-
1
-
-
0031614136
-
Computational applications of DNA structural scales
-
Glasgow, J. et al., (eds), AAAI Press, Menlo Park, CA
-
Baldi, P.F., Chauvin, Y., Brunak, S., Gorodkin, J. and Pederson, A.G. (1998) Computational applications of DNA structural scales. In Glasgow, J. et al., (eds), Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA, pp. 35-42.
-
(1998)
Intelligent Systems for Molecular Biology
, pp. 35-42
-
-
Baldi, P.F.1
Chauvin, Y.2
Brunak, S.3
Gorodkin, J.4
Pederson, A.G.5
-
2
-
-
84969565976
-
DNA structure, protein-DNA interactions, and DNA-protein expression
-
Altman, R. et al., (eds), World Scientific, Singapore
-
Baldi, P.F. and Lathrop, R.H. (2001) DNA structure, protein-DNA interactions, and DNA-protein expression. In Altman, R. et al., (eds), Pacific Symposium on Biocomputing. World Scientific, Singapore, pp. 101-102.
-
(2001)
Pacific Symposium on Biocomputing
, pp. 101-102
-
-
Baldi, P.F.1
Lathrop, R.H.2
-
3
-
-
0035236524
-
SAMIE: Statistical algorithm for modeling interaction energies
-
Altman, R. et al., (eds), World Scientific, Singapore
-
Benos, P.V., Lapedes, A.S., Fields, D.S. and Stormo, G.D. (2001) SAMIE: Statistical algorithm for modeling interaction energies. In Altman, R. et al., (eds), Pacific Symposium on Biocomputing. World Scientific, Singapore, pp. 115-126.
-
(2001)
Pacific Symposium on Biocomputing
, pp. 115-126
-
-
Benos, P.V.1
Lapedes, A.S.2
Fields, D.S.3
Stormo, G.D.4
-
5
-
-
0035900557
-
Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: Alteration of DNA binding specificity through alteration of DNA kinking
-
Chen, S., Gunasekera, A., Zhang, X., Kunkel, T.A., Ebright, R.H. and Berman, H.M. (2001) Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: Alteration of DNA binding specificity through alteration of DNA kinking. J. Mol. Biol., 314, 75-82.
-
(2001)
J. Mol. Biol.
, vol.314
, pp. 75-82
-
-
Chen, S.1
Gunasekera, A.2
Zhang, X.3
Kunkel, T.A.4
Ebright, R.H.5
Berman, H.M.6
-
6
-
-
0029642089
-
In vivo interaction of the E. coli integration host factor with its specific binding sites
-
Engelhorn, M., Boccard, F., Murtin, C., Prentki, P. and Geiselmann, J. (1995) In vivo interaction of the E. coli integration host factor with its specific binding sites. Nucleic Acids Res., 23, 2959-2965.
-
(1995)
Nucleic Acids Res.
, vol.23
, pp. 2959-2965
-
-
Engelhorn, M.1
Boccard, F.2
Murtin, C.3
Prentki, P.4
Geiselmann, J.5
-
7
-
-
0003437299
-
-
Distributed by the author., Department of Genetics, University of Washington, Seattle
-
Felsenstein, J. (1993) PHYLIP (Phylogeny inference package) version 3.5c.. Distributed by the author., Department of Genetics, University of Washington, Seattle.
-
(1993)
PHYLIP (Phylogeny Inference Package) Version 3.5c.
-
-
Felsenstein, J.1
-
8
-
-
0025180835
-
Searching for and predicting the activity of sites for DNA binding proteins
-
Goodrich, J.A., Schwartz, M.L. and McClure, W.R. (1990) Searching for and predicting the activity of sites for DNA binding proteins. Nucleic Acids Res., 18, 4993-5000.
-
(1990)
Nucleic Acids Res.
, vol.18
, pp. 4993-5000
-
-
Goodrich, J.A.1
Schwartz, M.L.2
McClure, W.R.3
-
9
-
-
0036953237
-
DNA topology-mediated control of global gene expression in E. coli
-
in press
-
Hatfield, G.W. and Benham, C.J. (2002) DNA topology-mediated control of global gene expression in E. coli. Ann. Rev. Genet. (in press).
-
(2002)
Ann. Rev. Genet.
-
-
Hatfield, G.W.1
Benham, C.J.2
-
10
-
-
0033120215
-
Structure-based prediction of DNA target sites by regulatory proteins
-
Kono, H. and Sarai, A. (1999) Structure-based prediction of DNA target sites by regulatory proteins. Proteins: Structure, Function, and Genetics, 35, 114-131.
-
(1999)
Proteins: Structure, Function, and Genetics
, vol.35
, pp. 114-131
-
-
Kono, H.1
Sarai, A.2
-
11
-
-
0027912333
-
Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment
-
Lawrence, C.E., Altschul, S.F., Boguski, M.S., Liu, J.S., Neuwald, A.F. and Wootton, J.C. (1993) Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science, 262, 208-214.
-
(1993)
Science
, vol.262
, pp. 208-214
-
-
Lawrence, C.E.1
Altschul, S.F.2
Boguski, M.S.3
Liu, J.S.4
Neuwald, A.F.5
Wootton, J.C.6
-
12
-
-
0034894475
-
Conformational model for binding site recognition by the E. coli MetJ transcription factor
-
Liu, R., Blackwell, T.W. and States, D.J. (2001) Conformational model for binding site recognition by the E. coli MetJ transcription factor. Bioinformatics, 17, 622-633.
-
(2001)
Bioinformatics
, vol.17
, pp. 622-633
-
-
Liu, R.1
Blackwell, T.W.2
States, D.J.3
-
13
-
-
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
-
14
-
-
0035221367
-
A structure-based approach for prediction of protein binding sites ingene upstream regions
-
Altman, R. et al., (eds), World Scientific, Singapore
-
Mandel-Gutfreund, Y., Baron, A. and Margalit, H. (2001) A structure-based approach for prediction of protein binding sites ingene upstream regions. In Altman, R. et al., (eds), Pacific Symposium on Biocomputing. World Scientific, Singapore, pp. 139-150.
-
(2001)
Pacific Symposium on Biocomputing
, pp. 139-150
-
-
Mandel-Gutfreund, Y.1
Baron, A.2
Margalit, H.3
-
15
-
-
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, 11 163-11 168.
-
(1998)
Proc. Natl Acad. Sci. USA
, vol.95
-
-
Olson, W.K.1
Gorin, A.A.2
Lu, X.J.3
Hock, L.M.4
Zhurkin, V.B.5
-
17
-
-
0031052180
-
Making DNA do a U-turn: IHF and related proteins
-
Rice, P.A. (1997) Making DNA do a U-turn: IHF and related proteins. Curr. Opin. Struct. Biol., 7, 86-93.
-
(1997)
Curr. Opin. Struct. Biol.
, vol.7
, pp. 86-93
-
-
Rice, P.A.1
-
18
-
-
0030451819
-
Crystal structure of an IHF-DNA complex: A protein-induced DNA U-turn
-
Rice, P.A., Yang, S.W., Mizuuchi, K. and Nash, H.A. (1996) Crystal structure of an IHF-DNA complex: A protein-induced DNA U-turn. Cell, 87, 1295-1306.
-
(1996)
Cell
, vol.87
, pp. 1295-1306
-
-
Rice, P.A.1
Yang, S.W.2
Mizuuchi, K.3
Nash, H.A.4
-
19
-
-
0034201441
-
EMBOSS: The European molecular biology open software suite
-
Rice, P.A., Longden, I. and Bleasby, A. (2000) EMBOSS: The European molecular biology open software suite. Trends Genet., 16, 276-277.
-
(2000)
Trends Genet.
, vol.16
, pp. 276-277
-
-
Rice, P.A.1
Longden, I.2
Bleasby, A.3
-
20
-
-
1442314837
-
Target prediction of transcription factors: Refinement of structure-based method
-
Matsuda, H. et al., (eds), Genome Informatics Series 12, Universal Academy Press, Tokyo
-
Sarai, A., Selvaraj, S., Gromiha, M.M., Siebers, J.G., Prabakaran, P. and Kono, H. (2001) Target prediction of transcription factors: Refinement of structure-based method. In Matsuda, H. et al., (eds), Genome Informatics 2001, Genome Informatics Series 12, Universal Academy Press, Tokyo, pp. 384-385.
-
(2001)
Genome Informatics 2001
, pp. 384-385
-
-
Sarai, A.1
Selvaraj, S.2
Gromiha, M.M.3
Siebers, J.G.4
Prabakaran, P.5
Kono, H.6
-
21
-
-
0035584142
-
Strong minor groove base conservation in sequence logos implies DNA distortion or base flipping during replication and transcription initiation
-
Schneider, T.D. (2001) Strong minor groove base conservation in sequence logos implies DNA distortion or base flipping during replication and transcription initiation. Nucleic Acids Res., 29, 4881-4891.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 4881-4891
-
-
Schneider, T.D.1
-
23
-
-
0035077729
-
Genome organisation and chromatin structure in E. coli
-
Ussery, D., Larsen, T.S., Wilkes, K.T., Friis, C., Worning, P., Krogh, A. and Brunak, S. (2001) Genome organisation and chromatin structure in E. coli. Biochimie, 83, 201-212.
-
(2001)
Biochimie
, vol.83
, pp. 201-212
-
-
Ussery, D.1
Larsen, T.S.2
Wilkes, K.T.3
Friis, C.4
Worning, P.5
Krogh, A.6
Brunak, S.7
-
24
-
-
0032483307
-
Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies
-
van Helden, J., André,B. and Collado-Vides, J. (1998) Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J. Mol. Biol., 281, 827-842.
-
(1998)
J. Mol. Biol.
, vol.281
, pp. 827-842
-
-
Van Helden, J.1
André, B.2
Collado-Vides, J.3
-
25
-
-
0034566082
-
Mining for putative regulatory elements in the yeast genome using gene expression data
-
Altman, R. et al., (eds), AAAI Press, Menlo Park, CA
-
Vilo, J., Brazma, A., Jonassen, I., Robinson, A. and Ukkonen, E. (2000) Mining for putative regulatory elements in the yeast genome using gene expression data. In Altman, R. et al., (eds), Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA, pp. 384-394.
-
(2000)
Intelligent Systems for Molecular Biology
, pp. 384-394
-
-
Vilo, J.1
Brazma, A.2
Jonassen, I.3
Robinson, A.4
Ukkonen, E.5
|