CMB_2024v14n2

Computational Molecular Biology 2024, Vol.14, No.2, 45-53 http://bioscipublisher.com/index.php/cmb 53 Paulevé L., Kolcák J., Chatain T., and Haar S., 2020, Reconciling qualitative abstract and scalable modeling of biological networks, Nature Communications, 11(1): 4256. https://doi.org/10.1038/s41467-020-18112-5. Pavlopoulos G.A., Secrier M., Moschopoulos C.N., Soldatos T., Kossida S., Aerts J., Schneider R., and Bagos P., 2011, Using graph theory to analyze biological networks, BioData Mining, 4: 1-27. https://doi.org/10.1186/1756-0381-4-10. Pham E., Li I., and Truong K., 2008, Computational modeling approaches for studying of synthetic biological networks, Current Bioinformatics, 3: 130-141. https://doi.org/10.2174/157489308784340667. Saadat pour A., and Albert R., 2013, Boolean modeling of biological regulatory networks: a methodology tutorial, Methods, 62(1): 3-12. https://doi.org/10.1016/j.ymeth.2012.10.012. Schneider M., and Antes I., 2021, SenseNet a tool for analysis of protein structure networks obtained from molecular dynamics simulations, PLoS ONE, 17(3): e0265194. https://doi.org/10.1371/journal.pone.0265194. Sen P., 2022, Flux balance analysis of metabolic networks for efficient engineering of microbial cell factories, Biotechnology and Genetic Engineering Reviews, 2022: 1-34. https://doi.org/10.1080/02648725.2022.2152631. Tyson J., Laomettachit T., and Kraikivski P., 2019, Modeling the dynamic behavior of biochemical regulatory networks, Journal of Theoretical Biology, 462: 514-527. https://doi.org/10.1016/j.jtbi.2018.11.034. Vidal-Limon A., Aguilar-Toalá J., and Liceaga A., 2022, Integration of molecular docking analysis and molecular dynamics simulations for studying food proteins and bioactive peptides, Journal of Agricultural and Food Chemistry, 70(4): 934-943. https://doi.org/10.1021/acs.jafc.1c06110. Wang Y.X.R., Li L., Li J.J., 2021, Network modeling in biology: statistical methods for gene and brain networks, Statistical Science: A Review Journal of the Institute of Mathematical Statistics, 36(1): 89. https://doi.org/10.1214/20-sts792. Wang B., Xie Z., Chen J., and Wu Y., 2018, Integrating structural information to study the dynamics of protein-protein interactions in cells, Structure, 26(10):1414-1424. https://doi.org/10.1016/j.str.2018.07.010. Wang S., Fan K., Luo N., Cao Y., Wu F., Zhang C., Heller K., and You L., 2019, Massive computational acceleration by using neural networks to emulate mechanism-based biological models, Nature Communications, 10(1): 4354. https://doi.org/10.1038/s41467-019-12342-y. Wang X., Zhang Y., and Wen T., 2021, Progress on genome-scale metabolic models integrated with multi-omics data, Chinese Science Bulletin, 13(7): 855. https://doi.org/10.1360/tb-2020-1468. Wang Z., and Gao H., 2010, Dynamics analysis of gene regulatory networks, International Journal of Systems Science, 41: 1-4. https://doi.org/10.1080/00207720903477952.

RkJQdWJsaXNoZXIy MjQ4ODYzNA==