He S, Wang X, Du Z, Liang P, Zhong Y, Wang L, Zhang YY*, Shen Y*. Physiological and transcriptomic responses to cold waves of the most cold-tolerant mangrove, Kandelia obovata. Front Plant Sci. 2023.14:1069055.
Guo Z, Ma D, Li J, Wei M, Zhang L, Zhou L, Zhou X, He S, Wang L, Shen Y*, Li QQ*, Zheng HL*.Genome-wide identification and characterization of aquaporins in mangrove plant Kandelia obovata and its role in response to the intertidal environment. Plant Cell Environ. 2022. 45(6):1698-1718.
Hao S, Hu W, Ye C, Shen Y, Li QQ*. Plastid development of albino viviparous propagules in the woody mangrove species of Kandelia obovata. Tree Physiol. 2022. 42(11):2353-2368.
Ni X, Shen Y*. Transgenerational Effects of Hexavalent Chromium on Marine Medaka (Oryzias melastigma) Reveal Complex Transgenerational Adaptation in Offspring. Biomolecules. 2021. 11(2):138. d
Li HQ, Li H, Zhou XY, Shen Y*, Su JQ*.Distinct patterns of abundant and rare subcommunities in paddy soil during wetting-drying cycles. Sci Total Environ. 2021. 785:147298.
Zhao Y, Zhong Y, Ye C, Liang P, Pan X, Zhang YY, Zhang Y*, Shen Y*. Multi-omics analyses on Kandelia obovata reveal its response to transplanting and genetic differentiation among populations. BMC Plant Biol. 2021. 21(1):341.
Liang P, Saqib HAS, Lin X, Zheng R, Qiu Y, Xie Y, Ma D, Shen Y* RNA-seq analyses of Marine Medaka (Oryzias melastigma) reveals salinity responsive transcriptomes in the gills and livers. Aquatic Toxicology. 2021;240:105970
Ni X, Shen Y*.Transgenerational Effects of Hexavalent Chromium on Marine Medaka ( Oryzias melastigma) Reveal Complex Transgenerational Adaptation in Offspring. Biomolecules; 2021; 11(2):138.
Lin J, Yu Z, Ye C, Hong L, Chu Y, Shen Y, Li QQ*. Alternative polyadenylated mRNAs behave as asynchronous rhythmic transcription in Arabidopsis. RNA Biol. 2021. 18(12):2594-2604.
Liang P, Saqib HAS, Ni X, Shen Y*. Long-read sequencing and de novo genome assembly of marine medaka (Oryzias melastigma) , BMC Genomics. 2020 16;21(1):640.
Ni X, Wan L, Liang P, Zheng R, Lin Z, Chen R, Pei M, Shen Y*.The acute toxic effects of hexavalent chromium on the liver of marine medaka (Oryzias melastigma). Comp Biochem Physiol C Toxicol Pharmacol. 2020;231:108734.
Fu H, Wang P, Wu X, Zhou X, Ji G, Shen Y, Gao Y, Li QQ*, Liang J*. Distinct genome-wide alternative polyadenylation during the response to silicon availability in the marine diatom Thalassiosira pseudonana. Plant J. 2019 99(1):67-80.
Hong L, Su W, Zhang Y, Ye C, Shen Y, Li Q Q.*. Transcriptome profiling during mangrove viviparity in response to abscisic acid. Sci Rep. 2018 15;8(1):770.
Lin J, Xu R, Wu X, Shen Y, Li QQ.*, Role of cleavage and polyadenylation specificity factor 100: anchoring poly(A) sites and modulating transcription termination, Plant Journal, 2017, 91(5): 829~839
Wu M, Liu S, Hu L, Qu H, Pan C, Lei P, Shen Y*, Yang M*. Global transcriptomic analysis of zebrafish in response to embryonic exposure to three antidepressants, amitriptyline, fluoxetine and mianserin. Aquat Toxicol. 2017; 192:274-283.
Lin J, Xu R, Wu X, Shen Y, Li QQ*.Role of cleavage and polyadenylation specificity factor 100: anchoring poly(A) sites and modulating transcription termination. Plant J. 2017; 91:829-839.
Cui Z, Shen Y, Chen KH, Mittal SK, Yang JY, Zhang G. KANK1 inhibits cell growth by inducing apoptosis though regulating CXXC5 in human malignant peripheral nerve sheath tumors. Sci Rep. 2017; 7:40325.
Fu H, Yang D, Su W, Ma L, Shen Y, Ji G, Ye X, Wu X, Li QQ.Genome-wide dynamics of alternative polyadenylation in rice. Genome Res. 26:1753-1760.
Shen Y, Chalopin D, Garcia T, Boswell M, Boswell W, Shiryev SA, Agarwala R, Volff JN, Postlethwait JH, Schartl M, Minx P, Warren WC, Walter RB. X. couchianus and X. hellerii genome models provide genomic variation insight among Xiphophorus species. BMC Genomics. 2016；17:37.
Schartl M， Shen Y, Maurus K, Walter R, Tomlinson C, Wilson RK, Postlethwait J, Warren WC. Whole Body Melanoma Transcriptome Response in Medaka. PLoS One. 2015; 10:e0143057.
Badenhorst D, Hillier LW, Literman R, Montiel EE, Radhakrishnan S, Shen Y, Minx P, Janes DE, Warren WC, Edwards SV, Valenzuela N. Physical Mapping and Refinement of the Painted Turtle Genome (Chrysemys picta) Inform Amniote Genome Evolution and Challenge Turtle-Bird Chromosomal Conservation. Genome Biol Evol. 2015;7 :2038-50
Yang K, Boswell M, Walter DJ, Downs KP, Gaston-Pravia K, Garcia T, Shen Y, Mitchell DL, Walter RB. UVB-induced Gene Expression in the Skin of Xiphophorus maculatus Jp 163 B. Comp Biochem Physiol C Toxicol Pharmacol. 2014; 163:86-94
Garcia TI, Matos I, Shen Y, Pabuwal V, Coelho MM, Wakamatsu Y, Schartl M, Walter RB. Novel method for analysis of allele specific expression in triploid Oryzias latipes reveals consistent pattern of allele exclusion. PLoS One. 2014;9:6
Schartl M*+, Walter RB*+, Shen Y, Garcia T, Catchen, JC, Amores A, Braasch I, Chalopin D, Volff JN, Fuerstenberg S, Boore J, Lesch KP, Bisazza A, Minx P, Wilson RK, Postlethwait J, and Warren CW. The genome of the platyfish, Xiphophorus maculatus: insights into complex traits. Nature Genetics. 2013; +co-first authors
Pabuwal V, Boswell M, Pasquali A, Wise SS, Kumar S, Shen Y, Garcia T, Lacerte C, Wise JP Jr, Wise JP Sr, Warren W, Walter RB. Transcriptomic analysis of cultured whale skin cells exposed to hexavalent chromium [Cr(VI)]. Aquat Toxicol. 2013; 134-135C:74-81.
Shen Y, Garcia T, Pabuwal V, Boswell M, Pasquali A, Beldorth I, Warren W, Schartl M, Cresko WA, Walter RB. Alternative strategies for development of a reference transcriptome for quantification of allele specific expression in organisms having sparse genomic resources. Comp Biochem Physiol Part D Genomics Proteomics. 2012; 8:11-16.
Shen Y, Venu RC, Nobuta K, Wu X, Notibula V, Demirci C, Meyers BC, Wang GL, and Li QQ. Transcriptome Dynamics Through Alternative Polyadenylation in Developmental and Environmental Responses in Plants Revealed by Deep Sequencing. Genome Research. 2011, 21:1478-1486.
Garcia T, Shen Y, Douglas Crawford D, Oleksiak MF, Whitehead A, Walter RB. RNA-Seq reveals complex genetic response to deepwater horizon oil release in Fundulus grandis. BMC genomics. 2012; 13:474.
Shen Y, Catchen J, Garcia T, Amores A, Beldroth I, Wagner JR, Zhang Z, Postlethwait JH, Warren W , Schartl M, and Walter RB. Identification of SNPs between Xiphophorus Lines and Species for Assessing Allele Specific Gene Expression within Interspecies Hybrids. Comparative Biochemistry and Physiology Part C: Toxicology and Pharmacology. 2012 ,155:102-108.
Downs KP, Shen Y, Pasquali A, Beldorth I, Savage M, Gallier K, Garcia T, Booth RE, Walter RB. Characterization of telomeres and telomerase expression in Xiphophorus. Comparative Biochemistry and Physiology Part C: Toxicology and Pharmacology. 2012, 155: 89-94.
Garcia T, Shen Y, Catchen J, Amores A, Schartl M, Postlethwait JH and Walter RB. Effects of short read quality and quantity on a de novo vertebrate Transcriptome assembly. Comparative Biochemistry and Physiology Part C: Toxicology and Pharmacology. 2012,155:95-101.
Zheng J, Xing D, Wu X, Shen Y, Kroll DM and Li QQ. Ratio-based Analysis of Differential mRNA Processing and Expression (RADPRE) of a Polyadenylation Factor Mutant Using Arabidopsis Genomic Tiling Microarray. PLoS ONE 2011, 6:e14719.
Ji G, Wu X, Shen Y, Huang J, Wang Z and Li QQ. Dec 2010. Classification-Based Prediction Models of Messenger RNA Polyadenylation Sites. J Theor Biol. Aug 2010,265:287-96
Shen Y, Ji G, Haas B, Wu X, Zheng, J, Reese, G, Li, QQ. Genome level analysis of rice mRNA 3'-end processing signals and alternative polyadenylation. Nucleic Acids Research. May 2008, 36:3150-3161.
Shen Y, Liu Y, Liu L, Liang C, Li QQ. Distinct genome-wide alternative polyadenylation during the response to silicon availability in the marine diatom Thalassiosira pseudonana. Genetics. 2008, 179:167-176.
Liang C, Liu Y, Liu L, Davis AC, Shen Y and Li QQ. Expressed sequence tags with cDNA termini: previously overlooked resources for gene annotation and transcriptome exploration in Chlamydomonas reinhardtii. Genetics. 2008, 179:83-93.
Ji G, Zheng J, Shen Y, Wu X, Jiang R, Lin Y, Loke JC, Davis KM, Reese GJ, Li QQ. Predictive modeling of plant messenger RNA polyadenylation sites. BMC Bioinformatics. Feb 2007, 7: 43.
Ji G, Wu XH, Zheng J, Shen Y and Li QQ. 2007.Modeling Plant mRNA Poly(A) sites: Software Design and Implementation. Journal of Computational and Theoretical Nanoscience. Nov 2007, 4:1365-1368.
Zhong X, Zhang C, Cui Y, Shen Y, Zhang Y, Yang Z. Isolation and Analysis of a High Expression Promoter in Rice. Chinese Journal of Biotechnology. Sep 2007, 23:836-840.
Shen Y, Chen DH. Effect of Different Light Cycle on Growth of Microcystis aeruginosa and Microcystis viridis. Journal of Lake Science. Jun 2005,16: 285-288.
Shen Y, Jiang H, Jin JP, Zhang ZB, Xi B, He YY, Wang G, Wang C, Qian L, LiX, Yu QB, Liu HJ, Chen DH, Gao JH, Huang H, Shi TL, Yang ZN. Development of Genome-Wide DNA Polymorphism Database for Map-Based Cloning of Rice Genes. Plant Physiol. July 2004, 135: 1198-1205.
