-
1
-
-
0037174671
-
Transcriptional regulatory networks in Saccharomyces cerevisiae
-
10.1126/science.1075090 12399584
-
Lee TI Rinaldi NJ Robert F Odom DT Bar-Joseph Z, et al Transcriptional regulatory networks in Saccharomyces cerevisiae Science 2002, 298:799-804. 10.1126/science.1075090 12399584
-
(2002)
Science
, vol.298
, pp. 799-804
-
-
Lee, T.I.1
Rinaldi, N.J.2
Robert, F.3
Odom, D.T.4
Bar-Joseph, Z.5
-
2
-
-
4544352942
-
Transcriptional regulatory code of a eukaryotic genome
-
10.1038/nature02800 15343339
-
Harbison CT Gordon DB Lee TI Rinaldi NJ Macisaac KD, et al Transcriptional regulatory code of a eukaryotic genome Nature 2004, 431:99-104. 10.1038/nature02800 15343339
-
(2004)
Nature
, vol.431
, pp. 99-104
-
-
Harbison, C.T.1
Gordon, D.B.2
Lee, T.I.3
Rinaldi, N.J.4
Macisaac, K.D.5
-
3
-
-
2942582468
-
Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data
-
407845 15113405 10.1186/1471-2105-5-31
-
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. 407845 15113405 10.1186/ 1471-2105-5-31
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 31
-
-
Gao, F.1
Foat, B.C.2
Bussemaker, H.J.3
-
4
-
-
33744501241
-
Bayesian error analysis model for reconstructing transcriptional regulatory networks
-
1472417 16702552 10.1073/pnas.0600164103
-
Sun N Carroll RJ Zhao H Bayesian error analysis model for reconstructing transcriptional regulatory networks Proc Natl Acad Sci USA 2006, 103:7988-7993. 1472417 16702552 10.1073/pnas.0600164103
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 7988-7993
-
-
Sun, N.1
Carroll, R.J.2
Zhao, H.3
-
5
-
-
41849143338
-
Statistical modeling of transcription factor binding affinities predicts regulatory interactions
-
2266803 18369429 10.1371/journal.pcbi.1000039
-
Manke T Roider HG Vingron M Statistical modeling of transcription factor binding affinities predicts regulatory interactions PLoS Comput Biol 2008, 4(3):e1000039. 2266803 18369429 10.1371/journal.pcbi.1000039
-
(2008)
PLoS Comput Biol
, vol.4
, Issue.3
-
-
Manke, T.1
Roider, H.G.2
Vingron, M.3
-
6
-
-
38349030979
-
Inferring transcriptional interactions and regulator activities from experimental data
-
18182844
-
Wang RS Zhang XS Chen L Inferring transcriptional interactions and regulator activities from experimental data Mol Cells 2007, 24:307-315. 18182844
-
(2007)
Mol Cells
, vol.24
, pp. 307-315
-
-
Wang, R.S.1
Zhang, X.S.2
Chen, L.3
-
8
-
-
15944378903
-
Post-translational modifications influence transcription factor activity: A view from the ETS superfamily
-
10.1002/bies.20198 15714552
-
Tootle T Rebay I Post-translational modifications influence transcription factor activity: A view from the ETS superfamily Bioessays 2005, 27:285-298. 10.1002/bies.20198 15714552
-
(2005)
Bioessays
, vol.27
, pp. 285-298
-
-
Tootle, T.1
Rebay, I.2
-
9
-
-
0345824737
-
Network component analysis: Reconstruction of regulatory signals in biological systems
-
307600 14673099 10.1073/pnas.2136632100
-
Liao J Boscolo R Yang YL Tran LM Sabatti C Roychowdhury W Network component analysis: Reconstruction of regulatory signals in biological systems Proc Natl Acad Sci USA 2003, 100:15522-15527. 307600 14673099 10.1073/pnas.2136632100
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 15522-15527
-
-
Liao, J.1
Boscolo, R.2
Yang, Y.L.3
Tran, L.M.4
Sabatti, C.5
Roychowdhury, W.6
-
10
-
-
0345743695
-
Transcriptome-based determination of multiple transcription regulator activities in Escherichia coli by using network component analysis
-
327201 14694202 10.1073/pnas.0305287101
-
Kao K Yang Y Boscolo R Sabatti C Roychowdhury V Liao J Transcriptome-based determination of multiple transcription regulator activities in Escherichia coli by using network component analysis Proc Natl Acad Sci USA 2004, 101:641-646. 327201 14694202 10.1073/ pnas.0305287101
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 641-646
-
-
Kao, K.1
Yang, Y.2
Boscolo, R.3
Sabatti, C.4
Roychowdhury, V.5
Liao, J.6
-
11
-
-
23744491001
-
Predicting transcription factor activities from combined analysis of microarray and chip data: A partial least squares approach
-
1182396 15978125 10.1186/1742-4682-2-23
-
Boulesteix AL Strimmer K Predicting transcription factor activities from combined analysis of microarray and chip data: A partial least squares approach Theor Biol Med Model 2005, 2:23. 1182396 15978125 10.1186/ 1742-4682-2-23
-
(2005)
Theor Biol Med Model
, vol.2
, pp. 23
-
-
Boulesteix, A.L.1
Strimmer, K.2
-
12
-
-
15244338624
-
gNCA: A framework for determining transcription factor activity based on transcriptome: Identifiability and numerical implementation
-
10.1016/j.ymben.2004.12.001 15781421
-
Tran L Brynildsen M, et al gNCA: A framework for determining transcription factor activity based on transcriptome: Identifiability and numerical implementation Metabolic Engineering 2005, 7:128-141. 10.1016/j.ymben.2004.12.001 15781421
-
(2005)
Metabolic Engineering
, vol.7
, pp. 128-141
-
-
Tran, L.1
Brynildsen, M.2
-
14
-
-
33745431808
-
Deciphering principles of transcription regulation in eukaryotic genomes
-
Nguyen DH Dhaeseleer P Deciphering principles of transcription regulation in eukaryotic genomes Mol Syst Bio 2006:mSb4100054.
-
(2006)
Mol Syst Bio
-
-
Nguyen, D.H.1
Dhaeseleer, P.2
-
15
-
-
33947409985
-
Factor analysis for gene regulatory networks and transcription factor activity profiles
-
1821042 17319944 10.1186/1471-2105-8-61
-
Pournara I Wernisch L Factor analysis for gene regulatory networks and transcription factor activity profiles BMC Bioinformatics 2007, 8:61. 1821042 17319944 10.1186/1471-2105-8-61
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 61
-
-
Pournara, I.1
Wernisch, L.2
-
16
-
-
36448970861
-
Inferring transcriptional regulatory network from high-throughput data
-
10.1093/bioinformatics/btm465 17890736
-
Wang RS Wang Y Zhang XS Chen L Inferring transcriptional regulatory network from high-throughput data Bioinformatics 2007, 23:3056-3064. 10.1093/bioinformatics/btm465 17890736
-
(2007)
Bioinformatics
, vol.23
, pp. 3056-3064
-
-
Wang, R.S.1
Wang, Y.2
Zhang, X.S.3
Chen, L.4
-
17
-
-
0347444723
-
MicroRNAs: Genomics, biogenesis, mechanism, and function
-
10.1016/S0092-8674(04)00045-5 14744438
-
Bartel DP MicroRNAs: Genomics, biogenesis, mechanism, and function Cell 2004, 116:281-297. 10.1016/S0092-8674(04)00045-5 14744438
-
(2004)
Cell
, vol.116
, pp. 281-297
-
-
Bartel, D.P.1
-
18
-
-
3042767202
-
MicroRNAs: Small RNAs with a big role in gene regulation
-
10.1038/nrg1379 15211354
-
He L Hannon G MicroRNAs: Small RNAs with a big role in gene regulation Nature Reviews Genetics 2004, 5:522-531. 10.1038/nrg1379 15211354
-
(2004)
Nature Reviews Genetics
, vol.5
, pp. 522-531
-
-
He, L.1
Hannon, G.2
-
19
-
-
4344682527
-
The small RNA regulators of Escherichia coli: Roles and mechanisms
-
10.1146/annurev.micro.58.030603.123841 15487940
-
Gottesman S The small RNA regulators of Escherichia coli: Roles and mechanisms Annu Rev Microbiol 2004, 58:303-328. 10.1146/ annurev.micro.58.030603.123841 15487940
-
(2004)
Annu Rev Microbiol
, vol.58
, pp. 303-328
-
-
Gottesman, S.1
-
20
-
-
36649025655
-
OncomiRs: The discovery and progress of microRNAs in cancers
-
2098778 17894887 10.1186/1476-4598-6-60
-
Cho WC OncomiRs: The discovery and progress of microRNAs in cancers Molecular Cancer 2007, 6:60. 2098778 17894887 10.1186/1476-4598-6-60
-
(2007)
Molecular Cancer
, vol.6
, pp. 60
-
-
Cho, W.C.1
-
21
-
-
58149179989
-
miR2Disease: A manually curated database for microRNA deregulation in human disease
-
10.1093/nar/gkn714 18927107
-
Jiang Q Wang Y Hao Y Juan L Teng M Zhang X Li M Wang G Liu Y miR2Disease: A manually curated database for microRNA deregulation in human disease Nucleic Acids Res 2009, 37:D98-D104. 10.1093/nar/gkn714 18927107
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Jiang, Q.1
Wang, Y.2
Hao, Y.3
Juan, L.4
Teng, M.5
Zhang, X.6
Li, M.7
Wang, G.8
Liu, Y.9
-
22
-
-
41949102707
-
myRiad roles for the miR-17-92 cluster in development and disease
-
10.1016/j.cell.2008.04.001 18423194
-
Mendell JT myRiad roles for the miR-17-92 cluster in development and disease Cell 2008, 133:217-222. 10.1016/j.cell.2008.04.001 18423194
-
(2008)
Cell
, vol.133
, pp. 217-222
-
-
Mendell, J.T.1
-
23
-
-
42949131237
-
Computational methods for microRNA target prediction
-
10.1016/S0076-6879(07)27004-1 17720479
-
Watanabe Y Tomita M Kanai A Computational methods for microRNA target prediction Methods Enzymol 2007, 427:65-86. 10.1016/ S0076-6879(07)27004-1 17720479
-
(2007)
Methods Enzymol
, vol.427
, pp. 65-86
-
-
Watanabe, Y.1
Tomita, M.2
Kanai, A.3
-
24
-
-
34249025114
-
Prediction of microRNA targets
-
10.1016/j.drudis.2007.04.002 17532529
-
Maziére P Enright AJA Prediction of microRNA targets Drug Discov Today 2007, 12:452-458. 10.1016/j.drudis.2007.04.002 17532529
-
(2007)
Drug Discov Today
, vol.12
, pp. 452-458
-
-
Maziére, P.1
Enright, A.J.A.2
-
25
-
-
0344232733
-
MicroRNAs: Runts of the genome assert themselves
-
10.1016/j.cub.2003.11.017 14654021
-
Lai EC MicroRNAs: Runts of the genome assert themselves Curr Biol 2003, 13:R925-R936. 10.1016/j.cub.2003.11.017 14654021
-
(2003)
Curr Biol
, vol.13
-
-
Lai, E.C.1
-
26
-
-
33645528966
-
Post-transcriptional small RNA pathways in plants: Mechanisms and regulations
-
10.1101/gad.1410506 16600909
-
Vaucheret H Post-transcriptional small RNA pathways in plants: mechanisms and regulations Genes Dev 2006, 20:759-771. 10.1101/ gad.1410506 16600909
-
(2006)
Genes Dev
, vol.20
, pp. 759-771
-
-
Vaucheret, H.1
-
27
-
-
0141860088
-
Coupled degradation of a small regulatory RNA and its mRNA targets in Escherichia coli
-
218075 12975324 10.1101/gad.1127103
-
Massé E Escorcia FE Gottesman S Coupled degradation of a small regulatory RNA and its mRNA targets in Escherichia coli Genes & Development 2003, 17:2374-2383. 218075 12975324 10.1101/gad.1127103
-
(2003)
Genes & Development
, vol.17
, pp. 2374-2383
-
-
Massé, E.1
Escorcia, F.E.2
Gottesman, S.3
-
28
-
-
34748871477
-
Regulation of gene expression by small non-coding RNAs: A quantitative view
-
2013925 17893699 10.1038/msb4100181
-
Shimoni Y Friedlander G Hetzroni G Niv G Altuvia S Biham O Margali H Regulation of gene expression by small non-coding RNAs: A quantitative view Molecular Systems Biology 2007, 3:138. 2013925 17893699 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
Margali, H.7
-
29
-
-
34548668642
-
Quantitative characteristics of gene regulation by small RNA
-
1994261 17713988 10.1371/journal.pbio.0050229
-
Levine E Zhang KTZ Hwa T Quantitative characteristics of gene regulation by small RNA PLoS Biol 2007, 5:e229. 1994261 17713988 10.1371/ journal.pbio.0050229
-
(2007)
PLoS Biol
, vol.5
-
-
Levine, E.1
Zhang, K.T.Z.2
Hwa, T.3
-
30
-
-
54049118804
-
A quantitative comparison of sRNA-based and protein-based gene regulation
-
2583084 18854820 10.1038/msb.2008.58
-
Mehta P Goyal S Wingreen N A quantitative comparison of sRNA-based and protein-based gene regulation Molecular Systems Biology 2008, 4:221. 2583084 18854820 10.1038/msb.2008.58
-
(2008)
Molecular Systems Biology
, vol.4
, pp. 221
-
-
Mehta, P.1
Goyal, S.2
Wingreen, N.3
-
31
-
-
58149382580
-
MicroRNA regulation of a cancer network: Consequences of the feedback loops involving miR-17-92, E2F, and Myc
-
2598727 19066217 10.1073/pnas.0811166106
-
Aguda BD Kim Y Piper-Hunter M Friedman A Marsh C MicroRNA regulation of a cancer network: Consequences of the feedback loops involving miR-17-92, E2F, and Myc Proc Natl Acad Sci USA 2008, 105:19678-83. 2598727 19066217 10.1073/pnas.0811166106
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 19678-19683
-
-
Aguda, B.D.1
Kim, Y.2
Piper-Hunter, M.3
Friedman, A.4
Marsh, C.5
-
32
-
-
41349120349
-
Computational modeling of post-transcriptional gene regulation by microRNAs
-
10.1089/cmb.2007.0184 18333757
-
Khanin R Vinciotti V Computational modeling of post-transcriptional gene regulation by microRNAs Journal of Computational Biology 2008, 15:305-316. 10.1089/cmb.2007.0184 18333757
-
(2008)
Journal of Computational Biology
, vol.15
, pp. 305-316
-
-
Khanin, R.1
Vinciotti, V.2
-
33
-
-
3142564584
-
The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae
-
10.1016/j.cell.2004.06.009 15242645
-
Lenz D Mok K Lilley B Kulkarni R Wingreen N Bassler B The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae Cell 2004, 118:69-82. 10.1016/ j.cell.2004.06.009 15242645
-
(2004)
Cell
, vol.118
, pp. 69-82
-
-
Lenz, D.1
Mok, K.2
Lilley, B.3
Kulkarni, R.4
Wingreen, N.5
Bassler, B.6
-
34
-
-
33644873438
-
RegulonDB (version 5.0): Escherichia coli k-12 transcriptional regulatory network, operon organization, and growth conditions
-
1347518 16381895 10.1093/nar/gkj156
-
Salgado H Gama-Castro S Peralta-Gil M, et al. RegulonDB (version 5.0): Escherichia coli k-12 transcriptional regulatory network, operon organization, and growth conditions Nucleic Acids Res 2006, 34:D394-D397. 1347518 16381895 10.1093/nar/gkj156
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Salgado, H.1
Gama-Castro, S.2
Peralta-Gil, M.3
-
35
-
-
33644875073
-
NPInter: The noncoding RNAs and protein related biomacromolecules interaction database
-
1347388 16381834 10.1093/nar/gkj025
-
Wu T Wang J Liu C Zhang y Shi B Zhu X Zhang Z Skogerb G Chen L Lu H Zhao Y Chen R NPInter: The noncoding RNAs and protein related biomacromolecules interaction database Nucleic Acids Res 2006, 34:D150-D152. 1347388 16381834 10.1093/nar/gkj025
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Wu, T.1
Wang, J.2
Liu, C.3
Zhang, Y.4
Shi, B.5
Zhu, X.6
Zhang, Z.7
Skogerb, G.8
Chen, L.9
Lu, H.10
Zhao, Y.11
Chen, R.12
-
36
-
-
0027327859
-
CAP interacts with RNA polymerase in solution in the absence of promoter DNA
-
10.1038/364548a0 8393148
-
Heyduk T Lee J Ebright Y Blatter E Zhou Y Ebright R CAP interacts with RNA polymerase in solution in the absence of promoter DNA Nature 1993, 364:548-549. 10.1038/364548a0 8393148
-
(1993)
Nature
, vol.364
, pp. 548-549
-
-
Heyduk, T.1
Lee, J.2
Ebright, Y.3
Blatter, E.4
Zhou, Y.5
Ebright, R.6
-
37
-
-
13244289800
-
Genome-wide expression analysis indicates that FNR of Escherichia coli K-12 regulates a large number of genes of unknown function
-
545700 15659690 10.1128/JB.187.3.1135-1160.2005
-
Kang Y Weber KD Qiu Y Kiley P Blattner FR Genome-wide expression analysis indicates that FNR of Escherichia coli K-12 regulates a large number of genes of unknown function J Bacteriol 2005, 187:1135-60. 545700 15659690 10.1128/JB.187.3.1135-1160.2005
-
(2005)
J Bacteriol
, vol.187
, pp. 1135-1160
-
-
Kang, Y.1
Weber, K.D.2
Qiu, Y.3
Kiley, P.4
Blattner, F.R.5
-
38
-
-
0037216801
-
Requirement of ArcA for Redox Regulation in Escherichia coli under Microaerobic but Not Anaerobic or Aerobic Conditions
-
141817 12486057 10.1128/JB.185.1.204-209.2003
-
Alexeeva S Hellingwerf kJ de Mattos MJT Requirement of ArcA for Redox Regulation in Escherichia coli under Microaerobic but Not Anaerobic or Aerobic Conditions J Bacteriol 2003, 185:204-209. 141817 12486057 10.1128/JB.185.1.204-209.2003
-
(2003)
J Bacteriol
, vol.185
, pp. 204-209
-
-
Alexeeva, S.1
Hellingwerf, K.J.2
de Mattos, M.J.T.3
-
39
-
-
0028008417
-
Division inhibition gene dicf of Escherichia coli reveals a widespread group of prophage sequences in bacterial genomes
-
205167 7508908
-
Faubladier M Bouch JP Division inhibition gene dicf of Escherichia coli reveals a widespread group of prophage sequences in bacterial genomes J Bacteriol 1994, 176:1150-1156. 205167 7508908
-
(1994)
J Bacteriol
, vol.176
, pp. 1150-1156
-
-
Faubladier, M.1
Bouch, J.P.2
-
40
-
-
13244281760
-
Implication of membrane localization of target mRNA in the action of a small RNA: Mechanism of post-transcriptional regulation of glucose transporter in escherichia coli
-
546511 15650111 10.1101/gad.1270605
-
Kawamoto H Morita T Shimizu A Inada T Aiba H Implication of membrane localization of target mRNA in the action of a small RNA: Mechanism of post-transcriptional regulation of glucose transporter in escherichia coli Genes Dev 2005, 19:328-338. 546511 15650111 10.1101/gad.1270605
-
(2005)
Genes Dev
, vol.19
, pp. 328-338
-
-
Kawamoto, H.1
Morita, T.2
Shimizu, A.3
Inada, T.4
Aiba, H.5
-
41
-
-
0034730125
-
A trans-acting RNA as a control switch in Escherichia coli: DsrA modulates function by forming alternative structures
-
27626 10954740 10.1073/pnas.170281497
-
Lease RA Belfort M A trans-acting RNA as a control switch in Escherichia coli: DsrA modulates function by forming alternative structures Proc Natl Acad Sci USA 2000, 97:9919-9924. 27626 10954740 10.1073/ pnas.170281497
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, pp. 9919-9924
-
-
Lease, R.A.1
Belfort, M.2
|