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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.


s ·nr: a visual analytics framework for contextual analyses of private and public RNA-seq data.

Klemm P, Frommolt P, Kornfeld JW.

BMC Genomics. 2019 Jan 24;20(1):85. doi: 10.1186/s12864-018-5396-0.


Small RNA sequencing of sessile serrated polyps identifies microRNA profile associated with colon cancer.

Kanth P, Hazel MW, Boucher KM, Yang Z, Wang L, Bronner MP, Boylan KE, Burt RW, Westover M, Neklason DW, Delker DA.

Genes Chromosomes Cancer. 2019 Jan;58(1):23-33. doi: 10.1002/gcc.22686. Epub 2018 Nov 18.


Bioinformatic analysis of endogenous and exogenous small RNAs on lipoproteins.

Allen RM, Zhao S, Ramirez Solano MA, Zhu W, Michell DL, Wang Y, Shyr Y, Sethupathy P, Linton MF, Graf GA, Sheng Q, Vickers KC.

J Extracell Vesicles. 2018 Aug 13;7(1):1506198. doi: 10.1080/20013078.2018.1506198. eCollection 2018.


Upregulation of miR-370 and miR-543 is associated with reduced expression of heat shock protein 40 in spinocerebellar ataxia type 3.

Evert BO, Nalavade R, Jungverdorben J, Matthes F, Weber S, Rajput A, Bonn S, Brüstle O, Peitz M, Krauß S.

PLoS One. 2018 Aug 7;13(8):e0201794. doi: 10.1371/journal.pone.0201794. eCollection 2018.


Expanding the miRNA Transcriptome of Human Kidney and Renal Cell Carcinoma.

Sage AP, Minatel BC, Marshall EA, Martinez VD, Stewart GL, Enfield KSS, Lam WL.

Int J Genomics. 2018 Jul 3;2018:6972397. doi: 10.1155/2018/6972397. eCollection 2018.


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.


MicroRNA expression profiles of bovine monocyte-derived macrophages infected in vitro with two strains of Streptococcus agalactiae.

Lewandowska-Sabat AM, Hansen SF, Solberg TR, Østerås O, Heringstad B, Boysen P, Olsaker I.

BMC Genomics. 2018 Apr 10;19(1):241. doi: 10.1186/s12864-018-4591-3.


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.


Small RNA Sequencing of Sporadic Amyotrophic Lateral Sclerosis Cerebrospinal Fluid Reveals Differentially Expressed miRNAs Related to Neural and Glial Activity.

Waller R, Wyles M, Heath PR, Kazoka M, Wollff H, Shaw PJ, Kirby J.

Front Neurosci. 2018 Jan 9;11:731. doi: 10.3389/fnins.2017.00731. eCollection 2017.


Regional and subtype-dependent miRNA signatures in sporadic Creutzfeldt-Jakob disease are accompanied by alterations in miRNA silencing machinery and biogenesis.

Llorens F, Thüne K, Martí E, Kanata E, Dafou D, Díaz-Lucena D, Vivancos A, Shomroni O, Zafar S, Schmitz M, Michel U, Fernández-Borges N, Andréoletti O, Del Río JA, Díez J, Fischer A, Bonn S, Sklaviadis T, Torres JM, Ferrer I, Zerr I.

PLoS Pathog. 2018 Jan 22;14(1):e1006802. doi: 10.1371/journal.ppat.1006802. eCollection 2018 Jan.


decodeRNA- predicting non-coding RNA functions using guilt-by-association.

Lefever S, Anckaert J, Volders PJ, Luypaert M, Vandesompele J, Mestdagh P.

Database (Oxford). 2017 Jan 1;2017. doi: 10.1093/database/bax042.


Current Research on Non-Coding Ribonucleic Acid (RNA).

Wang J, Samuels DC, Zhao S, Xiang Y, Zhao YY, Guo Y.

Genes (Basel). 2017 Dec 5;8(12). pii: E366. doi: 10.3390/genes8120366. Review.


Discovering cancer vulnerabilities using high-throughput micro-RNA screening.

Nikolic I, Elsworth B, Dodson E, Wu SZ, Gould CM, Mestdagh P, Marshall GM, Horvath LG, Simpson KJ, Swarbrick A.

Nucleic Acids Res. 2017 Dec 15;45(22):12657-12670. doi: 10.1093/nar/gkx1072.


Small non-coding RNA transcriptome of the NCI-60 cell line panel.

Marshall EA, Sage AP, Ng KW, Martinez VD, Firmino NS, Bennewith KL, Lam WL.

Sci Data. 2017 Oct 24;4:170157. doi: 10.1038/sdata.2017.157.


DJ-1 is a redox sensitive adapter protein for high molecular weight complexes involved in regulation of catecholamine homeostasis.

Piston D, Alvarez-Erviti L, Bansal V, Gargano D, Yao Z, Szabadkai G, Odell M, Puno MR, Björkblom B, Maple-Grødem J, Breuer P, Kaut O, Larsen JP, Bonn S, Møller SG, Wüllner U, Schapira AHV, Gegg ME.

Hum Mol Genet. 2017 Oct 15;26(20):4028-4041. doi: 10.1093/hmg/ddx294. Erratum in: Hum Mol Genet. 2018 Feb 1;27(3):576.


unitas: the universal tool for annotation of small RNAs.

Gebert D, Hewel C, Rosenkranz D.

BMC Genomics. 2017 Aug 22;18(1):644. doi: 10.1186/s12864-017-4031-9.


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 in the Host Response to Viral Infections of Veterinary Importance.

Samir M, Vaas LA, Pessler F.

Front Vet Sci. 2016 Oct 17;3:86. eCollection 2016. Review.

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