Chapter: Genomic Applications of the Neyman-Pearson Classification Paradigm
16. Li, J.J. and Tong, X. (2016). Genomic applications of the Neyman-Pearson classification paradigm. Big Data Analytics in Genomics. Springer (New York).
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 ]
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 ]
Chapter 24: Transcriptome analysis using next-generation sequencing
13. Li, J.J., Huang, H., Qian, M., and Zhang, X. (2015). Chapter 24: Transcriptome analysis using next-generation sequencing. Advanced Medical Statistics (2nd Edition).
A quantitative proteomic analysis of cellular responses to high glucose media in Chinese hamster ovary cells
12. 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.
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 ]
Comparative analysis of regulatory information and circuits across distant species
9. 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. [ […]
Comparison of D. melanogaster and C. elegans developmental stages, tissues, and cells by modENCODE RNA-seq data
8. 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. [ Press release ] [ Top 10 papers selected at the 2014 RECOMB/ISCB Conference on Regulatory & Systems Genomics ]
System wide analyses have underestimated protein abundances and transcriptional importance in animals
7. 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. [ Press release ] [ Guest post on “Bits of DNA” blog ] [ PeerJ Picks 2015″ Collection ] [ Top Bioinformatics Papers – June 2015″ Collection ] [ Top 5 most […]