Selected Publications-
Functional and Evolutionary Genomics

  1. Gao, B. and Gupta, R.S. (2011) Microbial systematics in the post-genomics era. Antonie Van Leeuwenhoek. (In press).
  2. Ahmod, N.Z., Gupta, R.S. and Shah, H.N. (2011) Identification of a Bacillus anthracis specific indel in the yeaC gene and Development of a Rapid Pyrosequencing Assay for distinguishing B. anthracis from the B. cereus group. J. Microbiol. Methods (In press)
  3. Naushad, H.S. and Gupta, R.S. (2011) Molecular signatures (conserved indels) in protein sequences that are specific for the order Pasteurellales and distinguish two of its main clades. Antonie Van Leeuwenhoek. Aug 10, (Epub ahead of print)
  4. Gupta, R. S. (2011) Origin of diderm (Gram-negative) bacteria: antibiotic selection pressure rather than endosymbiosis likely led to the evolution of bacterial cells with two membranes. Antonie Van Leeuwenhoek. 100(2): 171-82. [Abstract]
  5. Gupta, R. S. and Bhandari, V. (2011) Phylogeny and molecular signatures for the phylum Thermotogae and its subgroups. Antonie Van Leeuwenhoek. 100(1): 1-34. [Abstract]
  6. Gupta, R. S. and Shami, A. (2011) Molecular signatures for the Crenarchaeota and theThaumarchaeota. Antonie Van Leeuwenhoek. 99(2): 133-57. [Abstract
  7. Gupta, R. S. (2010) Molecular signatures for the main phyla of photosynthetic bacteria and their subgroups. Photosynth Res. 104(2-3): 357-72. [Abstract]
  8. Lorenzini, E., Singer, A., Singh, B., Lam, R., Skarina, T., Chirgadze, N. Y., Savchenko, A. and Gupta, R. S. (2010) Structure and protein-protein interaction studies on Chlamydia trachomatis protein CT670 (YscO Homolog). J Bacteriol. 192(11): 2746-56. [Abstract]
  9. Gupta, R. S. and Mathews, D. W. (2010) Signature proteins for the major clades of Cyanobacteria. BMC Evol Biol. 10: 24. [Abstract]
  10. Gupta, R. S. (2009) Protein signatures (molecular synapomorphies) that are distinctive characteristics of the major cyanobacterial clades. Int J Syst Evol Microbiol. 59(Pt 10): 2510-26. [Abstract]
  11. Gao, B., Sugiman-Marangos, S., Junop, M. S. and Gupta, R. S. (2009) Structural and phylogenetic analysis of a conserved actinobacteria-specific protein (ASP1; SCO1997) from Streptomyces coelicolor. BMC Struct Biol. 9: 40. [Abstract]
  12. Gupta, R. S. and Gao B. (2009) Phylogenomic analyses of clostridia and identification of novel protein signatures that are specific to the genus Clostridium sensu stricto (cluster I). Int J Syst Evol Microbiol. 59(Pt 2): 285-94. [Abstract]
  13. Gao, B., Mohan, R. and Gupta, R. S. (2009) Phylogenomics and protein signatures elucidating the evolutionary relationships among the Gammaproteobacteria. Int J Syst Evol Microbiol. 59(Pt 2): 234-47. [Abstract]
  14. Singh, B. and Gupta, R. S. (2009) Conserved inserts in the Hsp60 (GroEL) and Hsp70 (DnaK) proteins are essential for cellular growth. Mol Genet Genomics. 281(4): 361-73. [Abstract]
  15. Griffiths, E. and Gupta, R. S. (2007) Identification of signature proteins that are distinctive of the Deinococcus-Thermus phylum. Int Microbiol. 10(3): 201-8. [Abstract]
  16. Gupta, R. S. and Mok, A. (2007) Phylogenomics and signature proteins for the alpha proteobacteria and its main groups. BMC Microbiol. 7: 106. [Abstract]
  17. Gupta, R. S. and Lorenzini, E. (2007) Phylogeny and molecular signatures (conserved proteins and indels) that are specific for the Bacteroidetes and Chlorobi species. BMC Evol Biol. 7: 71. [Abstract]
  18. Gao, B. and Gupta, R. S. (2007) Phylogenomic analysis of proteins that are distinctive of Archaea and its main subgroups and the origin of methanogenesis. BMC Genomics. 8: 86. [Abstract]
  19. Gupta, R. S. and Griffiths, E. (2006) Chlamydiae-specific proteins and indels: novel tools for studies. Trends in Microbiology. 14: 527-535. [Abstract]
  20. Gupta, R. S and Sneath, P.H.A. (2006) Application of the Character Compatibility Approach to Generalized Molecular Sequence Data: Branching Order of the Proteobacterial Subdivisions. J. Mol. Evol. 64: 90-100. [Abstract]
  21. Ventura, M., Canchaya, C., Fitzgerald, G. F., Gupta, R. S. and van Sinderen, D. (2006) Genomics as a means to understand bacterial phylogeny and ecological adaptation: the case of bifidobacteria. Antonie van Leeuwenhoek. Oct 26 (Epub) [Abstract]
  22. Gupta, R. S. (2006) Molecular signatures (unique proteins and conserved Indels) that are specific for the epsilon proteobacteria (Campylobacterales).BMC Genomics. 2006 Jul 4;7(1):167. [Abstract]
  23. Griffiths, E. and Gupta, R. S. (2006) Lateral Transfers of Serine Hydroxymethyltransferase (glyA) and UDP-N-Acetylglucosamine Enolpyruvyl Transferase (murA) Genes from Free-living Actinobacteria to the Parasitic Chlamydiae. J. Mol. Evol. 63: 283-296. [Abstract]
  24. Griffiths, E., Ventresca, M. S. & Gupta, R. S. (2006) BLAST screening of chlamydial genomes to identify signature proteins that are unique for the Chlamydiales, Chlamydiaceae, Chlamydophila and Chlamydia groups of species. BMC Genomics 7: 14. [Abstract]
  25. Gao, B., Parmanathan, R. and Gupta, R. S. (2006) Signature proteins that are distinctive characteristics of Actinobacteria and their subgroups. Antonie van Leeuwenhoek, 90: 69-91. [Abstract]
  26. Griffiths, E. and Gupta, R. S. (2006) Molecular Signatures in protein sequences that are characteristics of the phylum Aquificae. Int. J. Syst. Evol. Microbiol. 56: 99-107. [Abstract]
  27. Gao, B. and Gupta, R. S. (2005) Conserved indels in protein sequences that are characteristics of the phylum Actinobacteria. Int. J. Syst. Evol. Microbiol. 55: 2401-2412. [Abstract]
  28. Gupta, R. S. (2005) Protein Signatures distinctive of Alpha proteobacteria and its Subgroups and a Model for Alpha-proteobacterial Evolution. Crit. Rev. Microbiol. 31: 101-135. [Abstract]
  29. Griffiths, E., Petrich, A., & Gupta, R. S. (2005) Conserved Indels in Essential Proteins that are Distinctive Characteristics of Chlamydiales and Provide Novel Means for Their Identification. Microbiology, 151: 2647-2657. [Abstract]
  30. Kainth, P. and Gupta, R. S. (2005) Signature proteins that are distinctive of Alpha Proteobacteria. BMC Genomics, 6:94. [Abstract]
  31. Gupta, R. S. (2005) Molecular Sequences and the Early History of Life. In “Microbial Evolution: Concepts and Controversies” J. Sapp (Ed.) Oxford University, pp 160-183. [PDF]
  32. Gupta, R. S. (2005). Protein Signatures Distinctive of Alpha Proteobacteria and Its Subgroups and a Model for α-Proteobacterial Evolution. Crit. Rev. Micrbiol. 31: 101-135. [PDF]
  33. Griffiths, E. and Gupta, R. S. (2004) Signature Sequences in Diverse Proteins Provide Evidence for the Late Divergence of the Order Aquificales. International Microbiol. 7: 41-52. [Abstract
  34. Gupta, R.S. (2004) The phylogeny and signature sequences characteristics of Fibrobacteres, Chlorobi and Bacteroidetes. Crit. Rev. in Microbiol. 30: 123-143. [Abstract] [PDF]
  35. Griffiths, E. and Gupta, R.S. (2004) Distinctive protein signatures provide molecular markers and evidence for the monophyletic nature of the Deinococcus-Thermus phylum. J. Bacteriol. 186: 3097-3107. [Abstract]
  36. Gupta, R. S. (2003) Evolutionary Relationships among Photosynthetic Bacteria. Photosynth. Res. 76: 173-183. [PDF]
  37. Gupta, R. S., Pereira, M., Chandrasekera, C. and Johari, V. (2003) Molecular Signatures in Protein Sequences that are Distinctive of Cyanobacterial and Plastid Homologs. Int. J. Syst. Evol. Microbiol. 53: 1833-1842. [Abstract]
  38. Griffiths, E. and Gupta, R. S. (2002) Protein Signatures distinctive of Chlamydial species: Horizontal transfer of Cell Wall Biosynthesis genes glmU . from Archaea to Chlamydiae and murA between Chlamydiae and Streptomyces. Microbiology 148: 2541-2549. [Abstract]
  39. Gupta, R. S. (2002) Phylogeny of Bacteria: Are we now close to understanding it? ASM News, 284: 284-291. [PDF]
  40. Gupta, R. S. and Griffiths, E. (2002) Critical Issues in Bacterial Phylogeny. Theoret. Pop. Biol. 61: 423-434. [Abstract] [PDF]
  41. Gupta, R. S. (2001) Branching order and the phylogenetic placements of species from completed bacterial genomes based on conserved indels found in various proteins. International Microbiol. 4: 187-202. [Abstract]
  42. Griffiths E, Gupta RS. (2001) The use of signature sequences in different proteins to determine the relative branching order of bacterial divisions: evidence that Fibrobacter diverged at a similar time to Chlamydia and the Cytophaga- Flavobacterium-Bacteroides division. Microbiology,147:2611-22. [Abstract]
  43. Gupta, R.S.(2000) The natural evolutionary relationships among prokaryotes. Crit. Rev. Microbiol. 26: 111-131. [PDF] [See also the Article by Sherrie Lyons in Perspectives in Biology and Medicine, 2002]
  44. Gupta, R.S. (2000) Phylogeny of Proteobacteria: Relationships to other eubacterial phyla and to eukaryotes. FEMS Microbiol. Rev. 24: 367-402. [Abstract]
  45. Gupta, R.S. (2000) Evolutionary Relationships among Bacteria: Does 16S rRNA provide all the answers? ASM News 66: 189-190.
  46. Gupta, R.S., Mukhtar, T. and Singh, B. (1999) Phylogenetic Placements of Heliobacteria chlorum, Chloroflexus auranticus and Chlorobium tepidum Based on Protein Signature Sequences : Implications Regarding Origin of Photosynthesis. Mol. Microbiol. 32: 891-906. [Abstract]
  47. Gupta, R.S. and Soltys, B.J. (1999) Lateral gene transfer, genome surveys and the Phylogeny of Prokaryotes (Comments) Science 286: 1443a. [PDF]
  48. Gupta, R.S. (1999) Origin of Eukaryotic cells: Was metabolic symbiosis based on hydrogen the driving force? Trends in Biochem. Sci. 24: 423. [Abstract]
  49. Gupta, R. S. (1999) Protein phylogenies and a new proposal for the classification of organisms unifying cell structure and molecular sequence data. In Endocytobiology VII, E. Wagner et al. (Eds.), University of Geneva; 271-289
  50. Gupta, R.S. (1998) Protein phylogenies and signature sequences: A reappraisal of evolutionary relationships among archaebacteria, eubacteria and eukaryotes. Microbiol. Mol. Biol. Rev. 62: 1435-1491. [Abstract]
  51. Gupta, R.S. (1998) What are archaebacteria: life's third domain or monoderm prokaryotes related to Gram-positive bacteria? A new proposal for the classification of prokaryotic organisms. Mol. Microbiol. 29: 695-708. [Abstract]
  52. Gupta, R.S. (1998) Life's third domain (Archaea): An established fact or an endangered paradigm? A new proposal for classification of organisms based on protein sequences and cell structure.Theoret. Pop. Biol. 54: 91-104. [Abstract]
  53. Gupta, R.S. and Johari, V. (1998) Signature sequences in diverse proteins provide evidence of a close evolutionary relationship between the Deinococcus-Thermus group and Cyanobacteria. J. Mol. Evol. 46: 716-720. [Abstract]
  54. Gupta, R. S., Bustard, K, Falah, M. and Singh, D. (1997) Sequencing of heat shock protein 70 (DnaK) homologs from Deinococcus proteolyticus and Thermomicrobium roseum and their integeration in a protein based phylogeny of prokaryotes. J. Bacteriol. 179, 345-357. [Abstract]
  55. Gupta, R.S. and Golding, G.B. (1996) The origin of the eukaryotic cell. Trends Biochem. Sci. 21: 166-171. [Abstract]
  56. Soltys, B.J., Falah, M.S. and Gupta, R.S. (1996) Identification of endoplasmic reticulum in the primitive eukaryote Giardia lamblia using cryoelectron microscopy and antibody to Bip. J. Cell Science 109: 1909-1917. [Abstract]
  57. Golding, G.B. and Gupta, R.S. (1995) Protein based phylogenies support a chimeric origin for the eukaryotic genome. Mol. Biol. Evol. 12: 1-6. [Abstract]
  58. Gupta, R.S. (1995) Microreview: Evolution of the chaperonin families (HSP60, HSP10 and Tcp-1) of proteins and the origin of eukaryotic cells. Mol. Microbiol. 15: 1-11. [Abstract]
  59. Gupta, R.S., Aitken, K., Falah, M. and Singh, B. (1994) Cloning of Giardia lamblia hsp70 homologs: Implications regarding origin of eukaryotic cells and of endoplasmic reticulum. Proc. Natl. Acad. Sci. USA 91: 2895-2899. [Abstract]
  60. Soltys, B.J. and Gupta, R.S. (1994) Presence and cellular distribution of a 60 kDa protein related to hsp60 in Giardia lamblia. J. Parasitol. 80: 580-590. [Abstract]
  61. Gupta, R.S. and Singh, B. (1994) Phylogenetic analysis of 70 kD heat shock protein sequences suggests a chimeric origin for the eukaryotic cell nucleus. Current Biol. 4: 1104-1114. [Abstract]
  62. Falah, M. and Gupta, R.S. (1994) Cloning of the hsp70 (dnaK) gene from Rhizobium meliloti and Pseudomonas cepacia: Phylogenetic analyses of mitochondrial origin based on a highly conserved protein sequence. J. Bacteriol. 176: 7748-7753. [Abstract]
  63. Gupta, R.S. and Golding, G.B. (1993) Evolution of HSP70 gene and its implications regarding relationships between archaebacteria, eubacteria and eukaryotes. J. Mol. Evol. 37: 573-582. [Abstract]
  64. Gupta, R.S. and Singh, B. (1992) Cloning of the HSP70 gene from Halobacterium marismortuii: relatedness of halobacterial HSP70 to its eubacterial homologs and a model for the evolution of HSP70 gene. J. Bacteriol. 174: 4594-4605. [Abstract



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