-
2
-
-
10744226222
-
Computational discovery of gene modules and regulatory networks
-
Bar-Joseph Z., Gerber G.K., Lee T.I., Rinaldi N.J., Yoo J.Y., Robert F., Gordon D.B., Fraenkel E., Jaahhola T.S., Young R.A., and Gifford D.K. Computational discovery of gene modules and regulatory networks. Nature Biotechnology 21 (2003) 1337-1342
-
(2003)
Nature Biotechnology
, vol.21
, pp. 1337-1342
-
-
Bar-Joseph, Z.1
Gerber, G.K.2
Lee, T.I.3
Rinaldi, N.J.4
Yoo, J.Y.5
Robert, F.6
Gordon, D.B.7
Fraenkel, E.8
Jaahhola, T.S.9
Young, R.A.10
Gifford, D.K.11
-
3
-
-
4344697782
-
An EA framework for biclustering of gene expression data
-
S. Bleuler, A. Prelić, E. Zitzler, An EA framework for biclustering of gene expression data, in: Proceedings of Congress on Evolutionary Computation, 2004, pp. 166-173.
-
(2004)
Proceedings of Congress on Evolutionary Computation
, pp. 166-173
-
-
Bleuler, S.1
Prelić, A.2
Zitzler, E.3
-
4
-
-
2342646842
-
Lsimpute: accurate estimation of missing values in microarray data with least squares methods
-
Bo T.H., Dysvik B., and Jonassen I. Lsimpute: accurate estimation of missing values in microarray data with least squares methods. Nucleic Acids Research 32 (2004) 1-8
-
(2004)
Nucleic Acids Research
, vol.32
, pp. 1-8
-
-
Bo, T.H.1
Dysvik, B.2
Jonassen, I.3
-
5
-
-
1242316281
-
Chip-chip: considerations for the design analysis and application of genome-wide chromatin immunoprecipitation experiments
-
Buck M.J., and Lieb J.D. Chip-chip: considerations for the design analysis and application of genome-wide chromatin immunoprecipitation experiments. Genomics 83 (2004) 349-360
-
(2004)
Genomics
, vol.83
, pp. 349-360
-
-
Buck, M.J.1
Lieb, J.D.2
-
6
-
-
0742306815
-
Computational prediction of transcription-factor binding site locations
-
Bulyk M.L. Computational prediction of transcription-factor binding site locations. Genome Biology 5 (2003) 1-11
-
(2003)
Genome Biology
, vol.5
, pp. 1-11
-
-
Bulyk, M.L.1
-
8
-
-
0034566393
-
-
Y. Cheng, G.M. Church, Biclustering of gene expression data, in: Proceedings of ISMB 2000, 2000, pp. 93-103.
-
Y. Cheng, G.M. Church, Biclustering of gene expression data, in: Proceedings of ISMB 2000, 2000, pp. 93-103.
-
-
-
-
9
-
-
0032112293
-
A genome-wide transcriptional analysis of the mitotic cell cycle
-
Cho R.J., Campbell M.J., Winzeler L.A., Steinmetz L., Conway A., Wodicka L., Wolfsberg T.G., Gabrielian A.E., Landsman D., Lockhart D.J., and Davis R.W. A genome-wide transcriptional analysis of the mitotic cell cycle. Molecular Cell 2 (1998) 65-73
-
(1998)
Molecular Cell
, vol.2
, pp. 65-73
-
-
Cho, R.J.1
Campbell, M.J.2
Winzeler, L.A.3
Steinmetz, L.4
Conway, A.5
Wodicka, L.6
Wolfsberg, T.G.7
Gabrielian, A.E.8
Landsman, D.9
Lockhart, D.J.10
Davis, R.W.11
-
14
-
-
0037057374
-
Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering
-
research0059.1-0059.22
-
Gasch A.P., and Eisen M.B. Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering. Genome Biology 3 (2002) research0059.1-0059.22
-
(2002)
Genome Biology
, vol.3
-
-
Gasch, A.P.1
Eisen, M.B.2
-
15
-
-
0034515528
-
A clustering algorithm based on graph connectivity
-
Hartuv E., and Shamir R. A clustering algorithm based on graph connectivity. Information Processing Letters 76 (2000) 175-181
-
(2000)
Information Processing Letters
, vol.76
, pp. 175-181
-
-
Hartuv, E.1
Shamir, R.2
-
16
-
-
0034609791
-
The large-scale organization of metabolic networks
-
Jeong H., Tombor B., Albert R., Oltval Z.N., and Barabasi A.-L. The large-scale organization of metabolic networks. Nature 407 (2000) 651-654
-
(2000)
Nature
, vol.407
, pp. 651-654
-
-
Jeong, H.1
Tombor, B.2
Albert, R.3
Oltval, Z.N.4
Barabasi, A.-L.5
-
17
-
-
14644416505
-
Identifying time-lagged gene clusters using gene expression data
-
Ji L., and Tan K.L. Identifying time-lagged gene clusters using gene expression data. Bioinformatics 21 (2005) 509-516
-
(2005)
Bioinformatics
, vol.21
, pp. 509-516
-
-
Ji, L.1
Tan, K.L.2
-
18
-
-
0037461033
-
Dynamic modeling of genetic networks using genetic algorithm and S-system
-
Kikuchi S., Tominaga D., Arita M., Takahashi K., and Tomita M. Dynamic modeling of genetic networks using genetic algorithm and S-system. Bioinformatics 19 (2003) 643-650
-
(2003)
Bioinformatics
, vol.19
, pp. 643-650
-
-
Kikuchi, S.1
Tominaga, D.2
Arita, M.3
Takahashi, K.4
Tomita, M.5
-
19
-
-
33745797057
-
Unraveling condition specific gene transcriptional regulatory networks in Saccharomyces Cerevisiae
-
Kim H., Hu W., and Kluger Y. Unraveling condition specific gene transcriptional regulatory networks in Saccharomyces Cerevisiae. BMC Bioinformatics 7 (2006) 165
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 165
-
-
Kim, H.1
Hu, W.2
Kluger, Y.3
-
21
-
-
14044267561
-
Biclustering in gene expression data by tendency
-
J. Liu, J. Yang, W. Wang, Biclustering in gene expression data by tendency, in: Proceedings of the 2004 Computational Systems Bioinformatics Conference (CSB 2004), 2004, pp. 1-12.
-
(2004)
Proceedings of the 2004 Computational Systems Bioinformatics Conference (CSB
, pp. 1-12
-
-
Liu, J.1
Yang, J.2
Wang, W.3
-
23
-
-
33646191891
-
A linear time biclustering algorithm for time series gene expression data
-
WABI 2005. Casadio R., and Myers G. (Eds), Springer Verlag, Berlin
-
Madeira S.C., and Oliveira A.L. A linear time biclustering algorithm for time series gene expression data. In: Casadio R., and Myers G. (Eds). WABI 2005. LNBI vol. 3692 (2005), Springer Verlag, Berlin 39-52
-
(2005)
LNBI
, vol.3692
, pp. 39-52
-
-
Madeira, S.C.1
Oliveira, A.L.2
-
24
-
-
0037208166
-
TRANSFAC: transcriptional regulation from patterns to profiles
-
Matys V., Fricke E., Geffers R., Gossling E., Haubrock M., Hehl R., Hornischer K., Karas D., Kel A., et al. TRANSFAC: transcriptional regulation from patterns to profiles. Nucleic Acids Research 31 (2003) 374-378
-
(2003)
Nucleic Acids Research
, vol.31
, pp. 374-378
-
-
Matys, V.1
Fricke, E.2
Geffers, R.3
Gossling, E.4
Haubrock, M.5
Hehl, R.6
Hornischer, K.7
Karas, D.8
Kel, A.9
-
25
-
-
33748417841
-
Multi-objective evolutionary biclustering of gene expression data
-
Mitra S., and Banka H. Multi-objective evolutionary biclustering of gene expression data. Pattern Recognition 39 (2006) 2464-2477
-
(2006)
Pattern Recognition
, vol.39
, pp. 2464-2477
-
-
Mitra, S.1
Banka, H.2
-
26
-
-
33748433501
-
Special issue on bioinformatics
-
Mitra S., and Pedrycz W. Special issue on bioinformatics. Pattern Recognition 39 12 (2006)
-
(2006)
Pattern Recognition
, vol.39
, Issue.12
-
-
Mitra, S.1
Pedrycz, W.2
-
27
-
-
0024365536
-
Defining the sequence specificity of DNA-binding proteins by selecting binding sites from random-sequence oligonucleotides: analysis of yeast GCN4 protein
-
Oliphant A., Brandl C., and Struhl K. Defining the sequence specificity of DNA-binding proteins by selecting binding sites from random-sequence oligonucleotides: analysis of yeast GCN4 protein. Molecular Cell Biology 9 (1989) 2944-2949
-
(1989)
Molecular Cell Biology
, vol.9
, pp. 2944-2949
-
-
Oliphant, A.1
Brandl, C.2
Struhl, K.3
-
28
-
-
0141998079
-
The maximum edge biclique problem is NP-complete
-
Peeters R. The maximum edge biclique problem is NP-complete. Discrete Applied Mathematics 131 (2003) 651-654
-
(2003)
Discrete Applied Mathematics
, vol.131
, pp. 651-654
-
-
Peeters, R.1
-
29
-
-
0142179209
-
Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data
-
Qian J., Lin J., Luscombe N.M., Yu H., and Gerstein M. Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data. Bioinformatics 19 (2003) 1917-1926
-
(2003)
Bioinformatics
, vol.19
, pp. 1917-1926
-
-
Qian, J.1
Lin, J.2
Luscombe, N.M.3
Yu, H.4
Gerstein, M.5
-
30
-
-
0034515772
-
Coordinate regulation of yeast ribosomal protein genes is associated with targeted recruitment of esa1 histone acetylase
-
Reid J.L., Iyer V.R., Brown P.O., and Struhl K. Coordinate regulation of yeast ribosomal protein genes is associated with targeted recruitment of esa1 histone acetylase. Molecular Cell 6 (2000) 1297-1307
-
(2000)
Molecular Cell
, vol.6
, pp. 1297-1307
-
-
Reid, J.L.1
Iyer, V.R.2
Brown, P.O.3
Struhl, K.4
-
31
-
-
0034704248
-
Genome-wide location and function of DNA binding proteins
-
Ren B., Robert F., Wyrick J.J., Aparicio O., Jennings E.G., Simon I., Zeitlinger J., Schreiber J., Hannett N., et al. Genome-wide location and function of DNA binding proteins. Science 290 (2000) 2306-2309
-
(2000)
Science
, vol.290
, pp. 2306-2309
-
-
Ren, B.1
Robert, F.2
Wyrick, J.J.3
Aparicio, O.4
Jennings, E.G.5
Simon, I.6
Zeitlinger, J.7
Schreiber, J.8
Hannett, N.9
-
32
-
-
15944367731
-
Reconstructing biological networks using conditional correlation analysis
-
Rice J.J., Tu Y., and Stolovitzky G. Reconstructing biological networks using conditional correlation analysis. Bioinformatics 21 (2005) 765-773
-
(2005)
Bioinformatics
, vol.21
, pp. 765-773
-
-
Rice, J.J.1
Tu, Y.2
Stolovitzky, G.3
-
33
-
-
0037941585
-
Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data
-
Segal E., Shapira M., Regev A., Pe'er D., Botstein D., Koller D., and Friedman N. Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nature Genetics 34 (2003) 166-176
-
(2003)
Nature Genetics
, vol.34
, pp. 166-176
-
-
Segal, E.1
Shapira, M.2
Regev, A.3
Pe'er, D.4
Botstein, D.5
Koller, D.6
Friedman, N.7
-
34
-
-
0031742022
-
Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces Cerevisiae by microarray hybridization
-
Spellman P.T., Sherlock G., Zhang M.Q., Iyer V.R., Anders K., Eisen M.B., Brown P.O., Botstein D., and Futcher B. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces Cerevisiae by microarray hybridization. Molecular Biology of the Cell 9 (1998) 3273-3297
-
(1998)
Molecular Biology of the Cell
, vol.9
, pp. 3273-3297
-
-
Spellman, P.T.1
Sherlock, G.2
Zhang, M.Q.3
Iyer, V.R.4
Anders, K.5
Eisen, M.B.6
Brown, P.O.7
Botstein, D.8
Futcher, B.9
-
36
-
-
0034072450
-
DNA binding sites: representation and discovery
-
Stormo G. DNA binding sites: representation and discovery. Bioinformatics 16 (2000) 16-23
-
(2000)
Bioinformatics
, vol.16
, pp. 16-23
-
-
Stormo, G.1
-
37
-
-
33846008592
-
Biclustering algorithms: a survey
-
Handbook of Computational Molecular Biology. Aluru S. (Ed), Chapman & Hall/CRC, USA
-
Tanay A., Sharan R., and Shamir R. Biclustering algorithms: a survey. In: Aluru S. (Ed). Handbook of Computational Molecular Biology. Computer and Information Science Series (2005), Chapman & Hall/CRC, USA 26-1
-
(2005)
Computer and Information Science Series
, pp. 26-1
-
-
Tanay, A.1
Sharan, R.2
Shamir, R.3
-
38
-
-
0033028596
-
Systematic determination of genetic network architecture
-
Tavazoie S., Hughes J.D., Campbell M.J., Cho R.J., and Church G.M. Systematic determination of genetic network architecture. Nature Genetics 22 (1999) 281-285
-
(1999)
Nature Genetics
, vol.22
, pp. 281-285
-
-
Tavazoie, S.1
Hughes, J.D.2
Campbell, M.J.3
Cho, R.J.4
Church, G.M.5
-
39
-
-
0035999974
-
Clustering gene expression data using a graph-theoretic approach: an application of minimum spanning trees
-
Xu Y., Olman V., and Xu D. Clustering gene expression data using a graph-theoretic approach: an application of minimum spanning trees. Bioinformatics 18 (2002) 536-545
-
(2002)
Bioinformatics
, vol.18
, pp. 536-545
-
-
Xu, Y.1
Olman, V.2
Xu, D.3
-
40
-
-
24744462678
-
A time-series biclustering algorithm for revealing co-regulated genes
-
Y. Zhang, H. Zha, C.H. Chu, A time-series biclustering algorithm for revealing co-regulated genes, in: Proceedings of the International Conference on Information Technology: Coding and Computing (ITCC'05), 2005, pp. 32-37.
-
(2005)
Proceedings of the International Conference on Information Technology: Coding and Computing (ITCC'05)
, pp. 32-37
-
-
Zhang, Y.1
Zha, H.2
Chu, C.H.3
|