Graph theory and network analysis for evolutionary modeling in biological and social systems
Sagar Ranesagarrane@aitpune.edu.inDepartment of Computer EngineeringArmy Institute of TechnologyPune, Maharashtra, 411015, IndiaView full profile → , Jaya Chitranshijaya.chitranshi@sims.eduSymbiosis Institute of Management StudiesSymbiosis International (Deemed) UniversityPune, Maharashtra, 411020, IndiaView full profile → , Anant Kaulageanant.kaulage@mituniversity.edu.inSchool of ComputingMIT Art, Design and Technology UniversityPune, Maharashtra, 412201, IndiaView full profile → , *Abhinav MishraCorresponding authorabhinav.mishra.orp@chitkara.edu.inChitkara Centre for Research and DevelopmentChitkara UniversityBarotiwala, Himachal Pradesh, 174103, IndiaView full profile → , Tushar Jadhavtushar.jadhav@vit.eduDepartment of Electronics and TelecommunicationVishwakarma Institute of Technology, PunePune, Maharashtra, IndiaView full profile → , Anchal Guptaanchal.gupta.orp@chitkara.edu.inCentre of Research Impact and OutcomeChitkara UniversityRajpura, Punjab, 140417, IndiaView full profile →
* Corresponding author · click or hover a name for details
- Received:
- 05 Nov 2024
- Published Online:
- 02 Sep 2025
- Article type:
- Research Article
- Language:
- EN
- Article no.:
- JDMSC-2374
- Pages:
- 1993–2003
Abstract
Keywords
Subject Classifications
References
[1] S. Käser, L. I. Vazquez-Salazar, M. Meuwly, and K. Töpfer, “Neural network potentials for chemistry: Concepts, applications and prospects,” Digital Discovery, vol. 2, pp. 28–58 (2023).
[2] M. Dautle, S. Zhang, and Y. Chen, “scTIGER: A deep-learning method for inferring gene regulatory networks from case versus control scRNA-seq datasets,” International Journal of Molecular Sciences, vol. 24, p. 13339 (2023).
[3] T. Zhang and G. Wong, “Gene expression data analysis using Hellinger correlation in weighted gene co-expression networks (WGCNA),” Computational and Structural Biotechnology Journal, vol. 20, pp. 3851–3863 (2022).
[4] D. Mercatelli, L. Scalambra, L. Triboli, F. Ray, and F. M. Giorgi, “Gene regulatory network inference resources: A practical overview,” Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, vol. 1863, p. 194430 (2020).
[5] N. J. Zade, N. P. Lanke, B. S. Madan, N. P. Katariya, P. Ghutke, and P. Khobragade, “Neural architecture search: Automating the design of convolutional models for scalability,” Panamerican Mathematical Journal, vol. 34, no. 4, pp. 178–193 (Dec. 2024). [Online]. Available: https://doi.org/10.52783/pmj.v34.i4.1877
[6] X. Han, B. Wang, C. Situ, Y. Qi, H. Zhu, Y. Li, and X. Guo, “scapGNN: A graph neural network–based framework for active pathway and gene module inference from single-cell multi-omics data,” PLoS Biology, vol. 21, p. e3002369 (2023).
[7] M. Ramezani, A. Ahadinia, A. Ziaei Bideh, and H. R. Rabiee, “Joint inference of diffusion and structure in partially observed social networks using coupled matrix factorization,” ACM Transactions on Knowledge Discovery from Data (TKDD), vol. 17, pp. 1–28 (2023).
[8] H. U. Karakurt and P. Pir, “Integration of transcriptomic profile of SARS-CoV-2 infected normal human bronchial epithelial cells with metabolic and protein-protein interaction networks,” Turkish Journal of Biology, vol. 44, pp. 168–177, ( 2020).
[9] G. Galindez, S. Sadegh, J. Baumbach, T. Kacprowski, and M. List, “Network-based approaches for modeling disease regulation and progression,” Computational and Structural Biotechnology Journal, vol. 21, pp. 780–795 (2023).
[10] M. E. Karabekmez, H. Taymaz-Nikerel, S. Eraslan, and B. Kirdar, “Time-dependent re-organization of biological processes by the analysis of the dynamic transcriptional response of yeast cells to doxorubicin,” Molecular Omics, vol. 17, pp. 572–582 (2021).
[11] Y. Wu, M. T. Judge, A. S. Edison, and J. Arnold, “Uncovering in vivo biochemical patterns from time-series metabolic dynamics,” PLoS ONE, vol. 17, p. e0268394 (2022).




