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Peer Reviewed Publications (*corresponding author, +graduate student,     #undergraduate student)


   Lu Z+ and  Lin Z*,  The origin and evolution of a distinct mechanism of transcription initiation in yeasts.  preprint available at bioRxiv doi: https://doi.org/10.1101/2020.04.04.025502 

    Zhang L*, Yang JR, Zhang G*, Lin Z*. Genomic variations of COVID-19 suggest multiple outbreak sources of transmission.  preprint available at medRxiv 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 ciaa112[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 [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 2019 : jeb.213918 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.; 2019 msz229, [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 

Prior to Joining SLU

    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 ]

Other Publications

Zhenguo Lin Gene Transfer from Organelles to Nuclei Visualized Molecular Evolution Forum 2012-07

Zhenguo Lin Instant Insecticide Resistance by Symbiosis Molecular Evolution Forum 2012-06

Zhenguo Lin Evolution of a Poison-Resistance Gene through Introgression Molecular Evolution Forum 2012-04


5 Fat Loss Keys

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