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Improved maize reference genome with single-molecule technologies.
Jiao Y, Peluso P, Shi J, Liang T, Stitzer MC, Wang B, Campbell MS, Stein JC, Wei X, Chin CS, Guill K, Regulski M, Kumari S, Olson A, Gent J, Schneider KL, Wolfgruber TK, May MR, Springer NM, Antoniou E, McCombie WR, Presting GG, McMullen M, Ross-Ibarra J, Dawe RK, Hastie A, Rank DR, Ware D. Jiao Y, et al. Among authors: shi j. Nature. 2017 Jun 22;546(7659):524-527. doi: 10.1038/nature22971. Epub 2017 Jun 12. Nature. 2017. PMID: 28605751 Free PMC article.
The maize W22 genome provides a foundation for functional genomics and transposon biology.
Springer NM, Anderson SN, Andorf CM, Ahern KR, Bai F, Barad O, Barbazuk WB, Bass HW, Baruch K, Ben-Zvi G, Buckler ES, Bukowski R, Campbell MS, Cannon EKS, Chomet P, Dawe RK, Davenport R, Dooner HK, Du LH, Du C, Easterling KA, Gault C, Guan JC, Hunter CT, Jander G, Jiao Y, Koch KE, Kol G, Köllner TG, Kudo T, Li Q, Lu F, Mayfield-Jones D, Mei W, McCarty DR, Noshay JM, Portwood JL 2nd, Ronen G, Settles AM, Shem-Tov D, Shi J, Soifer I, Stein JC, Stitzer MC, Suzuki M, Vera DL, Vollbrecht E, Vrebalov JT, Ware D, Wei S, Wimalanathan K, Woodhouse MR, Xiong W, Brutnell TP. Springer NM, et al. Among authors: shi j. Nat Genet. 2018 Sep;50(9):1282-1288. doi: 10.1038/s41588-018-0158-0. Epub 2018 Jul 30. Nat Genet. 2018. PMID: 30061736
Maize centromere structure and evolution: sequence analysis of centromeres 2 and 5 reveals dynamic Loci shaped primarily by retrotransposons.
Wolfgruber TK, Sharma A, Schneider KL, Albert PS, Koo DH, Shi J, Gao Z, Han F, Lee H, Xu R, Allison J, Birchler JA, Jiang J, Dawe RK, Presting GG. Wolfgruber TK, et al. Among authors: shi j. PLoS Genet. 2009 Nov;5(11):e1000743. doi: 10.1371/journal.pgen.1000743. Epub 2009 Nov 20. PLoS Genet. 2009. PMID: 19956743 Free PMC article.
Widespread gene conversion in centromere cores.
Shi J, Wolf SE, Burke JM, Presting GG, Ross-Ibarra J, Dawe RK. Shi J, et al. PLoS Biol. 2010 Mar 9;8(3):e1000327. doi: 10.1371/journal.pbio.1000327. PLoS Biol. 2010. PMID: 20231874 Free PMC article.
Diversity and evolution of centromere repeats in the maize genome.
Bilinski P, Distor K, Gutierrez-Lopez J, Mendoza GM, Shi J, Dawe RK, Ross-Ibarra J. Bilinski P, et al. Among authors: shi j. Chromosoma. 2015 Mar;124(1):57-65. doi: 10.1007/s00412-014-0483-8. Epub 2014 Sep 5. Chromosoma. 2015. PMID: 25190528
Single-molecule sequencing and optical mapping yields an improved genome of woodland strawberry (Fragaria vesca) with chromosome-scale contiguity.
Edger PP, VanBuren R, Colle M, Poorten TJ, Wai CM, Niederhuth CE, Alger EI, Ou S, Acharya CB, Wang J, Callow P, McKain MR, Shi J, Collier C, Xiong Z, Mower JP, Slovin JP, Hytönen T, Jiang N, Childs KL, Knapp SJ. Edger PP, et al. Among authors: shi j. Gigascience. 2018 Feb 1;7(2):1-7. doi: 10.1093/gigascience/gix124. Gigascience. 2018. PMID: 29253147 Free PMC article.
Sequence of the supernumerary B chromosome of maize provides insight into its drive mechanism and evolution.
Blavet N, Yang H, Su H, Solanský P, Douglas RN, Karafiátová M, Šimková L, Zhang J, Liu Y, Hou J, Shi X, Chen C, El-Walid M, McCaw ME, Albert PS, Gao Z, Zhao C, Ben-Zvi G, Glick L, Kol G, Shi J, Vrána J, Šimková H, Lamb JC, Newton K, Dawe RK, Doležel J, Ji T, Baruch K, Cheng J, Han F, Birchler JA, Bartoš J. Blavet N, et al. Among authors: shi x, shi j. Proc Natl Acad Sci U S A. 2021 Jun 8;118(23):e2104254118. doi: 10.1073/pnas.2104254118. Proc Natl Acad Sci U S A. 2021. PMID: 34088847 Free PMC article.
Elevated protein lactylation promotes immunosuppressive microenvironment and therapeutic resistance in pancreatic ductal adenocarcinoma.
Sun K, Zhang X, Shi J, Huang J, Wang S, Li X, Lin H, Zhao D, Ye M, Zhang S, Qiu L, Yang M, Liao C, He L, Lao M, Song J, Lu N, Ji Y, Yang H, Liu L, Liu X, Chen Y, Yao S, Xu Q, Lin J, Mao Y, Zhou J, Zhi X, Sun K, Lu X, Bai X, Liang T. Sun K, et al. Among authors: shi j. J Clin Invest. 2025 Jan 30:e187024. doi: 10.1172/JCI187024. Online ahead of print. J Clin Invest. 2025. PMID: 39883522
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