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Items: 14

1.
2.

Single-cell mRNA profiling reveals the hierarchical response of miRNA targets to miRNA induction.

Rzepiela AJ, Ghosh S, Breda J, Vina-Vilaseca A, Syed AP, Gruber AJ, Eschbach K, Beisel C, van Nimwegen E, Zavolan M.

Mol Syst Biol. 2018 Aug 27;14(8):e8266. doi: 10.15252/msb.20188266.

3.

miRAW: A deep learning-based approach to predict microRNA targets by analyzing whole microRNA transcripts.

Pla A, Zhong X, Rayner S.

PLoS Comput Biol. 2018 Jul 13;14(7):e1006185. doi: 10.1371/journal.pcbi.1006185. eCollection 2018 Jul.

4.

mirDIP 4.1-integrative database of human microRNA target predictions.

Tokar T, Pastrello C, Rossos AEM, Abovsky M, Hauschild AC, Tsay M, Lu R, Jurisica I.

Nucleic Acids Res. 2018 Jan 4;46(D1):D360-D370. doi: 10.1093/nar/gkx1144.

5.

CRISPR Genome Engineering for Human Pluripotent Stem Cell Research.

Chaterji S, Ahn EH, Kim DH.

Theranostics. 2017 Oct 7;7(18):4445-4469. doi: 10.7150/thno.18456. eCollection 2017. Review.

6.

Combinatorial ensemble miRNA target prediction of co-regulation networks with non-prediction data.

Davis JA, Saunders SJ, Mann M, Backofen R.

Nucleic Acids Res. 2017 Sep 6;45(15):8745-8757. doi: 10.1093/nar/gkx605.

7.

RIsearch2: suffix array-based large-scale prediction of RNA-RNA interactions and siRNA off-targets.

Alkan F, Wenzel A, Palasca O, Kerpedjiev P, Rudebeck AF, Stadler PF, Hofacker IL, Gorodkin J.

Nucleic Acids Res. 2017 May 5;45(8):e60. doi: 10.1093/nar/gkw1325.

8.

High-throughput identification of C/D box snoRNA targets with CLIP and RiboMeth-seq.

Gumienny R, Jedlinski DJ, Schmidt A, Gypas F, Martin G, Vina-Vilaseca A, Zavolan M.

Nucleic Acids Res. 2017 Mar 17;45(5):2341-2353. doi: 10.1093/nar/gkw1321.

9.

Learning to Predict miRNA-mRNA Interactions from AGO CLIP Sequencing and CLASH Data.

Lu Y, Leslie CS.

PLoS Comput Biol. 2016 Jul 20;12(7):e1005026. doi: 10.1371/journal.pcbi.1005026. eCollection 2016 Jul.

10.

Improving microRNA target prediction with gene expression profiles.

Ovando-Vázquez C, Lepe-Soltero D, Abreu-Goodger C.

BMC Genomics. 2016 May 17;17:364. doi: 10.1186/s12864-016-2695-1.

11.

Improving microRNA target prediction by modeling with unambiguously identified microRNA-target pairs from CLIP-ligation studies.

Wang X.

Bioinformatics. 2016 May 1;32(9):1316-22. doi: 10.1093/bioinformatics/btw002. Epub 2016 Jan 6.

12.

MicroRNA target prediction using thermodynamic and sequence curves.

Ghoshal A, Shankar R, Bagchi S, Grama A, Chaterji S.

BMC Genomics. 2015 Nov 25;16:999. doi: 10.1186/s12864-015-1933-2. Erratum in: BMC Genomics. 2016;17:216.

13.

Villain of Molecular Biology: Why are we not reproducible in research?

Bhardwaj V.

F1000Res. 2015 Jul 30;4:438. doi: 10.12688/f1000research.6854.1. eCollection 2015.

14.

Predicting effective microRNA target sites in mammalian mRNAs.

Agarwal V, Bell GW, Nam JW, Bartel DP.

Elife. 2015 Aug 12;4. doi: 10.7554/eLife.05005.

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