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Sonika Bhatnagar
Professor and Head, Department of Biological Sciences and Engineering
Qualification
Ph.D (Biophysics), A.I.I.M.S
Phone
011-25000110
Email
ecc999@gmail.com

Bio-sketch

Dr. Sonika Bhatnagar completed her Ph.D. and Post-Doctoral work in Department of Biophysics, AIIMS. She has been involved with the BSE Department since its inception. She has worked towards developing the curricula, laboratories and other infrastructure in the Department. She carried out an international consultancy assignment and was awarded the Innocentive solver award for shortlisting of five top therapeutic targets for obesity in 2003. Her work lies in the area of systems biology and structural study of protein -protein interactions as novel drug targets using machine learning, and genomics & proteomics. Collaborative projects have also been established for molecular Biology, drug design & discovery for cardiovascular disease drug design and study of stress response in bacteria. 

·Google scholar: https://scholar.google.co.in/citations?user=TrytHiwAAAAJ&hl=en

·LinkedIn: https://www.linkedin.com/in/sbnsit/?originalSubdomain=in

·Researchgate: https://www.researchgate.net/profile/Sonika_Bhatnagar

 

Research specialization: Application of Computational and Structural Biology tools for gaining insights into Cardiovascular Disease and Bacterial Stress response with a long term focus on Drug target selection, Drug design and Repurposing.

Experience: Almost 20 years of post Ph.D. research experience and 20+ years teaching experience in Structural and Computational Biology with project training of UG, PG and doctoral students.

Administrative experience:
1. Chief Proctor, NSUT since 2023
2. HOD, Department of BSE, NSUT since September 2018
3. HOD, Department of BSE, NSIT since September 2017

 

Areas of Interest

  • Cardiovascular Disease and Bacterial Stress response;
  • Molecular mechanisms of disease and Drug target selection;
  • Drug design and Repurposing. 

 

Financial support received 

  • PI: ICMR funded project: Implementation of Machine learning for improvement of patient care in Covid-19 for Rs. 29.36 Lakhs (2022-25) 
  •  PI: ICMR funded project: System level Host pathogen interaction studies in COVID- 19 for therapeutics and pharmacovigilance. Rs. 36.82 Lakhs (2022-25). 
  •  Project mentor: CSIR funded JRF “Development of novel inhibitors for atherosclerosis” 2017-2022  
  •  Co-PI: Collaborative project between NSIT and JNU entitled “Development of novel antibiotics of control of infectious diseases in pathogenic bacteria through induction of programmed cell death”. 2012-15. PI: Sonika Bhatnagar and Co-PI: Rakesh Bhatnagar.  
  • Project mentor: ICMR funded SRF, Ms. Pallavi Mohanty working in a project entitled Modeling of Protein-Protein Interactions in Cardiovascular Disease for Mining of Novel Drug Targets under Dr. Sonika Bhatnagar from 2013-2016.  
  • PI, DST young scientist project – Structure-based design of peptide inhibitors of mammalian 15-lipoxygenase, a target in atherogenesis. 2002- 2005. 
  • CSIR research project – Design of specific antagonists for the human endothelin A receptor. 2000-2002.

  Awards received 

  •  Commendable Research Award from NSUT on 2nd March 2022. 
  •  Dr. Sarvepalli Radhakrishnan distinguished Professor of Biotechnology Award from IMRF in 2021 
  •  Prof Sonika Bhatnagar: Kalpana Chawla Memorial Excellence Award for Woman achiever in Higher Education at Guru Kashi University, Talwandi Sabo, Bathinda, India on 1st February, 2020. 
  •  Awardee, Identification of the top 5 biological targets for the discovery and development of pharmaceuticals to treat Obesity for Innocentive Inc., an e business venture of Eli Lilly, 25th September, 2003.
     
Publications in International Journal

1. Tayal S, Singh V, Bhatnagar S. 3D-QSAR and ADMET studies of morpholino-pyrimidine inhibitors of DprE1 from Mycobacterium tuberculosis. Journal of Biomolecular Structure and Dynamics. 2023 Dec 13:1-20.
2. Gupta S, Gupta, D and Bhatnagar S. Analysis of SARS-CoV-2 Genome Evolutionary Patterns. Microbiology Spectrum. 2023. Accepted.
3. 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.
4. 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.
5. Singh N, Rai S, Bhatnagar R, Bhatnagar S. Network analysis of host-pathogen protein interactions in microbe induced cardiovascular diseases. In Silico Biol. 2021;14(3-4):115- 133. 5. Singh, N. and Bhatnagar, S.
6. Machine Learning for Prediction of Drug Targets in Microbe Associated Cardiovascular Diseases by Incorporating Host-pathogen Interaction Network Parameters. Mol. Inf. 2021;2100115. https://doi.org/10.1002/minf.202100115
7. Rai, S, Bhatia, V and Bhatnagar, S. Drug Repurposing for Hyperlipidemia Associated Disorders: An Integrative Network Biology and Machine Learning Approach. Computational Biology and Chemistry 2021 DOI: 10.1016/j.compbiolchem.2021.107505

8. Singh N, Bhatia V, Singh S, Bhatnagar S. MorCVD: A Unified Database for Host- Pathogen Protein-Protein Interactions of Cardiovascular Diseases Related to Microbes. Sci Rep. 2019 Mar 11;9(1):4039. doi: 10.1038/s41598-019-40704-5.
9. Kandari D, Gopalani M, Gupta M, Joshi H, Bhatnagar S, Bhatnagar R. 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. 2019 Jan 11;9:3314.
10. Rai S, Mohanty P, Bhatnagar S. Modeling, dynamics and phosphoinositide binding of the pleckstrin homology domain of two novel PLCs: η1 and η2. J Mol Graph Model. 2018 Oct; 85:130-144.
11. Mohanty P, Bhatnagar S. Structure of focal adhesion kinase in healthy heart versus pathological cardiac hypertrophy: A modeling and simulation study. J Mol Graph Model. 2018 Mar; 80:15-24.
12. Joon S, Gopalani M, Rahi A, Kulshreshtha P, Gogoi H, Bhatnagar S, et al. Biochemical characterization of the GTP-sensing protein, CodY of Bacillus anthracis. Pathog Dis. 2017 Jun 01;75(4).
13. Rai S, Bhatnagar S. Novel Lipidomic Biomarkers in Hyperlipidemia and Cardiovascular Diseases: An Integrative Biology Analysis. OMICS. 2017 Mar;21(3):132-42.
14. Dhiman A, Rahi A, Gopalani M, Bajpai S, Bhatnagar S, Bhatnagar R. Role of the recognition helix of response regulator WalR from Bacillus anthracis in DNA binding and specificity. Int J Biol Macromol. 2017 Mar; 96:257-264.
15. Mohanty P, Bhatnagar S. Structural basis of focal adhesion targeting domain- mediated signaling in cardiac hypertrophy. J Recept Signal Transduct Res. 2016 Apr 8:1-13.
16. Novel Lipidomic Biomarkers in Hyperlipidemia and Cardiovascular Diseases: An Integrative Biology Analysis. Rai S, Bhatnagar S. OMICS. 2017 Mar;21(3):132-142.
17. Calcium-induced conformational changes of Thrombospondin-1 signature domain: implications for vascular disease. Gupta A, Agarwal R, Singh A, Bhatnagar S. J Recept Signal Transduct Res. 2016 Aug 2:1-13.
18. A Network Biology Approach to Decipher Stress Response in Bacteria Using Escherichia coli As a Model. Nagar SD, Aggarwal B, Joon S, Bhatnagar R, Bhatnagar S. OMICS. 2016 May;20(5):310-24.
19. Gupta A, Bhatnagar S. Vasoregression: A Shared Vascular Pathology Underlying Macrovascular And Microvascular Pathologies? OMICS. 2015 Dec;19(12):733-53.
20. Integrative analysis of ocular complications in atherosclerosis unveils pathway 2 convergence and crosstalk (2014) Gupta A, Mohanty P, Bhatnagar S. J Recept Signal Transduct Res. Jul 23:1-16.
21. Structural basis of Bacillus anthracis MoxXT disruption and the modulation of MoxT ribonuclease activity by rationally designed peptides (2014) Verma S, Kumar S, Gupta VP, Gourinath S, Bhatnagar S, Bhatnagar R Epub J Biomol Struct Dyn.
22. Linkage, Mobility, and Selfishness in the MazF Family of Bacterial Toxins: A Snapshot of Bacterial Evolution (2013) Chopra N, Pathak A, Bhatnagar R, Bhatnagar S. Genome biol and evol 5, 2268-2284.

23. Modeling of Plasmodium falciparum Telomerase Reverse Transcriptase Ternary Complex: Repurposing of Nucleoside Analog Inhibitors (2014) Mohanty P, Gupta A, and Bhatnagar S. Drug Repurposing, Rescue, and Repositioning.
24. Functional characterization of WalRK: A two-component signal transduction system from Bacillus anthracis (2014) Dhiman A, Bhatnagar S, Kulshreshtha P, Bhatnagar R. FEBS Open Bio. 4: 65-76.
25. Positive selection and evolution of dengue type-3 virus in the Indian subcontinent. Bedi SK, Prasad A, Mathur K, Bhatnagar S. (2013) J Vector Borne Dis. 50,188-96.
26. Modeling of the structure and interactions of the B. anthracis antitoxin, MoxX: deletion mutant studies highlight its modular structure and repressor function (2011) Chopra N, Agarwal S, Verma S, Bhatnagar S, Bhatnagar R. J Comput Aided Mol Des. 25, 275-91.
27. Mining human genome for novel purinergic P2Y receptors: a sequence analysis and molecular modeling approach (2011) Bhatnagar S, Mishra S, Pathak R. J Recept Signal Transduct Res. 31, 75-84.
28. The PemK Toxin of Bacillus anthracis is a ribonuclease: An insight into its active site, structure and function. (2010) Agarwal S, Mishra NK, Bhatnagar S, Bhatnagar R J. Biol. Chem. 285, 7254-70.
29. Singh A, Thakur PK, Meena M, Dhiraj K, Bhatnagar S, Dubey AK, et al. Interaction between Basic 7S Globulin and Leginsulin in Soybean [Glycine max]: A Structural Insight Letters in Drug Design & Discovery. 2014;11(2): 231-239.
30. Dhiman A, Bhatnagar S, Kulshreshtha P, Bhatnagar R. Functional characterization of WalRK: A two-component signal transduction system from Bacillus anthracis. FEBS Open Bio. 2014;4:65-76.
31. Chopra N, Saumitra, Pathak A, Bhatnagar R, Bhatnagar S. Linkage, mobility, and selfishness in the MazF family of bacterial toxins: a snapshot of bacterial evolution. Genome Biol Evol. 2013;5(12):2268-84.
32. Bedi SK, Prasad A, Mathur K, Bhatnagar S. Positive selection and evolution of dengue type-3 virus in the Indian subcontinent. J Vector Borne Dis. 2013 Sep;50(3):188-96.
33. Chopra N, Agarwal S, Verma S, Bhatnagar S, Bhatnagar R. Modeling of the structure and interactions of the B. anthracis antitoxin, MoxX: deletion mutant studies highlight its modular structure and repressor function. J Comput Aided Mol Des. 2011 Mar;25(3):275- 91.
34. Bhatnagar S, Mishra S, Pathak R. Mining human genome for novel purinergic P2Y receptors: a sequence analysis and molecular modeling approach. J Recept Signal Transduct Res. 2011 Feb;31(1):75-84. 3
35. Agarwal S, Mishra NK, Bhatnagar S, Bhatnagar R. PemK toxin of Bacillus anthracis is a ribonuclease: an insight into its active site, structure, and function. J Biol Chem. 2010 Mar 5;285(10):7254-70.
36. Pathak R, Bhatnagar S, Dubey AK. Mechanisms underlying the opposing effects of P2Y receptors on the cell cycle. J Recept Signal Transduct Res. 2008;28(6):505-29.
37. Bhatnagar S, Srivastava D, Jayadev MS, Dubey AK. Molecular variants and derivatives of insulin for improved glycemic control in diabetes. Prog Biophys Mol Biol. 2006 Jul;91(3):199-228.

38. Rao GS, Bhatnagar S, and Ahuja V. Structure-based design of a novel peptide inhibitor of HIV-1 integrase: a computer modeling approach. J Biomol Struct Dyn. 2002;20(1): p. 31- 8.
39. Bhatnagar S, Rao GS. 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. J Biomol Struct Dyn. 2000 Jun;17(6):957-64.
40. Bhatnagar S, Rao GS, Singh TP. The role of dehydro-alanine in the design of peptides. Biosystems. 1995;34(1-3): p. 143-8.

Publications in National Journal

 

Publications in National Conferences

 

Publications in International Conferences

 

Books/Book Chapters

1. Nirupma S and Bhatnagar S, (2023) Biological interaction networks and their application for microbial pathogenesis in Systems Biology approaches for Host-pathogen Interaction Analysis EDs Tashfeen Ashraf: Elsevier. 

2. Transcriptional Regulators in Bacillus anthracis: A Potent Biothreat Agent. Joon, S, Bhatnagar, S, Bhatnagar, R. Recent Developments in Microbial Technologies, 367 377.

3. Rai S, Bhatnagar S (2016). Computational Methods for Prediction of Protein-Protein Interactions: PPI Prediction Methods (pp. 184-214). Hershey, PA (USA): IGI Global,. 

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

5. Denoising, Clustering, Classification and Representation of Microarray Data for Disease Diagnostics" authored by Bharadwaj N, Wadhwa S, Goel P, Sethi I, Arora CS, Goel A, Bhatnagar S and Parthasarathy H in Research Developments in Computer Vision and Image Processing: Methodologies and Applications" (Editors: Srivastava R, S. K. Singh, Dr. K. K. Shukla, IIT (BHU), Pubs: IGI Global, USA. 

6. Introduction to Bioinformatics. Sonika Bhatnagar and A.K. Dubey in Niscair e- book on Recombinant DNA Technology and Biotechnology available online at: http://nsdl.niscair.res.in/bitstream/123456789/633/1/Bioinformatics.pdf 

7. 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 

8. 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.


 

Publications (Click to expand)

1. Singh N, Bhatia V, Singh S, Bhatnagar S. MorCVD: A Unified Database for Host-Pathogen Protein-Protein Interactions of Cardiovascular Diseases Related to Microbes. Sci Rep. 2019 Mar 11;9(1):4039. doi: 10.1038/s41598-019-40704-5.

2. Kandari D, Gopalani M, Gupta M, Joshi H, Bhatnagar S, Bhatnagar R. 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. 2019 Jan 11;9:3314.

3. Rai S, Mohanty P, Bhatnagar S. Modeling, dynamics and phosphoinositide binding of the pleckstrin homology domain of two novel PLCs: η1 and η2. J Mol Graph Model. 2018 Oct; 85:130-144.

4. Mohanty P, Bhatnagar S. Structure of focal adhesion kinase in healthy heart versus pathological cardiac hypertrophy: A modeling and simulation study. J Mol Graph Model. 2018 Mar; 80:15-24.

5. Joon S, Gopalani M, Rahi A, Kulshreshtha P, Gogoi H, Bhatnagar S, et al. Biochemical characterization of the GTP-sensing protein, CodY of Bacillus anthracis. Pathog Dis. 2017 Jun 01;75(4).

6. Rai S, Bhatnagar S. Novel Lipidomic Biomarkers in Hyperlipidemia and Cardiovascular Diseases: An Integrative Biology Analysis. OMICS. 2017 Mar;21(3):132-42.

7. Dhiman A, Rahi A, Gopalani M, Bajpai S, Bhatnagar S, Bhatnagar R. Role of the recognition helix of response regulator WalR from Bacillus anthracis in DNA binding and specificity. Int J Biol Macromol. 2017 Mar;96:257-64.

8. Gupta A, Agarwal R, Singh A, Bhatnagar S. Calcium-induced conformational changes of Thrombospondin-1 signature domain: implications for vascular disease. J Recept Signal Transduct Res. 2017 Jun; 37(3):239-51.

9. Gupta A, Mohanty P, Bhatnagar S (2016). Protein Structure Prediction using Homology Modeling: Methods and Tools in Methods and Algorithms for Molecular Docking-Based Drug Design and Discovery (p. 339-359). Editors: S Dastmalchi,  MH Mivehroud. IGI Global, (Hershey) USA.

10. Rai S, Bhatnagar S (2016). Computational Methods for Prediction of Protein-Protein Interactions: PPI Prediction Methods in Handbook of Research on Computational Intelligence Applications in Bioinformatics (p. 184-214). Editors: S Dash and B Subudhi. IGI Global, (Hershey) USA.

11. 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. 2016 May;20(5):310-24.

12. Mohanty P, Bhatnagar S. Structural basis of focal adhesion targeting domain-mediated signaling in cardiac hypertrophy. J Recept Signal Transduct Res. 2016 Apr 8:1-13.

13. Rai S, Bhatnagar S. Hyperlipidemia, Disease Associations, and Top 10 Potential Drug Targets: A Network View. OMICS. 2016 Mar;20(3):152-68.

14. Gupta A, Bhatnagar S. Vasoregression: A Shared Vascular Pathology Underlying Macrovascular And Microvascular Pathologies? OMICS. 2015 Dec;19(12):733-53.

15. Mohanty P, Gupta A, and Bhatnagar S. Modeling of Plasmodium falciparum Telomerase Reverse Transcriptase Ternary Complex: Repurposing of Nucleoside Analog Inhibitors. Assay Drug Dev Technol. 2015 Dec;13(10):628-37.

16. Gupta A, Mohanty P, Bhatnagar S. Integrative analysis of ocular complications in atherosclerosis unveils pathway convergence and crosstalk. J Recept Signal Transduct Res. 2015 Apr;35(2):149-64.

17. Verma S, Kumar S, Gupta VP, Gourinath S, Bhatnagar S, Bhatnagar R. Structural basis of Bacillus anthracis MoxXT disruption and the modulation of MoxT ribonuclease activity by rationally designed peptides. J Biomol Struct Dyn. 2015;33(3):606-24.

18. Singh A, Thakur PK, Meena M, Dhiraj K, Bhatnagar S, Dubey AK, et al. Interaction between Basic 7S Globulin and Leginsulin in Soybean [Glycine max]: A Structural Insight Letters in Drug Design & Discovery. 2014;11(2): 231-239.

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

20. Bharadwaj N, Goel P, Arora CS, Bhatnagar S, Parthasarathy H (2014). Denoising, Clustering, Classification and Representation of Microarray Data for Disease Diagnostics in Research Developments in Computer Vision and Image Processing: Methodologies and Applications (p. 149-174). Editor: R. Srivastava, SK Singh, KK Shukla. IGI Global, (Hershey) USA.

21. Chopra N, Saumitra, Pathak A, Bhatnagar R, Bhatnagar S. Linkage, mobility, and selfishness in the MazF family of bacterial toxins: a snapshot of bacterial evolution. Genome Biol Evol. 2013;5(12):2268-84.

22. Bedi SK, Prasad A, Mathur K, Bhatnagar S. Positive selection and evolution of dengue type-3 virus in the Indian subcontinent. J Vector Borne Dis. 2013 Sep;50(3):188-96.

23. Chopra N, Agarwal S, Verma S, Bhatnagar S, Bhatnagar R. Modeling of the structure and interactions of the B. anthracis antitoxin, MoxX: deletion mutant studies highlight its modular structure and repressor function. J Comput Aided Mol Des. 2011 Mar;25(3):275-91.

24. Bhatnagar S, Mishra S, Pathak R. Mining human genome for novel purinergic P2Y receptors: a sequence analysis and molecular modeling approach. J Recept Signal Transduct Res. 2011 Feb;31(1):75-84.

25. Agarwal S, Mishra NK, Bhatnagar S, Bhatnagar R. PemK toxin of Bacillus anthracis is a ribonuclease: an insight into its active site, structure, and function. J Biol Chem. 2010 Mar 5;285(10):7254-70.

26. Pathak R, Bhatnagar S, Dubey AK. Mechanisms underlying the opposing effects of P2Y receptors on the cell cycle. J Recept Signal Transduct Res. 2008;28(6):505-29.

27. Dubey AK, Jayadev MSK, Bhatnagar S (2007). Emerging infectious diseases in humans in Microbes for Human life. Editor: AK Verma. I K International Publishing House, (New Delhi) India.

28. Dubey AK, Bhatnagar S (2006). Bioinformatics in Niscair e-book on Recombinant DNA Technology and Biotechnology. Editors: AK Dubey, P. Gunasekaran, VC Kalia. National Science Digital Library, (New Delhi) India.

29. Bhatnagar S, Srivastava D, Jayadev MS, Dubey AK. Molecular variants and derivatives of insulin for improved glycemic control in diabetes. Prog Biophys Mol Biol. 2006 Jul;91(3):199-228.

30. Bhatnagar S, Jayadev MSK, Dubey AK (2004). Genomics in Pathogenicity and Diversity of Flaviviruses in Microbial Diversity in Current Prespectives and Potential Applications (p 1075-1096). Editors: T. Satyanaranyan and BN Johri. I K International Publishing House, (New Delhi) India.

31. Rao GS, Bhatnagar S. In silico structure-based design of a potent, mutation resilient, small peptide inhibitor of HIV-1 reverse transcriptase. J Biomol Struct Dyn. 2003 Oct;21(2):171-8.

32. Rao GS, Bhatnagar S, and Ahuja V. Structure-based design of a novel peptide inhibitor of HIV-1 integrase: a computer modeling approach. J Biomol Struct Dyn. 2002;20(1): p. 31-8.

33. Bhatnagar S, Rao GS. 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. J Biomol Struct Dyn. 2000 Jun;17(6):957-64.

34. Bhatnagar S, Rao GS, Singh TP. The role of dehydro-alanine in the design of peptides. Biosystems. 1995;34(1-3): p. 143-8.

 

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