An Integer Programming approach to novel transcript reconstruction from paired-end RNA-Seq reads

2012 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2012

Volumn , Issue , 2012, Pages 369-376

  Mangul, Serghei ^a   Caciula, Adrian ^a   Al Seesi, Sahar ^b   Brinza, Dumitru ^c   Banday, Abdul Rouf ^d   Kanadia, Rahul ^d  

^a GEORGIA STATE UNIVERSITY   (United States)

^b University of Connecticut   (United States)

^c Life Technologies Corporation   (United States)

^d UNIVERSITY OF CONNECTICUT   (United States)

Author keywords

Algorithms

Indexed keywords

FRAGMENT LENGTHS; GENE EXPRESSION PROFILING; GRAPH-BASED; INTEGER PROGRAM; MAXIMAL PATH; SYNTHETIC DATASETS; TRANSCRIPTOMES;

ALGORITHMS; GENE EXPRESSION; INTEGER PROGRAMMING; RNA;

BIOINFORMATICS;

EID: 84869420829     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/2382936.2382983     Document Type: Conference Paper

References (22)

1. I. Astrovskaya, B. Tork, S. Mangul, K. Westbrooks, I. Mandoiu, P. Balfe, and A. Zelikovsky. Inferring viral quasispecies spectra from 454 pyrosequencing reads. BMC Bioinformatics, 12(Suppl 6):S1, 2011.
2. K. F. Au, H. Jiang, L. Lin, Y. Xing, and W. H. Wong. Detection of splice junctions from paired-end rna-seq data by splicemap. Nucleic Acids Research, 2010.
3. A. Derti, P. Garrett-Engele, K. D. MacIsaac, R. C. Stevens, S. Sriram, R. Chen, C. A. Rohl, J. M. Johnson, and T. Babak. A quantitative atlas of polyadenylation in five mammals. Genome Research, 22(6):1173-1183, 2012.
4. J. Feng, W. Li, and T. Jiang. Inference of isoforms from short sequence reads. In Proc. RECOMB, pages 138-157, 2010.
5. M. Garber, M. G. Grabherr, M. Guttman, and C. Trapnell. Computational methods for transcriptome annotation and quantification using RNA-seq. Nature Methods, 8(6):469-477, May 2011.
6. M. Grabherr. Full-length transcriptome assembly from rna-seq data without a reference genome. Nature biotechnology, 29(7):644-652, 2011.
7. M. Guttman, M. Garber, J. Levin, J. Donaghey, J. Robinson, X. Adiconis, L. Fan, M. Koziol, A. Gnirke, C. Nusbaum, J. Rinn, E. Lander, and A. Regev. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nature Biotechnology, 28(5):503-510, 2010.
8. B. Li, V. Ruotti, R. Stewart, J. Thomson, and C. Dewey. RNA-Seq gene expression estimation with read mapping uncertainty. Bioinformatics, 26(4):493-500, 2010.
9. W. Li, J. Feng, and T. Jiang. IsoLasso: A LASSO Regression Approach to RNA-Seq Based Transcriptome Assembly. Lecture Notes in Computer Science, 6577:168-+, 2011.
10. Y. Y. Lin, P. Dao, F. Hach, M. Bakhshi, F. Mo, A. Lapuk, C. Collins, and S. C. Sahinalp. Cliiq: Accurate comparative detection and quantification of expressed isoforms in a population. Proc. 12th Workshop on Algorithms in Bioinformatics, 2012.
11. S. Mangul, A. Caciula, I. Mandoiu, and A. Zelikovsky. Rna-seq based discovery and reconstruction of unannotated transcripts in partially annotated genomes. In Bioinformatics and Biomedicine Workshops (BIBMW), 2011 IEEE International Conference on, pages 118 -123, nov. 2011.
12. T. R. Mercer, D. J. Gerhardt, M. E. Dinger, J. Crawford, C. Trapnell, J. A. Jeddeloh, J. S. Mattick, and J. L. Rinn. Targeted RNA sequencing reveals the deep complexity of the human transcriptome. Nature Biotechnology, 30(1):99-104, 2012.
13. A. Mortazavi, B. Williams, K. McCue, L. Schaeffer, and B. Wold. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature methods, 2008.
14. M. Nicolae, S. Mangul, I. Mandoiu, and A. Zelikovsky. Estimation of alternative splicing isoform frequencies from rna-seq data. Algorithms for Molecular Biology, 6:9, 2011.
15. S. Pal, R. Gupta, H. Kim, P. Wickramasinghe, V. Baubet, L. C. Showe, N. Dahmane, and R. V. Davuluri. Alternative transcription exceeds alternative splicing in generating the transcriptome diversity of cerebellar development. Genome Research, 2011.
16. P. A. Pevzner. 1-Tuple DNA sequencing: computer analysis. J Biomol Struct Dyn, 7(1):63-73, Aug. 1989.
17. A. Roberts, H. Pimentel, C. Trapnell, and L. Pachter. Identification of novel transcripts in annotated genomes using rna-seq. Bioinformatics, 2011.
18. G. Robertson, J. Schein, R. Chiu, R. Corbett, M. Field, S. D. Jackman, K. Mungall, S. Lee, H. M. Okada, J. Q. Qian, and et al. De novo assembly and analysis of rna-seq data. Nature Methods, 7(11):909-912, 2010.
19. J. M. Rothberg, W. Hinz, T. M. Rearick, J. Schultz, W. Mileski, M. Davey, J. H. Leamon, K. Johnson, M. J. Milgrew, M. Edwards, J. Hoon, J. F. Simons, D. Marran, J. W. Myers, J. F. Davidson, A. Branting, J. R. Nobile, B. P. Puc, D. Light, T. A. Clark, M. Huber, J. T. Branciforte, I. B. Stoner, S. E. Cawley, M. Lyons, Y. Fu, N. Homer, M. Sedova, X. Miao, B. Reed, J. Sabina, E. Feierstein, M. Schorn, M. Alanjary, E. Dimalanta, D. Dressman, R. Kasinskas, T. Sokolsky, J. A. Fidanza, E. Namsaraev, K. J. McKernan, A. Williams, G. T. Roth, and J. Bustillo. An integrated semiconductor device enabling non-optical genome sequencing. Nature, 475(7356):348-352, 2011.
20. C. Trapnell, L. Pachter, and S. Salzberg. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics, 25(9):1105-1111, 2009.
21. C. Trapnell, B. Williams, G. Pertea, A. Mortazavi, G. Kwan, M. van Baren, S. Salzberg, B. Wold, and L. Pachter. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature biotechnology, 28(5):511-515, 2010.
22. E. Wang, R. Sandberg, S. Luo, I. Khrebtukova, L. Zhang, C. Mayr, S. Kingsmore, G. Schroth, and C. Burge. Alternative isoform regulation in human tissue transcriptomes. Nature, 456(7221):470-476, 2008.