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Zhenguo Lin, Ph.D.

Associate Professor
Biology

Courses Taught

Genetics, Genomics, Bioinformatics I, Bioinformatics II, Molecular Phylogenetic Analysis

Education

Ph.D., Pennsylvania State University

Research Interests

We are broadly interested in studying the evolution of genomes and gene regulation using fungal species as a model system. The main focus of our research is to better understand the regulation and evolution of transcription initiation mechanisms. We apply high-throughput sequencing, bioinformatics, and molecular biology approaches to achieve our research aims. More information about the research program of my lab is available at www.zlinlab.org

Labs and Facilities

Lin Lab webpage: www.zlinlab.org

Publications and Media Placements

*corresponding author, +graduate student mentee, #undergraduate student mentee

Chen J+, Bermingham JR‡*, Minx P, Kremitzky M, Lin Z*, Warren DE*.  A new chromosome-level genome assembly for western painted turtle Chrysemys picta belli, a model for extreme physiological adaptations. Preprint available at bioRxiv; 2025;  doi: 10.1101/2025.04.01.646645 

Zhan Y+., Hu Z+, Lu Z+ and Lin Z*. The Patterns of Alternative TSS Usage Explain the Highly Heterogeneous Landscape of 5’UTR Lengths in Eukaryotes. NAR Genomics and Bioinformatics; 2025; lqaf152, doi:  10.1093/nargab/lqaf152

Poonia P, Valabhoju V, Li T, Iben J, Niu X+, Lin Z, Hinnebusch AG. Yeast poly(A)-binding protein (Pab1) controls translation initiation in vivo primarily by blocking mRNA decapping and decay. Nucleic Acids Research; 2025; 53(5). doi:  10.1093/nar/gkaf143

Roshan P, Biswas A, Ahmed S, Anagnos S, Luebbers R, Harish K, Li M, Nguyen N, Zhou G, Tedeschi F, Hathuc V, Lin Z, Hamilton Z, Origanti S. Sequestration of ribosomal subunits as inactive 80S by targeting eIF6 limits mitotic exit and cancer progression. Nucleic Acids Research; 2025; 53(4). doi: 10.1093/nar/gkae1272

Gardner C‡., Chen J+., Hadfield C., Lu Z+., Debruin D., Zhan, Y+., Donlin MJ.,  Ahn TH*. and Lin Z*.  Chromosome-level Subgenome-aware de novo  Assembly of  Saccharomyces bayanus  Provides Insight into Genome Divergence after Hybridization. Genome Research; 2024;34(11):2133-46. doi: 10.1101/gr.279364.124.

Hu Z+, Chen J+, Olatoye MO, Zhang H. and Lin Z*. Transcriptome-wide expression landscape and starch synthesis pathway co-expression network in sorghum. Plant Genome; 2024; 17, e20448.  doi: 10.1002/tpg2.20448.

Li, S., Wei L, Gao Q, M. Xu M, Wang Y,  Lin Z, P. Holford P, Chen ZH and  Zhang L. "Molecular and phylogenetic evidence of parallel expansion of anion channels in plants." Plant Physiology; 2024;194;2533-2548; kiad687, doi: 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. "Origin and evolution of the triploid cultivated banana genome." Nature Genetics; 2024; 56:136-142; doi: 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; 2023; 51:9314-9336; doi 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; 18:2671-2698;  doi: 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. doi: 10.7554/eLife.85545

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; 2023; 9,eadg0328; 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;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

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.

Lu Z+ and Lin Z*, The origin and evolution of a distinct mechanism of transcription initiation in yeasts. Genome Research. 2021; 31:51-63; 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.

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

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

Zhang L, Shen FM, Chen F, Lin Z. Origin and Evolution of the 2019 Novel Coronavirus. Clin Infect Dis 2020. 71: 882-883.

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. J Exp Biol 2020. 223.

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. Front Synaptic Neurosci 2020. 12: 1.

Mullis A+, Lu Z+, Zhan Y+, Wang TY, Rodriguez J+, Rajeh A#, Chatrath A, Lin Z*. Parallel Concerted Evolution of Ribosomal Protein Genes in Fungi and Its Adaptive Significance. Molecular biology and evolution 2020. 37: 455-468.

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

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

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

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

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

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

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

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

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

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

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

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

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.

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

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.

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

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

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

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

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

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

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.

Lin Z*, Ma H, and Nei M. Ultraconserved coding regions outside the homeobox of mammalian Hox genes. BMC Evol Biol; 2008, 8:260.

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.

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. USA; 2006, 103:10328-10333.

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.