Samir K Brahmachari

Summary

Affiliation: Institute of Genomics and Integrative Biology
Country: India

Publications

  1. pmc Crowd sourcing a new paradigm for interactome driven drug target identification in Mycobacterium tuberculosis
    Rohit Vashisht
    Council of Scientific and Industrial Research, Delhi, India
    PLoS ONE 7:e39808. 2012
  2. pmc Introducing the medical bioinformatics in Journal of Translational Medicine
    Samir K Brahmachari
    CSIR Institute of Genomics and Integrative Biology, Mall Road, New Delhi, 110007, India
    J Transl Med 10:202. 2012
  3. pmc Polymorphisms of TNF-enhancer and gene for FcgammaRIIa correlate with the severity of falciparum malaria in the ethnically diverse Indian population
    Swapnil Sinha
    Division of Molecular and Structural Biology, Central Drug Research Institute, Post Box 173, Chattar Manzil, Mahatma Gandhi Marg, Lucknow 226001, India
    Malar J 7:13. 2008
  4. pmc Variations in host genes encoding adhesion molecules and susceptibility to falciparum malaria in India
    Swapnil Sinha
    Division of Molecular and Structural Biology, Central Drug Research Institute, Post Box 173, Chattar Manzil, Mahatma Gandhi Marg, Lucknow 226001, India
    Malar J 7:250. 2008
  5. pmc Systems medicine and integrated care to combat chronic noncommunicable diseases
    Jean Bousquet
    Department of Respiratory Diseases, Arnaud de Villeneuve Hospital, CHU Montpellier, INSERM CESP U1018, Villejuif, France
    Genome Med 3:43. 2011
  6. pmc Comparative analysis of chromatin landscape in regulatory regions of human housekeeping and tissue specific genes
    Mythily Ganapathi
    Dr B R Ambedkar Centre for Biomedical Research, University of Delhi, Delhi 110007, India
    BMC Bioinformatics 6:126. 2005
  7. doi request reprint Genetic susceptibility to schizophrenia: role of dopaminergic pathway gene polymorphisms
    Meenal Gupta
    Functional Genomics Unit, Institute of Genomics and Integrative Biology Council of Scientific and Industrial Research, Mall Road, Delhi 110 007, India
    Pharmacogenomics 10:277-91. 2009
  8. ncbi request reprint SYNGR1 is associated with schizophrenia and bipolar disorder in southern India
    Ranjana Verma
    Functional Genomics Unit, Institute of Genomics and Integrative Biology CSIR, Delhi University Campus, Mall Road, Delhi, 110007, India
    J Hum Genet 50:635-40. 2005
  9. ncbi request reprint Abundance of dinucleotide repeats and gene expression are inversely correlated: a role for gene function in addition to intron length
    Vineet K Sharma
    G N Ramachandran Knowledge Centre for Genome Informatics, Institute of Genomics and Integrative Biology, Delhi, India
    Physiol Genomics 31:96-103. 2007
  10. pmc Expoldb: expression linked polymorphism database with inbuilt tools for analysis of expression and simple repeats
    Vineet K Sharma
    G N Ramachandran Knowledge Centre for Genome Informatics, Institute of Genomics and Integrative Biology, Mall Road, Delhi 110 007, India
    BMC Genomics 7:258. 2006

Detail Information

Publications44

  1. pmc Crowd sourcing a new paradigm for interactome driven drug target identification in Mycobacterium tuberculosis
    Rohit Vashisht
    Council of Scientific and Industrial Research, Delhi, India
    PLoS ONE 7:e39808. 2012
    ..The fact that five of the 17 predicted drug targets are already experimentally validated either genetically or biochemically lends credence to our unique approach...
  2. pmc Introducing the medical bioinformatics in Journal of Translational Medicine
    Samir K Brahmachari
    CSIR Institute of Genomics and Integrative Biology, Mall Road, New Delhi, 110007, India
    J Transl Med 10:202. 2012
    ..The section welcomes studies on the development of Biomedical Informatics for translational medicine and clinical applications, including tools, methodologies and data integration...
  3. pmc Polymorphisms of TNF-enhancer and gene for FcgammaRIIa correlate with the severity of falciparum malaria in the ethnically diverse Indian population
    Swapnil Sinha
    Division of Molecular and Structural Biology, Central Drug Research Institute, Post Box 173, Chattar Manzil, Mahatma Gandhi Marg, Lucknow 226001, India
    Malar J 7:13. 2008
    ..The aim of this study was to examine the possible contribution of genetic variants in the TNF and FCGR2A genes in determining severity/resistance to P. falciparum malaria in Indian subjects...
  4. pmc Variations in host genes encoding adhesion molecules and susceptibility to falciparum malaria in India
    Swapnil Sinha
    Division of Molecular and Structural Biology, Central Drug Research Institute, Post Box 173, Chattar Manzil, Mahatma Gandhi Marg, Lucknow 226001, India
    Malar J 7:250. 2008
    ..The aim of this study was to investigate the association of SNPs of three adhesion molecule genes, ICAM1, PECAM1 and CD36, with severity of falciparum malaria in a malaria-endemic and a non-endemic region of India...
  5. pmc Systems medicine and integrated care to combat chronic noncommunicable diseases
    Jean Bousquet
    Department of Respiratory Diseases, Arnaud de Villeneuve Hospital, CHU Montpellier, INSERM CESP U1018, Villejuif, France
    Genome Med 3:43. 2011
    ..This systems medicine strategy, which will take a holistic approach to disease, is designed to allow the results to be used globally, taking into account the needs and specificities of local economies and health systems...
  6. pmc Comparative analysis of chromatin landscape in regulatory regions of human housekeeping and tissue specific genes
    Mythily Ganapathi
    Dr B R Ambedkar Centre for Biomedical Research, University of Delhi, Delhi 110007, India
    BMC Bioinformatics 6:126. 2005
    ..In-silico analysis can yield important insights into this aspect, facilitating comparison of two or more classes of genes comprising of a large number of genes within each group...
  7. doi request reprint Genetic susceptibility to schizophrenia: role of dopaminergic pathway gene polymorphisms
    Meenal Gupta
    Functional Genomics Unit, Institute of Genomics and Integrative Biology Council of Scientific and Industrial Research, Mall Road, Delhi 110 007, India
    Pharmacogenomics 10:277-91. 2009
    ....
  8. ncbi request reprint SYNGR1 is associated with schizophrenia and bipolar disorder in southern India
    Ranjana Verma
    Functional Genomics Unit, Institute of Genomics and Integrative Biology CSIR, Delhi University Campus, Mall Road, Delhi, 110007, India
    J Hum Genet 50:635-40. 2005
    ..Our results support SYNGR1 as a probable susceptibility gene for SCZ and BPAD. Also, the observed association of SYNGR1 with both SCZ and BPAD suggests the likely involvement of a common pathway in the etiology of these disorders...
  9. ncbi request reprint Abundance of dinucleotide repeats and gene expression are inversely correlated: a role for gene function in addition to intron length
    Vineet K Sharma
    G N Ramachandran Knowledge Centre for Genome Informatics, Institute of Genomics and Integrative Biology, Delhi, India
    Physiol Genomics 31:96-103. 2007
    ..These observations suggest that negative selection of (TG/CA)(n>or=12) microsatellites in the evolution of the highly expressed genes was also controlled by gene function in addition to intron length...
  10. pmc Expoldb: expression linked polymorphism database with inbuilt tools for analysis of expression and simple repeats
    Vineet K Sharma
    G N Ramachandran Knowledge Centre for Genome Informatics, Institute of Genomics and Integrative Biology, Mall Road, Delhi 110 007, India
    BMC Genomics 7:258. 2006
    ..A facilitating step towards understanding the basis for gene expression variability is associating genome wide transcription patterns with potential cis modifiers of gene expression...
  11. ncbi request reprint ALU-ring elements in the primate genomes
    Deepak Grover
    Functional Genomics Unit, Institute of Genomics and Integrative Biology, Mall Road, Delhi, India
    Genetica 124:273-89. 2005
    ..Moreover, these are the repeats with highest copy number in the human genome. We have highlighted different facets of their interaction with the genome and changing paradigms regarding their role in genome organization...
  12. ncbi request reprint MLC1 gene is associated with schizophrenia and bipolar disorder in Southern India
    Ranjana Verma
    Functional Genomics Unit, Institute of Genomics and Integrative Biology CSIR, Delhi, India
    Biol Psychiatry 58:16-22. 2005
    ..A missense mutation in MLC1 (putative cation-channel gene on 22q13) co-segregating with periodic catatonic schizophrenia has been reported. We have investigated the relationship of MLC1 with SCZ and BPAD in Southern India...
  13. pmc EGLN1 involvement in high-altitude adaptation revealed through genetic analysis of extreme constitution types defined in Ayurveda
    Shilpi Aggarwal
    Genomics and Molecular Medicine, Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research, New Delhi 110007, India
    Proc Natl Acad Sci U S A 107:18961-6. 2010
    ....
  14. ncbi request reprint Association of DRD2 gene variant with schizophrenia
    Ritushree Kukreti
    GenoMed Lab, Gene Quest Laboratory, Nicholas Piramal India Ltd at Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110007, India
    Neurosci Lett 392:68-71. 2006
    ..The results suggest that the synonymous SNP His313 in DRD2 may be associated with the illness. However, there is a need for further replication studies with larger sample sets...
  15. pmc dbSMR: a novel resource of genome-wide SNPs affecting microRNA mediated regulation
    Manoj Hariharan
    GN Ramachandran Knowledge Center for Genome Informatics, Institute of Genomics and Integrative Biology CSIR, Delhi, India
    BMC Bioinformatics 10:108. 2009
    ..Single Nucleotide Polymorphisms (SNPs) can contribute to alterations in the structure of regions flanking them, thereby influencing the accessibility for miRNA binding...
  16. ncbi request reprint microRNA: an emerging therapeutic
    Vinod Scaria
    GN Ramachandran Knowledge Centre for Genome Informatics, Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi, India
    ChemMedChem 2:789-92. 2007
  17. doi request reprint Association studies of catechol-O-methyltransferase (COMT) gene with schizophrenia and response to antipsychotic treatment
    Meenal Gupta
    Institute of Genomics and Integrative Biology, Delhi, India
    Pharmacogenomics 10:385-97. 2009
    ..We investigated the catechol-O-methyltrasferase (COMT) gene, which is a strong functional and positional candidate gene for schizophrenia and therapeutic response to antipsychotic medication...
  18. ncbi request reprint CoPS: Comprehensive Peptide Signature database
    Tulika Prakash
    G N R Knowledge Center for Genome Informatics, Institute of Genomics and Integrative Biology, Formerly Centre for Biochemical Technology, CSIR, Delhi University Campus, Mall Road, Delhi 110 007, India
    Bioinformatics 20:2886-8. 2004
    ..AVAILABILITY: The database can be freely accessed through the following URL: http://203.195.151.46/copsv2/index.html or http://203.90.127.70/copsv2/index.html..
  19. ncbi request reprint Assessing natural variations in gene expression in humans by comparing with monozygotic twins using microarrays
    Anu Sharma
    Functional Genomics Unit, G N Ramachandran Knowledge Center for Genome Informatics, Institute of Genomics and Integrative Biology, Delhi, India
    Physiol Genomics 21:117-23. 2005
    ..Gene expression profiling in monozygotic twins can provide useful data for the assessment of natural variation in gene expression in humans...
  20. ncbi request reprint Alu repeat analysis in the complete human genome: trends and variations with respect to genomic composition
    Deepak Grover
    Functional Genomics Unit, Institute of Genomics and Integrative Biology IGIB, CSIR, Mall Road, Delhi 110007, India
    Bioinformatics 20:813-7. 2004
    ..The objective of this study is to investigate the factors that influence the distribution of Alu repeat elements in the human genome. Such analysis is expected to yield insights into various aspects of gene regulation in primates...
  21. ncbi request reprint Host-virus genome interactions: macro roles for microRNAs
    Vinod Scaria
    GN Ramachandran Knowledge Center for Genome Informatics, Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110 007, India
    Cell Microbiol 9:2784-94. 2007
    ..This review discusses the intricacies of host-virus cross-talk mediated by microRNAs. Recent trends in this field and the challenges that need to be addressed are also discussed...
  22. ncbi request reprint Recognition and analysis of protein-coding genes in severe acute respiratory syndrome associated coronavirus
    Ramakant Sharma
    Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110 007, India
    Bioinformatics 20:1074-80. 2004
    ..Computational approach to identify protein-coding genes and their putative functions will help in designing experimental protocols...
  23. doi request reprint Genetic profile of patients with epilepsy on first-line antiepileptic drugs and potential directions for personalized treatment
    Sandeep Grover
    Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research, India
    Pharmacogenomics 11:927-41. 2010
    ....
  24. doi request reprint Social networks to biological networks: systems biology of Mycobacterium tuberculosis
    Rohit Vashisht
    CSIR Open Source Drug Discovery Unit, New Delhi, India
    Mol Biosyst 9:1584-93. 2013
    ..Furthermore, we highlight the strength of such collated structured data in the context of drug target prediction based on systems level analysis of pathogen...
  25. pmc Human cellular microRNA hsa-miR-29a interferes with viral nef protein expression and HIV-1 replication
    Jasmine K Ahluwalia
    Institute of Genomics and Integrative Biology IGIB CSIR, Delhi, India
    Retrovirology 5:117. 2008
    ..Computational predictions revealed earlier that the HIV-1 genome includes regions that may be potentially targeted by human miRNAs. Here we report the functionality of predicted miR-29a target site in the HIV-1 nef gene...
  26. ncbi request reprint Clusters of proteins in archaeal and bacterial proteomes using compositional analysis
    Tannistha Nandi
    G N Ramachandran Knowledge Centre for Genome Informatics, Institute of Genomics and Integrative Biology, Mall Road, Delhi 110 007, India
    In Silico Biol 4:573-91. 2004
    ..Our computational procedure can serve as a useful addition to the existing tools for carrying out in silico proteomics...
  27. ncbi request reprint Pharmacogenomics: a path to predictive medicine for schizophrenia
    Simone Gupta
    Institute of Genomics and Integrative Biology CSIR, Delhi University Campus, Delhi 110007, India
    Pharmacogenomics 7:31-47. 2006
    ..Coupling our knowledge of genetic polymorphisms with clinical response data promises a bright future for rapid advances in personalized medicine...
  28. ncbi request reprint Conformational analysis of invariant peptide sequences in bacterial genomes
    Tulika Prakash
    G N R Knowledge Centre for Genome Informatics, Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110007, India
    J Mol Biol 345:937-55. 2005
    ..The study indicates that these SD peptides may act as chain-reversal signatures, guiding the proteins to adopt appropriate folds. In some cases the invariant signature peptides may also act as folding nuclei (FN) of the proteins...
  29. pmc Posttranscriptional regulation of interleukin-10 expression by hsa-miR-106a
    Amit Sharma
    Molecular Immunogenetics Laboratory, Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India
    Proc Natl Acad Sci U S A 106:5761-6. 2009
    ..In summary, our results showed that IL-10 expression may be regulated by miR-106a, which is in turn transcriptionally regulated by Egr1 and Sp1...
  30. ncbi request reprint (TG:CA)(n) repeats in human housekeeping genes
    Vineet K Sharma
    G N Ramachandran Knowledge Centre for Genome Informatics, Institute of Genomics and Integrative Biology, Mall Road, Delhi 110 007, India
    J Biomol Struct Dyn 21:303-10. 2003
    ..the genes belonging to the functional class of 'signalling and communication' had a positive association with repeats in contrast to the genes belonging to the 'information' class that were negatively associated with repeats...
  31. pmc Host-virus interaction: a new role for microRNAs
    Vinod Scaria
    GN Ramachandran Knowledge Center for Genome Informatics, Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110 007, India
    Retrovirology 3:68. 2006
    ....
  32. pmc Evolution and distribution of RNA polymerase II regulatory sites from RNA polymerase III dependant mobile Alu elements
    Ravi Shankar
    Functional Genomics Unit, Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110007, India
    BMC Evol Biol 4:37. 2004
    ....
  33. pmc Whole genome expression and biochemical correlates of extreme constitutional types defined in Ayurveda
    Bhavana Prasher
    Genomics and Molecular Medicine, Functional Genomics Unit, Institute of Genomics and Integrative Biology, CSIR, Delhi, India
    J Transl Med 6:48. 2008
    ..In this study, we explore whether the different constitution types as described in Ayurveda has molecular correlates...
  34. pmc (TG/CA)n repeats in human gene families: abundance and selective patterns of distribution according to function and gene length
    Vineet K Sharma
    G N Ramachandran Knowledge Centre for Genome Informatics, Institute of Genomics and Integrative Biology, Mall Road, Delhi 110 007, India
    BMC Genomics 6:83. 2005
    ..Here, we report analysis of the distribution of (TG/CA)n repeats in human gene families...
  35. ncbi request reprint A novel complexity measure for comparative analysis of protein sequences from complete genomes
    Tannistha Nandi
    Institute of Genomics and Integrative Biology, Centre for Biochemical Technology, Mall Road, Delhi 110 007, India
    J Biomol Struct Dyn 20:657-68. 2003
    ..Further, it was observed that a few bacterial pathogens (Mycobacterium tuberculosis, Pseudomonas aeruginosa) have high fraction of low complexity proteins. The program ScanCom is available from the authors as a PERL script (UNIX system)...
  36. pmc A role for voltage-dependent anion channel Vdac1 in polyglutamine-mediated neuronal cell death
    Tanay Ghosh
    Institute of Genomics and Integrative Biology IGIB, New Delhi, India
    PLoS ONE 2:e1170. 2007
    ....
  37. ncbi request reprint Variations in angiotensin-converting enzyme gene insertion/deletion polymorphism in Indian populations of different ethnic origins
    M A Qadar Pasha
    Functional Genomics Unit, Centre for Biochemical Technology, Mall Road, Delhi 110 007, India
    J Biosci 27:67-70. 2002
    ..56 3.13%. The results suggested ethnic heterogeneity with a significant gene cline with higher insertion allele frequency. Such population-based data on various polymorphisms can ultimately be exploited in pharmacogenomics...
  38. ncbi request reprint Nonrandom distribution of alu elements in genes of various functional categories: insight from analysis of human chromosomes 21 and 22
    Deepak Grover
    Functional Genomics Unit, Institute of Genomics and Integrative Biology Formerly Centre for Biochemical Technology, CSIR, Delhi, India
    Mol Biol Evol 20:1420-4. 2003
    ..We suggest that Alu elements might be involved in regulatory mechanisms and are therefore differentially selected in primate genomes...
  39. ncbi request reprint A nonsense mutation in the synaptogyrin 1 gene in a family with schizophrenia
    Ranjana Verma
    Functional Genomics Unit, Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research, Delhi University Campus, Delhi, India
    Biol Psychiatry 55:196-9. 2004
    ..Because Synaptogyrin 1 (SYNGR1), associated with presynaptic vesicles in neuronal cells, lies within 1 million base pairs of this marker, it is a potential candidate gene for schizophrenia...
  40. doi request reprint Open source drug discovery--a new paradigm of collaborative research in tuberculosis drug development
    Anshu Bhardwaj
    Council of Scientific and Industrial Research, Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110 001, India
    Tuberculosis (Edinb) 91:479-86. 2011
    ..Hopefully what LINUX the World Wide Web have done for the information technology, Open Source Drug Discovery will do for drug discovery...
  41. ncbi request reprint Targets for human encoded microRNAs in HIV genes
    Manoj Hariharan
    G N Ramachandran Knowledge Center for Genome Informatics, Institute of Genomics and Integrative Biology, Mall Road, Delhi 110 007, India
    Biochem Biophys Res Commun 337:1214-8. 2005
    ..This is the first report of human microRNAs which can target crucial HIV-1 genes including the nef gene, which plays an important role in delayed disease progression...
  42. ncbi request reprint Study of the single nucleotide polymorphism (SNP) at the palindromic sequence of hypersensitive site (HS)4 of the human beta-globin locus control region (LCR) in Indian population
    Ritushree Kukreti
    Functional Genomics Unit, Centre for Biochemical Technology CSIR, Delhi University Campus, Delhi, India
    Am J Hematol 69:77-9. 2002
    ..We also observed linkage disequilibrium between the A/G polymorphism and the AT-rich motif of the LCR HS2 region, suggesting that the G allele could be an evolutionarily new mutation in the study population...
  43. pmc Role of histidine interruption in mitigating the pathological effects of long polyglutamine stretches in SCA1: A molecular approach
    Somdutta Sen
    Functional Genomics Unit, Institute of Genomics and Integrative Biology Formerly Centre for Biochemical Technology, CSIR, Delhi 110007, India
    Protein Sci 12:953-62. 2003
    ..Our present study also reveals that besides histidine interruption, proline interruption in polyglutamine stretches can lower their aggregation propensity...