An accurate and robust imputation for single cell RNA-seq data
26. Li, W.V. and Li, J.J. (2018). An accurate and robust imputation method scImpute for single-cell RNA-seq data. Nature Communications 9:997. [ UCLA NEWS ] [ SOFTWARE ]
Neyman-Pearson (NP) classification algorithms and NP receiver operating characteristics (NP-ROC)
25. Tong, X.*, Feng, Y.*, and Li, J.J. (2018). Neyman-Pearson classification algorithms and NP receiver operating characteristics. Science Advances 4(2):eaao1659. [ SOFTWARE ] [ VIDEO ] [ Francis X. Diebold’s Blog on NP Classification ]
Quantitating Translational Control: mRNA Abundance-Dependent and Independent Contributions and the mRNA Sequences That Specify Them
22. Li, J.J., Chew, G.-L., and Biggin, M.D. (2017). Quantitating translational control: mRNA abundancee-dependent and independent contributions and the mRNA sequences that specify them. Nucleic Acids Research 45(20):11821-11836. [ Highlight talk at RECOMB 2018 ]
TROM: a testing-based method for finding transcriptomic similarity of biological samples
19. Li, W.V., Chen, Y., and Li, J.J. (2017). TROM: a testing-based method for finding transcriptomic similarity of biological samples. Statistics in Biosciences 9(1):105-136. [ SOFTWARE ]
Correspondence of D. melanogaster and C. elegans developmental stages revealed by alternative splicing characteristics of conserved exons
18. Gao, R. and Li, J.J. (2017). Correspondence of D. melanogaster and C. elegans developmental stages revealed by alternative splicing characteristics of conserved exons. BMC Genomics 18:234.
Large-scale mapping of mammalian transcriptomes identifies conserved genes associated with different cell states
17. Yang, Y.*, Yang, Y.T.*, Yuan, J., Lu, Z.J., and Li, J.J. (2017). Large-scale mapping of mammalian transcriptomes identifies conserved genes associated with different cell states. Nucleic Acids Research 45(4):1657-1672. [ DATA ]
Epigenome overlap measure (EPOM) for comparing tissue/cell types based on chromatin states
14. Li, W.V., Razaee, Z.S., and Li, J.J. (2016). Epigenome overlap measure (EPOM) for comparing tissue/cell types based on chromatin states. BMC Genomics 17(Supp 1):10. [ SOFTWARE ]
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 ]
Statistics requantitates the central dogma
11. Li, J.J. and Biggin, M.D. (2015). Statistics requantitates the central dogma. Science 347(6226):1066-1067. [ UCLA NEWS ] [ Interview at Significance 12(3):8 ]
Comparative analysis of the transcriptome across distant species
10. Gerstein, M.B.*, Rozowsky, J.*, Yan, K.K.*, Wang, D.*, Cheng, C.*, Brown, J.B.*, Davis, C.A.*, Hillier, L*, Sisu, C.*, Li, J.J.*, Pei, B.*, Harmanci, A.O.*, Duff, M.O.*, Djebali, S.*, and 82 other authors from the modENCODE consortium (2014). Comparative analysis of the transcriptome across distant species. Nature 512(7515):445-448. [ NIH NEWS ]