Methodological Advances in Molecular Biology: Techniques, Applications, and Challenges

Authors

  • Anita M Patil-Nikam
  • Chechare Gayatri Vitthal
  • Sayali Baban Gajare
  • S. Prasanna
  • Karpagavalli Shanmugasundaram

Keywords:

Molecular Biology, Machine Learning, Convolutional Neural Network, Biomolecular Data Analysis, Computational Biology.

Abstract

This research examines the modern methodological developments in molecular biology as combined with computation and machine learning algorithms to increase interpretation of the biological data and diagnostic. The algorithm of four repute, namely Support Vector Machine (SVM), Random Forest (RF), Convolutional Neural Network (CNN), and k-Nearest Neighbors (k-NN) were used to evaluate the performance of their application to molecular datasets towards tasks such as gene expression classification, protein structure prediction and molecular pattern recognition. In the case of testing each algorithm’s efficiency, the study used synthetic and real-world datasets. Experiments showed that the CNN model produced a better result than other models with an accuracy of 94.6%, followed by RF’s accuracy of 91.2% as well as SVM and k-NN with 89.5% and 87.3% respectively. CNN also exhibited the highest sensitivity and specificity ate the levels of 95.1% and 93.2% respectively, which is why it is highly-suitable for image-based molecular applications. Two comparison tables and five measures of performance evaluation tables were utilized in presenting and analyzing results over algorithms. In addition, the literature review on recent studies supported the applicability of the combination of AI and molecular methods to overcome old-fashioned difficulties of scalability, accuracy and data complexity. The results indicate a great potential for introducing advanced algorithms in the molecular biology transmission channels with a view to improve the efficiency of research, diagnostics, and the development of therapeutic regimes

Downloads

Download data is not yet available.

References

ADÃO FILIPE, PÁDUA LUÍS and SOUSA, J.J., 2025. Evaluating Soil Degradation in Agricultural Soil with Ground-Penetrating Radar: A Systematic Review of Applications and Challenges. Agriculture, 15(8), pp. 852.

AFONSO, L., COSTA, J., ANA, M.C., VALENTE, R., LOPES, E., TOMASINO, M.P., ÁGATHA GIL, OLIVEIRA-RODRIGUES, C., ISABEL, S.P., LÓPEZ, A., SUAREZ-BREGUA, P. and MAGALHÃES, C., 2024. Environmental DNA as a complementary tool for biodiversity monitoring: A multi-technique and multi-trophic approach to investigate cetacean distribution and feeding ecology. PLoS One, 19(10),.

AFRIZAL, M.N., GOFUR, A., SARI, M.S. and MUNZIL, 2025. Technology-supported differentiated biology education: Trends, methods, content, and impacts. Eurasia Journal of Mathematics, Science and Technology Education, 21(3),.

ALEMU, R., SHAREW, N.T., ARSANO, Y.Y., AHMED, M., TEKOLA-AYELE, F., MERSHA, T.B. and AMARE, A.T., 2025. Multi-omics approaches for understanding gene-environment interactions in noncommunicable diseases: techniques, translation, and equity issues. Human Genomics, 19, pp. 1-27.

ANA CLÁUDIA MARTINS BRAGA,GOMES TORRES, MATHIAS, C., SUELEN CRISTINA, S.B., KOHLER, A.F., MYLENA, L.C. and BLANES, L., 2024. Advancements in LAMP-Based Diagnostics: Emerging Techniques and Applications in Viral Detection with a Focus on Herpesviruses in Transplant Patient Management. International Journal of Molecular Sciences, 25(21), pp. 11506.

BARAZESH, P., HAJIHASSANI, H., MOTALEBI, F., NEIRESI, S.M.H., HAJIHASSANI, R. and MEHRABIAN, A.R., 2025. Unlocking the Healing Potential: A Comprehensive Review of Ecology and Biology of Medical‐Grade Honey in Wound Management and Tissue Regeneration. Health Science Reports, 8(1),.

CLEMENT, A., FERNÁNDEZ-DÍAZ RAÚL, TIMMONS, P.B., ALESSANDRO, A., GÓMEZ HANSEL and SHIELDS, D.C., 2025. Molecular Modelling in Bioactive Peptide Discovery and Characterisation. Biomolecules, 15(4), pp. 524.

DELORD, C., ARNAUD‐HAOND, S., LEONE, A., ROLLAND, J. and NIKOLIC, N., 2024. Unraveling the Complexity of the Ne/Nc Ratio for Conservation of Large and Widespread Pelagic Fish Species: Current Status and Challenges. Evolutionary Applications, 17(10),.

DOUARD, N., SAMET, A., GIAKOS, G. and CAVALLUCCI, D., 2025. Quantifying Interdisciplinarity in Scientific Articles Using Deep Learning Toward a TRIZ-Based Framework for Cross-Disciplinary Innovation. Machine Learning and Knowledge Extraction, 7(1), pp. 7.

GARCÍA-GONZÁLEZ, N., GONÇALVES-SÁNCHEZ, J., GÓMEZ-NIETO, R., GONÇALVES-ESTELLA, J.,M. and LÓPEZ, D.,E., 2024. Advances and Challenges in Gene Therapy for Neurodegenerative Diseases: A Systematic Review. International Journal of Molecular Sciences, 25(23), pp. 12485.

GONZÁLEZ-SÁNCHEZ MARÍA, RAMÍREZ-EXPÓSITO, M.J. and MARTÍNEZ-MARTOS, J.M., 2025. Pathophysiology, Clinical Heterogeneity, and Therapeutic Advances in Amyotrophic Lateral Sclerosis: A Comprehensive Review of Molecular Mechanisms, Diagnostic Challenges, and Multidisciplinary Management Strategies. Life, 15(4), pp. 647.

HALKIOPOULOS, C., GKINTONI, E., AROUTZIDIS, A. and ANTONOPOULOU, H., 2025. Advances in Neuroimaging and Deep Learning for Emotion Detection: A Systematic Review of Cognitive Neuroscience and Algorithmic Innovations. Diagnostics, 15(4), pp. 456.

HIDENORI, T., 2025. Biomolecules Interacting with Long Noncoding RNAs. Biology, 14(4), pp. 442.

HUANG, G., LI, Y., ZHANG, Y., WEN, W., ZHAO, C. and GUO, X., 2025. Overcoming Challenges in Plant Biomechanics: Methodological Innovations and Technological Integration. Advanced Science, 12(10),.

JIANG, W., YE, W., TAN, X. and YUN-JUAN BAO, 2025. Network-based multi-omics integrative analysis methods in drug discovery: a systematic review. Biodata Mining, 18, pp. 1-29.

KAMZEEVA, P.N., ALFEROVA, V.A., KORSHUN, V.A., VARIZHUK, A.M. and ARALOV, A.V., 2025. 5′-UTR G-Quadruplex-Mediated Translation Regulation in Eukaryotes: Current Understanding and Methodological Challenges. International Journal of Molecular Sciences, 26(3), pp. 1187.

KAYA, C., 2025. Optimizing Crop Production With Plant Phenomics Through High‐Throughput Phenotyping and AI in Controlled Environments. Food and Energy Security, 14(1),.

KERVEZEE, L., DASHTI, H.S., PILZ, L.K., SKARKE, C. and RUBEN, M.D., 2024. Using routinely collected clinical data for circadian medicine: A review of opportunities and challenges. PLOS Digital Health, 3(5),.

KHAN, T., VADIVEL, G., AYYASAMY, K., MURUGESAN, G. and SEBAEY, T.A., 2025. Advances in Conductive Biomaterials for Cardiac Tissue Engineering: Design, Fabrication, and Functional Integration. Polymers, 17(5), pp. 620.

KOLAŠINAC, S.,M., PEĆINAR, I., GAJIĆ, R., MUTAVDŽIĆ, D. and ZORA P DAJIĆ STEVANOVIĆ, 2025. Raman Spectroscopy in the Characterization of Food Carotenoids: Challenges and Prospects. Foods, 14(6), pp. 953.

LI, H., SHANG, Y., ZENG, J. and MATSUSAKI, M., 2024. Technology for the formation of engineered microvascular network models and their biomedical applications. Nano Convergence, 11(1), pp. 10.

LI, T., LUO, Y., LIU, C., LU, X. and FENG, B., 2025. Archaeal Lipids: Extraction, Separation, and Identification via Natural Product Chemistry Perspective. International Journal of Molecular Sciences, 26(7), pp. 3167.

LIU, P., WEN, S., ZHU, S., HU, X. and WANG, Y., 2025. Microbial Degradation of Soil Organic Pollutants: Mechanisms, Challenges, and Advances in Forest Ecosystem Management. Processes, 13(3), pp. 916.

LORD, S., JOHNSTON, H., SAMANT, R. and LAI, Y., 2024. Ubiquitylomics: An Emerging Approach for Profiling Protein Ubiquitylation in Skeletal Muscle. Journal of Cachexia, Sarcopenia and Muscle, 15(6), pp. 2281-2294.

LUCIDO, A., BASALLO, O., MARIN-SANGUINO, A., ELEIWA, A., MARTINEZ, E.S., VILAPRINYO, E., SORRIBAS, A. and ALVES, R., 2025. Multiscale Mathematical Modeling in Systems Biology: A Framework to Boost Plant Synthetic Biology. Plants, 14(3), pp. 470.

MARTINS WILLE, A.C., MACHADO, M.I., SAMIRA, H.S., HANNA CÂMARA, D.J., MARIA EDUARDA DE FRAGA-FERREIRA, DE SOUZA MELLO, E., GREMSKI, L.H. and SILVIO, S.V., 2025. Brown Spider Venom Phospholipases D: From Potent Molecules Involved in Pathogenesis of Brown Spider Bites to Molecular Tools for Studying Ectosomes, Ectocytosis, and Its Applications. Toxins, 17(2), pp. 70...

.

Downloads

Published

2025-05-20

How to Cite

1.
Patil-Nikam AM, Gayatri Vitthal C, Gajare SB, Prasanna S, Shanmugasundaram K. Methodological Advances in Molecular Biology: Techniques, Applications, and Challenges. J Neonatal Surg [Internet]. 2025May20 [cited 2025Sep.19];14(24S):798-80. Available from: https://www.jneonatalsurg.com/index.php/jns/article/view/6143

Most read articles by the same author(s)