S Balaji

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. ncbi request reprint The two faces of short-range evolutionary dynamics of regulatory modes in bacterial transcriptional regulatory networks
    S Balaji
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Bioessays 29:625-9. 2007
  2. ncbi request reprint Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast
    S Balaji
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda 20894, USA
    J Mol Biol 360:213-27. 2006
  3. pmc Comparison of transcription regulatory interactions inferred from high-throughput methods: what do they reveal?
    S Balaji
    National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894, USA
    Trends Genet 24:319-23. 2008
  4. pmc Interplay between network structures, regulatory modes and sensing mechanisms of transcription factors in the transcriptional regulatory network of E. coli
    S Balaji
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    J Mol Biol 372:1108-22. 2007
  5. ncbi request reprint Uncovering a hidden distributed architecture behind scale-free transcriptional regulatory networks
    S Balaji
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    J Mol Biol 360:204-12. 2006
  6. pmc The natural history of the WRKY-GCM1 zinc fingers and the relationship between transcription factors and transposons
    M Madan Babu
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 34:6505-20. 2006
  7. pmc Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture
    Raja Jothi
    Biostatistics Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
    Mol Syst Biol 5:294. 2009
  8. pmc HPC2 and ubinuclein define a novel family of histone chaperones conserved throughout eukaryotes
    S Balaji
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Mol Biosyst 5:269-75. 2009
  9. ncbi request reprint Estimating the prevalence and regulatory potential of the telomere looping effect in yeast transcription regulation
    M Madan Babu
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Cell Cycle 5:2354-63. 2006
  10. pmc Robustness and evolvability in natural chemical resistance: identification of novel systems properties, biochemical mechanisms and regulatory interactions
    Thiago M Venancio
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Mol Biosyst 6:1475-91. 2010

Collaborators

Detail Information

Publications18

  1. ncbi request reprint The two faces of short-range evolutionary dynamics of regulatory modes in bacterial transcriptional regulatory networks
    S Balaji
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Bioessays 29:625-9. 2007
    ..These relationships might be shaped by the differences in the adaptive value and mode of operation of different regulatory interactions...
  2. ncbi request reprint Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast
    S Balaji
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda 20894, USA
    J Mol Biol 360:213-27. 2006
    ..We believe that the results presented here might provide a framework for testing the role of co-regulatory associations in eukaryotic transcriptional control...
  3. pmc Comparison of transcription regulatory interactions inferred from high-throughput methods: what do they reveal?
    S Balaji
    National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894, USA
    Trends Genet 24:319-23. 2008
    ..Through a detailed analysis of the latter, we predict components of the system responding to protein-aggregation stress...
  4. pmc Interplay between network structures, regulatory modes and sensing mechanisms of transcription factors in the transcriptional regulatory network of E. coli
    S Balaji
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    J Mol Biol 372:1108-22. 2007
    ....
  5. ncbi request reprint Uncovering a hidden distributed architecture behind scale-free transcriptional regulatory networks
    S Balaji
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    J Mol Biol 360:204-12. 2006
    ..Thus, an "over-engineered" backup system in the form of distributed architecture is likely to be a major determinant of the "evolvability" of the gene expression in organisms faced with environmental diversity...
  6. pmc The natural history of the WRKY-GCM1 zinc fingers and the relationship between transcription factors and transposons
    M Madan Babu
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 34:6505-20. 2006
    ..We also use the WRKY-GCM1 superfamily as an example to illustrate the importance of transposons in the emergence of new TFs in different lineages...
  7. pmc Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture
    Raja Jothi
    Biostatistics Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
    Mol Syst Biol 5:294. 2009
    ..We propose that the interplay between network organization and TF dynamics could permit differential utilization of the same underlying network by distinct members of a clonal cell population...
  8. pmc HPC2 and ubinuclein define a novel family of histone chaperones conserved throughout eukaryotes
    S Balaji
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Mol Biosyst 5:269-75. 2009
    ..Hence, we propose that Hpc2p homologs are probably involved in recruitment of the ancient conserved histone-loading Hir-Asf1 complex to different lineage-specific chromatin reorganization processes...
  9. ncbi request reprint Estimating the prevalence and regulatory potential of the telomere looping effect in yeast transcription regulation
    M Madan Babu
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Cell Cycle 5:2354-63. 2006
    ..Based on these observations, we also propose that genome-wide chromatin immunoprecipitation data might be useful to systematically uncover long-range chromatin looping effects in gene expression...
  10. pmc Robustness and evolvability in natural chemical resistance: identification of novel systems properties, biochemical mechanisms and regulatory interactions
    Thiago M Venancio
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Mol Biosyst 6:1475-91. 2010
    ..Further, we find evidence that cellular exploration of survival strategies under chemical stress and secondary metabolism draw from a common pool of biochemical players (e.g. acetyltransferases and a novel NTN hydrolase)...
  11. ncbi request reprint Evolutionary genomics of nucleo-cytoplasmic large DNA viruses
    Lakshminarayan M Iyer
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Virus Res 117:156-84. 2006
    ....
  12. pmc The RAGNYA fold: a novel fold with multiple topological variants found in functionally diverse nucleic acid, nucleotide and peptide-binding proteins
    S Balaji
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 35:5658-71. 2007
    ..3) We also present evidence for a bacterial origin of the GYF domain and propose how this version of the fold might have been utilized in peptide interactions in the context of nucleoprotein complexes...
  13. pmc High-confidence mapping of chemical compounds and protein complexes reveals novel aspects of chemical stress response in yeast
    Thiago M Venancio
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Mol Biosyst 6:175-81. 2010
    ..It is therefore conceivable that some of these complexes identified here might have roles in molding the evolution of chemical resistance and response...
  14. pmc Reconstructing the ubiquitin network: cross-talk with other systems and identification of novel functions
    Thiago M Venancio
    National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894, USA
    Genome Biol 10:R33. 2009
    ..While several studies have concentrated on structure-function relationships and evolution of individual components of the Ub-system, a study of the system as a whole is largely lacking...
  15. pmc Discovery of the principal specific transcription factors of Apicomplexa and their implication for the evolution of the AP2-integrase DNA binding domains
    S Balaji
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 33:3994-4006. 2005
    ....
  16. ncbi request reprint Adhesion molecules and other secreted host-interaction determinants in Apicomplexa: insights from comparative genomics
    Vivek Anantharaman
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    Int Rev Cytol 262:1-74. 2007
    ..It also suggests that the ancestral parasite had O-linked glycosylation of surface proteins which was partially or entirely lost in hematozoan lineages...
  17. ncbi request reprint General trends in the evolution of prokaryotic transcriptional regulatory networks
    M Madan Babu
    National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA
    Genome Dyn 3:66-80. 2007
    ..In turn, as phylogenetic diversification proceeds, this process appears to have favored repeated convergence to scale-free-like structures, albeit with different regulatory hubs...
  18. pmc Detection of a secreted metalloprotease within the nuclei of liver cells
    Ryan C Hunt
    Laboratory of Hemostasis, Division of Hematology, Center for Biologic, Food and Drug Administration, Bethesda, Maryland 20892, USA
    Mol Biosyst 7:2012-8. 2011
    ....