-
1
-
-
33847070442
-
The role of chromatin during transcription
-
Li B., Carey M., Workman JL The role of chromatin during transcription. Cell 2007; 128 (4). 707-719.
-
(2007)
Cell
, vol.128
, Issue.4
, pp. 707-719
-
-
Li, B.1
Carey, M.2
Workman, J.L.3
-
2
-
-
39449088572
-
Genome-wide approaches to studying chromatin modifications
-
Schones DE, Zhao K. Genome-wide approaches to studying chromatin modifications. Nature Reviews Genetics 2008; 9 (3). 179-191.
-
(2008)
Nature Reviews Genetics
, vol.9
, Issue.3
, pp. 179-191
-
-
Schones, D.E.1
Zhao, K.2
-
3
-
-
40449138572
-
Post-transcriptional gene regulation: From genome-wide studies to principles
-
Halbeisen RE, Galgano A., Scherrer T., Gerber AP Post-transcriptional gene regulation: from genome-wide studies to principles. Cellular and Molecular Life Sciences 2008; 65 (5). 798-813.
-
(2008)
Cellular and Molecular Life Sciences
, vol.65
, Issue.5
, pp. 798-813
-
-
Halbeisen, R.E.1
Galgano, A.2
Scherrer, T.3
Gerber, A.P.4
-
4
-
-
0035945567
-
Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF
-
Iyer VR, Horak CE, Scafe CS, Botstein D., Snyder M., Brown PO Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 2001; 409 (6819). 533-538.
-
(2001)
Nature
, vol.409
, Issue.6819
, pp. 533-538
-
-
Iyer, V.R.1
Horak, C.E.2
Scafe, C.S.3
Botstein, D.4
Snyder, M.5
Brown, P.O.6
-
5
-
-
0034704248
-
Genome-wide location and function of DNA binding proteins
-
Ren B., Robert F., Wyrick JJ et al. Genome-wide location and function of DNA binding proteins. Science 2000; 290 (5500). 2306-2309.
-
(2000)
Science
, vol.290
, Issue.5500
, pp. 2306-2309
-
-
Ren, B.1
Robert, F.2
Wyrick, J.J.3
-
6
-
-
33750442923
-
Genome-wide analysis of estrogen receptor binding sites
-
Carroll JS, Meyer CA, Song J. et al. Genome-wide analysis of estrogen receptor binding sites. Nature Genetics 2006; 38: 1289-1297.
-
(2006)
Nature Genetics
, vol.38
, pp. 1289-1297
-
-
Carroll, J.S.1
Meyer, C.A.2
Song, J.3
-
7
-
-
33646865180
-
Control of developmental regulators by Polycomb in human embryonic stem cells
-
Lee TI, Jenner RG, Boyer LA et al. Control of developmental regulators by Polycomb in human embryonic stem cells. Cell 2006; 125: 301-313.
-
(2006)
Cell
, vol.125
, pp. 301-313
-
-
Lee, T.I.1
Jenner, R.G.2
Boyer, L.A.3
-
8
-
-
34250159524
-
Genome-wide mapping of in vivo protein-DNA interactions
-
Johnson DS, Mortazavi A., Myers RM, Wold B. Genome-wide mapping of in vivo protein-DNA interactions. Science 2007; 316: 1497-1502.
-
(2007)
Science
, vol.316
, pp. 1497-1502
-
-
Johnson, D.S.1
Mortazavi, A.2
Myers, R.M.3
Wold, B.4
-
9
-
-
34547633677
-
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing
-
Robertson G., Hirst M., Bainbridge M. et al. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nature Methods 2007; 4: 651-657.
-
(2007)
Nature Methods
, vol.4
, pp. 651-657
-
-
Robertson, G.1
Hirst, M.2
Bainbridge, M.3
-
10
-
-
15544375816
-
DIP-chip: Rapid and accurate determination of DNA-binding specificity
-
Liu X., Noll DM, Lieb JD, Clarke ND DIP-chip: rapid and accurate determination of DNA-binding specificity. Genome Research 2005; 15 (3). 421-427.
-
(2005)
Genome Research
, vol.15
, Issue.3
, pp. 421-427
-
-
Liu, X.1
Noll, D.M.2
Lieb, J.D.3
Clarke, N.D.4
-
11
-
-
9644268153
-
Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays
-
Mukherjee S., Berger MF, Jona G. et al. Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays. Nature Genetics 2004; 36 (12). 1331-1339.
-
(2004)
Nature Genetics
, vol.36
, Issue.12
, pp. 1331-1339
-
-
Mukherjee, S.1
Berger, M.F.2
Jona, G.3
-
12
-
-
17944372930
-
Serial regulation of transcriptional regulators in the yeast cell cycle
-
Simon I., Barnett J., Hannett N. et al. Serial regulation of transcriptional regulators in the yeast cell cycle. Cell 2001; 106 (6). 697-708.
-
(2001)
Cell
, vol.106
, Issue.6
, pp. 697-708
-
-
Simon, I.1
Barnett, J.2
Hannett, N.3
-
13
-
-
2942582468
-
Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data
-
Gao F., Foat BC, Bussemaker HJ Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data. BMC Bioinformatics 2004; 5: 31.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 31
-
-
Gao, F.1
Foat, B.C.2
Bussemaker, H.J.3
-
14
-
-
39149093082
-
Statistical methods to infer cooperative binding among transcription factors in Saccharomyces cerevisiae
-
Datta D., Zhao H. Statistical methods to infer cooperative binding among transcription factors in Saccharomyces cerevisiae. Bioinformatics 2008; 24 (4). 545-552.
-
(2008)
Bioinformatics
, vol.24
, Issue.4
, pp. 545-552
-
-
Datta, D.1
Zhao, H.2
-
15
-
-
0032561246
-
The transcriptional program of sporulation in budding yeast
-
Chu S., DeRisi J., Eisen M. et al. The transcriptional program of sporulation in budding yeast. Science 1998; 282 (5389). 699-705.
-
(1998)
Science
, vol.282
, Issue.5389
, pp. 699-705
-
-
Chu, S.1
Derisi, J.2
Eisen, M.3
-
16
-
-
0033637153
-
Genomic expression programs in the response of yeast cells to environmental changes
-
Gasch AP, Spellman PT, Kao CM et al. Genomic expression programs in the response of yeast cells to environmental changes. Molecular Biology of the Cell 2000; 11 (12). 4241-4257.
-
(2000)
Molecular Biology of the Cell
, vol.11
, Issue.12
, pp. 4241-4257
-
-
Gasch, A.P.1
Spellman, P.T.2
Kao, C.M.3
-
17
-
-
0034616930
-
Functional discovery via a compendium of expression profiles
-
Hughes TR, Marton MJ, Jones AR et al. Functional discovery via a compendium of expression profiles. Cell 2000; 102 (1). 109-126.
-
(2000)
Cell
, vol.102
, Issue.1
, pp. 109-126
-
-
Hughes, T.R.1
Marton, M.J.2
Jones, A.R.3
-
18
-
-
0031742022
-
Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization
-
Spellman PT, Sherlock G., Zhang MQ et al. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Molecular Biology of the Cell 1998; 9 (12). 3273-3297.
-
(1998)
Molecular Biology of the Cell
, vol.9
, Issue.12
, pp. 3273-3297
-
-
Spellman, P.T.1
Sherlock, G.2
Zhang, M.Q.3
-
19
-
-
0037197892
-
Precision and functional specificity in mRNA decay
-
Wang Y., Liu CL, Storey JD, Tibshirani RJ, Herschlag D., Brown PO Precision and functional specificity in mRNA decay. Proceedings of the National Academy of Sciences of the United States of America 2002; 99 (9). 5860-5865.
-
(2002)
Proceedings of the National Academy of Sciences of the United States of America
, vol.99
, Issue.9
, pp. 5860-5865
-
-
Wang, Y.1
Liu, C.L.2
Storey, J.D.3
Tibshirani, R.J.4
Herschlag, D.5
Brown, P.O.6
-
20
-
-
38349030979
-
Inferring transcriptional interactions and regulator activities from experimental data
-
Wang RS, Zhang XS, Chen L. Inferring transcriptional interactions and regulator activities from experimental data. Molecular Cell 2007; 24 (3). 307-315.
-
(2007)
Molecular Cell
, vol.24
, Issue.3
, pp. 307-315
-
-
Wang, R.S.1
Zhang, X.S.2
Chen, L.3
-
21
-
-
0034710924
-
Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks
-
Butte AJ, Tamayo P., Slonim D., Golub TR, Kohane IS Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks. Proceedings of the National Academy of Sciences of the United States of America 2000; 97 (22). 12182-12186.
-
(2000)
Proceedings of the National Academy of Sciences of the United States of America
, vol.97
, Issue.22
, pp. 12182-12186
-
-
Butte, A.J.1
Tamayo, P.2
Slonim, D.3
Golub, T.R.4
Kohane, I.S.5
-
23
-
-
33947305781
-
ARACNE: An algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context
-
Margolin AA, Nemenman I., Basso K. et al. ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics 2006; 7 (Suppl 1). S7.
-
(2006)
BMC Bioinformatics
, vol.7
, Issue.1
, pp. 7
-
-
Margolin, A.A.1
Nemenman, I.2
Basso, K.3
-
24
-
-
15944367731
-
Reconstructing biological networks using conditional correlation analysis
-
Rice JJ, Tu Y., Stolovitzky G. Reconstructing biological networks using conditional correlation analysis. Bioinformatics 2005; 21 (6). 765-773.
-
(2005)
Bioinformatics
, vol.21
, Issue.6
, pp. 765-773
-
-
Rice, J.J.1
Tu, Y.2
Stolovitzky, G.3
-
26
-
-
0036191190
-
Inference of a genetic network by a combined approach of cluster analysis and graphical Gaussian modeling
-
Toh H., Horimoto K. Inference of a genetic network by a combined approach of cluster analysis and graphical Gaussian modeling. Bioinformatics 2002; 18 (2). 287-297.
-
(2002)
Bioinformatics
, vol.18
, Issue.2
, pp. 287-297
-
-
Toh, H.1
Horimoto, K.2
-
27
-
-
15944399178
-
Sparse graphical models for exploring gene expression data
-
Dobra A., Hans C., Jones B., Nevins JR, Yao G., West M. Sparse graphical models for exploring gene expression data. Journal of Multivariate Analysis 2004; 90 (1). 196-212.
-
(2004)
Journal of Multivariate Analysis
, vol.90
, Issue.1
, pp. 196-212
-
-
Dobra, A.1
Hans, C.2
Jones, B.3
Nevins, J.R.4
Yao, G.5
West, M.6
-
28
-
-
33645568358
-
Gradient directed regularization for sparse Gaussian concentration graphs, with applications to inference of genetic networks
-
Li H., Gui J. Gradient directed regularization for sparse Gaussian concentration graphs, with applications to inference of genetic networks. Biostatistics 2006; 7 (2). 302-317.
-
(2006)
Biostatistics
, vol.7
, Issue.2
, pp. 302-317
-
-
Li, H.1
Gui, J.2
-
29
-
-
33747163541
-
High-dimensional graphs and variable selection with the Lasso
-
Meinshausen N., Buhlmann P. High-dimensional graphs and variable selection with the Lasso. Annals of Statistics 2006; 34 (3). 1436.
-
(2006)
Annals of Statistics
, vol.34
, Issue.3
, pp. 1436
-
-
Meinshausen, N.1
Buhlmann, P.2
-
30
-
-
66549116888
-
Partial correlation estimation by joint sparse regression models
-
Peng J., Wang P., Zhou N., Zhu J. Partial correlation estimation by joint sparse regression models. Journal of the American Statistical Association 2009; 104 (486). 735-746.
-
(2009)
Journal of the American Statistical Association
, vol.104
, Issue.486
, pp. 735-746
-
-
Peng, J.1
Wang, P.2
Zhou, N.3
Zhu, J.4
-
31
-
-
25144501141
-
A Bayesian regression approach to the inference of regulatory networks from gene expression data
-
Rogers S., Girolami M. A Bayesian regression approach to the inference of regulatory networks from gene expression data. Bioinformatics 2005; 21 (14). 3131-3137.
-
(2005)
Bioinformatics
, vol.21
, Issue.14
, pp. 3131-3137
-
-
Rogers, S.1
Girolami, M.2
-
32
-
-
27844521293
-
A shrinkage approach to large-scale covariance matrix estimation and implications for functional genomics
-
Schafer J., Strimmer K. A shrinkage approach to large-scale covariance matrix estimation and implications for functional genomics. Statistical Applications in Genetics and Molecular Biology 2005; 4: Article 32.
-
(2005)
Statistical Applications in Genetics and Molecular Biology
, vol.4
-
-
Schafer, J.1
Strimmer, K.2
-
33
-
-
15944364151
-
An empirical Bayes approach to inferring large-scale gene association networks
-
Schafer J., Strimmer K. An empirical Bayes approach to inferring large-scale gene association networks. Bioinformatics 2005; 21 (6). 754-764.
-
(2005)
Bioinformatics
, vol.21
, Issue.6
, pp. 754-764
-
-
Schafer, J.1
Strimmer, K.2
-
34
-
-
46749151407
-
Weighted lasso in graphical Gaussian modeling for large gene network estimation based on microarray data
-
Shimamura T., Imoto S., Yamaguchi R., Miyano S. Weighted lasso in graphical Gaussian modeling for large gene network estimation based on microarray data. Genome Informatics 2007; 19: 142-153.
-
(2007)
Genome Informatics
, vol.19
, pp. 142-153
-
-
Shimamura, T.1
Imoto, S.2
Yamaguchi, R.3
Miyano, S.4
-
36
-
-
55249119797
-
Heuristic approach to sparse approximation of gene regulatory networks
-
Andrecut M., Huang S., Kauffman SA Heuristic approach to sparse approximation of gene regulatory networks. Journal of Computational Biology 2008; 15 (9). 1173-1186.
-
(2008)
Journal of Computational Biology
, vol.15
, Issue.9
, pp. 1173-1186
-
-
Andrecut, M.1
Huang, S.2
Kauffman, S.A.3
-
38
-
-
0038048325
-
Inferring genetic networks and identifying compound mode of action via expression profiling
-
Gardner TS, di Bernardo D., Lorenz D., Collins JJ Inferring genetic networks and identifying compound mode of action via expression profiling. Science 2003; 301 (5629). 102-105.
-
(2003)
Science
, vol.301
, Issue.5629
, pp. 102-105
-
-
Gardner, T.S.1
Bernardo, D.2
Lorenz, D.3
Collins, J.J.4
-
40
-
-
0033707946
-
Peĝ€™er D. Using Bayesian networks to analyze expression data
-
Friedman N., Linial M., Nachman I., Peĝ€™er D. Using Bayesian networks to analyze expression data. Journal of Computational Biology 2000; 7 (3-4). 601-620.
-
(2000)
Journal of Computational Biology
, vol.7
, Issue.3-4
, pp. 601-620
-
-
Friedman, N.1
Linial, M.2
Nachman, I.3
-
42
-
-
49549100459
-
Learning causal Bayesian network structures from experimental data
-
Ellis B., Wong WH Learning causal Bayesian network structures from experimental data. Journal of the American Statistical Association 2008; 103 (482). 778-789.
-
(2008)
Journal of the American Statistical Association
, vol.103
, Issue.482
, pp. 778-789
-
-
Ellis, B.1
Wong, W.H.2
-
43
-
-
4143058645
-
Gene networks inference using dynamic Bayesian networks
-
Perrin BE, Ralaivola L., Mazurie A., Bottani S., Mallet J., dĝ€™Alche-Buc F. Gene networks inference using dynamic Bayesian networks. Bioinformatics 2003; 19 (Suppl 2). ii138-48.
-
(2003)
Bioinformatics
, vol.19
, Issue.2
, pp. 138-48
-
-
Perrin, B.E.1
Ralaivola, L.2
Mazurie, A.3
Bottani, S.4
Mallet, J.5
Dĝalche-Buc, F.6
-
44
-
-
12744261506
-
A new dynamic Bayesian network (DBN) approach for identifying gene regulatory networks from time course microarray data
-
Zou M., Conzen SD A new dynamic Bayesian network (DBN) approach for identifying gene regulatory networks from time course microarray data. Bioinformatics 2005; 21 (1). 71-79.
-
(2005)
Bioinformatics
, vol.21
, Issue.1
, pp. 71-79
-
-
Zou, M.1
Conzen, S.D.2
-
46
-
-
0344464762
-
Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic Bayesian networks
-
Husmeier D. Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic Bayesian networks. Bioinformatics 2003; 19 (17). 2271-2282.
-
(2003)
Bioinformatics
, vol.19
, Issue.17
, pp. 2271-2282
-
-
Husmeier, D.1
-
47
-
-
34547844096
-
Comparing association network algorithms for reverse engineering of large-scale gene regulatory networks: Synthetic versus real data
-
Soranzo N., Bianconi G., Altafini C. Comparing association network algorithms for reverse engineering of large-scale gene regulatory networks: synthetic versus real data. Bioinformatics 2007; 23 (13). 1640-1647.
-
(2007)
Bioinformatics
, vol.23
, Issue.13
, pp. 1640-1647
-
-
Soranzo, N.1
Bianconi, G.2
Altafini, C.3
-
48
-
-
33749825955
-
Comparative evaluation of reverse engineering gene regulatory networks with relevance networks, graphical gaussian models and bayesian networks
-
Werhli AV, Grzegorczyk M., Husmeier D. Comparative evaluation of reverse engineering gene regulatory networks with relevance networks, graphical gaussian models and bayesian networks. Bioinformatics 2006; 22 (20). 2523-2531.
-
(2006)
Bioinformatics
, vol.22
, Issue.20
, pp. 2523-2531
-
-
Werhli, A.V.1
Grzegorczyk, M.2
Husmeier, D.3
-
49
-
-
33645307955
-
Inference of gene regulatory networks and compound mode of action from time course gene expression profiles
-
Bansal M., Gatta GD, di Bernardo D. Inference of gene regulatory networks and compound mode of action from time course gene expression profiles. Bioinformatics 2006; 22 (7). 815-822.
-
(2006)
Bioinformatics
, vol.22
, Issue.7
, pp. 815-822
-
-
Bansal, M.1
Gatta, G.D.2
Di Bernardo, D.3
-
50
-
-
4644238174
-
Reconstructing genetic networks from time ordered gene expression data using Bayesian method with global search algorithm
-
Wang SC Reconstructing genetic networks from time ordered gene expression data using Bayesian method with global search algorithm. Journal of Bioinformatics and Computational Biology 2004; 2 (3). 441-458.
-
(2004)
Journal of Bioinformatics and Computational Biology
, vol.2
, Issue.3
, pp. 441-458
-
-
Wang, S.C.1
-
51
-
-
0014658880
-
Biochemical systems analysis. II. The steady-state solutions for an n-pool system using a power-law approximation
-
Savageau MA Biochemical systems analysis. II. The steady-state solutions for an n-pool system using a power-law approximation. Journal of Theoretical Biology 1969; 25 (3). 370-379.
-
(1969)
Journal of Theoretical Biology
, vol.25
, Issue.3
, pp. 370-379
-
-
Savageau, M.A.1
-
52
-
-
0014649230
-
Biochemical systems analysis. I. Some mathematical properties of the rate law for the component enzymatic reactions
-
Savageau MA Biochemical systems analysis. I. Some mathematical properties of the rate law for the component enzymatic reactions. Journal of Theoretical Biology 1969; 25 (3). 365-369.
-
(1969)
Journal of Theoretical Biology
, vol.25
, Issue.3
, pp. 365-369
-
-
Savageau, M.A.1
-
53
-
-
33747813561
-
The Inferelator: An algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo
-
Bonneau R., Reiss DJ, Shannon P. et al. The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo. Genome Biology 2006; 7 (5). R36.
-
(2006)
Genome Biology
, vol.7
, Issue.5
, pp. 36
-
-
Bonneau, R.1
Reiss, D.J.2
Shannon, P.3
-
54
-
-
0032441150
-
Cluster analysis and display of genome-wide expression patterns
-
Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns. Proceedings of the National Academy of Sciences of the United States of America 1998; 95 (25). 14863-14868.
-
(1998)
Proceedings of the National Academy of Sciences of the United States of America
, vol.95
, Issue.25
, pp. 14863-14868
-
-
Eisen, M.B.1
Spellman, P.T.2
Brown, P.O.3
Botstein, D.4
-
56
-
-
44449136102
-
Bayesian biclustering of gene expression data
-
Gu J., Liu JS Bayesian biclustering of gene expression data. BMC Genomics 2008; 9 (Suppl 1). S4.
-
(2008)
BMC Genomics
, vol.9
, Issue.1
, pp. 4
-
-
Gu, J.1
Liu, J.S.2
-
58
-
-
1542357674
-
Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data
-
Tanay A., Sharan R., Kupiec M., Shamir R. Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data. Proceedings of the National Academy of Sciences of the United States of America 2004; 101 (9). 2981-2986.
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, Issue.9
, pp. 2981-2986
-
-
Tanay, A.1
Sharan, R.2
Kupiec, M.3
Shamir, R.4
-
59
-
-
0037941585
-
Module networks: Identifying regulatory modules and their condition-specific regulators from gene expression data
-
Segal E., Shapira M., Regev A. et al. Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nature Genetics 2003; 34 (2). 166-176.
-
(2003)
Nature Genetics
, vol.34
, Issue.2
, pp. 166-176
-
-
Segal, E.1
Shapira, M.2
Regev, A.3
-
60
-
-
2442446708
-
Genome-wide discovery of transcriptional modules from DNA sequence and gene expression
-
Segal E., Yelensky R., Koller D. Genome-wide discovery of transcriptional modules from DNA sequence and gene expression. Bioinformatics 2003; 19 (Suppl 1). i273-82.
-
(2003)
Bioinformatics
, vol.19
, Issue.1
, pp. 273-82
-
-
Segal, E.1
Yelensky, R.2
Koller, D.3
-
61
-
-
33746067911
-
Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks
-
Reiss DJ, Baliga NS, Bonneau R. Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks. BMC Bioinformatics 2006; 7: 280.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 280
-
-
Reiss, D.J.1
Baliga, N.S.2
Bonneau, R.3
-
62
-
-
10744226222
-
Computational discovery of gene modules and regulatory networks
-
Bar-Joseph Z., Gerber GK, Lee TI et al. Computational discovery of gene modules and regulatory networks. Nature Biotechnology 2003; 21 (11). 1337-1342.
-
(2003)
Nature Biotechnology
, vol.21
, Issue.11
, pp. 1337-1342
-
-
Bar-Joseph, Z.1
Gerber, G.K.2
Lee, T.I.3
-
63
-
-
33745128746
-
Inferring transcriptional modules from ChIP-chip, motif and microarray data
-
Lemmens K., Dhollander T., De Bie T. et al. Inferring transcriptional modules from ChIP-chip, motif and microarray data. Genome Biology 2006; 7 (5). R37.
-
(2006)
Genome Biology
, vol.7
, Issue.5
, pp. 37
-
-
Lemmens, K.1
Dhollander, T.2
De Bie, T.3
-
64
-
-
13844319583
-
Inference of combinatorial regulation in yeast transcriptional networks: A case study of sporulation
-
Wang W., Cherry JM, Nochomovitz Y., Jolly E., Botstein D., Li H. Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation. Proceedings of the National Academy of Sciences of the United States of America 2005; 102 (6). 1998-2003.
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, Issue.6
, pp. 1998-2003
-
-
Wang, W.1
Cherry, J.M.2
Nochomovitz, Y.3
Jolly, E.4
Botstein, D.5
Li, H.6
-
65
-
-
73449121698
-
Statistical methods for inference of genetic networks and regulatory modules
-
Emmert-Streid, Dehmer, eds. Wiley VCH, Verlag GmbH & Co. KGaA;
-
Li H. Statistical methods for inference of genetic networks and regulatory modules. In Emmert-Streid, Dehmer, eds. Analysis of microarray data: network-based approaches. Wiley VCH, Verlag GmbH & Co. KGaA; 2008: 143-167.
-
(2008)
Analysis of Microarray Data: Network-based Approaches
, pp. 143-167
-
-
Li, H.1
-
66
-
-
34848855728
-
Bayesian hierarchical model for transcriptional module discovery by jointly modeling gene expression and ChIP-chip data
-
Liu X., Jessen WJ, Sivaganesan S., Aronow BJ, Medvedovic M. Bayesian hierarchical model for transcriptional module discovery by jointly modeling gene expression and ChIP-chip data. BMC Bioinformatics 2007; 8: 283.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 283
-
-
Liu, X.1
Jessen, W.J.2
Sivaganesan, S.3
Aronow, B.J.4
Medvedovic, M.5
-
67
-
-
34548390720
-
Statistical reconstruction of transcription factor activity using Michaelis-Menten kinetics
-
Khanin R., Vinciotti V., Mersinias V., Smith CP, Wit E. Statistical reconstruction of transcription factor activity using Michaelis-Menten kinetics. Biometrics 2007; 63 (3). 816-823.
-
(2007)
Biometrics
, vol.63
, Issue.3
, pp. 816-823
-
-
Khanin, R.1
Vinciotti, V.2
Mersinias, V.3
Smith, C.P.4
Wit, E.5
-
68
-
-
0036396542
-
Rationalization of gene regulation by a eukaryotic transcription factor: Calculation of regulatory region occupancy from predicted binding affinities
-
Liu X., Clarke ND Rationalization of gene regulation by a eukaryotic transcription factor: calculation of regulatory region occupancy from predicted binding affinities. Journal of Molecular Biology 2002; 323 (1). 1-8.
-
(2002)
Journal of Molecular Biology
, vol.323
, Issue.1
, pp. 1-8
-
-
Liu, X.1
Clarke, N.D.2
-
69
-
-
14844307159
-
Inferring quantitative models of regulatory networks from expression data
-
Nachman I., Regev A., Friedman N. Inferring quantitative models of regulatory networks from expression data. Bioinformatics 2004; 20 (Suppl 1). i248-256.
-
(2004)
Bioinformatics
, vol.20
, Issue.1
, pp. 248-256
-
-
Nachman, I.1
Regev, A.2
Friedman, N.3
-
70
-
-
34547844132
-
Connecting quantitative regulatory-network models to the genome
-
Pan Y., Durfee T., Bockhorst J., Craven M. Connecting quantitative regulatory-network models to the genome. Bioinformatics 2007; 23 (13). i367-376.
-
(2007)
Bioinformatics
, vol.23
, Issue.13
, pp. 367-376
-
-
Pan, Y.1
Durfee, T.2
Bockhorst, J.3
Craven, M.4
-
71
-
-
20844452570
-
A stochastic differential equation model for quantifying transcriptional regulatory network in Saccharomyces cerevisiae
-
Chen KC, Wang TY, Tseng HH, Huang CY, Kao CY A stochastic differential equation model for quantifying transcriptional regulatory network in Saccharomyces cerevisiae. Bioinformatics 2005; 21 (12). 2883-2890.
-
(2005)
Bioinformatics
, vol.21
, Issue.12
, pp. 2883-2890
-
-
Chen, K.C.1
Wang, T.Y.2
Tseng, H.H.3
Huang, C.Y.4
Kao, C.Y.5
-
72
-
-
4444339832
-
Quantitative characterization of the transcriptional regulatory network in the yeast cell cycle
-
Chen HC, Lee HC, Lin TY, Li WH, Chen BS Quantitative characterization of the transcriptional regulatory network in the yeast cell cycle. Bioinformatics 2004; 20 (12). 1914-1927.
-
(2004)
Bioinformatics
, vol.20
, Issue.12
, pp. 1914-1927
-
-
Chen, H.C.1
Lee, H.C.2
Lin, T.Y.3
Li, W.H.4
Chen, B.S.5
-
74
-
-
57149100747
-
Structural identification of piecewise-linear models of genetic regulatory networks
-
Porreca R., Drulhe S., de Jong H., Ferrari-Trecate G. Structural identification of piecewise-linear models of genetic regulatory networks. Journal of Computational Biology 2008; 15 (10). 1365-1380.
-
(2008)
Journal of Computational Biology
, vol.15
, Issue.10
, pp. 1365-1380
-
-
Porreca, R.1
Drulhe, S.2
De Jong, H.3
Ferrari-Trecate, G.4
-
75
-
-
58149120776
-
Modeling the dynamics of transcriptional gene regulatory networks for animal development
-
Ben-Tabou de-Leon S., Davidson EH Modeling the dynamics of transcriptional gene regulatory networks for animal development. Developmental Biology 2009; 325 (2). 317-328.
-
(2009)
Developmental Biology
, vol.325
, Issue.2
, pp. 317-328
-
-
Ben-Tabou De-Leon, S.1
Davidson, E.H.2
-
76
-
-
34249856850
-
Bayesian model-based inference of transcription factor activity
-
Rogers S., Khanin R., Girolami M. Bayesian model-based inference of transcription factor activity. BMC Bioinformatics 2007; 8 Suppl 2: S2.
-
(2007)
BMC Bioinformatics
, vol.8
, Issue.2
, pp. 2
-
-
Rogers, S.1
Khanin, R.2
Girolami, M.3
-
77
-
-
38049170632
-
Inferring activity changes of transcription factors by binding association with sorted expression profiles
-
Cheng C., Yan X., Sun F., Li LM Inferring activity changes of transcription factors by binding association with sorted expression profiles. BMC Bioinformatics 2007; 8: 452.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 452
-
-
Cheng, C.1
Yan, X.2
Sun, F.3
Li, L.M.4
-
78
-
-
47049084462
-
Estimating dynamic models for gene regulation networks
-
Cao J., Zhao H. Estimating dynamic models for gene regulation networks. Bioinformatics 2008; 24 (14). 1619-1624.
-
(2008)
Bioinformatics
, vol.24
, Issue.14
, pp. 1619-1624
-
-
Cao, J.1
Zhao, H.2
-
79
-
-
0345824737
-
Network component analysis: Reconstruction of regulatory signals in biological systems
-
Liao JC, Boscolo R., Yang YL, Tran LM, Sabatti C., Roychowdhury VP Network component analysis: reconstruction of regulatory signals in biological systems. Proceedings of the National Academy of Sciences of the United States of America 2003; 100 (26). 15522-15527.
-
(2003)
Proceedings of the National Academy of Sciences of the United States of America
, vol.100
, Issue.26
, pp. 15522-15527
-
-
Liao, J.C.1
Boscolo, R.2
Yang, Y.L.3
Tran, L.M.4
Sabatti, C.5
Roychowdhury, V.P.6
-
80
-
-
21844466280
-
DNA-protein binding and gene expression patterns. Science and Statistics: A Festschrift for Terry Speed
-
Zhao H., Wu B., Sun N. DNA-protein binding and gene expression patterns. Science and Statistics: A Festschrift for Terry Speed. IMS Lecture Notes-Monograph Series 2003; 40: 259-274.
-
(2003)
IMS Lecture Notes-Monograph Series
, vol.40
, pp. 259-274
-
-
Zhao, H.1
Wu, B.2
Sun, N.3
-
81
-
-
33748905107
-
Modelling the network of cell cycle transcription factors in the yeast Saccharomyces cerevisiae
-
Cokus S., Rose S., Haynor D., Gronbech-Jensen N., Pellegrini M. Modelling the network of cell cycle transcription factors in the yeast Saccharomyces cerevisiae. BMC Bioinformatics 2006; 7: 381.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 381
-
-
Cokus, S.1
Rose, S.2
Haynor, D.3
Gronbech-Jensen, N.4
Pellegrini, M.5
-
82
-
-
34547840186
-
Group SCAD regression analysis for microarray time course gene expression data
-
Wang L., Chen G., Li H. Group SCAD regression analysis for microarray time course gene expression data. Bioinformatics 2007; 23 (12). 1486-1494.
-
(2007)
Bioinformatics
, vol.23
, Issue.12
, pp. 1486-1494
-
-
Wang, L.1
Chen, G.2
Li, H.3
-
83
-
-
15944376548
-
A statistical method for constructing transcriptional regulatory networks using gene expression and sequence data
-
Xing B., van der Laan MJ A statistical method for constructing transcriptional regulatory networks using gene expression and sequence data. Journal of Computational Biology 2005; 12 (2). 229-246.
-
(2005)
Journal of Computational Biology
, vol.12
, Issue.2
, pp. 229-246
-
-
Xing, B.1
Van Der Laan, M.J.2
-
84
-
-
33645107349
-
Bayesian sparse hidden components analysis for transcription regulation networks
-
Sabatti C., James GM Bayesian sparse hidden components analysis for transcription regulation networks. Bioinformatics 2006; 22 (6). 739-746.
-
(2006)
Bioinformatics
, vol.22
, Issue.6
, pp. 739-746
-
-
Sabatti, C.1
James, G.M.2
-
85
-
-
27744472292
-
Inference of transcriptional regulatory network by two-stage constrained space factor analysis
-
Yu T., Li KC Inference of transcriptional regulatory network by two-stage constrained space factor analysis. Bioinformatics 2005; 21 (21). 4033-4038.
-
(2005)
Bioinformatics
, vol.21
, Issue.21
, pp. 4033-4038
-
-
Yu, T.1
Li, K.C.2
-
86
-
-
23744491001
-
Predicting transcription factor activities from combined analysis of microarray and ChIP data: A partial least squares approach
-
Boulesteix AL, Strimmer K. Predicting transcription factor activities from combined analysis of microarray and ChIP data: a partial least squares approach. Theoretical Biology & Medical Modelling 2005; 2: 23.
-
(2005)
Theoretical Biology & Medical Modelling
, vol.2
, pp. 23
-
-
Boulesteix, A.L.1
Strimmer, K.2
-
87
-
-
33947409985
-
Factor analysis for gene regulatory networks and transcription factor activity profiles
-
Pournara I., Wernisch L. Factor analysis for gene regulatory networks and transcription factor activity profiles. BMC Bioinformatics 2007; 8: 61.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 61
-
-
Pournara, I.1
Wernisch, L.2
-
88
-
-
3142550629
-
Multilevel modeling and inference of transcription regulation
-
Tanay A., Shamir R. Multilevel modeling and inference of transcription regulation. Journal of Computational Biology 2004; 11 (2-3). 357-375.
-
(2004)
Journal of Computational Biology
, vol.11
, Issue.2-3
, pp. 357-375
-
-
Tanay, A.1
Shamir, R.2
-
89
-
-
41349101972
-
Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models
-
Hirose O., Yoshida R., Imoto S. et al. Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models. Bioinformatics 2008; 24 (7). 932-942.
-
(2008)
Bioinformatics
, vol.24
, Issue.7
, pp. 932-942
-
-
Hirose, O.1
Yoshida, R.2
Imoto, S.3
-
90
-
-
2442691914
-
Modeling gene expression from microarray expression data with state-space equations
-
Wu FX, Zhang WJ, Kusalik AJ Modeling gene expression from microarray expression data with state-space equations. Pacific Symposium on Biocomputing 2004: 581-592.
-
(2004)
Pacific Symposium on Biocomputing
, pp. 581-592
-
-
Wu, F.X.1
Zhang, W.J.2
Kusalik, A.J.3
-
91
-
-
3142744689
-
Modeling T-cell activation using gene expression profiling and state-space models
-
Rangel C., Angus J., Ghahramani Z. et al. Modeling T-cell activation using gene expression profiling and state-space models. Bioinformatics 2004; 20 (9). 1361-1372.
-
(2004)
Bioinformatics
, vol.20
, Issue.9
, pp. 1361-1372
-
-
Rangel, C.1
Angus, J.2
Ghahramani, Z.3
-
92
-
-
13844253637
-
A Bayesian approach to reconstructing genetic regulatory networks with hidden factors
-
Beal MJ, Falciani F., Ghahramani Z., Rangel C., Wild DL A Bayesian approach to reconstructing genetic regulatory networks with hidden factors. Bioinformatics 2005; 21 (3). 349-356.
-
(2005)
Bioinformatics
, vol.21
, Issue.3
, pp. 349-356
-
-
Beal, M.J.1
Falciani, F.2
Ghahramani, Z.3
Rangel, C.4
Wild, D.L.5
-
93
-
-
39149104076
-
Structural systems identification of genetic regulatory networks
-
Xiong H., Choe Y. Structural systems identification of genetic regulatory networks. Bioinformatics 2008; 24 (4). 553-560.
-
(2008)
Bioinformatics
, vol.24
, Issue.4
, pp. 553-560
-
-
Xiong, H.1
Choe, Y.2
-
94
-
-
33751008680
-
Probabilistic inference of transcription factor concentrations and gene-specific regulatory activities
-
DOI 10.1093/bioinformatics/btl473
-
Sanguinetti G., Lawrence ND, Rattray M. Probabilistic inference of transcription factor concentrations and gene-specific regulatory activities. Bioinformatics 2006; 22 (22). 2775-2781. (Pubitemid 44742398)
-
(2006)
Bioinformatics
, vol.22
, Issue.22
, pp. 2775-2781
-
-
Sanguinetti, G.1
Lawrence, N.D.2
Rattray, M.3
-
95
-
-
33645108505
-
Using a state-space model with hidden variables to infer transcription factor activities
-
Li Z., Shaw SM, Yedwabnick MJ, Chan C. Using a state-space model with hidden variables to infer transcription factor activities. Bioinformatics 2006; 22 (6). 747-754.
-
(2006)
Bioinformatics
, vol.22
, Issue.6
, pp. 747-754
-
-
Li, Z.1
Shaw, S.M.2
Yedwabnick, M.J.3
Chan, C.4
-
96
-
-
32944459703
-
Integrating mRNA decay information into co-regulation study
-
Chen L., Zhao H. Integrating mRNA decay information into co-regulation study. Journal of Computer Science and Technology 2005; 20: 434-438.
-
(2005)
Journal of Computer Science and Technology
, vol.20
, pp. 434-438
-
-
Chen, L.1
Zhao, H.2
-
97
-
-
53949098609
-
Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation
-
Shalem O., Dahan O., Levo M. et al. Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation. Molecular Systems Biology 2008; 4: 223.
-
(2008)
Molecular Systems Biology
, vol.4
, pp. 223
-
-
Shalem, O.1
Dahan, O.2
Levo, M.3
-
98
-
-
58549106607
-
High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites
-
Whitington T., Perkins AC, Bailey TL High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites. Nucleic Acids Research 2009; 37 (1). 14-25.
-
Nucleic Acids Research 2009;
, vol.37
, Issue.1
, pp. 14-25
-
-
Whitington, T.1
Perkins, A.C.2
Bailey, T.L.3
-
99
-
-
0035135420
-
Regulatory element detection using correlation with expression
-
Bussemaker HJ, Li H., Siggia ED Regulatory element detection using correlation with expression. Nature Genetics 2001; 27 (2). 167-171.
-
(2001)
Nature Genetics
, vol.27
, Issue.2
, pp. 167-171
-
-
Bussemaker, H.J.1
Li, H.2
Siggia, E.D.3
-
100
-
-
0036324753
-
An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments
-
Liu XS, Brutlag DL, Liu JS An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nature Biotechnology 2002; 20 (8). 835-839.
-
(2002)
Nature Biotechnology
, vol.20
, Issue.8
, pp. 835-839
-
-
Liu, X.S.1
Brutlag, D.L.2
Liu, J.S.3
-
101
-
-
0037453009
-
Integrating regulatory motif discovery and genome-wide expression analysis
-
Conlon EM, Liu XS, Lieb JD, Liu JS Integrating regulatory motif discovery and genome-wide expression analysis. Proceedings of the National Academy of Sciences of the United States of America 2003; 100 (6). 3339-3344.
-
(2003)
Proceedings of the National Academy of Sciences of the United States of America
, vol.100
, Issue.6
, pp. 3339-3344
-
-
Conlon, E.M.1
Liu, X.S.2
Lieb, J.D.3
Liu, J.S.4
-
102
-
-
0037177625
-
Genetic dissection of transcriptional regulation in budding yeast
-
Brem RB, Yvert G., Clinton R., Kruglyak L. Genetic dissection of transcriptional regulation in budding yeast. Science 2002; 296 (5568). 752-755.
-
(2002)
Science
, vol.296
, Issue.5568
, pp. 752-755
-
-
Brem, R.B.1
Yvert, G.2
Clinton, R.3
Kruglyak, L.4
-
103
-
-
4043128071
-
Genetic analysis of genome-wide variation in human gene expression
-
Morley M., Molony CM, Weber TM et al. Genetic analysis of genome-wide variation in human gene expression. Nature 2004; 430 (7001). 743-747.
-
(2004)
Nature
, vol.430
, Issue.7001
, pp. 743-747
-
-
Morley, M.1
Molony, C.M.2
Weber, T.M.3
-
104
-
-
0037456823
-
Genetics of gene expression surveyed in maize, mouse and man
-
Schadt EE, Monks SA, Drake TA et al. Genetics of gene expression surveyed in maize, mouse and man. Nature 2003; 422 (6929). 297-302.
-
(2003)
Nature
, vol.422
, Issue.6929
, pp. 297-302
-
-
Schadt, E.E.1
Monks, S.A.2
Drake, T.A.3
-
105
-
-
0042856391
-
Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors
-
Yvert G., Brem RB, Whittle J. et al. Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors. Nature Genetics 2003; 35 (1). 57-64.
-
(2003)
Nature Genetics
, vol.35
, Issue.1
, pp. 57-64
-
-
Yvert, G.1
Brem, R.B.2
Whittle, J.3
-
106
-
-
45149106353
-
Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks
-
Zhu J., Zhang B., Smith EN et al. Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks. Nature Genetics 2008; 40 (7). 854-861.
-
(2008)
Nature Genetics
, vol.40
, Issue.7
, pp. 854-861
-
-
Zhu, J.1
Zhang, B.2
Smith, E.N.3
-
107
-
-
33646920070
-
Iterative reconstruction of transcriptional regulatory networks: An algorithmic approach
-
Barrett CL, Palsson BO Iterative reconstruction of transcriptional regulatory networks: an algorithmic approach. PLoS Computational Biology 2006; 2 (5). e52.
-
(2006)
PLoS Computational Biology
, vol.2
, Issue.5
, pp. 52
-
-
Barrett, C.L.1
Palsson, B.O.2
-
108
-
-
0037687416
-
Reverse engineering gene networks: Integrating genetic perturbations with dynamical modeling
-
Tegner J., Yeung MK, Hasty J., Collins JJ Reverse engineering gene networks: integrating genetic perturbations with dynamical modeling. Proceedings of the National Academy of Sciences of the United States of America 2003; 100 (10). 5944-5949.
-
(2003)
Proceedings of the National Academy of Sciences of the United States of America
, vol.100
, Issue.10
, pp. 5944-5949
-
-
Tegner, J.1
Yeung, M.K.2
Hasty, J.3
Collins, J.J.4
-
109
-
-
54249124501
-
Learning biological networks: From modules to dynamics
-
Bonneau R. Learning biological networks: from modules to dynamics. Nature Chemical Biology 2008; 4 (11). 658-664.
-
(2008)
Nature Chemical Biology
, vol.4
, Issue.11
, pp. 658-664
-
-
Bonneau, R.1
-
110
-
-
7744225947
-
Transcriptional networks: Reverse-engineering gene regulation on a global scale
-
Chua G., Robinson MD, Morris Q., Hughes TR Transcriptional networks: reverse-engineering gene regulation on a global scale. Current Opinion in Microbiology 2004; 7 (6). 638-646.
-
(2004)
Current Opinion in Microbiology
, vol.7
, Issue.6
, pp. 638-646
-
-
Chua, G.1
Robinson, M.D.2
Morris, Q.3
Hughes, T.R.4
-
111
-
-
3343020085
-
Integrative analysis of cell cycle control in budding yeast
-
Chen KC, Calzone L., Csikasz-Nagy A., Cross FR, Novak B., Tyson JJ Integrative analysis of cell cycle control in budding yeast. Molecular Biology of the Cell 2004; 15 (8). 3841-3862.
-
(2004)
Molecular Biology of the Cell
, vol.15
, Issue.8
, pp. 3841-3862
-
-
Chen, K.C.1
Calzone, L.2
Csikasz-Nagy, A.3
Cross, F.R.4
Novak, B.5
Tyson, J.J.6
-
112
-
-
0242490789
-
Importance of input perturbations and stochastic gene expression in the reverse engineering of genetic regulatory networks: Insights from an identifiability analysis of an in silico network
-
Zak DE, Gonye GE, Schwaber JS, Doyle FJ, 3rd. Importance of input perturbations and stochastic gene expression in the reverse engineering of genetic regulatory networks: insights from an identifiability analysis of an in silico network. Genome Research 2003; 13 (11). 2396-2405.
-
(2003)
Genome Research
, vol.13
, Issue.11
, pp. 2396-2405
-
-
Zak, D.E.1
Gonye, G.E.2
Schwaber, J.S.3
Doyle III, F.J.4
-
113
-
-
57749195712
-
RNA-Seq: A revolutionary tool for transcriptomics
-
Wang Z., Gerstein M., Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nature Reviews Genetics 2009; 10 (1). 57-63.
-
(2009)
Nature Reviews Genetics
, vol.10
, Issue.1
, pp. 57-63
-
-
Wang, Z.1
Gerstein, M.2
Snyder, M.3
|