S.  Chowdhury and Sarkar, R. Rup, ?Drug targets and biomarker identification from computational study of human notch signaling pathway?, Clinical and Experimental Pharmacology and Physiology, vol. 3, no. 4, 2013.

S.  Mandal, Sinha, S., and Sarkar, R. Rup, ?Realistic host-vector transmission model for describing malaria prevalence pattern?, Bulletin of Mathematical Biology, vol. 75, no. 12, pp. 2499-2528, 2013.

S.  Chowdhury, Pradhan, R. N., and Sarkar, R. Rup, ?Structural and logical analysis of a comprehensive hedgehog signaling pathway to identify alternative drug targets for glioma, colon and pancreatic cancer?, Plos One, vol. 8, no. 7, p. e69132, 2013.

A.  Subramanian and Sarkar, R. Rup, ?Comparison of codon usage bias across leishmania and trypanosomatids to understand mRNA secondary structure, relative protein abundance and pathway functions?, Genomics, vol. 106, no. 4, pp. 232-241, 2015.

S.  Chowdhury and Sarkar, R. Rup, ?Comparison of human cell signaling pathway databases-evolution, drawbacks and challenges?, Database-the Journal of Biological Databases and Curation, p. Article Number: bau126, 2015.

A.  Subramanian and Sarkar, R. Rup, ?Data in support of large scale comparative codon usage analysis in leishmania and trypanosomatids?, Data Brief, vol. 4, no. C, pp. 269-272, 2015.

A.  Subramanian, Jhawar, J., and Sarkar, R. Rup, ?Dissecting leishmania infantum energy metabolism - a systems perspective?, Plos One, vol. 10, no. 9, p. Article Number: e0137976, 2015.

A.  Subramanian and Sarkar, R. Rup, ?Dynamics of gli regulation and a strategy to control cancerous situation: hedgehog signaling pathway revisited?, Journal of Biological Systems, vol. 23, no. 4, pp. 681-719, 2015.

R.  Bhowmick, Subramanian, A., and Sarkar, R. Rup, ?Exploring the differences in metabolic behavior of astrocyte and glioblastoma: a flux balance analysis approach?, Systems and Synthetic Biology, vol. 9, no. 4, pp. 159-177, 2015.

P.  Ganguli, Choudhury, S., Choudhury, S., and Sarkar, R. Rup, ?Identification of Th1/Th2 regulatory switch to promote healing response during Leishmaniasis: a computational approach?, EURASIP Journal on Bioinformatics and Systems Biology, vol. 1, 2015.

P.  Ganguli, Chowdhury, S., Bhowmick, R., and Sarkar, R. Rup, ?Temporal protein expression pattern in intracellular signalling cascade during T-cell activation: a computational study?, Journal of Biosciences, vol. 40, no. 4, pp. 769-789, 2015.

A.  Subramanian, Singh, V., and Sarkar, R. Rup, ?Understanding visceral leishmaniasis disease transmission and its control - a study based on mathematical modelling?, Mathematics, vol. 3, no. 3, pp. 913-344, 2015.

R. Rup Sarkar, ?Big Data Deluge in Biology: Challenges and Solutions?, Journal of Informatics and Data Mining, vol. 1, no. 2, pp. 1-3, 2016.

A.  Subramanian and Sarkar, R. Rup, ?Network structure and enzymatic evolution in Leishmania metabolism: a computational study?, in Proceedings of the International Symposium on Mathematical and Computational Biology-BIOMAT 2015, Roorkee, Uttarakhand, India, 2016.

N.  Sinha, Chowdhury, S., and Sarkar, R. Rup, ?Structural insight of NICD-MAML interactions: virtual screening, docking and molecular dynamics study for the identification of potential inhibitor?, Letters in Drug Design & Discovery, vol. 13, no. 4, pp. 301-313, 2016.

S.  Banerjee, Subramanian, A., Chattopadhyay, J., and Sarkar, R. Rup, ?Exploring the role of GS-GOGAT cycle in microcystin synthesis and regulation - a model based analysis?, Molecular Biosystems, vol. 13, no. 12, pp. 2603-2614, 2017.

S.  Nandi, Subramanian, A., and Sarkar, R. Rup, ?Integrative machine learning strategy for improved prediction of essential genes in Escherichia coli metabolism using flux-coupled features?, Molecular Biosystems, vol. 13, no. 8, pp. 1584-1596, 2017.

S.  Biswas, Subramanian, A., Elmojtaba, I. M., Chattopadhyay, J., and Sarkar, R. Rup, ?Optimal combinations of control strategies and cost-effective analysis for visceral leishmaniasis disease transmission?, PLoS ONE, vol. 12, no. 2, 2017.

A.  Subramanian and Sarkar, R. Rup, ?Revealing the mystery of metabolic adaptations using a genome scale model of Leishmania infantum?, Scientific Reports, vol. 7, no. Article Number: 10262, 2017.

A.  Subramanian and Sarkar, R. Rup, ?Evolutionary perspectives of genotype-phenotype factors in leishmania metabolism?, Journal of Molecular Evolution, vol. 86, no. 7, pp. 443-456, 2018.

P.  Ganguli and Sarkar, R. Rup, ? Exploring immuno-regulatory mechanisms in the tumor microenvironment: model and design of protocols for cancer remission?, Plos One, vol. 13, no. 9, 2018.

A.  Mahanta, Ganguli, P., Barah, P., Sarkar, R. Rup, Sarmah, N., Phukan, S., Bora, M., and Baruah, S., ?Integrative approaches to understand the Mastery in manipulation of host cytokine networks by protozoan parasites with emphasis on Plasmodium and Leishmania species?, Frontiers in Immunology, vol. 9, p. Article Number: 296, 2018.

S.  Bose, Dhawan, D., Nandi, S., Sarkar, R. Rup, and Ghosh, D., ?Machine learning prediction of interaction energies in rigid water clusters?, Physical Chemistry Chemical Physics , vol. 20, no. 35, pp. 22987-22996, 2018.

A.  Subramanian and Sarkar, R. Rup, ?Perspectives on leishmania species and stage-specific adaptive mechanisms?, Trends In Parasitology, vol. 34, no. 12, p. 10.1016/j.pt.2018.09.004, 2018.

S.  Banerjee, Sarkar, R. Rup, and Chattopadhyay, J., ?Effect of copper contamination on zooplankton epidemics?, Journal of Theoretical Biology, vol. 469, pp. 61-74, 2019.

S.  Chowdhury and Sarkar, R. Rup, ?Exploring notch pathway to elucidate phenotypic plasticity and intra-tumor heterogeneity in gliomas?, Scientific Reports, vol. 9, p. 9488, 2019.

N.  Sinha, Chowdhury, S., and Sarkar, R. Rup, ?Molecular basis of drug resistance in smoothened receptor: an in silico study of protein resistivity and specificity?, Proteins-Structure Function and Bioinformatics, 2019.

R.  Bhowmick and Sarkar, R. Rup, ?Differential suitability of reactive oxygen species and the role of glutathione in regulating paradoxical behavior in gliomas: a mathematical perspective?, PloS One, vol. 15, no. 6, p. e0235204, 2020.

S.  Nandi, Ganguli, P., and Sarkar, R. Rup, ?Essential gene prediction using limited gene essentiality information-an integrative semi-supervised machine learning strategy?, PloS One, vol. 15, no. 11, p. e0242943, 2020.

R.  Saurabh, Nandi, S., Sinha, N., Shukla, M., and Sarkar, R. Rup, ?Prediction of survival rate and effect of drugs on cancer patients with somatic mutations of genes: an AI-based approach?, Chemical Biology & Drug Design, vol. 96, no. 3, pp. 1005-1019, 2020.

M.  Chakravarty, Ganguli, P., Murahari, M., Sarkar, R. Rup, Peters, G. Johannes, and Mayur, Y. C., ?Study of combinatorial drug synergy of novel acridone derivatives with temozolomide using in-silico and in-vitro methods in the treatment of drug-resistant glioma?, Frontiers in Oncology, vol. 11, p. 625899, 2021.

G.  Panditrao, Bhowmick, R., Meena, C., and Sarkar, R. Rup, ?Emerging landscape of molecular interaction networks: opportunities, challenges and prospects?, Journal of Biosciences, vol. 47, no. 2, p. 24, 2022.

R.  Bhowmick and Sarkar, R. Rup, ?Identification of potential microRNAs regulating metabolic plasticity and cellular phenotypes in glioblastoma?, Molecular Genetics and Genomics, vol. 298, pp. 161-181, 2023.

A.  Murali and Sarkar, R. Rup, ?Mechano-immunology in microgravity?, Life Sciences in Space Research, vol. 37, pp. 50-64, 2023.

M.  Shukla and Sarkar, R. Rup, ?Differential cellular communication in tumor immune microenvironment during early and advanced stages of lung adenocarcinoma?, Molecular Genetics and Genomics, vol. 299, no. 1, p. 100, 2024.

A.  Murali and Sarkar, R. Rup, ?Dynamic cellular responses to gravitational forces: exploring the impact on white blood cell(s)?, Biomicrofluidics, vol. 18, no. 5, p. 054112, 2024.

M.  Shukla, Bhowmick, R., Ganguli, P., and Sarkar, R. Rup, ?Metabolic reprogramming and signalling cross-talks in tumour-immune interaction: a system-level exploration?, Royal Society Open Science , vol. 11, no. 3, 2024.

A.  Murali and Sarkar, R. Rup, ?Impact of gravitational forces on Red Blood Cell dynamics in biofluid suspension?, Life Sciences in Space Research, vol. 47, pp. 197-210, 2025.

S.  Gharui, Puntambekar, S., Sarkar, R. Rup, Narlikar, L., and Sengupta, D., ?Recognition of diverse GATA motifs necessitates multimodal GATA3-DNA binding?, Biochemical and Biophysical Research Communications, vol. 817, p. 153718, 2026.