Software
1. MaizeGGM, a maize gene network program. (Download)
Described in the following paper:
- 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. (*corresponding author) [Full Text]
Software (before 2016)
1. AtGGM2014, a program to query and utilize the Arabidopsis gene network AtGGM2014. (Download)
Described in the following paper:
- 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. [Full Text]
2. MotifIndexer, a program for de novo promoter motifs finding. (Download)
Described in the following paper:
- 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. [Full Text]
3. MotifNetwork, to analyze promoter motifs over an Arabidopsis gene network. (Download)
Described in the following paper:
- 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. [Full Text]
Note: These three pieces of software were developed during the PI’s postdoctoral work in the Dinesh-Kumar lab at UC Davis.
Datasets
Coming soon.
