Publication
Notation: ‡: co-first author; #: corresponding author
Pre-prints
21 Peipei Wang#, Melissa D Lehti-Shiu, Serena Lotreck, Kenia Segura Aba, Patrick J. Krysan, Shin-Han Shiu#. 2023. Prediction of plant complex traits via integration of multi-omics data. bioRxiv bioRxiv
Published
2024
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 BMC Genomics
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 Frontiers in Plant Science
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 Phytol 234(4):1521-1533 pubmed
16 Peipei Wang#, Ally Schumacher and Shin-Han Shiu#. 2022. Computational prediction of plant metabolic pathways. Curr Opin Plant Biol 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. Mol Biol Evol 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 Phytol 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. Proc Natl Acad Sci U S A 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. Proc Natl Acad Sci U S A 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 Biol Evol 10(10):2596–2613 pubmed
2017
5 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. BBA-Gene Regul Mech 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. Nat 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. Mol Phylogenetics Evol 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). Proc Natl Acad Sci U S A 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). J Integr Plant Biol 52(12):1109–1126 pubmed