-
1
-
-
0742305866
-
Network biology: Understanding the cell's functional organization
-
doi:10.1038/nrg1272
-
Barabasi, A. L., & Oltvai, Z. N. (2004). Network biology: Understanding the cell's functional organization. Nature Reviews. Genetics, 5(2), 101-113. doi:10.1038/nrg1272
-
(2004)
Nature Reviews. Genetics
, vol.5
, Issue.2
, pp. 101-113
-
-
Barabasi, A.L.1
Oltvai, Z.N.2
-
2
-
-
2542529262
-
Pajek-analysis and visualization of large networks
-
In M. Jünger & P. Mutzel (Eds.), Springer
-
Batagelj, V., & Mrvar, A. (2003). Pajek-analysis and visualization of large networks. In M. Jünger & P. Mutzel (Eds.), Graph drawing software (pp. 77-103). Springer.
-
(2003)
Graph Drawing Software
, pp. 77-103
-
-
Batagelj, V.1
Mrvar, A.2
-
3
-
-
22144454660
-
Genetical genomics analysis of a yeast segregant population for transcription network inference
-
doi:10.1534/genetics.105.041103
-
Bing, N., & Hoeschele, I. (2005). Genetical genomics analysis of a yeast segregant population for transcription network inference. Genetics, 170(2), 533-542. doi:10.1534/genetics.105.041103
-
(2005)
Genetics
, vol.170
, Issue.2
, pp. 533-542
-
-
Bing, N.1
Hoeschele, I.2
-
6
-
-
0042424655
-
Transcriptional regulatory cascades in development: Initial rates, not steady state, determine network kinetics
-
doi:10.1073/pnas.1533293100
-
Bolouri, H., & Davidson, E. H. (2003). Transcriptional regulatory cascades in development: Initial rates, not steady state, determine network kinetics. Proceedings of the National Academy of Sciences of the United States of America, 100(16), 9371-9376. doi:10.1073/pnas.1533293100
-
(2003)
Proceedings of the National Academy of Sciences of the United States of America
, vol.100
, Issue.16
, pp. 9371-9376
-
-
Bolouri, H.1
Davidson, E.H.2
-
7
-
-
0036843965
-
Gene networks: How to put the function in genomics
-
doi:10.1016/S0167-7799(02)02053-X
-
Brazhnik, P., de la Fuente, A., & Mendes, P. (2002). Gene networks: How to put the function in genomics. Trends in Biotechnology, 20(11), 467-472. doi:10.1016/S0167-7799(02)02053-X
-
(2002)
Trends in Biotechnology
, vol.20
, Issue.11
, pp. 467-472
-
-
Brazhnik, P.1
de la Fuente, A.2
Mendes, P.3
-
8
-
-
0033721503
-
Graph structure in the web
-
Broder, A., Kumar, R., Maghoul, F., Raghavan, P., Rajagopalan, S., Stata, R., et al. (2000). Graph structure in the Web. Computer Networks, 33(1-6), 309-320.
-
(2000)
Computer Networks
, vol.33
, Issue.1-6
, pp. 309-320
-
-
Broder, A.1
Kumar, R.2
Maghoul, F.3
Raghavan, P.4
Rajagopalan, S.5
Stata, R.6
-
9
-
-
1242316281
-
Chip-chip: Considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments
-
doi:10.1016/j. ygeno.2003.11.004
-
Buck, M. J., & Lieb, J. D. (2004). ChIP-chip: Considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics, 83(3), 349-360. doi:10.1016/j. ygeno.2003.11.004
-
(2004)
Genomics
, vol.83
, Issue.3
, pp. 349-360
-
-
Buck, M.J.1
Lieb, J.D.2
-
11
-
-
0034710924
-
Discovering functional relationships between rna expression and chemotherapeutic susceptibility using relevance networks
-
doi:10.1073/pnas.220392197
-
Butte, A. J., Tamayo, P., Slonim, D., Golub, T. R., & Kohane, I. S. (2000). 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, 97(22), 12182-12186. doi:10.1073/pnas.220392197
-
(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
-
12
-
-
20144383240
-
Uncovering regulatory pathways that affect hematopoietic stem cell function using 'genetical genomics.'
-
doi:10.1038/ng1497
-
Bystrykh, L., Weersing, E., Dontje, B., Sutton, S., Pletcher, M. T., & Wiltshire, T. (2005). Uncovering regulatory pathways that affect hematopoietic stem cell function using 'genetical genomics.'. Nature Genetics, 37(3), 225-232. doi:10.1038/ng1497
-
(2005)
Nature Genetics
, vol.37
, Issue.3
, pp. 225-232
-
-
Bystrykh, L.1
Weersing, E.2
Dontje, B.3
Sutton, S.4
Pletcher, M.T.5
Wiltshire, T.6
-
13
-
-
20344365760
-
The origin of correlations in metabolomic data
-
doi:10.1007/s11306-005-1107-3
-
Camacho, D., de la Fuente, A., & Mendes, P. (2005). The origin of correlations in metabolomic data. Metabolomics, 1(1), 53-63. doi:10.1007/s11306-005-1107-3
-
(2005)
Metabolomics
, vol.1
, Issue.1
, pp. 53-63
-
-
Camacho, D.1
de la Fuente, A.2
Mendes, P.3
-
14
-
-
33947728976
-
Beyond reductionism: Metabolic circularity as a guiding vision for a real biology of systems
-
doi:10.1002/pmic.200600431
-
Cornish-Bowden, A., Cardenas, M. L., Letelier, J. C., & Soto-Andrade, J. (2007). Beyond reductionism: Metabolic circularity as a guiding vision for a real biology of systems. Proteomics, 7(6), 839-845. doi:10.1002/pmic.200600431
-
(2007)
Proteomics
, vol.7
, Issue.6
, pp. 839-845
-
-
Cornish-Bowden, A.1
Cardenas, M.L.2
Letelier, J.C.3
Soto-Andrade, J.4
-
15
-
-
0003687180
-
-
New York, Springer-Verlag
-
Cowell, R. G., Dawid, A. P., Lauritzen, S. L., & Spiegelhalter, D. J. (1999). Probabilistic networks and expert systems. New York: Springer-Verlag.
-
(1999)
Probabilistic Networks and Expert Systems
-
-
Cowell, R.G.1
Dawid, A.P.2
Lauritzen, S.L.3
Spiegelhalter, D.J.4
-
16
-
-
0033736476
-
Genetic network inference: From co-expression clustering to reverse engineering
-
doi:10.1093/ bioinformatics/16.8.707
-
D'Haeseleer, P., Liang, S., & Somogyi, R. (2000). Genetic network inference: From co-expression clustering to reverse engineering. Bioinformatics (Oxford, England), 16(8), 707-726. doi:10.1093/ bioinformatics/16.8.707
-
(2000)
Bioinformatics (Oxford, England)
, vol.16
, Issue.8
, pp. 707-726
-
-
D'Haeseleer, P.1
Liang, S.2
Somogyi, R.3
-
17
-
-
12344321571
-
Discovery of meaningful associations in genomic data using partial correlation coefficients
-
doi:10.1093/bioinformatics/bth445
-
de la Fuente, A., Bing, N., Hoeschele, I., & Mendes, P. (2004). Discovery of meaningful associations in genomic data using partial correlation coefficients. Bioinformatics (Oxford, England), 20, 3565-3574. doi:10.1093/bioinformatics/bth445
-
(2004)
Bioinformatics (Oxford, England)
, vol.20
, pp. 3565-3574
-
-
de la Fuente, A.1
Bing, N.2
Hoeschele, I.3
Mendes, P.4
-
18
-
-
84898532348
-
-
Paper presented at the 2nd Int. Conf. Syst. Biol., California Institute of Technology, Pasadena, CA
-
de la Fuente, A., Brazhnik, P., & Mendes, P. (2001). A quantitative method for reverse engineering gene networks from microarray experiments using regulatory strengths. Paper presented at the 2nd Int. Conf. Syst. Biol., California Institute of Technology, Pasadena, CA.
-
(2001)
A Quantitative Method for Reverse Engineering Gene Networks from Microarray Experiments Using Regulatory Strengths
-
-
de la Fuente, A.1
Brazhnik, P.2
Mendes, P.3
-
19
-
-
0036683181
-
Linking the genes: Inferring quantitative gene networks from microarray data
-
doi:10.1016/S0168-9525(02)02692-6
-
de la Fuente, A., Brazhnik, P., & Mendes, P. (2002). Linking the genes: Inferring quantitative gene networks from microarray data. Trends in Genetics, 18(8), 395-398. doi:10.1016/S0168-9525(02)02692-6
-
(2002)
Trends in Genetics
, vol.18
, Issue.8
, pp. 395-398
-
-
de la Fuente, A.1
Brazhnik, P.2
Mendes, P.3
-
20
-
-
27744554166
-
Regulatory strength analysis for inferring gene networks
-
In K. B. N. & W. H. V. (Eds.), Wymondham, UK: Horizon Bioscience
-
de la Fuente, A., Brazhnik, P., & Mendes, P. (2004). Regulatory strength analysis for inferring gene networks. In K. B. N. & W. H. V. (Eds.), Metabolic engineering in the post genomic era (pp. 107-137). Wymondham, UK: Horizon Bioscience.
-
(2004)
Metabolic Engineering in the Post Genomic Era
, pp. 107-137
-
-
de la Fuente, A.1
Brazhnik, P.2
Mendes, P.3
-
21
-
-
0036041072
-
Quantifying gene networks with regulatory strengths
-
doi:10.1023/A:1020310504986
-
de la Fuente, A., & Mendes, P. (2002). Quantifying gene networks with regulatory strengths. Molecular Biology Reports, 29(1-2), 73-77. doi:10.1023/A:1020310504986
-
(2002)
Molecular Biology Reports
, vol.29
, Issue.1-2
, pp. 73-77
-
-
de la Fuente, A.1
Mendes, P.2
-
22
-
-
0001038826
-
Covariance selection
-
doi:10.2307/2528966
-
Dempster, A. P. (1972). Covariance selection. Biometrics, 28, 157-175. doi:10.2307/2528966
-
(1972)
Biometrics
, vol.28
, pp. 157-175
-
-
Dempster, A.P.1
-
26
-
-
33846400424
-
Large-scale mapping and validation of escherichia coli transcriptional regulation from a compendium of expression profiles
-
e8, doi:10.1371/journal.pbio.0050008
-
Faith, J. J., Hayete, B., Thaden, J. T., Mogno, I., Wierzbowski, J., & Cottarel, G. (2007). Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biology, 5(1), e8. doi:10.1371/journal.pbio.0050008
-
(2007)
PLoS Biology
, vol.5
, Issue.1
-
-
Faith, J.J.1
Hayete, B.2
Thaden, J.T.3
Mogno, I.4
Wierzbowski, J.5
Cottarel, G.6
-
27
-
-
38549140094
-
Regulondb (version 6.0): Gene regulation model of escherichia coli k-12 beyond transcription, active (experimental) annotated promoters and textpresso navigation
-
(Database issue), D120-D124. doi:10.1093/nar/gkm994
-
Gama-Castro, S., Jimenez-Jacinto, V., Peralta-Gil, M., Santos-Zavaleta, A., Penaloza-Spinola, M. I., & Contreras-Moreira, B. (2008). RegulonDB (version 6.0): Gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Research, 36(Database issue), D120-D124. doi:10.1093/nar/gkm994
-
(2008)
Nucleic Acids Research
, vol.36
-
-
Gama-Castro, S.1
Jimenez-Jacinto, V.2
Peralta-Gil, M.3
Santos-Zavaleta, A.4
Penaloza-Spinola, M.I.5
Contreras-Moreira, B.6
-
29
-
-
0038048325
-
Inferring genetic networks and identifying compound mode of action via expression profiling
-
doi:10.1126/ science.1081900
-
Gardner, T., di Bernardo, D., Lorenz, D., & Collins, J. (2003). Inferring genetic networks and identifying compound mode of action via expression profiling. Science, 301(5629), 102-105. doi:10.1126/ science.1081900
-
(2003)
Science
, vol.301
, Issue.5629
, pp. 102-105
-
-
Gardner, T.1
di Bernardo, D.2
Lorenz, D.3
Collins, J.4
-
30
-
-
0036578654
-
Topological and causal structure of the yeast transcriptional regulatory network
-
doi:10.1038/ng873
-
Guelzim, N., Bottani, S., Bourgine, P., & Kepes, F. (2002). Topological and causal structure of the yeast transcriptional regulatory network. Nature Genetics, 31(1), 60-63. doi:10.1038/ng873
-
(2002)
Nature Genetics
, vol.31
, Issue.1
, pp. 60-63
-
-
Guelzim, N.1
Bottani, S.2
Bourgine, P.3
Kepes, F.4
-
31
-
-
4544352942
-
Transcriptional regulatory code of a eukaryotic genome
-
doi:10.1038/ nature02800
-
Harbison, C. T., Gordon, D. B., Lee, T. I., Rinaldi, N. J., Macisaac, K. D., & Danford, T. W. (2004). Transcriptional regulatory code of a eukaryotic genome. Nature, 431(7004), 99-104. doi:10.1038/ nature02800
-
(2004)
Nature
, vol.431
, Issue.7004
, pp. 99-104
-
-
Harbison, C.T.1
Gordon, D.B.2
Lee, T.I.3
Rinaldi, N.J.4
Macisaac, K.D.5
Danford, T.W.6
-
33
-
-
0031811851
-
Regulondb: A database on transcriptional regulation in escherichia coli
-
doi:10.1093/nar/26.1.55
-
Huerta, A. M., Salgado, H., Thieffry, D., & Collado-Vides, J. (1998). RegulonDB: A database on transcriptional regulation in Escherichia coli. Nucleic Acids Research, 26(1), 55-59. doi:10.1093/nar/26.1.55
-
(1998)
Nucleic Acids Research
, vol.26
, Issue.1
, pp. 55-59
-
-
Huerta, A.M.1
Salgado, H.2
Thieffry, D.3
Collado-Vides, J.4
-
34
-
-
0034616930
-
Functional discovery via a compendium of expression profiles
-
doi:10.1016/ S0092-8674(00)00015-5
-
Hughes, T. R., Marton, M. J., Jones, A. R., Roberts, C. J., Stoughton, R., & Armour, C. D. (2000). Functional discovery via a compendium of expression profiles. Cell, 102(1), 109-126. doi:10.1016/ S0092-8674(00)00015-5
-
(2000)
Cell
, vol.102
, Issue.1
, pp. 109-126
-
-
Hughes, T.R.1
Marton, M.J.2
Jones, A.R.3
Roberts, C.J.4
Stoughton, R.5
Armour, C.D.6
-
35
-
-
0035945567
-
Genomic binding sites of the yeast cell-cycle transcription factors sbf and mbf
-
doi:10.1038/35054095
-
Iyer, V. R., Horak, C. E., Scafe, C. S., Botstein, D., Snyder, M., & Brown, P. O. (2001). Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature, 409(6819), 533-538. doi:10.1038/35054095
-
(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
-
36
-
-
0014671878
-
Homeostasis and differentiation in random genetic control networks
-
doi:10.1038/224177a0
-
Kauffman, S. (1969). Homeostasis and differentiation in random genetic control networks. Nature, 224(215), 177-178. doi:10.1038/224177a0
-
(1969)
Nature
, vol.224
, Issue.215
, pp. 177-178
-
-
Kauffman, S.1
-
37
-
-
33846818896
-
Regulatory network construction in arabidopsis by using genome-wide gene expression quantitative trait loci
-
doi:10.1073/pnas.0610429104
-
Keurentjes, J. J., Fu, J., Terpstra, I. R., Garcia, J. M., van den Ackerveken, G., & Snoek, L. B. (2007). Regulatory network construction in Arabidopsis by using genome-wide gene expression quantitative trait loci. Proceedings of the National Academy of Sciences of the United States of America, 104(5), 1708-1713. doi:10.1073/pnas.0610429104
-
(2007)
Proceedings of the National Academy of Sciences of the United States of America
, vol.104
, Issue.5
, pp. 1708-1713
-
-
Keurentjes, J.J.1
Fu, J.2
Terpstra, I.R.3
Garcia, J.M.4
van den Ackerveken, G.5
Snoek, L.B.6
-
38
-
-
0037174671
-
Transcriptional regulatory networks in saccharomyces cerevisiae
-
doi:10.1126/ science.1075090
-
Lee, T. I., Rinaldi, N. J., Robert, F., Odom, D. T., Bar-Joseph, Z., & Gerber, G. K. (2002). Transcriptional regulatory networks in Saccharomyces cerevisiae. Science, 298(5594), 799-804. doi:10.1126/ science.1075090
-
(2002)
Science
, vol.298
, Issue.5594
, pp. 799-804
-
-
Lee, T.I.1
Rinaldi, N.J.2
Robert, F.3
Odom, D.T.4
Bar-Joseph, Z.5
Gerber, G.K.6
-
39
-
-
40149095913
-
Transcription factors bind thousands of active and inactive regions in the drosophila blastoderm
-
doi:10.1371/journal.pbio.0060027
-
Li, X. Y., MacArthur, S., Bourgon, R., Nix, D., Pollard, D. A., & Iyer, V. N. (2008). Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biology, 6(2), e27. doi:10.1371/journal.pbio.0060027
-
(2008)
PLoS Biology
, vol.6
, Issue.2
-
-
Li, X.Y.1
Macarthur, S.2
Bourgon, R.3
Nix, D.4
Pollard, D.A.5
Iyer, V.N.6
-
40
-
-
0034934774
-
Promoter-specific binding of rap1 revealed by genome-wide maps of protein-dna association
-
doi:10.1038/ng569
-
Lieb, J. D., Liu, X., Botstein, D., & Brown, P. O. (2001). Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nature Genetics, 28(4), 327-334. doi:10.1038/ng569
-
(2001)
Nature Genetics
, vol.28
, Issue.4
, pp. 327-334
-
-
Lieb, J.D.1
Liu, X.2
Botstein, D.3
Brown, P.O.4
-
41
-
-
45149096374
-
Gene network inference via structural equation modeling in genetical genomics experiments
-
doi:10.1534/genetics.107.080069
-
Liu, B., de la Fuente, A., & Hoeschele, I. (2008). Gene network inference via structural equation modeling in genetical genomics experiments. Genetics, 178, 1763-1776. doi:10.1534/genetics.107.080069
-
(2008)
Genetics
, vol.178
, pp. 1763-1776
-
-
Liu, B.1
de la Fuente, A.2
Hoeschele, I.3
-
42
-
-
4644326931
-
Genomic analysis of regulatory network dynamics reveals large topological changes
-
doi:10.1038/nature02782
-
Luscombe, N. M., Babu, M. M., Yu, H., Snyder, M., Teichmann, S. A., & Gerstein, M. (2004). Genomic analysis of regulatory network dynamics reveals large topological changes. Nature, 431(7006), 308-312. doi:10.1038/nature02782
-
(2004)
Nature
, vol.431
, Issue.7006
, pp. 308-312
-
-
Luscombe, N.M.1
Babu, M.M.2
Yu, H.3
Snyder, M.4
Teichmann, S.A.5
Gerstein, M.6
-
43
-
-
0042093610
-
The connectivity structure, giant strong component and centrality of metabolic networks
-
doi:10.1093/bioinformatics/btg177
-
Ma, H. W., & Zeng, A. P. (2003). The connectivity structure, giant strong component and centrality of metabolic networks. Bioinformatics (Oxford, England), 19(11), 1423-1430. doi:10.1093/bioinformatics/btg177
-
(2003)
Bioinformatics (Oxford, England)
, vol.19
, Issue.11
, pp. 1423-1430
-
-
Ma, H.W.1
Zeng, A.P.2
-
44
-
-
63849106452
-
-
Submitted
-
Mancosu, G., Pieroni, E., Maggio, F., Fotia, G., Liu, B., Hoeschele, I., et al.(2008). Deciphering a genome-wide yeast gene network. Submitted.
-
(2008)
Deciphering a Genome-wide Yeast Gene Network
-
-
Mancosu, G.1
Pieroni, E.2
Maggio, F.3
Fotia, G.4
Liu, B.5
Hoeschele, I.6
-
45
-
-
47649086309
-
Chip-on-chip significance analysis reveals ubiquitous transcription factor binding
-
doi:10.1186/1471-2105-8-S8-S2
-
Margolin, A. A., Palomero, T., Ferrando, A. A., Califano, A., & Stolovitzky, G. (2007). ChIP-on-chip significance analysis reveals ubiquitous transcription factor binding. BMC Bioinformatics, 8(Suppl 8), S2. doi:10.1186/1471-2105-8-S8-S2
-
(2007)
BMC Bioinformatics
, vol.8
, Issue.SUPPL. 8
-
-
Margolin, A.A.1
Palomero, T.2
Ferrando, A.A.3
Califano, A.4
Stolovitzky, G.5
-
46
-
-
27644549928
-
Integrating genotypic and expression data in a segregating mouse population to identify 5-lipoxygenase as a susceptibility gene for obesity and bone traits
-
doi:10.1038/ng1619
-
Mehrabian, M., Allayee, H., Stockton, J., Lum, P. Y., Drake, T. A., & Castellani, L. W. (2005). Integrating genotypic and expression data in a segregating mouse population to identify 5-lipoxygenase as a susceptibility gene for obesity and bone traits. Nature Genetics, 37(11), 1224-1233. doi:10.1038/ng1619
-
(2005)
Nature Genetics
, vol.37
, Issue.11
, pp. 1224-1233
-
-
Mehrabian, M.1
Allayee, H.2
Stockton, J.3
Lum, P.Y.4
Drake, T.A.5
Castellani, L.W.6
-
47
-
-
3142536716
-
Exploration of essential gene functions via titratable promoter alleles
-
doi:10.1016/j. cell.2004.06.013
-
Mnaimneh, S., Davierwala, A. P., Haynes, J., Moffat, J., Peng, W. T., & Zhang, W. (2004). Exploration of essential gene functions via titratable promoter alleles. Cell, 118(1), 31-44. doi:10.1016/j. cell.2004.06.013
-
(2004)
Cell
, vol.118
, Issue.1
, pp. 31-44
-
-
Mnaimneh, S.1
Davierwala, A.P.2
Haynes, J.3
Moffat, J.4
Peng, W.T.5
Zhang, W.6
-
48
-
-
0014636204
-
Dynamics of synthesis, translation, and degradation of trp operon messenger rna in e. Coli
-
Morse, D. E., Mosteller, R. D., & Yanofsky, C. (1969). Dynamics of synthesis, translation, and degradation of trp operon messenger RNA in E. coli. Cold Spring Harbor Symposia on Quantitative Biology, 34, 725-740.
-
(1969)
Cold Spring Harbor Symposia on Quantitative Biology
, vol.34
, pp. 725-740
-
-
Morse, D.E.1
Mosteller, R.D.2
Yanofsky, C.3
-
49
-
-
0038718854
-
The structure and function of complex networks
-
doi:10.1137/S003614450342480
-
Newman, M. (2003). The structure and function of complex networks. SIAM Review, 45(2), 167-256. doi:10.1137/S003614450342480
-
(2003)
SIAM Review
, vol.45
, Issue.2
, pp. 167-256
-
-
Newman, M.1
-
52
-
-
40549110559
-
Protein networking: Insights into global functional organization of proteomes
-
doi:10.1002/pmic.200700767
-
Pieroni, E.,de la Fuente van Bentem, S., Mancosu, G., Capobianco, E., Hirt, H., &de la Fuente, A. (2008). Protein networking: Insights into global functional organization of proteomes. Proteomics, 8(4), 799-816. doi:10.1002/pmic.200700767
-
(2008)
Proteomics
, vol.8
, Issue.4
, pp. 799-816
-
-
Pieroni, E.1
de la Fuente van Bentem, S.2
Mancosu, G.3
Capobianco, E.4
Hirt, H.5
de la Fuente, A.6
-
53
-
-
0034704248
-
Genome-wide location and function of dna binding proteins
-
doi:10.1126/science.290.5500.2306
-
Ren, B., Robert, F., Wyrick, J. J., Aparicio, O., Jennings, E. G., & Simon, I. (2000). Genome-wide location and function of DNA binding proteins. Science, 290(5500), 2306-2309. doi:10.1126/science.290.5500.2306
-
(2000)
Science
, vol.290
, Issue.5500
, pp. 2306-2309
-
-
Ren, B.1
Robert, F.2
Wyrick, J.J.3
Aparicio, O.4
Jennings, E.G.5
Simon, I.6
-
54
-
-
9144270496
-
Regulondb (version 4.0): Transcriptional regulation, operon organization and growth conditions in escherichia coli k-12
-
(Database issue, doi:10.1093/ nar/gkh140
-
Salgado, H., Gama-Castro, S., Martinez-Antonio, A., Diaz-Peredo, E., Sanchez-Solano, F., & Peralta-Gil, M. (2004). RegulonDB (version 4.0): Transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12. Nucleic Acids Research, 32(Database issue), D303-D306. doi:10.1093/ nar/gkh140
-
(2004)
Nucleic Acids Research
, vol.32
-
-
Salgado, H.1
Gama-Castro, S.2
Martinez-Antonio, A.3
Diaz-Peredo, E.4
Sanchez-Solano, F.5
Peralta-Gil, M.6
-
55
-
-
33644873438
-
Regulondb (version 5.0): Escherichia coli k-12 transcriptional regulatory network, operon organization, and growth conditions
-
(Database issue), doi:10.1093/nar/gkj156
-
Salgado, H., Gama-Castro, S., Peralta-Gil, M., Diaz-Peredo, E., Sanchez-Solano, F., & Santos-Zavaleta, A. (2006a). RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions. Nucleic Acids Research, 34(Database issue), D394-D397. doi:10.1093/nar/gkj156
-
(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
-
56
-
-
0032947086
-
Regulondb (version 2.0): A database on transcriptional regulation in escherichia coli
-
doi:10.1093/nar/27.1.59
-
Salgado, H., Santos, A., Garza-Ramos, U., van Helden, J., Diaz, E., & Collado-Vides, J. (1999). RegulonDB (version 2.0): A database on transcriptional regulation in Escherichia coli. Nucleic Acids Research, 27(1), 59-60. doi:10.1093/nar/27.1.59
-
(1999)
Nucleic Acids Research
, vol.27
, Issue.1
, pp. 59-60
-
-
Salgado, H.1
Santos, A.2
Garza-Ramos, U.3
van Helden, J.4
Diaz, E.5
Collado-Vides, J.6
-
57
-
-
0033971476
-
Regulondb (version 3.0): Transcriptional regulation and operon organization in escherichia coli k-12
-
doi:10.1093/nar/28.1.65
-
Salgado, H., Santos-Zavaleta, A., Gama-Castro, S., Millan-Zarate, D., Blattner, F. R., & Collado-Vides, J. (2000). RegulonDB (version 3.0): Transcriptional regulation and operon organization in Escherichia coli K-12. Nucleic Acids Research, 28(1), 65-67. doi:10.1093/nar/28.1.65
-
(2000)
Nucleic Acids Research
, vol.28
, Issue.1
, pp. 65-67
-
-
Salgado, H.1
Santos-Zavaleta, A.2
Gama-Castro, S.3
Millan-Zarate, D.4
Blattner, F.R.5
Collado-Vides, J.6
-
58
-
-
0035162782
-
Regulondb (version 3.2): Transcriptional regulation and operon organization in escherichia coli k-12
-
doi:10.1093/nar/29.1.72
-
Salgado, H., Santos-Zavaleta, A., Gama-Castro, S., Millan-Zarate, D., Diaz-Peredo, E., & Sanchez-Solano, F. (2001). RegulonDB (version 3.2): Transcriptional regulation and operon organization in Escherichia coli K-12. Nucleic Acids Research, 29(1), 72-74. doi:10.1093/nar/29.1.72
-
(2001)
Nucleic Acids Research
, vol.29
, Issue.1
, pp. 72-74
-
-
Salgado, H.1
Santos-Zavaleta, A.2
Gama-Castro, S.3
Millan-Zarate, D.4
Diaz-Peredo, E.5
Sanchez-Solano, F.6
-
59
-
-
30644465547
-
The comprehensive updated regulatory network of escherichia coli k-12
-
doi:10.1186/1471-2105-7-5
-
Salgado, H., Santos-Zavaleta, A., Gama-Castro, S., Peralta-Gil, M., Penaloza-Spinola, M. I., & MartinezAntonio, A. (2006b). The comprehensive updated regulatory network of Escherichia coli K-12. BMC Bioinformatics, 7, 5. doi:10.1186/1471-2105-7-5
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 5
-
-
Salgado, H.1
Santos-Zavaleta, A.2
Gama-Castro, S.3
Peralta-Gil, M.4
Penaloza-Spinola, M.I.5
Martinezantonio, A.6
-
60
-
-
0035852686
-
Dynamic regulation of the tryptophan operon: A modeling study and comparison with experimental data
-
doi:10.1073/pnas.98.4.1364
-
Santillan, M., & Mackey, M. C. (2001). Dynamic regulation of the tryptophan operon: A modeling study and comparison with experimental data. Proceedings of the National Academy of Sciences of the United States of America, 98(4), 1364-1369. doi:10.1073/pnas.98.4.1364
-
(2001)
Proceedings of the National Academy of Sciences of the United States of America
, vol.98
, Issue.4
, pp. 1364-1369
-
-
Santillan, M.1
Mackey, M.C.2
-
61
-
-
22844446947
-
An integrative genomics approach to infer causal associations between gene expression and disease
-
doi:10.1038/ng1589
-
Schadt, E., Lamb, J., Yang, X., Zhu, J., Edwards, S., & Guhathakurta, D. (2005). An integrative genomics approach to infer causal associations between gene expression and disease. Nature Genetics, 37(7), 710. doi:10.1038/ng1589
-
(2005)
Nature Genetics
, vol.37
, Issue.7
, pp. 710
-
-
Schadt, E.1
Lamb, J.2
Yang, X.3
Zhu, J.4
Edwards, S.5
Guhathakurta, D.6
-
62
-
-
15944364151
-
An empirical bayes approach to inferring large-scale gene association networks
-
doi:10.1093/bioinformatics/bti062
-
Schäfer, J., & Strimmer, K. (2005a). An empirical Bayes approach to inferring large-scale gene association networks. Bioinformatics (Oxford, England), 21, 754-764. doi:10.1093/bioinformatics/bti062
-
(2005)
Bioinformatics (Oxford, England)
, vol.21
, pp. 754-764
-
-
Schäfer, J.1
Strimmer, K.2
-
63
-
-
27844521293
-
A shrinkage approach to large-scale covariance matrix estimation and implications for functional genomics
-
doi:10.2202/1544-6115.1175
-
Schäfer, J., & Strimmer, K. (2005b). A shrinkage approach to large-scale covariance matrix estimation and implications for functional genomics. Statistical Applications in Genetics and Molecular Biology, 4, 32. doi:10.2202/1544-6115.1175
-
(2005)
Statistical Applications in Genetics and Molecular Biology
, vol.4
, pp. 32
-
-
Schäfer, J.1
Strimmer, K.2
-
64
-
-
0036578795
-
Network motifs in the transcriptional regulation network of escherichia coli
-
doi:10.1038/ng881
-
Shen-Orr, S. S., Milo, R., Mangan, S., & Alon, U. (2002). Network motifs in the transcriptional regulation network of Escherichia coli. Nature Genetics, 31(1), 64-68. doi:10.1038/ng881
-
(2002)
Nature Genetics
, vol.31
, Issue.1
, pp. 64-68
-
-
Shen-Orr, S.S.1
Milo, R.2
Mangan, S.3
Alon, U.4
-
65
-
-
34748871477
-
Regulation of gene expression by small non-coding rnas: A quantitative view
-
doi:10.1038/msb4100181
-
Shimoni, Y., Friedlander, G., Hetzroni, G., Niv, G., Altuvia, S., & Biham, O. (2007). Regulation of gene expression by small non-coding RNAs: A quantitative view. Molecular Systems Biology, 3, 138. doi:10.1038/msb4100181
-
(2007)
Molecular Systems Biology
, vol.3
, pp. 138
-
-
Shimoni, Y.1
Friedlander, G.2
Hetzroni, G.3
Niv, G.4
Altuvia, S.5
Biham, O.6
-
66
-
-
0003614273
-
-
MIT Press
-
Spirtes, P., Glymour, C., & Scheines, R. (1993). Causation, prediction, and search. MIT Press.
-
(1993)
Causation, Prediction, and Search
-
-
Spirtes, P.1
Glymour, C.2
Scheines, R.3
-
67
-
-
0042526388
-
The mutual information: Detecting and evaluating dependencies between variables
-
Steuer, R., Kurths, J., Daub, C. O., Weise, J., & Selbig, J. (2002). The mutual information: Detecting and evaluating dependencies between variables. Bioinformatics (Oxford, England), 18(Suppl 2), S231-S240.
-
(2002)
Bioinformatics (Oxford, England)
, vol.18
, Issue.SUPPL. 2
-
-
Steuer, R.1
Kurths, J.2
Daub, C.O.3
Weise, J.4
Selbig, J.5
-
68
-
-
0042424602
-
Statistical significance for genomewide studies
-
doi:10.1073/ pnas.1530509100
-
Storey, J. D., & Tibshirani, R. (2003). Statistical significance for genomewide studies. Proceedings of the National Academy of Sciences of the United States of America, 100(16), 9440-9445. doi:10.1073/ pnas.1530509100
-
(2003)
Proceedings of the National Academy of Sciences of the United States of America
, vol.100
, Issue.16
, pp. 9440-9445
-
-
Storey, J.D.1
Tibshirani, R.2
-
70
-
-
0015823097
-
Boolean formalization of genetic control circuits
-
doi:10.1016/0022-5193(73)90247-6
-
Thomas, R. (1973). Boolean formalization of genetic control circuits. Journal of Theoretical Biology, 42(3), 563-585. doi:10.1016/0022-5193(73)90247-6
-
(1973)
Journal of Theoretical Biology
, vol.42
, Issue.3
, pp. 563-585
-
-
Thomas, R.1
-
71
-
-
10744230485
-
Global mapping of the yeast genetic interaction network
-
doi:10.1126/science.1091317
-
Tong, A. H., Lesage, G., Bader, G. D., Ding, H., Xu, H., & Xin, X. (2004). Global mapping of the yeast genetic interaction network. Science, 303(5659), 808-813. doi:10.1126/science.1091317
-
(2004)
Science
, vol.303
, Issue.5659
, pp. 808-813
-
-
Tong, A.H.1
Lesage, G.2
Bader, G.D.3
Ding, H.4
Xu, H.5
Xin, X.6
-
72
-
-
0037376655
-
Sniffers, buzzers, toggles, and blinkers: Dynamics of regulatory and signaling pathways in the cell
-
doi:10.1016/ S0955-0674(03)00017-6
-
Tyson, J. J., Chen, K. C., & Novak, B. (2003). Sniffers, buzzers, toggles, and blinkers: Dynamics of regulatory and signaling pathways in the cell. Current Opinion in Cell Biology, 15(2), 221-231. doi:10.1016/ S0955-0674(03)00017-6
-
(2003)
Current Opinion in Cell Biology
, vol.15
, Issue.2
, pp. 221-231
-
-
Tyson, J.J.1
Chen, K.C.2
Novak, B.3
-
73
-
-
37349079219
-
Genome-wide partial correlation analysis of escherichia coli microarray data
-
Veiga, D. F., Vicente, F. F., Grivet, M., de la Fuente, A., & Vasconcelos, A. T. (2007). Genome-wide partial correlation analysis of Escherichia coli microarray data. Genetics and Molecular Research, 6(4), 730-742.
-
(2007)
Genetics and Molecular Research
, vol.6
, Issue.4
, pp. 730-742
-
-
Veiga, D.F.1
Vicente, F.F.2
Grivet, M.3
de la Fuente, A.4
Vasconcelos, A.T.5
-
75
-
-
0036138322
-
How to reconstruct a large genetic network from n gene perturbations in fewer than n(2) easy steps
-
doi:10.1093/bioinformatics/17.12.1183
-
Wagner, A. (2001). How to reconstruct a large genetic network from n gene perturbations in fewer than n(2) easy steps. Bioinformatics (Oxford, England), 17(12), 1183-1197. doi:10.1093/bioinformatics/17.12.1183
-
(2001)
Bioinformatics (Oxford, England)
, vol.17
, Issue.12
, pp. 1183-1197
-
-
Wagner, A.1
-
76
-
-
0032482432
-
Collective dynamics of 'small-world' networks
-
doi:10.1038/30918
-
Watts, D. J., & Strogatz, S. H. (1998). Collective dynamics of 'small-world' networks. Nature, 393(6684), 440-442. doi:10.1038/30918
-
(1998)
Nature
, vol.393
, Issue.6684
, pp. 440-442
-
-
Watts, D.J.1
Strogatz, S.H.2
-
79
-
-
30044444291
-
Low-order conditional independence graphs for inferring genetic networks
-
Article 1
-
Wille, A., & Buhlmann, P. (2006). Low-order conditional independence graphs for inferring genetic networks. Stat. Appl. Genet. Mol. Biol., 5(1), Article 1.
-
(2006)
Stat. Appl. Genet. Mol. Biol
, vol.5
, Issue.1
-
-
Wille, A.1
Buhlmann, P.2
-
80
-
-
22044448669
-
Sparse graphical gaussian modeling of the isoprenoid gene network in arabidopsis thaliana
-
doi:10.1186/gb-2004-5-11-r92
-
Wille, A., Zimmermann, P., Vranova, E., Furholz, A., Laule, O., & Bleuler, S. (2004). Sparse graphical Gaussian modeling of the isoprenoid gene network in Arabidopsis thaliana. Genome Biology, 5(11), R92. doi:10.1186/gb-2004-5-11-r92
-
(2004)
Genome Biology
, vol.5
, Issue.11
-
-
Wille, A.1
Zimmermann, P.2
Vranova, E.3
Furholz, A.4
Laule, O.5
Bleuler, S.6
-
81
-
-
0037197936
-
Reverse engineering gene networks using singular value decomposition and robust regression
-
doi:10.1073/pnas.092576199
-
Yeung, M., Tegner, J., & Collins, J. (2002). Reverse engineering gene networks using singular value decomposition and robust regression. Proceedings of the National Academy of Sciences of the United States of America, 99(9), 6163-6168. doi:10.1073/pnas.092576199
-
(2002)
Proceedings of the National Academy of Sciences of the United States of America
, vol.99
, Issue.9
, pp. 6163-6168
-
-
Yeung, M.1
Tegner, J.2
Collins, J.3
-
82
-
-
3242806720
-
An integrative genomics approach to the reconstruction of gene networks in segregating populations
-
doi:10.1159/000078209
-
Zhu, J., Lum, P. Y., Lamb, J., GuhaThakurta, D., Edwards, S. W., & Thieringer, R. (2004). An integrative genomics approach to the reconstruction of gene networks in segregating populations. Cytogenetic and Genome Research, 105(2-4), 363-374. doi:10.1159/000078209
-
(2004)
Cytogenetic and Genome Research
, vol.105
, Issue.2-4
, pp. 363-374
-
-
Zhu, J.1
Lum, P.Y.2
Lamb, J.3
Guhathakurta, D.4
Edwards, S.W.5
Thieringer, R.6
|