Database created:

BambooInfoline: a database for North Bengal Bamboos (www.bamboodb.ind.in)
MycoSec: a database for Mycobacterium Secretome analysis (under submission)

Selected Papers:

1. Rai R, Swanson E, Sarkar I, Lama D, Abebe-Akele F, Simpson S, Morris K, Thomas W , Kar P, Gtari M, Sen A, and Tisa L (2017). Permanent Draft Genome sequence of French bean symbiont, Rhizobium sp. strain RSm-3, isolated from East-Himalayan region of India. Genome Announcement

2. Ghodhbane-Gtari F, N Beauchemin, M Louati, I Nouioui, A Ktari, K Hezbri, A Gueddou, A Chen, M Huntemann, N Ivanova, N Kyrpides, V Markowitz, K Mavrommatis, I Pagani, A Sen, L Wall, T Woyke, M Gtari, and L Tisa (2016). Permanent improved high quality draft genome sequence of Nocardia casuarinae strain BMG51109, an endophyte of actinorhizal root nodules of Casuarina glauca. GenomeA 4(4), pp.e00799-16

3. Ghodhbane-Gtari F, N Beauchemin, A Geddou, K Hezbri, A Ktari, M Louati, I Nouioui, A Chen, M Huntemann, N Ivanova, N Kyrpides, V Markowitz, K Mavrommatis, I Pagani, A Sen, L Wall, T Woyke, M Gtari, and L Tisa (2016) Permanent Draft Genome sequence of Nocardia sp. BMG111209, an actinobacterium isolated from nodules of Casuarina glauca. GenomeA 4.4 (2016): e00770-16.

4. Thakur S and Sen A (2016) Comparative analysis of metabolic machinery of Frankia along with other selected actinobacteria. Symbiosis. 70(1) 59–68. DOI 10.1007/s13199-016-0410-2.

5. Sarkar I, Normand P, Tisa S. L, Gtari M, Bothra A and Sen A. Characterization of PAS domains in Frankia and selected Actinobacteria and their possible interaction with other co-domains for environmental adaptation. Symbiosis. 70(1) 69–78.

6. Bose D, Sarkar I, Labar R, Oshone R, Ghazal R, Morris K, Abebe-Akele F, Thomas K W, Tisa S. L, Sen A. Comparative genomics of Prauserella sp. Am3,an actinobacterium isolated from root nodules of Alnus nepalensis in India. Symbiosis. 70(1) 49–58. DOI 10.1007/s13199-016-0401-3.

7. Tisa S. L., Oshone R, Sarkar I, Ktari A, Sen A, Gtari M. Genomic approaches toward understanding the actinorhizal symbiosis: an update on the status of the Frankia genomes. Symbiosis. 70(1) 5–16. DOI 10.1007/s13199-016-0390-2

8. Sghaier H, Hezbri K, Ghodhbane-Gtari F, Pujic P, Sen A, Daffonchio D, Boudabous A, Tisa LS, Klenk HP, Armengaud J, Normand P, Gtari M (2016). Stone-dwelling actinobacteria Blastococcus saxobsidens, Modestobacter marinus and Geodermatophilus obscurus proteogenomes. ISME J. 10, 21–29. doi: 10.1038/ismej..108.

9. Banerjee A, DK Sahoo, H Thatoi, BR Pati, KC Mondal, A Sen, PK Das Mohapatra (2015). Structural Characterization and Active Site Prediction of Bacterial Keratinase through Molecular Docking. J Bioinform 1:67-82

10. Roy A, Mukhopadhyay S, Sarkar I, Sen A (2015). Comparative investigation of the various determinants that influence the codon and amino acid usage patterns in the genus Bifidobacterium. World J Microbiol Biotechnol. doi: 10.1007/s11274-015-1850-1.

11. Sen A, V Daubin, D Abrouk, I Gifford, AM Berry, and P Normand (2014) The phylogeny of actinobacteria revisited in the light of complete genomes, the orders Frankiales and Micrococcales should be split into coherent entities. Proposal of Frankiales ord. nov., Geodermatophilales ord. nov., Acidothermales ord. nov. and Nakamurellales ord. nov. IJSEM. 64, 3821–3832.

12. Ghosh S, UK Mondal, A Sen and AK Bothra (2014). Comparative analysis and codon usage study of nifD, nifK and nifH genes linked with free living nitrogen fixing bacteria. Int. J. Integ. Biol. 15:7-10

13. Pal S, A Banerjee, PS Das, BR Pati, KC Mandal, B Chakraborty, A Sen and PKD Mohapatra (2014) Dengue virus type 4 evolution & genomics: a Bioinformatic approach. Ind J Biotechnol

14. Banerjee A, S Pal, T Pal, KC Mondal, BR Pati, A Sen and PKD Mohapatra (2014) Characterization of Bacillus proteases through protein-protein interaction: an in silico study of anthrax pathogenicity. Hum. Trad. Med. 4:e6.

15. Pal A, UK Mandal, S Mukherjee, A Sen and AK Bothra (2013). The Implication of Codon Usage Design and Expression Level in Determining the Nature of Selection and Functionality amongst the Amino Acid Biosynthetic Pathway coding sequences of Arthrobacter sp. FB24. Current Bioinformatics (published online).

16. Tisa LS, N Beauchemin, M Gtari, A Sen, and LG Wall (2013). What stories can the Frankia genomes tell us? J Biosciences 38:719–726.

17. Bhattacharya S, A Sen, S Thakur and LS Tisa (2013). Characterization of Hemoglobin from Actinorhizal Plants – An in-silico approach. J Biosciences 38:777–787.

18. Thakur S, AK Bothra and A Sen (2013) Functional divergence outlines the evolution of novel protein function in NifH/BchL protein family. J Biosciences 38:733–740.

19. Sur S, S Saha, LS. Tisa, AK Bothra and A Sen (2013) Characterization of pseudogenes in members of the order Frankineae. J Biosciences 38:727–732.

20. Thakur S, Normand P, Daubin V, Tisa LS and Sen A (2013). Contrasted evolutionary constraints on secreted and non-secreted proteomes of selected Actinobacteria. BMC Genomics doi:10.1186/1471-2164-14-474.

21. Ray A, Bhattacharya S, Bothra AK and Sen A. (2013) A Database for Mycobacterium secretome analysis: 'MycoSec' to accelerate global health research. Omics: A Journal of Integrative Biology 17:502-509.

22. Thakur S, AK Bothra and A Sen (2013). Exploring the genomes of symbiotic diazotrophs with relevance to biological nitrogen fixation. In R. Bandopadhyay and PB Kavi (ed). Agriculture bioinformatics. Springer publications Pp 235-257.

23. Thakur S, AK Bothra and A Sen (2013). Insights into the nitrogenase protein - an in silico approach. In: Biology of useful plants and microbes, A Sen (ed), Narosa Publishing House, New Delhi, India, pp 301-320.

24. Sur S, AK Bothra and A Sen (2013) Proteome analysis reveals the influence of isoelectric point and amino acid usages on the lifestyle of nitrogen fixing microorganisms. Ind J Biotechnol. 12: 88-97.

25. Thakur S, AK Bothra, S Sur and A Sen (2012) Molecular dynamics simulation of pr-1 protein from Solanum tuberosum provides an in-depth view of its structural features. In ‘Microbial Resources for Crop Improvement’; BN Chakraborty and U Chakraborty (ed.); Satish Serial Publishing House Pp 173-181.

26. Kundu, S, AK Bothra, LS Tisa and A Sen (2012). In silico analysis reveals the role of horizontally transferred genes (HGTs) in shaping the pathogenicity of Xanthomonas. Ind. J. Biotechnol. 11:404-411.

27. Saha, S, S Sur, A Bothra and A Sen (2012). A homology model for 16S rRNA tertiary structure of Frankia. NBU J Pl. Sc.6:89-94.

28. Mondal, U, A Sen and A Bothra (2012). Bioinformatics of pathogenic food bacteria. NBU J Pl. Sc.6:9-17.

29. Thakur S, A Bothra and A Sen (2012) In silico studies of NifH protein structure and its post-translational modification in Bradyrhizobium sp. ors278. Int. J Pharm Bio Sc

30. Sen A, S Thakur, A Bothra, S Sur and L Tisa (2012). Identification of TTA codon containing genes in Frankia and exploration of the role of tRNA in regulating these genes. Archives of Microbiology.194: 35-45.

31. Chakraborty D, UK Mondal, A Sen and AK Bothra (2011). Molecular dynamics simulation of hydrogenase isoenzyme formation protein HypC. IUP J Biotechnol. 5(3):56-64.

32. Sur S, AK Bothra and A Sen (2011). Bioinformatics of Nitrogen fixation – a review, In Recent studies in biodiversity and traditional knowledge in India. C Ghosh & AP Das (eds.) pp35-43.

33. Thakur S, Z Patra, M Biswal and A Sen (2011). Exploration of proteis with signal peptides and their respective genes in some actinomycetes: a bioinformatics approach. Int. J. Integrative Biol. 11(2): 97-102.

34. Mondal UK, A Sen and AK Bothra (2011). Characterization of pathogenic genes through condensed matrix method, case study through bacterial Zeta toxin. International journal of Genetic Engneering and Biotechnology. 2(1): 109-114.

35. Sur S, A Pal, AK Bothra and A Sen. (2005) Moderate codon bias is attributed to translational selection for nitrogen fixing genes of Bradyrhizobium japonicum USDA 110. Bioinformatics India. 3:59-64

36. Sur S, A Sen and AK Bothra (2006) Codon usage profiling and analysis of intergenic association of Frankia EuIK1 nif genes . Ind J Microbiol 46:363-369.

37. Sur S, A Sen and AK Bothra. (2007) Mutational drift prevails over translational efficiency in Frankia nif operons. Ind J Biotechnol 6:321-328.

38. Ghosh MK, S Sur and A Sen (2007) Nitrogen fixation in various microorganisms with special reference to Frankia. In Rhizosphere Biotechnology: Plant growth-Retrospect and prospect, ed. AK Roy, Scientific Publishers. pp 167-182.

39. Sen G, S Sur, D Bose, U Mondal, T Furnholm, A Bothra, L Tisa and A Sen (2007) Analysis of codon usage patterns and predicted highly expressed genes for six phytopathogenic Xanthomonas genomes shows a high degree of conservation. In silico Biology 7:0039 http://www.bioinfo.de/isb/2007/07/0039/

40. Sur S, A Sen & AK Bothra (2007). Codon usage analysis of some archaeal (methanogenic) nitrogen fixing genes: relationship to gene expression and bias. Bioinfo. Trends 2: 47-60.

41. Sen A, S Sur, AK Bothra, DR Benson, P Normand, and LS Tisa. (2008) The implication of life style on codon usage patterns and predicted highly expressed genes for three Frankia Genomes. Antonie van Leeuwenhoek 93(4) 335-346.

42. Sur S, M Bhattacharya, AK Bothra, LS Tisa and A Sen (2008). Bioinformatic analysis of codon usage patterns in a free living diazotroph, Azotobacter vinelandii. Biotechnology 7: 242-249.

43. Sur S, AK Bothra, M Bajwa, LS Tisa & A Sen (2008). In Silico analysis of Chlorobium genomes divulge insights into the subsistence of the bacteria. Res. J. Microbiol. 3: 600-613.

44. Thakur S, S Sur, D Bose, AK Goyal, T Mishra, R Rai, M Bhattacharya, AK Bothra and A Sen (2009) Molecular modeling of a pathogenesis related protein from Solanum tuberosum. NBU J Pl. Sc. 3: 15-19.

45. Sur S, B Bajwa, M Bajwa, B Basistha, AK Bothra and A Sen (2009) Investigation of codon and amino-acid usages in a Rhizobium phage. NBU J Pl. Sc. 3: 49-51.

46. Sur S, G Sen, S Thakur, AK Bothra and A Sen (2009) In silico analysis of evolution in swine flu viral genomes through re-assortment by promulgation and mutation. Biotechnol. 8:434-441.

47. Mondal U, A Sen, and A Bothra (2009) Comparison in motional properties of Staphylococcus aureus exfoliative toxins A and B as revealed by their MD simulation. Int. J. Integrative Biol. 8:19-24.

48. Sen A, S Sur, LS Tisa, AK Bothra, S Thakur and UK Mondal (2010) Homology modelling of the Frankia nitrogenase iron proteins. Symbiosis 50:37-44.

49. Sur S, A Bothra and A Sen (2010) Symbiotic nitrogen fixation-a bioinformatics perspective. Biotechnology DOI: 0000.19779-19779

50. Sur S, A Bothra, TC Ghosh and A Sen (2010) Investigation of the molecular evolution of nitrogen fixation using nucleotide triplet based condensed matrix method. Int. J. Integrative Biol.10: 59-65

51. Thakur S, AK Bothra, S Sur and A Sen (2010). Modeling and molecular dynamics simulation of PR-1 protein an integral part of plant defense. Int J of Biol and Chem Sci 4(4): 1251-1261.

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