I am looking for the same answers. The following is the results of my literature review:
First, three review papers should be checked:
- Lopes, M. and G. Bontempi (2013). "Experimental assessment of static and dynamic algorithms for gene regulation inference from time series expression data." Front Genet 4: 303.
- Kim, Y., et al. (2014). "Inference of dynamic networks using time-course data." Brief Bioinform 15(2): 212-228.
- Liu, Z. P. (2015). "Reverse Engineering of Genome-wide Gene Regulatory Networks from Gene Expression Data." Curr Genomics 16(1): 3-22.
According to the review paper, several packages are available currently for construct transcription regulatory network from time series expression data:
- GRNInfer, Huber group LASSO, these two can construct the regulatory network from multiple time series expression data.
- TDARACNE, DPC.
- Bayes network: Banjo, BNFinder, GlobalMIT
Hope this will help you. Any suggestions on this topic are welcome!