Bayesian transcriptome assembly

Genome Biology

Volumn 15, Issue 10, 2014, Pages

  Maretty, Lasse ^a   Sibbesen, Jonas Andreas ^a   Krogh, Anders ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; BAYESIAN LEARNING; COMPUTER PROGRAM; COMPUTER SIMULATION; DENDRITIC CELL; EMBRYONIC STEM CELL; INTERMETHOD COMPARISON; K562 CELL LINE; MEASUREMENT PRECISION; RNA SEQUENCE; SENSITIVITY ANALYSIS; TRANSCRIPTOME ASSEMBLY; TRANSCRIPTOMICS; VALIDITY; BAYES THEOREM; CELL LINE; EVALUATION STUDY; GENE EXPRESSION PROFILING; HUMAN; PROCEDURES; SEQUENCE ANALYSIS;

TRANSCRIPTOME;

ALGORITHMS; BAYES THEOREM; CELL LINE; COMPUTER SIMULATION; EMBRYONIC STEM CELLS; GENE EXPRESSION PROFILING; HUMANS; K562 CELLS; SEQUENCE ANALYSIS, RNA; SOFTWARE; TRANSCRIPTOME;

EID: 84924626858     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/s13059-014-0501-4     Document Type: Article

References (19)

1. Heber S, Alekseyev M, Sze S-H, Tang H, Pevzner PA: Splicing graphs and EST assembly problem. Bioinformatics (Oxford, England)2002, 18:181-188.
2. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L: Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol2010, 28:511-515.
3. Li W, Feng J, Jiang T: IsoLasso: a LASSO regression approach to RNA-Seq based transcriptome assembly. J Comput Biol2011, 18:1693-1707.
4. Li JJ, Jiang C-R, Brown JB, Huang H, Bickel PJ: Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation. Proc Nat Acad Sci USA2011, 108:19867-19872.
5. Li W, Jiang T: Transcriptome assembly and isoform expression level estimation from biased RNA-seq reads. Bioinformatics (Oxford, England)2012, 28:2914-2921.
6. Mezlini AM, Smith EJ, Fiume M, Buske O, Savich G, Shah S, Aparicion S, Chiang D, Goldenberg A, Brudno M: iReckon: Simultaneous isoform discovery and abundance estimation from RNA-seq data. Genome Res2012, 23:519-529.
7. Behr J, Kahles A, Zhong Y, Sreedharan VT, Drewe P, Rätsch G: MITIE: Simultaneous RNA-Seq-based transcript identification and quantification in multiple samples. Bioinformatics (Oxford, England)2013, 29:2529-2538.
8. Tomescu AI, Kuosmanen A, Rizzi R, Mäkinen V, Veli M: A novel min-cost flow method for estimating transcript expression with RNA-Seq. BMC Bioinformatics2013, 14:S15.
9. Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL: TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol2013, 14:R36.
10. Pachter L: Models for transcript quantification from RNA-Seq. (2011) arXiv 1104.3889v2
11. Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, Xue C, Marinov GK, Khatun J, Williams BA, Zaleski C, Rozowsky J, Röder M, Kokocinski F, Abdelhamid RF, Alioto T, Antoshechkin I, Baer MT, Bar NS, Batut P, Bell K, Bell I, Chakrabortty S, Chen X, Chrast J, Curado J, et al: Landscape of transcription in human cells. Nature2012, 489:101-108.
12. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A: Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol2011, 29:644-652.
13. Meyer LR, Zweig AS, Hinrichs AS, Karolchik D, Kuhn RM, Wong M, Sloan CA, Rosenbloom KR, Roe G, Rhead B, Raney BJ, Pohl A, Malladi VS, Li CH, Lee BT, Learned K, Kirkup V, Hsu F, Heitner S, Harte RA, Haeussler M, Guruvadoo L, Goldman M, Giardine BM, Fujita PA, Dreszer TR, Diekhans M, Cline MS, Clawson H, Barber GP, et al: The UCSC genome browser database: extensions and updates 2013. Nucleic Acids Res2013, 41:D64-D69.
14. Griebel T, Zacher B, Ribeca P, Raineri E, Lacroix V, Guigó R, Sammeth M: Modelling and simulating generic RNA-Seq experiments with the flux simulator. Nucleic Acids Res2012, 40:10073-10083.
15. Au KF, Sebastiano V, Afshar PT, Durruthy JD, Lee L, Williams BA, van Bakel H, Schadt EE, Reijo-Pera RA, Underwood JG, Wong WH: Characterization of the human ESC transcriptome by hybrid sequencing. Proc Nat Acad Sci USA2013, 110:E4821-E4830.
16. Schulz MH, Zerbino DR, Vingron M, Birney E: Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics (Oxford, England)2012, 28:1086-1092.
17. Trapnell C, Hendrickson DG, Sauvageau M, Goff L, Rinn JL, Pachter L: Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat Biotechnol2013, 31:46-53.
18. Bayesembler [https://github.com/bioinformatics-centre/bayesembler]
19. Langmead B, Salzberg SL: Fast gapped-read alignment with Bowtie 2. Nat Methods2012, 9:357-359.