Publications

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

26. Wang R+, Helbig I, Edmondson AC, Lin L, Xing Y+. (2023) Splicing defects in rare diseases: transcriptomics and machine learning strategies towards genetic diagnosis. Briefings in Bioinformatics, bbad284. (+joint corresponding authors)

25. Wang F*, Xu Y*, Wang R*, Zhang B, Smith N, Notaro A, Gaerlan S, Kutschera E, Kadash-Edmondson KE, Xing Y+, Lin L+ (2023) TEQUILA-seq: A versatile and low-cost method for targeted long-read RNA sequencing. Nature Communications, 14:4760. (+joint corresponding authors; *joint first authors)

24. Gao Y+*, Wang F*, Wang R, Kutschera E, Xu Y, Xie S, Wang Y, Kadash-Edmondson K, Lin L, Xing Y+ (2023) ESPRESSO: Robust discovery and quantification of transcript isoforms from error-prone long-read RNA-seq data. Science Advances, 9(3):eabq507. (*joint first authors, +joint corresponding authors).

23. Wang Z*, Pan Z*, Adhikari S, Harada BT, Shen L, Yuan W, Abeywardana T, Al-Hadid Q, Stark JM, He C, Lin L+, Yang Y+ (2021) m6A deposition is regulated by PRMT1‐mediated arginine methylation of METTL14 in its disordered C‐terminal region. EMBO, 40(5):e106309 (*joint first authors, +joint corresponding authors).

22. Xin R*, Gao Y*, Gao Y, Wang R, Kadash-Edmondson KE, Liu B, Wang Y, Lin L, Xing Y. (2021) isoCirc catalogs full-length circular RNA isoforms in human transcriptomes. Nature Communications, 12:266. (*joint first authors).

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. (+joint 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 YN, 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 JW, Ramachandran S, Zhang Y, Tseng YT, Shen S, Waldvogel HJ, Curtis MA, Faull RL, Troncosco JC, Pletnikova O, Ross CA, Davidson BL, Xing Y. (2016) Transcriptome sequencing reveals aberrant alternative splicing in Huntington’s disease. Hum Mol Genet, 25(16):3454-3466.

17. Ji X, Park JW, 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 JW*, Wang J*, Lu ZX, Lam MP, Ping P, Xing Y. (2016) The contribution of Alu exons to the human proteome. Genome Biol, 17:15. (*joint first authors).

15. Wang J*, Ma MC*, Mennie AK*, Pettus JM, Xu Y, Lin L, Traxler MG, Jakoubek J, Atanur SS, Aitman TJ, Xing Y, Kwitek AE. (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. (*joint first authors).

14. Lu ZX*, Huang Q*, Park JW*, Shen S, Lin L, Tokheim CJ, Henry MD, Xing Y. (2015) Transcriptome-wide landscape of pre-mRNA alternative splicing associated with metastatic colonization. Mol Cancer Res, 13(2):305-318. (*joint first authors).

13. Shen S*, Park JW*, Lu ZX, Lin L, Henry MD, Wu YN, 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. (*joint first authors).

12. Shen S*, Lin L*, Cai JJ, Jiang P, Kenkel EJ, Stroik MR, Sato S, Davidson BL, Xing Y. (2011) Widespread establishment and regulatory impact of Alu exons in human genes. Proc Natl Acad Sci USA, 108(7):2837-2842. (*joint 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 BL, Ying Y. (2010). Evolution of alternative splicing in primate brain transcriptomes. Hum Mol Genet, 19(15): 2958-29273. (*joint first authors).

9. Au KF, Jiang H, Lin L, Xing Y, Wong WH. (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 CJ. (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 WH, 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 JJ, Jiang P, Davidson BL, Ying Y. (2008) Diverse splicing patterns of exonized Alu elements in human tissues. PLoS Genet, 4(10):e1000225.

4. Lin L, Nemeth E, Goodnough JB, Thapa DR, 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 EV, Nemeth E, Goodnough JB, 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 YP, Ganz T. (2005) Competitive regulation of hepcidin mRNA by soluble and cell-associated hemojuvelin. Blood, 106(8):2884-2889.

1. Zewail A, Xie MW, Xing Y, Lin L, Zhang PF, Zou W, Saxe JP, 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(1):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.