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Items: 20

1.

Visualization of the small RNA transcriptome using seqclusterViz.

Pantano L, Pantano F, Marti E, Ho Sui S.

F1000Res. 2019 Feb 28;8. pii: ISCB Comm J-232. doi: 10.12688/f1000research.18142.1. eCollection 2019.

2.

Identifying and characterizing functional 3' nucleotide addition in the miRNA pathway.

Burroughs AM, Ando Y.

Methods. 2019 Jan 1;152:23-30. doi: 10.1016/j.ymeth.2018.08.006. Epub 2018 Aug 20. Review.

3.

IsopiRBank: a research resource for tracking piRNA isoforms.

Zhang H, Ali A, Gao J, Ban R, Jiang X, Zhang Y, Shi Q.

Database (Oxford). 2018 Jan 1;2018. doi: 10.1093/database/bay059.

4.

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.

5.

Identification of Conserved and Novel MicroRNAs in Blueberry.

Yue J, Lu X, Zhang H, Ge J, Gao X, Liu Y.

Front Plant Sci. 2017 Jun 30;8:1155. doi: 10.3389/fpls.2017.01155. eCollection 2017.

6.

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.

7.

DeAnnIso: a tool for online detection and annotation of isomiRs from small RNA sequencing data.

Zhang Y, Zang Q, Zhang H, Ban R, Yang Y, Iqbal F, Li A, Shi Q.

Nucleic Acids Res. 2016 Jul 8;44(W1):W166-75. doi: 10.1093/nar/gkw427. Epub 2016 May 13.

8.

miRMOD: a tool for identification and analysis of 5' and 3' miRNA modifications in Next Generation Sequencing small RNA data.

Kaushik A, Saraf S, Mukherjee SK, Gupta D.

PeerJ. 2015 Oct 20;3:e1332. doi: 10.7717/peerj.1332. eCollection 2015.

9.

miFRame: analysis and visualization of miRNA sequencing data in neurological disorders.

Backes C, Haas J, Leidinger P, Frese K, Großmann T, Ruprecht K, Meder B, Meese E, Keller A.

J Transl Med. 2015 Jul 14;13:224. doi: 10.1186/s12967-015-0594-x.

10.

Computational Approaches for the Analysis of ncRNA through Deep Sequencing Techniques.

Veneziano D, Nigita G, Ferro A.

Front Bioeng Biotechnol. 2015 Jun 3;3:77. doi: 10.3389/fbioe.2015.00077. eCollection 2015. Review.

11.

Oasis: online analysis of small RNA deep sequencing data.

Capece V, Garcia Vizcaino JC, Vidal R, Rahman RU, Pena Centeno T, Shomroni O, Suberviola I, Fischer A, Bonn S.

Bioinformatics. 2015 Jul 1;31(13):2205-7. doi: 10.1093/bioinformatics/btv113. Epub 2015 Feb 19.

12.

plantDARIO: web based quantitative and qualitative analysis of small RNA-seq data in plants.

Patra D, Fasold M, Langenberger D, Steger G, Grosse I, Stadler PF.

Front Plant Sci. 2014 Dec 23;5:708. doi: 10.3389/fpls.2014.00708. eCollection 2014.

13.

Research resources: comparative microRNA profiles in human corona radiata cells and cumulus oophorus cells detected by next-generation small RNA sequencing.

Tong XH, Xu B, Zhang YW, Liu YS, Ma CH.

PLoS One. 2014 Sep 4;9(9):e106706. doi: 10.1371/journal.pone.0106706. eCollection 2014.

14.

MAGI: a Node.js web service for fast microRNA-Seq analysis in a GPU infrastructure.

Kim J, Levy E, Ferbrache A, Stepanowsky P, Farcas C, Wang S, Brunner S, Bath T, Wu Y, Ohno-Machado L.

Bioinformatics. 2014 Oct;30(19):2826-7. doi: 10.1093/bioinformatics/btu377. Epub 2014 Jun 6.

15.

CAP-miRSeq: a comprehensive analysis pipeline for microRNA sequencing data.

Sun Z, Evans J, Bhagwate A, Middha S, Bockol M, Yan H, Kocher JP.

BMC Genomics. 2014 Jun 3;15:423. doi: 10.1186/1471-2164-15-423.

16.

Systematic characterization of small RNAome during zebrafish early developmental stages.

Yao Y, Ma L, Jia Q, Deng W, Liu Z, Zhang Y, Ren J, Xue Y, Jia H, Yang Q.

BMC Genomics. 2014 Feb 10;15:117. doi: 10.1186/1471-2164-15-117.

17.

Comparative proteome profile of human placenta from normal and preeclamptic pregnancies.

Wang F, Shi Z, Wang P, You W, Liang G.

PLoS One. 2013 Oct 18;8(10):e78025. doi: 10.1371/journal.pone.0078025. eCollection 2013.

18.

MicroRNA and piRNA profiles in normal human testis detected by next generation sequencing.

Yang Q, Hua J, Wang L, Xu B, Zhang H, Ye N, Zhang Z, Yu D, Cooke HJ, Zhang Y, Shi Q.

PLoS One. 2013 Jun 24;8(6):e66809. doi: 10.1371/journal.pone.0066809. Print 2013.

19.

mirTools 2.0 for non-coding RNA discovery, profiling, and functional annotation based on high-throughput sequencing.

Wu J, Liu Q, Wang X, Zheng J, Wang T, You M, Sheng Sun Z, Shi Q.

RNA Biol. 2013 Jul;10(7):1087-92. doi: 10.4161/rna.25193. Epub 2013 May 29.

20.

Rat mir-155 generated from the lncRNA Bic is 'hidden' in the alternate genomic assembly and reveals the existence of novel mammalian miRNAs and clusters.

Uva P, Da Sacco L, Del Cornò M, Baldassarre A, Sestili P, Orsini M, Palma A, Gessani S, Masotti A.

RNA. 2013 Mar;19(3):365-79. doi: 10.1261/rna.035394.112. Epub 2013 Jan 17.

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