-
2
-
-
33644839268
-
Automatic Discovery of Cross-Family Sequence Features Associated with Protein Function
-
M. Brameier, J. Haan, A. Krings, and R. MacCallum, "Automatic Discovery of Cross-Family Sequence Features Associated with Protein Function," BMC Bioinformatics, vol. 7, p. 16, 2006.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 16
-
-
Brameier, M.1
Haan, J.2
Krings, A.3
MacCallum, R.4
-
3
-
-
0003875050
-
Designing Efficient and Accurate Parallel Genetic Algorithms,
-
PhD dissertation, Univ. of Illinois at Urbana-Champaign
-
E. Cantú-Paz, "Designing Efficient and Accurate Parallel Genetic Algorithms," PhD dissertation, Univ. of Illinois at Urbana-Champaign, 1999.
-
(1999)
-
-
Cantú-Paz, E.1
-
4
-
-
33847197149
-
Preliminary Results for GAMI: A Genetic Algorithms Approach to Motif Inference
-
C.B. Congdon, C Fizer, N.W. Smith, H.R. Gaskins, J. Aman, G.M. Nava, and C Mattingly, "Preliminary Results for GAMI: A Genetic Algorithms Approach to Motif Inference," Proc. IEEE Symp. Computational Intelligence in Bioinformatics and Computational Biology (CIBCB '05), pp. 97-104, 2005.
-
(2005)
Proc. IEEE Symp. Computational Intelligence in Bioinformatics and Computational Biology (CIBCB '05)
, pp. 97-104
-
-
Congdon, C.B.1
Fizer, C.2
Smith, N.W.3
Gaskins, H.R.4
Aman, J.5
Nava, G.M.6
Mattingly, C.7
-
5
-
-
0034869173
-
Evolving Core Promoter Signal Motifs
-
May
-
D. Corne, A. Meade, and R. Sibly, "Evolving Core Promoter Signal Motifs," Proc. Congress Evolutionary Computation (CEC '01), pp. 1162-1169, May 2001.
-
(2001)
Proc. Congress Evolutionary Computation (CEC '01)
, pp. 1162-1169
-
-
Corne, D.1
Meade, A.2
Sibly, R.3
-
6
-
-
14944363825
-
NestedMICA: Sensitive Inference of Over-Represented Motifs in Nucleic Acid Sequence
-
T.A. Down and T.J.P. Hubbard, "NestedMICA: Sensitive Inference of Over-Represented Motifs in Nucleic Acid Sequence," Nucleic Acids Research, vol. 33, no. 5, pp. 1445-1453, 2005.
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.5
, pp. 1445-1453
-
-
Down, T.A.1
Hubbard, T.J.P.2
-
7
-
-
3142737815
-
Discovery of Sequence Motifs Related to Coexpression of Genes Using Evolutionary Computation
-
G. Fogel, D. Weekes, G. Varga, E. Dow, H. Harlow, J. Onyia, and C Su, "Discovery of Sequence Motifs Related to Coexpression of Genes Using Evolutionary Computation," Nucleic Acids Research, vol. 32, no. 13, pp. 3826-3835, 2004.
-
(2004)
Nucleic Acids Research
, vol.32
, Issue.13
, pp. 3826-3835
-
-
Fogel, G.1
Weekes, D.2
Varga, G.3
Dow, E.4
Harlow, H.5
Onyia, J.6
Su, C.7
-
9
-
-
27144445869
-
A Self-Adaptive Mate Selection Model for Genetic Programming
-
R. Fry, S. Smith, and A. Tyrrell, "A Self-Adaptive Mate Selection Model for Genetic Programming," Proc. IEEE Congress Evolutionary Computation (CEC '05), vol. 3, pp. 2707-2714, 2005.
-
(2005)
Proc. IEEE Congress Evolutionary Computation (CEC '05)
, vol.3
, pp. 2707-2714
-
-
Fry, R.1
Smith, S.2
Tyrrell, A.3
-
10
-
-
34547996100
-
Kohonen Maps Are Suitable for a Biologically Meaningful Classification of Transcription Factor Binding Site Matrices
-
K. Grote, R. Schneider, and T. Werner, "Kohonen Maps Are Suitable for a Biologically Meaningful Classification of Transcription Factor Binding Site Matrices," Proc. German Conf. Bioinformatics (GCB '99), 1999.
-
(1999)
Proc. German Conf. Bioinformatics (GCB '99)
-
-
Grote, K.1
Schneider, R.2
Werner, T.3
-
12
-
-
35048847106
-
Evolving Regular Expression-Based Sequence Classifiers for Protein Nuclear Localisation
-
Apr
-
A. Heddad, M. Brameier, and M. MacCallum, "Evolving Regular Expression-Based Sequence Classifiers for Protein Nuclear Localisation," Applications of Evolutionary Computing, Proc. EvoWork-shops '04, pp. 31-40, Apr. 2004.
-
(2004)
Applications of Evolutionary Computing, Proc. EvoWork-shops '04
, pp. 31-40
-
-
Heddad, A.1
Brameier, M.2
MacCallum, M.3
-
13
-
-
0345724915
-
Evolutionary Computation Method for Pattern Recognition of Cis-Acting Sites
-
Nov
-
D. Howard and K. Benson, "Evolutionary Computation Method for Pattern Recognition of Cis-Acting Sites," Biosystems, vol. 72, nos. 1-2, pp. 19-27, Nov. 2003.
-
(2003)
Biosystems
, vol.72
, Issue.1-2
, pp. 19-27
-
-
Howard, D.1
Benson, K.2
-
14
-
-
26444584579
-
Limitations and Potentials of Current Motif Discovery Algorithms
-
J. Hu, B. Li, and D. Kihara, "Limitations and Potentials of Current Motif Discovery Algorithms," Nucleic Acids Research, vol. 33, no. 15, pp. 4899-4913, 2005.
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.15
, pp. 4899-4913
-
-
Hu, J.1
Li, B.2
Kihara, D.3
-
15
-
-
0008954994
-
Biopattern Discovery by Genetic Programming
-
J.R. Koza et al, ed, pp
-
Y.-J. Hu, "Biopattern Discovery by Genetic Programming," Proc. Genetic Programming Conf, J.R. Koza et al., ed., pp. 152-157, 1998.
-
(1998)
Proc. Genetic Programming Conf
, pp. 152-157
-
-
Hu, Y.-J.1
-
16
-
-
0006837687
-
Automatic Display of Network Structures for Human Understanding
-
Technical Report 88-007, Dept. of Information Science, Univ. of Tokyo
-
T. Kamada and S. Kawai, "Automatic Display of Network Structures for Human Understanding," Technical Report 88-007, Dept. of Information Science, Univ. of Tokyo, 1988.
-
(1988)
-
-
Kamada, T.1
Kawai, S.2
-
17
-
-
4844223097
-
Detecting DNA Regulatory Motifs by Incorporating Positional Trends in Information Content
-
K.J. Kechris, E. van Zwet, P.J. Bickel, and M.B. Eisen, "Detecting DNA Regulatory Motifs by Incorporating Positional Trends in Information Content," Genome Biology, vol. 5, no. 7, p. R50, 2004.
-
(2004)
Genome Biology
, vol.5
, Issue.7
-
-
Kechris, K.J.1
van Zwet, E.2
Bickel, P.J.3
Eisen, M.B.4
-
18
-
-
34547705781
-
The Evolutionary Computation Approach to Motif Discovery in Biological Sequences
-
F. Rothlauf, ed, pp, June
-
M.A. Lones and A.M. Tyrrell, "The Evolutionary Computation Approach to Motif Discovery in Biological Sequences," Proc. Genetic and Evolutionary Computation Conf. (GECCO) Workshop Program, Workshop Biological Applications of Genetic and Evolutionary Computation, F. Rothlauf, ed., pp. 1-11, June 2005.
-
(2005)
Proc. Genetic and Evolutionary Computation Conf. (GECCO) Workshop Program, Workshop Biological Applications of Genetic and Evolutionary Computation
, pp. 1-11
-
-
Lones, M.A.1
Tyrrell, A.M.2
-
19
-
-
0037208166
-
TRANSFAC: Transcriptional Regulation, from Patterns to Profiles
-
Jan
-
V. Matys, E. Fricke, R. Geffers, E. Gssling, M. Haubrock, R. Hehl, K. Homischer, D. Karas, A.E. Kel, O.V. Kel-Margoulis, D.-U. Kloos, S. Land, B. Lewicki-Potapov, H. Michael, R. Münch, I. Reuter, S. Rotert, H. Saxel, M. Scheer, S. Thiele, and E. Wingender, "TRANSFAC: Transcriptional Regulation, from Patterns to Profiles," Nucleic Acids Research, vol. 31, no. 1, pp. 374-378, Jan. 2003.
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.1
, pp. 374-378
-
-
Matys, V.1
Fricke, E.2
Geffers, R.3
Gssling, E.4
Haubrock, M.5
Hehl, R.6
Homischer, K.7
Karas, D.8
Kel, A.E.9
Kel-Margoulis, O.V.10
Kloos, D.-U.11
Land, S.12
Lewicki-Potapov, B.13
Michael, H.14
Münch, R.15
Reuter, I.16
Rotert, S.17
Saxel, H.18
Scheer, M.19
Thiele, S.20
Wingender, E.21
more..
-
20
-
-
0343776188
-
The Eukaryotic Promoter Database (EPD)
-
R. Prier, V. Praz, T. Junier, C. Bonnard, and P. Bucher, "The Eukaryotic Promoter Database (EPD)," Nucleic Acids Research, vol. 28, pp. 302-303, 2000.
-
(2000)
Nucleic Acids Research
, vol.28
, pp. 302-303
-
-
Prier, R.1
Praz, V.2
Junier, T.3
Bonnard, C.4
Bucher, P.5
-
21
-
-
0041829442
-
Recent Advances in Computational Promoter Analysis in Understanding the Transcriptional Regulatory Network
-
Sept
-
P. Qiu, "Recent Advances in Computational Promoter Analysis in Understanding the Transcriptional Regulatory Network," Biochemical and Biophysical Research Comm., vol. 309, no. 3, pp. 495-501, Sept. 2003.
-
(2003)
Biochemical and Biophysical Research Comm
, vol.309
, Issue.3
, pp. 495-501
-
-
Qiu, P.1
-
22
-
-
0031684427
-
Combinatorial Pattern Discovery in Biological Sequences: The TEIRESIAS Algorithm
-
I. Rigoutsos and A. Floratos, "Combinatorial Pattern Discovery in Biological Sequences: The TEIRESIAS Algorithm," Bioinformatics, vol. 14, no. 1, pp. 55-67, 1998.
-
(1998)
Bioinformatics
, vol.14
, Issue.1
, pp. 55-67
-
-
Rigoutsos, I.1
Floratos, A.2
-
23
-
-
0036238824
-
The Evolution of Stochastic Regular Motifs for Protein Sequences
-
Feb
-
B.J. Ross, "The Evolution of Stochastic Regular Motifs for Protein Sequences," New Generation Computing, vol. 20, no. 2, pp. 187-213, Feb. 2002.
-
(2002)
New Generation Computing
, vol.20
, Issue.2
, pp. 187-213
-
-
Ross, B.J.1
-
24
-
-
0347125328
-
JASPAR: An Open-Access Database for Eukaryotic Transcription Factor Binding Profiles
-
Jan
-
A. Sandelin, W. Alkema, P. Engström, W.W. Wasserman, and B. Lenhard, "JASPAR: An Open-Access Database for Eukaryotic Transcription Factor Binding Profiles," Nucleic Acids Research, vol. 32, pp. D91-D94, Jan. 2004.
-
(2004)
Nucleic Acids Research
, vol.32
-
-
Sandelin, A.1
Alkema, W.2
Engström, P.3
Wasserman, W.W.4
Lenhard, B.5
-
25
-
-
0346230985
-
Integrated Analysis of Yeast Regulatory Sequences for Biologically Linked Clusters of Genes
-
July
-
A. Sandelin, A. Höglund, B. Lenhard, and W.W. Wasserman, "Integrated Analysis of Yeast Regulatory Sequences for Biologically Linked Clusters of Genes," Functional and Integrative Genomics, vol. 3, no. 3, pp. 125-134, July 2003.
-
(2003)
Functional and Integrative Genomics
, vol.3
, Issue.3
, pp. 125-134
-
-
Sandelin, A.1
Höglund, A.2
Lenhard, B.3
Wasserman, W.W.4
-
26
-
-
34247579156
-
A Survey of Motif Discovery Methods in an Integrated Framework
-
G.K. Sandve and F. Drablos, "A Survey of Motif Discovery Methods in an Integrated Framework," Biology Direct, vol. 1, no. 11, 2006.
-
(2006)
Biology Direct
, vol.1
, Issue.11
-
-
Sandve, G.K.1
Drablos, F.2
-
28
-
-
34547992071
-
A Clustering Method for Improving the Global Search Capability of Genetic Algorithms
-
F.M.G. França and C.E.C. Ribeiro, eds, pp
-
L. Schnitman and T. Yoneyama, "A Clustering Method for Improving the Global Search Capability of Genetic Algorithms," Proc. Sixth Brazilian Symp. Neural Networks (SBRN '00), F.M.G. França and C.E.C. Ribeiro, eds., pp. 32-37, 2000.
-
(2000)
Proc. Sixth Brazilian Symp. Neural Networks (SBRN '00)
, pp. 32-37
-
-
Schnitman, L.1
Yoneyama, T.2
-
29
-
-
3543059897
-
Multiple Sequence Alignment with Evolutionary Computation
-
C Shyu, L. Sheneman, and J.A. Foster, "Multiple Sequence Alignment with Evolutionary Computation," Genetic Programming and Evolvable Machines, vol. 5, no. 2, pp. 121-144, 2004.
-
(2004)
Genetic Programming and Evolvable Machines
, vol.5
, Issue.2
, pp. 121-144
-
-
Shyu, C.1
Sheneman, L.2
Foster, J.A.3
-
30
-
-
13444273342
-
Identifying TissueSelective Transcription Factor Binding Sites in Vertebrate Promoters
-
Feb
-
A.D. Smith, P. Sumazin, and M.Q. Zhang, "Identifying TissueSelective Transcription Factor Binding Sites in Vertebrate Promoters," Proc. Nat'l Academy Sciences of the USA, vol. 102, no. 5, pp. 1560-1565, Feb. 2005.
-
(2005)
Proc. Nat'l Academy Sciences of the USA
, vol.102
, Issue.5
, pp. 1560-1565
-
-
Smith, A.D.1
Sumazin, P.2
Zhang, M.Q.3
-
31
-
-
0034072450
-
DNA Binding Sites: Representation and Discovery
-
Jan
-
G. Stormo, "DNA Binding Sites: Representation and Discovery," Bioinformatics, vol. 16, no. 1, pp. 16-23, Jan. 2000.
-
(2000)
Bioinformatics
, vol.16
, Issue.1
, pp. 16-23
-
-
Stormo, G.1
-
32
-
-
35248880713
-
A Clustering Based Niching Method for Evolutionary Algorithms
-
E. Cantu-Paz, J.A. Foster, K. Deb, D. Davis, R. Roy, U.-M. O'Reilly, H.-G. Beyer, R. Standish, G. Kendall, S. Wilson, M. Harman, J. Wegener, D. Dasgupta, M.A. Potter, A.C. Schultz, K. Dowsland, N. Jonoska, and J. Miller, eds, pp, July
-
F. Streichert, G. Stein, H. Ulmer, and A. Zell, "A Clustering Based Niching Method for Evolutionary Algorithms," Proc. Genetic and Evolutionary Computation Conf. (GECCO '03), E. Cantu-Paz, J.A. Foster, K. Deb, D. Davis, R. Roy, U.-M. O'Reilly, H.-G. Beyer, R. Standish, G. Kendall, S. Wilson, M. Harman, J. Wegener, D. Dasgupta, M.A. Potter, A.C. Schultz, K. Dowsland, N. Jonoska, and J. Miller, eds., pp. 644-645, July 2003.
-
(2003)
Proc. Genetic and Evolutionary Computation Conf. (GECCO '03)
, pp. 644-645
-
-
Streichert, F.1
Stein, G.2
Ulmer, H.3
Zell, A.4
-
33
-
-
0043123063
-
Gibbs Recursive Sampler: Finding Transcription Factor Binding Sites
-
July
-
W. Thompson, E.C Rouchka, and C.E. Lawrence, "Gibbs Recursive Sampler: Finding Transcription Factor Binding Sites," Nucleic Acids Research, vol. 31, no. 13, pp. 3580-3585, July 2003.
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.13
, pp. 3580-3585
-
-
Thompson, W.1
Rouchka, E.C.2
Lawrence, C.E.3
-
34
-
-
21144439147
-
Assessing Computational Tools for the Discovery of Transcription Factor Binding Sites
-
Jan
-
M. Tompa, N. Li, T.L. Bailey, G.M. Church, B.D. 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. Rgnier, N. Simonis, S. Sinha, G. Thijs, J. van Helden, M. Vandenbogaert, Z. Weng, C. Workman, C. Ye, and Z. Zhu, "Assessing Computational Tools for the Discovery of Transcription Factor Binding Sites," Nature Biotechnology, vol. 23, no. 1, pp. 137-144, Jan. 2005.
-
(2005)
Nature Biotechnology
, vol.23
, Issue.1
, pp. 137-144
-
-
Tompa, M.1
Li, N.2
Bailey, T.L.3
Church, G.M.4
Moor, B.D.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
Rgnier, M.16
Simonis, N.17
Sinha, S.18
Thijs, G.19
van Helden, J.20
Vandenbogaert, M.21
Weng, Z.22
Workman, C.23
Ye, C.24
Zhu, Z.25
more..
-
35
-
-
0032562789
-
Identification of Regulatory Regions which Confer Muscle-Specific Gene Expression
-
Apr
-
W.W. Wasserman and J.W. Fickett, "Identification of Regulatory Regions which Confer Muscle-Specific Gene Expression," J. Molecular Biology, vol. 278, no. 1, pp. 167-181, Apr. 1998.
-
(1998)
J. Molecular Biology
, vol.278
, Issue.1
, pp. 167-181
-
-
Wasserman, W.W.1
Fickett, J.W.2
-
36
-
-
0037869270
-
The State of the Art of Mammalian Promoter Recognition
-
Mar
-
T. Werner, "The State of the Art of Mammalian Promoter Recognition," Briefings Bioinformatics, vol. 4, no. 1, pp. 22-30, Mar. 2003.
-
(2003)
Briefings Bioinformatics
, vol.4
, Issue.1
, pp. 22-30
-
-
Werner, T.1
-
37
-
-
12344325673
-
Training HMM Structure with Genetic Algorithm for Biological Sequence Analysis
-
Dec
-
K.-J. Won, A. Prügel-Bennett, and A. Krogh, "Training HMM Structure with Genetic Algorithm for Biological Sequence Analysis," Bioinformatics, vol. 20, no. 18, pp. 3613-3619, Dec. 2004.
-
(2004)
Bioinformatics
, vol.20
, Issue.18
, pp. 3613-3619
-
-
Won, K.-J.1
Prügel-Bennett, A.2
Krogh, A.3
-
38
-
-
0042697343
-
The Evolution of Transcriptional Regulation in Eukaryotes
-
Sept
-
G.A. Wray, M.W. Hahn, E. Abouheif, J.P. Balhoff, M. Pizer, M.V. Rockman, and L.A. Romano, "The Evolution of Transcriptional Regulation in Eukaryotes," Molecular Biology and Evolution, vol. 20, no. 9, pp. 1377-1419, Sept. 2003.
-
(2003)
Molecular Biology and Evolution
, vol.20
, Issue.9
, pp. 1377-1419
-
-
Wray, G.A.1
Hahn, M.W.2
Abouheif, E.3
Balhoff, J.P.4
Pizer, M.5
Rockman, M.V.6
Romano, L.A.7
-
39
-
-
0030310347
-
Extraction of Hidden Markov Model Representations of Signal Patterns in DNA Sequences
-
T. Yada, M. Ishikawa, H. Tanaka, and K. Asai, "Extraction of Hidden Markov Model Representations of Signal Patterns in DNA Sequences," Proc. Pacific Symp. Biocomputing, pp. 686-696, 1996.
-
(1996)
Proc. Pacific Symp. Biocomputing
, pp. 686-696
-
-
Yada, T.1
Ishikawa, M.2
Tanaka, H.3
Asai, K.4
|