Meena Kishore Sakharkar

Summary

Affiliation: Nanyang Technological University
Country: Singapore

Publications

  1. ncbi SEGE: A database on 'intron less/single exonic' genes from eukaryotes
    Meena K Sakharkar
    Department of Applied Physics, Stanford University, CA 94305, USA
    Bioinformatics 18:1266-7. 2002
  2. pmc Activity of Chitosans in combination with antibiotics in Pseudomonas aeruginosa
    San Tin
    Biomedical Engineering Research Centre, Nanyang Technological University, Singapore
    Int J Biol Sci 5:153-60. 2009
  3. pmc A combined computational-experimental analyses of selected metabolic enzymes in Pseudomonas species
    Deepak Perumal
    Advanced Design and Modeling Lab, Nanyang Technological University, Singapore
    Int J Biol Sci 4:309-17. 2008
  4. pmc Quantitative analysis on the characteristics of targets with FDA approved drugs
    Meena K Sakharkar
    ADAMs Lab, Mechanical, Aerospace Engineering, Nanyang Technological University, Singapore
    Int J Biol Sci 4:15-22. 2008
  5. ncbi Human genome -- from pieces to patterns
    Meena Kishore Sakharkar
    NCSV, MAE, Nanyang Technological University, 639798, Singapore
    Front Biosci 10:2576-84. 2005
  6. ncbi In vitro combinations of antibiotics and phytochemicals against Pseudomonas aeruginosa
    Meena K Sakharkar
    Biomedical Engineering Research Centre, Nanyang Technological University, Singapore
    J Microbiol Immunol Infect 42:364-70. 2009
  7. ncbi Huge proteins in the human proteome and their participation in hereditary diseases
    Meena Kishore Sakharkar
    Nanyang Centre for Supercomputing and Visualization, MAE, Nanyang Technological University, Singapore
    In Silico Biol 6:275-9. 2006
  8. ncbi An analysis on gene architecture in human and mouse genomes
    Meena Kishore Sakharkar
    Nanyang Centre for Supercomputing and Visualization, Nanyang Technological University, Singapore 639798
    In Silico Biol 5:347-65. 2005
  9. ncbi Alternatively spliced human genes by exon skipping--a database (ASHESdb)
    Meena Kishore Sakharkar
    Nanyang Centre for Supercomputing and Visualization, Nanyang Technological University, Singapore 639798
    In Silico Biol 5:221-5. 2005
  10. ncbi Insights to metabolic network evolution by fusion proteins
    Meena Kishore Sakharkar
    NCSV, MPE, Nanyang Technological University, Singapore 639798
    Front Biosci 10:1070-8. 2005

Collaborators

Detail Information

Publications25

  1. ncbi SEGE: A database on 'intron less/single exonic' genes from eukaryotes
    Meena K Sakharkar
    Department of Applied Physics, Stanford University, CA 94305, USA
    Bioinformatics 18:1266-7. 2002
    ..In this note, we describe a database for 'intron less' genes from eukaryotes. 'Intron less' eukaryotic genes having prokaryotic architecture will help to understand gene evolution in a much simpler way unlike 'intron containing' genes...
  2. pmc Activity of Chitosans in combination with antibiotics in Pseudomonas aeruginosa
    San Tin
    Biomedical Engineering Research Centre, Nanyang Technological University, Singapore
    Int J Biol Sci 5:153-60. 2009
    ..The findings suggest on the use of chitosans as enhancing agent in combination with antibiotics in pharmaceutical preparations...
  3. pmc A combined computational-experimental analyses of selected metabolic enzymes in Pseudomonas species
    Deepak Perumal
    Advanced Design and Modeling Lab, Nanyang Technological University, Singapore
    Int J Biol Sci 4:309-17. 2008
    ..These analyses connect and integrate systematic data generation, computational data interpretation, and experimental validation and represent a synergistic and powerful means for conducting biological research...
  4. pmc Quantitative analysis on the characteristics of targets with FDA approved drugs
    Meena K Sakharkar
    ADAMs Lab, Mechanical, Aerospace Engineering, Nanyang Technological University, Singapore
    Int J Biol Sci 4:15-22. 2008
    ..These quantitative characteristics could serve as criteria to search for promising targetable disease genes...
  5. ncbi Human genome -- from pieces to patterns
    Meena Kishore Sakharkar
    NCSV, MAE, Nanyang Technological University, 639798, Singapore
    Front Biosci 10:2576-84. 2005
    ..The existence of common exon-intron length patterns across unrelated genes suggests for their role of in gene assemblage and human genome design and architecture...
  6. ncbi In vitro combinations of antibiotics and phytochemicals against Pseudomonas aeruginosa
    Meena K Sakharkar
    Biomedical Engineering Research Centre, Nanyang Technological University, Singapore
    J Microbiol Immunol Infect 42:364-70. 2009
    ....
  7. ncbi Huge proteins in the human proteome and their participation in hereditary diseases
    Meena Kishore Sakharkar
    Nanyang Centre for Supercomputing and Visualization, MAE, Nanyang Technological University, Singapore
    In Silico Biol 6:275-9. 2006
    ..The genes for huge proteins are found to have more introns. Our analysis also shows greater involvement of huge proteins in hereditary diseases...
  8. ncbi An analysis on gene architecture in human and mouse genomes
    Meena Kishore Sakharkar
    Nanyang Centre for Supercomputing and Visualization, Nanyang Technological University, Singapore 639798
    In Silico Biol 5:347-65. 2005
    ..The results presented provide a framework for understanding the nature and patterns of exon-intron length distributions, the constraints on them and their role in genome design and evolution...
  9. ncbi Alternatively spliced human genes by exon skipping--a database (ASHESdb)
    Meena Kishore Sakharkar
    Nanyang Centre for Supercomputing and Visualization, Nanyang Technological University, Singapore 639798
    In Silico Biol 5:221-5. 2005
    ..1,229 human genes are identified to exhibit alternative splicing by exon skipping. Availability: http://sege.ntu.edu.sg/wester/ashes/...
  10. ncbi Insights to metabolic network evolution by fusion proteins
    Meena Kishore Sakharkar
    NCSV, MPE, Nanyang Technological University, Singapore 639798
    Front Biosci 10:1070-8. 2005
    ..In addition, we propose that fusion proteins have gained additive biochemical function for a balanced regulation of metabolic networks...
  11. ncbi Distributions of exons and introns in the human genome
    Meena Kishore Sakharkar
    Nanyang Centre for Supercomputing and Visualisation, N3 2c 113b, 50 Nanyang Avenue, Nanyang Technological University, Singapore
    In Silico Biol 4:387-93. 2004
    ..95 and r = 0.97, respectively. These results suggest their implication in genome design...
  12. pmc Types of inter-atomic interactions at the MHC-peptide interface: identifying commonality from accumulated data
    Png Eak Hock Adrian
    National University of Singapore, Department of Microbiology, Medical Drive, Singapore
    BMC Struct Biol 2:2. 2002
    ..The available x-ray crystallography data for these complexes in the Protein Databank (PDB) provides an opportunity to identify the prevalent types of such interactions at the binding interface...
  13. pmc Computational identification and experimental validation of PPRE motifs in NHE1 and MnSOD genes of human
    Gireedhar Venkatachalam
    Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
    BMC Genomics 10:S5. 2009
    ..Here we computationally identified PPAR binding regions in NHE1 and MnSOD. We further validated the predictions in vitro...
  14. pmc Genome SEGE: a database for 'intronless' genes in eukaryotic genomes
    Meena Kishore Sakharkar
    Nanyang Centre for Supercomputing and Visualization, School of Mechanical and Production Engineering, Nanyang Technological University, Singapore 639798
    BMC Bioinformatics 5:67. 2004
    ..Thus Genome SEGE, a database for 'intronless' genes in completely sequenced eukaryotic genomes, has been constructed. Availability: http://sege.ntu.edu.sg/wester/intronless..
  15. ncbi A report on single exon genes (SEG) in eukaryotes
    Meena Kishore Sakharkar
    Scool of Mechanical and Production Engineering, Nanyang Technological University, Singapore
    Front Biosci 9:3262-7. 2004
    ..The comparison suggests that the SEG fraction decreases with gene count (r = -0.80) and increases with gene density (r = 0.88) in these genomes. We also examined the distribution patterns of their protein lengths in different genomes...
  16. ncbi HLA-peptide binding prediction using structural and modeling principles
    Pandjassarame Kangueane
    School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore
    Methods Mol Biol 409:293-9. 2007
    ..Prediction of peptide binding to HLA alleles using structural and modeling principles has gained momentum in recent years. Here, we discuss the current status of such prediction...
  17. ncbi Grouping of class I HLA alleles using electrostatic distribution maps of the peptide binding grooves
    Pandjassarame Kangueane
    School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore
    Methods Mol Biol 409:175-81. 2007
    ..This grouping provides insight toward the inference for functional overlap among HLA alleles...
  18. ncbi Can ends justify the means? Digging deep for human fusion genes of prokaryotic origin
    Yu Yiting
    School of Mechanical and Production Engineering, Nanyang Center for Supercomputing and Visualization, Nanyang Technological University, Singapore 639798
    Front Biosci 9:2964-71. 2004
    ..The accredited biological functions for each of these proteins is made available as a database at http://sege.ntu.edu.sg/wester/fusion/..
  19. ncbi Intron position conservation across eukaryotic lineages in tubulin genes
    Bagavathi S Perumal
    NCSV, MAE, Nanyang Technological University, 639798, Singapore
    Front Biosci 10:2412-9. 2005
    ..Many intron positions are old and are conserved across different eukaryotic lineages and intron distribution patterns are consistent with 'introns-early' hypothesis...
  20. ncbi Generation of a dataset for studying ligand effect on homodimer interface
    Lei Li
    MAE, NTU, Singapore
    Front Biosci 10:1977-84. 2005
    ..We also found that ligands occupying = 7% interface area have negligible effect on dimer interaction...
  21. ncbi Identification of critical heterodimer protein interface parameters by multi-dimensional scaling in euclidian space
    Cui Zhanhua
    Nanyang Centre for Supercomputing and Visualization, School of Mechanical and Production Engineering, Nanyang Technological University, Singapore
    Front Biosci 10:844-52. 2005
    ..The significance of these parameters in subunit interaction is discussed...
  22. ncbi Mammalian specific mouse genes are evolving faster than mouse genes conserved across other eukaryotic lineages
    Iti Chaturvedi
    Advanced Design and Modeling Lab, Affiliated staff BioInformatics Research Centre, Nanyang Technological University, Singapore
    Front Biosci 12:3367-76. 2007
    ....
  23. ncbi Druggability of human disease genes
    Meena Kishore Sakharkar
    Nanyang Centre for Supercomputing and Visualization, School of Mechanical and Aerospace Engineering MAE, Nanyang Technological University, Singapore
    Int J Biochem Cell Biol 39:1156-64. 2007
    ..Our analyses underscore the utility of large genomic databases for in silico systematic drug target identification in the post-genomic era...
  24. ncbi Structural basis for HLA-A2 supertypes
    Pandjassarame Kangueane
    School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore
    Methods Mol Biol 409:155-62. 2007
    ..Nonetheless, the structural basis for HLA supertype-like function is not clearly known. Here, we use structural data to explain the molecular basis for HLA-A2 supertypes...
  25. ncbi A framework to sub-type HLA supertypes
    Pandjassarame Kangueane
    School of Mechanical and Production Engineering, Nanyang Technological University, Nanyang Centre for Supercomputing and Visualization, Singapore 639798
    Front Biosci 10:879-86. 2005
    ..A complete knowledge of this phenomenon finds utility in epitope design for the development of HLA based vaccines and immuno-therapeutics...