2018Publications

No.

Paper Information

1.      

Liu Y, Cao ZZ, Wang YN, Guo Y, Xu P, Yuan PF, Liu ZH, He Y,Wei WS. (2018) Genome-wide screening for functional long noncoding RNAs in human cells by Cas9 targeting of splice sites.Nat Biotechnol., 36: 1203-1210.

2.      

Zhou Z,Wei WS. (2018)PrePAIRing Cas9s for screening success.Nat Biotechnol., 36: 147-148.

3.      

Du XM, Huang G, He SP, Yang ZE, Sun GF, Ma XF, Li N, Zhang XY, Sun JL, Liu M, Jia YH, Pan ZE, Gong WF, Liu ZH, Zhu HQ, Ma L, Liu FY, Yang DG, Wang F, Fan W, Gong Q, Peng Z, Wang LR, Wang XY, Xu SJ, Shang HH, Lu CR, Zheng HK, Huang SW, Lin T,Zhu YX, Li FG. (2018) Resequencing of 243 diploid cotton accessions based on an updated A genome identifies the genetic basis of key agronomic traits.Nature Genet., 50: 796-802.

4.      

Li Q, Zhang X, Zhang ZG. (2018) CHAF1B Overexpression: A Brake for the Differentiation of Leukemia Cells.Cancer Cell,34: 693-694.

5.      

Zeng H, He B, Xia B, Bai DS, Lu XY, Cai JB, Chen L, Zhou AK, Zhu CX, Meng HW, Gao Y, Guo HS, He C, Dai Q,Yi CQ. (2018) Bisulfite-Free Nanoscale Analysis of 5-Hydroxymethylcytosine at Single Base Resolution.J Am Chem Soc., 140: 13190-13194.

6.      

Liu Y, Bhowmick T, Liu YQ, Gao XF, Mertens HDT, Svergun DI,Xiao JY, Zhang Y, Wang JH, Meijers R. (2018) Structural Basis for Draxin-Modulated Axon Guidance and Fasciculation by Netrin-1 through DCC.Neuron,97: 1261-1267.

7.      

Shu XT, Liu MH, Lu ZK, Zhu CX, Meng HW, Huang SH, Zhang XX,Yi CQ. (2018) Genome-wide mapping reveals that deoxyuridine is enriched in the human centromeric DNA.Nat Chem Biol., 14: 680-687.

8.      

Gao SX, Feng SM, Ning SK, Liu JY, Zhao HY, Xu YX, Shang JF, Li KJ, Li Q,Guo R, Xu DY. (2018) An OB-fold complex controls the repair pathways for DNA double-strand breaks.Nat Commun., 9: 3925.

9.      

Zhang H, Wang YR, Li J, Chen H, He XL, Zhang HW, Liang H,Lu J. (2018) Biosynthetic energy cost for amino acids decreases in cancer evolution.Nat Commun., 9: 4124.

10.   

Zhang H, Zhu QY, Cui JX, Wang YX, Chen MJ, Guo X, Tagliabracci VS, Dixon JE,Xiao JY. (2018) Structure and evolution of the Fam20 kinases.Nat Commun., 9: 1218.

11.   

Wang M, Tai C, Weinan E,Wei LP. (2018) DeFine: deep convolutional neural networks accurately quantify intensities of transcription factor-DNA binding and facilitate evaluation of functional non-coding variants.Nucleic Acids Res.,46: e69.

12.   

Luo SQ, He F, Luo JJ, Dou SQ, Wang YR, Guo AN,Lu J. (2018) Drosophila tsRNAs preferentially suppress general translation machinery via antisense pairing and participate in cellular starvation response.Nucleic Acids Res., 46: 5250-5268.

13.   

Li SQ, Xu ZY, Xu JW, Zuo LY, Yu CH, Zheng P, Gan HY, Wang XZ, Li LT, Sharma S, Chabes A, Li D, Wang S, Zheng SH, Li JB, Chen XF, Sun YJ, Xu DY, Han JH, Chan KM, Qi Z,Feng JX, Li Q.(2018) Rtt105 functions as a chaperone for replication protein A to preserve genome stability.EMBO J., 37:e99154.

14.   

Duan YG, Dou SQ, Zhang H, Wu CC, Wu MM,Lu J. (2018) Linkage of A-to-I RNA Editing in Metazoans and the Impact on Genome Evolution.Mol Biol Evol., 35: 132-148.

15.   

Ye AY, Dou YM, Yang XX, Wang S, Huang AY,Wei LP. (2018) A model for postzygotic mosaicisms quantifies the allele fraction drift, mutation rate, and contribution to de novo mutations.Genome Res., 28: 943-951.

16.   

Zhao XH, Jiang Y, Li J, Huq E, Chen ZJ, Xu DQ,Deng XW. (2018) COP1 SUPPRESSOR 4 promotes seedling photomorphogenesis by repressing CCA1 and PIF4 expression in Arabidopsis.Proc Natl Acad Sci U S A., 115: 11631-11636.

17.   

Liang K, Li NN, Wang X, Dai JY, Liu PL, Wang C, Chen XW, Gao N,Xiao JY. (2018) Cryo-EM structure of human mitochondrial trifunctional protein.Proc Natl Acad Sci US A., 115: 7039-7044.

18.   

Song QX, Ando A, Xu DQ, Fang L, Zhang TZ, Huq E, Qiao H,Deng XW, Chen ZJ. (2018) Diurnal down-regulation of ethylene biosynthesis mediates biomass heterosis.Proc Natl Acad Sci U S A.,115: 5606-5611.

19.   

Shi H, Lyu M, Luo YW, Liu SC, Li Y, He H, Wei N,Deng XW, Zhong SW. (2018) Genome-wide regulation of light-controlled seedling morphogenesis by three families of transcription factors.Proc Natl Acad Sci U S A.,115: 6482-6487.

20.   

Zhou YY,Yang L, Duan J, Cheng JK, Shen YP, Wang XJ, Han R, Li H, Li Z,Wang LH, William Terzaghi, Zhu DM, Chen HD,Deng XW, Li JG. (2018) Hinge region of Arabidopsis phyA plays an important role in regulating phyA function.Proc Natl Acad Sci U S A.,115: E11864-E11873.

21.   

Xu R, Xu YX, Huo W, Lv ZC, Yuan JS, Ning SK, Wang QS, Hou M, Gao G, Ji JG, Chen JJ,Guo R, Xu DY. (2018) Mitosis-specific MRN complex promotes a mitotic signaling cascade to regulate spindle dynamics and chromosome segregation.Proc Natl Acad Sci U S A.,115: E10079-E10088.

22.   

Yang JG, Xie XQ, Xiang N, Tian ZX, Dixon R,Wang YP. (2018) Polyprotein strategy for stoichiometric assembly of nitrogen fixation components for synthetic biology.Proc Natl Acad Sci U S A.,115: E8509-E8517.

23.   

Liu YC, Sun X, Driscoll C, Miquelle DG, Xu X, Mrartelli P, Uphyrkina O, Smith JLD, O'Brien SJ,Luo SJ. (2018) Genome-Wide Evolutionary Analysis of Natural History and Adaptation in the World's Tigers.Curr Biol., 28: 3840-3849.

24.   

Zhang H, Dou SQ, He F, Luo JJ, Wei LP,Lu J. (2018) Genome-wide maps of ribosomal occupancy provide insights into adaptive evolution and regulatory roles of uORFs during Drosophila development.PLoS Biol., 16: e2003903.

25.   

Yang CZ, Zang WC, Tang ZF, Ji YP, Xu RD, Yang YF, Luo AP, Hu B, Zhang ZM, Liu ZH,Zheng XF. (2018) A20/TNFAIP3 Regulates the DNA Damage Response and Mediates Tumor Cell Resistance to DNA-Damaging Therapy.Cancer Res.,78: 1069-1082.

26.   

Li JC, Liang WJ, Li Y,Qian WQ. (2018) APURINIC/APYRIMIDINIC ENDONUCLEASE2 and ZINC FINGER DNA 3'-PHOSPHOESTERASE Play Overlapping Roles in the Maintenance of Epigenome and Genome Stability.Plant Cell,30: a1954-1970.

27.   

Lin F, Jiang Y, Li J, Yan TT, Fan LM, Liang JS, Chen ZJ, Xu DQ,Deng XW. (2018) B-BOX DOMAIN PROTEIN28 Negatively Regulates Photomorphogenesis by Repressing the Activity of Transcription Factor HY5 and Undergoes COP1-Mediated Degradation.Plant Cell, 30: 2006-2019.

28.   

Guan FH, Yu JY, Yu J, Liu Y, Li Y, Feng XH, Huang KC,Chang ZY, Ye S.(2018) Lateral interactions between protofilaments of the bacterial tubulin homolog FtsZ are essential for cell division.Elife., 7: e35578.

29.   

Xiong XS, Li XY,Yi CQ. (2018) N-1-methyladenosine methylome in messenger RNA and non-coding RNA.Curr Opin Chem Biol., 45:179-186.

30.   

Liu Y,Cai H. (2018) The Lrp of Mycobacterium tuberculosis regulates the innate immune response of macrophages.Cell Mol Immunol., 15: 934-936.

31.   

Yuan RR, Lan JQ, Fang YX, Yu H, Zhang JZ, Huang JY,Qin GJ. (2018) The Arabidopsis USL1 controls multiple aspects of development by affecting late endosome morphology.New Phytol., 219: 1388-1405.

32.   

Xia M, Han X, He H, Yu RB, Zhen G, Jia XP, Cheng BJ,Deng XW. (2018) Improved de novo genome assembly and analysis of the Chinese cucurbit Siraitia grosvenorii, also known as monk fruit or luo-han-guo.Gigascience.,7: doi: 10.1093.

33.   

Peng LN, Cheng SJ, Lin Y, Cui QH, Luo YY, Chu JH, Shao MM, Fan WY, Chen YM, Lin A, Xi YY, Sun YX, Zhang L, Zhang C, Tan W,Gao G, Wu C, Lin DX. (2018) CCGD-ESCC: A Comprehensive Database for Genetic Variants Associated with Esophageal Squamous Cell Carcinoma in Chinese Population.Genomics Proteomics Bioinformatics., 16: 262-268.

34.   

Guan JH, Yu SY,Zheng XF. (2018) NEDDylation antagonizes ubiquitination of proliferating cell nuclear antigen and regulates the recruitment of polymerase eta in response to oxidative DNA damage.Protein Cell., 9: 365-379.

35.   

Yan XW, Yang JY, Xu JW,Feng JX, Li Q. (2018) Histone chaperone Spt16p is required for heterochromatin mediated silencing in budding yeast.Protein Cell., 9: 652-658.

36.   

Xu DQ, Jiang Y, Li J, Holm M,Deng XW. (2018) The B-Box Domain Protein BBX21 Promotes Photomorphogenesis.Plant Physiol., 176: 2365-2375.

37.   

Chen ZS, Liu XF, Wang DH, Chen R, Zhang XL, Xu ZH,Bai SN. (2018) Transcription Factor OsTGA10 Is a Target of the MADS Protein OsMADS8 and Is Required for Tapetum Development.Plant Physiol.,176: 819-835.

38.   

Wang XC, Yang M, Ren DQ, Terzaghi W,Deng XW,He GM. (2018) Cis-regulated alternative splicing divergence and its potential contribution to environmental responses inArabidopsis.Plant J., doi: 10.1111/tpj.14142.

39.   

Yang ZR,Li Y. (2018) Dissection of RNAi-based antiviral immunity in plants.Curr Opin Virol., 32: 88-99.

40.   

Yang B, Song Z, Li C, Jiang J, Zhou Y, Wang R, Wang Q. Ni C, Liang Q, Chen H,Fan LM. (2018) RSM1, an Arabidopsis MYB protein, interacts with HY5/HYH to modulate seed germination and seedling development in response to abscisic acid and salinity. PLoS Genet., 14: e1007839.

41.   

Huang AY, Yang XX, Wang S, Zheng XN, Wu QX, Ye AY,Wei LP. (2018) Distinctive types of postzygotic single-nucleotide mosaicisms in healthy individuals revealed by genome-wide profiling of multiple organs.PLoS Genet.,14: e1007395.

42.   

Yang Y, Nicolas M, Zhang JZ, Yu H, Guo DS, Yuan RR, Zhang TT, Yang JZ, Cubas P,Qin GJ. (2018) The TIE1 transcriptional repressor controls shoot branching by directly repressing BRANCHED1 in Arabidopsis.PLoS Genet.,14: e1007296.

43.   

Deng MJ, Tao J, E C, Ye ZY, Jiang Z, Yu J,Su XD. (2018) Novel Mechanism for Cyclic Dinucleotide Degradation Revealed by Structural Studies of Vibrio Phosphodiesterase V-cGAP3.J Mol Biol.,430: 5080-5093.

44.   

Fu XM, Wang Y, Shao HQ, Ma J, Song XW, Zhang M,Chang ZY. (2018) DegP functions as a critical protease for bacterial acid resistance.FEBS J., 285: 3525-3538.

45.   

Luo JJ, Wang YR, Yuan J, Zhao ZL,Lu J(2018) MicroRNA duplication accelerates the recruitment of new targets during vertebrate evolution.RNA,24: 787-802.

46.   

Xiong XS, Li XY, Wang K,Yi CQ. (2018) Perspectives on topology of the human m1A methylome at single nucleotide resolution.RNA,24: 1437-1442.

47.   

Zhang HM, Zhou YX, Wang YA, Zhao YG, Qiu YT, Zhang XY, Yue D, Zhou Z,Wei WS. (2018) A surrogate reporter system for multiplexable evaluation of CRISPR/Cas9 in targeted mutagenesis.Sci Rep., 8: 1042.

48.   

Ai C,Kong L. (2018) CGPS: A machine learning-based approach integrating multiple gene set analysis tools for better prioritization of biologically relevant pathways.J Genet Genomics., 45: 489-504.

49.   

Sun Y, Huang JY, Zhong S, Gu HY, He S,Qu LJ. (2018) Novel DYW-type pentatricopeptide repeat (PPR) protein BLX controls mitochondrial RNA editing and splicing essential for early seed development of Arabidopsis.J Genet Genomics.,45: 155-168.

50.   

Cheng SJ, Jiang S, Shi FY, Ding Y,Gao G. (2018) Systematic identification and annotation of multiple-variant compound effects at transcription factor binding sites in human genome.J Genet Genomics.,45: 373-379.

51.   

Zeng H, He B,Yi CQ,Peng JY. (2018)Liquid biopsies: DNA methylation analyses in circulating cell-free DNA.J Genet Genomics., 45:185-192.

52.   

Liu X, Yang MK, Wang Y, Chen Z, Zhang J, Lin XH, Ge F,Zhao JD. (2018) Effects of PSII Manganese-Stabilizing Protein Succinylation on Photosynthesis in the Model Cyanobacterium Synechococcus sp PCC 7002.Plant Cell Physiol., 59: 1466-1482.

53.   

Yang CH, Li JR, Wu QX, Yang XX, Huang AY, Zhang J, Ye AY, Dou YM, Yan LL, Zhou WZ, Kong L, Wang M, Ai C, Yang DC,Wei LP. (2018) AutismKB 2.0: a knowledgebase for the genetic evidence of autism spectrum disorder.Database, doi: 10.1093/database/bay106.

54.   

Liu YN, Luo MY, Jin ZC, Zhao M,Qu H. (2018) dbLGL: an online leukemia gene and literature database for the retrospective comparison of adult and childhood leukemia genetics with literature evidence.Database,doi: 10.1093/database/bay062.

55.   

Yang H, Wang XC, Wei YX, Deng Z, Liu H, Chen JS, Dai LJ, Xia ZH,He GM, Li DJ.(2018) Transcriptomic analyses reveal molecular mechanisms underlying growth heterosis and weakness of rubber tree seedlings.BMC Plant Biol., 18: 10.

56.   

Zeng FL, Hua Y, Liu XQ, Liu SJ, Lao KJ, Zhang Z,Kong DC. (2018) Gpn2 and Rba50 Directly Participate in the Assembly of the Rpb3 Subcomplex in the Biogenesis of RNA Polymerase II.Mol Cell Biol., 38:e00091-18.

57.   

Liu YN, Luo MY, Li QJ, Lu JC, Zhao M,Qu H. (2018) CIGene: a literature-based online resource for cancer initiation genes.BMC Genomics,19: 552.

58.   

Wang DH, Song W, Wei SW, Zheng YF, Chen ZS, Han JD, Zhang HT, Luo JC, Qin YM, Xu ZH,Bai SN. (2018) Characterization of the Ubiquitin C-Terminal Hydrolase and Ubiquitin-Specific Protease Families in Rice (Oryza sativa).Front Plant Sci.,9: 1636.

59.   

Liang L, Yang J, Gao ZX, Wang Q, Liang Q, Song ZH, Bi Y, Li CN, He H,Fan LM. (2018) SPINDLY is involved in ABA signaling bypassing the PYR/PYLs/RCARs-mediated pathway and partly through functional ABAR.Environ Exp Bot., 151: 43-54.

60.   

Pan JW, Huang DH, Guo ZL, Kuang Z, Zhang H, Xie XY, Ma ZF, Gao SP, Lerdau MT, Chu CC,Li L. (2018) Overexpression of microRNA408 enhances photosynthesis, growth, and seed yield in diverse plants.J Integr Plant Biol., 60: 323-340.

61.   

Wang YQ, Li J,Deng XW, Zhu DM. (2018) Arabidopsis noncoding RNA modulates seedling greening during deetiolation.Sci China Life Sci., 61: 199-203.

62.   

Bai SN, Ge H, Qian H. (2018) Structure for energy cycle: a unique status of the second law of thermodynamics for living systems.Sci China Life Sci., 61: 1266-1273.

63.   

Wang K,Yi CQ. (2018) Coupling Transcription and Translation via the Epitranscriptomic m6A Mark.Biochemistry., doi: 10.1021/acs.biochem.8b00903.

64.   

Li Y, Kumar S,Qian WQ. (2018) Active DNA demethylation: mechanism and role in plant development.Plant Cell Rep., 37: 77-85.

65.   

Du S, Qu LJ,Xiao JY. (2018) Crystal structures of the extracellular domains of the CrRLK1L receptor-like kinases ANXUR1 and ANXUR2.Protein Sci., 27: 886-892.

66.   

Li MZ, Zheng LJ, Shen J, Li XY, Zhang Q, Bai X, Wang QS,Ji JG. (2018)SIRT1 facilitates amyloid beta peptide degradation by upregulating lysosome number in primary astrocytes.Neural Regen Res., 13: 2005-2013.

67.   

Zhu W,Li LF, Deng MJ, Wang B, Li MF, Ding GF, Yang ZS, Medynski D, Lin XT, Ouyang Y, Lin JR, Li LY, Lin XL. (2018) Oxidation-resistant and thermostable forms of alpha-1 antitrypsin from Escherichia coli inclusion bodies.FEBS Open Bio., 8: 1711-1721.

68.   

Wang CG, Guan YK, Lv MZ, Zhang R, Guo ZY, Wei XM, Du XX, Yang J, Li T, Wan Y,Su XD, Huang XJ, Jiang ZF. (2018) Manganese Increases the Sensitivity of the cGAS-STING Pathway for Double-Stranded DNA and Is Required for the Host Defense against DNA Viruses.Immunity., 48: 675–687.

69.   

Westerman E, VanKuren N, Massardo D, Tanger-Trolander A,Zhang W, Hill RI, Perry M, Bayala E, Barr K, Chamberlain N, Douglas TE, Buerkle N, Palmer S, Kronfost MR. (2018) Aristaless controls butterfly wing color variation used in mimicry and mate choice.Curr Biol.,28: 3469-3474.

70.   

Zhang SM, Li C, Zhou YY, Wang XJ, Li H, Feng ZY, Chen HD, Qin GJ, Jin D, Terzaghi W, Gu HY., Qu LJ., Kang DM,Deng XW, Li JG. (2018) TANDEM ZINC-FINGER/PLUS3 Is a Key Component of Phytochrome A Signaling.Plant Cell, 30: 835-852.

71.   

Wang S, Shuai Y, Sun CY, Xue BX, Hou YP,Su XD, Sun YJ. (2018) Lighting up Live Cells with Smart Genetically Encoded Fluorescence Probes from GMars Family.ACS Sens., 3: 2269−2277.

72.   

Li Q, Lin F, Yang C, Wang J, Lin Y, Shen M, Park MS, Li T, Zhao JD. (2018) A Large-Scale Comparative Metagenomic Study Reveals the Functional Interactions in Six Bloom-Forming Microcystis-Epibiont Communities.Front Microbiol., 9: 746.

73.   

Wang J, Wang C, Li JH, Bai P, Li Q, Shen MY, Li RH, Li T,Zhao JD. (2018) Comparative genomics of degradative Novosphingobium strains with special reference to the microcystin-degrading Novosphingobium sp. THN1. Front Microbiol., 9: 2238.

74.   

Constantinides AE, Severin CC, Gumpper RH,Zheng XF, Luo M. (2018) Characterizations of the PB2 Cap Binding Domain Accelerate Inhibitor Design.Crystals, 8: 62.

75.   

Huang Y,Li Y. (2018) Secondary siRNAs rescue virus-infected plants.Nat Plant, 4: 136-137.

76.   

Hong L, Lu MD, Dinel MP, Blain P, Peng W,Gu HY, Masson JF. (2018) Hybridization conditions of oligonucleotide-capped gold nanoparticles for SPR sensing of microRNA.Biosens Bioelectron., 109: 230-236.

77.   

Li Y, Shao S, Xu X,Su XD, Sun YJ, Wei SC.(2018). MapZ Forms a Stable Ring Structure That Acts As a Nanotrack for FtsZ Treadmilling in Streptococcus mutans.ACS Nano., 12: 6137-6146.

78.   

Jin D, Wu M, Li BS, Bucker B, Keil P, Zhang SM, Li JG, Kang DM, Liu J, Dong J,Deng XW, Irish V, Wei N. (2018) The COP9 Signalosome regulates seed germination by facilitating protein degradation of RGL2 and ABI5.PLoS Genet.,14:e1007237.

79.   

Gaubert P, Antunes A, Meng H, Miao L, Peigne S, Justy F, Njiokou F, Dufour S, Danquah E, Alahakoon J, Verheyen E, Stanley WT, O'Brien SJ, Johnson WE,Luo SJ. (2018) The Complete Phylogeny of Pangolins: Scaling Up Resources for the Molecular Tracing of the Most Trafficked Mammals on Earth.J Hered., 109: 347-359.

80.   

Nallu S, Hill JA, Don K, Sahagun C,Zhang W, Meslin C, Snell-Rood E, Clark NL,Morehouse NI, Bergelson J, Wheat CW, Kronforst MR. Westerman E, Nitzany E, Palmer S, Kronforst MR. (2018) The molecular genetic basis of herbivory between butterflies and their host-plants.Nat Ecol Evol., 2: 1418-1427.

81.   

Li H, Zhu L, Chen H, Li T, Han Q, Wang S, Yao X, Feng H, Fan L, Gao S, Boyd R, Cao X, Zhu P, Li J, Keating A,Su XD, Zhao RC. (2018) Generation of Functional Hepatocytes from Human Adipose-Derived MYC+KLF4+GMNN+Stem Cells Analyzed by Single-Cell RNA-Seq Profiling.Stem CellsTransl Med., 7: 792-805.

82.   

Chen YO, Bao Y, Ma HZ, Yi ZZ, Zhou Z,Wei WS. (2018) [Gene editing technology and its research progress in China].Yi Chuan.40: 900-915. (in Chinese)