메뉴 건너뛰기




Volumn 8, Issue 3-4, 2012, Pages 171-191

Derivative scores from site accessibility and ranking of miRNA target predictions

Author keywords

Microrna; Multi objective optimisation; Pareto front; Rna secondary structure; Target prediction

Indexed keywords


EID: 84866244528     PISSN: 17445485     EISSN: 17445493     Source Type: Journal    
DOI: 10.1504/IJBRA.2012.048966     Document Type: Article
Times cited : (3)

References (44)
  • 1
    • 79952306458 scopus 로고    scopus 로고
    • Uncovering a tumor suppressor for triple-negative breast cancer
    • Albeck, J.G. and Brugge, J.S. (2011) 'Uncovering a tumor suppressor for triple-negative breast cancer', Cell, Vol. 144, pp.638-640.
    • (2011) Cell , vol.144 , pp. 638-640
    • Albeck, J.G.1    Brugge, J.S.2
  • 3
    • 57849114288 scopus 로고    scopus 로고
    • Computational identification of novel microRNA homologs in the chimpanzee genome
    • DOI 10.1016/j.compbiolchem.2008.07.024, PII S1476927108001035
    • Baev, V., Daskalova, E. and Minkov, I. (2009) 'Computational identification of novel microRNA homologs in the chimpanzee genome', Computational Biology and Chemistry, Vol. 33, pp.62-70. (Pubitemid 50254552)
    • (2009) Computational Biology and Chemistry , vol.33 , Issue.1 , pp. 62-70
    • Baev, V.1    Daskalova, E.2    Minkov, I.3
  • 4
    • 77955963884 scopus 로고    scopus 로고
    • Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites
    • Betel, D., Koppal, A., Agius, P., Sander, C. and Leslie, C. (2010) 'Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites', Genome Biology, Vol. 11, p.R90.
    • (2010) Genome Biology , vol.11
    • Betel, D.1    Koppal, A.2    Agius, P.3    Sander, C.4    Leslie, C.5
  • 7
    • 60149095444 scopus 로고    scopus 로고
    • Most mammalian mRNAs are conserved targets of microRNAs
    • Friedman, R.C., Farh, K.K., Burge, C.B. and Bartel, D.P. (2009) 'Most mammalian mRNAs are conserved targets of microRNAs', Genome Research, Vol. 9, pp.92-105.
    • (2009) Genome Research , vol.9 , pp. 92-105
    • Friedman, R.C.1    Farh, K.K.2    Burge, C.B.3    Bartel, D.P.4
  • 10
    • 34250805982 scopus 로고    scopus 로고
    • MicroRNA Targeting Specificity in Mammals: Determinants beyond Seed Pairing
    • DOI 10.1016/j.molcel.2007.06.017, PII S1097276507004078
    • Grimson, A., Farh, K.K., Johnston, W.K., Garrett-Engele, P., Lim, L.P. and Bartel, D.P. (2007) 'MicroRNA targeting specificity in mammals: determinants beyond seed pairing', Molecular Cell, Vol. 27, pp.91-105. (Pubitemid 46991392)
    • (2007) Molecular Cell , vol.27 , Issue.1 , pp. 91-105
    • Grimson, A.1    Farh, K.K.-H.2    Johnston, W.K.3    Garrett-Engele, P.4    Lim, L.P.5    Bartel, D.P.6
  • 12
    • 77955101812 scopus 로고    scopus 로고
    • Computational methods to identify miRNA targets
    • Hammell, M. (2010) 'Computational methods to identify miRNA targets', Seminars in Cell & Developmental Biology, Vol. 21, pp.738-744.
    • (2010) Seminars in Cell & Developmental Biology , vol.21 , pp. 738-744
    • Hammell, M.1
  • 13
    • 50849141708 scopus 로고    scopus 로고
    • MirWIP: MicroRNA target prediction based on microRNA-containing 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 microRNA-containing ribonucleoprotein-enriched transcripts', Nature Methods, Vol. 5, pp.813-819.
    • (2008) Nature Methods , 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
  • 14
    • 1542318824 scopus 로고    scopus 로고
    • Multicriteria gene screening for analysis of differential expression with DNA microarrays
    • Hero, A.O., Fleury, G. and Cerbourg, S. (2004) 'Multicriteria gene screening for analysis of differential expression with DNA microarrays', EURASIP Journal on Applied Signal Processing, Vol. 1, pp.43-52.
    • (2004) EURASIP Journal on Applied Signal Processing , vol.1 , pp. 43-52
    • Hero, A.O.1    Fleury, G.2    Cerbourg, S.3
  • 15
    • 34447288056 scopus 로고    scopus 로고
    • Bayesian inference of microRNA targets from sequence and expression data
    • DOI 10.1089/cmb.2007.R002
    • Huang, J.C., Morris, Q.D. and Frey, B.J. (2007) 'Bayesian inference of microRNA targets from sequence and expression data', Journal of Computational Biology, Vol. 14, pp.550-563. (Pubitemid 47047813)
    • (2007) Journal of Computational Biology , vol.14 , Issue.5 , pp. 550-563
    • Huang, J.C.1    Morris, Q.D.2    Frey, B.J.3
  • 17
    • 34748821761 scopus 로고    scopus 로고
    • The role of site accessibility in microRNA target recognition
    • Kertesz, M., Iovino, N., Unnerstall, U., Gaul, U. and Segal, E. (2007) 'The role of site accessibility in microRNA target recognition', Nature Genetics, Vol. 39, pp.1278-1248.
    • (2007) Nature Genetics , vol.39 , pp. 1248-1278
    • Kertesz, M.1    Iovino, N.2    Unnerstall, U.3    Gaul, U.4    Segal, E.5
  • 18
    • 33749645474 scopus 로고    scopus 로고
    • MiTarget: MicroRNA target-gene prediction using a support vector machine
    • Kim, S.K., Nam, J.W., Rhee, J.K., Lee, W.J. and Zhang, B.T. (2006) 'miTarget: microRNA target-gene prediction using a Support Vector Machine', BMC Bioinformatics, Vol. 7, pp.411.
    • (2006) BMC Bioinformatics , vol.7 , pp. 411
    • Kim, S.K.1    Nam, J.W.2    Rhee, J.K.3    Lee, W.J.4    Zhang, B.T.5
  • 21
    • 33747849920 scopus 로고    scopus 로고
    • RNAhybrid: MicroRNA target prediction easy, fast and flexible
    • Krüger, J. and Rehmsmeier, M. (2006) 'RNAhybrid: microRNA target prediction easy, fast and flexible', Nucleic Acids Research, Vol. 34, pp.451-454.
    • (2006) Nucleic Acids Research , vol.34 , pp. 451-454
    • Krüger, J.1    Rehmsmeier, M.2
  • 23
    • 0346094457 scopus 로고    scopus 로고
    • Prediction of mammalian microRNA targets
    • DOI 10.1016/S0092-8674(03)01018-3
    • Lewis, B.P., Shih, I.H., Jones-Rhoades, M.W., Bartel, D.P. and Burge, C.B. (2003) 'Prediction of mammalian microRNA targets', Cell, Vol. 115, pp.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
  • 24
    • 40549089550 scopus 로고    scopus 로고
    • Analysis of microRNA-target interactions by a target structure hybridization model
    • Long, D., Chan, C.Y. and Ding, Y. (2008) 'Analysis of microRNA-target interactions by a target structure hybridization model', Pacific Symposium on Biocomputing, Vol. 13, pp.64-74.
    • (2008) Pacific Symposium on Biocomputing , vol.13 , pp. 64-74
    • Long, D.1    Chan, C.Y.2    Ding, Y.3
  • 26
    • 34547212309 scopus 로고    scopus 로고
    • The MicroRNA miR-124 Promotes Neuronal Differentiation by Triggering Brain-Specific Alternative Pre-mRNA Splicing
    • DOI 10.1016/j.molcel.2007.07.015, PII S1097276507004881
    • A.Z.M. Dayem Ullah et al. Makeyev, E.V., Zhang, J.W., Carrasco, M.A. and Maniatis, T. (2007) 'The microRNA miR-124 promotes neuronal differentiation by triggering brain-specific alternative pre-mRNA splicing', Molecular Cell, Vol. 27, pp.435-448. (Pubitemid 47126944)
    • (2007) Molecular Cell , vol.27 , Issue.3 , pp. 435-448
    • Makeyev, E.V.1    Zhang, J.2    Carrasco, M.A.3    Maniatis, T.4
  • 28
    • 33846053464 scopus 로고    scopus 로고
    • MiRGen: A database for the study of animal microRNA genomic organization and function
    • DOI 10.1093/nar/gkl904
    • Megraw, M., Sethupathy, P., Corda, B. and Hatzigeorgiou, A.G. (2006) 'miRGen: a database for the study of animal microRNA genomic organization and function', Nucleic Acids Research, Vol. 35, pp.D149-D155. (Pubitemid 46056188)
    • (2007) Nucleic Acids Research , vol.35 , Issue.SUPPL. 1
    • Megraw, M.1    Sethupathy, P.2    Corda, B.3    Hatzigeorgiou, A.G.4
  • 29
    • 33748587841 scopus 로고    scopus 로고
    • A pattern-based method for the identification of microrna binding sites and their corresponding heteroduplexes
    • DOI 10.1016/j.cell.2006.07.031, PII S0092867406010993
    • Miranda, K.C., Huynh, T., Tay, Y., Ang, Y.S., Tam, W.L., Thomson, A.M., Lim, B. and Rigosos, I. (2006) 'A pattern-based method for the identification of microRNA binding sites and their corresponding heteroduplexes', Cell, Vol. 126, pp.1203-1217. (Pubitemid 44380294)
    • (2006) Cell , vol.126 , Issue.6 , pp. 1203-1217
    • Miranda, K.C.1    Huynh, T.2    Tay, Y.3    Ang, Y.-S.4    Tam, W.-L.5    Thomson, A.M.6    Lim, B.7    Rigoutsos, I.8
  • 30
    • 43449090367 scopus 로고    scopus 로고
    • MicroRNA-10a Binds the 5'UTR of Ribosomal Protein mRNAs and Enhances Their Translation
    • DOI 10.1016/j.molcel.2008.05.001, PII S1097276508003286
    • ørom, U.A, Nielsen, F.C. and Lund, A.H. (2008) 'MicroRNA-10a binds the 5'UTR of ribosomal protein mRNAs and enhances their translation', Molecular Cell, Vol. 30, pp.460-471. (Pubitemid 351672378)
    • (2008) Molecular Cell , vol.30 , Issue.4 , pp. 460-471
    • Orom, U.A.1    Nielsen, F.C.2    Lund, A.H.3
  • 32
    • 66749109861 scopus 로고    scopus 로고
    • Transcriptome-wide prediction of miRNA targets in human and mouse using FASTH
    • Ragan, C., Cloonan, N., Grimmond, S.M., Zuker, M. and Ragan, M.A. (2009) 'Transcriptome-wide prediction of miRNA targets in human and mouse using FASTH'. PLoS One, Vol. 4, pp.e5745.
    • (2009) PLoS One , vol.4
    • Ragan, C.1    Cloonan, N.2    Grimmond, S.M.3    Zuker, M.4    Ragan, M.A.5
  • 33
    • 79952478894 scopus 로고    scopus 로고
    • Quantitative prediction of miRNA-mRNA interaction based on equilibrium concentrations
    • Ragan, C., Zuker, M. and Ragan, M.A. (2011) 'Quantitative prediction of miRNA-mRNA interaction based on equilibrium concentrations'. PLoS Computational Biology, Vol. 7, pp.e1001090.
    • (2011) PLoS Computational Biology , vol.7
    • Ragan, C.1    Zuker, M.2    Ragan, M.A.3
  • 34
    • 4644237189 scopus 로고    scopus 로고
    • Fast and effective prediction of microRNA/target duplexes
    • DOI 10.1261/rna.5248604
    • Rehmsmeier, M., Steffen, P., Hochsmann, M. and Giegerich, R. (2004) 'Fast and effective prediction of microRNA/target duplexes', RNA, Vol. 10, pp.1507-1517. (Pubitemid 39288185)
    • (2004) RNA , vol.10 , Issue.10 , pp. 1507-1517
    • Rehmsmeier, M.1    Steffen, P.2    Hochsmann, M.3    Giegerich, R.4
  • 36
    • 77953879493 scopus 로고    scopus 로고
    • Multi-objective tag SNPs selection using evolutionary algorithms
    • Ting, C.K., Lin, W.T. and Huang, Y.T. (2010) 'Multi-objective tag SNPs selection using evolutionary algorithms', Bioinformatics, Vol. 26, pp.1446-1452.
    • (2010) Bioinformatics , vol.26 , pp. 1446-1452
    • Ting, C.K.1    Lin, W.T.2    Huang, Y.T.3
  • 38
    • 38849145861 scopus 로고    scopus 로고
    • Prediction of both conserved and nonconserved microRNA targets in animals
    • DOI 10.1093/bioinformatics/btm595
    • Wang, X. and El Naqa, I.M. (2008) 'Prediction of both conserved and nonconserved microRNA targets in animals', Bioinformatics, Vol. 24, pp.325-332. (Pubitemid 351189007)
    • (2008) Bioinformatics , vol.24 , Issue.3 , pp. 325-332
    • Wang, X.1    El Naqa, I.M.2
  • 39
    • 67650725491 scopus 로고    scopus 로고
    • Increasing MicroRNA target prediction confidence by the relative R2 method
    • Wang, H.Y. and Li, W.H. (2009) 'Increasing MicroRNA target prediction confidence by the relative R2 method', Journal of Theoretical Biology, Vol. 259, pp.793-798.
    • (2009) Journal of Theoretical Biology , vol.259 , pp. 793-798
    • Wang, H.Y.1    Li, W.H.2
  • 40
    • 58149186499 scopus 로고    scopus 로고
    • MiRecords: An integrated resource for microRNA-target interactions
    • Xiao, F., Zuo, Z., Cai, G., Kang, S., Gao, X. and Li, T. (2009) 'miRecords: an integrated resource for microRNA-target interactions', Nucleic Acids Research, Vol. 37, pp.105-110.
    • (2009) Nucleic Acids Research , vol.37 , pp. 105-110
    • Xiao, F.1    Zuo, Z.2    Cai, G.3    Kang, S.4    Gao, X.5    Li, T.6
  • 41
    • 67349149082 scopus 로고    scopus 로고
    • MicroRNA-145 regulates OCT4, SOX2, and KLF4 and represses pluripotency in human embryonic stem cells
    • Xu, N., Papagiannakopoulos, T., Pan, G., Thomson, J.A. and Kosik, K.S. (2009) 'MicroRNA-145 regulates OCT4, SOX2, and KLF4 and represses pluripotency in human embryonic stem cells', Cell, Vol. 137, pp.647-658.
    • (2009) Cell , vol.137 , pp. 647-658
    • Xu, N.1    Papagiannakopoulos, T.2    Pan, G.3    Thomson, J.A.4    Kosik, K.S.5
  • 42
    • 45849107663 scopus 로고    scopus 로고
    • The effect of central loops in miRNA:MRE duplexes on the efficiency of miRNA-mediated gene regulation
    • Ye, W., Lv, Q., Wong, C.K., Hu, S., Fu, C., Hua, Z., Cai, G., Li, G., Yang, B.B. and Zhang, Y. (2008) 'The effect of central loops in miRNA:MRE duplexes on the efficiency of miRNA-mediated gene regulation', PLoS One, Vol. 3, pp.e1719.
    • (2008) PLoS One , vol.3
    • Ye, W.1    Lv, Q.2    Wong, C.K.3    Hu, S.4    Fu, C.5    Hua, Z.6    Cai, G.7    Li, G.8    Yang, B.B.9    Zhang, Y.10
  • 43
    • 36448982458 scopus 로고    scopus 로고
    • Naïve Bayes for microRNA target predictions - Machine learning for microRNA targets
    • DOI 10.1093/bioinformatics/btm484
    • Yousef, M., Jung, S., Kossenkov, A.V., Showe, L.C. and Showe, M.K. (2007) 'Naïve Bayes for microRNA target predictions - machine learning for microRNA targets', Bioinformatics, Vol. 23, pp.2987-2992. (Pubitemid 350162862)
    • (2007) Bioinformatics , vol.23 , Issue.22 , pp. 2987-2992
    • Yousef, M.1    Jung, S.2    Kossenkov, A.V.3    Showe, L.C.4    Showe, M.K.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.