-
1
-
-
34249079154
-
Network motifs: Theory and experimental approaches
-
DOI 10.1038/nrg2102, PII NRG2102
-
Alon, U. 2007. Network motifs: theory and experimental approaches. Nat. Rev. Genet. 8, 450-461. (Pubitemid 46789247)
-
(2007)
Nature Reviews Genetics
, vol.8
, Issue.6
, pp. 450-461
-
-
Alon, U.1
-
2
-
-
49949116902
-
The impact of microRNAs on protein output
-
Baek, D., Villen, J., Shin, C., et al. 2008. The impact of microRNAs on protein output. Nature 455, 64-71.
-
(2008)
Nature
, vol.455
, pp. 64-71
-
-
Baek, D.1
Villen, J.2
Shin, C.3
-
3
-
-
58249088751
-
MicroRNAs: Target recognition and regulatory functions
-
Bartel, D.P. 2009. MicroRNAs: target recognition and regulatory functions. Cell 136, 215-233.
-
(2009)
Cell
, vol.136
, pp. 215-233
-
-
Bartel, D.P.1
-
4
-
-
0347444723
-
MicroRNAs: Genomics, biogenesis, mechanism, and function
-
Bartel, D.P. 2004. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116, 281-297.
-
(2004)
Cell
, vol.116
, pp. 281-297
-
-
Bartel, D.P.1
-
5
-
-
34548200846
-
DAISY: A new software tool to test global identifiability of biological and physiological systems
-
DOI 10.1016/j.cmpb.2007.07.002, PII S0169260707001605
-
Bellu, G., Saccomani, M.P., Audoly, S., et al. 2007. DAISY: a new software tool to test global identifiability of biological and physiological systems. Comput. Methods Programs Biomed. 88, 52-61. (Pubitemid 47331951)
-
(2007)
Computer Methods and Programs in Biomedicine
, vol.88
, Issue.1
, pp. 52-61
-
-
Bellu, G.1
Saccomani, M.P.2
Audoly, S.3
D'Angio, L.4
-
6
-
-
22844440427
-
Identification of hundreds of conserved and nonconserved human microRNAs
-
DOI 10.1038/ng1590
-
Bentwich, I., Avniel, A., Karov, Y., et al. 2005. Identification of hundreds of conserved and nonconserved human microRNAs. Nat. Genet. 37, 766-770. (Pubitemid 41754896)
-
(2005)
Nature Genetics
, vol.37
, Issue.7
, pp. 766-770
-
-
Bentwich, I.1
Avniel, A.2
Karov, Y.3
Aharonov, R.4
Gilad, S.5
Barad, O.6
Barzilai, A.7
Einat, P.8
Einav, U.9
Meiri, E.10
Sharon, E.11
Spector, Y.12
Bentwich, Z.13
-
7
-
-
4444339832
-
Quantitative characterization of the transcriptional regulatory network in the yeast cell cycle
-
Chen, H.C., Lee, H.C., Lin, T.Y., et al. 2004. Quantitative characterization of the transcriptional regulatory network in the yeast cell cycle. Bioinformatics 20, 1914-1927.
-
(2004)
Bioinformatics
, vol.20
, pp. 1914-1927
-
-
Chen, H.C.1
Lee, H.C.2
Lin, T.Y.3
-
8
-
-
20844452570
-
A stochastic differential equation model for quantifying transcriptional regulatory network in Saccharomyces cerevisiae
-
Chen, K.C., Wang, T.Y., Tseng, H.H., et al. 2005. A stochastic differential equation model for quantifying transcriptional regulatory network in Saccharomyces cerevisiae. Bioinformatics 21, 2883-2890.
-
(2005)
Bioinformatics
, vol.21
, pp. 2883-2890
-
-
Chen, K.C.1
Wang, T.Y.2
Tseng, H.H.3
-
10
-
-
28044455435
-
MicroPrimer: The biogenesis and function of microRNA
-
DOI 10.1242/dev.02070
-
Du, T., and Zamore, P.D. 2005. microPrimer: the biogenesis and function of microRNA. Development 132, 4645-4652. (Pubitemid 41685275)
-
(2005)
Development
, vol.132
, Issue.21
, pp. 4645-4652
-
-
Du, T.1
Zamore, P.D.2
-
11
-
-
79952289884
-
A curated database of miRNA-mediated feed-forward loops involving MYC as master regulator
-
El Baroudi, M., Cora, D., Bosia, C., et al. 2011. A curated database of miRNA-mediated feed-forward loops involving MYC as master regulator. PLoS ONE 6, e14742.
-
(2011)
PLoS ONE
, vol.6
-
-
El Baroudi, M.1
Cora, D.2
Bosia, C.3
-
12
-
-
77956520986
-
CircuitsDB: A database of mixed microRNA/transcription factor feedforward regulatory circuits in human and mouse
-
Friard, O., Re, A., Taverna, D., et al. 2010. CircuitsDB: a database of mixed microRNA/transcription factor feedforward regulatory circuits in human and mouse. BMC Bioinform. 11, 435.
-
(2010)
BMC Bioinform.
, vol.11
, pp. 435
-
-
Friard, O.1
Re, A.2
Taverna, D.3
-
13
-
-
60149095444
-
Most mammalian mRNAs are conserved targets of microRNAs
-
Friedman, R.C., Farh, K.K., Burge, C.B., et al. 2009. Most mammalian mRNAs are conserved targets of microRNAs. Genome Res. 19, 92-105.
-
(2009)
Genome Res
, vol.19
, pp. 92-105
-
-
Friedman, R.C.1
Farh, K.K.2
Burge, C.B.3
-
14
-
-
33644750115
-
MiRBase: MicroRNA sequences, targets and gene nomenclature
-
Griffiths-Jones, S., Grocock, R.J., van Dongen, S., et al. 2006. miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res. 34, D140-4.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Griffiths-Jones, S.1
Grocock, R.J.2
Van Dongen, S.3
-
15
-
-
84984765621
-
Canalization of development by microRNAs
-
Hornstein, E., and Shomron, N. 2006. Canalization of development by microRNAs. Nat. Genet. 38, S20-S24.
-
(2006)
Nat. Genet
, vol.38
-
-
Hornstein, E.1
Shomron, N.2
-
16
-
-
58149179989
-
MiR2Disease: A manually curated database for microRNA deregulation in human disease
-
Jiang, Q., Wang, Y., Hao, Y., et al. 2009. miR2Disease: a manually curated database for microRNA deregulation in human disease. Nucleic Acids Res. 37, D98-D104.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Jiang, Q.1
Wang, Y.2
Hao, Y.3
-
17
-
-
77349121900
-
Identification of novel non-coding RNAs using profiles of short sequence reads from next generation sequencing data
-
Jung, C.H., Hansen, M.A., Makunin, I.V., et al. 2010. Identification of novel non-coding RNAs using profiles of short sequence reads from next generation sequencing data. BMC Genomics 11, 77.
-
(2010)
BMC Genomics
, vol.11
, pp. 77
-
-
Jung, C.H.1
Hansen, M.A.2
Makunin, I.V.3
-
18
-
-
33746428728
-
A coherent feed-forward loop with a SUM input function prolongs flagella expression in Escherichia coli
-
2005.0006
-
Kalir, S., Mangan, S., and Alon, U. 2005. A coherent feed-forward loop with a SUM input function prolongs flagella expression in Escherichia coli. Mol. Syst. Biol. 1, 2005.0006.
-
(2005)
Mol. Syst. Biol
, vol.1
-
-
Kalir, S.1
Mangan, S.2
Alon, U.3
-
19
-
-
47349095809
-
The incoherent feed-forward loop can generate non-monotonic input functions for genes
-
Kaplan, S., Bren, A., Dekel, E., et al. 2008. The incoherent feed-forward loop can generate non-monotonic input functions for genes. Mol. Syst. Biol. 4, 203.
-
(2008)
Mol. Syst. Biol
, vol.4
, pp. 203
-
-
Kaplan, S.1
Bren, A.2
Dekel, E.3
-
20
-
-
70350125874
-
MicroRNA miR-27b impairs human adipocyte differentiation and targets PPARgamma
-
Karbiener, M., Fischer, C., Nowitsch, S., et al. 2009. microRNA miR-27b impairs human adipocyte differentiation and targets PPARgamma. Biochem. Biophys. Res. Commun. 390, 247-251.
-
(2009)
Biochem. Biophys. Res. Commun.
, vol.390
, pp. 247-251
-
-
Karbiener, M.1
Fischer, C.2
Nowitsch, S.3
-
21
-
-
41349120349
-
Computational modeling of post-transcriptional gene regulation by microRNAs
-
DOI 10.1089/cmb.2007.0184
-
Khanin, R., and Vinciotti, V. 2008. Computational modeling of post-transcriptional gene regulation by microRNAs. J. Comput. Biol. 15, 305-316. (Pubitemid 351450464)
-
(2008)
Journal of Computational Biology
, vol.15
, Issue.3
, pp. 305-316
-
-
Khanin, R.1
Vinciotti, V.2
-
22
-
-
0035955374
-
Identification of novel genes coding for small expressed RNAs
-
DOI 10.1126/science.1064921
-
Lagos-Quintana, M., Rauhut, R., Lendeckel, W., et al. 2001. Identification of novel genes coding for small expressed RNAs. Science 294, 853-858. (Pubitemid 33032103)
-
(2001)
Science
, vol.294
, Issue.5543
, pp. 853-858
-
-
Lagos-Quintana, M.1
Rauhut, R.2
Lendeckel, W.3
Tuschl, T.4
-
23
-
-
0037321349
-
New microRNAs from mouse and human
-
DOI 10.1261/rna.2146903
-
Lagos-Quintana, M., Rauhut, R., Meyer, J., et al. 2003. New microRNAs from mouse and human. RNA 9, 175-179. (Pubitemid 36206285)
-
(2003)
RNA
, vol.9
, Issue.2
, pp. 175-179
-
-
Lagos-Quintana, M.1
Rauhut, R.2
Meyer, J.3
Borkhardt, A.4
Tuschl, T.5
-
24
-
-
36849064251
-
Target-specific and global effectors in gene regulation by microRNA
-
DOI 10.1529/biophysj.107.118448
-
Levine, E., Ben Jacob, E., and Levine, H. 2007a. Target-specific and global effectors in gene regulation by MicroRNA. Biophys. J. 93, L52-4. (Pubitemid 350223788)
-
(2007)
Biophysical Journal
, vol.93
, Issue.11
-
-
Levine, E.1
Jacob, E.B.2
Levine, H.3
-
25
-
-
34548668642
-
Quantitative characteristics of gene regulation by small RNA
-
Levine, E., Zhang, Z., Kuhlman, T., et al. 2007b. Quantitative characteristics of gene regulation by small RNA. PLoS Biol. 5, e229.
-
(2007)
PLoS Biol
, vol.5
-
-
Levine, E.1
Zhang, Z.2
Kuhlman, T.3
-
26
-
-
11844278458
-
Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets
-
DOI 10.1016/j.cell.2004.12.035, PII S0092867404012607
-
Lewis, B.P., Burge, C.B., and Bartel, D.P. 2005. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120, 15-20. (Pubitemid 40094598)
-
(2005)
Cell
, vol.120
, Issue.1
, pp. 15-20
-
-
Lewis, B.P.1
Burge, C.B.2
Bartel, D.P.3
-
27
-
-
0346094457
-
Prediction of mammalian MicroRNA targets
-
DOI 10.1016/S0092-8674(03)01018-3
-
Lewis, B.P., Shih, I.H., Jones-Rhoades, M.W., et al. 2003. Prediction of mammalian microRNA targets. Cell 115, 787-798. (Pubitemid 38058492)
-
(2003)
Cell
, vol.115
, Issue.7
, pp. 787-798
-
-
Lewis, B.P.1
Shih, I.-H.2
Jones-Rhoades, M.W.3
Bartel, D.P.4
Burge, C.B.5
-
28
-
-
64249144494
-
A microRNA imparts robustness against environmental fluctuation during development
-
Li, X., Cassidy, J.J., Reinke, C.A., et al. 2009. A microRNA imparts robustness against environmental fluctuation during development. Cell 137, 273-282.
-
(2009)
Cell
, vol.137
, pp. 273-282
-
-
Li, X.1
Cassidy, J.J.2
Reinke, C.A.3
-
29
-
-
71049182983
-
Specialized or flexible feed-forward loop motifs: A question of topology
-
Macia, J., Widder, S., and Sole, R. 2009. Specialized or flexible feed-forward loop motifs: a question of topology. BMC Syst. Biol. 3, 84.
-
(2009)
BMC Syst. Biol
, vol.3
, pp. 84
-
-
MacIa, J.1
Widder, S.2
Sole, R.3
-
31
-
-
0037174670
-
Network motifs: Simple building blocks of complex networks
-
DOI 10.1126/science.298.5594.824
-
Milo, R., Shen-Orr, S., Itzkovitz, S., et al. 2002. Network motifs: simple building blocks of complex networks. Science 298, 824-827. (Pubitemid 35231534)
-
(2002)
Science
, vol.298
, Issue.5594
, pp. 824-827
-
-
Milo, R.1
Shen-Orr, S.2
Itzkovitz, S.3
Kashtan, N.4
Chklovskii, D.5
Alon, U.6
-
32
-
-
79952302623
-
The role of incoherent microRNA-mediated feedforward loops in noise buffering
-
Osella, M., Bosia, C., Corà, D., et al. 2011. The role of incoherent microRNA-mediated feedforward loops in noise buffering. PLoS Comput. Biol. 7, e1001101.
-
(2011)
PLoS Comput. Biol.
, vol.7
-
-
Osella, M.1
Bosia, C.2
Corà, D.3
-
33
-
-
70349334678
-
Genome-wide survey of microRNA-transcription factor feed-forward regulatory circuits in human
-
Re, A., Cora, D., Taverna, D., et al. 2009. Genome-wide survey of microRNA-transcription factor feed-forward regulatory circuits in human. Mol. Biosyst. 5, 854-867.
-
(2009)
Mol. Biosyst
, vol.5
, pp. 854-867
-
-
Re, A.1
Cora, D.2
Taverna, D.3
-
34
-
-
48549087683
-
Comparative transcriptomics of human multipotent stem cells during adipogenesis and osteoblastogenesis
-
Scheideler, M., Elabd, C., Zaragosi, L.E., et al. 2008. Comparative transcriptomics of human multipotent stem cells during adipogenesis and osteoblastogenesis. BMC Genomics 9, 340.
-
(2008)
BMC Genomics
, vol.9
, pp. 340
-
-
Scheideler, M.1
Elabd, C.2
Zaragosi, L.E.3
-
35
-
-
49949117302
-
Widespread changes in protein synthesis induced by microRNAs
-
Selbach, M., Schwanhausser, B., Thierfelder, N., et al. 2008. Widespread changes in protein synthesis induced by microRNAs. Nature 455, 58-63.
-
(2008)
Nature
, vol.455
, pp. 58-63
-
-
Selbach, M.1
Schwanhausser, B.2
Thierfelder, N.3
-
36
-
-
34547555796
-
Global and local architecture of the mammalian microRNA-transcription factor regulatory network
-
Shalgi, R., Lieber, D., Oren, M., et al. 2007. Global and local architecture of the mammalian microRNA-transcription factor regulatory network. PLoS Comput. Biol. 3, e131.
-
(2007)
PLoS Comput. Biol
, vol.3
-
-
Shalgi, R.1
Lieber, D.2
Oren, M.3
-
37
-
-
0036578795
-
Network motifs in the transcriptional regulation network of Escherichia coli
-
Shen-Orr, S.S., Milo, R., Mangan, S., et al. 2002. Network motifs in the transcriptional regulation network of Escherichia coli. Nat. Genet. 31, 64-68.
-
(2002)
Nat. Genet
, vol.31
, pp. 64-68
-
-
Shen-Orr, S.S.1
Milo, R.2
Mangan, S.3
-
38
-
-
34748871477
-
Regulation of gene expression by small non-coding RNAs: A quantitative view
-
Shimoni, Y., Friedlander, G., Hetzroni, G., et al. 2007. Regulation of gene expression by small non-coding RNAs: a quantitative view. Mol. Syst. Biol. 3, 138.
-
(2007)
Mol. Syst. Biol
, vol.3
, pp. 138
-
-
Shimoni, Y.1
Friedlander, G.2
Hetzroni, G.3
-
39
-
-
34249819336
-
MicroRNA-Mediated Feedback and Feedforward Loops Are Recurrent Network Motifs in Mammals
-
DOI 10.1016/j.molcel.2007.05.018, PII S109727650700319X
-
Tsang, J., Zhu, J., and van Oudenaarden, A. 2007. MicroRNA-mediated feedback and feedforward loops are recurrent network motifs in mammals. Mol. Cell 26, 753-767. (Pubitemid 46856248)
-
(2007)
Molecular Cell
, vol.26
, Issue.5
, pp. 753-767
-
-
Tsang, J.1
Zhu, J.2
Van Oudenaarden, A.3
-
40
-
-
77955840320
-
Numerical modelling of microRNA-mediated mRNA decay identifies novel mechanism of microRNA controlled mRNA downregulation
-
Vohradsky, J., Panek, J., and Vomastek, T. 2010. Numerical modelling of microRNA-mediated mRNA decay identifies novel mechanism of microRNA controlled mRNA downregulation. Nucleic Acids Res. 38, 4579-4585.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 4579-4585
-
-
Vohradsky, J.1
Panek, J.2
Vomastek, T.3
-
41
-
-
33846703173
-
Nonlinear differential equation model for quantification of transcriptional regulation applied to microarray data of Saccharomyces cerevisiae
-
DOI 10.1093/nar/gkl1001
-
Vu, T.T., and Vohradsky, J. 2007. Nonlinear differential equation model for quantification of transcriptional regulation applied to microarray data of Saccharomyces cerevisiae. Nucleic Acids Res. 35, 279-287. (Pubitemid 46189852)
-
(2007)
Nucleic Acids Research
, vol.35
, Issue.1
, pp. 279-287
-
-
Vu, T.T.1
Vohradsky, J.2
-
42
-
-
66049153398
-
Evolution under canalization and the dual roles of microRNAs: A hypothesis
-
Wu, C.I., Shen, Y., and Tang, T. 2009. Evolution under canalization and the dual roles of microRNAs: a hypothesis. Genome Res. 19, 734-743.
-
(2009)
Genome Res
, vol.19
, pp. 734-743
-
-
Wu, C.I.1
Shen, Y.2
Tang, T.3
|