Publications

        Research Papers: 37;  Reviews: 5;  Book Chapter: 2; Citations: 1254; h-index =17

            For details on citations of Beena's Publications go to: https://scholar.google.co.in/citations?user=ofN6G20AAAAJ&hl=en


    1. A simple alternative to stereotactic injection for brain specific knockdown of miRNA. Suryawanshi,H.*, Sarangdhar,M. A.*, Vij, M., Roshan, R., Singh, V. P., Ganguli, M., Pillai, B. JoVE, in press.
    2. This is a video paper demonstrating the use of a peptide to target anti-miRNA to the mouse brain. The results of the behavioural assays wherein mice showed ataxia-like phenotype is also shown.

    3. Cell based gene therapy against HIV. Dey R. and Pillai B. Gene Therapy, 2015, in press

    4. Brain-specific knockdown of miR-29 results in neuronal cell death and ataxia in mice. Roshan R, Shridhar S, Sarangdhar MA, Banik A, Chawla M, Garg M, Singh VP, Pillai B*. RNA. 2014 Jun 23. 
    5. In this paper, we used a peptide to target anti-miRNA to the mouse brain. Using this method we could avoid the tedious tissue-specific knockout methods. The microRNA, miR-29 was knocked down, and the mice showed defects in walking on a thin ledge and close foot-steps that is considered typical of ataxia.

    6. Non-coding RNA interact to regulate neuronal development and function. Iyengar BR, Choudhary A, Sarangdhar MA, Venkatesh KV, Gadgil CJ, Pillai B*. Front Cell Neurosci. 2014 Feb 24;8:47.

    7. A study on the influence of different promoter and 5'UTR (URM) cassettes from Arabidopsis thaliana on the expression level of the reporter gene β glucuronidase in tobacco  and cotton. Agarwal P, Garg V, Gautam T, Pillai B, Kanoria S, Burma PK*. Transgenic Res. 2014 Apr;23(2):351-63. 

    8. Hsp90-targeted miRNA-liposomal formulation for systemic antitumor effect.Pore SK, Choudhary A, Rathore B, Ganguly A, Sujitha P, Kumar CG, Agawane SB, Kumar JM, Scaria V, Pillai B, Banerjee R*.  Biomaterials. 2013 Sep;34(28):6804-17.

    9. Detection and knockdown of microRNA-34a using thioacetamido nucleic acid. Soni K, Gupta S, Gokhale SS, Dey R, Gunjal AD, Kumar VA*, Pillai B*. Nucleic Acid Ther. 2013 Jun;23(3):195-202. 
    10. The TANA modification developed by Dr. Vyjayanti Kumar's lab in National Chemical Laboratory, Pune, performs as well as commercially available Locked Nucleic Acid modified oligo in miRNA detection and knockdown.

    11. Comprehensive expression analyses of neural cell-type-specific miRNAs identify new determinants of the specification and maintenance of neuronal phenotypes. Jovičić A, Roshan R, Moisoi N, Pradervand S, Moser R, Pillai B*, Luthi-Carter R. J* Neurosci. 2013 Mar 20;33(12):5127-37. 
    12. Collaboratoive work: useful resource if you are looking for cell-type specific miRNA expression patterns in the brain.

    13. miR-34 is maternally inherited in Drosophila melanogaster and Danio rerio. Soni K, Choudhary A, Patowary A, Singh AR, Bhatia S, Sivasubbu S, Chandrasekaran S, Pillai B*. Nucleic Acids Res. 2013 Apr;41(8):4470-80. 
    14. We wondered what happens to the cytoplasmic miRNA of the oocyte when fertilization happens. Does it get degraded? Does it get inherited? If so, can it influence the gene expression pattern in the progeny? In this paper, we show that atleast miR_34 does get inherited maternally. Knocking down the maternally inherited miR-34 leads to deformities in the zebrafish brain. 

    15. Identification of novel targets for miR-29a using miRNA proteomics. Bargaje R, Gupta S, Sarkeshik A, Park R, Xu T, Sarkar M, Halimani M, Roy SS, Yates J*, Pillai B*.  PLoS One. 2012;7(8):e43243. 
    16. Can we find miRNA targets by looking at differentially expressed proteins in cells with altered levels of miRNA? Rhishi learnt proteomics in the Yates lab at Scripps and did part of the work at IGIB. We did find that miR-29 targets VDAC, but as a general approach it was not very successful, perhaps because of the limited number of proteins we could identify.

    17. Proximity of H2A.Z containing nucleosome to the transcription start site influences gene expression  levels in the mammalian liver and brain. Bargaje R, Alam MP, Patowary A, Sarkar M, Ali T, Gupta S, Garg M, Singh M, Purkanti R, Scaria V, Sivasubbu S, Brahmachari V*, Pillai B*. Nucleic Acids Res. 2012 Oct;40(18):8965-78. 

    18. Regulation of BACE1 by miR-29a/b in a  cellular model of Spinocerebellar Ataxia 17. Roshan R, Ghosh T, Gadgil M, Pillai B*. RNA Biol. 2012 Jun;9(6):891-9. 

    19. Magnetite (Fe3O4) nanocrystals affect the expression of genes involved in the TGF-beta signalling pathway. Khan JA, Mandal TK, Das TK, Singh Y, Pillai B, Maiti S*. Mol Biosyst. 2011 May;7(5):1481-6. 

    20. A kinetic model of TBP auto-regulation exhibits bistability. Gokhale SA, Roshan R, Khetan V, Pillai B, Gadgil CJ. Biol Direct. 2010 Aug 5;5:50. 

    21. Consensus miRNA expression profiles derived from interplatform normalization of microarray data. Bargaje R, Hariharan M, Scaria V, Pillai B*. RNA. 2010 Jan;16(1):16-25. 

    22. MicroRNAs: novel therapeutic targets in neurodegenerative diseases. Roshan R, Ghosh T, Scaria V, Pillai B*. Drug Discov Today. 2009 Dec;14(23-24):1123-9. 

    23. Incomplete penetrance and variable expressivity: is there a microRNA connection? Ahluwalia JK, Hariharan M, Bargaje R, Pillai B, Brahmachari V*. Bioessays.  2009 Sep;31(9):981-92. 

    24. Human cellular microRNA hsa-miR-29a interferes with viral nef protein expression and HIV-1 replication. Ahluwalia JK, Khan SZ, Soni K, Rawat P, Gupta A, Hariharan M, Scaria V, Lalwani M, Pillai B, Mitra D*, Brahmachari SK*. Retrovirology. 2008 Dec 23;5:117. 

    25. GASCO: genetic algorithm simulation for codon optimization. Sandhu KS, Pandey S, Maiti S, Pillai B*. In Silico Biol. 2008;8(2):187-92. 

    26. MicroRNA-mediated up-regulation of an alternatively polyadenylated variant of the mouse cytoplasmic {beta}-actin gene. Ghosh T, Soni K, Scaria V, Halimani M, Bhattacharjee C, Pillai B*. Nucleic Acids Res. 2008 Nov;36(19):6318-32. 

    27. A role for voltage-dependent anion channel Vdac1 in polyglutamine-mediated neuronal cell death. Ghosh T, Pandey N, Maitra A, Brahmachari SK, Pillai B*. PLoS One. 2007 Nov 14;2(11):e1170. 

    28. Host-virus genome interactions: macro roles for microRNAs. Scaria V, Hariharan M, Pillai B, Maiti S, Brahmachari SK. Cell Microbiol. 2007 Dec;9(12):2784-94. 

    29. Molecular effects of uptake of gold nanoparticles in HeLa cells. Khan JA, Pillai B, Das TK, Singh Y, Maiti S*. Chembiochem. 2007 Jul 23;8(11):1237-40. 

    30. microRNA: an emerging therapeutic. Scaria V, Hariharan M, Brahmachari SK, Maiti S, Pillai B*. ChemMedChem. 2007 Jun;2(6):789-92. 

    31. Relative levels of  RNA polII subunits differentially affect starvation response in budding yeast. Singh SR, Pillai B, Balakrishnan B, Naorem A, Sadhale PP*.  Biochem Biophys Res Commun. 2007 Apr 27;356(1):266-72. 

    32. Host-virus interaction: a new role for microRNAs. Scaria V, Hariharan M, Maiti S, Pillai B, Brahmachari SK*. Retrovirology. 2006 Oct 11;3:68. 

    33. DyNAVacS: an integrative tool for optimized DNA vaccine design. Harish N, Gupta R, Agarwal P, Scaria V*, Pillai B*. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W264-6. 

    34. Homocysteine- and cysteine-mediated growth defect is not associated with induction of oxidative stress response genes in yeast. Kumar A, John L, Alam MM, Gupta A, Sharma G, Pillai B, Sengupta S*. Biochem J. 2006 May 15;396(1):61-9. 

    35. Cigarette smoke extract induces changes in growth and gene expression of Saccharomyces cerevisiae. John L, Sharma G, Chaudhuri SP, Pillai B*. Biochem Biophys Res Commun. 2005 Dec 23;338(3):1578-86. 

    36. Targets for human encoded microRNAs in HIV genes. Hariharan M, Scaria V, Pillai B, Brahmachari SK*. Biochem Biophys Res Commun. 2005 Dec 2;337(4):1214-8.

    37. Genome-wide expression profile of steroid response in Saccharomyces cerevisiae. Banerjee D, Pillai B, Karnani N, Mukhopadhyay G, Prasad R*. Biochem Biophys Res Commun. 2004 Apr 30;317(2):406-13. 

    38. Domainal organization of the lower eukaryotic homologs of the yeast RNA polymerase II core subunit Rpb7 reflects functional conservation. Singh SR, Rekha N, Pillai B, Singh V, Naorem A, Sampath V, Srinivasan N, Sadhale PP*. Nucleic Acids Res. 2004 Jan 2;32(1):201-10.

    39. Whole genome expression profiles of yeast RNA polymerase II core subunit, Rpb4, in stress and nonstress conditions. Pillai B, Verma J, Abraham A, Francis P, Kumar Y, Tatu U, Brahmachari SK, Sadhale PP*. J Biol Chem. 2003 Jan 31;278(5):3339-46.

    40. RNA Isolation from High ‐ Phenolic Freeze‐ Dried Tea (Camellia sinensis) leaves. Jaiprakash,M., Pillai,B.,Venkatesh,P., Subramanian,N., Sinkar,V.P.and Sadhale,P.P.* Plant Molecular Biology Reporter. (2003).21: 465a–465g. 

    41. Genome‐wide expression profile of RNA polymerase II subunit mutant of yeast using microarray technology. Pillai B.,Brahmachari, S. K.and Sadhale, P.P*.Current Science. (2001). 81(5), 574‐578. 

    42. Rpb4, a non‐essential subunit of core RNA polymerase II of Saccharomyces cerevisiae is important for activated transcription of a subset of genes. Pillai,B., Sampath,V., Sharma,N., and Sadhale,P.P.* J. Biol. Chem. (2001). 276, 30641‐30647. 

    43. Modulation of polymerase II composition: a possible mode of transcriptional regulation of stress response in eukaryotes. Sadhale P. *, Sharma N., Pillai B., Katoch A., Acharya N. and Singh S. K.J. Biosci. (1998). 23, 331‐335. 

              

    BOOK CHAPTERS:

    1. Beena Pillai, "Non-coding RNA" in Gene and its Engineering,  (2015) ed. H. K. Das, Wiley Publications
    2. Mitali Mukerji, Beena Pillai, Somdatta Sinha & S. K. Brahmachari. Textbook of Biotechnology, (2005) ed. H. K. Das, Wiley Publications

    posted 18 Jun 2010, 09:41 by Beena Pillai   [ updated 7 Nov 2010, 08:02 ]


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