-
1
-
-
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
-
2
-
-
0035875327
-
Non-independence of Mnt repressoroperator interaction determined by a new quantitative multiple uorescence relative af®nity (QuMFRA) assay
-
Man, T.K. and Stormo, G.D. (2001) Non-independence of Mnt repressoroperator interaction determined by a new quantitative multiple uorescence relative af®nity (QuMFRA) assay. Nucleic Acids Res., 29, 2471±2478.
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 2471-2478
-
-
Man, T.K.1
Stormo, G.D.2
-
3
-
-
0036493201
-
Nucleotides of transcription factor binding sites exert interdependent effects on the binding af®nities of transcription factors
-
Bulyk, M.L., Johnson, P.L.F. and Church, G.M. (2002) Nucleotides of transcription factor binding sites exert interdependent effects on the binding af®nities of transcription factors. Nucleic Acids Res., 30, 1255±1261.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 1255-1261
-
-
Bulyk, M.L.1
Johnson, P.L.F.2
Church, G.M.3
-
4
-
-
0036966431
-
A statistical model for investigating binding probabilities of DNA nucleotide sequences using microarrays
-
Lee, M.-L.T., Bulyk, M.L., Whitmore, G.A. and Church, G.M. (2003) A statistical model for investigating binding probabilities of DNA nucleotide sequences using microarrays. Biometrics, 58, 981±988.
-
(2003)
Biometrics
, vol.58
, pp. 981-988
-
-
Lee, M.-L.T.1
Bulyk, M.L.2
Whitmore, G.A.3
Church, G.M.4
-
5
-
-
0037109192
-
Additivity in protein± DNA interactions: how good an approximation is it?
-
Benos, P., 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.1
Bulyk, M.L.2
Stormo, G.D.3
-
6
-
-
85156186944
-
A hierarchical bayesian markovian model for motifs in biopolymer sequences
-
Becker, S., Thrun, S. and Obermayer, K. (eds), MIT Press, Cambridge, MA, in press
-
Xing, E.P., Jordan, M.I., Karp, R.M. and Russell, S. (2002) A hierarchical bayesian markovian model for motifs in biopolymer sequences. In Becker, S., Thrun, S. and Obermayer, K. (eds), Advances in Neural Information Processing Systems 15. MIT Press, Cambridge, MA, in press. Available at http://www.cs.berkeley.edu/-epxing/
-
(2002)
Advances in Neural Information Processing Systems 15
-
-
Xing, E.P.1
Jordan, M.I.2
Karp, R.M.3
Russell, S.4
-
7
-
-
0038716277
-
Modeling dependencies in protein-dna binding sites
-
Vingron, M., Istrail, S., Pevzner, P. and Waterman, M. (eds), ACM Press, New York, NY, in press
-
Barash, Y., Elidan, G., Friedman, N. and Kaplan, T. (2003) Modeling dependencies in protein-dna binding sites. In Vingron, M., Istrail, S., Pevzner, P. and Waterman, M. (eds), Proceedings of the Seventh Annual International Conference on Research in Computational Molecular Biology. ACM Press, New York, NY, in press. Available at http:// www.cs.huji.ac.il/labs/compbio/TFBN/
-
(2003)
Proceedings of the Seventh Annual International Conference on Research in Computational Molecular Biology
-
-
Barash, Y.1
Elidan, G.2
Friedman, N.3
Kaplan, T.4
-
8
-
-
0031652639
-
Detecting non-adjoining correlations within signals in DNA
-
Istrail, S., Pevzner, P. and Waterman, M. (eds), The Association for Computing Machinery, New York, NY
-
Agarwal, P. and Bafna, V. (1998) Detecting non-adjoining correlations within signals in DNA. In Istrail, S., Pevzner, P. and Waterman, M. (eds), Second Annual Conference on Research in Computational Molecular Biology. The Association for Computing Machinery, New York, NY, pp. 2±7.
-
(1998)
Second Annual Conference on Research in Computational Molecular Biology
, pp. 2-7
-
-
Agarwal, P.1
Bafna, V.2
-
9
-
-
0036324753
-
An algorithm for ®nding 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 ®nding 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
-
10
-
-
0003516147
-
-
Cambridge University Press, Cambridge, UK
-
Durbin, R., Eddy, S.R., Krogh, A. and Mitchison, G. (1998) Biological Sequence Analysis. Cambridge University Press, Cambridge, UK.
-
(1998)
Biological Sequence Analysis
-
-
Durbin, R.1
Eddy, S.R.2
Krogh, A.3
Mitchison, G.4
-
11
-
-
0028784743
-
MATRIX SEARCH 1.0: a computer program that scans DNA sequences for transcriptional elements using a database of weight matrices
-
Chen, Q.K., Hertz, J.Z. and Stormo, G.D. (1995) MATRIX SEARCH 1.0: a computer program that scans DNA sequences for transcriptional elements using a database of weight matrices. Comput. Appl. Biol. Sci., 11, 563±566.
-
(1995)
Comput. Appl. Biol. Sci
, vol.11
, pp. 563-566
-
-
Chen, Q.K.1
Hertz, J.Z.2
Stormo, G.D.3
-
12
-
-
0034628901
-
Computational identi®cation of cis-regulatory elements associated with functionally coherent groups of genes in Saccharomyces cerevisiae
-
Hughes, J.D., Estep, P.W., Tavazoie, S. and Church, G.M. (2000) Computational identi®cation of cis-regulatory elements associated with functionally coherent groups of genes in Saccharomyces cerevisiae. J. Mol. Biol., 296, 1205±1214.
-
(2000)
J. Mol. Biol
, vol.296
, pp. 1205-1214
-
-
Hughes, J.D.1
Estep, P.W.2
Tavazoie, S.3
Church, G.M.4
-
13
-
-
0033565546
-
Computer analysis of transcription regulatory patterns in completely sequenced bacterial genomes
-
Mironov, A.A., Koonin, E.V., Roytberg, M.A. and Gelfand, M.S. (1999) Computer analysis of transcription regulatory patterns in completely sequenced bacterial genomes. Nucleic Acids Res., 27, 2981±2989.
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 2981-2989
-
-
Mironov, A.A.1
Koonin, E.V.2
Roytberg, M.A.3
Gelfand, M.S.4
-
14
-
-
0023147228
-
Selection of DNA binding sites by regulatory proteins I: 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 I: 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
-
15
-
-
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
-
16
-
-
0002629270
-
Maximum likelihood from incomplete data via the EM algorithm
-
Dempster, A.P., Laird, N.M. and Rubin, D.B. (1977) Maximum likelihood from incomplete data via the EM algorithm. J. R. Stat. Soc. B, 39, 1±38.
-
(1977)
J. R. Stat. Soc. B
, vol.39
, pp. 1-38
-
-
Dempster, A.P.1
Laird, N.M.2
Rubin, D.B.3
-
18
-
-
0035172256
-
The TRANSFAC system on gene expression regulation
-
Wingender, E., Chen, X., Fricke, E., Geffers, R., Hehl, R., Liebich, I., Krull, M., Matys, V., Michael, H., OhnhaÈuser, R., PruÈû, M., Schacherer, F., Thiele, S. and Urbach, S. (2001) The TRANSFAC system on gene expression regulation. Nucleic Acids Res., 29, 281±283.
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 281-283
-
-
Wingender, E.1
Chen, X.2
Fricke, E.3
Geffers, R.4
Hehl, R.5
Liebich, I.6
Krull, M.7
Matys, V.8
Michael, H.9
OhnhaÈuser, R.10
PruÈû, M.11
Schacherer, F.12
Thiele, S.13
Urbach, S.14
-
19
-
-
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
-
20
-
-
0033977960
-
SELEX_DB: an activated database on selected randomized DNA/RNA sequences addressed to genomic sequence annotation
-
Ponomarenko, J.V., Orlova, G.V., Ponomarenko, M.P., Lavryushev, S.V., Frolov, A.S., Zybova, S.V. and Kolchanov, N.A. (2000) SELEX_DB: an activated database on selected randomized DNA/RNA sequences addressed to genomic sequence annotation. Nucleic Acids Res., 28, 205±208.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 205-208
-
-
Ponomarenko, J.V.1
Orlova, G.V.2
Ponomarenko, M.P.3
Lavryushev, S.V.4
Frolov, A.S.5
Zybova, S.V.6
Kolchanov, N.A.7
-
21
-
-
0031742022
-
Comprehensive identi®cation of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization
-
Spellman, P.T., Sherlock, G., Iyer, V.R., Zhang, M., Anders, K., Eisen, M.B., Brown, P.O., Botstein, D. and Futcher, B. (1998) Comprehensive identi®cation of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell, 9, 3273±3297.
-
(1998)
Mol. Biol. Cell
, vol.9
, pp. 3273-3297
-
-
Spellman, P.T.1
Sherlock, G.2
Iyer, V.R.3
Zhang, M.4
Anders, K.5
Eisen, M.B.6
Brown, P.O.7
Botstein, D.8
Futcher, B.9
-
22
-
-
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..
-
23
-
-
0028714603
-
Neural networks for determining protein speci®city and multiple alignment of binding sites
-
Altman, R., Brutlag, D., Karp, P., Lathrop, R. and Searls, D. (eds), AAAI Press, Menlo Park, CA
-
Heumann, J.M., Lapedes, A.S. and Stormo, G.D. (1994) Neural networks for determining protein speci®city and multiple alignment of binding sites. In Altman, R., Brutlag, D., Karp, P., Lathrop, R. and Searls, D. (eds), Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA, pp. 188±194.
-
(1994)
Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology
, pp. 188-194
-
-
Heumann, J.M.1
Lapedes, A.S.2
Stormo, G.D.3
-
25
-
-
0031269184
-
On the optimality of the simple Bayesian classi®er under zero-one loss
-
Domingos, P. and Pazzani, M. (1997) On the optimality of the simple Bayesian classi®er under zero-one loss. Machine Learning, 29, 103±130.
-
(1997)
Machine Learning
, vol.29
, pp. 103-130
-
-
Domingos, P.1
Pazzani, M.2
-
26
-
-
0027377256
-
A weighted array method for splicing and signal analysis
-
Zhang, M. and Marr, T. (1993) A weighted array method for splicing and signal analysis. Comput. Appl. Biol. Sci., 9, 499±509.
-
(1993)
Comput. Appl. Biol. Sci
, vol.9
, pp. 499-509
-
-
Zhang, M.1
Marr, T.2
-
27
-
-
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
-
28
-
-
0028685490
-
Fitting a mixture model by expectation maximization to discover motifs in biopolymers
-
Altman, R., Brutlag, D., Karp, P., Lathrop, R. and Searls, D. (eds), AAAI Press, Menlo Park, CA
-
Bailey, T.L. and Elkan, C. (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. In Altman, R., Brutlag, D., Karp, P., Lathrop, R. and Searls, D. (eds), Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA, pp. 28±36.
-
(1994)
Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology
, pp. 28-36
-
-
Bailey, T.L.1
Elkan, C.2
-
29
-
-
0035228215
-
BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes
-
Altman, R., Dunker, A., Hunter, L., Lauderdale, K. and Klein, T. (eds), World Scienti®c Publishers, NJ
-
Liu, X., Brutlag, D.L. and Liu, J.S. (2001) BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. In Altman, R., Dunker, A., Hunter, L., Lauderdale, K. and Klein, T. (eds), Paci®c Symposium on Biocomputing 2001. World Scienti®c Publishers, NJ, pp. 127±138.
-
(2001)
Paci®c Symposium on Biocomputing 2001
, pp. 127-138
-
-
Liu, X.1
Brutlag, D.L.2
Liu, J.S.3
-
30
-
-
2342453339
-
Designing committees of models through deliberate weighting of data points
-
Christensen, S.W., Sinclair, I. and Reed, P.A.S. (2003) Designing committees of models through deliberate weighting of data points. J. Machine Learning Res., 4, 39±66.
-
(2003)
J. Machine Learning Res
, vol.4
, pp. 39-66
-
-
Christensen, S.W.1
Sinclair, I.2
Reed, P.A.S.3
|