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]

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]

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]

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]

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]

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]

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]

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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