-
1
-
-
70349334678
-
Genome-wide survey of microRNA - transcription factor feed-forward regulatory circuits in human
-
Angela, R., Davide, C., Daniela, T. and Caselle, M. (2009) 'Genome-wide survey of microRNA - transcription factor feed-forward regulatory circuits in human', Mol. BioSyst., Vol. 5, pp.854-867.
-
(2009)
Mol. BioSyst.
, vol.5
, pp. 854-867
-
-
Angela, R.1
Davide, C.2
Daniela, T.3
Caselle, M.4
-
2
-
-
12344252023
-
Neuronal subtype-specific genes that control corticospinal motor neuron development in vivo
-
Arlotta, P., Molyneaux, B.J., Chen, J., Inoue, J., Kominami, R. and Macklis, J.D. (2005) 'Neuronal subtype-specific genes that control corticospinal motor neuron development in vivo', Neuron, Vol. 45, No. 2, pp.207-221.
-
(2005)
Neuron
, vol.45
, Issue.2
, pp. 207-221
-
-
Arlotta, P.1
Molyneaux, B.J.2
Chen, J.3
Inoue, J.4
Kominami, R.5
Macklis, J.D.6
-
3
-
-
23944514849
-
Regulation by let-7 and lin-4 microRNAs results in target mRNA degradation
-
Bagga, S., Bracht, J., Hunter, S., Massirer, K., Holtz, J., Eachus, R. and Pasquinelli, A.E. (2005) 'Regulation by let-7 and lin-4 microRNAs results in target mRNA degradation', Cell, Vol. 122, pp.553-563.
-
(2005)
Cell
, vol.122
, pp. 553-563
-
-
Bagga, S.1
Bracht, J.2
Hunter, S.3
Massirer, K.4
Holtz, J.5
Eachus, R.6
Pasquinelli, A.E.7
-
4
-
-
0347444723
-
MicroRNAs: Genomics, biogenesis, mechanism, and function
-
Bartel, D.P. (2004) 'MicroRNAs: genomics, biogenesis, mechanism, and function', Cell, Vol. 116, pp.281-297.
-
(2004)
Cell
, vol.116
, pp. 281-297
-
-
Bartel, D.P.1
-
5
-
-
33847172327
-
Clustering by passing messages between data points
-
Frey, B.J. and Dueck, D. (2007) 'Clustering by passing messages between data points', Science, Vol. 315, pp.972-976.
-
(2007)
Science
, vol.315
, pp. 972-976
-
-
Frey, B.J.1
Dueck, D.2
-
7
-
-
47149083435
-
Message passing clustering (MPC): A knowledge-based framework for clustering under biological constraints
-
Geng, H.M., Deng, X. and Ali, H.H. (2008) 'Message passing clustering (MPC): a knowledge-based framework for clustering under biological constraints', International Journal of Data Mining and Bioinformatics, Vol. 2, No. 2, pp.95-120.
-
(2008)
International Journal of Data Mining and Bioinformatics
, vol.2
, Issue.2
, pp. 95-120
-
-
Geng, H.M.1
Deng, X.2
Ali, H.H.3
-
8
-
-
61849143920
-
MicroRNA target prediction by expression analysis of host genes
-
Gennarino, V.A., Sardiello, M., Avellino, R., Meola, N., Maselli, V., Anand, S., Cutillo, L., Ballabio, A. and Banfi, S. (2009) 'MicroRNA target prediction by expression analysis of host genes', Genome Research, Vol. 19, No. 3, pp.481-490.
-
(2009)
Genome Research
, vol.19
, Issue.3
, pp. 481-490
-
-
Gennarino, V.A.1
Sardiello, M.2
Avellino, R.3
Meola, N.4
Maselli, V.5
Anand, S.6
Cutillo, L.7
Ballabio, A.8
Banfi, S.9
-
9
-
-
50849141708
-
MirWIP: MicroRNA target prediction based on microRNAcontaining ribonucleoprotein-enriched transcripts
-
Hammell, M., Long, D., Zhang, L., Lee, A., Carmack, C.S., Han, M., Ding, Y. and Ambros, V. (2008) 'MirWIP: microRNA target prediction based on microRNAcontaining ribonucleoprotein-enriched transcripts', Nature Method, Vol. 5, pp.813-819.
-
(2008)
Nature Method
, vol.5
, pp. 813-819
-
-
Hammell, M.1
Long, D.2
Zhang, L.3
Lee, A.4
Carmack, C.S.5
Han, M.6
Ding, Y.7
Ambros, V.8
-
10
-
-
33745765418
-
Detecting microRNA targets by linking sequence, microRNA and gene expression data
-
Huang, J.C., Morris, Q.D. and Frey, B.J. (2006) 'Detecting microRNA targets by linking sequence, microRNA and gene expression data', Proc. RECOMB, Vol. 3909, pp.114-129.
-
(2006)
Proc. RECOMB
, vol.3909
, pp. 114-129
-
-
Huang, J.C.1
Morris, Q.D.2
Frey, B.J.3
-
11
-
-
34447288056
-
Bayesian learning of microRNA targets from sequence and expression data
-
Huang, J.C., Morris, Q.D. and Frey, B.J. (2007) 'Bayesian learning of microRNA targets from sequence and expression data', Journal of Computational Biology, Vol. 14, pp.550-563.
-
(2007)
Journal of Computational Biology
, vol.14
, pp. 550-563
-
-
Huang, J.C.1
Morris, Q.D.2
Frey, B.J.3
-
12
-
-
40549138450
-
Comparing sequence and expression for predicting microRNA targets using genMiR3
-
Huang, J.C., Frey, B.J. and Morris, Q.D. (2008) 'Comparing sequence and expression for predicting microRNA targets using genMiR3', Pacific Symposium for Biocomputing, Vol. 13, pp.52-63.
-
(2008)
Pacific Symposium for Biocomputing
, vol.13
, pp. 52-63
-
-
Huang, J.C.1
Frey, B.J.2
Morris, Q.D.3
-
13
-
-
14044251458
-
Human microRNA targets
-
John, B., Enright, A.J., Aravin, A., Tuschl, T., Sander, C. and Marks, D.S. (2004) 'Human microRNA targets', PLoS Biology, Vol. 2, p.363.
-
(2004)
PLoS Biology
, vol.2
, pp. 363
-
-
John, B.1
Enright, A.J.2
Aravin, A.3
Tuschl, T.4
Sander, C.5
Marks, D.S.6
-
14
-
-
0347357618
-
A microRNA controlling left/right neuronal asymmetry in caenorhabditis elegans
-
Johnston, R.J. and Hobert, O. (2003) 'A microRNA controlling left/right neuronal asymmetry in caenorhabditis elegans', Nature, Vol. 426, pp.845-849.
-
(2003)
Nature
, vol.426
, pp. 845-849
-
-
Johnston, R.J.1
Hobert, O.2
-
15
-
-
33644756532
-
A genome-wide map of conserved microRNA targets in C. elegans
-
Lall, S., Grün, D., Krek, A., Chen, K., Wang, Y.L., Dewey, C.N., Sood, P., Colombo, T., Bray, N., Macmenamin, P., Kao, H.L., Gunsalus, K.C., Pachter, L., Piano, F. and Rajewsky, N. (2006) 'A genome-wide map of conserved microRNA targets in C. elegans', Current Biology, Vol. 16, pp.460-471.
-
(2006)
Current Biology
, vol.16
, pp. 460-471
-
-
Lall, S.1
Grün, D.2
Krek, A.3
Chen, K.4
Wang, Y.L.5
Dewey, C.N.6
Sood, P.7
Colombo, T.8
Bray, N.9
Macmenamin, P.10
Kao, H.L.11
Gunsalus, K.C.12
Pachter, L.13
Piano, F.14
Rajewsky, N.15
-
16
-
-
0027751663
-
The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14
-
Lee, R.C., Feinbaum, R.L. and Ambros, V. (1993) 'The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14', Cell, Vol. 75, pp.843-854.
-
(1993)
Cell
, vol.75
, pp. 843-854
-
-
Lee, R.C.1
Feinbaum, R.L.2
Ambros, V.3
-
17
-
-
11844278458
-
Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets
-
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, Vol. 120, pp.15-20.
-
(2005)
Cell
, vol.120
, pp. 15-20
-
-
Lewis, B.P.1
Burge, C.B.2
Bartel, D.P.3
-
18
-
-
13944282215
-
Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs
-
Lim, L.P., Lau, N.C., Garrett-Engele, P., Grimson, A., Schelter, J.M., Castle, J., Bartel, D.P., Linsley, P.S. and Johnson, J.M. (2005) 'Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs', Nature, Vol. 433, pp.769-773.
-
(2005)
Nature
, vol.433
, pp. 769-773
-
-
Lim, L.P.1
Lau, N.C.2
Garrett-Engele, P.3
Grimson, A.4
Schelter, J.M.5
Castle, J.6
Bartel, D.P.7
Linsley, P.S.8
Johnson, J.M.9
-
19
-
-
20444460289
-
MicroRNA expression profiles classify human cancers
-
Lu, J., Getz, G., Miska, E.A., Alvarez-Saavedra, E., Lamb, J., Peck, D., Sweet-Cordero, A., Ebert, B.L., Mak, R.H., Ferrando, A.A., Downing, J.R., Jacks, T., Horvitz, H.R. and Golub, T.R. (2005) 'MicroRNA expression profiles classify human cancers', Nature, Vol. 435, pp.834-838.
-
(2005)
Nature
, vol.435
, pp. 834-838
-
-
Lu, J.1
Getz, G.2
Miska, E.A.3
Alvarez-Saavedra, E.4
Lamb, J.5
Peck, D.6
Sweet-Cordero, A.7
Ebert, B.L.8
Mak, R.H.9
Ferrando, A.A.10
Downing, J.R.11
Jacks, T.12
Horvitz, H.R.13
Golub, T.R.14
-
20
-
-
33745248430
-
MicroRNA target predictions in animals
-
Rajewsky, N. (2006) 'MicroRNA target predictions in animals', Nature Genetics, Suppl., Vol. 38, pp.S8-S13.
-
(2006)
Nature Genetics, Suppl.
, vol.38
-
-
Rajewsky, N.1
-
21
-
-
0347201147
-
Multiclass cancer diagnosis using tumor gene expression signatures
-
Ramaswamy, S., Tamayo, P., Rifkin, R., Mukherjee, S., Yeang, C.H., Angelo, M., Ladd, C., Reich, M., Latulippe, E., Mesirov, J.P., Poggio, T., Gerald, W., Loda, M., Lander, E.S. and Golub, T.R. (2001) 'Multiclass cancer diagnosis using tumor gene expression signatures', Proc. Natl. Acad. Sci. USA, Vol. 98, pp.15149-15154.
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 15149-15154
-
-
Ramaswamy, S.1
Tamayo, P.2
Rifkin, R.3
Mukherjee, S.4
Yeang, C.H.5
Angelo, M.6
Ladd, C.7
Reich, M.8
Latulippe, E.9
Mesirov, J.P.10
Poggio, T.11
Gerald, W.12
Loda, M.13
Lander, E.S.14
Golub, T.R.15
-
22
-
-
4644237189
-
Fast and effective prediction of microRNA/target duplexes
-
Rehmsmeier, M., Steffen, P., Hochsmann, M. and Giegerich, R. (2004) 'Fast and effective prediction of microRNA/target duplexes', RNA, Vol. 10, pp.1507-1517.
-
(2004)
RNA
, vol.10
, pp. 1507-1517
-
-
Rehmsmeier, M.1
Steffen, P.2
Hochsmann, M.3
Giegerich, R.4
-
23
-
-
15544371346
-
Gene regulation at the single-cell level
-
Rosenfeld, N., Young, J.W., Alon, U., Swain, P.S. and Elowitz, M.B. (2005) 'Gene regulation at the single-cell level', Science, Vol. 307, No. 5717, pp.1962-1965.
-
(2005)
Science
, vol.307
, Issue.5717
, pp. 1962-1965
-
-
Rosenfeld, N.1
Young, J.W.2
Alon, U.3
Swain, P.S.4
Elowitz, M.B.5
-
24
-
-
33750318273
-
A guide through present computational approaches for the identification of mammalian microRNA targets
-
Sethupathy, P., Megraw, M. and Hatzigeorgiou, A.G. (2006a) 'A guide through present computational approaches for the identification of mammalian microRNA targets', Nature Method, Vol. 3, pp.881-886.
-
(2006)
Nature Method
, vol.3
, pp. 881-886
-
-
Sethupathy, P.1
Megraw, M.2
Hatzigeorgiou, A.G.3
-
25
-
-
31044444975
-
TarBase: A comprehensive database of experimentally supported animal microRNA targets
-
Sethupathy, P., Corda, B. and Hatziegeorgiou, A.G. (2006b) 'TarBase: a comprehensive database of experimentally supported animal microRNA targets', RNA, Vol. 12, pp.192-197.
-
(2006)
RNA
, vol.12
, pp. 192-197
-
-
Sethupathy, P.1
Corda, B.2
Hatziegeorgiou, A.G.3
-
26
-
-
28944439309
-
Animal microRNAs confer robustness to gene expression and have a significant impact on 3'UTR evolution
-
Stark, A., Brennecke, J., Bushati, N., Russell, R.B. and Cohen, S.M. (2005) 'Animal microRNAs confer robustness to gene expression and have a significant impact on 3'UTR evolution', Cell, Vol. 123, No. 6, pp.1133-1146.
-
(2005)
Cell
, vol.123
, Issue.6
, pp. 1133-1146
-
-
Stark, A.1
Brennecke, J.2
Bushati, N.3
Russell, R.B.4
Cohen, S.M.5
-
27
-
-
29444452573
-
Molecular taxonomy of major neuronal classes in the adult mouse forebrain
-
Sugino, K., Hempel, C.M., Miller, M.N., Hattox, A.M., Shapiro, P., Wu, C., Huang, Z.J. and Nelson, S.B. (2005) 'Molecular taxonomy of major neuronal classes in the adult mouse forebrain', Nature Neuroscience, Vol. 9, pp.99-107.
-
(2005)
Nature Neuroscience
, vol.9
, pp. 99-107
-
-
Sugino, K.1
Hempel, C.M.2
Miller, M.N.3
Hattox, A.M.4
Shapiro, P.5
Wu, C.6
Huang, Z.J.7
Nelson, S.B.8
-
28
-
-
34047267329
-
An E2F/miR-20a auto-regulatory feed-back loop
-
Sylvestre, Y., Guire, V.D., Querido, E., Mukhopadhyay, U.K., Bourdeau, V., Major, F., Ferbeyre, G. and Chartrand, P. (2006) 'An E2F/miR-20a auto-regulatory feed-back loop', J. Biol. Chem., Vol. 282, pp.2135-2143.
-
(2006)
J. Biol. Chem.
, vol.282
, pp. 2135-2143
-
-
Sylvestre, Y.1
Guire, V.D.2
Querido, E.3
Mukhopadhyay, U.K.4
Bourdeau, V.5
Major, F.6
Ferbeyre, G.7
Chartrand, P.8
-
29
-
-
2442537233
-
Gene regulatory network growth by duplication
-
Teichmann, S.A. and Babu, M.M. (2004) 'Gene regulatory network growth by duplication', Nature Genetics, Vol. 36, pp.492-496.
-
(2004)
Nature Genetics
, vol.36
, pp. 492-496
-
-
Teichmann, S.A.1
Babu, M.M.2
-
30
-
-
0034960264
-
Missing value estimation methods for DNA microarrays
-
Troyanskaya, O., Cantor, M., Sherlock, G., Brown, P., Hastie, T., Tibshirani, R., Botstein, D. and Altman, R.B. (2001) 'Missing value estimation methods for DNA microarrays' Bioinformatics, Vol. 17, pp.520-525.
-
(2001)
Bioinformatics
, vol.17
, pp. 520-525
-
-
Troyanskaya, O.1
Cantor, M.2
Sherlock, G.3
Brown, P.4
Hastie, T.5
Tibshirani, R.6
Botstein, D.7
Altman, R.B.8
-
31
-
-
34249819336
-
MicroRNA-mediated feedback and feedforward loops are recurrent network motifs in mammals
-
Tsang, J., Zhu, J. and Oudenaarden, A. (2007) 'MicroRNA-mediated feedback and feedforward loops are recurrent network motifs in mammals', Molecular Cell, Vol. 26, pp.753-767.
-
(2007)
Molecular Cell
, vol.26
, pp. 753-767
-
-
Tsang, J.1
Zhu, J.2
Oudenaarden, A.3
-
32
-
-
33645472191
-
Systematic identification of microRNA functions by combining target prediction and expression profiling
-
Wang, X.W. and Wang, X.H. (2006) 'Systematic identification of microRNA functions by combining target prediction and expression profiling', Nucleic Acids Research, Vol. 34, pp.1646-1652.
-
(2006)
Nucleic Acids Research
, vol.34
, pp. 1646-1652
-
-
Wang, X.W.1
Wang, X.H.2
-
33
-
-
42949131237
-
Computational methods for microRNA target prediction
-
Watanabe, Y., Tomita, M. and Kanai, A. (2007) 'Computational methods for microRNA target prediction', Methods Enzymol., Vol. 427, pp.65-86.
-
(2007)
Methods Enzymol.
, vol.427
, pp. 65-86
-
-
Watanabe, Y.1
Tomita, M.2
Kanai, A.3
-
34
-
-
38549150275
-
MiRBase: Tools for microRNA genomics
-
Database Issue
-
Griffiths-Jones, S., Saini, H.K., van Dongen, S. and Enright, A.J. (2008) 'MiRBase: tools for microRNA genomics', NAR, Vol. 36 Database Issue, pp.D154-D158.
-
(2008)
NAR
, vol.36
-
-
Griffiths-Jones, S.1
Saini, H.K.2
Van Dongen, S.3
Enright, A.J.4
-
35
-
-
34047234690
-
Characterization and identification of microRNA core promoters in four model species
-
Zhou, X., Ruan, J., Wang, G. and Zhang, W. (2007a) 'Characterization and identification of microRNA core promoters in four model species', PLoS Comput Biology, Vol. 3, p.e37.
-
(2007)
PLoS Comput Biology
, vol.3
-
-
Zhou, X.1
Ruan, J.2
Wang, G.3
Zhang, W.4
-
36
-
-
38349138548
-
Inter- and intra-combinatorial regulation by transcription factors and microRNAs
-
Zhou, Y., Ferguson, J., Chang, J.T. and Kluger, Y. (2007b) 'Inter- and intra-combinatorial regulation by transcription factors and microRNAs', BMC Genomics, Vol. 8, p.396.
-
(2007)
BMC Genomics
, vol.8
, pp. 396
-
-
Zhou, Y.1
Ferguson, J.2
Chang, J.T.3
Kluger, Y.4
|