< Centre of Excellence in Systems Biology and Biomedical Engineering

Biophysics



About:

The aim of this group is to integrate different aspects of systems biology into an interdisciplinary platform to understand the regulation of cellular architecture. Our investigation ranges from the regulation of macromolecular nanomachines to that of the entire metabolic and transcriptional regulatory networks. We also study the co-ordinated response of cellular regulatory networks to various environmental stimulus and their pervasive roles in reshaping the gene expression profile. Combination of a diversity of computational techniques allows us to depict novel roadmaps of drug targeting, remodeling of metabolic regulation to enhance worldwide rice yield.












Mr. Saurav Mallik
Junior Research Assistant
Center of Excellence, TEQIP Phase-II
Department of Biophysics, Molecular Biology and Bioinformatics
University of Calcutta
Email:saurav.bmb@gmail.com
 Mr.Saurav Mallik








Rumdeep Kaur Grewal
Project Research Associates
Center of Excellence, TEQIP Phase-II
Department of Biophysics, Molecular Biology and Bioinformatics
University of Calcutta
Email:saurav.bmb@gmail.com
Rumdeep Kaur Grewal








Yasmin Begum
Project Research Associates
Center of Excellence, TEQIP Phase-II
Department of Biophysics, Molecular Biology and Bioinformatics
University of Calcutta
Email:saurav.bmb@gmail.com
Yasmin Begum








Dr. Sudip Kundu
Professor
Department Of Biophysics molecular biology and bioinformatics
University of Calcutta






Publications:

  1. Mallik, S., & Kundu, S. (2013). A Comparison of Structural and Evolutionary Attributes of Escherichia coli and Thermus thermophilus Small Ribosomal Subunits: Signatures of Thermal Adaptation. PLoS One, 8(8), e69898. PMID: 23940533.

  2. Mallik, S., & Kundu, S. (2015). Molecular interactions within the halophilic, thermophilic, and mesophilic prokaryotic ribosomal complexes: clues to environmental adaptation. Journal of Biomolecular Structure and Dynamics, 3 (3):639-56.

  3. Mallik, S., Akashi, H., Kundu, S. (2014). The co-evolution among the protein-rRNA constituents of ribosome is maintained by assembly constraints; Poster-P17; SMBE Satellite Meeting/NIG International Symposium: 'The Causes of Genome Evolution', March 14-17; Toray Conference Center, Mishima, Japan. DOI: 10.13140/2.1.3674.3365.

  4. Bhattacherjee, A., Mallik, S., Kundu, S. (2015). Compensatory mutations occur within the electrostatic interaction range of deleterious mutations in protein structure, Journal of Molecular Evolution, 80(1): 10-12.

  5. Mallik, S., Akashi, H., Kundu, S. (2015). Assembly constraints drive co-evolution among ribosomal constituents, Nucleic Acids Research, 43(11): 5352-5363.

  6. Mallik, S., & Kundu, S. (2015). Co-evolutionary constraints of globular proteins correlate with their folding rates. FEBS Letters, 589(17): 2179-2185 [recommended by F1000Prime].

  7. Mallik, S., Das, S., & Kundu, S. (2015). Predicting protein folding rate change upon point mutation using residue-level co-evolutionary information. Proteins, 84(1): 3-8.

  8. Chatterjee, A., Sudip K. (2015) Revisiting the chlorophyll biosynthesis pathway using genome scale metabolic model of Oryza sativa japonica. Scientific Reports 5, 14975. doi:10.1038/srep14975.

  9. Deb, A., Sudip K. (2015) Deciphering Cis-Regulatory Element Mediated Combinatorial Regulation in Rice under Blast Infected Condition. PLoS One 10(9), e0137295.

  10. Shaw, R., Sudip K. (2015) Flux Balance Analysis of Genome Scale Metabolic Model of Rice (Oryza sativa): Aiming to Increase Biomass. Journal of Biosciences 40(4), 819-828.

  11. Mal, C., Deb, A., Aftabuddin, Md, Sudip K. (2015) A network analysis of miRNA mediated gene regulation of rice: crosstalk among biological processes. Molecular BioSystems , 11, 2273-2280.

  12. Aftabuddin, Md, Mal, C., Deb, A., Sudip K. (2014) C2Analyzer: Co-target- Co-function Analyzer. Genomics, proteomics & bioinformatics 12.3: 133-136.

  13. Mallik, S., Akashi, H., Kundu, S. (2014). The co-evolution among the protein-rRNA constituents of ribosome is maintained by assembly constraints; Poster-P17; SMBE Satellite Meeting/NIG International Symposium: 'The Causes of Genome Evolution', March 14-17; Toray Conference Center, Mishima, Japan. DOI: 10.13140/2.1.3674.3365.

  14. Shaw R, Kundu S, (2014), Random weighting through linear programming into intracellular transporters of rice metabolic network. Proc. of Pattern recognition and machine intelligence.

  15. Huma, B., Kundu, S. (2015) "C2 pathway analysis in rice through stoichiometric metabolic modelling" at the 2015 NNMCB National Meeting at CSIR-NCL and IISER Pune. Awarded for Best Poster Presentation.

  16. Huma, B., Kundu, S., Poolman, M., Fell, D. (2014) "Revisiting photorespiration: its interactions and energetics" (in collaboration with Department of Biological & Medical Sciences, Oxford Brookes University) at the 2014 International Study Group for Systems Biology (ISGSB) meeting at Durham University, UK.

  17. Huma, B., Kundu, S. (2014) "Energetics and interactions of photorespiration: an elementary modes analysis" at the annual conference, 2014 of Indian Biophysical Society (IBS) at the Saha Institute of Nuclear Physics, Kolkata.

  18. Chatterjee, A., Kundu, S. (2015) ;Revisiting the chlorophyll synthesis pathway using genome scale meatbolic model of Oryza sativa japonica; at the NNMCB National Meeting, December 27-30, 2015 at NCL & IISER, Pune.

  19. Chatterjee, A., Kundu, S. (2014) ;Revisiting the chlorophyll synthesis pathway using genome scale meatbolic model of Oryza sativa japonica;, Annual Meeting of Indian Biophysical Society (MADALS-2014), 7-10 Feb-2014 at SINP, Kolkata.

  20. Chatterjee, A., Kundu, S. (2012) ;Revisiting the chlorophyll synthesis pathway using genome scale meatbolic model of Oryza sativa japonica;, BBSRC workshop on Development of Metabolic Models to Support Systems Biology Approaches to Bioenergy Research, Oct 15th- 19th, 2012 at ICGEB, New Delhi.



Collaborations:

  • Prof. Hiroshi Akashi, Department of Evolutionary genomics, National Institute of Genetics, Japan.

  • Prof. David Fell, Department of Biological and Medical Sciences - Faculty of Health and Life Sciences, Oxford Brooks University.

  • Dr. Rahul Shaw, Yale-NUS College, Singapore.