2023
Ying Zhen*#, Michel A.K. Dongmo*, Ryan J. Harrigan, Kristen Ruegg, Qi Fu, Rachid Hanna, Timothy C. Bonebrake, Thomas B. Smith. Strong habitat-specific phenotypic plasticity but no genome-wide differentiation across a rainforest gradient in an African butterfly. Evolution (2023). 77: 1430–1443. 
Adam H. Freedman, Ryan J. Harrigan, Ying Zhen, Alison M. Hamilton, Thomas B. Smith. Evidence for ecotone speciation across an African rainforest-savanna gradient. Molecular Ecology (2023). 32(9): 2287-2230.
Lu Yang, Flora Borne, Anja Betz, Matthew L. Aardema, Ying Zhen, Julie Peng, Regina Visconti, Mariana Wu, Bartholomew P. Roland, Aaron D. Talsma, Michael J. Palladino, Georg Petschenka, Peter Andolfatto#. Predatory fireflies and their toxic firefly prey have evolved distinct toxin resistance strategies Current Biology (2023). 33(23): 5160.
2022
Tianyu Wang, Lina Shi, Ying Zhen#. Gut-Specific Cardenolide-Resistant Sodium Pump Primed an Omnivore to Feed on Toxic Oleander. IScience (2022). 25 (12): 105616.
Chengqi Zhu#, Xiaodong Xu, Ying Zhen#. Systematic review of the firefly genus Emeia Fu, Ballantyne & Lambkin, 2012 (Coleoptera, Lampyridae) from China. ZooKeys (2022). 1113 (July): 153–166.
Chengqi Zhu#, Xiaodong Xu, Ying Zhen#. Two New Species of Pyrocoelia Gorham (Coleoptera: Lampyridae) from Southwest China. Zootaxa (2022). 5162 (2): 173–182.
Victoria L. Sork, Shawn J. Cokus, Sorel T. Fitz-Gibbon, Aleksey V. Zimin, Daniela Puiu, Jesse A. Garcia, Paul F. Gugger, Claudia L. Henriquez, Ying Zhen, Kirk E. Lohmueller, Matteo Pellegrini, Steven L. Salzberg. High-quality genome and methylomes illustrate features underlying evolutionary success of oaks. Nature Communications (2022). 13 (1), 1-15.
Jianhua Luo*, Qi Yang*, Xiaofeng Zhang*, Yuanyuan Zhang*, Li Wan*, Xiechao Zhan, Yao Zhou, Liuqing He, Danyang Li, Dazhi Jin, Ying Zhen, Jing Huang, Yanyan Li#, and Liang Tao#. TFPI is a colonic crypt receptor for TcdB from hypervirulent clade 2 C. difficile. Cell (2022). 185 (6), 980-994.
2021
Ying Zhen#, Christian D. Huber, Robert W. Davies, Kirk E. Lohmueller#. Greater strength of selection and higher proportion of beneficial amino acid changing mutations in humans compared with mice and Drosophila melanogaster. Genome Research (2021). 31:110–120.
Thomas B. Smith, Trevon L. Fuller, Ying Zhen, Virginia Zaunbrecher, Henri A. Thomassen, Kevin Njabo, Nicola M. Anthony. Genomic vulnerability and socio-economic threats under climate change in an African rainforest bird. Evolutionary Applications (2021). 14(5): 1239-1247.
2020
Katy Morgan, Jean-François Mboumba, Stephan Ntie, Patrick Mickala, Courtney A Miller, Ying Zhen, Ryan J Harrigan, Vinh Le Underwood, Kristen Ruegg, Eric B Fokam, Geraud C Tasse Taboue, Paul R Sesink Clee, Trevon Fuller, Thomas B Smith, Nicola M Anthony. Precipitation and vegetation shape patterns of genomic and craniometric variation in the central African rodent Praomys misonnei. Proceedings of the Royal Society B (2020). 287(1930): 20200449.
Enhui Shen, Kangli Zhu, Danyang Li, Zhenrui Pan, Yun Luo, Qiao Bian, Liuqing He, Xiaojun Song, Ying Zhen, Dazhi Jin, Liang Tao. Subtyping analysis reveals new variants and accelerated evolution of Clostridioides difficile toxin B. Communications Biology (2020). 3(1): 1-8.
2018
Bridgett M. vonHoldt, Rebecca Y. Kartzinel, Christian D. Huber, Vinh Le Underwood, Ying Zhen, Kristen Ruegg, Kirk E. Lohmueller, Thomas B. Smith. Growth factor gene IGF1 is associated with bill size in the black-bellied seedcracker Pyrenestes ostrinus. Nature Communications (2018). 9:4855.
2017
Ying Zhen#, Ryan J. Harrigan, Kristen Ruegg, Eric C. Anderson, Thomas C. Ng, Sirena Lao, Kirk E. Lohmueller, and Thomas B. Smith. Genomic divergence across ecological gradients in the Central African rainforest songbird (Andropadus virens). Molecular Ecology (2017). 26: 4966–4977.
Kyle J. McCulloch, Furong Yuan, Ying Zhen, Matthew L. Aardema, Gilbert Smith, Jorge Llorente-Bousquets, Peter Andolfatto and Adriana D. Briscoe. Sexual Dimorphism and Retinal Mosaic Diversification Following the Evolution of a Violet Receptor in Butterflies. Molecular Biology and Evolution (2017). 34(9): 2271–2284.
2012
Ying Zhen, Matthew L Aardema, Edgar M Medina, Molly Schumer, Peter Andolfatto. Parallel molecular evolution in an herbivore community. Science (2012). 337:1634-1637.
Matthew L. Aardema, Ying Zhen, Peter Andolfatto. The evolution of cardenolide-resistant forms of Na+,K+-ATPase in Danainae butterflies. Molecular Ecology (2012). 21(2): 340-349.
Ying Zhen and Peter Andolfatto. Methods to detect selection on non-coding DNA. Chapter 6, Evolutionary Genomics: statistical and computational methods, Volume 2, Methods in Molecular Biology (2012), 856(1).
2011
Ying Zhen#, Preeti Dhakal and Mark C. Ungerer. Fitness benefits and costs of cold acclimation in Arabidopsis thaliana. American Naturalist (2011). 178(1): 44-52.
2010
Takeshi Kawakami, Suzanne C. Strakosh, Ying Zhen, and Mark C. Ungerer. Different scales of Ty1/copia-like retrotransposon proliferation in the genomes of three diploid hybrid sunflower species. Heredity (2010). 104: 341-350.
2008
Ying Zhen, Mark C Ungerer. Relaxed selection on the CBF/DREB1 regulatory genes and reduced freezing tolerance in the southern range of Arabidopsis thaliana. Molecular Biology and Evolution (2008), 25(12):2547-2555.
Ying Zhen, Mark C Ungerer. Clinal variation in freezing tolerance among natural accessions of Arabidopsis thaliana. New Phytologist (2008). 177(2): 419–427.
2007
Fei He, D Kang, Y Ren, Li-Jia Qu, Ying Zhen and Hongya Gu. Genetic diversity of the natural populations of Arabidopsis thaliana in China. Heredity (2007). 99: 423–431.
2006
Mark C Ungerer, Suzanne C Strakosh, Ying Zhen. Genome expansion in three hybrid sunflower species is associated with retrotransposon proliferation. Current Biology (2006). 16(20): R872-R873.