E. Wang, R. Sandberg, S. Luo, I. Khrebtukova, L. Zhang et al., Alternative isoform regulation in human tissue transcriptomes, Nature, vol.15, issue.7221, pp.470-476, 2008.
DOI : 10.1038/nature07509

A. Mortazavi, B. Williams, K. Mccue, L. Schaeffer, and B. Wold, Mapping and quantifying mammalian transcriptomes by RNA-Seq, Nature Methods, vol.14, issue.7, pp.621-628, 2008.
DOI : 10.1038/nmeth.1226

M. Grabherr, B. Haas, M. Yassour, J. Levin, D. Thompson et al., Full-length transcriptome assembly from RNA-Seq data without a reference genome, Nature Biotechnology, vol.30, issue.7, pp.644-652, 2011.
DOI : 10.1101/GR.229202. ARTICLE PUBLISHED ONLINE BEFORE MARCH 2002

G. Robertson, J. Schein, and R. Chiu, De novo assembly and analysis of RNA-seq data, Nature Methods, vol.7, issue.11, pp.909-912, 2010.
DOI : 10.1038/nbt0509-455

M. Schulz, D. Zerbino, M. Vingron, and E. Birney, Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels, Bioinformatics, vol.28, issue.8, pp.1086-1092, 2012.
DOI : 10.1093/bioinformatics/bts094

G. Sacomoto, J. Kielbassa, R. Chikhi, R. Uricaru, P. Antoniou et al., Kissplice: de?novo calling alternative splicing events from RNA?seq data, BMC Bioinform, vol.13, p.5, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00784407

E. Birmelé, P. Crescenzi, R. Ferreira, R. Grossi, V. Lacroix et al., Efficient Bubble Enumeration in Directed Graphs, String Processing and Infor? mation Retrieval, pp.118-129, 2012.
DOI : 10.1007/978-3-642-34109-0_13

T. Cormen, C. Leiserson, R. Rivest, and C. Stein, Introduction to algo? rithms, 2001.

R. Chikhi and G. Rizk, Space-Efficient and Exact de Bruijn Graph Representation Based on a Bloom Filter, Bioinformatics. WABI, Lecture Notes in Computer Science, vol.7534, pp.236-248, 2012.
DOI : 10.1007/978-3-642-33122-0_19

URL : https://hal.archives-ouvertes.fr/hal-00753930

K. Salikhov, G. Sacomoto, and G. Kucherov, Using cascading bloom filters to improve the memory usage for de Brujin graphs, Algorithms in Bioinformatics. WABI, Lecture notes in computer science, pp.364-376, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00824697

R. Ahuja, K. Mehlhorn, J. Orlin, and R. Tarjan, Faster algorithms for the shortest path problem, Journal of the ACM, vol.37, issue.2, pp.213-223, 1990.
DOI : 10.1145/77600.77615

M. Chen, R. Chowdhury, V. Ramachandran, D. Roche, and L. Tong, Prior? ity queues and Dijkstra's algorithm, 2007.

P. Flicek, M. Amode, D. Barrell, K. Beal, K. Billis et al., Ensembl 2014, Nucleic Acids Research, vol.42, issue.D1, pp.749-755, 2014.
DOI : 10.1093/nar/gkt1196

A. Dobin, C. Davis, F. Schlesinger, J. Drenkow, C. Zaleski et al., STAR: ultrafast universal RNA-seq aligner, Bioinformatics, vol.29, issue.1, pp.15-21, 2013.
DOI : 10.1093/bioinformatics/bts635

C. Li, S. Mccormick, and D. Simchi?levi, The complexity of finding two disjoint paths with min-max objective function, Discrete Applied Mathematics, vol.26, issue.1, 1990.
DOI : 10.1016/0166-218X(90)90024-7

M. Bussieck and M. Lübbecke, The vertex set of a 01-polytope is strongly P-enumerable, Computational Geometry, vol.11, issue.2, pp.103-109, 1998.
DOI : 10.1016/S0925-7721(98)00021-2