Savithramma Dinesh-Kumar Department of Plant Biology and the Genome Center, University of California, USA
1 protocol

Shisong Ma
  • University of California
Research focus
  • Plant science
  • 2 Author merit


Ph.D. in Biology, University of Illinois at Urbana-Champaign, 2007

Current position

Assistant Project Scientist, Department of Plant Biology & Genome Center, University of California, Davis


  1. Ma, S., Shah, S., Bohnert, H. J., Snyder, M. and Dinesh-Kumar, S. P. (2013). Incorporating motif analysis into gene co-expression networks reveals novel modular expression pattern and new signaling pathways. PLoS Genet 9(10): e1003840.
  2. Padmanabhan, M. S., Ma, S., Burch-Smith, T. M., Czymmek, K., Huijser, P. and Dinesh-Kumar, S. P. (2013). Novel positive regulatory role for the SPL6 transcription factor in the N TIR-NB-LRR receptor-mediated plant innate immunity. PLoS Pathog 9(3): e1003235.
  3. Ma, S., Bachan, S., Porto, M., Bohnert, H. J., Snyder, M. and Dinesh-Kumar, S. P. (2012). Discovery of stress responsive DNA regulatory motifs in Arabidopsis. PLoS One 7(8): e43198.
  4. Lee, H. Y., Bowen, C. H., Popescu, G. V., Kang, H. G., Kato, N., Ma, S., Dinesh-Kumar, S., Snyder, M. and Popescu, S. C. (2011). Arabidopsis RTNLB1 and RTNLB2 Reticulon-like proteins regulate intracellular trafficking and activity of the FLS2 immune receptor. Plant Cell 23(9): 3374-3391.
  5. Miura, K., Lee, J., Gong, Q., Ma, S., Jin, J. B., Yoo, C. Y., Miura, T., Sato, A., Bohnert, H. J. and Hasegawa, P. M. (2011). SIZ1 regulation of phosphate starvation-induced root architecture remodeling involves the control of auxin accumulation. Plant Physiol 155(2): 1000-1012.
  6. Ma, S. and Bohnert, H. J. (2008). Gene networks in Arabidopsis thaliana for metabolic and environmental functions. Mol Biosyst 4(3): 199-204.
  7. Li, P., Ma, S. and Bohnert, H. J. (2008). Coexpression characteristics of trehalose-6-phosphate phosphatase subfamily genes reveal different functions in a network context. Physiol Plant 133(3): 544-556.
  8. Ma, S., Gong, Q. and Bohnert, H. J. (2007). An Arabidopsis gene network based on the graphical Gaussian model. Genome Res 17(11): 1614-1625.
  9. Ma, S. and Bohnert, H. J. (2007). Integration of Arabidopsis thaliana stress-related transcript profiles, promoter structures, and cell-specific expression. Genome Biol 8(4): R49.
  10. Lee, J., Nam, J., Park, H. C., Na, G., Miura, K., Jin, J. B., Yoo, C. Y., Baek, D., Kim, D. H., Jeong, J. C., Kim, D., Lee, S. Y., Salt, D. E., Mengiste, T., Gong, Q., Ma, S., Bohnert, H. J., Kwak, S. S., Bressan, R. A., Hasegawa, P. M. and Yun, D. J. (2007). Salicylic acid-mediated innate immunity in Arabidopsis is regulated by SIZ1 SUMO E3 ligase. Plant J 49(1): 79-90.
  11. Ma, S., Gong, Q. and Bohnert, H. J. (2006). Dissecting salt stress pathways. J Exp Bot 57(5): 1097-1107.
  12. Bohnert, H. J., Gong, Q., Li, P. and Ma, S. (2006). Unraveling abiotic stress tolerance mechanisms--getting genomics going. Curr Opin Plant Biol 9(2): 180-188.
  13. Gong, Q., Li, P., Ma, S., Indu Rupassara, S. and Bohnert, H. J. (2005). Salinity stress adaptation competence in the extremophile Thellungiella halophila in comparison with its relative Arabidopsis thaliana. Plant J 44(5): 826-839.
  14. Ma, S., Quist, T. M., Ulanov, A., Joly, R. and Bohnert, H. J. (2004). Loss of TIP1;1 aquaporin in Arabidopsis leads to cell and plant death. Plant J 40(6): 845-859.
  15. Inan, G., Zhang, Q., Li, P., Wang, Z., Cao, Z., Zhang, H., Zhang, C., Quist, T. M., Goodwin, S. M., Zhu, J., Shi, H., Damsz, B., Charbaji, T., Gong, Q., Ma, S., Fredricksen, M., Galbraith, D. W., Jenks, M. A., Rhodes, D., Hasegawa, P. M., Bohnert, H. J., Joly, R. J., Bressan, R. A. and Zhu, J. K. (2004). Salt cress. A halophyte and cryophyte Arabidopsis relative model system and its applicability to molecular genetic analyses of growth and development of extremophiles. Plant Physiol 135(3): 1718-1737.
2 Protocols published
SGR-based Reporter to Assay Plant Transcription Factor-promoter Interactions
Authors:  Shisong Ma and Savithramma Dinesh-Kumar, date: 08/20/2014, view: 8892, Q&A: 0
We developed an in vivo method to assay plant transcription factor (TF)–promoter interactions using the transient expression system in Nicotiana benthamiana (N. benthamiana) plants. The system uses the Arabidopsis stay ...
Gene Networks Based on the Graphical Gaussian Model
Author:  Shisong Ma, date: 02/20/2012, view: 13184, Q&A: 1
This protocol describes how to build a gene network based on the graphical Gaussian model (GGM) from large scale microarray data. GGM uses partial correlation coefficient (pcor) to infer co-expression relationship between genes. Compared to the ...
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