Publications on PubMed and Google Scholar
Current and former members of the JSB Group are in bold
author* indicates equal contribution 
author indicates corresponding author(s)
Li, J.J., Tong, X., and Bickel, P.J. (2019). Generalized R2 measures for a mixture of bivariate linear dependences. arXiv[ SOFTWARE ]


Li, W.V.*, Li, S.*, Tong, X., Deng, L., Shi, H., and Li, J.J. (2019). AIDE: annotation-assisted isoform discovery and abundance estimation with high precision. Genome Research in press. [ SOFTWARE ]
Li, J.J., Chew, G.-L., and Biggin, M.D. (2019). Quantitation of cis-translational control by general mRNA sequence features in eukaryotes. Genome Biology 20:162. [ CODE ] | [ PDF ]
Ge, X.*, Zhang, H.*, Xie, L., Li, W.V., Kwon, S.B., and Li, J.J. (2019). EpiAlign: an alignment-based bioinformatic tool for comparing chromatin state sequences. Nucleic Acids Research gkz287. [ SOFTWARE ] [ WEBSITE ] | [ PDF ]
Razaee, Z.S., Amini, A.A., and Li, J.J. (2019). Matched bipartite block model with covariates. Journal of Machine Learning Research 20:1-44. | [ PDF ]
Li, J.J. (2019). Review of "Statistical modeling and machine learning for molecular biology" by Moses, A.M. ‚ÄčThe American Statistician 73(1):103-104. | [ PDF ]
Duong, D., Ahmad, W.U., Eskin, E., Chang, K.-W., and Li, J.J. (2019). Word and sentence embedding tools to measure semantic similarity of Gene Ontology terms by their definitions. Journal of Computational Biology 26(1):38-52. [ SOFTWARE ] | [ PDF ]


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. | [ PDF ]
Burke, J.E., Longhurst, A.D., Merkurjev, D., Sales-Lee, J., Rao, B., Moresco, J.J., Yates III, J.R., Li, J.J., and Madhani, H.D. (2018). Spliceosome profiling visualizes operations of a dynamic RNP at nucleotide resolution. Cell 173(4):1014–1030.e17. | [ PDF ]
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 ] | [ PDF ]
Tong, X.*, Feng, Y.*, and Li, J.J. (2018). Neyman-Pearson (NP) classification algorithms and NP receiver operating characteristics (NP-ROC). Science Advances 4(2):eaao1659. [ SOFTWARE ] [ VIDEO ] | [ PDF ]
Zhang, Y., Harris, C.J., Liu, Q., Liu, W., Ausin, I., Long, Y., Xiao, L., Feng, L., Chen, X., Xie, Y., Chen, X., Zhan, L., Feng, S., Li, J.J., Wang, H., Zhai, J., and Jacobsen. S.E. (2018). Large-scale comparative epigenomics reveals hierarchical regulation of non-CG methylation in Arabidopsis. Proc Natl Acad Sci. USA 115(5):E1069-E1074. | [ PDF ]


Jonassaint, C.R., Kang, C., Abrams, D.M., Li, J.J.Mao, J.Jia, Y., Long, Q., Sanger M., Jonassaint, J.C., De Castro, L., and Shah, N. (2017). Understanding patterns and correlates of daily pain using the sickle cell disease mobile application to record symptoms via technology (SMART). British Journal of Haematology. | [ PDF ]
Clifton, S.M., Kang, C.Li, J.J., Long, Q., Shah, N., and Abrams, D.M. (2017). Hybrid statistical and mechanistic mathematical model guides mobile health intervention for chronic pain. Journal of Computational Biology 24(7):675-688. | [ PDF ]
Tong, X. and Li, J.J. (2017). Discussion of "Random-projection ensemble classification" by Cannings, T.I. and Samworth, R.J. Journal of the Royal Statistical Society: Series B 79(4):1025-1026. | [ PDF ]
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 ] | [ PDF ]
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. | [ PDF ]


Li, J.J. and Tong, X. (2016). Genomic applications of the Neyman–Pearson classification paradigm. Big Data Analytics in Genomics. Springer (New York).
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 ] | [ PDF ]


Li, J.J., Huang, H., Qian, M., and Zhang, X. (2015). Chapter 24: Transcriptome analysis using next-generation sequencing. Advanced Medical Statistics (2nd Edition).
Liu, Z., Dai, S., Bones, J., Ray, S., Cha, S., Karger, B. L., Li, J.J., Wilson, L., Hinckle, G., and Rossomando, A. (2015). A quantitative proteomic analysis of cellular responses to high glucose media in Chinese hamster ovary cells. Biotechnology Progress 31(4):1026-38. | [ PDF ]
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 ] | [ PDF ]


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 ] | [ PDF ]
Boyle, A., Araya, C., Brdlik, C., Cayting, P., Cheng, C., Cheng, Y., Gardner, K., Hillier, L., Janette, J., Jiang, L., Kasper, D., Kawli, T., Kheradpour, P., Kundaje, A., Li, J.J., and 25 other authors from the modENCODE and ENCODE consortia (2014). Comparative analysis of regulatory information and circuits across distant species. Nature 512(7515):453-456. [ NIH news ] | [ PDF ]


Fisher, W.W., Li, J.J., Hammonds, A.S., Brown, J.B., Pfeiffer, B., Weiszmann, R., MacArthur, S., Thomas, S., Stamatoyannopoulos, J.A., Eisen, M.B., Bickel, P.B., Biggin, M.D., and Celniker, S.E. (2012). DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila. Proc Natl Acad Sci. USA 109(52):21330–21335. | [ PDF ]
Gao, Q., Ho, C., Jia, Y., Li, J.J., and Huang, H. (2012). Biclustering of linear patterns in gene expression data (CLiP). Journal of Computational Biology 19(6):619-631. | [ PDF ]
Li, J., Li, J., and Chen, B. (2012). Oct4 was a novel target of Wnt signaling pathway. Molecular and Cellular Biochemistry 362:233–240. | [ PDF ]


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 ] | [ PDF ]


MacArthur, S.*, Li, X.Y.*, Li, J.*, Brown, J.B., Chu, H.C., Zeng, L., Grondona, B.P., Hechmer, A., Simirenko, L., Keranen, S.V., Knowles, D.W., Stapleton, M., Bickel, P., Biggin, M.D., and Eisen, M.B. (2009). Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions. Genome Biology 10:R80. [ Faculty of 1000 recommendation ] | [ PDF ]