By analyzing gene distribution patterns, we reconstruct a phylogenetic network of 191 prokaryotes.
We compare the target genes of the three regulators to the known regulators of sporulation [ 11, 17] and, based on the overlapped targets (Table 3), we reconstruct a sporulation network of the core transcriptional regulations with minimal protein-protein interactions (PPI) added from literature (Fig. 4).
We first used EGN (e-value ≤ 1E-20, hidentityity ≥ 30% ) to reconstruct a genome network of 131 cellular organisms, 2,211 plasmids and 3,477 viral genomes, harboring either cellular chromosomes or genomes of mobile genetic elements at its nodes, connected when they shared sequences from the same similarity cluster, as in Halary et al.[ 25].
Age-structured demographic and spatial dynamics of the focal population are reconstructed in a network of 415 ponds embedded in a heterogeneous landscape.
Based on these measurements, we reconstructed a parsimony network of haplotypes with a 95% connection probability limit using TCS 1.21 [ 53].
We showed that by confronting and integrating two independent sources, we were able to semi-automatically reconstruct a core metabolic network of A. thaliana, whose properties are comparable to existing manually reconstructed networks of other species.
We have reconstructed an integrated network of eicosanoid metabolism and signaling based on the KEGG pathway database and the literature and have developed a kinetic model.
Computed tomography image data from two different patients were used to reconstruct a nearly complete network of the major arteries from head to foot.
Here we proposed a systematic approach that incorporates discrete dynamic modeling and experimental data to reconstruct a phenotype-specific network of cell signaling.
As a future work, we plan to relax the conditions on the restricted LGT networks in order to be able to reconstruct a broader class of networks and discover new algorithms for reconstructing such networks from biologically significant data.
