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Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing.

Yassour M, Kaplan T, Fraser HB, Levin JZ, Pfiffner J, Adiconis X, Schroth G, Luo S, Khrebtukova I, Gnirke A, Nusbaum C, Thompson DA, Friedman N, Regev A.

Proc Natl Acad Sci U S A. 2009 Mar 3;106(9):3264-9. doi: 10.1073/pnas.0812841106. Epub 2009 Feb 10.


Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach.

Bainbridge MN, Warren RL, Hirst M, Romanuik T, Zeng T, Go A, Delaney A, Griffith M, Hickenbotham M, Magrini V, Mardis ER, Sadar MD, Siddiqui AS, Marra MA, Jones SJ.

BMC Genomics. 2006 Sep 29;7:246.


Genome-wide profiling of untranslated regions by paired-end ditag sequencing reveals unexpected transcriptome complexity in yeast.

Kang YN, Lai DP, Ooi HS, Shen TT, Kou Y, Tian J, Czajkowsky DM, Shao Z, Zhao X.

Mol Genet Genomics. 2015 Feb;290(1):217-24. doi: 10.1007/s00438-014-0913-6. Epub 2014 Sep 12.


Extensive transcriptional heterogeneity revealed by isoform profiling.

Pelechano V, Wei W, Steinmetz LM.

Nature. 2013 May 2;497(7447):127-31. doi: 10.1038/nature12121. Epub 2013 Apr 24.


Meiosis-induced alterations in transcript architecture and noncoding RNA expression in S. cerevisiae.

Kim Guisbert KS, Zhang Y, Flatow J, Hurtado S, Staley JP, Lin S, Sontheimer EJ.

RNA. 2012 Jun;18(6):1142-53. doi: 10.1261/rna.030510.111. Epub 2012 Apr 26.


Detection and analysis of alternative splicing in Yarrowia lipolytica reveal structural constraints facilitating nonsense-mediated decay of intron-retaining transcripts.

Mekouar M, Blanc-Lenfle I, Ozanne C, Da Silva C, Cruaud C, Wincker P, Gaillardin C, Neuvéglise C.

Genome Biol. 2010;11(6):R65. doi: 10.1186/gb-2010-11-6-r65. Epub 2010 Jun 23.


Sampling the Arabidopsis transcriptome with massively parallel pyrosequencing.

Weber AP, Weber KL, Carr K, Wilkerson C, Ohlrogge JB.

Plant Physiol. 2007 May;144(1):32-42. Epub 2007 Mar 9.


Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing.

Morin R, Bainbridge M, Fejes A, Hirst M, Krzywinski M, Pugh T, McDonald H, Varhol R, Jones S, Marra M.

Biotechniques. 2008 Jul;45(1):81-94. doi: 10.2144/000112900.


Noncanonical transcript forms in yeast and their regulation during environmental stress.

Yoon OK, Brem RB.

RNA. 2010 Jun;16(6):1256-67. doi: 10.1261/rna.2038810. Epub 2010 Apr 26.


Genome-wide bioinformatic and molecular analysis of introns in Saccharomyces cerevisiae.

Spingola M, Grate L, Haussler D, Ares M Jr.

RNA. 1999 Feb;5(2):221-34.


Alternative Splicing in Next Generation Sequencing Data of Saccharomyces cerevisiae.

Schreiber K, Csaba G, Haslbeck M, Zimmer R.

PLoS One. 2015 Oct 15;10(10):e0140487. doi: 10.1371/journal.pone.0140487. eCollection 2015.


SpliceJumper: a classification-based approach for calling splicing junctions from RNA-seq data.

Chu C, Li X, Wu Y.

BMC Bioinformatics. 2015;16 Suppl 17:S10. doi: 10.1186/1471-2105-16-S17-S10. Epub 2015 Dec 7.


Quantification of the yeast transcriptome by single-molecule sequencing.

Lipson D, Raz T, Kieu A, Jones DR, Giladi E, Thayer E, Thompson JF, Letovsky S, Milos P, Causey M.

Nat Biotechnol. 2009 Jul;27(7):652-8. doi: 10.1038/nbt.1551. Epub 2009 Jul 5.


Correlation between the secondary structure of pre-mRNA introns and the efficiency of splicing in Saccharomyces cerevisiae.

Rogic S, Montpetit B, Hoos HH, Mackworth AK, Ouellette BF, Hieter P.

BMC Genomics. 2008 Jul 29;9:355. doi: 10.1186/1471-2164-9-355.


Massively parallel sequencing of the polyadenylated transcriptome of C. elegans.

Hillier LW, Reinke V, Green P, Hirst M, Marra MA, Waterston RH.

Genome Res. 2009 Apr;19(4):657-66. doi: 10.1101/gr.088112.108. Epub 2009 Jan 30.


Differentially expressed alternatively spliced genes in malignant pleural mesothelioma identified using massively parallel transcriptome sequencing.

Dong L, Jensen RV, De Rienzo A, Gordon GJ, Xu Y, Sugarbaker DJ, Bueno R.

BMC Med Genet. 2009 Dec 31;10:149. doi: 10.1186/1471-2350-10-149.


A large-scale full-length cDNA analysis to explore the budding yeast transcriptome.

Miura F, Kawaguchi N, Sese J, Toyoda A, Hattori M, Morishita S, Ito T.

Proc Natl Acad Sci U S A. 2006 Nov 21;103(47):17846-51. Epub 2006 Nov 13.


Autoregulation of the mRNA export factor Yra1p requires inefficient splicing of its pre-mRNA.

Preker PJ, Guthrie C.

RNA. 2006 Jun;12(6):994-1006. Epub 2006 Apr 17.

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