Bulk RNA-seq isoform discovery and quantification – The Junction of Statistics and Biology

AIDE: annotation-assisted isoform discovery and abundance estimation from RNA-seq data

36. Li, W.V.*, Li, S.*, Tong, X., Deng, L., Shi, H., and Li, J.J. (2019). AIDE: annotation-assisted isoform discovery with high precision. Genome Research 29:2056-2072. [ UCLA NEWS ] [ SOFTWARE ] [ DATA ] [ COVER ART ]

Modeling and analysis of RNA-seq data: a review from a statistical perspective

29. Li, W.V. and Li, J.J. (2018). Modeling and analysis of RNA-seq data: a review from a statistical perspective. Quantitative Biology 6(3):195-209.

MSIQ: Joint Modeling of Multiple RNA-seq Samples for Accurate Isoform Quantification

27. Li, W.V.*, Zhao, A., Zhang, S., and Li, J.J.* (2018). MSIQ: joint modeling of multiple RNA-seq samples for accurate isoform quantification. Annals of Applied Statistics 12(1):510-539. [ SOFTWARE ] [ COLOR PDF ]

NMFP: a non-negative matrix factorization based preselection method to increase accuracy of identifying mRNA isoforms from RNA-seq data.

15. Ye, Y. and Li, J.J. (2016). NMFP: a non-negative matrix factorization based preselection method to increase accuracy of identifying mRNA isoforms from RNA-seq data. BMC Genomics 17(Supp 1):11. [ SOFTWARE ]

Sparse linear modeling of RNA-seq data for isoform discovery and abundance estimation

2. Li, J.J., Jiang, C.-R., Brown, B.J., Huang, H., and Bickel, P.J. (2011). Sparse linear modeling of RNA-seq data for isoform discovery and abundance estimation. Proc Natl Acad Sci. USA 108(50):19867-19872. [ SOFTWARE ]