-
1
-
-
0028685490
-
Fitting a mixture model by expectation maximization to discover motifs in biopolymers
-
AAAI Press, Menlo Park, California
-
Bailey, T.L. and Elkan, C. (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. In Proceedings of the 2nd International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, California, 28-36.
-
(1994)
Proceedings of the 2nd International Conference on Intelligent Systems for Molecular Biology
, pp. 28-36
-
-
Bailey, T.L.1
Elkan, C.2
-
2
-
-
0038716277
-
Modeling dependence in protein-DNA binding sites
-
RECOMB'03. Berlin, Germany, April 2003
-
Barash, Y., Elidan, G., Friedman ,N. and Kaplan, T. (2003) Modeling dependence in protein-DNA binding sites. RECOMB'03. Berlin, Germany, April 2003.
-
(2003)
-
-
Barash, Y.1
Elidan, G.2
Friedman, N.3
Kaplan, T.4
-
3
-
-
0037109192
-
Additivity in protein-DNA interactions: How good an approximation is it?
-
Benos, P.V., Bulyk, M.L. and Stormo, G.D. (2002a) 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
-
4
-
-
0036977044
-
Probabilistic code for DNA recognition by proteins of the EGR family
-
Benos, P.V., Lapedes ,A.S. and Stormo, G.D. (2002b) Probabilistic code for DNA recognition by proteins of the EGR family. J. Mol. Biol., 323, 701-727.
-
(2002)
J. Mol. Biol.
, vol.323
, pp. 701-727
-
-
Benos, P.V.1
Lapedes, A.S.2
Stormo, G.D.3
-
5
-
-
0036493201
-
Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities 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 affinities 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
-
6
-
-
0022358896
-
Rigorous pattern-recognition methods for DNA sequence: Analysis of promoter sequences from Escherichia coli
-
Galas, D.J., Eggert, M. and Waterman, M.S. (1985) Rigorous pattern-recognition methods for DNA sequence: analysis of promoter sequences from Escherichia coli. J. Mol. Biol., 186, 117-128.
-
(1985)
J. Mol. Biol.
, vol.186
, pp. 117-128
-
-
Galas, D.J.1
Eggert, M.2
Waterman, M.S.3
-
7
-
-
0029962489
-
ParaMEME: A parallel implementation and a web interface for a DNA and protein motif discovery tool
-
Grundy, W.N., Bailey, T.L. and Elkan, C.P. (1996) ParaMEME: a parallel implementation and a web interface for a DNA and protein motif discovery tool. Comput. Appl. Biosci., 12, 303-310.
-
(1996)
Comput. Appl. Biosci.
, vol.12
, pp. 303-310
-
-
Grundy, W.N.1
Bailey, T.L.2
Elkan, C.P.3
-
8
-
-
0037361669
-
Discovery of sequence patterns using a stochastic dictionary model
-
Gupta, M. and Liu, J.S. (2003) Discovery of sequence patterns using a stochastic dictionary model. J. Amer. Stat. Assoc., 98, 55-66.
-
(2003)
J. Amer. Stat. Assoc.
, vol.98
, pp. 55-66
-
-
Gupta, M.1
Liu, J.S.2
-
9
-
-
0034949169
-
Role for E2F in control of both DNA replication and mitotic functions as revealed from DNA microarray analysis
-
Ishida, S., Huang, E., Zuzan ,H., Spang, R., Leone, G., West, M. and Nevins, J.R. (2001) Role for E2F in control of both DNA replication and mitotic functions as revealed from DNA microarray analysis. Mol. Cell. Biol., 21, 4684-4699.
-
(2001)
Mol. Cell. Biol.
, vol.21
, pp. 4684-4699
-
-
Ishida, S.1
Huang, E.2
Zuzan, H.3
Spang, R.4
Leone, G.5
West, M.6
Nevins, J.R.7
-
10
-
-
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.N. and Wootton, J. (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.N.5
Wootton, J.6
-
11
-
-
0025320805
-
An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences
-
Lawrence, C.E. and Reilly ,A.A. (1990) An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences. Proteins, 7, 41-51.
-
(1990)
Proteins
, vol.7
, pp. 41-51
-
-
Lawrence, C.E.1
Reilly, A.A.2
-
12
-
-
79951870792
-
The collapsed Gibbs sampler in Bayesian computations with applications to a gene regulation problem
-
Liu, J.S. (1994) The collapsed Gibbs sampler in Bayesian computations with applications to a gene regulation problem. JASA, 89, 958-966.
-
(1994)
JASA
, vol.89
, pp. 958-966
-
-
Liu, J.S.1
-
14
-
-
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., 6, 127-138.
-
(2001)
Pac. Symp. Biocomput.
, vol.6
, pp. 127-138
-
-
Liu, X.1
Brutlag, D.L.2
Liu, J.S.3
-
15
-
-
0036324753
-
An algorithm for finding protein-DNA interaction sites with applications to chromatin immunoprecipitation microarray experiments
-
Liu, X., Brutlag, D.L. and Liu, J.S. (2002) An algorithm for finding protein-DNA interaction sites with applications to chromatin immunoprecipitation microarray experiments. Nat. Biotechnol., 20, 835-839.
-
(2002)
Nat. Biotechnol.
, vol.20
, pp. 835-839
-
-
Liu, X.1
Brutlag, D.L.2
Liu, J.S.3
-
16
-
-
84950424966
-
Bayesian models for multiple local sequence alignment and Gibbs sampling strategies
-
Liu, J.S., Neuwald, A.N. and Lawrence, C.E. (1995) Bayesian models for multiple local sequence alignment and Gibbs sampling strategies. JASA, 90, 1156-1170.
-
(1995)
JASA
, vol.90
, pp. 1156-1170
-
-
Liu, J.S.1
Neuwald, A.N.2
Lawrence, C.E.3
-
17
-
-
0035252592
-
E2Fs regulate the expression of genes involved in differentiation, development, proliferation, and apoptosis
-
Muller, H., Bracken, A.P., Vernell, R., Moroni, M.C., Christians, F., Grassilli, E., Prosperini, E., Vigo, E., Oliner, J.D. and Helin, K. (2001) E2Fs regulate the expression of genes involved in differentiation, development, proliferation, and apoptosis. Genes Dev., 15, 267-285.
-
(2001)
Genes Dev.
, vol.15
, pp. 267-285
-
-
Muller, H.1
Bracken, A.P.2
Vernell, R.3
Moroni, M.C.4
Christians, F.5
Grassilli, E.6
Prosperini, E.7
Vigo, E.8
Oliner, J.D.9
Helin, K.10
-
18
-
-
0029144601
-
Gibbs motif sampling - Detection of bacterial outer-membrane protein repeats
-
Neuwald, A.F., Liu, J.S. and Lawrence, C.E. (1995) Gibbs motif sampling - detection of bacterial outer-membrane protein repeats. Protein Sci., 4, 1618-1632.
-
(1995)
Protein Sci.
, vol.4
, pp. 1618-1632
-
-
Neuwald, A.F.1
Liu, J.S.2
Lawrence, C.E.3
-
19
-
-
0037080483
-
E2F integrates cell cycle progression with DNA repair, replication, and G(2)/M checkpoints
-
Ren, B., Cam, H., Takahashi ,Y., Volkert, T., Terragni, J., Young, R.A. and Dynlacht ,B.D. (2002) E2F integrates cell cycle progression with DNA repair, replication, and G(2)/M checkpoints. Genes Dev., 16, 245-256.
-
(2002)
Genes Dev.
, vol.16
, pp. 245-256
-
-
Ren, B.1
Cam, H.2
Takahashi, Y.3
Volkert, T.4
Terragni, J.5
Young, R.A.6
Dynlacht, B.D.7
-
20
-
-
0031787969
-
Finding DNA regulatory motifs within unaligned non-coding sequences clustered by whole genome mRNA quantization
-
Roth, F.R., Hughes ,J.D., Estep, P.E. and Church ,G.M. (1998) Finding DNA regulatory motifs within unaligned non-coding sequences clustered by whole genome mRNA quantization. Nat. Biotechnol., 16, 939-945.
-
(1998)
Nat. Biotechnol.
, vol.16
, pp. 939-945
-
-
Roth, F.R.1
Hughes, J.D.2
Estep, P.E.3
Church, G.M.4
-
21
-
-
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
-
22
-
-
0000133199
-
Identifying protein-binding sites from unaligned DNA fragments
-
Stormo, G.D. and Hartzell, G.W. (1989) Identifying protein-binding sites from unaligned DNA fragments. Proc. Natl Acad. Sci., USA, 86, 1183-1187.
-
(1989)
Proc. Natl. Acad. Sci. USA
, vol.86
, pp. 1183-1187
-
-
Stormo, G.D.1
Hartzell, G.W.2
-
23
-
-
0033976586
-
TRANSFAC: An integral system for gene expression regulation
-
Wingender, E., Chen, X., Hehl, R., Karas, H., Liebich, I., Matys, V., Meinhardt, T., Pruss, M., Reuter, I. and Schacherer, F. (2000) TRANSFAC: an integral system for gene expression regulation. Nucleic Acids Res., 28, 316-319.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 316-319
-
-
Wingender, E.1
Chen, X.2
Hehl, R.3
Karas, H.4
Liebich, I.5
Matys, V.6
Meinhardt, T.7
Pruss, M.8
Reuter, I.9
Schacherer, F.10
|