Publications

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Here is a chronological list of our publications. To understand the main findings of these publications, please visit the Projects page.
  1. Chaubey, D., Joshi, D. C., Dayal, S., Verma, S., Sachidanandan, C., & Pillai, B. (2026). Bucky ball mRNA is responsive to the total RNA content in the fertilized zebrafish oocyte . Biochemical and Biophysical Research Communications, 807, 153328. PubMed
  2. Joshi, D. C., Kadam, A., Sachidanandan, C., & Pillai, B. (2025). A comprehensive analysis of the inherited lncRNA and circRNA repertoire of zebrafish . Bioinformatics Advances, 5(1), vbaf139. PubMed
  3. 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. PubMed
  4. Bandesh K, Pal M, Balakrishnan A, Gautam P, Jha P, Tandon N, Pillai B, Bharadwaj D. (2023). A novel antisense lncRNA, ARBAG harboring an RNA destabilizing GWAS variant for C-peptide dictates the transcript isoforms of GABRA6 in cerebellum . Human Molecular Genetics, 32(19), 2929–2939. PubMed
  5. Pal M, Chaubey D, Tanwar M, Pillai B. (2023). A Novel Cis-Regulatory lncRNA, Kalnc2, Downregulates Kalrn Protein-Coding Transcripts in Mouse Neuronal Cells . Noncoding RNA, 9(1). PubMed
  6. Rawat RS, Bhambri A, Pal M, Roy A, Jain S, Pillai B, Konar A. (2022). Early life stressful experiences escalate aggressive behavior in adulthood via changes in transthyretin expression and function . eLife, 11. PubMed
  7. Rawat J, Bhambri A, Pandey U, Banerjee S, Pillai B, Gadgil M. (2022). Amino acid abundance and composition in cell culture medium affects trace metal tolerance and cholesterol synthesis . Biotechnology Progress, e3298. PubMed
  8. Kathpalia P, Konar A, Pillai B. (2021). Home laboratory: interactive science from the kitchen . Nature, 596(7873), 486. PubMed
  9. 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. (2021). Multiple Alu Exonization in 3'UTR of a Primate-Specific Isoform of CYP20A1 Creates a Potential miRNA Sponge . Genome Biology and Evolution, 13(1). PubMed
  10. Singh Patel S, Zunjarrao S, Pillai B. (2020). Neev, a novel long non-coding RNA, is expressed in chaetoblasts during regeneration of Eisenia fetida . Journal of Experimental Biology, 223(Pt 8). PubMed
  11. Bhambri A, Pinto A, Pillai B. (2020). Interferon mediated neuroinflammation in polyglutamine disease is not caused by RNA toxicity . Cell Death & Disease, 11(1), 3. PubMed
  12. Ramasamy S, Sharma S, Iyengar BR, Vellarikkal SK, Sivasubbu S, Maiti S, Pillai B. (2019). Identification of novel circadian transcripts in the zebrafish retina . Journal of Experimental Biology, 222(Pt 1). PubMed
  13. Sarangdhar MA, Chaubey D, Srikakulam N, Pillai B. (2018). Parentally inherited long non-coding RNA Cyrano is involved in zebrafish neurodevelopment . Nucleic Acids Research, 46(18), 9726–9735. PubMed
  14. 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. (2018). Large scale changes in the transcriptome of Eisenia fetida during regeneration . PLoS One, 13(9), e0204234. PubMed
  15. Roshan R, Choudhary A, Bhambri A, Bakshi B, Ghosh T, Pillai B. (2017). microRNA dysregulation in polyglutamine toxicity of TATA-box binding protein is mediated through STAT1 in mouse neuronal cells . Journal of Neuroinflammation, 14(1), 155. PubMed
  16. Iyengar BR, Pillai B, Venkatesh KV, Gadgil CJ. (2017). Systematic comparison of the response properties of protein and RNA mediated gene regulatory motifs . Molecular BioSystems, 13(6), 1235–1245. PubMed
  17. Sarangdhar MA, Chaubey D, Bhatt A, Km M, Kumar M, Ranjan S, Pillai B. (2017). A Novel Long Non-coding RNA, durga Modulates Dendrite Density and Expression of kalirin in Zebrafish . Frontiers in Molecular Neuroscience, 10, 95. PubMed
  18. Dey R, Soni K, Saravanan S, Balakrishnan P, Kumar V, Boobalan J, Solomon SS, Scaria V, Solomon S, Brahmachari SK, Pillai B. (2016). Anti-HIV microRNA expression in a novel Indian cohort . Scientific Reports, 6, 28279. PubMed
  19. Sharma S, Hussain S, Soni K, Singhal P, Tripathi R, Ramachandran VG, Sharma S, Das S, Pillai B, Bharadwaj M. (2016). Novel MicroRNA signatures in HPV-mediated cervical carcinogenesis in Indian women . Tumour Biology, 37(4), 4585–4595. PubMed
  20. Suryawanshi H, Sarangdhar MA, Vij M, Roshan R, Singh VP, Ganguli M, Pillai B. (2015). A Simple Alternative to Stereotactic Injection for Brain Specific Knockdown of miRNA . Journal of Visualized Experiments, (106), e53307. PubMed
  21. Dhamija N, Choudhary D, Ladha JS, Pillai B, Mitra D. (2015). Tat predominantly associates with host promoter elements in HIV-1-infected T-cells - regulatory basis of transcriptional repression of c-Rel . FEBS Journal, 282(3), 595–610. PubMed
  22. Roshan R, Shridhar S, Sarangdhar MA, Banik A, Chawla M, Garg M, Singh VP, Pillai B. (2014). Brain-specific knockdown of miR-29 results in neuronal cell death and ataxia in mice . RNA, 20(8), 1287–1297. PubMed
  23. Agarwal P, Garg V, Gautam T, Pillai B, Kanoria S, Burma PK. (2014). 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 Research, 23(2), 351–363. PubMed
  24. Iyengar BR, Choudhary A, Sarangdhar MA, Venkatesh KV, Gadgil CJ, Pillai B. (2014). Non-coding RNA interact to regulate neuronal development and function . Frontiers in Cellular Neuroscience, 8, 47. PubMed
  25. Pore SK, Choudhary A, Rathore B, Ganguly A, Sujitha P, Kumar CG, Agawane SB, Kumar JM, Scaria V, Pillai B, Banerjee R. (2013). Hsp90-targeted miRNA-liposomal formulation for systemic antitumor effect . Biomaterials, 34(28), 6804–6817. PubMed
  26. Soni K, Gupta S, Gokhale SS, Dey R, Gunjal AD, Kumar VA, Pillai B. (2013). Detection and knockdown of microRNA-34a using thioacetamido nucleic acid . Nucleic Acid Therapeutics, 23(3), 195–202. PubMed
  27. Soni K, Choudhary A, Patowary A, Singh AR, Bhatia S, Sivasubbu S, Chandrasekaran S, Pillai B. (2013). miR-34 is maternally inherited in Drosophila melanogaster and Danio rerio . Nucleic Acids Research, 41(8), 4470–4480. PubMed
  28. Jovičić A, Roshan R, Moisoi N, Pradervand S, Moser R, Pillai B, Luthi-Carter R. (2013). Comprehensive expression analyses of neural cell-type-specific miRNAs identify new determinants of the specification and maintenance of neuronal phenotypes . Journal of Neuroscience, 33(12), 5127–5137. PubMed
  29. 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. (2012). Proximity of H2A.Z containing nucleosome to the transcription start site influences gene expression levels in the mammalian liver and brain . Nucleic Acids Research, 40(18), 8965–8978. PubMed
  30. Bargaje R, Gupta S, Sarkeshik A, Park R, Xu T, Sarkar M, Halimani M, Roy SS, Yates J, Pillai B. (2012). Identification of novel targets for miR-29a using miRNA proteomics . PLoS One, 7(8), e43243. PubMed
  31. Roshan R, Ghosh T, Gadgil M, Pillai B. (2012). Regulation of BACE1 by miR-29a/b in a cellular model of Spinocerebellar Ataxia 17 . RNA Biology, 9(6), 891–899. PubMed
  32. Khan JA, Mandal TK, Das TK, Singh Y, Pillai B, Maiti S. (2011). Magnetite (Fe3O4) nanocrystals affect the expression of genes involved in the TGF-beta signalling pathway . Molecular BioSystems, 7(5), 1481–1486. PubMed
  33. Gokhale SA, Roshan R, Khetan V, Pillai B, Gadgil CJ. (2010). A kinetic model of TBP auto-regulation exhibits bistability . Biology Direct, 5, 50. PubMed
  34. Bargaje R, Hariharan M, Scaria V, Pillai B. (2010). Consensus miRNA expression profiles derived from interplatform normalization of microarray data . RNA, 16(1), 16–25. PubMed
  35. Roshan R, Ghosh T, Scaria V, Pillai B. (2009). MicroRNAs: novel therapeutic targets in neurodegenerative diseases . Drug Discovery Today, 14(23-24), 1123–1129. PubMed
  36. Ahluwalia JK, Hariharan M, Bargaje R, Pillai B, Brahmachari V. (2009). Incomplete penetrance and variable expressivity: is there a microRNA connection? . BioEssays, 31(9), 981–992. PubMed
  37. Ahluwalia JK, Khan SZ, Soni K, Rawat P, Gupta A, Hariharan M, Scaria V, Lalwani M, Pillai B, Mitra D, Brahmachari SK. (2008). Human cellular microRNA hsa-miR-29a interferes with viral nef protein expression and HIV-1 replication . Retrovirology, 5, 117. PubMed
  38. Ghosh T, Soni K, Scaria V, Halimani M, Bhattacharjee C, Pillai B. (2008). MicroRNA-mediated up-regulation of an alternatively polyadenylated variant of the mouse cytoplasmic β-actin gene . Nucleic Acids Research, 36(19), 6318–6332. PubMed
  39. Sandhu KS, Pandey S, Maiti S, Pillai B. (2008). GASCO: genetic algorithm simulation for codon optimization . In Silico Biology, 8(2), 187–192. PubMed
  40. Scaria V, Hariharan M, Pillai B, Maiti S, Brahmachari SK. (2007). Host-virus genome interactions: macro roles for microRNAs . Cellular Microbiology, 9(12), 2784–2794. PubMed
  41. Ghosh T, Pandey N, Maitra A, Brahmachari SK, Pillai B. (2007). A role for voltage-dependent anion channel Vdac1 in polyglutamine-mediated neuronal cell death . PLoS One, 2(11), e1170. PubMed
  42. Khan JA, Pillai B, Das TK, Singh Y, Maiti S. (2007). Molecular effects of uptake of gold nanoparticles in HeLa cells . ChemBioChem, 8(11), 1237–1240. PubMed
  43. Scaria V, Hariharan M, Brahmachari SK, Maiti S, Pillai B. (2007). microRNA: an emerging therapeutic . ChemMedChem, 2(6), 789–792. PubMed
  44. Singh SR, Pillai B, Balakrishnan B, Naorem A, Sadhale PP. (2007). Relative levels of RNA polII subunits differentially affect starvation response in budding yeast . Biochemical and Biophysical Research Communications, 356(1), 266–272. PubMed
  45. Scaria V, Hariharan M, Maiti S, Pillai B, Brahmachari SK. (2006). Host-virus interaction: a new role for microRNAs . Retrovirology, 3, 68. PubMed
  46. Harish N, Gupta R, Agarwal P, Scaria V, Pillai B. (2006). DyNAVacS: an integrative tool for optimized DNA vaccine design . Nucleic Acids Research, 34(Web Server issue), W264–W266. PubMed
  47. Kumar A, John L, Alam MM, Gupta A, Sharma G, Pillai B, Sengupta S. (2006). Homocysteine- and cysteine-mediated growth defect is not associated with induction of oxidative stress response genes in yeast . Biochemical Journal, 396(1), 61–69. PubMed
  48. John L, Sharma G, Chaudhuri SP, Pillai B. (2005). Cigarette smoke extract induces changes in growth and gene expression of Saccharomyces cerevisiae . Biochemical and Biophysical Research Communications, 338(3), 1578–1586. PubMed
  49. Hariharan M, Scaria V, Pillai B, Brahmachari SK. (2005). Targets for human encoded microRNAs in HIV genes . Biochemical and Biophysical Research Communications, 337(4), 1214–1218. PubMed
  50. Banerjee D, Pillai B, Karnani N, Mukhopadhyay G, Prasad R. (2004). Genome-wide expression profile of steroid response in Saccharomyces cerevisiae . Biochemical and Biophysical Research Communications, 317(2), 406–413. PubMed
  51. Singh SR, Rekha N, Pillai B, Singh V, Naorem A, Sampath V, Srinivasan N, Sadhale PP. (2004). Domainal organization of the lower eukaryotic homologs of the yeast RNA polymerase II core subunit Rpb7 reflects functional conservation . Nucleic Acids Research, 32(1), 201–210. PubMed
  52. Pillai B, Verma J, Abraham A, Francis P, Kumar Y, Tatu U, Brahmachari SK, Sadhale PP. (2003). Whole genome expression profiles of yeast RNA polymerase II core subunit, Rpb4, in stress and nonstress conditions . Journal of Biological Chemistry, 278(5), 3339–3346. PubMed