Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing, Nature Genetics, vol.76, issue.12, pp.1413-1428, 2008. ,
DOI : 10.1016/j.molcel.2004.12.004
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation, Nature Biotechnology, vol.25, issue.5, pp.511-526, 2010. ,
DOI : 10.1038/nbt.1621
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3146043
Alternative isoform regulation in human tissue transcriptomes, Nature, vol.15, issue.7221, pp.470-476, 2008. ,
DOI : 10.1038/nature07509
Landscape of transcription in human cells, Nature, vol.474, issue.7414, pp.101-119, 2012. ,
DOI : 10.1038/nature11233
URL : https://hal.archives-ouvertes.fr/hal-01216755
Transcriptomic landscape of breast cancers through mRNA sequencing, Scientific Reports, vol.25, issue.1, p.264, 2012. ,
DOI : 10.1038/srep00264
The transcriptional landscape and mutational profile of lung adenocarcinoma, Genome Research, vol.22, issue.11 ,
DOI : 10.1101/gr.145144.112
Integrative analysis of the melanoma transcriptome, Genome Research, vol.20, issue.4, pp.413-440, 2010. ,
DOI : 10.1101/gr.103697.109
Whole Transcriptome Sequencing Reveals Gene Expression and Splicing Differences in Brain Regions Affected by Alzheimer's Disease, PLoS ONE, vol.154, issue.1, p.16266, 2011. ,
DOI : 10.1371/journal.pone.0016266.s006
Ab initio reconstruction of cell type???specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs, Nature Biotechnology, vol.10, issue.5, pp.503-513, 2010. ,
DOI : 10.1038/nbt.1633
CLIIQ: Accurate Comparative Detection and Quantification of Expressed Isoforms in a Population, Algorithms in bioinformatics. Lecture notes in computer science, pp.178-89, 2012. ,
DOI : 10.1007/978-3-642-33122-0_14
MITIE: Simultaneous RNA-Seq-based transcript identification and quantification in multiple samples, Bioinformatics, vol.29, issue.20, pp.2529-2567, 2013. ,
DOI : 10.1093/bioinformatics/btt442
A novel min-cost flow method for estimating transcript expression with RNA-seq, BMC Bioinforma, vol.14, issue.5, p.15, 2013. ,
CLASS: constrained transcript assembly of RNA-seq reads, BMC Bioinformatics, vol.14, issue.Suppl 5, p.14, 2013. ,
DOI : 10.1093/bioinformatics/btp120
Inference of Isoforms from Short Sequence Reads, Journal of Computational Biology, vol.18, issue.3, pp.305-326, 2011. ,
DOI : 10.1089/cmb.2010.0243
iReckon: Simultaneous isoform discovery and abundance estimation from RNA-seq data, Genome Research, vol.23, issue.3, pp.519-548, 2013. ,
DOI : 10.1101/gr.142232.112
Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation, Proceedings of the National Academy of Sciences, vol.108, issue.50, pp.19867-72, 2011. ,
DOI : 10.1073/pnas.1113972108
IsoLasso: A LASSO Regression Approach to RNA-Seq Based Transcriptome Assembly, Journal of Computational Biology, vol.18, issue.11, pp.1693-707, 2011. ,
DOI : 10.1089/cmb.2011.0171
StringTie enables improved reconstruction of a transcriptome from RNA-seq reads, Nature Biotechnology, vol.16, issue.3, pp.290-295, 2015. ,
DOI : 10.1038/nbt.3122
Simultaneous Isoform Discovery and Quantification from RNA-Seq, Statistics in Biosciences, vol.27, issue.19, pp.100-118, 2013. ,
DOI : 10.1007/s12561-012-9069-2
Introduction to linear optimization Athena Scientific, 1997. ,
An integrated encyclopedia of DNA elements in the human genome, Nature, vol.489, issue.7414, pp.57-74, 2012. ,
Modelling and simulating generic RNA-Seq experiments with the flux simulator, Nucleic Acids Research, vol.40, issue.20, pp.10073-83, 2012. ,
DOI : 10.1093/nar/gks666
URL : https://hal.archives-ouvertes.fr/hal-00744755
The UCSC Known Genes, Bioinformatics, vol.22, issue.9, pp.1036-1082, 2006. ,
DOI : 10.1093/bioinformatics/btl048
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions, Genome Biology, vol.14, issue.4, p.36, 2013. ,
DOI : 10.1186/gb-2009-10-3-r25
Genome-guided transcript assembly by integrative analysis of RNA sequence data, Nature Biotechnology, vol.25, issue.4, pp.341-347, 2014. ,
DOI : 10.1093/nar/gkm259
Identification of novel transcripts in annotated genomes using RNA-Seq, Bioinformatics, vol.27, issue.17, pp.2325-2329, 2011. ,
DOI : 10.1093/bioinformatics/btr355
Estimation of alternative splicing isoform frequencies from RNA-Seq data, Algorithms for Molecular Biology, vol.6, issue.1, p.9, 2011. ,
DOI : 10.1186/1471-2164-10-221
NCBI Reference Sequences: current status, policy and new initiatives, Nucleic Acids Research, vol.37, issue.Database, pp.32-38, 2009. ,
DOI : 10.1093/nar/gkn721
Ensembl 2014, Nucleic Acids Research, vol.42, issue.D1, pp.749-55, 2014. ,
DOI : 10.1093/nar/gkt1196
URL : http://doi.org/10.1093/nar/gkt1196
The UCSC Genome Browser database: 2014 update, Nucleic Acids Research, vol.42, issue.D1, pp.764-770, 2014. ,
DOI : 10.1093/nar/gkt1168
Native Elongating Transcript Sequencing Reveals Human Transcriptional Activity at Nucleotide Resolution, Cell, vol.161, issue.3, pp.541-54, 2015. ,
DOI : 10.1016/j.cell.2015.03.010
Exact Transcriptome Reconstruction from Short Sequence Reads, Algorithms in bioinformatics. Lecture notes in computer science, pp.50-63, 2008. ,
DOI : 10.1007/978-3-540-87361-7_5
URL : https://hal.archives-ouvertes.fr/hal-00428220
Full-length transcriptome assembly from RNA-Seq data without a reference genome, Nature Biotechnology, vol.30, issue.7, pp.644-52, 2011. ,
DOI : 10.1101/GR.229202. ARTICLE PUBLISHED ONLINE BEFORE MARCH 2002
FlyBase: improvements to the bibliography, Nucleic Acids Research, vol.41, issue.D1, pp.751-758, 2013. ,
DOI : 10.1093/nar/gks1024
Splicing graphs and EST assembly problem, Bioinformatics, vol.18, issue.Suppl 1, pp.181-189, 2002. ,
DOI : 10.1093/bioinformatics/18.suppl_1.S181
URL : http://bioinformatics.oxfordjournals.org/cgi/content/short/18/suppl_1/S181
Least angle regression, Ann Stat, vol.32, issue.2, pp.407-99, 2004. ,
Regularization Paths for Generalized Linear Models via Coordinate Descent, Journal of Statistical Software, vol.33, issue.1, pp.1-22, 2010. ,
DOI : 10.18637/jss.v033.i01
On choosing a dense subgraph, Proceedings of 1993 IEEE 34th Annual Foundations of Computer Science ,
DOI : 10.1109/SFCS.1993.366818