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Publications

† First Authors * Corresponding Author

2021

  1. miR-Hy: A robust shallow-deep learning system for plant microRNA discovery
    Sagar Gupta† and Ravi Shankar*
    Communicated, 2021  
  2. DeepPlnc: Discovering plant lncRNAs through multimodal deep learning on sequential data
    Ritu†, Sagar Gupta†, Nitesh Kumar Sharma, Ravi Shankar*
    Communicated, 2021  
  3. RBPSpot: Learning on Appropriate Contextual Information for RBP Binding Sites Discovery
    Nitesh Kumar Sharma†, Sagar Gupta, Prakash Kumar, Ashwani Kumar, Upendra Kumar Pradhan, Ravi Shankar*
    bioRxiv, 2021  Read research article here 
    Accepted
  4. miRbiom: Machine-Learning on Bayesian Causal Nets of RBP-miRNA interactions successfully predicts miRNA profiles
    Upendra Kumar Pradhan†, Nitesh Kumar Sharma†, Prakash Kumar, Ashwani Kumar, Sagar Gupta, Ravi Shankar*
    PLoS ONE, 2021  Read research article here 
  5. The first draft genome of Picrorhiza kurrooa, an endangered medicinal herb from Himalaya
    Tanvi Sharma†, Nitesh Kumar Sharma†, Prakash Kumar, Ganesh Panzade, Tanuja Rana, Mohit Kumar Swarnkar, Anil Kumar Singh, Dharam Singh, Ravi Shankar*, Sanjay Kumar*
    Scientific Reports, 2021  Read research article here 
  6. In Silico Approach for Identifying Natural Lead Molecules Against SARS-COV2
    Shiv Shankar Gupta†, Ashwani Kumar†, Ravi Shankar*, Upendra Sharma*
    Journal of Molecular Graphics and Modelling, 2021  Read research article here

2020

  1. Comparative transcriptome analysis of Rheum australe, an endangered medicinal herb, in its natural habitat and those grown in controlled growth chambers
    Deep Mala†, Supriya Awasthi†, Nitesh Kumar Sharma, Mohit Kumar Swarnkar, Ravi Shankar*, Sanjay Kumar*
    Scientific Reports, 2020  Read research article here
  2. The dynamic aspects of RNA regulation (book chapter)
    Ravi Shankar†
    RNA-based Regulation in Human Health and Disease. Elsevier (2020), doi.org/10.1016/B978-0-12-817193-6.00004-2  Book link here

2019

  1. Regulation of color transition in purple tea (Camellia sinensis)
    Manglesh Kumari†, Shweta Thakur, Ajay Kumar, Robin Joshi, Prakash Kumar, Ravi Shankar, Rajiv Kumar*
    Planta (2019) 251: 35, doi.org/10.1007/s00425-019-03328-7  Read research article here
  2. Plant Regulomics Portal (PRP): A comprehensive integrated regulatory information and analysis portal for plant genomes
    Ganesh Panzade†, Indu Gangwar, Supriya Awasthi, Nitesh Sharma, Ravi Shankar*
    Database, Volume 2019, 2019, baz130, doi.org/10.1093/database/baz130  Read research article here
  3. 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
    Nisha Dhiman†, Nitesh Kumar Sharma†, Pooja Thapa†, Isha Sharma, Mohit Kumar Swarnkar, Amit Chawla, Ravi Shankar* & Amita Bhattacharya*
    Scientific Reports, 2019;doi:10.1038/s41598-019-49446-w Read research article here

2018

  1. miR-876-3p regulates glucose homeostasis and insulin sensitivity by targeting adiponectin.
    Sujith Rajan, Ganesh Panzade, Ankita Srivastava, Kripa Shankar, Rajesh Pandey, Abhishek Gupta, Durgesh Kumar, Salil Varshney, Muheeb beg, Raj Kumar Mishra, Ravi Shankar* and Anil Gaikwad*
    Journal of Endocrinology, 2 July 2018 Read research article here
  2. Transcriptome and Co-Expression Network Analyses Identify Key Genes Regulating Nitrogen Use Efficiency in Brassica juncea L.
    Parul Goel†, Nitesh Kumar Sharma†, Monika Bhuria, Vishal Sharma, Rohit Chauhan, Shivalika Pathania, Mohit Kumar Swarnkar, Vandna Chawla, Vishal Acharya, Ravi Shankar* and Anil Kumar Singh*
    Scientific Reports, 2018;doi:10.1038/s41598-018-25826-6 Read research article here

2017

  1. Detecting the Molecular System Signatures of Idiopathic Pulmonary Fibrosis through Integrated Genomic Analysis
    Indu Gangwar†, Nitesh Kumar Sharma†, Ganesh Panzade, Supriya Awasthi, Anurag Agrawal, and Ravi Shankar*
    Scientific Reports, 2017;doi:10.1038/s41598-017-01765-6 Read research article here

2016

  1. Comparative Transcriptome Analysis of Chinary, Assamica and Cambod tea (Camellia sinensis) Types during Development and Seasonal Variation using RNA-seq Technology.
    Ajay Kumar†, Vandna Chawla†, Eshita Sharma, Pallavi Mahajan, Ravi Shankar*, Sudesh Kumar Yadav*
    Scientific Reports, 2016;doi:10.1038/srep37244  Read research article here
  2. Genome-wide regulatory dynamics of G-Quadruplexes in human malaria parasite Plasmodium falciparum.
    Deeksha Bhartiya†, Vandna Chawla†, Sourav Ghosh, Ravi Shankar, Niti Kumar
    Genomics, Oct 2016, doi.org/10.1016/j.ygeno.2016.10.004   Read research article here.
  3. Transcriptome Analysis Reveals Candidate Genes involved in Blister Blight defense in Tea (Camellia sinensis (L) Kuntze)
    Kuldip Jayaswall, Pallavi Mahajan, Gagandeep Singh, Rajni Parmar, Romit Seth, Aparnashree Raina , Mohit k Swarnkar, Anil Singh, Ravi Shankar, Ram K Sharma
    Scientific Reports, 2016 Jul 28;6:30412. doi: 10.1038/srep30412. Read research article here
  4. Identifying wrong assemblies in de novo short read primary sequence assembly contigs.
    Vandna Chawla, Rajnish Kumar, and Ravi Shankar*.
    Journal Of Biosciences, September 2016, Volume 41, Issue 3.
    Read research article here
    Article Altmetric Score = 15. Click here for article popularity details.
  5. Global de novo protein-protein interactome elucidates interactions of drought responsive proteins in horsegram (Macrotyloma uniflorum).
    Bhardwaj Jyoti†, Gangwar Indu†, Panzade Ganesh, Shankar Ravi*, Kumar Sudesh*.
    Journal of proteome research; May 10, 2016; doi:10.1021/acs.jproteome.5b01114
    Click here to read the article.
  6. Transcriptome analysis of stem wood of Nothapodytes nimmoniana (Graham) Mabb. identifies genes associated with biosynthesis of camptothecin, an anti-carcinogenic molecule.
    Manjunath BL, Singh HR, Ravikanth G, Karaba NN, Shankar R, Kumar S, Uma Shankeer R.
    J Biosci. 2016 Mar;41(1):119-31.  Click here to read the article.

2015

  1. Expression of SOD and APX genes positively regulates secondary cell wall biosynthesis and promotes plant growth and yield in Arabidopsis under salt stress. Amrina Shafi, Rohit Chauhan, Tejpal Gill, Mohit K. Swarnkar, Yelam Sreenivasulu, Sanjay Kumar, Neeraj Kumar, Ravi Shankar, Paramvir Singh Ahuja, Anil Kumar Singh Plant Mol. Biol., April 2015, Volume 87, Issue 6, pp 615-631   Click here to read the article.

  2. A Deluge of Complex Repeats: The Solanum Genome. Mrigaya Mehra, Indu Gangwar and Ravi Shankar*. PLoS ONE 10(8): e0133962. doi:10.1371/journal.pone.0133962 
    Click here to read the article.

  3. A legion of potential regulatory sRNAs exists beyond the typical microRNAs microcosm.,
    Ashwani Jha, Ganesh Panzade, Rajesh Pandey and Ravi Shankar*.
    Nucleic Acids Research, 2015, doi: 10.1093/nar/gkv871 
    Click here to read the article.
    Article Altmetric Score = 13

2014

  1. Poster: Novel to Reference Free miRNA Discovery: NGS powered miRNA discovery with miR-BAG and miReader. Ashwani Jha, Jennifer Clancy, Thomas Preiss Ravi Shankar*. 35th Annual Lorne Genome Conference 2014 held in Lorne, Victoria, Australia, February 16–18, 2014
    Related Reference : http://genomebiology.com/2014/15/4/304

  2. RNA-seq-mediated transcriptome analysis of actively growing and winter dormant shoots identifies non-deciduous habit of evergreen tree tea during winters.
    Asosii Paul†, Ashwani Jha†, Shruti Bhardwaj, Sewa Singh, Ravi Shankar*, Sanjay Kumar*.
    Sci. Rep., 2014. doi:10.1038/srep05932. Read research article here

  3. miRNAting control of DNA methylation. Ashwani Jha and Ravi Shankar*. J Biosci. 39 365-380, June 2014.
    Read research article here.

  4. Transcriptome sequencing of rhizome tissue of Sinopodophyllum hexandrum at two temperatures. A Kumari, HR Singh, A Jha, MK Swarnkar, R Shankar, S KumarA Kumari, HR Singh, A Jha, MK Swarnkar, R Shankar*, S Kumar*.
    BMC Genomics, 15 (1), 871  Read research article here

2013

  1. Comprehensive Transcriptomic Study on horse gram (Macrotyloma uniflorum): De novo Assembly, Functional Characterization and Comparative Analysis in Relation to Drought Stress.
    Jyoti Bhardwaj†, Rohit Chauhan†, Mohit Swarnkar, R Chahota, R Shankar* and S Yadav*.
    BMC Genomics. 2013 14:647, September 2013.   Read research article here

  2. miReader: Discovering novel miRNAs in species without sequenced genome.
    Ashwani Jha† and Ravi Shankar*†
    PLoS ONE 8(6): e66857. doi:10.1371/journal.pone.0066857  Read research article here
    Download miReader Download @ souceforge

  3. De-novo sequence assembly and transcriptome analysis of Venturia inaequalis , the deadly apple scab pathogen.
    Karnika Thakur†, Vandna Chawla†, Shammi Bhatti, Mohit Kumar Swarnkar, Jagdeep Kaur, Ravi Shankar*, Gopaljee Jha*.
    PLoS ONE 8(1): e53937. doi:10.1371/journal.pone.0053937  (PLOS dedicated this article to mark the rise of Indian Science, celebrating National Science Day.) Read research article here

2012

  1. miR-BAG: Bagging Based Identification of MicroRNA Precursors.
    Ashwani Jha†, Rohit Chauhan†, Mrigaya Mehra†, Heikham Russiachand Singh, Ravi Shankar* PLoS ONE 7(9): e45782. doi:10.1371/journal.pone.0045782
    Read research article here

  2. De novo sequencing and characterization of Picrorhiza kurrooa transcriptome at two temperatures showed major transcriptome adjustments.
    Parul Gahlan†, Heikham Russiachand Singh†, Ravi Shankar*, Niharika Sharma, Anita Kumari, Vandna Chawla, Paramvir Singh Ahuja, Sanjay Kumar*.
    BMC Genomics, 13:126, March, 2012. Read research article here

2011

  1. Employing Machine Learning for Reliable miRNA target Identification in Plants.
    Ashwani Jha and Ravi Shankar*.
    BMC Genomics 2011, 12:636.
    Read research article here

  2. The Regulatory Epicenter of microRNAs.
    Ashwani Jha, Mrigaya Mehra, Ravi Shankar*.
    J Biosci. 2011 Sep;36(4):621-38.
    Read research article here

2010

  1. "The Bioinformatics of Next Generation Sequencing": A meeting report.
    Journal of Mol. Cell Biol. (Oxford University Press) 2010.
    Ravi Shankar*.
    Read article here

  2. Flanking region sequence information to refine microRNA target predictions.
    Heikham R and Shankar R* J. Biosci. 2010 35 105-118.Read research article here