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Items: 1 to 20 of 72

1.

Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts.

Sun L, Luo H, Bu D, Zhao G, Yu K, Zhang C, Liu Y, Chen R, Zhao Y.

Nucleic Acids Res. 2013 Sep;41(17):e166. doi: 10.1093/nar/gkt646. Epub 2013 Jul 27.

2.

De novo approach to classify protein-coding and noncoding transcripts based on sequence composition.

Luo H, Bu D, Sun L, Chen R, Zhao Y.

Methods Mol Biol. 2014;1182:203-7. doi: 10.1007/978-1-4939-1062-5_18.

PMID:
25055913
3.

PLEK: a tool for predicting long non-coding RNAs and messenger RNAs based on an improved k-mer scheme.

Li A, Zhang J, Zhou Z.

BMC Bioinformatics. 2014 Sep 19;15:311. doi: 10.1186/1471-2105-15-311.

4.

iSeeRNA: identification of long intergenic non-coding RNA transcripts from transcriptome sequencing data.

Sun K, Chen X, Jiang P, Song X, Wang H, Sun H.

BMC Genomics. 2013;14 Suppl 2:S7. doi: 10.1186/1471-2164-14-S2-S7. Epub 2013 Feb 15.

5.

LNCipedia: a database for annotated human lncRNA transcript sequences and structures.

Volders PJ, Helsens K, Wang X, Menten B, Martens L, Gevaert K, Vandesompele J, Mestdagh P.

Nucleic Acids Res. 2013 Jan;41(Database issue):D246-51. doi: 10.1093/nar/gks915. Epub 2012 Oct 5.

6.

Computational discovery of human coding and non-coding transcripts with conserved splice sites.

Rose D, Hiller M, Schutt K, Hackermüller J, Backofen R, Stadler PF.

Bioinformatics. 2011 Jul 15;27(14):1894-900. doi: 10.1093/bioinformatics/btr314. Epub 2011 May 26.

PMID:
21622663
7.

Novel software package for cross-platform transcriptome analysis (CPTRA).

Zhou X, Su Z, Sammons RD, Peng Y, Tranel PJ, Stewart CN Jr, Yuan JS.

BMC Bioinformatics. 2009 Oct 8;10 Suppl 11:S16. doi: 10.1186/1471-2105-10-S11-S16.

8.

Screening non-coding RNAs in transcriptomes from neglected species using PORTRAIT: case study of the pathogenic fungus Paracoccidioides brasiliensis.

Arrial RT, Togawa RC, Brigido Mde M.

BMC Bioinformatics. 2009 Aug 4;10:239. doi: 10.1186/1471-2105-10-239.

9.

Identification of long non-protein coding RNAs in chicken skeletal muscle using next generation sequencing.

Li T, Wang S, Wu R, Zhou X, Zhu D, Zhang Y.

Genomics. 2012 May;99(5):292-8. doi: 10.1016/j.ygeno.2012.02.003. Epub 2012 Feb 20.

10.

deepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns.

Langenberger D, Pundhir S, Ekstrøm CT, Stadler PF, Hoffmann S, Gorodkin J.

Bioinformatics. 2012 Jan 1;28(1):17-24. doi: 10.1093/bioinformatics/btr598. Epub 2011 Nov 3.

11.

A non-biased framework for the annotation and classification of the non-miRNA small RNA transcriptome.

Pantano L, Estivill X, Martí E.

Bioinformatics. 2011 Nov 15;27(22):3202-3. doi: 10.1093/bioinformatics/btr527. Epub 2011 Oct 5.

PMID:
21976421
12.

Identification of long non-coding transcripts with feature selection: a comparative study.

Ventola GM, Noviello TM, D'Aniello S, Spagnuolo A, Ceccarelli M, Cerulo L.

BMC Bioinformatics. 2017 Mar 23;18(1):187. doi: 10.1186/s12859-017-1594-z.

13.

Refining transcriptional programs in kidney development by integration of deep RNA-sequencing and array-based spatial profiling.

Thiagarajan RD, Cloonan N, Gardiner BB, Mercer TR, Kolle G, Nourbakhsh E, Wani S, Tang D, Krishnan K, Georgas KM, Rumballe BA, Chiu HS, Steen JA, Mattick JS, Little MH, Grimmond SM.

BMC Genomics. 2011 Sep 5;12:441. doi: 10.1186/1471-2164-12-441.

14.

miRExpress: analyzing high-throughput sequencing data for profiling microRNA expression.

Wang WC, Lin FM, Chang WC, Lin KY, Huang HD, Lin NS.

BMC Bioinformatics. 2009 Oct 12;10:328. doi: 10.1186/1471-2105-10-328.

15.

Transcriptome analysis for Caenorhabditis elegans based on novel expressed sequence tags.

Shin H, Hirst M, Bainbridge MN, Magrini V, Mardis E, Moerman DG, Marra MA, Baillie DL, Jones SJ.

BMC Biol. 2008 Jul 8;6:30. doi: 10.1186/1741-7007-6-30.

16.

miREvo: an integrative microRNA evolutionary analysis platform for next-generation sequencing experiments.

Wen M, Shen Y, Shi S, Tang T.

BMC Bioinformatics. 2012 Jun 21;13:140. doi: 10.1186/1471-2105-13-140.

17.

nocoRNAc: characterization of non-coding RNAs in prokaryotes.

Herbig A, Nieselt K.

BMC Bioinformatics. 2011 Jan 31;12:40. doi: 10.1186/1471-2105-12-40.

18.

Identification of protein coding regions in RNA transcripts.

Tang S, Lomsadze A, Borodovsky M.

Nucleic Acids Res. 2015 Jul 13;43(12):e78. doi: 10.1093/nar/gkv227. Epub 2015 Apr 13.

19.

Identifying differentially expressed transcripts from RNA-seq data with biological variation.

Glaus P, Honkela A, Rattray M.

Bioinformatics. 2012 Jul 1;28(13):1721-8. doi: 10.1093/bioinformatics/bts260. Epub 2012 May 3.

20.

Transcriptome analysis of the silkworm (Bombyx mori) by high-throughput RNA sequencing.

Li Y, Wang G, Tian J, Liu H, Yang H, Yi Y, Wang J, Shi X, Jiang F, Yao B, Zhang Z.

PLoS One. 2012;7(8):e43713. doi: 10.1371/journal.pone.0043713. Epub 2012 Aug 23.

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