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- Comprehensive genomic characterization of squamous cell lung cancers. Cancer Genome Atlas Research Network. Nature 489(7417):519-25, 2012. Erratum in: Nature 491(7423):288, 2012.
- DiffSplice: the genome-wide detection of differential splicing events with RNA-seq. Hu Y, Huang Y, Du Y, Orellana CF, Singh D, Johnson AR, Monroy A, Kuan PF, Hammond SM, Makowski L, Randell SH, Chiang DY, Hayes DN, Jones C, Liu Y, Prins JF, Liu J. Nucleic Acids Res 41(2):e39, 2013.
- A robust method for transcript quantification with RNA-seq data. Huang Y, Hu Y, Jones CD, MacLeod JN, Chiang DY, Liu Y, Prins JF, Liu J. J Comput Biol 20(3):167-87, 2013.
- A Probabilistic Framework for Aligning Paired-end RNA-seq Data. Hu Y, Wang K, He X, Chiang DY, Prins JF, Liu J. Bioinformatics 26:1950-1957, 2010.
- MapSplice: Mapping RNA-seq Reads for Splice Junction Discovery. Wang K, Singh D, Zeng Z, Huang Y, Coleman S, He X, Perou C, MacLeod JN, Chiang DY, Prins JF, Liu J. Nucleic Acids Research Methods Online 38(18):1-14, 2010.