1. Gupta, S., Jyoti, Bhati, U., Kesarwani, V. and Shankar, R., 2024. PTF-Vāc: Ab-initio discovery of plant transcription factors binding sites using deep co-learning encoders-decoders. bioRxiv, pp.2024-01.

  2. Choudhary, S., Shanu, K., Hegde, A.S., Kesarwani, V., Kumar, R., shankar, R., Devi, S. and Srivatsan, V., 2024. Nutritional quality and microbial diversity of Chhurpe from different milk sources: an ethnic fermented food of high-altitude regions of the Western Himalayas. Discover Food, 4(1), p.10.


  1. Gupta, S., Kesarwani, V., Bhati, U., Jyoti and Shankar, R., 2023. Deep co-learning on transcription factors and their binding regions attains impeccable universality in plants. bioRxiv, pp.2023-11.
  2. Jyoti, Ritu, Gupta, S. and Shankar, R., 2023. Comprehensive evaluation of plant transcription factors binding sites discovery tools. bioRxiv, pp.2023-11.
  3. Suresh, P.S., Kesarwani, V., Kumari, S., Shankar, R. and Sharma, U., 2023. Flavonoids from Aerial Parts of Cissampelos pareira L. as Antimalarial Agents: Computational Validation of Ethnopharmacological Relevance. South African Journal of Botany, 163, pp.10-19.
  4. Gupta, S. and Shankar, R., 2023. miWords: transformer-based composite deep learning for highly accurate discovery of pre-miRNA regions across plant genomes. Briefings in Bioinformatics, 24(2), p.bbad088.
  5. Suresh, P.S., Kesarwani, V., Kumari, S., Shankar, R. and Sharma, U., 2023. Bisbenzylisoquinolines from Cissampelos pareira L. as antimalarial agents: Molecular docking, pharmacokinetics analysis, and molecular dynamic simulation studies. Computational Biology and Chemistry, 104, p.107826.


  1. Bhattacharyya, P., Sharma, T., Yadav, A., Lalthafamkimi, L., Swarnkar, M.K., Joshi, R., Shankar, R. and Kumar, S., 2022. De novo transcriptome based insights into secondary metabolite biosynthesis in Malaxis acuminata (Jeevak)–A therapeutically important orchid. Frontiers in Plant Science, 13, p.954467.
  2. Rathore, N., Kumar, P., Mehta, N., Swarnkar, M.K., Shankar, R. and Chawla, A., 2022. Time-series RNA-Seq transcriptome profiling reveals novel insights about cold acclimation and de-acclimation processes in an evergreen shrub of high altitude. Scientific Reports, 12(1), p.15553.
  3. Ritu, Gupta, S., Sharma, N.K. and Shankar, R., 2022. DeepPlnc: Bi-modal deep learning for highly accurate plant lncRNA discovery. Genomics, 114(5), p.110443.


  1. Kumari, M., Pradhan, U.K., Joshi, R., Punia, A., Shankar, R. and Kumar, R., 2021. In-depth assembly of organ and development dissected Picrorhiza kurroa proteome map using mass spectrometry. BMC Plant Biology, 21(1), pp.1-18.
  2. Sharma, N.K., Gupta, S., Kumar, A., Kumar, P., Pradhan, U.K. and Shankar, R., 2021. RBPSpot: Learning on appropriate contextual information for RBP binding sites discovery. IScience, 24(12).
  3. Pradhan, U.K., Sharma, N.K., Kumar, P., Kumar, A., Gupta, S. and Shankar, R., 2021. miRbiom: Machine-learning on Bayesian causal nets of RBP-miRNA interactions successfully predicts miRNA profiles. Plos one, 16(10), p.e0258550.
  4. Sharma, T., Sharma, N.K., Kumar, P., Panzade, G., Rana, T., Swarnkar, M.K., Singh, A.K., Singh, D., Shankar, R. and Kumar, S., 2021. The first draft genome of Picrorhiza kurrooa, an endangered medicinal herb from Himalayas. Scientific Reports, 11(1), p.14944.
  5. Gupta, S.S., Kumar, A., Shankar, R. and Sharma, U., 2021. In silico approach for identifying natural lead molecules against SARS-COV-2. Journal of molecular graphics and modelling, 106, p.107916.


  1. Mala, D., Awasthi, S., Sharma, N.K., Swarnkar, M.K., Shankar, R. and Kumar, S., 2021. Comparative transcriptome analysis of Rheum australe, an endangered medicinal herb, growing in its natural habitat and those grown in controlled growth chambers. Scientific Reports, 11(1), p.3702.
  2. Shankar, R., 2020. The dynamic aspects of RNA regulation. In Rna-Based Regulation in Human Health and Disease (pp. 85-115). Academic Press.


  1. Kumari, M., Thakur, S., Kumar, A., Joshi, R., Kumar, P., Shankar, R. and Kumar, R., 2020. Regulation of color transition in purple tea (Camellia sinensis). Planta, 251, pp.1-18.
  2. Panzade, G., Gangwar, I., Awasthi, S., Sharma, N. and Shankar, R., 2019. Plant Regulomics Portal (PRP): a comprehensive integrated regulatory information and analysis portal for plant genomes. Database, 2019, p.baz130.
  3. Dhiman, N., Sharma, N.K., Thapa, P., Sharma, I., Kumar Swarnkar, M., Chawla, A., Shankar, R. and Bhattacharya, A., 2019. De novo transcriptome provides insights into the growth behaviour and resveratrol and trans-stilbenes biosynthesis in Dactylorhiza hatagirea-An endangered alpine terrestrial orchid of western Himalaya. Scientific Reports, 9(1), p.13133.


  1. Rajan, S., Panzade, G., Srivastava, A., Shankar, K., Pandey, R., Kumar, D., Gupta, S., Gupta, A., Varshney, S., Beg, M. and Mishra, R.K., 2018. miR-876-3p regulates glucose homeostasis and insulin sensitivity by targeting adiponectin. Journal of Endocrinology, 239(1), pp.1-17.
  2. Goel, P., Sharma, N.K., Bhuria, M., Sharma, V., Chauhan, R., Pathania, S., Swarnkar, M.K., Chawla, V., Acharya, V., Shankar, R. and Singh, A.K., 2018. Transcriptome and co-expression network analyses identify key genes regulating nitrogen use efficiency in Brassica juncea L. Scientific Reports, 8(1), p.7451.


  1. Gangwar, I., Kumar Sharma, N., Panzade, G., Awasthi, S., Agrawal, A. and Shankar, R., 2017. Detecting the molecular system signatures of idiopathic pulmonary fibrosis through integrated genomic analysis. Scientific reports, 7(1), p.1554.


  1. Kumar, A., Chawla, V., Sharma, E., Mahajan, P., Shankar, R. and Yadav, S.K., 2016. Comparative transcriptome analysis of chinary, assamica and cambod tea (Camellia sinensis) types during development and seasonal variation using RNA-seq technology. Scientific reports, 6(1), p.37244.
  2. Bhartiya, D., Chawla, V., Ghosh, S., Shankar, R. and Kumar, N., 2016. Genome-wide regulatory dynamics of G-quadruplexes in human malaria parasite Plasmodium falciparum. Genomics, 108(5-6), pp.224-231.
  3. Jayaswall, K., Mahajan, P., Singh, G., Parmar, R., Seth, R., Raina, A., Swarnkar, M.K., Singh, A.K., Shankar, R. and Sharma, R.K., 2016. Transcriptome analysis reveals candidate genes involved in blister blight defense in tea (Camellia sinensis (L) Kuntze). Scientific reports, 6(1), p.30412.
  4. Chawla, V., Kumar, R. and Shankar, R., 2016. Identifying wrong assemblies in de novo short read primary sequence assembly contigs. Journal of biosciences, 41, pp.455-474.
  5. Bhardwaj, J., Gangwar, I., Panzade, G., Shankar, R. and Yadav, S.K., 2016. Global de novo protein–protein interactome elucidates interactions of drought-responsive proteins in horse gram (Macrotyloma uniflorum). Journal of Proteome Research, 15(6), pp.1794-1809.
  6. Manjunatha, B.L., Singh, H.R., Ravikanth, G., Nataraja, K.N., Shankar, R., Kumar, S. and Shaanker, R.U., 2016. Transcriptome analysis of stem wood of Nothapodytes nimmoniana (Graham) Mabb. identifies genes associated with biosynthesis of camptothecin, an anti-carcinogenic molecule. Journal of biosciences, 41, pp.119-131.


  1. Shafi, A., Chauhan, R., Gill, T., Swarnkar, M.K., Sreenivasulu, Y., Kumar, S., Kumar, N., Shankar, R., Ahuja, P.S. and Singh, A.K., 2015. Expression of SOD and APX genes positively regulates secondary cell wall biosynthesis and promotes plant growth and yield in Arabidopsis under salt stress. Plant Molecular Biology, 87, pp.615-631.
  2. Mehra, M., Gangwar, I. and Shankar, R., 2015. A deluge of complex repeats: the Solanum genome. Plos one, 10(8), p.e0133962.
  3. Jha, A., Panzade, G., Pandey, R. and Shankar, R., 2015. A legion of potential regulatory sRNAs exists beyond the typical microRNAs microcosm. Nucleic acids research, 43(18), pp.8713-8724.


  1. Paul, A., Jha, A., Bhardwaj, S., Singh, S., Shankar, R. and Kumar, S., 2014. RNA-seq-mediated transcriptome analysis of actively growing and winter dormant shoots identifies non-deciduous habit of evergreen tree tea during winters. Scientific Reports, 4(1), p.5932.
  2. Jha, A. and Shankar, R., 2014. MiRNAting control of DNA methylation. Journal of biosciences, 39, pp.365-380.
  3. Kumari, A., Singh, H.R., Jha, A., Swarnkar, M.K., Shankar, R. and Kumar, S., 2014. Transcriptome sequencing of rhizome tissue of Sinopodophyllum hexandrum at two temperatures. BMC genomics, 15, pp.1-17.


  1. Bhardwaj, J., Chauhan, R., Swarnkar, M.K., Chahota, R.K., Singh, A.K., Shankar, R. and Yadav, S.K., 2013. Comprehensive transcriptomic study on horse gram (Macrotyloma uniflorum): De novo assembly, functional characterization and comparative analysis in relation to drought stress. BMC genomics, 14, pp.1-18.
  2. Jha, A. and Shankar, R., 2013. miReader: discovering novel miRNAs in species without sequenced genome. PloS one, 8(6), p.e66857.
  3. Thakur, K., Chawla, V., Bhatti, S., Swarnkar, M.K., Kaur, J., Shankar, R. and Jha, G., 2013. De novo transcriptome sequencing and analysis for Venturia inaequalis, the devastating apple scab pathogen. PloS one, 8(1), p.e53937.


  1. Jha, A., Chauhan, R., Mehra, M., Singh, H.R. and Shankar, R., 2012. miR-BAG: bagging based identification of microRNA precursors.
  2. Gahlan, P., Singh, H.R., Shankar, R., Sharma, N., Kumari, A., Chawla, V., Ahuja, P.S. and Kumar, S., 2012. De novo sequencing and characterization of Picrorhiza kurrooa transcriptome at two temperatures showed major transcriptome adjustments. BMC genomics, 13(1), pp.1-21.


  1. Jha, A. and Shankar, R., 2011. Employing machine learning for reliable miRNA target identification in plants. BMC genomics, 12, pp.1-18.
  2. Jha, A., Mehra, M. and Shankar, R., 2011. The regulatory epicenter of miRNAs. Journal of biosciences, 36, pp.621-638.


  1. Shankar, R., 2011. The bioinformatics of next generation sequencing: a meeting report. Journal of molecular cell biology, 3(3), pp.147-150.
  2. Heikham, R. and Shankar, R., 2010. Flanking region sequence information to refine microRNA target predictions. Journal of biosciences, 35, pp.105-118.