Publication
Notation: ‡: co-first author; #: corresponding author
Pre-prints
25 Ruidong Jia‡; Xinyi Zuo‡; Liting Zou‡; Li Wang; Letian Lin; Zhiqing Wang; Yuexia Zhang; Xingyu Chen; Fanrui Meng; Hantang Huang; Lan Lan; Zhimei Li; Fei Wang; Yuxuan Jin; Hongyan Shan; Rui Zhang#; Hongzhi Kong#; Peipei Wang#. 2026. Haplotype-resolved genome assembly advances genetic understanding of trait diversity in Phalaenopsis orchids. bioRxiv
24 Jingwei Ma‡, Zhenglin Wang‡, Liting Zou‡, Xiaoxue Wang, Xinyi Zuo, Fei Wang, Zhiqing Wang, Zhimei Li, Lin Li#, Peipei Wang#. 2025. Usefulness of scRNA-seq data in predicting plant metabolic pathway genes. bioRxiv
Published
2025
23 review Fei Wang‡, Xinyi Zuo‡, Angel Wingho SZE‡, Zhimei Li, Tao Xie, Hongyan Shan, Rui Zhang#, Ruidong Jia#, Hongzhi Kong#, Peipei Wang#. 2025. Molecular mechanisms underlying floral trait formation in Phalaenopsis orchids. Horticulture Research uhaf340 Horticulture Research
22 Peipei Wang#, Fanrui Meng, Christina B Del Azodi, Kenia Segura Aba, Michael D. Casler, Shin-Han Shiu#. 2025. Optimizing genomic prediction for complex traits via investigating multiple factors in switchgrass. Plant Physiology 198(3):kiaf188 pubmed
2024
21 Peipei Wang#, Melissa D Lehti-Shiu, Serena Lotreck, Kenia Segura Aba, Patrick J. Krysan, Shin-Han Shiu#. 2024. Prediction of plant complex traits via integration of multi-omics data. Nature Communications 15(1):6856 pubmed behind the paper
20 Wenhui Bai, Cheng Li, Wei Li, Xiaohong Han#, Peipei Wang#, Li Wang#. 2024. Machine learning assists prediction of genes responsible for plant specialized metabolite biosynthesis by integrating multi-omics data. BMC Genomics 25:418 pubmed
2023
19 Peipei Wang#, Pengxiang Fan#, Yan Bao#, Wei Li#, Li Wang#. 2023. Editorial: Omics Data-based Identification of Plant Specialized Metabolic Genes. Frontiers in Plant Science 14:1209334 pubmed
2022
18 Thilanka Ranaweera, Brianna N.I. Brown, Peipei Wang#, Shin-Han Shiu#. 2022. Temporal regulation of cold transcriptional response in switchgrass. Frontiers in Plant Science 13:998400 pubmed
17 Peipei Wang‡, Fanrui Meng‡, Paityn Donaldson, Sarah Horan, Nicholas L. Panchy, Elyse Vischulis, Eamon Winship, Jeffrey K. Conner, Patrick J Krysan, Shin-Han Shiu#, Melissa D. Lehti-Shiu#. 2022. High throughput measurement of plant fitness traits with an object detection method using Faster R-CNN. New Phytologist 234(4):1521-1533 pubmed
16 review Peipei Wang#, Ally Schumacher and Shin-Han Shiu#. 2022. Computational prediction of plant metabolic pathways. Current Opinion in Plant Biology 66:102171 pubmed
15 Bethany Moore#‡, Yun Lee‡, Peipei Wang, Christina Azodi, Erich Grotewold, and Shin-Han Shiu#. 2022. Modeling temporal and hormonal regulation of plant transcriptional response to wounding. Plant Cell 34(2): 867–888 pubmed.
2021
14 Siobhan A. Cusack, Peipei Wang, Serena G. Lotreck, Bethany M. Moore, Fanrui Meng, Jeffrey K. Conner, Patrick J. Krysan, Melissa D. Lehti-Shiu, Shin-Han Shiu#. 2021. Predictive models of genetic redundancy in Arabidopsis thaliana. Molecular Biology and Evolution 38(8):3397-3414 pubmed
13 Peipei Wang, Bethany M. Moore, Sahra Uygun, Melissa D. Lehti-Shiu, Cornelius S. Barry, Shin-Han Shiu#. 2021. Optimizing the use of gene expression data to predict plant metabolic pathway memberships. New Phytologist 231(1):475-489 pubmed
12 Peipei Wang, Fanrui Meng, Bethany M. Moore, Shin-Han Shiu#. 2021. Impact of short-read sequencing on the misassembly of a plant genome. BMC Genomics 22(1):99 pubmed
2020
11 Bethany M Moore, Peipei Wang, Pengxiang Fan, Aaron Lee, Bryan Leong, Yann-Ru Lou, Craig A Schenck, Koichi Sugimoto, Robert Last, Melissa D Lehti-Shiu, Cornelius S Barry, Shin-Han Shiu#. 2020. Within and cross species predictions of plant specialized metabolism genes using transfer learning. in silico Plants 2(1): diaa005 pubmed
10 Rui Zhang‡, Xuehao Fu‡, Caiyao Zhao‡, Jie Cheng‡, Hong Liao, Peipei Wang, Xu Yao, Xiaoshan Duan, Yi Yuan, Guixia Xu, Elena M Kramer, Hongyan Shan, Hongzhi Kong#. 2020. Identification of the key regulatory genes involved in elaborate petal development and specialized character formation in Nigella damascena (Ranunculaceae). Plant Cell 32(10): 3095-3112 pubmed
9 Pengxiang Fan, Peipei Wang, Yann-Ru Lou, Bryan J Leong, Bethany M Moore, Craig A Schenck, Rachel Combs, Pengfei Cao, Federica Brandizzi, Shin-Han Shiu, Robert Last#. 2020. Evolution of a plant gene cluster in Solanaceae and emergence of metabolic diversity. eLife 9:e56717 pubmed
8 Yan Bao‡#, Weimeng Song‡, Peipei Wang, Xiang Yu, Bei Li, Chunmei Jiang, Shin-Han Shiu, Hongxia Zhang#, Diane C Bassham#. 2020. COST1 regulates autophagy to control plant drought tolerance. Proceedings of the National Academy of Sciences of the United States of America 117(13):7482-7493 pubmed
2019
7 Bethany M. Moore, Peipei Wang, Pengxiang Fan, Bryan Leong, Craig A. Schenck, John P. Lloyd, Melissa D. Lehti-Shiu, Robert L. Last, Eran Pichersky, Shin-Han Shiu#. 2019. Robust predictions of specialized metabolism genes through machine learning. Proceedings of the National Academy of Sciences of the United States of America 116(6):2344-2353 pubmed
2018
6 Peipei Wang, Bethany M Moore, Nicholas L Panchy, Fanrui Meng, Melissa D Lehti-Shiu, Shin-Han Shiu#. 2018. Factors influencing gene family size variation among related species in a plant family, Solanaceae. Genome Biology and Evolution 10(10):2596–2613 pubmed
2017
5 review Melissa D. Lehti-Shiu, Nicholas Panchy, Peipei Wang, Sahra Uygun, Shin-Han Shiu#. 2017. Diversity, expansion, and evolutionary novelty of plant DNA-binding transcription factor families. Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms 1860(1):3-20 pubmed
2016
4 Peipei Wang‡, Hong Liao‡, Wengen Zhang‡, Xianxian Yu, Rui Zhang, Hongyan Shan, Xiaoshan Duan, Xu Yao, Hongzhi Kong#. 2016. Flexibility in the structure of spiral flowers and its underlying mechanisms. Nature Plants 2:15188 pubmed
2015
3 Jinhua Ran, Tingting Shen, Wenjuan Liu, Peipei Wang, Xiaoquan Wang#. 2015. Mitochondrial introgression and complex biogeographic history of the genus Picea. Molecular Phylogenetics and Evolution 93:63-76 pubmed
2013
2 Rui Zhang‡, Chunce Guo‡, Wengen Zhang‡, Peipei Wang, Lin Li, Xiaoshan Duan, Qinggao Du, Liang Zhao, Hongyan Shan, Scott A. Hodges, Elena M. Kramer, Yi Ren, Hongzhi Kong#. 2013. Disruption of the petal identity gene APETALA3-3 is highly correlated with loss of petals within the buttercup family (Ranunculaceae). Proceedings of the National Academy of Sciences of the United States of America 110(13):5074-5079 pubmed
2010
1 Jinhua Ran‡, Peipei Wang‡, Huijuan Zhao, Xiaoquan Wang#. 2010. A test of seven candidate barcode regions from the plastome in Picea (Pinaceae). Journal of Integrative Plant Biology 52(12):1109–1126 pubmed