M.  Gadgil, Lian, W., Gadgil, C. J., Kapur, V., and Wu, W. S., ?Analysis of the use of genomic DNA as a universal reference in two channel DNA microarrays?, BMC Genomics, vol. 6, p. Article Number. 66, 2005.

C. J.  Gadgil, Lee, C. Hyeong, and Othmer, H. G., ?Stochastic model for first order reaction networks?, Bulletin of Mathematical Biology, vol. 67, no. 5, pp. 901?946, 2005.

C. J.  Gadgil, ?Stochastic modeling of biological reactions?, Journal of the Indian Institute of Science, vol. 88, no. 1, pp. 45-55, 2008.

C. J.  Gadgil and Kulkarni, B. D., ?Autocatalysis: a unit process of biological systems?, Chemical Engineering Progress, vol. 105, no. 3, p. 8, 2009.

C. J.  Gadgil and Kulkarni, B. D., ?Autocatalysis in biological systems?, Aiche Journal, vol. 55, no. 3, pp. 556-562, 2009.

V.  Vijayan, Bulsara, B., Gadgil, C. J., and Gadgil, M., ?Comparison of feature selection and classification combinations for cancer classification using microarray data?,  International Journal of Bioinformatics Research and Applications, vol. 5, no. 4, pp. 417-431 , 2009.

C. J.  Gadgil, ?Size-independent differences between the mean of discrete stochastic systems and the corresponding continuous deterministic systems?, Bulletin of Mathematical Biology, vol. 71, no. 7, pp. 1599-1611, 2009.

S. A.  Gokhale, Roshan, R., Khetan, V., Pillai, B., and Gadgil, C. J., ?Kinetic model of TBP auto-regulation exhibits bistability?, Biology Direct, vol. 5, p. 50, 2010.

K.  Subramanian and Gadgil, C. J., ?Robustness of the drosophila segment polarity network to transient perturbations?, IET Systems Biology, vol. 4, no. 2, pp. 169-176, 2010.

S. A.  Gokhale, Nyayanit, D., and Gadgil, C. J., ?Systems view of the protein expression process?, Systems and Synthetic Biology, vol. 5, no. 3, pp. 139?150, 2011.

S. A.  Gokhale and Gadgil, C. J., ?Analysis of miRNA regulation suggests an explanation for `unexpected' increase in target protein levels?, Molecular Biosystems, vol. 8, no. 3, pp. 760-765, 2012.

S.  Gokhale and Gadgil, C. J., ?Mathematical model identifies conditions for 'unexpected' increase in target protein levels due to miRNA regulation?,  Mol. BioSyst., vol. 8, no. 3, pp. 760-765, 2012.

P.  Ganju, Natarajan, V. T., Singh, A., Vijayan, V., Dani, P. P., Kar, H. K., Natarajan, K., Gadgil, C. J., Rani, R., and Gokhale, R. S., ?Novel mechanism involved in temporal regulation of skin pigmentation homeostasis?, Journal of Investigative Dermatology, vol. 132, p. S128, 2012.

S. A.  Gokhale, Hariharan, M., Brahmachari, S. K., and Gadgil, C. J., ?Simple method for incorporating dynamic effects of intronic miRNA mediated regulation?, Molecular Biosystems, vol. 8, no. 8, pp. 2145-2152, 2012.

V.  Vijayan, Deshpande, P., Gadgil, C. J., and Gadgil, M., ?Comparison of methods for identifying periodically varying genes?, International Journal of Bioinformatics Research and Applications, vol. 9, no. 1, pp. 53-70, 2013.

V. T.  Natarajan, Ganju, P., Singh, A., Vijayan, V., Kirty, K., Yadav, S., Puntambekar, S., Bajaj, S., Dani, P. P., Kar, H. K., Gadgil, C. J., Natarajan, K., Rani, R., and Gokhale, R. S., ?IFN-gamma signaling maintains skin pigmentation homeostasis through regulation of melanosome maturation?, Proceedings of the National Academy of Sciences of the United States of America, vol. 111, no. 6, pp. 2301-2306, 2014.

B. R.  Iyengar, Choudhary, A., Sarangdhar, M. A., Venkatesh, K. V., Gadgil, C. J., and Pillai, B., ?Non-coding RNA interact to regulate neuronal development and function?, Frontiers in Cellular Neuroscience, vol. 8, p. 47, 2014.

D.  Nyayanit and Gadgil, C. J., ?Mathematical modeling of combinatorial regulation suggests that apparent positive regulation of targets by miRNA could be an artifact resulting from competition for mRNA?, RNA-A Publication of the RNA Society, vol. 21, no. 3, pp. 307-319, 2015.

S. A.  Gokhale and Gadgil, C. J., ?Ranking of reactions based on sensitivity of protein noise depends on the choice of noise measure?, Plos One, vol. 10, no. 12, p. Article Number: e0143867, 2015.

S. S.  Puntambekar, Nyayanit, D., Saxena, P., and Gadgil, C. J., ?Identification of unintuitive features of sumoylation through mathematical modeling?, Journal of Biological Chemistry, vol. 291, no. 18, p. 9458-+, 2016.

A.  Singh, Gotherwal, V., Junni, P., Vijayan, V., Tiwari, M., Ganju, P., Kumar, A., Sharma, P., Fatima, T., Gupta, A., Holla, A., Kar, H. K., Khanna, S., Thukral, L., Malik, G., Natarajan, K., Gadgil, C. J., Lahesmaa, R., Natarajan, V. T., Rani, R., and Gokhale, R. S., ?Mapping architectural and transcriptional alterations in non-lesional and lesional epidermis in vitiligo?, Scientific Reports, vol. 7, no. Article Number: 9860, 2017.

B. Ravi Iyengar, Pillai, B., Venkatesh, K. V., and Gadgil, C. J., ?Systematic comparison of the response properties of protein and RNA mediated gene regulatory motifs?, Molecular BioSystems, vol. 13  , no. 6 , pp. 1235-1245, 2017.

P. A.  Dnyane, Puntambekar, S. S., and Gadgil, C. J., ?Method for identification of sensitive nodes in boolean models of biological networks?, IET Systems Biology, vol. 12, no. 1, pp. 1-6, 2018.

A.  Sreejan, Gadgil, M., and Gadgil, C. J., ?Mathematical model of the multi-amino acid multi-transporter system predicts uptake flux in CHO cells?, Journal of Biotechnology, vol. 344, pp. 40-49, 2022.

S.  Hegde, Sreejan, A., Gadgil, C. J., and Ratnaparkhi, G. S., ?SUMOylation of dorsal attenuates Toll/NF-kappa B signaling?, Genetics, vol. 221, no. 3, 2022.

A.  Ramachandran and Gadgil, C. J., ?Physiologically-based pharmacokinetic model for tuberculosis drug disposition at extrapulmonary sites?, CPT-Pharmacometrics & Systems Pharmacology, vol. 12, no. 9, pp. 1274-1284, 2023.