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Automated analysis of small RNA datasets with RAPID.

Karunanithi S, Simon M, Schulz MH.

PeerJ. 2019 Apr 10;7:e6710. doi: 10.7717/peerj.6710. eCollection 2019.


Human Novel MicroRNA Seq-915_x4024 in Keratinocytes Contributes to Skin Regeneration by Suppressing Scar Formation.

Zhao F, Lang H, Wang Z, Zhang T, Zhang D, Wang R, Lin X, Liu X, Shi P, Pang X.

Mol Ther Nucleic Acids. 2019 Mar 1;14:410-423. doi: 10.1016/j.omtn.2018.12.016. Epub 2019 Jan 10.


miRNomes involved in imparting thermotolerance to crop plants.

Gahlaut V, Baranwal VK, Khurana P.

3 Biotech. 2018 Dec;8(12):497. doi: 10.1007/s13205-018-1521-7. Epub 2018 Nov 24. Review.


The evolutionary dynamics of microRNAs in domestic mammals.

Penso-Dolfin L, Moxon S, Haerty W, Di Palma F.

Sci Rep. 2018 Nov 19;8(1):17050. doi: 10.1038/s41598-018-34243-8.


QsRNA-seq: a method for high-throughput profiling and quantifying small RNAs.

Fishman A, Light D, Lamm AT.

Genome Biol. 2018 Aug 14;19(1):113. doi: 10.1186/s13059-018-1495-0.


miR-MaGiC improves quantification accuracy for small RNA-seq.

Russell PH, Vestal B, Shi W, Rudra PD, Dowell R, Radcliffe R, Saba L, Kechris K.

BMC Res Notes. 2018 May 15;11(1):296. doi: 10.1186/s13104-018-3418-2.


miR-126-5p by direct targeting of JNK-interacting protein-2 (JIP-2) plays a key role in Theileria-infected macrophage virulence.

Haidar M, Rchiad Z, Ansari HR, Ben-Rached F, Tajeri S, Latre De Late P, Langsley G, Pain A.

PLoS Pathog. 2018 Mar 23;14(3):e1006942. doi: 10.1371/journal.ppat.1006942. eCollection 2018 Mar.


Oasis 2: improved online analysis of small RNA-seq data.

Rahman RU, Gautam A, Bethune J, Sattar A, Fiosins M, Magruder DS, Capece V, Shomroni O, Bonn S.

BMC Bioinformatics. 2018 Feb 14;19(1):54. doi: 10.1186/s12859-018-2047-z.


Genome-wide profiling of the PIWI-interacting RNA-mRNA regulatory networks in epithelial ovarian cancers.

Singh G, Roy J, Rout P, Mallick B.

PLoS One. 2018 Jan 10;13(1):e0190485. doi: 10.1371/journal.pone.0190485. eCollection 2018.


LncRNA Structural Characteristics in Epigenetic Regulation.

Wang C, Wang L, Ding Y, Lu X, Zhang G, Yang J, Zheng H, Wang H, Jiang Y, Xu L.

Int J Mol Sci. 2017 Dec 8;18(12). pii: E2659. doi: 10.3390/ijms18122659. Review.


Mirnovo: genome-free prediction of microRNAs from small RNA sequencing data and single-cells using decision forests.

Vitsios DM, Kentepozidou E, Quintais L, Benito-Gutiérrez E, van Dongen S, Davis MP, Enright AJ.

Nucleic Acids Res. 2017 Dec 1;45(21):e177. doi: 10.1093/nar/gkx836.


Circulating microRNAs and Bioinformatics Tools to Discover Novel Diagnostic Biomarkers of Pediatric Diseases.

Baldassarre A, Felli C, Prantera G, Masotti A.

Genes (Basel). 2017 Sep 19;8(9). pii: E234. doi: 10.3390/genes8090234. Review.


Association of microRNAs with Argonaute proteins in the malaria mosquito Anopheles gambiae after blood ingestion.

Fu X, Dimopoulos G, Zhu J.

Sci Rep. 2017 Jul 26;7(1):6493. doi: 10.1038/s41598-017-07013-1.


QuickMIRSeq: a pipeline for quick and accurate quantification of both known miRNAs and isomiRs by jointly processing multiple samples from microRNA sequencing.

Zhao S, Gordon W, Du S, Zhang C, He W, Xi L, Mathur S, Agostino M, Paradis T, von Schack D, Vincent M, Zhang B.

BMC Bioinformatics. 2017 Mar 20;18(1):180. doi: 10.1186/s12859-017-1601-4.


CPSS 2.0: a computational platform update for the analysis of small RNA sequencing data.

Wan C, Gao J, Zhang H, Jiang X, Zang Q, Ban R, Zhang Y, Shi Q.

Bioinformatics. 2017 Oct 15;33(20):3289-3291. doi: 10.1093/bioinformatics/btx066.


MicroRNAs As Potential Targets for Abiotic Stress Tolerance in Plants.

Shriram V, Kumar V, Devarumath RM, Khare TS, Wani SH.

Front Plant Sci. 2016 Jun 14;7:817. doi: 10.3389/fpls.2016.00817. eCollection 2016. Review.


Evaluation of microRNA alignment techniques.

Ziemann M, Kaspi A, El-Osta A.

RNA. 2016 Aug;22(8):1120-38. doi: 10.1261/rna.055509.115. Epub 2016 Jun 9.


miARma-Seq: a comprehensive tool for miRNA, mRNA and circRNA analysis.

Andrés-León E, Núñez-Torres R, Rojas AM.

Sci Rep. 2016 May 11;6:25749. doi: 10.1038/srep25749. Erratum in: Sci Rep. 2018 Jan 08;8:46928.


A survey of best practices for RNA-seq data analysis.

Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A, Szcześniak MW, Gaffney DJ, Elo LL, Zhang X, Mortazavi A.

Genome Biol. 2016 Jan 26;17:13. doi: 10.1186/s13059-016-0881-8. Review. Erratum in: Genome Biol. 2016;17(1):181.


Structure Prediction: New Insights into Decrypting Long Noncoding RNAs.

Yan K, Arfat Y, Li D, Zhao F, Chen Z, Yin C, Sun Y, Hu L, Yang T, Qian A.

Int J Mol Sci. 2016 Jan 21;17(1). pii: E132. doi: 10.3390/ijms17010132. Review.

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