Publications on PubMed and Google Scholar 2016
- Yang, Y., Yang, Y.T., Yuan, J., Lu, Z.J.† and Li, J.J.† (2016). Large-scale mapping of mammalian transcriptomes identifies conserved genes associated with different cell states. Nucleic Acids Research. [pdf]
- Li, W.V., Chen, Y. and Li, J.J.† (2016). TROM: A testing-based method for finding transcriptomic similarity of biological samples. Statistics in Biosciences. [pdf] [arXiv pdf]
- Li, J.J.† and Tong, X. (2016). Genomic applications of the Neyman-Pearson classification paradigm. Chapter in Big Data Analytics in Genomics. Springer (New York). Hardcopy ISBN: 978-3-319-41278-8.
- 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. [pdf]
- 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. [pdf]
2015
- 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.
2014
- 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. [pdf] [NIH news]
- 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. [pdf] [NIH news]
- Li, J.J., Huang, H., Bickel, P.B., and Brenner, S.E. (2014). Comparison of D. melanogaster and C. elegans developmental stages, tissues, and cells by modENCODE RNA-seq data. Genome Research 24(7):1086-1101. [pdf] [press release] [data]
- Li, J.J., Bickel, P.B., and Biggin, M.D. (2014). System wide analyses have underestimated protein abundances and transcriptional importance in animals. PeerJ 2:e270. [pdf] [ArXiv version] [press release]
2012
- 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]
- The ENCODE Project Consortium (2012). An integrated encyclopedia of DNA elements in the human genome. Nature 489(7414):57–74. [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.
2011
2009
- 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. [pdf]
Current and former members of the Li Group are in bold
* indicates equal contribution
† indicates corresponding authors
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