Kulshreshtha, A., & Bhatnagar, S. (2026). Impact of loss-of-function variations of PCSK9 on LDLR interaction and dynamics: Implications for heart function. Biochemical and biophysical research communications, 799, 153224.

Singh, V., Pant, T., Kumar, Y., Bhatnagar, S. (2025). Novel potent heterocyclicGrb2–SH2 domain antagonists as potential anti-proliferative agents. Biochemical andBiophysical Research Communications, 760, 151680.

Sharma, A., Tayal, S., Bhatnagar, S. (2025). Analysis of stress response in multiple bacterial pathogens using a network biology approach. Scientific Reports, 15(1), 15342.

Kulshreshtha, A., & Bhatnagar, S. (2025). Structural effect of the H992D/H418D mutation of angiotensin-converting enzyme in the Indian population: implications for health and disease. Journal of Biomolecular Structure and Dynamics, 43(14), 7631–7648.

Singh V, Kumar Y, Bhatnagar S. Robustaflavone as a novel scaffold for inhibitors of native and auto-proteolysed human neutrophil elastase. SAR QSAR Environ Res. 2024 ;35(8):729-756.

Tayal S, Bhatnagar S. Role of molecular mimicry in the SARS-CoV-2-human interactome for pathogenesis of cardiovascular diseases: An update to ImitateDB. Comput Biol Chem. 2023;106:107919.

Gupta S, Gupta D, Bhatnagar S. Analysis of SARS-CoV-2 genome evolutionary patterns. Microbiol Spectr. 2024 ;12(2):e0265423.

Tayal S, Singh V, Bhatnagar S. 3D-QSAR and ADMET studies of morpholino- pyrimidine inhibitors of DprE1 from Mycobacterium tuberculosis. J Biomol Struct Dyn. 2023 Dec 19:1-20.

Singh V, Singh N, Pradhan A, Kumar Y, Bhatnagar S. Structure-activity relationships of dihydropyrimidone inhibitors against native and auto-processed human neutrophil elastase. Comput Biol Med. 2023 Jul;161:107004.

Tayal S, Bhatia V, Mehrotra T, Bhatnagar S. ImitateDB: A database for domain and motif mimicry incorporating host and pathogen protein interactions. Amino Acids. 2022;54(6):923-934.

Singh, N., Rai, S., Bhatnagar, R., & Bhatnagar, S. (2021). Network analysis of host-pathogen protein interactions in microbe induced cardiovascular diseases. In silico biology, 14(3-4), 115–133.

Singh, N., & Bhatnagar, S. (2022). Machine Learning for Prediction of Drug Targets in Microbe Associated Cardiovascular Diseases by Incorporating Host-pathogen Interaction Network Parameters. Molecular informatics, 41(3), e2100115.

Rai, S., Bhatia, V., & Bhatnagar, S. (2021). Drug repurposing for hyperlipidemia associated disorders: An integrative network biology and machine learning approach. Computational biology and chemistry, 92, 107505.

Singh, N., Bhatia, V., Singh, S. et al. MorCVD: A Unified Database for Host-Pathogen Protein-Protein Interactions of Cardiovascular Diseases Related to Microbes. Sci Rep 9, 4039 (2019). 

Kandari D, Gopalani M, Gupta M, Joshi H, Bhatnagar S and Bhatnagar R (2019) Identification, Functional Characterization, and Regulon Prediction of the Zinc Uptake Regulator (zur) of Bacillus anthracis – An Insight Into the Zinc Homeostasis of the Pathogen. Front. Microbiol. 9:3314.

Mohanty P, Bhatnagar S. In Silico Screening to Identify Inhibitors of Growth Factor Receptor 2–Focal Adhesion Kinase Interaction for Therapeutic Treatment of Pathological Cardiac Hypertrophy. ASSAY and Drug Development Technologies. 2019;17(2):58-67.

Rai, S., Mohanty, P., & Bhatnagar, S. (2018). Modeling, dynamics and phosphoinositide binding of the pleckstrin homology domain of two novel PLCs: η1 and η2. Journal of molecular graphics & modelling, 85, 130–144. 

Mohanty, P., & Bhatnagar, S. (2018). Structure of focal adhesion kinase in healthy heart versus pathological cardiac hypertrophy: A modeling and simulation study. Journal of molecular graphics & modelling, 80, 15–24. 

Joon, S., Gopalani, M., Rahi, A., Kulshreshtha, P., Gogoi, H., Bhatnagar, S., & Bhatnagar, R. (2017). Biochemical characterization of the GTP-sensing protein, CodY of Bacillus anthracis. Pathogens and disease, 75(4), 10.1093/femspd/ftx048. 

Rai, S., & Bhatnagar, S. (2017). Novel Lipidomic Biomarkers in Hyperlipidemia and Cardiovascular Diseases: An Integrative Biology Analysis. Omics : a journal of integrative biology, 21(3), 132–142. 

Dhiman, A., Rahi, A., Gopalani, M., Bajpai, S., Bhatnagar, S., & Bhatnagar, R. (2017). Role of the recognition helix of response regulator WalR from Bacillus anthracis in DNA binding and specificity. International journal of biological macromolecules, 96, 257–264.

Mohanty, P., & Bhatnagar, S. (2017). Structural basis of focal adhesion targeting domain-mediated signaling in cardiac hypertrophy. Journal of Receptors and Signal Transduction, 37(1), 38–50. 

Gupta, A., Agarwal, R., Singh, A., & Bhatnagar, S. (2017). Calcium-induced conformational changes of Thrombospondin-1 signature domain: implications for vascular disease. Journal of receptor and signal transduction research, 37(3), 239–251. 

Nagar SD, Aggarwal B, Joon S, Bhatnagar R, Bhatnagar S. A Network Biology Approach to Decipher Stress Response in Bacteria Using Escherichia coli As a Model. OMICS: A Journal of Integrative Biology. 2016;20(5):310-324.

Rai S, Bhatnagar S. Hyperlipidemia, Disease Associations, and Top 10 Potential Drug Targets: A Network View. OMICS: A Journal of Integrative Biology. 2016;20(3):152-168.

Gupta, A., & Bhatnagar, S. (2015). Vasoregression: A Shared Vascular Pathology Underlying Macrovascular And Microvascular Pathologies?. Omics : a journal of integrative biology, 19(12), 733–753. 

Gupta, A., Mohanty, P., & Bhatnagar, S. (2015). Integrative analysis of ocular complications in atherosclerosis unveils pathway convergence and crosstalk. Journal of Receptors and Signal Transduction, 35(2), 149–164. 

Verma, S., Kumar, S., Gupta, V. P., Gourinath, S., Bhatnagar, S., & Bhatnagar, R. (2015). Structural basis of Bacillus anthracis MoxXT disruption and the modulation of MoxT ribonuclease activity by rationally designed peptides. Journal of Biomolecular Structure and Dynamics, 33(3), 606–624. 

Mohanty, P., Gupta, A., & Bhatnagar, S. (2015). Modeling of Plasmodium falciparum Telomerase Reverse Transcriptase Ternary Complex: Repurposing of Nucleoside Analog Inhibitors. Assay and drug development technologies, 13(10), 628–637.

Dhiman, A., Bhatnagar, S., Kulshreshtha, P., & Bhatnagar, R. (2014). Functional characterization of WalRK: A two-component signal transduction system from Bacillus anthracis. FEBS Open Bio, 4, 65–76.

Singh, A., Thakur, P. K., Meena, M., Kumar, D., Bhatnagar, S., & Hassan, I. (2014). Interaction between basic 7S globulin and leginsulin in soybean [Glycine max]: A structural insight. Letters in Drug Design & Discovery, 11(2), 231-239.

Bedi, S. K., Prasad, A., Mathur, K., & Bhatnagar, S. (2013). Positive selection and evolution of dengue type-3 virus in the Indian subcontinent. Journal of vector borne diseases, 50(3), 188–196.

Chopra, N., Saumitra, Pathak, A., Bhatnagar, R., & Bhatnagar, S. (2013). Linkage, mobility, and selfishness in the MazF family of bacterial toxins: a snapshot of bacterial evolution. Genome biology and evolution, 5(12), 2268–2284.

Chopra, N., Agarwal, S., Verma, S., Bhatnagar, S., & Bhatnagar, R. (2011). Modeling of the structure and interactions of the B. anthracis antitoxin, MoxX: deletion mutant studies highlight its modular structure and repressor function. Journal of computer-aided molecular design, 25(3), 275–291.

Bhatnagar, S., Mishra, S., & Pathak, R. (2011). Mining human genome for novel purinergic P2Y receptors: a sequence analysis and molecular modeling approach. Journal of receptor and signal transduction research, 31(1), 75–84.

Chopra, N., Agarwal, S., Verma, S., Bhatnagar, S., & Bhatnagar, R. (2011). Modeling of the structure and interactions of the B. anthracis antitoxin, MoxX: deletion mutant studies highlight its modular structure and repressor function. Journal of computer-aided molecular design, 25(3), 275–291.

Agarwal, S., Mishra, N. K., Bhatnagar, S., & Bhatnagar, R. (2010). PemK toxin of Bacillus anthracis is a ribonuclease: an insight into its active site, structure, and function. The Journal of biological chemistry, 285(10), 7254–7270.

Pathak, R., Bhatnagar, S., & Dubey, A. K. (2008). Mechanisms Underlying the Opposing Effects of P2Y Receptors on the Cell Cycle. Journal of Receptors and Signal Transduction, 28(6), 505–529.

Bhatnagar, S., Srivastava, D., Jayadev, M. S., & Dubey, A. K. (2006). Molecular variants and derivatives of insulin for improved glycemic control in diabetes. Progress in biophysics and molecular biology, 91(3), 199–228.

Rao, G. S., & Bhatnagar, S. (2003). In silico structure-based design of a potent, mutation resilient, small peptide inhibitor of HIV-1 reverse transcriptase. Journal of biomolecular structure & dynamics, 21(2), 171–178.

Rao, G. S., Bhatnagar, S., & Ahuja, V. (2002). Structure-based design of a novel peptide inhibitor of HIV-1 integrase: a computer modeling approach. Journal of biomolecular structure & dynamics, 20(1), 31–38.

Bhatnagar, S., & Rao, G. S. (2000). Molecular modeling of the complex of endothelin-1 (ET-1) with the endothelin type A (ET(A)) receptor and the rational design of a peptide antagonist. Journal of biomolecular structure & dynamics, 17(6), 957–964.

Bhatnagar, S., Rao, G. S., & Singh, T. P. (1995). The role of dehydro-alanine in the design of peptides. Bio Systems, 34(1-3), 143–148.

Research Articles

Book Chapters

Singh, N., & Bhatnagar, S. (2022). Biological interaction networks and their application for microbial pathogenesis. In A. Ashraf (Ed.), Systems Biology Approaches for Host-Pathogen Interaction Analysis (pp. 259–280).

Joon, S., Bhatnagar, S., Bhatnagar, R. (2021). Transcriptional Regulators in Bacillus anthracis: A Potent Biothreat Agent. In: Prasad, R., Kumar, V., Singh, J., Upadhyaya, C.P. (eds) Recent Developments in Microbial Technologies. Environmental and Microbial Biotechnology. Springer, Singapore.

Rai, S. & Bhatnagar, S. (2016). Computational Methods for Prediction of Protein-Protein Interactions: PPI Prediction Methods. In S. Dash & B. Subudhi (Eds.), Handbook of Research on Computational Intelligence Applications in Bioinformatics (pp. 184-215). IGI Global Scientific Publishing.

Gupta A, Mohanty P, Bhatnagar S (2016). Protein Structure Prediction using Homology Modeling: Methods and Tools (pp. 339-359). Hershey, PA (USA): IGI Global Scientific Publishing.

Baharadwaj, N., Wadhwa, S., Goel, P., Sethi, I., Arora, C. S., Goel, A., Bhatnagar, S., & Parthasarathy, H. (2014). De-Noising, Clustering, Classification, and Representation of Microarray Data for Disease Diagnostics. In R. Srivastava, S. Singh, & K. Shukla (Eds.), Research Developments in Computer Vision and Image Processing: Methodologies and Applications (pp. 149-174). IGI Global Scientific Publishing.

Introduction to Bioinformatics. Sonika Bhatnagar and A.K. Dubey in Niscair e-book on Recombinant DNA Technology and Biotechnology

Emerging infectious diseases in humans MSK Jayadev, D. Srivastava, Sonika Bhatnagar, and A.K.Dubey In Microbes for Human life. Editor: Ajit. K. Verma 2007

Genomics in Pathogenicity and Diversity of Flaviviruses. Sonika Bhatnagar, MSK Jayadev and A.K.Dubey in Microbial Diversity Eds. T. Satyanarayan and B.N.Johri. 2004, pp1075-1096.