A.  Raghunathan, Shin, S., and Daefler, S., ?Systems approach to investigating host-pathogen interactions in infections with the biothreat agent Francisella. constraints-based model of Francisella tularensis?, BMC Systems Biology, vol. 4, p. 118, 2010.

N.  Jamshidi and Raghunathan, A., ?Cell scale host-pathogen modeling: another branch in the evolution of constraint-based methods?, Frontiers in Microbiology, vol. 6, p. Article Number: 1032, 2015.

A.  Raghunathan and Athale, C. A., ?Modelling natural and synthetic biological networks?, Current Science, vol. 113, no. 7, pp. 1221-1222, 2017.

D.  Banerjee, Parmar, D., Bhattacharya, N., Ghanate, A. D., Panchagnula, V., and Raghunathan, A., ?Scalable metabolite supplementation strategy against antibiotic resistant pathogen Chromobacterium violaceum induced by NAD(+)/NADH(+) imbalanceA scalable metabolite supplementation strategy against antibiotic resistant pathogen Chromobacterium violaceu?, BMC Syst Biol. , vol. 11, no. 1, 2017.

S. Rupa Chris Immanuel, Banerjee, D., Rajankar, M. P., and Raghunathan, A., ? Integrated constraints based analysis of an engineered violacein pathway in escherichia coli?, Biosystems , vol. 171, pp. 10-19, 2018.

A.  Raghunathan and Jamshidi, N., ?Integrated host-pathogen metabolic reconstructions?, Methods in Molecular Biology, vol. 1716, pp. 197-217, 2018.

S. Rupa C.  Immanuel, Ghanate, A. D., Parmar, D. S., Marriage, F., Panchagnula, V., Day, N. J., and Raghunathan, A., ?Integrative analysis of rewired central metabolism in temozolomide resistant cells?, Biochemical and Biophysical Research Communications, vol. 495, no. 2, pp. 2010-2016, 2018.

D.  Banerjee and Raghunathan, A., ?Knowledge, attitude and practice of antibiotic use and antimicrobial resistance: a study post the 'Red Line' initiative?, Current Science, vol. 114, no. 9, pp. 1866-1877, 2018.

D.  Banerjee and Raghunathan, A., ?Constraints-based analysis identifies NAD(+) recycling through metabolic reprogramming in antibiotic resistant Chromobacterium violaceum?, PLoS One, vol. 14, no. 1, p. Article Number: e0210008, 2019.

S. Rupa Chris Immanuel, Ghanate, A. D., Parmar, D. S., Yadav, R., Uthup, R., Panchagnula, V., and Raghunathan, A., ?Integrated genetic and metabolic landscapes predict vulnerabilities of temozolomide resistant glioblastoma cells?, npj Systems Biology and Applications, vol. 7, no. 1, p. 2, 2021.

D.  Sengupta and Raghunathan, A., ?Rise of the superbugs: what we need to know overview of antimicrobial resistance?, Resonance, vol. 26, no. 9, pp. 1251 - 1266, 2021.

D.  Niveditha, Khan, S., Khilari, A., Nadkarni, S., Bhalerao, U., Kadam, P., Yadav, R., Kanekar, J. B., Shah, N., Likhitkar, B., Sawant, R., Thakur, S., Tupekar, M., Nagar, D., Rao, A. G., Jagtap, R., Jogi, S., Belekar, M., Pathak, M., Shah, P., Ranade, S., Phadke, N., Das, R., Joshi, S., Karyakarte, R., Ghose, A., Kadoo, N., Shashidhara, L. S., Monteiro, J. Merwin, Shanmugam, D., Raghunathan, A., and Karmodiya, K., ?Tale of two waves: Delineating diverse genomic and transmission landscapes driving the COVID-19 pandemic in Pune, India?, Journal of Infection and Public Health, vol. 16, no. 8, pp. 1290-1300, 2023.

M. S.  Asokan, Joan, R. Florina, Babji, S., Dayma, G., Nadukkandy, P., Subrahmanyam, V., Pandey, A., Malagi, G., Arya, P., Mahajan, V., Bhavikatti, J., Pawar, K., Thorat, A., Shah, P., Goud, R. B., Roy, B., Rajukutty, S., Immanuel, S., Agarwal, D., Saha, S., Shivaraj, A., Panikulam, P., Shome, R., Gulzar, S. - E. - J., Sharma, A. U., Naik, A., Talashi, S., Belekar, M., Yadav, R., Khude, P., V, M., Shivalingaiah, S., Deshmukh, U., Bhise, C., Joshi, M., Inbaraj, L. Raja, Chandrasingh, S., Ghose, A., Jamora, C., Karumbati, A. S., Sundaramurthy, V., Johnson, A., Ramesh, N., Chetan, N., Parthiban, C., Ahmed, A., Rakshit, S., Adiga, V., D'souza, G., Rale, V., George, C. Elizabeth, John, J., Kawade, A., Chaturvedi, A., Raghunathan, A., Dias, M., Bhosale, A., Raghu, P., Shashidhara, L. S., yakarnam, A. V., Bal, V., Kang, G., and Mayor, S., ?Immunogenicity of SARS-CoV-2 vaccines BBV152 (COVAXIN®) and ChAdOx1 nCoV-19 (COVISHIELD?) in seronegative and seropositive individuals in India: a multicentre, nonrandomised observational study?, Lancet Regional Health - Southeast Asia, vol. 22, 2024.

H.  Joshi, Isar, J., Rangaswamy, V., and Raghunathan, A., ?Advances in metabolic engineering and fermentation for 3-hydroxypropionic acid biosynthesis: a comprehensive review?, World Journal of Microbiology & Biotechnology, vol. 41, no. 10, p. 352, 2025.

M.  Belekar, Kavatalkar, V., Yadav, R., and Raghunathan, A., ?Integrated analysis of mitochondrial ETC inhibition reveals genotype-specific heterogeneity of drug response in glioblastoma?, Biochemical and Biophysical Research Communications, vol. 787, p. 152798, 2025.

S.  Sharma, Subrahmanyam, Y. Venkata, Gupta, P., Vadivel, S., Deepa, M., Tandon, A., Sreedevi, S., Ram, U., Narad, P., Parmar, D., Anjana, R. Mohan, Raghunathan, A., Balasubramanyam, M., Mohan, V., Sengupta, A., Adamski, J., Saravanan, P., Panchagnula, V., Usharani, D., and Gokulakrishnan, K., ?Precision integrated identification of predictive first-trimester metabolomics signatures for early detection of gestational diabetes mellitus?, Cardiovascular Diabetology, vol. 24, no. 1, p. 434, 2025.