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 XiphophorusmaculatusJp 163 B.Comp BiochemPhysiol C ToxicolPharmacol. 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 Oryziaslatipes reveals consistent pattern of allele exclusion. PLoS One. 2014;9:6
Schartl M*+, Walter RB*+, Shen Y, GarciaT, 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, Xiphophorusmaculatus: insights into complex traits. Nature Genetics. 2013; 45:567-72
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)]. AquatToxicol. 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 PlantsRevealed 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 XiphophorusLines and Species for Assessing Allele Specific Gene Expression within Interspecies Hybrids. Comparative Biochemistry and Physiology Part C: Toxicology and Pharmacology. 2012 ,155:102-108.
Kevin P. Downs, Yingjia Shen, Amanda Pasquali, Ion Beldorth, Markita Savage, Katelyn Gallier, Tzintzuni Garcia, Rachell E. Booth, Ronald B. Walter..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. Genome level analysis of Chlamydomonasreinhardtii mRNA 3'-end processing signals and alternative polyadenylation. 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 Chlamydomonasreinhardtii. 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 Microcystisaeruginosa and Microcystisviridis. 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, Li X, 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.
Shen Y, Garcia T, Walter RB. Gene Expression Analysis Using RNA-Seq from Organisms Lacking Substantial Genomic Resources. Systems and Computational Biology - Molecular and Cellular Experimental Systems, 2011, ISBN: 978-953-307-280-7
