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Publications

Publications

Peer-reviewed Selected Publication:
  1. Nature-inspired Enzyme engineering and sustainable catalysis: biochemical clues from the world of plants and extremophiles (2023), Chatterjee A., Puri S., Sharma P. K., Deepa PR*. and Chowdhury S.*, Front. Bioeng. Biotechnol. (Accepted).
  2. Transforming growth factor- β mediated regulation of epigenome is required for epithelial to mesenchymal transition associated features in liver cancer cells (2023), Srivastava A., Sharma H., Chowdhury S., Chowdhury R. and Mukherjee S*. Heliyon 9:e14565.
  3. Transcriptomic analysis reveals differential adaptation of colorectal cancer cells to low and acute doses of cisplatin (2023), Saini H., Dave R., Chatterjee S., Mandloi A., Sharma H., Daiya A., Mukherjee S. and Chowdhury R*. and Chowdhury S.*, Gene 864:147304.
  4. Epigenetic adaptations in drug-tolerant tumor cells (2023), Mani N., Daiya A., Chowdhury R., Mukherjee S.* and Chowdhury S.*,  Advances in Cancer Research 158:293
  5. Chloroquine induces transitory attenuation of proliferation of human lung cancer cells through regulation of mutant P53 and YAP. (2023), Saini H., Choudhary M., Sharma H., Chowdhury S., Mukherjee S. and Chowdhury R. Mol Biol Rep 50:1045.
  6. Silver nanoparticle-induced alteration of mitochondrial and ER homeostasis affects human breast cancer cell fate. (2022), Dey S., Fageria L., Sharma A., Mukherjee S., Pande S., Chowdhury R. and Chowdhury S.* Toxicology Reports 9:1977.
  7. Interleukin-6 Induced Proliferation is Attenuated by Transforming Growth Factor-b-Induced Signaling in Human Hepatocellular Carcinoma Cells, Srivastava A., Sharma H., Khanna S., Tejasvini SB, Chowdhury S., Chowdhury R. and Mukherjee S. Front Oncol. 2022 Jan 20;11:811941.
  8. A genome wide expression profile of non-coding RNAs in human osteosarcoma cells as they acquire resistance to cisplatin. (2021), Sharma H.,Niveditha D., Chowdhury, R. Mukherjee, S. and Chowdhury S*. Discover Oncology 12:43.  
  9. Dynamic alterations of H3K4me3 and H3K27me3 at ADAM17 and Jagged-1 gene promoters cause inflammatory switch of endothelial cells. Katakia YT, Pandya-Thakkar N, Thakar S, Sakhuja A, Goyal R, Sharma H, Dave R, Mandloi A, Basu S, Nigam I, Kuncharam BVR, Chowdhury S, Majumder S. Journal of Cellular Physiology, 2021 (Accepted).
  10. Verteporfin disrupts multiple steps of autophagy and regulates p53 to sensitize osteosarcoma cells. (2021), Saini H., Sharma H., Mukherjee S., Chowdhury S. and Chowdhury R. Cancer Cell Int. 21:52
  11. Differential response of photosynthetic apparatus towards alkaline pH treatment in NIES-39 and PCC 7345 strains of Arthrospira platensis, (2021), Jangir, M.M., Chowdhury, S*. and Bhagavatula, Int. Microbiol. 24:219-31. 
  12. Multistimuli responsive heteroleptic Iridium (III) complex: Role of Hydrogen bonding in probing solvent, pH and Bovine Serum Albumin (BSA). (2020), Kachawal V., Sharma P K., Sarmah, A., Chowdhury S*. and Laskar I. R. J. Mater. Chem. C 8:6605-14.
  13. Common and unique microRNAs in multiple carcinomas regulate similar network of pathways to mediate cancer progression. (2020), Niveditha D., Jasoria M., Narayan J., Majumder S, Mukherjee, S., Chowdhury, R. and Chowdhury S*. Sci. Rep 10:2331-41.
  14. Transcriptomic analysis associated with reversal of cisplatin sensitivity in drug resistant osteosarcoma cells after a drug holiday. (2019), Niveditha D., Sharma H., Majumder S, Mukherjee, S., Chowdhury, R. and Chowdhury S*. BMC Cancer 19:1045-1058.
  15. Drug tolerant cells: An emerging target with unique transcriptomic features. (2019), Niveditha D., Sharma H., Sahu A., Majumder S., Chowdhury R. and Chowdhury S*. Cancer Informatics 18: 1-5
  16. Dysregulated expression but redundant function of the long non-coding RNA Hotair in diabetic kidney disease. (2019) Majumder S, Hadden MJ, Thieme K, Batchu SN, Niveditha D, Chowdhury S, Yerra VG, Advani SL, Bowskill BB, Liu Y, Vakili H, Alghamdi TA, White KE, Geldenhuys L, Siddiqi FS, Advani A.  Diabetologia 62(11): 2129.
  17. Analysis of seven putative Na+/H+ antiporters of Arthrospira platensis NIES-39 using transcription profiling and in-silico studies: an indication towards alkaline pH  acclimation (2019), Jangir M. M., Vani B. and Chowdhury S*. Physiology and Molecular Biology of Plants 25 (5): 1175 
  18. Evolution of endonuclease IV protein family: an in silico analysis (2019), Kanchan S., Sharma, P and Chowdhury S*., 3Biotech 9 (5): 168.  
  19. Autophagy Regulated by Gain of Function Mutant p53 Enhances Proteasomal Inhibitor-Mediated Cell Death through Induction of ROS and ERK in Lung Cancer Cells (2019), Saini H., Hakeem I., Mukherjee S., Chowdhury S. and Chowdhury R., Journal of Oncology, 6164807.  
  20. Refined template selection and combination algorithm significantly improves template based modelling accuracy (2019), Runthala A. and Chowdhury S*., Journal of Bioinformatics and Computational Biology 17 (2), 1950006.
  21. A global transcriptomic pipeline decoding core network of genes involved in stages leading to acquisition of drug-resistance to cisplatin in osteosarcoma cells (2019), Niveditha D., Mukherjee S., Majumder S., Chowdhury R. and Chowdhury S*., Bioinformatics 35 (10), 1701-1711.
  22. In-Silico analysis of Endonuclease III protein family identifies key residues and processes during evolution (2015), Kanchan S., Mehrotra R. and Chowdhury S*., J. Mol. Evol. 81(1-2), 54-67.
  23. Evolutionary pattern of four representative DNA repair proteins across six model organisms: an in-silico analysis (2014), Kanchan S., Mehrotra R. and Chowdhury S*., Network Modeling Analysis in Health Informatics and Bioinformatics 3 (1), 70-80.
  24. Novel mutations in the antifolate drug resistance marker genes among Plasmodium vivax isolates exhibiting severe manifestations (2012), Garg S., Saxena, V., Lumb V., Pakalapati, D., P.A., Boopathi, Subudhi A. K., Chowdhury S. Sanjay K. Kochar, Dhanpat K. Kochar, Y.D. Sharma, Das A.K., Experimental Parasitology 132, 410–416.
  25. Denatured-state ensemble and the early-stage folding of the G29A mutant of the B-domain of protein A (2005), Chowdhury S., Lei H. and Duan Y., J. Phys. Chem. B. 109, 9073-9081.
  26. Characterizing the rate-limiting step of Trp-cage folding by all-atom molecular dynamics simulations (2004), Chowdhury, S., Mathew C. Lee and Duan Y., J. Phys. Chem. B  108, 13855-13865.
  27. Fs-21 Peptides Can Form Both Single Helix and Helix-Turn-Helix (2004), Zhang W., Lei H., Chowdhury, S. and Duan, Y., J. Phys. Chem. B. 108, 7479-7489. 
  28. A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase QM calculations (2003), Duan Y., Wu C., Chowdhury S., Lee M. C., G. Xiong et al., J. Comp. Chem. 16, 1999-2012.
  29. Ab initio folding simulation of the Trp-cage mini-protein approaches NMR resolution (2003), Chowdhury, S., Lee M. C., Xiong G. M., Duan Y., J. Mol. Biol. 327, 711-717.
  30. Breaking non-native hydrophobic clusters is the rate-limiting step in the folding of an alanine-based peptide (2003), Chowdhury, S., Zhang W., Wu C., Xiong G. M. and Duan Y., Biopolymers 68, 63-75.
  31. G-quadruplex structure can be stable with only some coordination sites being occupied by cations: A six-nanosecond molecular dynamics study (2001), Chowdhury S. and Bansal M., J. Phys. Chem. B 105, 7572-7578.
  32. A nanosecond molecular dynamics study of antiparallel d(G)7 quadruplex structures: effect of the coordinated cations (2001), Chowdhury S. and Bansal M., J. Biomol. Struct. Dyn., 18, 647-669.
  33. Modelling studies on neurodegenerative disease-causing triplet repeat sequences d(GGC/GCC)(n) and d(CAG/CTG)(n) (2001), Chowdhury S. and Bansal M., J. Biosciences 26, 649-665.
  34. Effect of coordinated ions on structure and flexibility of parallel G-quadruplexes: A molecular dynamics study (2000), Chowdhury S. and Bansal M., J. Biomol. Struct. Dyn. 18, 11-28.
Book Chapter :
  1. Analysis of Transcriptomic Data Generated from Drug Treated Cancer Cell Line (2022), Kushwaha S., Mukherjee S., Chowdhury R. and Chowdhury S. In: Baiocchi, M. (eds) Cancer Drug Resistance. Methods in Molecular Biology, vol 2535. Humana, New York, NY.
  2. Understanding the binding affinity and specificity of miRNAs: A molecular dynamics study (2022), Kushwaha S., Mandloi A. and Chowdhury S. In: Srinivas R., Kumar, R., Dutta, M. (eds) Advances in Computational Modeling and Simulation Lectures Notes in Mechanical Engineering. Springer, Singapore.
  3. Secondary and tertiary structure prediction of proteins: A Bioinformatics approach (2015), Kesheri M., Kanchan S., Chowdhury S. and Sinha R.P. in Complex System Modelling and Control Through Intelligent Soft Computations Studies in Fuzziness and Soft Computing, Volume 319 (Ed: Quanmin Zhu and Ahmad Taher Azar), Springer International Publishing Switzerland, pp 541-569.
  4. Unsolved problems of ambient computationally intelligent TBM algorithms (2015), Runthala A. and Chowdhury S, in Hybrid Soft Computing Approaches: Research and Applications. Vol- 611 (Eds. Bhattacharyya Siddhartha,  Dutta Paramartha, Chakraborty Susanta), Springer India, pp 75-105.
  5. Protein Structure Prediction: Are we there yet? (2013), Runthala A. and Chowdhury S., in Knowledge-Based Systems in Biomedicine and Computational Life Science, Springer-Verlag Monograph Volume, Editor(s): Tuan D. Pham and Lakhmi C. Jain, Volume 450, 2013, pp 79-115
  6. Exploring the structural repertoire of guanine-rich DNA sequences: Computer modelling studies (1999), Bansal M., M. Ravi Kiran and Chowdhury S., in Computational Molecular Biology, Theoretical Computational  Chemistry, Vol. -8 (Ed. J. Leszczynski), Elsevier Science, pp 279-323, 1999.
Book:
Title: "Cyanobacterial Stresses: An Ecophysiological, Biotechnological and Bioinformatic Approach" by Minu Kesheri, Swarna Kanchan, Shibasish Chowdhury
Publisher: LAMBERT Academic Publishing 
ISBN-13: 9778-3848438839
 
* Corresponding Author 

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