.
, vol.316
, pp. 903-918
-
-
Audit, B.1
Vaillant, C.2
Arneodo, A.3
d'Aubenton-Carafa, Y.4
Thermes, C.5
-
23
-
-
0029900290
-
Common DNA structural features exhibited by eukaryotic ribosomal gene promoters
-
Marilley,M. and Pasero,P. (1996) Common DNA structural features exhibited by eukaryotic ribosomal gene promoters. Nucleic Acids Res., 24, 2204-2211.
-
(1996)
Nucleic Acids Res.
, vol.24
, pp. 2204-2211
-
-
Marilley, M.1
Pasero, P.2
-
24
-
-
0033302046
-
Curved DNA in promoter sequences
-
Gabrielian,A.E., Landsman,D. and Bolshoy,A. (1999) Curved DNA in promoter sequences. In Silico Biol., 1, 183-196.
-
(1999)
Silico Biol.
, vol.1
, pp. 183-196
-
-
Gabrielian, A.E.1
Landsman, D.2
Bolshoy, A.3
-
25
-
-
0036049774
-
DNA structural variation affects complex formation and promoter melting in ribosomal RNA transcription
-
Marilley,M., Radebaugh,C.A., Geiss,G.K., Laybourn,P.J. and Paule,M.R. (2002) DNA structural variation affects complex formation and promoter melting in ribosomal RNA transcription. Mol. Genet. Genomics, 267, 781-791.
-
(2002)
Mol. Genet. Genomics
, vol.267
, pp. 781-791
-
-
Marilley, M.1
Radebaugh, C.A.2
Geiss, G.K.3
Laybourn, P.J.4
Paule, M.R.5
-
26
-
-
7444244495
-
Core promoter elements of eukaryotic genes have a highly distinctive mechanical property
-
Fukue,Y., Sumida,N., Nishikawa,J. and Ohyama,T. (2004) Core promoter elements of eukaryotic genes have a highly distinctive mechanical property. Nucleic Acids Res., 32, 5834-5840.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 5834-5840
-
-
Fukue, Y.1
Sumida, N.2
Nishikawa, J.3
Ohyama, T.4
-
27
-
-
0035021811
-
Identification and characterization of the potential promoter regions of 1031 kinds of human genes
-
Suzuki,Y., Tsunoda,T., Sese,J., Taira,H., Mizushima-Sugano,J., Hata,H., Ota,T., Isogai,T., Tanaka,T., Nakamura,Y. et al. (2001) Identification and characterization of the potential promoter regions of 1031 kinds of human genes. Genome Res., 11, 677-684.
-
(2001)
Genome Res.
, vol.11
, pp. 677-684
-
-
Suzuki, Y.1
Tsunoda, T.2
Sese, J.3
Taira, H.4
Mizushima-Sugano, J.5
Hata, H.6
Ota, T.7
Isogai, T.8
Tanaka, T.9
Nakamura, Y.10
-
28
-
-
0034991911
-
Diverse transcriptional initiation revealed by fine, large-scale mapping of mRNA start sites
-
Suzuki,Y., Taira,H., Tsunoda,T., Mizushima-Sugano,J., Sese,J., Hata,H., Ota,T., Isogai,T., Tanaka,T., Morishita,S. et al. (2001) Diverse transcriptional initiation revealed by fine, large-scale mapping of mRNA start sites. EMBO Rep., 2, 388-393.
-
(2001)
EMBO Rep.
, vol.2
, pp. 388-393
-
-
Suzuki, Y.1
Taira, H.2
Tsunoda, T.3
Mizushima-Sugano, J.4
Sese, J.5
Hata, H.6
Ota, T.7
Isogai, T.8
Tanaka, T.9
Morishita, S.10
-
29
-
-
0036081146
-
DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs
-
Suzuki,Y., Yamashita,R., Nakai,K. and Sugano,S. (2002) DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs. Nucleic Acids Res., 30, 328-331.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 328-331
-
-
Suzuki, Y.1
Yamashita, R.2
Nakai, K.3
Sugano, S.4
-
30
-
-
0347756647
-
DBTSS, DataBase of Transcriptional Start Sites: Progress report 2004 Nucleic
-
Suzuki,Y., Yamashita,R., Sugano,S. and Nakai,K. (2004) DBTSS, DataBase of Transcriptional Start Sites: Progress report 2004. Nucleic Acids Res., 32, D78-D81.
-
(2004)
Acids Res.
, vol.32
-
-
Suzuki, Y.1
Yamashita, R.2
Sugano, S.3
Nakai, K.4
-
31
-
-
20244377471
-
Functional annotation of a full-length Arabidopsis cDNA collection
-
Seki,M., Narusaka,M., Kamiya,A., Ishida,J., Satou,M., Sakurai,T., Nakajima,M., Enju,A., Akiyama,K., Oono,Y. et al. (2002) Functional annotation of a full-length Arabidopsis cDNA collection. Science, 296, 141-145.
-
(2002)
Science
, vol.296
, pp. 141-145
-
-
Seki, M.1
Narusaka, M.2
Kamiya, A.3
Ishida, J.4
Satou, M.5
Sakurai, T.6
Nakajima, M.7
Enju, A.8
Akiyama, K.9
Oono, Y.10
-
32
-
-
0038376923
-
Computational approaches to identify promoters and cis-regulatory elements in plant genomes
-
Rombauts,S., Florquin,K., Lescot,M., Marchal,K., Rouze,P. and van de Peer,Y. (2003) Computational approaches to identify promoters and cis-regulatory elements in plant genomes. Plant Physiol., 132, 1162-1176.
-
(2003)
Plant Physiol.
, vol.132
, pp. 1162-1176
-
-
Rombauts, S.1
Florquin, K.2
Lescot, M.3
Marchal, K.4
Rouze, P.5
van de Peer, Y.6
-
33
-
-
0033976523
-
Discovery and modeling of transcriptional regulatory regions
-
Fickett,J.W. and Wasserman,W.W. (2000) Discovery and modeling of transcriptional regulatory regions. Curr. Opin. Biotechnol., 11, 19-24.
-
(2000)
Curr. Opin. Biotechnol.
, vol.11
, pp. 19-24
-
-
Fickett, J.W.1
Wasserman, W.W.2
-
34
-
-
0037108159
-
The RNA polymerase II core promoter: A key component in the regulation of gene expression
-
Butler,J.E. and Kadonaga,J.T. (2002) The RNA polymerase II core promoter: A key component in the regulation of gene expression. Genes Dev., 16, 2583-2592.
-
(2002)
Genes Dev.
, vol.16
, pp. 2583-2592
-
-
Butler, J.E.1
Kadonaga, J.T.2
-
35
-
-
2642665514
-
A contiguous 60 kb genomic stretch from barley reveals molecular evidence for gene islands in a monocot genome
-
Panstruga,R., Buschges,R., Piffanelli,P. and Schulze-Lefert,P. (1998) A contiguous 60 kb genomic stretch from barley reveals molecular evidence for gene islands in a monocot genome. Nucleic Acids Res., 26, 1056-1062.
-
(1998)
Nucleic Acids Res.
, vol.26
, pp. 1056-1062
-
-
Panstruga, R.1
Buschges, R.2
Piffanelli, P.3
Schulze-Lefert, P.4
-
36
-
-
0033539168
-
CpG islands as genomic footprints of promoters that are associated with replication origins
-
Antequera,F. and Bird,A. (1999) CpG islands as genomic footprints of promoters that are associated with replication origins. Curr. Biol., 9, R661-R667.
-
(1999)
Curr. Biol.
, vol.9
-
-
Antequera, F.1
Bird, A.2
-
37
-
-
0034920129
-
Gene-associated CpG islands in plants as revealed by analyses of genomic sequences
-
Ashikawa,I. (2001) Gene-associated CpG islands in plants as revealed by analyses of genomic sequences. Plant J., 26, 617-625.
-
(2001)
Plant J.
, vol.26
, pp. 617-625
-
-
Ashikawa, I.1
-
38
-
-
0037133565
-
Comprehensive analysis of CpG islands in human chromosomes 21 and 22
-
Takai,D. and Jones,P.A. (2002) Comprehensive analysis of CpG islands in human chromosomes 21 and 22. Proc. Natl Acad. Sci. USA, 99, 3740-3745.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 3740-3745
-
-
Takai, D.1
Jones, P.A.2
-
39
-
-
0023216891
-
CpG islands in vertebrate genomes
-
Gardiner-Garden,M. and Frommer,M. (1987) CpG islands in vertebrate genomes. J. Mol. Biol., 196, 261-282.
-
(1987)
J. Mol. Biol.
, vol.196
, pp. 261-282
-
-
Gardiner-Garden, M.1
Frommer, M.2
-
40
-
-
0032729435
-
Exploring expression data: Identification and analysis of coexpressed genes
-
Heyer,L.J., Kruglyak,S. and Yooseph,S. (1999) Exploring expression data: identification and analysis of coexpressed genes. Genome Res., 9, 1106-1115.
-
(1999)
Genome Res.
, vol.9
, pp. 1106-1115
-
-
Heyer, L.J.1
Kruglyak, S.2
Yooseph, S.3
-
41
-
-
0034062083
-
Analysis of large-scale gene expression data
-
Sherlock,G. (2000) Analysis of large-scale gene expression data. Curr. Opin. Immunol., 12, 201-205.
-
(2000)
Curr. Opin. Immunol.
, vol.12
, pp. 201-205
-
-
Sherlock, G.1
-
42
-
-
0036080361
-
Adaptive quality-based clustering of gene expression profiles
-
De Smet,F., Mathys,J., Marchal,K., Thijs,G., De Moor,B. and Moreau,Y. (2002) Adaptive quality-based clustering of gene expression profiles. Bioinformatics, 18, 735-746.
-
(2002)
Bioinformatics
, vol.18
, pp. 735-746
-
-
De Smet, F.1
Mathys, J.2
Marchal, K.3
Thijs, G.4
De Moor, B.5
Moreau, Y.6
-
43
-
-
0033572893
-
No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution
-
Workman,C. and Krogh,A. (1999) No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution. Nucleic Acids Res., 27, 4816-4822.
-
(1999)
Nucleic Acids Res.
, vol.27
, pp. 4816-4822
-
-
Workman, C.1
Krogh, A.2
-
44
-
-
0141519339
-
Widespread selection for local RNA secondary structure in coding regions of bacterial genes
-
Katz,L. and Burge,C.B. (2003) Widespread selection for local RNA secondary structure in coding regions of bacterial genes. Genome Res., 13, 2042-2051.
-
(2003)
Genome Res.
, vol.13
, pp. 2042-2051
-
-
Katz, L.1
Burge, C.B.2
-
45
-
-
0026966646
-
A training algorithm for optimal margin classifiers
-
Haussler,D. (ed.), ACM Press, New York, NY, USA
-
Boser,B., Guyon,I. and Vapnik,V.N. (1992) A training algorithm for optimal margin classifiers. In Haussler,D. (ed.), Proceedings of COLT. ACM Press, New York, NY, USA, pp. 144-152.
-
(1992)
Proceedings of COLT
, pp. 144-152
-
-
Boser, B.1
Guyon, I.2
Vapnik, V.N.3
-
47
-
-
0031882652
-
New core promoter element in RNA polymerase II-dependent transcription: Sequence-specific DNA binding by transcription factor IIB
-
Lagrange,T., Kapanidis,A.N., Tang,H., Reinberg,D. and Ebright,R.H. (1998) New core promoter element in RNA polymerase II-dependent transcription: Sequence-specific DNA binding by transcription factor IIB. Genes Dev., 12, 34-44.
-
(1998)
Genes Dev.
, vol.12
, pp. 34-44
-
-
Lagrange, T.1
Kapanidis, A.N.2
Tang, H.3
Reinberg, D.4
Ebright, R.H.5
-
48
-
-
0037201434
-
The DPE, a core promoter element for transcription by RNA polymerase II
-
Kadonaga,J.T. (2002) The DPE, a core promoter element for transcription by RNA polymerase II. Exp. Mol. Med., 34, 259-264.
-
(2002)
Exp. Mol. Med.
, vol.34
, pp. 259-264
-
-
Kadonaga, J.T.1
-
49
-
-
0025278259
-
Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences
-
Bucher,P. (1990) Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences. J. Mol. Biol., 212, 563-578.
-
(1990)
J. Mol. Biol.
, vol.212
, pp. 563-578
-
-
Bucher, P.1
-
50
-
-
85134575899
-
PoSSuMsearch: Fast and sensitive matching of position specific scoring matrices using enhanced suffix arrays
-
Proceedings of the German Conference on Bioinformatics 2004
-
Beckstette,M., Strothmann,D., Homann,R., Giegerich,R. and Kurtz,S. (2004) PoSSuMsearch: Fast and sensitive matching of position specific scoring matrices using enhanced suffix arrays. In Proceedings of the German Conference on Bioinformatics 2004. GI Lecture Notes in Informatics, 53, 53-64.
-
(2004)
GI Lecture Notes in Informatics
, vol.53
, pp. 53-64
-
-
Beckstette, M.1
Strothmann, D.2
Homann, R.3
Giegerich, R.4
Kurtz, S.5
-
51
-
-
0031614136
-
Computational applications of DNA structural scales
-
Baldi,P., Chauvin,Y., Brunak,S., Gorodkin,J. and Pedersen,A.G. (1998) Computational applications of DNA structural scales. Proc. Int. Conf. Intell. Syst. Mol. Biol., 6, 35-42.
-
(1998)
Proc. Int. Conf. Intell. Syst. Mol. Biol.
, vol.6
, pp. 35-42
-
-
Baldi, P.1
Chauvin, Y.2
Brunak, S.3
Gorodkin, J.4
Pedersen, A.G.5
-
52
-
-
0030590260
-
How proteins recognize the TATA box
-
Juo,Z.S., Chiu,T.K., Leiberman,P.M., Baikalov,I., Berk,A.J. and Dickerson,R.E. (1996) How proteins recognize the TATA box. J. Mol. Biol., 261, 239-254.
-
(1996)
J. Mol. Biol.
, vol.261
, pp. 239-254
-
-
Juo, Z.S.1
Chiu, T.K.2
Leiberman, P.M.3
Baikalov, I.4
Berk, A.J.5
Dickerson, R.E.6
-
53
-
-
0033573008
-
TATA element recognition by the TATA box-binding protein has been conserved throughout evolution
-
Patikoglou,G.A., Kim,J.L., Sun,L., Yang,S.H., Kodadek,T. and Burley,S.K. (1999) TATA element recognition by the TATA box-binding protein has been conserved throughout evolution. Genes Dev., 13, 3217-3230.
-
(1999)
Genes Dev.
, vol.13
, pp. 3217-3230
-
-
Patikoglou, G.A.1
Kim, J.L.2
Sun, L.3
Yang, S.H.4
Kodadek, T.5
Burley, S.K.6
-
54
-
-
0035805499
-
DNA bends in TATA-binding protein-TATA complexes in solution are DNA sequence-dependent
-
Wu,J., Parkhurst,K.M., Powell,R.M., Brenowitz,M. and Parkhurst,L.J. (2001) DNA bends in TATA-binding protein-TATA complexes in solution are DNA sequence-dependent. J. Biol. Chem., 276, 14614-14622.
-
(2001)
J. Biol. Chem.
, vol.276
, pp. 14614-14622
-
-
Wu, J.1
Parkhurst, K.M.2
Powell, R.M.3
Brenowitz, M.4
Parkhurst, L.J.5
-
55
-
-
0034718503
-
An initiation element in the yeast CUP1 promoter is recognized by RNA polymerase II in the absence of TATA box-binding protein if the DNA is negatively supercoiled
-
Leblanc,B.P., Benham,C.J. and Clark,D.J. (2000) An initiation element in the yeast CUP1 promoter is recognized by RNA polymerase II in the absence of TATA box-binding protein if the DNA is negatively supercoiled. Proc. Natl Acad. Sci. USA, 97, 10745-10750.
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 10745-10750
-
-
Leblanc, B.P.1
Benham, C.J.2
Clark, D.J.3
-
56
-
-
0035477896
-
Core promoters: Active contributors to combinatorial gene regulation
-
Smale,S.T. (2001) Core promoters: Active contributors to combinatorial gene regulation. Genes Dev., 15, 2503-2508.
-
(2001)
Genes Dev.
, vol.15
, pp. 2503-2508
-
-
Smale, S.T.1
-
57
-
-
25444522648
-
Genome wide analysis of Arabidopsis core promoters
-
Molina,C. and Grotewold,E.R. (2005) Genome wide analysis of Arabidopsis core promoters. BMC Genomics, 6, 25.
-
(2005)
BMC Genomics
, vol.6
, pp. 25
-
-
Molina, C.1
Grotewold, E.R.2
-
58
-
-
0012253746
-
Computational analysis of core promoters in the Drosophila genome
-
RESEARCH0087
-
Ohler,U., Liao,G.C., Niemann,H. and Rubin,G.M. (2002) Computational analysis of core promoters in the Drosophila genome. Genome Biol., 3, RESEARCH0087.
-
(2002)
Genome Biol.
, vol.3
-
-
Ohler, U.1
Liao, G.C.2
Niemann, H.3
Rubin, G.M.4
-
59
-
-
0037246944
-
PlantProm: A database of plant promoter sequences
-
Shahmuradov,I.A., Gammerman,A.J., Hancock,J.M., Bramley,P.M. and Solovyev,V.V. (2003) PlantProm: A database of plant promoter sequences. Nucleic Acids Res., 31, 114-117.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 114-117
-
-
Shahmuradov, I.A.1
Gammerman, A.J.2
Hancock, J.M.3
Bramley, P.M.4
Solovyev, V.V.5
-
60
-
-
0036123111
-
Computational detection and location of transcription start sites in mammalian genomic DNA
-
Down,T.A. and Hubbard,T.J. (2002) Computational detection and location of transcription start sites in mammalian genomic DNA. Genome Res., 12, 458-461.
-
(2002)
Genome Res.
, vol.12
, pp. 458-461
-
-
Down, T.A.1
Hubbard, T.J.2
-
61
-
-
0037352074
-
Computer model for recognition of functional transcription start sites in RNA polymerase II promoters of vertebrates
-
Bajic,V.B., Seah,S.H., Chong,A., Krishnan,S.P., Koh,J.L. and Brusic,V. (2003) Computer model for recognition of functional transcription start sites in RNA polymerase II promoters of vertebrates. J. Mol. Graph Model., 21, 323-332.
-
(2003)
J. Mol. Graph Model.
, vol.21
, pp. 323-332
-
-
Bajic, V.B.1
Seah, S.H.2
Chong, A.3
Krishnan, S.P.4
Koh, J.L.5
Brusic, V.6
-
63
-
-
0035224747
-
Joint modeling of DNA sequence and physical properties to improve eukaryotic promoter recognition
-
Ohler,U., Niemann,H., Liao,G.C. and Rubin,G.M. (2001) Joint modeling of DNA sequence and physical properties to improve eukaryotic promoter recognition. Bioinformatics, 17 (Suppl. 1), S199-S206.
-
(2001)
Bioinformatics
, vol.17
, Issue.SUPPL. 1
-
-
Ohler, U.1
Niemann, H.2
Liao, G.C.3
Rubin, G.M.4
-
64
-
-
8444235368
-
Content analysis of the core promoter region of human genes
-
Bajic,V.B., Choudhary,V. and Hock,C.K. (2004) Content analysis of the core promoter region of human genes. In Silico Biol., 4, 109-125.
-
(2004)
Silico Biol.
, vol.4
, pp. 109-125
-
-
Bajic, V.B.1
Choudhary, V.2
Hock, C.K.3
-
65
-
-
0018143102
-
An optimized potential function for the calculation of nucleic acid interaction energies: Base stacking
-
Ornstein,R.L., Rein,R., Breen,D.L. and Macelroy,R.D. (1987) An optimized potential function for the calculation of nucleic acid interaction energies: Base stacking. Biopolymers, 17, 2341-2360.
-
(1987)
Biopolymers
, vol.17
, pp. 2341-2360
-
-
Ornstein, R.L.1
Rein, R.2
Breen, D.L.3
Macelroy, R.D.4
-
66
-
-
0030003963
-
Propeller-twisting of base-pairs and the conformational mobility of dinucleotide steps in DNA
-
el Hassan,M.A. and Calladine,C.R. (1996) Propeller-twisting of base-pairs and the conformational mobility of dinucleotide steps in DNA. J. Mol. Biol., 259, 95-103.
-
(1996)
J. Mol. Biol.
, vol.259
, pp. 95-103
-
-
el Hassan, M.A.1
Calladine, C.R.2
-
67
-
-
0023001414
-
Sequence periodicities in chicken nucleosome core DNA
-
Satchwell,S.C., Drew,H.R. and Travers,A.A. (1986) Sequence periodicities in chicken nucleosome core DNA. J. Mol. Biol., 191, 659-675.
-
(1986)
J. Mol. Biol.
, vol.191
, pp. 659-675
-
-
Satchwell, S.C.1
Drew, H.R.2
Travers, A.A.3
-
68
-
-
0010118486
-
The A-form of DNA: In search of the biological role
-
Ivanov,V.I. and Minchenkova,L.E. (1995) The A-form of DNA: In search of the biological role. Mol. Biol., 28, 780-788.
-
(1995)
Mol. Biol.
, vol.28
, pp. 780-788
-
-
Ivanov, V.I.1
Minchenkova, L.E.2
-
69
-
-
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
-
70
-
-
0001550068
-
Predicting DNA duplex stability from the base sequence
-
Breslauer,K.J., Frank,R., Blocker,H. and Marky,L.A. (1986) Predicting DNA duplex stability from the base sequence. Proc. Natl Acad. Sci. USA, 83, 3746-3750.
-
(1986)
Proc. Natl. Acad. Sci. USA
, vol.83
, pp. 3746-3750
-
-
Breslauer, K.J.1
Frank, R.2
Blocker, H.3
Marky, L.A.4
-
71
-
-
0029859713
-
Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes
-
Sugimoto,N., Nakano,S., Yoneyama,M. and Honda,K. (1996) Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. Nucleic Acids Res., 24, 4501-4505.
-
(1996)
Nucleic Acids Res.
, vol.24
, pp. 4501-4505
-
-
Sugimoto, N.1
Nakano, S.2
Yoneyama, M.3
Honda, K.4
-
73
-
-
0032998464
-
Statistical mechanical simulation of polymeric DNA melting with MELTSIM
-
Blake,R.D., Bizzaro,J.W., Blake,J.D., Day,G.R., Delcourt,S.G., Knowles,J., Marx, K.A. and SantaLucia,J.,Jr (1999) Statistical mechanical simulation of polymeric DNA melting with MELTSIM. Bioinformatics, 15, 370-375.
-
(1999)
Bioinformatics
, vol.15
, pp. 370-375
-
-
Blake, R.D.1
Bizzaro, J.W.2
Blake, J.D.3
Day, G.R.4
Delcourt, S.G.5
Knowles, J.6
Marx, K.A.7
SantaLucia Jr., J.8
-
74
-
-
0028936684
-
Translational positioning of nucleosomes on DNA: The role of sequence-dependent isotropic DNA bending stiffness
-
Sivolob,A.V. and Khrapunov,S.N. (1995) Translational positioning of nucleosomes on DNA: The role of sequence-dependent isotropic DNA bending stiffness. J. Mol. Biol., 247, 918-931.
-
(1995)
J. Mol. Biol.
, vol.247
, pp. 918-931
-
-
Sivolob, A.V.1
Khrapunov, S.N.2
-
75
-
-
0028931709
-
B-DNA twisting correlates with base-pair morphology
-
Gorin,A.A., Zhurkin,V.B. and Olson,W.K. (1995) B-DNA twisting correlates with base-pair morphology. J. Mol. Biol., 247, 34-48.
-
(1995)
J. Mol. Biol.
, vol.247
, pp. 34-48
-
-
Gorin, A.A.1
Zhurkin, V.B.2
Olson, W.K.3
-
76
-
-
0025184633
-
Polarized electronic spectra of Z-DNA single crystals
-
Ho,P.S., Zhou,G.W. and Clark,L.B. (1990) Polarized electronic spectra of Z-DNA single crystals. Biopolymers, 30, 151-163.
-
(1990)
Biopolymers
, vol.30
, pp. 151-163
-
-
Ho, P.S.1
Zhou, G.W.2
Clark, L.B.3
|