-
1
-
-
0002759539
-
Unsupervised learning of multiple motifs in biopolymers using expectation maximization
-
Bailey T.L., Elkan C. Unsupervised learning of multiple motifs in biopolymers using expectation maximization. Machine Learning 1995, 21:51-80.
-
(1995)
Machine Learning
, vol.21
, pp. 51-80
-
-
Bailey, T.L.1
Elkan, C.2
-
2
-
-
0028685490
-
-
Fitting a mixture model by expectation maximization to discover motifs in biopolymers, in: Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, AAAI Press, Menlo Park, California
-
T.L. Bailey, C. Elkan, Fitting a mixture model by expectation maximization to discover motifs in biopolymers, in: Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, AAAI Press, Menlo Park, California, 1994, pp. 28-36.
-
(1994)
, pp. 28-36
-
-
Bailey, T.L.1
Elkan, C.2
-
3
-
-
0023948822
-
Selection of DNA binding sites by regulatory proteins: the LexA protein and the argine repressor use different strategies for functional specificity
-
Berg O.G. Selection of DNA binding sites by regulatory proteins: the LexA protein and the argine repressor use different strategies for functional specificity. Nucleic Acids Research 1988, 16:5089-5105.
-
(1988)
Nucleic Acids Research
, vol.16
, pp. 5089-5105
-
-
Berg, O.G.1
-
4
-
-
0023147228
-
Selection of DNA binding sites by regulatory proteins: statistical-mechanical theory and application to operators and promoters
-
Berg O.G., von Hippel P.H. Selection of DNA binding sites by regulatory proteins: statistical-mechanical theory and application to operators and promoters. Journal of Molecular Biology 1987, 193:723-750.
-
(1987)
Journal of Molecular Biology
, vol.193
, pp. 723-750
-
-
Berg, O.G.1
von Hippel, P.H.2
-
5
-
-
84886053679
-
-
A genetic-based EM motif-finding algorithm for biological sequence analysis, in: Proceedings of IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology
-
C. Bi, A genetic-based EM motif-finding algorithm for biological sequence analysis, in: Proceedings of IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, 2007, pp. 275-282.
-
(2007)
, pp. 275-282
-
-
Bi, C.1
-
6
-
-
68649104708
-
A Monte Carlo EM algorithm for de novo motif discovery in biomolecular sequences
-
Bi C. A Monte Carlo EM algorithm for de novo motif discovery in biomolecular sequences. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2009, 6:370-386.
-
(2009)
IEEE/ACM Transactions on Computational Biology and Bioinformatics
, vol.6
, pp. 370-386
-
-
Bi, C.1
-
8
-
-
34248191269
-
SEAM: a stochastic EM-type algorithm for motif-finding in biopolymer sequences
-
Bi C. SEAM: a stochastic EM-type algorithm for motif-finding in biopolymer sequences. Journal of Bioinformatics and Computational Biology 2007, 5:47-77.
-
(2007)
Journal of Bioinformatics and Computational Biology
, vol.5
, pp. 47-77
-
-
Bi, C.1
-
9
-
-
60849096092
-
DNA motif alignment through evolving a population of Markov chains
-
Bi C. DNA motif alignment through evolving a population of Markov chains. BMC Bioinformatics 2009, 10:S13.
-
(2009)
BMC Bioinformatics
, vol.10
-
-
Bi, C.1
-
10
-
-
38649088564
-
Data augmentation algorithms for detecting conserved domains in protein sequences: a comparative study
-
Bi C. Data augmentation algorithms for detecting conserved domains in protein sequences: a comparative study. Journal of Proteome Research 2008, 7:192-210.
-
(2008)
Journal of Proteome Research
, vol.7
, pp. 192-210
-
-
Bi, C.1
-
11
-
-
39749102250
-
A comparative study on computational two-block motif detection: algorithms and applications
-
Bi C., Leeder J.S., Vyhlidal C.A. A comparative study on computational two-block motif detection: algorithms and applications. Molecular Pharmaceutics 2008, 5:3-16.
-
(2008)
Molecular Pharmaceutics
, vol.5
, pp. 3-16
-
-
Bi, C.1
Leeder, J.S.2
Vyhlidal, C.A.3
-
12
-
-
77956339979
-
-
Comparison of optimization techniques for sequence pattern discovery by maximum-likelihood, Pattern Recognition Letters, doi:10.1016/j.patrec.2009.09.005
-
C. Bi, Comparison of optimization techniques for sequence pattern discovery by maximum-likelihood, Pattern Recognition Letters (2010), doi:10.1016/j.patrec.2009.09.005.
-
(2010)
-
-
Bi, C.1
-
14
-
-
0030376179
-
Stochastic versions of the EM algorithm: an experimental study in the mixture case
-
Celeux G., Diebolt J. Stochastic versions of the EM algorithm: an experimental study in the mixture case. Journal of Statistical Computation and Simulation 1996, 55:287-314.
-
(1996)
Journal of Statistical Computation and Simulation
, vol.55
, pp. 287-314
-
-
Celeux, G.1
Diebolt, J.2
-
15
-
-
32444449634
-
-
MDGA: motif discovery using a genetic algorithm, in: Proceedings of GECCO
-
D. Che, Y. Song, K. Rasheed, MDGA: motif discovery using a genetic algorithm, in: Proceedings of GECCO, 2005, pp. 447-452.
-
(2005)
, pp. 447-452
-
-
Che, D.1
Song, Y.2
Rasheed, K.3
-
16
-
-
0021245317
-
Cyclic AMP receptor protein: role in transcription activation
-
De Crombrugghe B., Busby S., Buc H. Cyclic AMP receptor protein: role in transcription activation. Science 1984, 224:831-838.
-
(1984)
Science
, vol.224
, pp. 831-838
-
-
De Crombrugghe, B.1
Busby, S.2
Buc, H.3
-
18
-
-
3042666256
-
MUSCLE: multiple sequence alignment with high accuracy and high thoughput
-
Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high thoughput. Nucleic Acids Research 2004, 32:1792-1797.
-
(2004)
Nucleic Acids Research
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
19
-
-
34250305146
-
-
The ENCODE Project Consortium, Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project, Science
-
The ENCODE Project Consortium, Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project, Science 447 (2007) 799-816.
-
(2007)
, vol.447
, pp. 799-816
-
-
-
20
-
-
35248875630
-
Exploring the conditional coagulation of yeast gene expression through fuzzy k-means clustering
-
Gasch A.P., Eisen M.B. Exploring the conditional coagulation of yeast gene expression through fuzzy k-means clustering. BMC Bioinformatics 2002, 3:1.
-
(2002)
BMC Bioinformatics
, vol.3
, pp. 1
-
-
Gasch, A.P.1
Eisen, M.B.2
-
21
-
-
0002555793
-
-
Do not worry, be messy, in: Proceedings of the Fourth International Conference on Genetic Algorithms, Morgan Kaufmann Publishers, California
-
D.E. Goldberg, K. Deb, B. Korb, Do not worry, be messy, in: Proceedings of the Fourth International Conference on Genetic Algorithms, Morgan Kaufmann Publishers, California, 1991, pp. 24-30.
-
(1991)
, pp. 24-30
-
-
Goldberg, D.E.1
Deb, K.2
Korb, B.3
-
22
-
-
33748765218
-
Computational biology: towards deciphering gene regulatory information in mammalian genomes
-
Ji H., Wong W.H. Computational biology: towards deciphering gene regulatory information in mammalian genomes. Biometrics 2006, 62:645-663.
-
(2006)
Biometrics
, vol.62
, pp. 645-663
-
-
Ji, H.1
Wong, W.H.2
-
23
-
-
0035946917
-
Computer-assisted identification of cell cycle-related genes: new targets for E2F transcription factors
-
Kel A.E., Kel-Margoulis O.V., Farnham P.J., Bartley S.M., Wingender E., Zhang M.Q. Computer-assisted identification of cell cycle-related genes: new targets for E2F transcription factors. Journal of Molecular Biology 2001, 309:99-120.
-
(2001)
Journal of Molecular Biology
, vol.309
, pp. 99-120
-
-
Kel, A.E.1
Kel-Margoulis, O.V.2
Farnham, P.J.3
Bartley, S.M.4
Wingender, E.5
Zhang, M.Q.6
-
24
-
-
0035878743
-
Estrogen receptor interaction with estrogen response elements
-
Klinge C.M. Estrogen receptor interaction with estrogen response elements. Nucleic Acids Research 2001, 29:2905-2919.
-
(2001)
Nucleic Acids Research
, vol.29
, pp. 2905-2919
-
-
Klinge, C.M.1
-
25
-
-
27344452492
-
A tutorial for competent memetic algorithms: model, taxonomy and design issues
-
Krasnogor N., Smith J. A tutorial for competent memetic algorithms: model, taxonomy and design issues. IEEE Transactions on Evolutionary Computation 2005, 9:474-488.
-
(2005)
IEEE Transactions on Evolutionary Computation
, vol.9
, pp. 474-488
-
-
Krasnogor, N.1
Smith, J.2
-
26
-
-
0025320805
-
An expectation maximization algorithm for the identification and characterization of common sites in unaligned biopolymer sequences
-
Lawrence C.E., Reilly A.A. An expectation maximization algorithm for the identification and characterization of common sites in unaligned biopolymer sequences. Proteins: Structure, Function and Genetics 1990, 7:41-51.
-
(1990)
Proteins: Structure, Function and Genetics
, vol.7
, pp. 41-51
-
-
Lawrence, C.E.1
Reilly, A.A.2
-
28
-
-
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., Wootton J.C. Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science 1993, 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
-
29
-
-
0035228215
-
BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes
-
Liu X., Brutlag D.L., Liu J.S. BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Pacific Symposium on Biocomputing 2001, 127-138.
-
(2001)
Pacific Symposium on Biocomputing
, pp. 127-138
-
-
Liu, X.1
Brutlag, D.L.2
Liu, J.S.3
-
30
-
-
4544358562
-
-
FMGA: finding motifs by genetic algorithm, in: Proceedings of BIBE
-
F.F.M. Liu, J.J.P. Tsai, R.M. Chen, S.N. Chen, S.H. Shih, FMGA: finding motifs by genetic algorithm, in: Proceedings of BIBE, 2004, p. 459.
-
(2004)
, pp. 459
-
-
Liu, F.F.M.1
Tsai, J.J.P.2
Chen, R.M.3
Chen, S.N.4
Shih, S.H.5
-
31
-
-
33646229522
-
Practical strategies for discovering regulatory DNA sequence motifs
-
MacIsaac K.D., Fraenkel E. Practical strategies for discovering regulatory DNA sequence motifs. PLoS Computational Biology 2006, 2:e36.
-
(2006)
PLoS Computational Biology
, vol.2
-
-
MacIsaac, K.D.1
Fraenkel, E.2
-
32
-
-
0033725892
-
Learning mixture models using a genetic version of the EM algorithm
-
Martinez A.M., Vitria J. Learning mixture models using a genetic version of the EM algorithm. Pattern Recognition Letters 2000, 21:759-769.
-
(2000)
Pattern Recognition Letters
, vol.21
, pp. 759-769
-
-
Martinez, A.M.1
Vitria, J.2
-
34
-
-
0029872694
-
SAGA: sequence alignment by genetic algorithm
-
Notredame C., Higgins D.G. SAGA: sequence alignment by genetic algorithm. Nucleic Acids Research 1996, 24:1515-1524.
-
(1996)
Nucleic Acids Research
, vol.24
, pp. 1515-1524
-
-
Notredame, C.1
Higgins, D.G.2
-
35
-
-
0035224579
-
An algorithm for finding signals of unknown length in DNA sequences
-
Pavesi G., Mauri G., Pesole G.G. An algorithm for finding signals of unknown length in DNA sequences. Bioinformatics 2001, 17:S207-S214.
-
(2001)
Bioinformatics
, vol.17
-
-
Pavesi, G.1
Mauri, G.2
Pesole, G.G.3
-
37
-
-
0034565285
-
-
Combinatorial approaches to finding subtle signals in DNA sequences, in: Proceedings of ISCB
-
P.A. Pevzner, S-H. Sze, Combinatorial approaches to finding subtle signals in DNA sequences, in: Proceedings of ISCB, 2000, pp. 269-278.
-
(2000)
, pp. 269-278
-
-
Pevzner, P.A.1
Sze, S-H.2
-
38
-
-
33644873438
-
RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions
-
Salgado H., Gama-Castro S., Peralta-Gil M., Diaz-Peredo E., Sanchez-Solano F., Santos-Zavaleta A., Martinez-Flores I., Jimenez-Jacinto V., Bonavides-Martinez C., Segura-Salazar J., Martinez-Antonio A., Collado-Vides J. RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions. Nucleic Acids Research 2006, 34:D394-D397.
-
(2006)
Nucleic Acids Research
, vol.34
-
-
Salgado, H.1
Gama-Castro, S.2
Peralta-Gil, M.3
Diaz-Peredo, E.4
Sanchez-Solano, F.5
Santos-Zavaleta, A.6
Martinez-Flores, I.7
Jimenez-Jacinto, V.8
Bonavides-Martinez, C.9
Segura-Salazar, J.10
Martinez-Antonio, A.11
Collado-Vides, J.12
-
39
-
-
0347125328
-
JASPAR: an open-access database for eukaryotic transcription factor binding profiles
-
Sandelin A., Alkema W., Engstrom P., Wasserman W.W., Lenhard B. JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Research 2004, 32:D91-D94.
-
(2004)
Nucleic Acids Research
, vol.32
-
-
Sandelin, A.1
Alkema, W.2
Engstrom, P.3
Wasserman, W.W.4
Lenhard, B.5
-
40
-
-
84901431286
-
-
Motif discovery in upstream sequences of coordinately expressed genes, in: Proceedings of CEC
-
M. Stine, D. Dasgupta, S. Mukatira, Motif discovery in upstream sequences of coordinately expressed genes, in: Proceedings of CEC, 2003, pp. 1596-1603.
-
(2003)
, pp. 1596-1603
-
-
Stine, M.1
Dasgupta, D.2
Mukatira, S.3
-
42
-
-
0036108622
-
A Gibbs sampling method to detect over-represented motifs in the upstream regions of co-expressed genes
-
Thijs G., Marchal K., Lescot M., Rombauts S., De Moor B., Roze P., Moreau Y. A Gibbs sampling method to detect over-represented motifs in the upstream regions of co-expressed genes. Journal of Computational Biology 2002, 9:447-464.
-
(2002)
Journal of Computational Biology
, vol.9
, pp. 447-464
-
-
Thijs, G.1
Marchal, K.2
Lescot, M.3
Rombauts, S.4
De Moor, B.5
Roze, P.6
Moreau, Y.7
-
43
-
-
0027968068
-
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 1994, 22:4673-4680.
-
(1994)
Nucleic Acids Research
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
44
-
-
24644457706
-
BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark
-
Thompson J.D., Koehl P., Ripp R., Poch O. BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark. Proteins 2005, 61:127-136.
-
(2005)
Proteins
, vol.61
, pp. 127-136
-
-
Thompson, J.D.1
Koehl, P.2
Ripp, R.3
Poch, O.4
-
45
-
-
0028679709
-
On the complexity of multiple sequence alignment
-
Wang L., Jiang T. On the complexity of multiple sequence alignment. Journal of Computational Biology 1994, 1:337-348.
-
(1994)
Journal of Computational Biology
, vol.1
, pp. 337-348
-
-
Wang, L.1
Jiang, T.2
-
48
-
-
84950432017
-
A Monte Carlo implementation of the EM algorithm and the poor man's data augmentation algorithms
-
Wei G.C.G., Tanner M.A. A Monte Carlo implementation of the EM algorithm and the poor man's data augmentation algorithms. Journal of the American Statistical Association 1990, 85:699-704.
-
(1990)
Journal of the American Statistical Association
, vol.85
, pp. 699-704
-
-
Wei, G.C.G.1
Tanner, M.A.2
-
49
-
-
33745611139
-
GAME: detecting cis-regulatory elements using genetic algorithm
-
Wei Z., Jensen S.T. GAME: detecting cis-regulatory elements using genetic algorithm. Bioinformatics 2006, 22:1577-1584.
-
(2006)
Bioinformatics
, vol.22
, pp. 1577-1584
-
-
Wei, Z.1
Jensen, S.T.2
-
50
-
-
0002210265
-
On the convergence properties of the EM algorithm
-
Wu C.F.J. On the convergence properties of the EM algorithm. The Annals of Statistics 1983, 11:95-103.
-
(1983)
The Annals of Statistics
, vol.11
, pp. 95-103
-
-
Wu, C.F.J.1
|