Publications

Research Publications, peer reviewed (print of other media):

21. Zheng Z., Wu M., Zhang J., Fu W., Xu N., Lao Y., Lin L.*, Xu H*. (2019) The natural compound neobractatin induces cell cycle arrest by regulating E2F1 and Gadd45α. Front Oncol, 9:654. (*Co-corresponding authors).

20. Wang J., Pan Y., Shen S., Lin L., Xing Y. (2017) rMATS-DVR: rMATS discovery of differential variants in RNA. Bioinformatics, 33(14): 2216-2217. [software]

19. Park E., Guo J., Shen S., Demirdjian L., Wu Y.N., Lin L., Xing Y. (2017) Population and allelic variation of A-to-I RNA editing in human transcriptomes. Genome Biol, 18(1): 143.

18. Lin L., Park J.W., Ramachandran S., Zhang Y., Tseng Y.T., Shen S., Waldvogel H.J., Curtis M.A., Faull R.L., Troncosco J.C., Pletnikova O., Ross C.A., Davidson B.L., Xing Y. (2016) Transcriptome sequencing reveals aberrant alternative splicing in Huntington’s disease. Hum Mol Genet, 25(16): 3454-3466.

17. Ji X., Park J.W., Bahrami-Samani E., Lin L., Duncan-Lewis C., Pherribo G., Xing Y., Liebhaber S. (2016) αCP binding to a cytosine-rich subset of polypyrimidine tracts drives a novel pathway of cassette exon splicing in the mammalian transcriptome. Nucleic Acids Res, 44(5): 2283-2297.

16. Lin L.*, Jiang P.*, Park J.W.*, Wang J.*, Lu Z.X., Lam M.P., Ping P., Xing Y. (2016) The contribution of Alu exons to the human proteome. Genome Biol, 17: 15. (*Co-first authors).

15. Wang J.*, Ma M.C.*, Mennie A.K.*, Pettus J.M., Xu Y., Lin L., Traxler M.G., Jakoubek J., Atanur S.S., Aitman T.J., Xing Y., Kwitek A.E. (2015) Systems biology with high-throughput sequencing reveals genetic mechanisms underlying the metabolic syndrome in the Lyon hypertensive rat. Circ Cardiovasc Genet, 8(2): 316-326. (*Co-first authors).

14. Lu Z.X.*, Huang Q.*, Park J.W.*, Shen S., Lin L., Tokheim C.J., Henry M.D., Xing Y. (2015) Transcriptome-wide landscape of pre-mRNA alternative splicing associated with metastatic colonization. Mol Cancer Res, 13(2): 305-318. (*Co-first authors).

13. Shen S.*, Park J.W.*, Lu Z.X., Lin L., Henry M.D., Wu Y.N., Zhou Q., Xing Y. (2014) rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data. Proc Natl Acad Sci USA, 111(51): E5593-601. (*Co-first authors).

12. Shen S.*, Lin L.*, Cai J.J., Jiang P., Kenkel E.J., Stroik M.R., Sato S., Davidson B.L., Xing Y. (2011) Widespread establishment and regulatory impact of Alu exons in human genes. Proc Natl Acad Sci USA, 108(7): 2837-2842. (*Co-first authors).

11. Liu S., Lin L., Jiang P., Wang D., Xing Y. (2011) A comparison of RNA-Seq and high-density exon array for detecting differential gene expression between closely related species. Nucleic Acids Res, 39(2): 578-588.

10. Lin L*, Shen S.*, Jiang P., Sato S., Davidson B.L., Ying Y. (2010). Evolution of alternative splicing in primate brain transcriptomes. Hum Mol Genet, 19(15): 2958-29273. (*Co-first authors).

9. Au K.F., Jiang H., Lin L., Xing Y., Wong W.H. (2010) Detection of splice junctions from paired-end RNA-seq data by SpliceMap. Nucleic Acids Res, 38(14): 4570-4578.

8. Lu H., Lin L., Sato S., Xing Y., Lee C.J. (2009) Predicting functional alternative splicing by measuring RNA selection pressure from multigenome alignments. PLoS Comput Biol, 5(12): e1000608.

7. Lin L., Liu S., Brockway H., Seok J., Jiang P., Wong W.H., Xing Y. (2009) Using high-density exon arrays to profile gene expression in closely related species. Nucleic Acids Res, 37(12): e90.

6. Lin L., Jiang P, Shen S, Sato S, Davidson BL, Xing Y( 2009) Large-scale analysis of exonized mammalian-wide interspersed repeats in primate genomes. Hum Mol Genet, 18(12): 2204-2214.

5. Lin L., Shen S., Tye A., Cai J.J., Jiang P., Davidson B.L., Ying Y. (2008) Diverse splicing patterns of exonized Alu elements in human tissues. PLoS Genet, 4(10).

4. Lin L., Nemeth E., Goodnough J.B., Thapa D.R., Gabayan V., Ganz T. (2008) Soluble hemojuvelin is released by proprotein convertase-mediated cleavage at a conserved polybasic RNRR site. Blood Cells Mol Dis, 40(1): 122-131.

3. Lin L., Valore E.V., Nemeth E., Goodnough J.B., Gabayan V., Ganz T. (2007) Iron transferrin regulates hepcidin synthesis in primary hepatocyte culture through hemojuvelin and BMP2/4. Blood, 110(6): 2182-2189.

2. Lin L., Goldberg Y.P., Ganz T. (2005) Competitive regulation of hepcidin mRNA by soluble and cell-associated hemojuvelin. Blood, 106(8): 2884-2889.

1. Zewail A., Xie M.W., Xing Y., Lin L., Zhang P.F., Zou W., Saxe J.P., Huang J. (2003) Novel functions of the phosphatidylinositol metabolic pathway discovered by a chemical genomics screen with wortmannin. Proc Nat Acad Sci USA, 100(6): 3345-3350.

Research Publications, peer-reviewed reviews:

2. Park E., Pan Z., Zhang Z., Lin L., Xing Y. (2018) The expanding landscape of alternative splicing variation in human populations. Am J Hum Genet, 102(1): 11-26.

1. Zhang Z., Park E., Lin L., Xing Y. (2018) A panoramic view of RNA modifications: exploring new frontiers. Genome Biology, 19(11).

Patents

The Regents of the Univ CA; Xenon Pharm, Inc.: Competitive Regulation of Hepcidin mRNA by Soluble and Cell-Associated Hemojuvelin. United States Patent Number 7,745,407, 2010.