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Items: 1 to 20 of 133

1.

Exome RNA sequencing reveals rare and novel alternative transcripts.

Halvardson J, Zaghlool A, Feuk L.

Nucleic Acids Res. 2013 Jan 7;41(1):e6. doi: 10.1093/nar/gks816. Epub 2012 Aug 31.

2.

CLASS: constrained transcript assembly of RNA-seq reads.

Song L, Florea L.

BMC Bioinformatics. 2013;14 Suppl 5:S14. doi: 10.1186/1471-2105-14-S5-S14. Epub 2013 Apr 10.

3.

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
4.

Deep sequencing the circadian and diurnal transcriptome of Drosophila brain.

Hughes ME, Grant GR, Paquin C, Qian J, Nitabach MN.

Genome Res. 2012 Jul;22(7):1266-81. doi: 10.1101/gr.128876.111. Epub 2012 Apr 3.

5.

SSP: an interval integer linear programming for de novo transcriptome assembly and isoform discovery of RNA-seq reads.

Safikhani Z, Sadeghi M, Pezeshk H, Eslahchi C.

Genomics. 2013 Nov-Dec;102(5-6):507-14. doi: 10.1016/j.ygeno.2013.10.003. Epub 2013 Oct 23.

6.

Alternative Splicing Signatures in RNA-seq Data: Percent Spliced in (PSI).

Schafer S, Miao K, Benson CC, Heinig M, Cook SA, Hubner N.

Curr Protoc Hum Genet. 2015 Oct 6;87:11.16.1-14. doi: 10.1002/0471142905.hg1116s87.

PMID:
26439713
7.

Transcriptome analyses of the human retina identify unprecedented transcript diversity and 3.5 Mb of novel transcribed sequence via significant alternative splicing and novel genes.

Farkas MH, Grant GR, White JA, Sousa ME, Consugar MB, Pierce EA.

BMC Genomics. 2013 Jul 18;14:486. doi: 10.1186/1471-2164-14-486.

8.

Targeted LncRNA Sequencing with the SeqCap RNA Enrichment System.

Tan JC, Bouriakov VD, Feng L, Richmond TA, Burgess D.

Methods Mol Biol. 2016;1402:73-100. doi: 10.1007/978-1-4939-3378-5_8.

PMID:
26721485
9.

Exome versus transcriptome sequencing in identifying coding region variants.

Ku CS, Wu M, Cooper DN, Naidoo N, Pawitan Y, Pang B, Iacopetta B, Soong R.

Expert Rev Mol Diagn. 2012 Apr;12(3):241-51. doi: 10.1586/erm.12.10. Review.

PMID:
22468815
10.

Characterization of pseudorabies virus transcriptome by Illumina sequencing.

Oláh P, Tombácz D, Póka N, Csabai Z, Prazsák I, Boldogkői Z.

BMC Microbiol. 2015 Jul 1;15:130. doi: 10.1186/s12866-015-0470-0.

11.

Knowledge-based reconstruction of mRNA transcripts with short sequencing reads for transcriptome research.

Seok J, Xu W, Jiang H, Davis RW, Xiao W.

PLoS One. 2012;7(2):e31440. doi: 10.1371/journal.pone.0031440. Epub 2012 Feb 1.

12.

ORMAN: optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms.

Dao P, Numanagić I, Lin YY, Hach F, Karakoc E, Donmez N, Collins C, Eichler EE, Sahinalp SC.

Bioinformatics. 2014 Mar 1;30(5):644-51. doi: 10.1093/bioinformatics/btt591. Epub 2013 Oct 15.

PMID:
24130305
13.

A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome.

Sultan M, Schulz MH, Richard H, Magen A, Klingenhoff A, Scherf M, Seifert M, Borodina T, Soldatov A, Parkhomchuk D, Schmidt D, O'Keeffe S, Haas S, Vingron M, Lehrach H, Yaspo ML.

Science. 2008 Aug 15;321(5891):956-60. doi: 10.1126/science.1160342. Epub 2008 Jul 3.

14.

Reliable identification of genomic variants from RNA-seq data.

Piskol R, Ramaswami G, Li JB.

Am J Hum Genet. 2013 Oct 3;93(4):641-51. doi: 10.1016/j.ajhg.2013.08.008. Epub 2013 Sep 26.

15.

Discover hidden splicing variations by mapping personal transcriptomes to personal genomes.

Stein S, Lu ZX, Bahrami-Samani E, Park JW, Xing Y.

Nucleic Acids Res. 2015 Dec 15;43(22):10612-22. doi: 10.1093/nar/gkv1099. Epub 2015 Nov 17.

16.

FDM: a graph-based statistical method to detect differential transcription using RNA-seq data.

Singh D, Orellana CF, Hu Y, Jones CD, Liu Y, Chiang DY, Liu J, Prins JF.

Bioinformatics. 2011 Oct 1;27(19):2633-40. doi: 10.1093/bioinformatics/btr458. Epub 2011 Aug 8.

17.

PASTA: splice junction identification from RNA-sequencing data.

Tang S, Riva A.

BMC Bioinformatics. 2013 Apr 4;14:116. doi: 10.1186/1471-2105-14-116.

18.

Quantitative visualization of alternative exon expression from RNA-seq data.

Katz Y, Wang ET, Silterra J, Schwartz S, Wong B, Thorvaldsdóttir H, Robinson JT, Mesirov JP, Airoldi EM, Burge CB.

Bioinformatics. 2015 Jul 15;31(14):2400-2. doi: 10.1093/bioinformatics/btv034. Epub 2015 Jan 22.

19.

A Comprehensive RNA Sequencing Analysis of the Adeno-Associated Virus (AAV) Type 2 Transcriptome Reveals Novel AAV Transcripts, Splice Variants, and Derived Proteins.

Stutika C, Gogol-Döring A, Botschen L, Mietzsch M, Weger S, Feldkamp M, Chen W, Heilbronn R.

J Virol. 2015 Nov 11;90(3):1278-89. doi: 10.1128/JVI.02750-15.

20.

A systematic comparison and evaluation of high density exon arrays and RNA-seq technology used to unravel the peripheral blood transcriptome of sickle cell disease.

Raghavachari N, Barb J, Yang Y, Liu P, Woodhouse K, Levy D, O'Donnell CJ, Munson PJ, Kato GJ.

BMC Med Genomics. 2012 Jun 29;5:28. doi: 10.1186/1755-8794-5-28.

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