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MicroRNA transcription start site prediction with multi-objective feature selection.

Bhattacharyya M, Feuerbach L, Bhadra T, Lengauer T, Bandyopadhyay S.

Stat Appl Genet Mol Biol. 2012 Jan 6;11(1):Article 6. doi: 10.2202/1544-6115.1743.


Identifying transcriptional start sites of human microRNAs based on high-throughput sequencing data.

Chien CH, Sun YM, Chang WC, Chiang-Hsieh PY, Lee TY, Tsai WC, Horng JT, Tsou AP, Huang HD.

Nucleic Acids Res. 2011 Nov;39(21):9345-56. doi: 10.1093/nar/gkr604. Epub 2011 Aug 5.


Identification and analysis of the proximal promoters of microRNA genes in Arabidopsis.

Zhao X, Zhang H, Li L.

Genomics. 2013 Mar;101(3):187-94. doi: 10.1016/j.ygeno.2012.12.004. Epub 2013 Jan 4.


Genomic analysis of rice microRNA promoters and clusters.

Cui X, Xu SM, Mu DS, Yang ZM.

Gene. 2009 Feb 15;431(1-2):61-6. doi: 10.1016/j.gene.2008.11.016. Epub 2008 Nov 24.


Features of mammalian microRNA promoters emerge from polymerase II chromatin immunoprecipitation data.

Corcoran DL, Pandit KV, Gordon B, Bhattacharjee A, Kaminski N, Benos PV.

PLoS One. 2009;4(4):e5279. doi: 10.1371/journal.pone.0005279. Epub 2009 Apr 23.


MicroRNA genes are transcribed by RNA polymerase II.

Lee Y, Kim M, Han J, Yeom KH, Lee S, Baek SH, Kim VN.

EMBO J. 2004 Oct 13;23(20):4051-60. Epub 2004 Sep 16.


MultiMiTar: a novel multi objective optimization based miRNA-target prediction method.

Mitra R, Bandyopadhyay S.

PLoS One. 2011;6(9):e24583. doi: 10.1371/journal.pone.0024583. Epub 2011 Sep 15.


microTSS: accurate microRNA transcription start site identification reveals a significant number of divergent pri-miRNAs.

Georgakilas G, Vlachos IS, Paraskevopoulou MD, Yang P, Zhang Y, Economides AN, Hatzigeorgiou AG.

Nat Commun. 2014 Dec 10;5:5700. doi: 10.1038/ncomms6700.


Prediction of plant pre-microRNAs and their microRNAs in genome-scale sequences using structure-sequence features and support vector machine.

Meng J, Liu D, Sun C, Luan Y.

BMC Bioinformatics. 2014 Dec 30;15:423. doi: 10.1186/s12859-014-0423-x.


miRT: a database of validated transcription start sites of human microRNAs.

Bhattacharyya M, Das M, Bandyopadhyay S.

Genomics Proteomics Bioinformatics. 2012 Oct;10(5):310-6. doi: 10.1016/j.gpb.2012.08.005. Epub 2012 Sep 29.


Genomic analysis of silkworm microRNA promoters and clusters.

Huang Y, Shen XJ, Zou Q, Huang JS, Tang SM.

Mol Biol (Mosk). 2011 Mar-Apr;45(2):225-30.


RNA polymerase II binding patterns reveal genomic regions involved in microRNA gene regulation.

Wang G, Wang Y, Shen C, Huang YW, Huang K, Huang TH, Nephew KP, Li L, Liu Y.

PLoS One. 2010 Nov 2;5(11):e13798. doi: 10.1371/journal.pone.0013798.


Genomic features and computational identification of human microRNAs under long-range developmental regulation.

Sheng Y, Previti C.

BMC Genomics. 2011 May 27;12:270. doi: 10.1186/1471-2164-12-270.


Identifying cell-specific microRNA transcriptional start sites.

Hua X, Chen L, Wang J, Li J, Wingender E.

Bioinformatics. 2016 Aug 15;32(16):2403-10. doi: 10.1093/bioinformatics/btw171. Epub 2016 Apr 19.


GPMiner: an integrated system for mining combinatorial cis-regulatory elements in mammalian gene group.

Lee TY, Chang WC, Hsu JB, Chang TH, Shien DM.

BMC Genomics. 2012;13 Suppl 1:S3. doi: 10.1186/1471-2164-13-S1-S3. Epub 2012 Jan 17.


Predicting human microRNA precursors based on an optimized feature subset generated by GA-SVM.

Wang Y, Chen X, Jiang W, Li L, Li W, Yang L, Liao M, Lian B, Lv Y, Wang S, Wang S, Li X.

Genomics. 2011 Aug;98(2):73-8. doi: 10.1016/j.ygeno.2011.04.011. Epub 2011 May 14.


miTarget: microRNA target gene prediction using a support vector machine.

Kim SK, Nam JW, Rhee JK, Lee WJ, Zhang BT.

BMC Bioinformatics. 2006 Sep 18;7:411.


Using a kernel density estimation based classifier to predict species-specific microRNA precursors.

Chang DT, Wang CC, Chen JW.

BMC Bioinformatics. 2008 Dec 12;9 Suppl 12:S2. doi: 10.1186/1471-2105-9-S12-S2.


DNA methylation patterns facilitate the identification of microRNA transcription start sites: a brain-specific study.

Bhadra T, Bhattacharyya M, Feuerbach L, Lengauer T, Bandyopadhyay S.

PLoS One. 2013 Jun 24;8(6):e66722. doi: 10.1371/journal.pone.0066722. Print 2013. Erratum in: PLoS One. 2013;8(12). doi:10.1371/annotation/dd8f4acc-3859-46e2-9136-20b6b4d08d21.


TargetMiner: microRNA target prediction with systematic identification of tissue-specific negative examples.

Bandyopadhyay S, Mitra R.

Bioinformatics. 2009 Oct 15;25(20):2625-31. doi: 10.1093/bioinformatics/btp503. Epub 2009 Aug 19.


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