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Context-specific microRNA analysis: identification of functional microRNAs and their mRNA targets.

Bossel Ben-Moshe N, Avraham R, Kedmi M, Zeisel A, Yitzhaky A, Yarden Y, Domany E.

Nucleic Acids Res. 2012 Nov;40(21):10614-27. doi: 10.1093/nar/gks841. Epub 2012 Sep 12.


Transcriptome dynamics of the microRNA inhibition response.

Wen J, Leucci E, Vendramin R, Kauppinen S, Lund AH, Krogh A, Parker BJ.

Nucleic Acids Res. 2015 Jun 18. pii: gkv603. [Epub ahead of print]


ToppMiR: ranking microRNAs and their mRNA targets based on biological functions and context.

Wu C, Bardes EE, Jegga AG, Aronow BJ.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W107-13. doi: 10.1093/nar/gku409. Epub 2014 May 14.


The co-inertia approach in identification of specific microRNA in early and advanced atherosclerosis plaque.

Jovanović I, Zivković M, Jovanović J, Djurić T, Stanković A.

Med Hypotheses. 2014 Jul;83(1):11-5. doi: 10.1016/j.mehy.2014.04.019. Epub 2014 Apr 23.


miMsg: a target enrichment algorithm for predicted miR-mRNA interactions based on relative ranking of matched expression data.

Rijlaarsdam MA, Rijlaarsdam DJ, Gillis AJ, Dorssers LC, Looijenga LH.

Bioinformatics. 2013 Jul 1;29(13):1638-46. doi: 10.1093/bioinformatics/btt246. Epub 2013 May 1.


Similarity-based methods for potential human microRNA-disease association prediction.

Chen H, Zhang Z.

BMC Med Genomics. 2013 Apr 9;6:12. doi: 10.1186/1755-8794-6-12.


Isolation and identification of cell-specific microRNAs targeting a messenger RNA using a biotinylated anti-sense oligonucleotide capture affinity technique.

Hassan T, Smith SG, Gaughan K, Oglesby IK, O'Neill S, McElvaney NG, Greene CM.

Nucleic Acids Res. 2013 Apr 1;41(6):e71. doi: 10.1093/nar/gks1466. Epub 2013 Jan 15.


Heart structure-specific transcriptomic atlas reveals conserved microRNA-mRNA interactions.

Vacchi-Suzzi C, Hahne F, Scheubel P, Marcellin M, Dubost V, Westphal M, Boeglen C, Büchmann-Møller S, Cheung MS, Cordier A, De Benedetto C, Deurinck M, Frei M, Moulin P, Oakeley E, Grenet O, Grevot A, Stull R, Theil D, Moggs JG, Marrer E, Couttet P.

PLoS One. 2013;8(1):e52442. doi: 10.1371/journal.pone.0052442. Epub 2013 Jan 2.


Inferring microRNA regulation of mRNA with partially ordered samples of paired expression data and exogenous prediction algorithms.

Godsey B, Heiser D, Civin C.

PLoS One. 2012;7(12):e51480. doi: 10.1371/journal.pone.0051480. Epub 2012 Dec 19.


MiRGator v3.0: a microRNA portal for deep sequencing, expression profiling and mRNA targeting.

Cho S, Jang I, Jun Y, Yoon S, Ko M, Kwon Y, Choi I, Chang H, Ryu D, Lee B, Kim VN, Kim W, Lee S.

Nucleic Acids Res. 2013 Jan;41(Database issue):D252-7. doi: 10.1093/nar/gks1168. Epub 2012 Nov 27.


Integrated miRNA, mRNA and protein expression analysis reveals the role of post-transcriptional regulation in controlling CHO cell growth rate.

Clarke C, Henry M, Doolan P, Kelly S, Aherne S, Sanchez N, Kelly P, Kinsella P, Breen L, Madden SF, Zhang L, Leonard M, Clynes M, Meleady P, Barron N.

BMC Genomics. 2012 Nov 21;13:656. doi: 10.1186/1471-2164-13-656.


OrbId: Origin-based identification of microRNA targets.

Filshtein TJ, Mackenzie CO, Dale MD, Dela-Cruz PS, Ernst DM, Frankenberger EA, He C, Heath KL, Jones AS, Jones DK, King ER, Maher MB, Mitchell TJ, Morgan RR, Sirobhushanam S, Halkyard SD, Tiwari KB, Rubin DA, Borchert GM, Larson ED.

Mob Genet Elements. 2012 Jul 1;2(4):184-192.


Alternative mRNA fates identified in microRNA-associated transcriptome analysis.

Carroll AP, Tran N, Tooney PA, Cairns MJ.

BMC Genomics. 2012 Oct 19;13:561. doi: 10.1186/1471-2164-13-561.


MicroRNAs and cardiac sarcoplasmic reticulum calcium ATPase-2 in human myocardial infarction: expression and bioinformatic analysis.

Boštjančič E, Zidar N, Glavač D.

BMC Genomics. 2012 Oct 15;13:552. doi: 10.1186/1471-2164-13-552.


Toward a combinatorial nature of microRNA regulation in human cells.

Balaga O, Friedman Y, Linial M.

Nucleic Acids Res. 2012 Oct;40(19):9404-16. doi: 10.1093/nar/gks759. Epub 2012 Aug 16.


Antagonism pattern detection between microRNA and target expression in Ewing's sarcoma.

Martignetti L, Laud-Duval K, Tirode F, Pierron G, Reynaud S, Barillot E, Delattre O, Zinovyev A.

PLoS One. 2012;7(7):e41770. doi: 10.1371/journal.pone.0041770. Epub 2012 Jul 25.


Differential association of microRNAs with polysomes reflects distinct strengths of interactions with their mRNA targets.

Molotski N, Soen Y.

RNA. 2012 Sep;18(9):1612-23. doi: 10.1261/rna.033142.112. Epub 2012 Jul 26.


Identification of new microRNA-regulated genes by conserved targeting in plant species.

Chorostecki U, Crosa VA, Lodeyro AF, Bologna NG, Martin AP, Carrillo N, Schommer C, Palatnik JF.

Nucleic Acids Res. 2012 Oct;40(18):8893-904. doi: 10.1093/nar/gks625. Epub 2012 Jul 5.


MiR-137 targets estrogen-related receptor alpha and impairs the proliferative and migratory capacity of breast cancer cells.

Zhao Y, Li Y, Lou G, Zhao L, Xu Z, Zhang Y, He F.

PLoS One. 2012;7(6):e39102. doi: 10.1371/journal.pone.0039102. Epub 2012 Jun 18.


PsRobot: a web-based plant small RNA meta-analysis toolbox.

Wu HJ, Ma YK, Chen T, Wang M, Wang XJ.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W22-8. doi: 10.1093/nar/gks554. Epub 2012 Jun 12.

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