21. Han E, Geng Z, Qin Y, Wang Y, and Ma S. 2024. Single-cell network analysis reveals gene expression programs for Arabidopsis root development and metabolism. Plant Communications  5:100978. [Full text] [中文解读]

        构建了拟南芥根系单细胞基因共表达网络，鉴定出调控根系不同细胞类型发育和代谢的基因模块

20. Xu Y, Wang Y, and Ma S. 2024. SingleCellGGM enables gene expression program identification from single-cell transcriptomes and facilitates universal cell label transfer. Cell Reports Methods  4:100813. [Full text] [中文解读] [软件下载]

        开发出一种针对单细胞数据的基因共表达网络分析算法 SingleCellGGM

19. Peng Y, Liu Y, Wang Y, Geng Z, Qin Y, and Ma S. 2024. Stomatal maturomics: hunting genes regulating guard cell maturation and function formation from single-cell transcriptomes. Journal of Genetics and Genomics 51:1286-1299 [Full text] [中文解读]

提出气孔成熟组学的研究方法，并据此发现两个气孔环形刚度调控基因

18. Wang Y, Zhang Y, Yu N, Li B, Gong J, Mei Y, Bao J, and Ma S. 2023. Decoding transcriptional regulation via a human gene expression predictor. Journal of Genetics and Genomics. [Full text] [中文解读] [软件下载]

开发了用于预测人类基因模块上游转录因子预测工具EXPLICIT-Human

17. 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 190:1526-1542 [Full text] [中文解读]

系统鉴定了调控水稻重要农艺性状的性状基因模块，验证OsOPS1调控水稻种子大小

16. 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 (#共同一作) [Full text] [中文解读] [软件下载]

开发系统预测激酶组功能的算法 EXPLICIT-Kinase，验证 Raf6 激酶调控气孔运动

15. 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. (#共同一作) （Plant Journal 杂志2021年Outstanding Paper Award）[Full text] [中文解读] [软件下载]

开发了拟南芥转录调控网络 EXPLICIT ，用于分析转录调控因子

14. 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.

13. 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) (*共同通讯作者)

12. 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. (*共同通讯作者)

11. 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.

10. 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. (*共同通讯作者)

9. 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. (*共同通讯作者)

8. 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.

7. 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. (*共同通讯作者)

6. 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.

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

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

3. 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.

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

1. 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.

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