Publications

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  1. Dayal, S., Chaubey, D., Joshi, D. C., Ranmale, S., & Pillai, B. (2024). Noncoding RNAs: Emerging regulators of behavioral complexity. Wiley interdisciplinary reviews. RNA, 15(3), e1847.

  2. Bandesh K, Pal M, Balakrishnan A, Gautam P, Jha P, Tandon N, Pillai B, Bharadwaj D. A novel antisense lncRNA, ARBAG harboring an RNA destabilizing GWAS variant for C-peptide dictates the transcript isoforms of GABRA6 in cerebellum. Hum Mol Genet. 2023 Sep 16;32(19):2929-2939. doi: 10.1093/hmg/ddad119. PMID: 37498167.

  3. Pal M, Chaubey D, Tanwar M, Pillai B. A Novel Cis-Regulatory lncRNA, Kalnc2, Downregulates Kalrn Protein-Coding Transcripts in Mouse Neuronal Cells. Noncoding RNA. 2023 Jan 13;9(1). doi: 10.3390/ncrna9010007. PubMed PMID: 36649036.

  4. Rawat RS, Bhambri A, Pal M, Roy A, Jain S, Pillai B, Konar A. Early life stressful experiences escalate aggressive behavior in adulthood via changes in transthyretin expression and function. Elife. 2022 Oct 13;11. doi: 10.7554/eLife.77968. PubMed PMID: 36226913; PubMed Central PMCID: PMC9633068.

  5. Rawat J, Bhambri A, Pandey U, Banerjee S, Pillai B, Gadgil M. Amino acid abundance and composition in cell culture medium affects trace metal tolerance and cholesterol synthesis. Biotechnol Prog. 2022 Aug 24;:e3298. doi: 10.1002/btpr.3298. [Epub ahead of print] PubMed PMID: 36053936.

  6. Kathpalia P, Konar A, Pillai B. Home laboratory: interactive science from the kitchen. Nature. 2021 Aug;596(7873):486. doi: 10.1038/d41586-021-02278-z. PubMed PMID: 34429540.

  7. Bhattacharya A, Jha V, Singhal K, Fatima M, Singh D, Chaturvedi G, Dholakia D, Kutum R, Pandey R, Bakken TE, Seth P, Pillai B, Mukerji M. Multiple Alu Exonization in 3'UTR of a Primate-Specific Isoform of CYP20A1 Creates a Potential miRNA Sponge. Genome Biol Evol. 2021 Jan 7;13(1). doi: 10.1093/gbe/evaa233. PubMed PMID: 33434274; PubMed Central PMCID: PMC7802813.

  8. Singh Patel S, Zunjarrao S, Pillai B. Neev, a novel long non-coding RNA, is expressed in chaetoblasts during regeneration of Eisenia fetida. J Exp Biol. 2020 Apr 16;223(Pt 8). doi: 10.1242/jeb.216754. PubMed PMID: 32098889.

  9. Bhambri A, Pinto A, Pillai B. Interferon mediated neuroinflammation in polyglutamine disease is not caused by RNA toxicity. Cell Death Dis. 2020 Jan 2;11(1):3. doi: 10.1038/s41419-019-2193-x. PubMed PMID: 31919387; PubMed Central PMCID: PMC6952400.

  10. Ramasamy S, Sharma S, Iyengar BR, Vellarikkal SK, Sivasubbu S, Maiti S, Pillai B. Identification of novel circadian transcripts in the zebrafish retina. J Exp Biol. 2019 Jan 10;222(Pt 1). doi: 10.1242/jeb.192195. PubMed PMID: 30446534.

  11. Sarangdhar MA, Chaubey D, Srikakulam N, Pillai B. Parentally inherited long non-coding RNA Cyrano is involved in zebrafish neurodevelopment. Nucleic Acids Res. 2018 Oct 12;46(18):9726-9735. doi: 10.1093/nar/gky628. PubMed PMID: 30011017; PubMed Central PMCID: PMC6182166.

  12. Bhambri A, Dhaunta N, Patel SS, Hardikar M, Bhatt A, Srikakulam N, Shridhar S, Vellarikkal S, Pandey R, Jayarajan R, Verma A, Kumar V, Gautam P, Khanna Y, Khan JA, Fromm B, Peterson KJ, Scaria V, Sivasubbu S, Pillai B. Large scale changes in the transcriptome of Eisenia fetida during regeneration. PLoS One. 2018;13(9):e0204234. doi: 10.1371/journal.pone.0204234. eCollection 2018. PubMed PMID: 30260966; PubMed Central PMCID: PMC6160089.

  13. Roshan R, Choudhary A, Bhambri A, Bakshi B, Ghosh T, Pillai B. microRNA dysregulation in polyglutamine toxicity of TATA-box binding protein is mediated through STAT1 in mouse neuronal cells. J Neuroinflammation. 2017 Aug 3;14(1):155. doi: 10.1186/s12974-017-0925-3. PubMed PMID: 28774347; PubMed Central PMCID: PMC5543588.

  14. Iyengar BR, Pillai B, Venkatesh KV, Gadgil CJ. Systematic comparison of the response properties of protein and RNA mediated gene regulatory motifs. Mol Biosyst. 2017 May 30;13(6):1235-1245. doi: 10.1039/c6mb00808a. PubMed PMID: 28485414.

  15. Sarangdhar MA, Chaubey D, Bhatt A, Km M, Kumar M, Ranjan S, Pillai B. A Novel Long Non-coding RNA, durga Modulates Dendrite Density and Expression of kalirin in Zebrafish. Front Mol Neurosci. 2017;10:95. doi: 10.3389/fnmol.2017.00095. eCollection 2017. PubMed PMID: 28442991; PubMed Central PMCID: PMC5385350.

  16. Dey R, Soni K, Saravanan S, Balakrishnan P, Kumar V, Boobalan J, Solomon SS, Scaria V, Solomon S, Brahmachari SK, Pillai B. Anti-HIV microRNA expression in a novel Indian cohort. Sci Rep. 2016 Jun 20;6:28279. doi: 10.1038/srep28279. PubMed PMID: 27320691; PubMed Central PMCID: PMC4913240.

  17. Sharma S, Hussain S, Soni K, Singhal P, Tripathi R, Ramachandran VG, Sharma S, Das S, Pillai B, Bharadwaj M. Novel MicroRNA signatures in HPV-mediated cervical carcinogenesis in Indian women. Tumour Biol. 2016 Apr;37(4):4585-95. doi: 10.1007/s13277-015-4248-7. Epub 2015 Oct 27. PubMed PMID: 26508022.

  18. Suryawanshi H, Sarangdhar MA, Vij M, Roshan R, Singh VP, Ganguli M, Pillai B. A Simple Alternative to Stereotactic Injection for Brain Specific Knockdown of miRNA. J Vis Exp. 2015 Dec 26;(106):e53307. doi: 10.3791/53307. PubMed PMID: 26779762; PubMed Central PMCID: PMC4780854.

  19. Dhamija N, Choudhary D, Ladha JS, Pillai B, Mitra D. Tat predominantly associates with host promoter elements in HIV-1-infected T-cells - regulatory basis of transcriptional repression of c-Rel. FEBS J. 2015 Feb;282(3):595-610. doi: 10.1111/febs.13168. Epub 2014 Dec 22. PubMed PMID: 25472883.

  20. Roshan R, Shridhar S, Sarangdhar MA, Banik A, Chawla M, Garg M, Singh VP, Pillai B. Brain-specific knockdown of miR-29 results in neuronal cell death and ataxia in mice. RNA. 2014 Aug;20(8):1287-97. doi: 10.1261/rna.044008.113. Epub 2014 Jun 23. PubMed PMID: 24958907; PubMed Central PMCID: PMC4105753.

  21. Agarwal P, Garg V, Gautam T, Pillai B, Kanoria S, Burma PK. 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. Transgenic Res. 2014 Apr;23(2):351-63. doi: 10.1007/s11248-013-9757-9. Epub 2013 Sep 27. PubMed PMID: 24072400.

  22. Iyengar BR, Choudhary A, Sarangdhar MA, Venkatesh KV, Gadgil CJ, Pillai B. Non-coding RNA interact to regulate neuronal development and function. Front Cell Neurosci. 2014;8:47. doi: 10.3389/fncel.2014.00047. eCollection 2014. Review. PubMed PMID: 24605084; PubMed Central PMCID: PMC3932439.

  23. Pore SK, Choudhary A, Rathore B, Ganguly A, Sujitha P, Kumar CG, Agawane SB, Kumar JM, Scaria V, Pillai B, Banerjee R. Hsp90-targeted miRNA-liposomal formulation for systemic antitumor effect. Biomaterials. 2013 Sep;34(28):6804-17. doi: 10.1016/j.biomaterials.2013.05.054. Epub 2013 Jun 14. PubMed PMID: 23773821.

  24. Soni K, Gupta S, Gokhale SS, Dey R, Gunjal AD, Kumar VA, Pillai B. Detection and knockdown of microRNA-34a using thioacetamido nucleic acid. Nucleic Acid Ther. 2013 Jun;23(3):195-202. doi: 10.1089/nat.2012.0411. Epub 2013 May 6. PubMed PMID: 23647235

  25. Soni K, Choudhary A, Patowary A, Singh AR, Bhatia S, Sivasubbu S, Chandrasekaran S, Pillai B. miR-34 is maternally inherited in Drosophila melanogaster and Danio rerio. Nucleic Acids Res. 2013 Apr;41(8):4470-80. doi: 10.1093/nar/gkt139. Epub 2013 Mar 6. PubMed PMID: 23470996; PubMed Central PMCID: PMC3632126

  26. Jovičić A, Roshan R, Moisoi N, Pradervand S, Moser R, Pillai B, Luthi-Carter R. Comprehensive expression analyses of neural cell-type-specific miRNAs identify new determinants of the specification and maintenance of neuronal phenotypes. J Neurosci. 2013 Mar 20;33(12):5127-37. doi: 10.1523/JNEUROSCI.0600-12.2013. PubMed PMID: 23516279; PubMed Central PMCID: PMC6705001.

  27. 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. Proximity of H2A.Z containing nucleosome to the transcription start site influences gene expression levels in the mammalian liver and brain. Nucleic Acids Res. 2012 Oct;40(18):8965-78. doi: 10.1093/nar/gks665. Epub 2012 Jul 19. PubMed PMID: 22821566; PubMed Central PMCID: PMC3467062.

  28. Bargaje R, Gupta S, Sarkeshik A, Park R, Xu T, Sarkar M, Halimani M, Roy SS, Yates J, Pillai B. Identification of novel targets for miR-29a using miRNA proteomics. PLoS One. 2012;7(8):e43243. doi: 10.1371/journal.pone.0043243. Epub 2012 Aug 27. PubMed PMID: 22952654; PubMed Central PMCID: PMC3428309.

  29. Roshan R, Ghosh T, Gadgil M, Pillai B. Regulation of BACE1 by miR-29a/b in a cellular model of Spinocerebellar Ataxia 17. RNA Biol. 2012 Jun;9(6):891-9. doi: 10.4161/rna.19876. Epub 2012 Jun 1. PubMed PMID: 22664922.

  30. Khan JA, Mandal TK, Das TK, Singh Y, Pillai B, Maiti S. Magnetite (Fe3O4) nanocrystals affect the expression of genes involved in the TGF-beta signalling pathway. Mol Biosyst. 2011 May;7(5):1481-6. doi: 10.1039/c0mb00192a. Epub 2011 Feb 19. PubMed PMID: 21336377.

  31. Gokhale SA, Roshan R, Khetan V, Pillai B, Gadgil CJ. A kinetic model of TBP auto-regulation exhibits bistability. Biol Direct. 2010 Aug 5;5:50. doi: 10.1186/1745-6150-5-50. PubMed PMID: 20687914; PubMed Central PMCID: PMC2928763.

  32. Bargaje R, Hariharan M, Scaria V, Pillai B. Consensus miRNA expression profiles derived from interplatform normalization of microarray data. RNA. 2010 Jan;16(1):16-25. doi: 10.1261/rna.1688110. Epub 2009 Nov 30. PubMed PMID: 19948767; PubMed Central PMCID: PMC2802026.

  33. Roshan R, Ghosh T, Scaria V, Pillai B. MicroRNAs: novel therapeutic targets in neurodegenerative diseases. Drug Discov Today. 2009 Dec;14(23-24):1123-9. doi: 10.1016/j.drudis.2009.09.009. Epub 2009 Oct 12. Review. PubMed PMID: 19822222.

  34. Ahluwalia JK, Hariharan M, Bargaje R, Pillai B, Brahmachari V. Incomplete penetrance and variable expressivity: is there a microRNA connection?. Bioessays. 2009 Sep;31(9):981-92. doi: 10.1002/bies.200900066. PubMed PMID: 19642110.

  35. Ahluwalia JK, Khan SZ, Soni K, Rawat P, Gupta A, Hariharan M, Scaria V, Lalwani M, Pillai B, Mitra D, Brahmachari SK. Human cellular microRNA hsa-miR-29a interferes with viral nef protein expression and HIV-1 replication. Retrovirology. 2008 Dec 23;5:117. doi: 10.1186/1742-4690-5-117. PubMed PMID: 19102781; PubMed Central PMCID: PMC2635386.

  36. Ghosh T, Soni K, Scaria V, Halimani M, Bhattacharjee C, Pillai B. MicroRNA-mediated up-regulation of an alternatively polyadenylated variant of the mouse cytoplasmic {beta}-actin gene. Nucleic Acids Res. 2008 Nov;36(19):6318-32. doi: 10.1093/nar/gkn624. Epub 2008 Oct 3. PubMed PMID: 18835850; PubMed Central PMCID: PMC2577349.

  37. Sandhu KS, Pandey S, Maiti S, Pillai B. GASCO: genetic algorithm simulation for codon optimization. In Silico Biol. 2008;8(2):187-92. PubMed PMID: 18928205.

  38. Scaria V, Hariharan M, Pillai B, Maiti S, Brahmachari SK. Host-virus genome interactions: macro roles for microRNAs. Cell Microbiol. 2007 Dec;9(12):2784-94. doi: 10.1111/j.1462-5822.2007.01050.x. Epub 2007 Oct 18. Review. PubMed PMID: 17944962.

  39. Ghosh T, Pandey N, Maitra A, Brahmachari SK, Pillai B. A role for voltage-dependent anion channel Vdac1 in polyglutamine-mediated neuronal cell death. PLoS One. 2007 Nov 14;2(11):e1170. doi: 10.1371/journal.pone.0001170. PubMed PMID: 18000542; PubMed Central PMCID: PMC2064964.

  40. Khan JA, Pillai B, Das TK, Singh Y, Maiti S. Molecular effects of uptake of gold nanoparticles in HeLa cells. Chembiochem. 2007 Jul 23;8(11):1237-40. doi: 10.1002/cbic.200700165. PubMed PMID: 17569092.

  41. Scaria V, Hariharan M, Brahmachari SK, Maiti S, Pillai B. microRNA: an emerging therapeutic. ChemMedChem. 2007 Jun;2(6):789-92. doi: 10.1002/cmdc.200600278. Review. PubMed PMID: 17410618

  42. Singh SR, Pillai B, Balakrishnan B, Naorem A, Sadhale PP. Relative levels of RNA polII subunits differentially affect starvation response in budding yeast. Biochem Biophys Res Commun. 2007 Apr 27;356(1):266-72. doi: 10.1016/j.bbrc.2007.02.120. Epub 2007 Mar 1. PubMed PMID: 17346670.

  43. Scaria V, Hariharan M, Maiti S, Pillai B, Brahmachari SK. Host-virus interaction: a new role for microRNAs. Retrovirology. 2006 Oct 11;3:68. doi: 10.1186/1742-4690-3-68. Review. PubMed PMID: 17032463; PubMed Central PMCID: PMC1626483.

  44. Harish N, Gupta R, Agarwal P, Scaria V, Pillai B. DyNAVacS: an integrative tool for optimized DNA vaccine design. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W264-6. doi: 10.1093/nar/gkl242. PubMed PMID: 16845007; PubMed Central PMCID: PMC1538838.

  45. Kumar A, John L, Alam MM, Gupta A, Sharma G, Pillai B, Sengupta S. Homocysteine- and cysteine-mediated growth defect is not associated with induction of oxidative stress response genes in yeast. Biochem J. 2006 May 15;396(1):61-9. doi: 10.1042/BJ20051411. PubMed PMID: 16433631; PubMed Central PMCID: PMC1449999.

  46. John L, Sharma G, Chaudhuri SP, Pillai B. Cigarette smoke extract induces changes in growth and gene expression of Saccharomyces cerevisiae. Biochem Biophys Res Commun. 2005 Dec 23;338(3):1578-86. doi: 10.1016/j.bbrc.2005.10.122. Epub 2005 Nov 2. PubMed PMID: 16289044.

  47. Hariharan M, Scaria V, Pillai B, Brahmachari SK. Targets for human encoded microRNAs in HIV genes. Biochem Biophys Res Commun. 2005 Dec 2;337(4):1214-8. doi: 10.1016/j.bbrc.2005.09.183. Epub 2005 Oct 7. PubMed PMID: 16236258.

  48. Banerjee D, Pillai B, Karnani N, Mukhopadhyay G, Prasad R. Genome-wide expression profile of steroid response in Saccharomyces cerevisiae. Biochem Biophys Res Commun. 2004 Apr 30;317(2):406-13. doi: 10.1016/j.bbrc.2004.03.053. PubMed PMID: 15063773

  49. Singh SR, Rekha N, Pillai B, Singh V, Naorem A, Sampath V, Srinivasan N, Sadhale PP. Domainal organization of the lower eukaryotic homologs of the yeast RNA polymerase II core subunit Rpb7 reflects functional conservation. Nucleic Acids Res. 2004;32(1):201-10. doi: 10.1093/nar/gkh163. Print 2004. PubMed PMID: 14704357; PubMed Central PMCID: PMC373273.

  50. Pillai B, Verma J, Abraham A, Francis P, Kumar Y, Tatu U, Brahmachari SK, Sadhale PP. Whole genome expression profiles of yeast RNA polymerase II core subunit, Rpb4, in stress and nonstress conditions. J Biol Chem. 2003 Jan 31;278(5):3339-46. doi: 10.1074/jbc.M112180200. Epub 2002 Nov 11. PubMed PMID: 12429747.

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