Publications

Zhang Y, Han E, Peng Y, Wang Y, Wang Y, Geng Z, Xu Y, Geng H, Qian Y, and Ma S. 2022. Rice network analysis identified gene modules associated with agronomic traits. Plant Physiology accepted.

Peng Y^#, Zuo W^#, Zhou H, Miao F, Zhang Y, Qin Y, Liu Y, Long Y, and Ma S. 2022. EXPLICIT-Kinase: a gene expression predictor for dissecting the functions of the Arabidopsis kinome. Journal of Integrative Plant Biology (^#co-first author) [Full Text]

Geng H^#, Wang M^#, Gong J^#, Xu Y, and Ma S. 2021. An Arabidopsis expression predictor enables inference of transcriptional regulators for gene modules. Plant Journal 107: 597-612. (^#co-first author) [Full Text] (Outstanding Paper Award 2021, by Plant Journal)

Lee D, Lal NK, Lin ZD, Ma S, Liu J, Castro B, Toruno T, Dinesh-Kumar SP, and Coaker G. 2020. Regulation of reactive oxygen species during plant immunity through phosphorylation and ubiquitination of RBOHD. Nature Communications 11:1838. [Full Text]

Shen Y, Liu J, Geng H, Zhang J, Liu Y, Zhang H, Xing S, Du J^*, Ma S^*, and Tian Z*. 2018. De novo assembly of a Chinese soybean genome. Science China Life Sciences 61:871-884. (^*co-corresponding author) [Full Text]

Ma S^*, Ding Z, Li P^*. 2017. Maize network analysis revealed gene modules involved in development, nutrients utilization, metabolism, and stress response. BMC Plant Biology 17:131. (^*co-corresponding author) [Full Text]

Feng B, Ma S, Chen S, Zhu N, Zhang S, Yu B, Yu Y, Le B, Chen X, Dinesh-Kumar SP, Shan L, He P. 2016. PARylation of the forkhead-associated domain protein DAWDLE regulates plant immunity. EMBO Reports 17:1799-1813.

Ma S^*, Bohnert HJ, Dinesh-Kumar SP^*. 2015. AtGGM2014, an Arabidopsis gene co-expression network for functional studies. Science China Life Sciences 58: 276-286. (^*co-corresponding author)

Ma S^*, Shah S, Bohnert HJ, Snyder M, Dinesh-Kumar SP^*. 2013. Incorporating Motif Analysis into Gene Co-expression Networks Reveals Novel Modular Expression Pattern and New Signaling Pathways. Plos Genetics 9: e1003840. (^*co-corresponding author)

Padmanabhan MS, Ma S, Burch-Smith TM, Czymmek K, Huijser P, Dinesh-Kumar SP. 2013. Novel Positive Regulatory Role for the SPL6 Transcription Factor in the N TIR-NB-LRR Receptor-Mediated Plant Innate Immunity. Plos Pathogens 9: e1003235.

Ma S^*, Bachan S, Porto M, Bohnert HJ, Snyder M, Dinesh-Kumar SP^*. 2012. Discovery of stress responsive DNA regulatory motifs in Arabidopsis. PLoS One 7: e43198. (^*co-corresponding author)

Lee HY, Bowen CH, Popescu GV, Kang H-G, Kato N, Ma S, Dinesh-Kumar S, Snyder M, Popescu SC. 2011. Arabidopsis RTNLB1 and RTNLB2 Reticulon-Like Proteins Regulate Intracellular Trafficking and Activity of the FLS2 Immune Receptor. Plant Cell 23: 3374-3391.

Ma S, Bohnert HJ. 2007. Integration of Arabidopsis thaliana stress-related transcript profiles, promoter structures, and cell-specific expression. Genome Biology 8: R49.

Ma S, Gong Q, Bohnert HJ. 2007. An Arabidopsis gene network based on the graphical Gaussian model. Genome Research 17: 1614-1625.

Bohnert H, Gong Q, Li P, Ma S. 2006. Unraveling abiotic stress tolerance mechanisms – getting genomics going. Current Opinion in Plant Biology 9: 180-188.

Ma S, Gong Q, Bohnert H. 2006. Dissecting salt stress pathways. Journal of Experimental Botany 57: 1097-1107.

Gong Q, Li P, Ma S, Rupassara S, Bohnert H. 2005. Salinity stress adaptation competence in the extremophile Thellungiella halophila in comparison with its relative Arabidopsis thaliana. Plant Journal 44: 826-839.