Computational Identification of Key Molecular Targets and Signaling Pathways in Asthma-Associated Inflammation

Authors

  • Bachary Endersson School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, USA.

Keywords:

asthma, inflammation, network medicine, systems biology, machine learning, target identification, signaling pathways, computational infrastructure

Abstract

Asthma is a highly heterogeneous inflammatory disorder of the airways shaped by diverse molecular, cellular, and environmental determinants. The computational identification of key molecular targets and signaling pathways in asthma-associated inflammation has become a major systems-level research challenge because single-target and single-pathway approaches cannot adequately capture the regulatory complexity of the disease. This paper examines the conceptual architecture, data infrastructure, inference methods, and governance structures required for robust computational target discovery in asthma. It situates target identification within a broader socio-technical framework in which multi-omics data, network biology, machine learning, and clinical phenotyping interact through modular analytical pipelines. The discussion emphasizes structural trade-offs between mechanistic interpretability and predictive performance, between data completeness and representational diversity, and between innovation speed and regulatory accountability. It further considers deployment sustainability, algorithmic fairness, and policy implications for translating computational predictions into reproducible biomedical knowledge. Rather than proposing a single computational method, the paper develops a system-level perspective on how computational infrastructures can be designed to prioritize verifiable molecular targets, reduce bias, and align prediction with clinical and public health needs. The analysis concludes that durable progress in asthma target identification depends not only on algorithmic sophistication but also on coherent governance of data, models, evidence standards, and translational incentives.

References

1. Lambrecht, B. N., & Hammad, H. (2015). The immunology of asthma. Nature Immunology, 16(1), 45-56. https://doi.org/10.1038/ni.3049

2. Holgate, S. T. (2012). Innate and adaptive immune responses in asthma. Nature Medicine, 18(5), 673-683. https://doi.org/10.1038/nm.2781

3. Barabasi, A.-L., Gulbahce, N., & Loscalzo, J. (2011). Network medicine: A network-based approach to human disease. Nature Reviews Genetics, 12(1), 56-68. https://doi.org/10.1038/nrg2918

4. Wenzel, S. E. (2012). Asthma phenotypes: The evolution from clinical to molecular approaches. Nature Medicine, 18(5), 716-725. https://doi.org/10.1038/nm.2678

5. Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S., & Mesirov, J. P. (2005). Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences, 102(43), 15545-15550. https://doi.org/10.1073/pnas.0506580102

6. Reimand, J., Isserlin, R., Voisin, V., Kucera, M., Tannus-Lopes, C., Rostamianfar, A., Wadi, L., Meyer, M., Wong, J., Xu, C., Merico, D., & Bader, G. D. (2019). Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap. Nature Protocols, 14(2), 482-517. https://doi.org/10.1038/s41596-018-0101-9

7. Kanehisa, M., Furumichi, M., Sato, Y., Ishiguro-Watanabe, M., & Tanabe, M. (2021). KEGG for taxonomy-based analysis of pathways and genomes. Nucleic Acids Research, 49(D1), D545-D551. https://doi.org/10.1093/nar/gkaa970

8. Szklarczyk, D., Gable, A. L., Nastou, K. C., Lyon, D., Kirsch, R., Pyysalo, S., Doncheva, N. T., Legeay, M., Fang, T., Bork, P., Jensen, L. J., & von Mering, C. (2021). The STRING database in 2021: Customizable protein-protein networks, and functional characterization of user-uploaded gene measurement sets. Nucleic Acids Research, 49(D1), D605-D612. https://doi.org/10.1093/nar/gkaa1077

9. LeCun, Y., Bengio, Y., & Hinton, G. (2015). Deep learning. Nature, 521(7553), 436-444. https://doi.org/10.1038/nature14539

10. Wang, Yinyin, et al. "HerbSyner_Finder: a network community-based model for identifying synergistic combinations from herbal medicines and complex systems." Targetome 2.2 (2026).

11. Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003). Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Research, 13(11), 2498-2504. https://doi.org/10.1101/gr.1239303

12. Woodruff, P. G., Boushey, H. A., Dolganov, G. M., Barker, C. S., Yang, Y. H., Donnelly, S., Ellwanger, A., Sidhu, S. S., Dao-Pick, T. P., Pantoja, C., Erle, D. J., & Fahy, J. V. (2007). Genome-wide profiling identifies epithelial cell genes associated with asthma and with treatment response to corticosteroids. Proceedings of the National Academy of Sciences, 104(40), 15858-15863. https://doi.org/10.1073/pnas.0707413104

13. Lotvall, J., Akdis, C. A., Bacharier, L. B., Bjermer, L., Casale, T. B., Custovic, A., Lemanske, R. F., Wardlaw, A. J., Wenzel, S. E., & Greenberger, P. A. (2011). Asthma endotypes: A new approach to classification of disease entities within the asthma syndrome. Journal of Allergy and Clinical Immunology, 127(2), 355-360. https://doi.org/10.1016/j.jaci.2010.11.037

14. Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., Harris, M. A., Hill, D. P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J. C., Richardson, J. E., Ringwald, M., Rubin, G. M., & Sherlock, G. (2000). Gene Ontology: Tool for the unification of biology. Nature Genetics, 25(1), 25-29. https://doi.org/10.1038/75556

15. Wilkinson, M. D., Dumontier, M., Aalbersberg, I. J., Appleton, G., Axton, M., Baak, A., Blomberg, N., Boiten, J. W., da Silva Santos, L. B., Bourne, P. E., Bouwman, J., Brookes, A. J., Clark, T., Crosas, M., Dillo, I., Dumon, O., Edmunds, S., Evelo, C. T., Finkers, R., ... Mons, B. (2016). The FAIR Guiding Principles for scientific data management and stewardship. Scientific Data, 3, 160018. https://doi.org/10.1038/sdata.2016.18

16. Obermeyer, Z., Powers, B., Vogeli, C., & Mullainathan, S. (2019). Dissecting racial bias in an algorithm used to manage the health of populations. Science, 366(6464), 447-453. https://doi.org/10.1126/science.aax2342

17. Mittelstadt, B. D., Allo, P., Taddeo, M., Wachter, S., & Floridi, L. (2016). The ethics of algorithms: Mapping the debate. Big Data & Society, 3(2), 2053951716679679. https://doi.org/10.1177/2053951716679679

18. Vayena, E., Blasimme, A., & Cohen, I. G. (2018). Machine learning in medicine: Addressing ethical challenges. PLoS Medicine, 15(11), e1002689. https://doi.org/10.1371/journal.pmed.1002689

19. Turing, A. M. (1950). Computing machinery and intelligence. Mind, 59(236), 433-460. https://doi.org/10.1093/mind/LIX.236.433

20. Gillespie, T. (2014). The relevance of algorithms. In T. Gillespie, P. J. Boczkowski, & K. A. Foot (Eds.), Media technologies: Essays on communication, materiality, and society (pp. 167-194). MIT Press. https://doi.org/10.7551/mitpress/9780262525374.003.0009

Downloads

Published

2026-06-30

How to Cite

Bachary Endersson. (2026). Computational Identification of Key Molecular Targets and Signaling Pathways in Asthma-Associated Inflammation. International Journal of Clinical and Translational Medicine, 1(1). Retrieved from https://ijctmed.org/index.php/home/article/view/186