Research:

Publications:

1. Das, M., Haberer, G., Panda, A., Das Laha, S., Ghosh, T C., A R Schäffner 2016. Expression Pattern Similarities Support the Prediction of Orthologs Retaining Common Functions after Gene Duplication Events. Plant Physiol 171(4): 2343-2357.

2. Saha D, Podder S, T C Ghosh 2016. Overlapping Regions in HIV-1 Genome Act as Potential Sites for Host-Virus Interaction. Front Microbiol. 2016 Nov 4;7:1735. eCollection 2016.

3. Sen K, Sarkar A, Maji RK, Ghosh Z, Gupta S, T C Ghosh 2016. Deciphering the cross-talking of human competitive endogenous RNAs in K562 chronic myelogenous leukemia cell line Mol Biosyst. 2016 Nov 15;12(12):3633-3642

4. Acharya, D., T.C. Ghosh 2016. Global analysis of human duplicated genes reveals the relative importance of whole-genome duplicates originated in the early vertebrate evolution. BMC Genomics Jan 22;17(1):71. doi: 10.1186/s12864-016-2392-0.

5. Biswas, K., Chakraborty, S., Podder, S., T.C. Ghosh 2016. Insights into the DN/Ds ratio heterogeneity between brain specific genes and widely expressed genes in species of different complexity. Genomics 108: 11-17.

6. Saha, D., Podder, S., Panda, A., T.C. Ghosh  2016. Overlapping genes: A significant genomic correlate of prokaryotic growth rates. Gene  582(2):143-147.

7. Chakraborty, S., Panda, A., T.C. Ghosh 2016. Exploring the evolutionary rate differences between human disease and non-disease genes. Genomics 108: 18-24.

8. Acharya, D., Mukherjee, D., Podder S., T.C. Ghosh 2015. Investigating different duplication pattern of essential genes in mouse and human. PLoS One Mar 9;10(3):e0120784. 

9. Mukherjee, S., Panda, A., T.C. Ghosh 2015. Elucidating evolutionary features and functional implications of orphan genes in Leishmania major. Infect Genet Evol 32:330- 337. 

10. Saha, D., Panda, A., Podder, S., T.C. Ghosh 2015. Overlapping genes: a new strategy of thermophilic stress tolerance in prokaryotes. Extremophiles 19: 345-353.

11. Mukherjee, D., Mukherjee, A., T.C. Ghosh 2015. Evolutionary Rate Heterogeneity of Primary and Secondary Metabolic Pathway Genes in Arabidopsis thaliana. Genome Biol Evol 8: 17-28.

12. Begum, T., T.C. Ghosh 2014. Elucidating the genotype-phenotype relationships and network perturbations of human shared and specific disease genes from an evolutionary perspective. Genome Biol Evol 6: 2741-2753.

13. Panda, A., Podder, S., Chakraborty, S., T.C. Ghosh 2014. GC-made protein disorder sheds new light on vertebrate evolution. Genomics 104: 530-537. 

14. Panda, A., T.C. Ghosh 2014. Prevalent structural disorder carries signature of prokaryotic adaptation to oxic atmosphere. Gene 548: 134-141.

15. Das, J., Podder, S., T.C. Ghosh 2014. Insights into the miRNA regulations in human disease genes. BMC Genomics Nov 21;15:1010. doi: 10.1186/1471-2164-15-1010.

16. Sen, K., T.C. Ghosh 2013. Pseudogenes and their composers: delving in the 'debris' of human genome. Briefings in Functional Genomics 12: 536-547.

17. Chakraborty, S., T.C. Ghosh 2013. Evolutionary rate heterogeneity of core and attachment proteins in yeast protein complexes. Genome Biol Evol 5: 1366-1375.

18. Das, J., Chakraborty, S., Podder, S., T.C. Ghosh 2013. Complex-forming proteins escape the robust regulations of miRNA in human. FEBS Lett. 587, 2284-2287.

19. Kahali, B., T.C. Ghosh 2013. Disorderness in Escherichia coli proteome: perception of folding fidelity and protein-protein interactions. J Biomol Struct Dynamics 31, 472-476.

20. Podder, S.,  T.C. Ghosh 2012. Evolutionary Dynamics of Human Autoimmune Disease Genes and Malfunctioned Immunological Genes. BMC Evol Biol Jan 25;12(1):10. [Epub ahead of print].

21. Sen, K., T.C. Ghosh 2012. Evolutionary conservation and disease gene association of the human genes composing pseudogenes. Gene 501,164-170. 

22. Panda, A., Begum, T., T.C. Ghosh 2012. Insights into the evolutionary features of human neurodegenerative diseases. PLoS One 7(10):e48336. doi: 10.1371/journal.pone.0048336. Epub 2012 Oct 30.

23. Sen, K., Podder, S., T.C. Ghosh 2011. On the quest for selective constraints shaping the expressivity of the genes casting retropseudogenes in human. BMC Genomics (2011) Aug 8;12:401.

24. Kahali, B., Ahmad, S., T.C. Ghosh 2011. Selective constraints in yeast genes with   differential expressivity: Codon pair usage and mRNA stability perspectives. Gene  481, 76-82. 

25. Bagchi, A., T.C. Ghosh 2011. New Direction to the Solution of Protein Folding Problem. J Biomol Struct Dynamics 28, 653-654. 

26. Podder, S., T.C. Ghosh 2011. Insights into the Molecular Correlates Modulating Functional Compensation between Monogenic and Polygenic Disease Gene Duplicates in Human. Genomics 97, 200-204.

27. Podder, S., T.C. Ghosh 2010. Exploring the differences in evolutionary rates between monogenic and polygenic disease genes in human. Mol Biol Evol 27:934- 941.

28. Basak, S., Mukhopadhyay, P., Gupta, S.K., T.C. Ghosh 2010. Genomic adaptation   of prokaryotic organisms at high temperature. Bioinformation 4(8): 352-356.

29. Mukhopadhyay P., T.C. Ghosh 2010. Relationship between gene compactness and base composition in rice and human genome. J Biomol Struct Dynamics 27:477-488. 

30. Singh,  H., Andrabi, M.,  Kahali, B., Ghosh T.C.,  Kochetov A.V., Ahmad S., 2010. On nucleotide solvent accessibility in RNA structure. Gene 463: 41-48. 

31. Begum, T., T.C. Ghosh 2010. Understanding the Effect of Secondary Structures and Aggregation on Human Protein Folding Class Evolution. J Mol Evol 71: 60-69. 

32. Bhattacharya, T., T.C. Ghosh 2010. Protein Connectivity and Protein Complexity Promotes Human Gene Duplicability in a Mutually Exclusive Manner. DNA Research 17: 261-270. 

33. Sur, S., Bothra, A.,  Ghosh, T.C.,  A. Sen 2010. Investigation of the molecular evolution of nitrogen fixation using nucleotide triplet based condensed matrix method. International J Integrative Biology 10, 59-65.

34. Sen, K., Podder, S., T.C. Ghosh 2010. Insights into the genomic features and evolutionary impact of the genes configuring duplicated pseudogenes in human. FEBS Letters 584: 4015-4018.

35. Chakraborty, S., Kahali, B., T.C. Ghosh 2010. Protein complex forming ability is favored over the features of interacting partners in determining the evolutionary rates of proteins in the yeast protein-protein interaction networks. BMC Syst Biol 2010 Nov 12;4(1):155. 

36. Podder, S., Mukhopadhyay, P., T.C. Ghosh 2009. Multifunctionality dominantly determines the rate of human housekeeping and tissue specific interacting protein evolution. Gene 439: 11-16.

37. Manna, B., Bhattacharya, T., Kahali, B.,  T.C. Ghosh 2009. Evolutionary constraints on hub and non-hub proteins in human protein interaction network: insight from protein connectivity and intrinsic disorder. Gene 434: 50-55.

38. Kahali, B.,  Ahmad, S., T.C. Ghosh 2009. Exploring the evolutionary rate differences of party hub and date hub proteins in Saccharomyces cerevisiae protein-protein interaction network 2008. Gene 429: 18-22.

39. Mandal, U.K., Das, B., Ghosh T.C., Sen, A., A.K. Bothra  2008. Nucleotide Triplet Based Molecular Phylogeny of class-I and class II Aminoacyl t-RNA Synthetase in three Domain of Life Process: Bacteria, Archaea and Eukarya. J Biomol Struct  Dynamics 26: 321-328.

40. Mukhopadhyay, P., Basak, S., T.C. Ghosh 2008. Differential Selective Constraints Shaping Codon Usage Pattern of Housekeeping and Tissue Specific Homologous Genes of rice and Arabidopsis. DNA Research 15: 347-356.

41. Kahali, B., Basak, S., T.C. Ghosh 2008. Delving deeper into the unexpected correlation between gene expressivity and codon usage bias of Escherichia coli genome. J Biomol Struct  Dynamics 25: 655-662.

42. Patra, S.K., A. Patra, F. Rizzi, Ghosh T. C.,  S. Bettuzzi  2008. Demethylation of (Cytosine-5-C-methyl) DNA and regulation of transcription in the epigenetic pathways of cancer development. Cancer Metastasis Rev 27: 315-334.

43. Bagchi, A., T.C. Ghosh 2008. Structural interaction between DsrE, DsrF and DsrH in Dsr operon. A. Bagchi and T.C. Ghosh. J Biomol Struct Dynamics 25: 517-524.

44. D’Onofrio, G., Ghosh, T.C., S. Saccone 2007. Different functional classes of genes are characterized by different compositional properties. FEBS Letters 581: 5819-5824.

45. Bagchi,  A., and T.C. Ghosh. 2007.Homology modeling and molecular dynamics study of the interactions of SoxY and SoxZ: The central player of biochemical oxidation of sulfur anions in Pseudaminobacter salicylatoxidans. Res J Microbiol.  2: 569-576.

46. Bagchi, A., and T.C. Ghosh. 2007. Structural insight into the functionality of the transcriptional regulator SoxR from Paracoccus pantotrophus in sulfur oxidation operon  Res J Microbiol. 2: 735-741. 

47. Basak, S., Roy, S., T.C. Ghosh 2007. On the origin of synonymous codon usage divergence between thermophilic and mesophilic prokaryotes. FEBS Letters 581: 5825-5830.

48. Mukhopadhyay, P.,  Basak, S., T. C. Ghosh 2007. Synonymous codon usage in different protein secondary structural classes of human genes: Implication for increased non-randomness of GC3 rich genes towards protein stability. J Biosciences 32: 947-963. 

49. Mukhopadhyay, P.,  Basak, S.,  T. C. Ghosh 2007. Nature of selective constraints on synonymous codon usage of rice differs in GC-poor and GC-rich genes. Gene 400: 71-81.

50. Kahali, B., Basak, S., T.C. Ghosh 2007. Reinvestigating the codon and amino acid usage of S. cerevisiae genome: A new insight from protein secondary structure analysis.  Biochem Biophys Res Commun 354: 693-699.

51. Sau, K., Gupta, S.K., Sau, S., Mandal, S.C., T.C. Ghosh 2007. Studies on synonymous codon and amino acid usage biases in the broad-host range bacteriophage KVP40. J. Microbiol.  45: 58-63.

52. Basak, S., T.C. Ghosh 2006. .Temperature Adaptation of Synonymous Codon Usage in Different Functional Categories of Genes: A Comparative Study betweenMethanococcus jannaschii and Methanococcus maripaludis Homologous Genes. FEBS Letters 580: 3895-3899.

53. Bagchi, A., and T.C. Ghosh. 2006. Structural and functional characterization of SoxW – a thioredoxin involved in the transport of reductants during sulfur oxidation by the global sulfur oxidation reaction cycle. Res. J Microbiol.1: 392-400.

54. Bagchi, A.,  and T.C. Ghosh. 2006. Structural identification of the interactions of SoxA and SoxX during the oxidation of sulfur anions via the novel global sulfur oxidizing (Sox) operon. Res. J Microbiol.1: 172-182.

55. Bagchi,  A., T.C. Ghosh 2006. Structural study of two proteins SigE and ORF1 to predict their roles in the biochemical oxidation of sulfur anions via the global sulfur oxidation operon (sox). Comp Biol Chem 30: 227-232.

56. Joy, F., Basak, S., Gupta, S.K., Das, P.J., Ghosh, S.K., T.C. Ghosh 2006. Compositional correlations in canine genome reflects similarity with human genes. J Biochem Mol Biol 39: 240-246. 

57. Sau, K., Gupta, S.K., Sau, S., Mandal, S.C., T.C. Ghosh 2006. Factors influencing synonymous codon and amino acid usage biases in Mimivirus. BioSystems 85: 107-113.

58. Banerjee, T.,  T.C. Ghosh 2006. Gene expression Level Shapes the Amino Acid Usages in Prochlorococcus marinus  MED4. J Biomol Struct Dynamics 23: 547-554.

59. Bagchi, A., T.C. Ghosh 2006. Structural insight into the interactions of SoxV, SoxW and SoxS in the process of transport of reductants during sulfur oxidation by the novel global sulfur oxidation reaction cycle. Biophys Chem 119: 7-13.

60. Bagchi, A., T.C. Ghosh 2005. Structural identification of a novel thioredoxin SoxS: prediction of the function in the process of transport of reductants during sulfur oxidation by the novel global sulfur oxidation reaction cycle. J Mol Struct – Theochem 758: 113-118.

61. Banerjee, T., Gupta, S.K., T.C. Ghosh 2005. Compositional transitions between Oryza sativa and Arabidopsis thaliana genes are linked to the functional change of encoded proteins. Plant Science 170: 267-273.

62. Bagchi, A.,  T.C. Ghosh 2005. A structural study towards the understanding of the interactions of SoxY, SoxZ and SoxB leading to the oxidation of sulfur anions via the novel global sulfur oxidizing (sox) operon. Biochem Biophys Res Commun  335: 609-615.

63. Sahu, K., Sau, S., Mandal, S.C., T.C. Ghosh 2005. Factors influencing the synonymous codon and amino acid usage bias in an AT-rich P. aeruginosa phage PhiKZ. Acta Biochim Biophys Sin 37: 625-633.

64. Gupta, S.K., Banerjee, T.,  Basak, S., Sahu, K., Sau, S., T.C. Ghosh 2005. Studies on codon usage in Thermoplasma acidophilum and its possible implications on the occurrences of lateral gene transfer. J Basic Microbiol 45: 344-354. 

65. Sahu, K., Gupta, S.K., Sau, S., T.C. Ghosh 2005. Synonymous codon usage bias in 16 Staphylococcus aureus phages: Implication in phage therapy. Virus Res 113: 123-131.

66. Sahu, K., Gupta, S.K., Sau, S., T.C. Ghosh 2005. Comparative analysis of the base composition and codon usages in fourteen mycobacteriophage genomes. J Biomol Struct Dynamics 23: 63-72. 

67. Banerjee, T., Gupta, S.K., T.C. Ghosh 2005. Role of mutational bias and natural selection on genome-wide nucleotide bias in prokaryotic organisms. BioSystems 81: 11-18. 

68. Basak, S., T.C. Ghosh 2005. On the origin of genomic adaptation at high temperature for prokaryotic organisms.  Biochem Biophys Res Commun  330: 629-632. 

69. Banerjee, T., Gupta, S.K., T.C. Ghosh 2005. Towards a resolution on the inherent methodological weakness of the “effective number of codons used by a gene”. Biochem Biophys Res Commun 330: 1015-1018.

70. D’Onofrio, G., T.C. Ghosh 2005. The compositional transition of vertebrate genomes: an analysis of the secondary structure of the proteins encoded by human genes. Gene 345: 27-33. 

71. Basak, S., Mandal, S., T.C. Ghosh 2005. Correlations between genomic GC levels and optimal growth temperatures: some comments. Biochem Biophys Res Commun 327: 969-970. 

72. Basak, S., Banerjee, T., Gupta, S.K., T.C. Ghosh 2004. Investigation on the Causes of Codon and Amino Acid Usages Variation Between  Thermophilic Aquifex aeolicus  and Mesophilic Bacillus subtilis.    J Biomol Struct  Dynamics 22: 205-214. 

73. Banerjee, T., Basak, S., Gupta,S.K., T.C. Ghosh 2004. Evolutionary Forces in Shaping the Codon and Amino Acid Usages in Blochmannia floridanus. J Biomol Struct  Dynamics 22: 13-24. 

74. Sau, K.,  Gupta, S.K., Ghosh T.C.,  S. Sau 2004. Synonymous codon usage analysis of mycobacteriophage Bxz1 and its plating bacteria M. smegmatis: identification of highly and lowly expressed genes of Bxz1 and the possible function of its tRNA species. J Biochem Mol Biol  37: 487-492.

75. Subramaniyam, V., Gupta, S.K., T.C. Ghosh 2004. Shannon’s uncertainty principle and gene expression levels. V. Subramaniyam, Current Science 86: 1142-1147. 

76. Gupta, S.K.,  Bhattacharyya, T.K., T.C. Ghosh 2004. Synonymous codon usage in Lactococcus lactis: Mutational Bias Versus Translational Selection. J Biomol Struct Dynamics 21: 527-535. 

77. Gupta, S.K., T.C. Ghosh 2003. Reinvestigation on the causes of genomic GC variation between the orthologous genes of Mycobacterium tuberculosis and Mycobacterium leprae. Biochem Biophys Res Commun 303: 65-68.

78. D’Onofrio, G., Ghosh T.C., G. Bernardi 2002. The base composition of the human genes is correlated with the secondary  structures of the encoded proteins.  Gene 300:179-187.

79. Gupta, S.K., Bhattacharyya T.K., T.C. Ghosh 2002. Compositional correlation and codon usage studies in Buchnera aphidicola. Indian J Biochem Biophys 39: 35-48.

80. Gupta, S.K., T.C. Ghosh 2001. Gene expressivity is the main factor in dictating the codon usage variation among the genes in Pseudomonas aeruginosa. Gene 273: 63-70. 

81. Khetawat, D., Ghosh T.C., Bhattacharya, M.K., Bhattacharya, S.K., S. Chakrabarti 2001. Molecular characterization of the VP7 gene of Rotavirus isolated from a clinical sample of Calcutta, India., Virus Res 74: 53-58.

82. Mandal, D., Jana,  S.,  Panda, S., Bhattacharya, S., Ghosh T.C.,  Bhattacharya, S.K., S. Chakrabarti 2000. Distribution of HIV-I subtypes among female sex workers of Calcutta, India. Indian J Med Res 112: 165-172.

83. Ghosh, T.C., Gupta, S.K., S. Majumdar 2000.  Studies on codon usage in Entamoeba histolytica. Intl J  Parasitology 30: 715-722. 

84. Gupta, S.K., Majumdar, S.,  Bhattacharya, T.K., T.C. Ghosh 2000. Studies on the relationships between the synonymous codon usage and protein secondary  structural units. Biochem Biophys Res Commun 269: 692-696. 

85. Gupta, S.K., T.C. Ghosh 2000. CUCG: A non-redundant codon usage database from complete genomes. Current Science 78: 28-29. 

86. Majumdar S., Gupta S.K., Sundararajan V.S., T.C. Ghosh 1999. Compositional correlation studies among the three different codon positions in 12 bacterial genomes. Biochem Biophys Res Commun 266: 66-71.

87. Gupta, S.K., T.C. Ghosh 1997. Similarities inferred from the studies of long range correlations among mitochondrial DNA sequences. Indian J Biochem Biophys 34: 259-265. 

88. Gupta, S.K., T.C. Ghosh 1996. Genolyte: a PC-based computer program for visualisation of genomic DNA sequences. Indian J Biochem Biophys 33: 152-155. 

89. Pal, M.K., T.C. Ghosh 1991.Binding of dyes by Teichoic Acid in competition with other polyanions. Makromol Chem.192: 467-471.

90. Pal, M.K., Ghosh T.C.,  J.K. Ghosh 1990. Studies on conformation and metal ion binding by Teichoic Acid of Staphylococcus Aureus. Biopolymers 30: 273-277. 

91. Pal, M.K., T.C. Ghosh 1990. Induction of Metachromasia and Circular Dichroism in the dye 1,9 dimethyl methylene blue by S. Aureus wall teichoic acid. Indian J Biochem Biophys  27: 176-178. 

92. Pal, M.K., T.C. Ghosh 1988. Teichoic Acid: Induction of Metachromasia and Circular Dichroism in pinacyanol dye. Makromol Chem. Rapid Commun. 9: 97-100. 

Book chapter 

Chakraborty, S., Podder, S., Kahali, B., Begum, T., Sen, K., Ghosh, T C. 2011. Insights into Eukaryotic Interacting Protein evolution in Evolutionary Biology – Concepts, Biodiversity, Macroevolution and Genome Evolution edited by Pierre Pontarotti, Springer.

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