@article{Heber:2002aa,
author = {Heber, Steffen and Alekseyev, Max and Sze, Sing-Hoi and Tang, Haixu and Pevzner, Pavel A},
title = {{Splicing graphs and EST assembly problem}},
journal = {Bioinformatics (Oxford, England)},
year = {2002},
volume = {18 Suppl 1},
pages = {S181--8}
}

@article{Seshagiri:2012gr,
author = {Seshagiri, Somasekar and Stawiski, Eric W and Durinck, Steffen and Modrusan, Zora and Storm, Elaine E and Conboy, Caitlin B and Chaudhuri, Subhra and Guan, Yinghui and Janakiraman, Vasantharajan and Jaiswal, Bijay S and Guillory, Joseph and Ha, Connie and Dijkgraaf, Gerrit J P and Stinson, Jeremy and Gnad, Florian and Huntley, Melanie A and Degenhardt, Jeremiah D and Haverty, Peter M and Bourgon, Richard and Wang, Weiru and Koeppen, Hartmut and Gentleman, Robert and Starr, Timothy K and Zhang, Zemin and Largaespada, David A and Wu, Thomas D and de Sauvage, Frederic J},
title = {{Recurrent R-spondin fusions in colon cancer}},
journal = {Nature},
year = {2012},
volume = {488},
number = {7413},
pages = {660--664},
month = aug
}

@article{Lawrence:2013hi,
author = {Lawrence, Michael and Huber, Wolfgang and Pag{\`e}s, Herv{\'e} and Aboyoun, Patrick and Carlson, Marc and Gentleman, Robert and Morgan, Martin T and Carey, Vincent J},
title = {{Software for Computing and Annotating Genomic Ranges}},
journal = {PLoS Computational Biology},
year = {2013},
volume = {9},
number = {8},
pages = {e1003118},
month = aug
}

@article{Venables:2008aa,
author = {Venables, Julian P and Klinck, Roscoe and Bramard, Anne and Inkel, Lyna and Dufresne-Martin, Genevieve and Koh, ChuShin and Gervais-Bird, Julien and Lapointe, Elvy and Froehlich, Ulrike and Durand, Mathieu and Gendron, Daniel and Brosseau, Jean-Philippe and Thibault, Philippe and Lucier, Jean-Francois and Tremblay, Karine and Prinos, Panagiotis and Wellinger, Raymund J and Chabot, Benoit and Rancourt, Claudine and Elela, Sherif A},
title = {{Identification of alternative splicing markers for breast cancer}},
journal = {Cancer Research},
year = {2008},
volume = {68},
number = {22},
pages = {9525--9531},
month = nov
}

@article{Katz:2010aa,
author = {Katz, Yarden and Wang, Eric T and Airoldi, Edoardo M and Burge, Christopher B},
title = {{Analysis and design of RNA sequencing experiments for identifying isoform regulation}},
journal = {Nature Methods},
year = {2010},
volume = {7},
number = {12},
pages = {1009--1015},
month = dec
}

@article{Anders:2012es,
author = {Anders, S and Reyes, A and Huber, W},
title = {{Detecting differential usage of exons from RNA-seq data}},
journal = {Genome Research},
year = {2012},
volume = {22},
number = {10},
pages = {2008--2017},
month = oct
}

@article{Ritchie:2015fa,
author = {Ritchie, Matthew E and Phipson, Belinda and Wu, Di and Hu, Yifang and Law, Charity W and Shi, Wei and Smyth, Gordon K},
title = {{limma powers differential expression analyses for RNA-sequencing and microarray studies}},
journal = {Nucleic Acids Research},
year = {2015},
volume = {43},
number = {7},
pages = {e47},
month = apr
}

@article{Dobin:2013fg,
author = {Dobin, Alexander and Davis, Carrie A and Schlesinger, Felix and Drenkow, Jorg and Zaleski, Chris and Jha, Sonali and Batut, Philippe and Chaisson, Mark and Gingeras, Thomas R},
title = {{STAR: ultrafast universal RNA-seq aligner}},
journal = {Bioinformatics},
year = {2013},
volume = {29},
number = {1},
pages = {15--21},
month = jan
}

@article{Kim:2015be,
author = {Kim, Daehwan and Langmead, Ben and Salzberg, Steven L},
title = {{HISAT: a fast spliced aligner with low memory requirements}},
journal = {Nature Methods},
year = {2015},
volume = {12},
number = {4},
pages = {357--360},
month = apr
}

@article{Wu:2010ep,
author = {Wu, Thomas D and Nacu, Serban},
title = {{Fast and SNP-tolerant detection of complex variants and splicing in short reads}},
journal = {Bioinformatics},
year = {2010},
volume = {26},
number = {7},
pages = {873--881},
month = apr
}

@article{Goldstein:2016hc,
author = {Goldstein, Leonard D and Cao, Yi and Pau, Gregoire and Lawrence, Michael and Wu, Thomas D and Seshagiri, Somasekar and Gentleman, Robert},
title = {{Prediction and Quantification of Splice Events from RNA-Seq Data}},
journal = {PLoS ONE},
year = {2016},
volume = {11},
number = {5},
pages = {e0156132}
}
