Li, S., Wei L, Gao Q, M. Xu M, Wang Y,  Lin Z, P. Holford P, Chen ZH and  Zhang L (2023). "Molecular and phylogenetic evidence of parallel expansion of anion channels in plants." Plant Physiology. kiad687, https://doi.org/10.1093/plphys/kiad687

    Li, X., Yu S Cheng Z, Chang X, Yun Y, Jiang M, Chen X, Wen X, Li H, Zhu W, Xu S,  Xu Y, Wang X, Zhang C,  Wu Q, Hu J, Lin Z, Aury JM, Van de Peer Y, Wang Z,  Zhou X, Wang J, Lu Pand Zhang L (2023). "Origin and evolution of the triploid cultivated banana genome." Nature Genetics. Dec 11. https://doi.org/10.1038/s41588-023-01589-3 .

    Vijjamarri A.K.; Gupta N; Onu C; Niu  X⁺; Zhang F; Kumar R; Lin Z; Greenberg M; Hinnebusch AG.  mRNA decapping activators Pat1 and Dhh1 regulate transcript abundance and translation to tune cellular responses to nutrient availability. Nucleic Acids Research, gkad584 (2023), https://doi.org/10.1093/nar/gkad584

    Wang J., Alwin BL., Lai Y., Dong H., Xu L., Fu XY., Lin Z., Shi PY., Lu TK., Luo D, Jaffrey SR., Dedon PC., A systems-level mass spectrometry-based technique for accurate and sensitive quantification of the RNA cap epitranscriptome. Nature Protocols. (2023)  https://doi.org/10.1038/s41596-023-00857-0 

    Vijjamarri A.K., Niu X⁺., Vandermeulen M.D., Onu C., Zhang F., Qiu H., Gupta N., Gaikwad S., Greenberg M.L., Cullen P.J., Lin Z., Hinnebusch AG.  Decapping factor Dcp2 controls mRNA abundance and translation to adjust metabolism and filamentation to nutrient availability. eLife, (2023) 12:e85545.

    Wang Z., Pu J., Richards C., Giannetti E., Cong H., Lin Z. and Chung H. (2023) Evolution of a fatty acyl-CoA elongase underlies desert adaptation in Drosophila. Science Advances, 9,eadg0328(2023).DOI:10.1126/sciadv.adg03283.

    Liu H, Liu X, Chang X, Chen F, Lin Z, Zhang L. Large-scale analyses of angiosperm Flowering Locus T genes reveal duplication and functional divergence in monocots. Front Plant Sci. 2023 Jan 4;13:1039500. doi: 10.3389/fpls.2022.1039500.

    Lu Z⁺, Berry K, Hu Z, Zhan Y⁺, Ahn TH*, and Lin Z*.  TSSr: an R package for comprehensive analyses of TSS sequencing data. NAR: Genomics and Bioinformatics; 2021, 3 (4), lqab108, [Full Text | PDF]

    Rosato M, Hoelscher B, Lin Z, Agwu C, Xu F. Transcriptome analysis provides genome annotation and expression profiles in the central nervous system of Lymnaea stagnalis at different ages. BMC Genomics 2021 22:637.[Full Text | PDF]

    Lu Z⁺ and  Lin Z*,  The origin and evolution of a distinct mechanism of transcription initiation in yeasts. Genome Research. 2021; 31:51-63; [Full Text | PDF]  Cover story.

    Zhang H^‡, Lu Z^+‡, Zhan Y⁺, Rodriguez J⁺, Lu C*, Xue Y*, Lin Z*.  Distinct roles of nucleosome sliding and histone modifications in controlling the fidelity of transcription initiation. RNA Biology. 2020; doi: 10.1080/15476286.2020.1860389. [ PDF ]

    Chang X, Wei L, Lu Z⁺, Chen ZH, Chen F, Lai Z, Lin Z*, Zhang L*. Origins and stepwise expansion of R2R3-MYB transcription factors for the terrestrial adaptation of plants. Frontiers in Plant Science. 2020; 11:575360. doi: 10.3389/fpls.2020.575360. 

    Zhang L*, Yang JR, Zhang G*, Lin Z*. Genomic variations of COVID-19 suggest multiple outbreak sources of transmission.   preprint available at medRxiv 2020 doi: https://doi.org/10.1101/2020.02.25.20027953

    Zhang L, Shen FM, Chen F, Lin Z. Origin and evolution of the 2019 novel coronavirus. Clinical Infectious Diseases. 2020; 71: 882-883 [Full Text | PDF]

    Mersman BA, Jolly SN, Lin Z, Xu F. Gap Junction Coding Innexin in Lymnaea stagnalis: Sequence Analysis and Characterization in Tissues and the Central Nervous System  Frontiers in Synaptic Neuroscience. 2020; 12: 1  [Full Text | PDF]

    Fanter CE, Lin Z, Keenan SW, Janzen FJ, Mitchell TS, Warren DE. Development-specific transcriptomic profiling suggests new mechanisms for anoxic survival in the ventricle of overwintering turtles. Journal of Experimental Biology. 2020 223  doi: 10.1242/jeb.213918 [Full Text | PDF]

    Mullis A^+‡, Lu Z^+‡, Zhan Y^+‡, Wang TY, Rodriguez J^§, Rajeh A^#, Chatrath A^#, and Lin Z*. Concerted evolution of ribosomal protein genes in fungi and its adaptive significance. Mol. Biol. Evol.; 2020; 37: 455-468, [Full Text | PDF]

    Wang J, Chew BLA, Lai Y, Dong H, Xu L, Balamkundu S, Cai WM, Cui L, Liu CF, Fu XY, Lin Z, Shi PY, Lu TK, Luo D, Jaffrey SR, and Dedon PC, Quantifying the RNA cap epitranscriptome reveals novel caps in cellular and viral RNA. Nucleic Acid Research 2019; 47(20):e130,  [Full Text | PDF]

    Chen F, Song Y, Li X, Zhang X, Tang H, Lin Z, and Zhang L. Genome sequences of horticultural plants: past, present, and future. Horticulture Research  2019; 6:112  [Full Text | PDF]

    Lu Z⁺ and  Lin Z*,  Pervasive and Dynamic Transcription Initiation in Saccharomyces cerevisiae, Genome Research 2019. 29:1198-1210;  [Full Text | PDF]

    McMillan J^#‡, Lu Z^+‡, Rodriguez JS, Ahn T-H*, Lin Z*. YeasTSS: An Integrative Web Database of Yeast Transcription Start Sites. Database (Oxford) 2019 baz048,  [Full Text | PDF]   

    Vijayraghavan S, Kozmin SG, Strope PK, Skelly DA, Lin Z, Kennell J, Magwene PM, Dietrich FS. and McCusker JH. Mitochondrial Genome Variation Affects Multiple Respiration and Non-respiration Phenotypes in Saccharomyces cerevisiae. Genetics 2019; 211(2):773-86; [Full Text ] 

    Chen F, Zhang L, Lin Z, Cheng ZM. Identification of a novel fused gene family implicates convergent evolution in eukaryotic calcium signaling. BMC Genomics 2018; 19:306   [Full Text | PDF]   

    Rajeh A^#, Lv J, and Lin Z*. Heterogeneous rates of genome rearrangement contributed to the disparity of species richness in Ascomycota. BMC Genomics 2018; 19:282  [Full Text | PDF]

    Chen F, Dong W, Zhang, J, Guo X, Lin Z, Tang H, Zhang L. The sequenced angiosperm genomes and genome databases.  Frontiers in Plant Science 2018; 9:418.  [Full Text | PDF]

    Chen F, Hu Y,  Vannozzi A, Wu K, Cai H, Qin Y, Mullis A⁺, Lin Z*, and Zhang, L*. The WRKY transcription factor family in model plants and crops. Critical Reviews in Plant Sciences. 2018; 36:311-335  [Full Text | PDF]

    Wang B, Han X, Bai Y, Lin Z, Qiu M, Nie X, Wang S, Zhang F, Zhuang Z, Yuan J, Wang S. Effects of nitrogen metabolism on growth and aflatoxin biosynthesis in Aspergillus flavus. J Hazard Mater. 2017; 324(Pt B):691-700. [ Full text  |PDF ] 

    Zhang L, Chen F, Zhang GQ, Zhang YQ, Niu S, Xiong JS, Lin Z, Cheng Z, Liu ZJ.Origin and mechanism of crassulacean acid metabolism in orchids as implied by comparative transcriptomics and genomics of the carbon fixation pathway. The Plant Journal 2016; 86: 175-185  [ Full text  |PDF ] 

    Li Y, Zhang W, Zheng D, Zhou Z, Yu W, Zhang L, Feng L, Liang X, Guan W, Zhou J, Chen J, and Lin Z*. Genomic Evolution of Saccharomyces cerevisiae under Chinese Rice Wine Fermentation. Genome Biol. Evol. 2014; 6: 2516-2526  [ Full text  |PDF ] 

    Lin Z and Li WH. Comparative Genomics and Evolutionary Genetics of Yeast Carbon Metabolism in Molecular Mechanisms in Yeast Carbon Metabolism J. Piškur and C. Compagno Editors. 2014 Springer Berlin Heidelberg. p. 97-120. [full text | PDF ]

    Zhu Y, Lin Z, and Nakhleh L. Evolution After Whole-genome Duplication: A Network Perspective. G3: Genes Genomes Genetics 2013; 3:2049-2057 [ Full text  |PDF ] 

    Lin Z, Wang TY, Tsai BS, Wu FT, Yu FJ, Tseng YJ, Sung HM, and Li WH. Identifying cis-regulatory changes involved in the evolution of aerobic fermentation in yeasts. Genome Biol. Evol. 2013; 5:1065-1078.  [ Full text  |PDF ] 

    Li Y, Zhang L, Ball RL, Liang X, Li J, Lin Z, and Liang H. Comparative analysis of somatic copy-number alterations across different human cancer types reveals two distinct classes of breakpoint hotspots. Hum. Mol. Genet.  2012; 21:4957-4965 [ Full text  |PDF ] 

    Lin Z, and Li WH.  Evolution of 5’untranslated region length and gene expression reprogramming in yeasts.  Mol. Biol. Evol. 2012; 29:81-89 [ Full text |PDF ]

    Lin Z, and Li WH.  The evolution of aerobic fermentation in Schizosaccharomyces pombe was associated with regulatory reprogramming but not nucleosome reorganization.  Mol. Biol. Evol. 2011; 28: 1407-1413  [ Full text  |PDF]

    Lin Z, and Li WH. Expansion of hexose transporter genes was associated with evolution of aerobic fermentation in yeasts. Mol. Biol. Evol. 2011; 28: 131-142 [ Full text |PDF ]

    Lin Z, Wu WS, Liang H, Woo Y and Li WH. Spatial distributions of cis regulatory elements and nucleosomes in yeast promoters and their effects on transcriptional regulation. BMC Genomics 2010; 11:581 [ Full text |PDF ]

    Zhou X, Lin Z, and Ma H.  Phylogenetic detection of numerous gene duplications shared by animals fungi and plants. Genome Biology 2010; 11: R38 [Full text| PDF ]

    Li Y, Liang H, Gu Z,  Lin Z, Guan W, Zhou L, Li Y, and Li WH. Detecting positive selection in the budding yeast genome. J Evol Biol. 2009; 22: 2430. [Full text | PDF ]

    Lin Z*, Ma H, and Nei M. Ultraconserved coding regions outside the homeobox of mammalian Hox genes.  BMC Evol Biol. 2008; 8: 260. [ Full text |PDF ] Review of this publication  at   

    Lin Z, Nei M, and Ma H. The origins and early evolution of DNA mismatch repair genes: multiple horizontal gene transfers and co-evolution. Nucleic Acids Res. 2007; 35 7591-7603. [ Full text | PDF ]

    Lin Z, Kong H, Nei M, and Ma H. Origins and evolution of the recA/RAD51 gene family: evidence for ancient gene duplication and endosymbiotic gene transfer.Proc. Natl. Acad. Sci. U S A. 2006; 103 10328-10333. [ Full text | PDF ]  

    Li W, Yang X, Lin Z, Timofejeva L, Xiao R, Makaroff CA, and Ma H. TheAtRAD51C gene is required for normal meiotic chromosome synapsis and double-stranded break repair in Arabidopsis. Plant Physiol. 2005; 138 965-976.  [ Full text | PDF ]