-
1
-
-
4544295425
-
Environmentally induced foregut remodeling by PHA-4/FoxA and DAF-12/NHR
-
W. Ao, J. Gaudet, W.J. Kent, S. Muttumu, and S.E. Mango Environmentally induced foregut remodeling by PHA-4/FoxA and DAF-12/NHR Science 305 5691 2004 1743 1746
-
(2004)
Science
, vol.305
, Issue.5691
, pp. 1743-1746
-
-
Ao, W.1
Gaudet, J.2
Kent, W.J.3
Muttumu, S.4
Mango, S.E.5
-
2
-
-
0002759539
-
Unsupervised learning of multiple motifs in biopolymers using expectation maximization
-
T.L. Bailey, and C. Elkan Unsupervised learning of multiple motifs in biopolymers using expectation maximization Mach. Learn. 21 1-2 1995 51 80
-
(1995)
Mach. Learn.
, vol.21
, Issue.12
, pp. 51-80
-
-
Bailey, T.L.1
Elkan, C.2
-
6
-
-
33645748095
-
What are DNA sequence motifs?
-
P. D'haeseleer What are DNA sequence motifs? Nat. Biotechnol. 24 4 2006 423 425
-
(2006)
Nat. Biotechnol.
, vol.24
, Issue.4
, pp. 423-425
-
-
D'Haeseleer, P.1
-
7
-
-
0344376570
-
Finding composite regulatory patterns in DNA sequences
-
E. Eskin, and P.A. Pevzner Finding composite regulatory patterns in DNA sequences Bioinformatics 18 Suppl 1 2002 S354 S363
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 1
-
-
Eskin, E.1
Pevzner, P.A.2
-
8
-
-
19544379737
-
A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length
-
A.V. Favorov, M.S. Gelfand, A.V. Gerasimova, D.A. Ravcheev, A.A. Mironov, and V.J. Makeev A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length Bioinformatics 21 10 2005 2240 2245
-
(2005)
Bioinformatics
, vol.21
, Issue.10
, pp. 2240-2245
-
-
Favorov, A.V.1
Gelfand, M.S.2
Gerasimova, A.V.3
Ravcheev, D.A.4
Mironov, A.A.5
Makeev, V.J.6
-
9
-
-
3142737815
-
Discovery of sequence motifs related to coexpression of genes using evolutionary computation
-
G.B. Fogel, D.G. Weekes, G. Varga, E.R. Dow, H.B. Harlow, J.E. Onyia, and C. Su Discovery of sequence motifs related to coexpression of genes using evolutionary computation Nucl. Acids Res. 32 13 2004 3826 3835
-
(2004)
Nucl. Acids Res.
, vol.32
, Issue.13
, pp. 3826-3835
-
-
Fogel, G.B.1
Weekes, D.G.2
Varga, G.3
Dow, E.R.4
Harlow, H.B.5
Onyia, J.E.6
Su, C.7
-
10
-
-
57149097863
-
Evolutionary computation for discovery of composite transcription factor binding sites
-
G.B. Fogel, V.W. Porto, G. Varga, E.R. Dow, A.M. Craven, D.M. Powers, H.B. Harlow, E.W. Su, J.E. Onyia, and C. Su Evolutionary computation for discovery of composite transcription factor binding sites Nucl. Acids Res. 36 21 2008 e142
-
(2008)
Nucl. Acids Res.
, vol.36
, Issue.21
, pp. 142
-
-
Fogel, G.B.1
Porto, V.W.2
Varga, G.3
Dow, E.R.4
Craven, A.M.5
Powers, D.M.6
Harlow, H.B.7
Su, E.W.8
Onyia, J.E.9
Su, C.10
-
11
-
-
1242264319
-
Finding functional sequence elements by multiple local alignment
-
M.C. Frith, U. Hansen, J.L. Spouge, and Z. Weng Finding functional sequence elements by multiple local alignment Nucl. Acids Res. 32 1 2004 189 200
-
(2004)
Nucl. Acids Res.
, vol.32
, Issue.1
, pp. 189-200
-
-
Frith, M.C.1
Hansen, U.2
Spouge, J.L.3
Weng, Z.4
-
13
-
-
79959398526
-
Solving the motif discovery problem by using differential evolution with Pareto tournaments
-
González-Álvarez, D.L.; Vega-Rodríguez, M.A.; Gómez-Pulido, J.A.; Sánchez-Pérez, J.M.; 2010a. Solving the motif discovery problem by using differential evolution with Pareto tournaments. In: Proceedings of the 2010 IEEE Congress on Evolutionary Computation (CEC'10), pp. 4140-4147.
-
(2010)
Proceedings of the 2010 IEEE Congress on Evolutionary Computation (CEC'10)
, pp. 4140-4147
-
-
González-Álvarez, D.L.1
Vega-Rodríguez, M.A.2
Gómez-Pulido, J.A.3
Sánchez-Pérez, J.M.4
-
14
-
-
85038026212
-
A multiobjective variable neighborhood search for solving the motif discovery problem
-
González-Álvarez, D.L.; Vega-Rodríguez, M.A.; Gómez-Pulido, J.A.; Sánchez-Pérez, J.M.; 2010b. A multiobjective variable neighborhood search for solving the motif discovery problem. In: International Workshop on Soft Computing Models in Industrial Applications (SOCO'10), vol. 73, pp. 39-46.
-
(2010)
International Workshop on Soft Computing Models in Industrial Applications (SOCO'10)
, vol.73
, pp. 39-46
-
-
González-Álvarez, D.L.1
Vega-Rodríguez, M.A.2
Gómez-Pulido, J.A.3
Sánchez-Pérez, J.M.4
-
15
-
-
79955779768
-
Finding motifs in DNA sequences applying a multiobjective artificial bee colony (MOABC) algorithm
-
González-Álvarez, D.L.; Vega-Rodríguez, M.A.; Gómez-Pulido, J.A.; Sánchez-Pérez, J.M.; 2011a. Finding motifs in DNA sequences applying a multiobjective artificial bee colony (MOABC) algorithm. In: Proceedings of 8th European Conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics (EVOBIO'11), Lecture Notes in Computer Science, vol. 6623/2011, pp. 89-100.
-
(2011)
Proceedings of 8th European Conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics (EVOBIO'11), Lecture Notes in Computer Science
, vol.6623
, Issue.2011
, pp. 89-100
-
-
González-Álvarez, D.L.1
Vega-Rodríguez, M.A.2
Gómez-Pulido, J.A.3
Sánchez-Pérez, J.M.4
-
16
-
-
79957953014
-
Applying a multiobjective gravitational search algorithm (MO-GSA) to discover motifs
-
González-Álvarez, D.L.; Vega-Rodríguez, M.A.; Gómez-Pulido, J.A.; Sánchez-Pérez, J.M.; 2011b. Applying a multiobjective gravitational search algorithm (MO-GSA) to discover motifs. In: International Work Conference on Artificial Neural Networks (IWANN'11), Lecture Notes in Computer Science, vol. 6692/2011, pp. 372-379.
-
(2011)
International Work Conference on Artificial Neural Networks (IWANN'11), Lecture Notes in Computer Science
, vol.6692
, Issue.2011
, pp. 372-379
-
-
González-Álvarez, D.L.1
Vega-Rodríguez, M.A.2
Gómez-Pulido, J.A.3
Sánchez-Pérez, J.M.4
-
18
-
-
0032826179
-
Identifying DNA and protein patterns with statistically significant alignments of multiple sequences
-
G.Z. Hertz, and G.D. Stormo Identifying DNA and protein patterns with statistically significant alignments of multiple sequences Bioinformatics 15 7-8 1999 563 577
-
(1999)
Bioinformatics
, vol.15
, Issue.78
, pp. 563-577
-
-
Hertz, G.Z.1
Stormo, G.D.2
-
19
-
-
0025372992
-
Identification of consensus patterns in unaligned DNA sequences known to be functionally related
-
G.Z. Hertz, G.W. Hartzell, and G.D. Stormo Identification of consensus patterns in unaligned DNA sequences known to be functionally related Comput. Appl. Biosci. 6 2 1990 81 92
-
(1990)
Comput. Appl. Biosci.
, vol.6
, Issue.2
, pp. 81-92
-
-
Hertz, G.Z.1
Hartzell, G.W.2
Stormo, G.D.3
-
20
-
-
35148827874
-
An Idea Based on Honey Bee Swarm for Numerical Optimization
-
Turkey
-
Karaboga, D.; 2005. An Idea Based on Honey Bee Swarm for Numerical Optimization. Technical Report-tr06, Erciyes University, Turkey.
-
(2005)
Technical Report-tr06, Erciyes University
-
-
Karaboga, D.1
-
21
-
-
56349123312
-
MOGAMOD: Multi-objective genetic algorithm for motif discovery
-
M. Kaya MOGAMOD: Multi-objective genetic algorithm for motif discovery Expert Syst. Appl. 36 2 2009 1039 1047
-
(2009)
Expert Syst. Appl.
, vol.36
, Issue.2
, pp. 1039-1047
-
-
Kaya, M.1
-
22
-
-
4544358562
-
FMGA: Finding motifs by genetic algorithm
-
Liu, F.F.M.; Tsai, J.J.P.; Chen, R.M.; Chen, S.N.; Shih, S.H.; 2004. FMGA: finding motifs by genetic algorithm. In: Fourth IEEE Symposium on Bioinformatics and Bioengineering (BIBE'04), pp. 459-466.
-
(2004)
Fourth IEEE Symposium on Bioinformatics and Bioengineering (BIBE'04)
, pp. 459-466
-
-
Liu, F.F.M.1
Tsai, J.J.P.2
Chen, R.M.3
Chen, S.N.4
Shih, S.H.5
-
23
-
-
84976657294
-
The complexity of some problems on subsequences and supersequences
-
D. Maier The complexity of some problems on subsequences and supersequences J. ACM 25 2 1978 322 336
-
(1978)
J. ACM
, vol.25
, Issue.2
, pp. 322-336
-
-
Maier, D.1
-
25
-
-
0029144601
-
Gibbs motif sampling: Detection of bacterial outer membrane protein repeats
-
A.F. Neuwald, J.S. Liu, and C.E. Lawrence Gibbs motif sampling: detection of bacterial outer membrane protein repeats Protein Sci. 4 8 1995 1618 1632
-
(1995)
Protein Sci.
, vol.4
, Issue.8
, pp. 1618-1632
-
-
Neuwald, A.F.1
Liu, J.S.2
Lawrence, C.E.3
-
26
-
-
0029872694
-
SAGA: Sequence alignment by genetic algorithm
-
C. Notredame, and D.G. Higgins SAGA: sequence alignment by genetic algorithm Nucl. Acids Res. 24 8 1996 1515 1524
-
(1996)
Nucl. Acids Res.
, vol.24
, Issue.8
, pp. 1515-1524
-
-
Notredame, C.1
Higgins, D.G.2
-
27
-
-
0035224579
-
An algorithm for finding signals of unknown length in DNA sequences
-
G. Pavesi, G. Mauri, and G. Pesole An algorithm for finding signals of unknown length in DNA sequences Bioinformatics 17 Suppl 1 2001 S207 S214
-
(2001)
Bioinformatics
, vol.17
, Issue.SUPPL. 1
-
-
Pavesi, G.1
Mauri, G.2
Pesole, G.3
-
30
-
-
42249099020
-
Shuffling biological sequences with motif constraints
-
R. Rivière, D. Barth, J. Cohen, and A. Denise Shuffling biological sequences with motif constraints J. Discrete Algorithms 6 2 2008 192 204
-
(2008)
J. Discrete Algorithms
, vol.6
, Issue.2
, pp. 192-204
-
-
Rivière, R.1
Barth, D.2
Cohen, J.3
Denise, A.4
-
31
-
-
0031787969
-
Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation
-
F.P. Roth, J.D. Hughes, P.W. Estep, and G.M. Church Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation Nat. Biotechnol. 16 10 1998 939 945
-
(1998)
Nat. Biotechnol.
, vol.16
, Issue.10
, pp. 939-945
-
-
Roth, F.P.1
Hughes, J.D.2
Estep, P.W.3
Church, G.M.4
-
35
-
-
0042905768
-
YMF: A program for discovery of novel transcription factor binding sites by statistical overrepresentation
-
S. Sinha, and M. Tompa YMF: A program for discovery of novel transcription factor binding sites by statistical overrepresentation Nucl. Acids Res. 31 13 2003 3586 3588
-
(2003)
Nucl. Acids Res.
, vol.31
, Issue.13
, pp. 3586-3588
-
-
Sinha, S.1
Tompa, M.2
-
36
-
-
0000852513
-
Multi-objective function optimization using non-dominated sorting genetic algorithms
-
N. Srinivas, and K. Deb Multi-objective function optimization using non-dominated sorting genetic algorithms Evolut. Comput. 2 3 1995 221 248
-
(1995)
Evolut. Comput.
, vol.2
, Issue.3
, pp. 221-248
-
-
Srinivas, N.1
Deb, K.2
-
37
-
-
84901431286
-
Motif discovery in upstream sequences of coordinately expressed genes
-
Stine, M.; Dasgupta, D.; Mukatira, S.; 2003. Motif discovery in upstream sequences of coordinately expressed genes. In: The 2003 Congress on Evolutionary Computation (CEC'03), vol. 3, pp. 1596-1603.
-
(2003)
The 2003 Congress on Evolutionary Computation (CEC'03)
, vol.3
, pp. 1596-1603
-
-
Stine, M.1
Dasgupta, D.2
Mukatira, S.3
-
38
-
-
0142000477
-
Differential evolution - A simple and efficient heuristic for global optimization over continuous spaces
-
R. Storn, and K. Price Differential evolution - a simple and efficient heuristic for global optimization over continuous spaces J. Global Optim. 11 4 1997 341 359
-
(1997)
J. Global Optim.
, vol.11
, Issue.4
, pp. 341-359
-
-
Storn, R.1
Price, K.2
-
39
-
-
0036137323
-
A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling
-
G. Thijs, M. Lescot, K. Marchal, S. Rombauts, B. De Moor, P. Rouzé, and Y. Moreau A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling Bioinformatics 17 12 2001 1113 1122
-
(2001)
Bioinformatics
, vol.17
, Issue.12
, pp. 1113-1122
-
-
Thijs, G.1
Lescot, M.2
Marchal, K.3
Rombauts, S.4
De Moor, B.5
Rouzé, P.6
Moreau, Y.7
-
40
-
-
21144439147
-
Assessing computational tools for the discovery of transcription factor binding sites
-
M. Tompa, N. Li, T.L. Bailey, G.M. Church, B. De Moor, E. Eskin, A.V. Favorov, M.C. Frith, Y. Fu, W.J. Kent, V.J. Makeev, A.A. Mironov, W.S. Noble, G. Pavesi, G. Pesole, M. Regnier, N. Simonis, S. Sinha, G. Thijs, J. van Helden, M. Vandenbogaert, C. Weng, Z. Workman, C. Ye, and Z. Zhu Assessing computational tools for the discovery of transcription factor binding sites Nat. Biotechnol. 23 1 2005 137 144
-
(2005)
Nat. Biotechnol.
, vol.23
, Issue.1
, pp. 137-144
-
-
Tompa, M.1
Li, N.2
Bailey, T.L.3
Church, G.M.4
De Moor, B.5
Eskin, E.6
Favorov, A.V.7
Frith, M.C.8
Fu, Y.9
Kent, W.J.10
Makeev, V.J.11
Mironov, A.A.12
Noble, W.S.13
Pavesi, G.14
Pesole, G.15
Regnier, M.16
Simonis, N.17
Sinha, S.18
Thijs, G.19
Van Helden, J.20
Vandenbogaert, M.21
Weng, C.22
Workman, Z.23
Ye, C.24
Zhu, Z.25
more..
-
41
-
-
0032483307
-
Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies
-
J. van Helden, B. Andre, and J. Collado-Vides Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies J. Mol. Biol. 281 5 1998 827 842
-
(1998)
J. Mol. Biol.
, vol.281
, Issue.5
, pp. 827-842
-
-
Van Helden, J.1
Andre, B.2
Collado-Vides, J.3
-
42
-
-
0034656326
-
Discovering regulatory elements in non-coding sequences by analysis of spaced dyads
-
J. van Helden, A.F. Rios, and J. Collado-Vides Discovering regulatory elements in non-coding sequences by analysis of spaced dyads Nucl. Acids Res. 28 8 2000 1808 1818
-
(2000)
Nucl. Acids Res.
, vol.28
, Issue.8
, pp. 1808-1818
-
-
Van Helden, J.1
Rios, A.F.2
Collado-Vides, J.3
-
43
-
-
31744438420
-
A faster algorithm for calculating hypervolume
-
L. While, P. Hingston, L. Barone, and S. Huband A faster algorithm for calculating hypervolume IEEE Trans. Evolut. Comput. 10 1 2006 29 38
-
(2006)
IEEE Trans. Evolut. Comput.
, vol.10
, Issue.1
, pp. 29-38
-
-
While, L.1
Hingston, P.2
Barone, L.3
Huband, S.4
-
44
-
-
0029960055
-
TRANSFAC: A database on transcription factors and their DNA binding sites
-
E. Wingender, P. Dietze, H. Karas, and R. Knuppel TRANSFAC: a database on transcription factors and their DNA binding sites Nucl. Acids Res. 24 1 1996 238 241
-
(1996)
Nucl. Acids Res.
, vol.24
, Issue.1
, pp. 238-241
-
-
Wingender, E.1
Dietze, P.2
Karas, H.3
Knuppel, R.4
-
45
-
-
0033655171
-
ANN-Spec: A method for discovering transcription factor binding sites with improved specificity
-
Workman, C.T.; Stormo, G.D.; 2000. ANN-Spec: a method for discovering transcription factor binding sites with improved specificity. In: Pacific Symposium on Biocomputing, pp. 467-478.
-
(2000)
Pacific Symposium on Biocomputing
, pp. 467-478
-
-
Workman, C.T.1
Stormo, G.D.2
-
46
-
-
65949083121
-
Genetic algorithm for dyad pattern finding in DNA sequences
-
F. Zare-Mirakabad, H. Ahrabian, M. Sadeghi, S. Hashemifar, A. Nowzari-Dalini, and B. Goliaei Genetic algorithm for dyad pattern finding in DNA sequences Genes Genet. Syst. 84 1 2009 81 93
-
(2009)
Genes Genet. Syst.
, vol.84
, Issue.1
, pp. 81-93
-
-
Zare-Mirakabad, F.1
Ahrabian, H.2
Sadeghi, M.3
Hashemifar, S.4
Nowzari-Dalini, A.5
Goliaei, B.6
-
47
-
-
0033318858
-
Multiobjective evolutionary algorithms: A comparative case study and the strength Pareto approach
-
E. Zitzler, and L. Thiele Multiobjective evolutionary algorithms: a comparative case study and the strength Pareto approach IEEE Trans. Evolut. Comput. 3 4 1999 257 271
-
(1999)
IEEE Trans. Evolut. Comput.
, vol.3
, Issue.4
, pp. 257-271
-
-
Zitzler, E.1
Thiele, L.2
-
48
-
-
0034199979
-
Comparison of multiobjective evolutionary algorithms: Empirical results
-
E. Zitzler, K. Deb, and L. Thiele Comparison of multiobjective evolutionary algorithms: empirical results Evolut. Comput. 8 2 2000 173 195
-
(2000)
Evolut. Comput.
, vol.8
, Issue.2
, pp. 173-195
-
-
Zitzler, E.1
Deb, K.2
Thiele, L.3
|