Zhenguo Lin, Ph.D.

Assistant Professor

Courses Taught

Genomics, Bioinformatics I, Bioinformatics II


 Ph.D., Pennsylvania State University

Research Interests

The main research interests of Lin's laboratory are in understanding the evolutionary dynamics of genomic architecture, content and sequences in different lineages of organisms, and in elucidating its impacts on the evolution of biological novelty and diversity through integrated analyses of genomic, transcriptomic and epigenomic data. These studies tackle fundamental biological questions, but are also directly and indirectly related to many human diseases, especially human cancers. Specifically, current research projects in his laboratory are to develop innovative approaches by integrating computational and experimental tools to address:

  • Evolutionary dynamics of genome architecture and chromosome subtelomeric regions
  • Evolution of promoter structure and gene regulation
  • Genetic basis underlying the evolution of biological novelty and complexity.

Labs and Facilities

Lin's laboratory applies both computational and experimental approaches to study the evolution of genome and gene regulation. There are a variety of research opportunities for undergraduate and graduate students with different research interests and expertise. Students will a chance to learn useful techniques and skills in genomics, bioinformatics, molecular biology, and genetics. Students are also encouraged to conceive, design and conduct their own research projects. Highly motivated students are welcome to contact Lin for research opportunities.

Publications and Media Placements

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, In press

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(9):2516-26.

Lin, Z. and W.-H. Li. Comparative Genomics and Evolutionary Genetics of Yeast Carbon Metabolism. Molecular Mechanisms in Yeast Carbon Metabolism. J. Piškur and C. Compagno, Springer Berlin Heidelberg: 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 Biology and Evolution; 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. Human Molecular Genetics; 2012:21:4957-4965

Lin, Z., and Li, WH. Evolution of 5'untranslated region length and gene expression reprogramming in yeasts. Molecular Biology and Evolution; 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. Molecular Biology and Evolution; 2011: 28: 1407-1413

Lin, Z., and Li, WH. Expansion of hexose transporter genes was associated with evolution of aerobic fermentation in yeasts. Molecular Biology and Evolution; 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 evidence for abundant ancient gene duplication in early eukaryotes. 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. Journal of Evolutionary Biology; 2009; 22: 2430.

Lin, Z., Ma, H., and Nei, M. Ultraconserved coding regions outside the homeobox of mammalian Hox genes. BMC Evolutionary Biology; 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 Research; 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. Proceedings of the National Academy of Sciences USA; 2006; 103: 10328-10333.

Li, W., Yang, X., Lin, Z., Timofejeva, L., Xiao, R., Makaroff, C.A., and Ma, H. The AtRAD51C gene is required for normal meiotic chromosome synapsis and double-stranded break repair in Arabidopsis. Plant Physiology; 2005; 138: 965-976.