Dr. Ravi Shankar

Funded Project Grants Attracted As PI

• Project titled "Computation investigation into the role of alternative splicing in cellular differentiation, tissue regeneration, diseases and evaluation", sanctioned for funding by the DBT, Government of India.
• Project titled "National Network Project of CSIR-IHBT, Palampur " , sanctioned for funding by the DBT, Government of India.
• Project titled "The Himalayan Centre for High-throughput Computational Biology (HiCHiCoB)", sanctioned for funding by the DBT, Government of India.
• Project titled "iPRESS: Integrated Plant REgulomics Software & Server", sanctioned for funding by the CSIR, India.
• Project titled" Exploration of RBP-RNA interactions to reveal the post-transcriptional regulatory impact and development of related tools and resource server", sanctioned for funding by the Department of Biotechnology.
• Project titled "Epigenetic and transcriptional regulation by small RNAs: a computational approach", sanctioned for funding by the Department of Science and Technology.
• Project titled "Identification of De novo non-coding transcripts in Human Brain [HUNT]", Project Funded under "Encouraging and Motivating Pursuit of World Class Exploratory Research " [EMPOWER] CSIR, India.
• Project titled "Regulatory system Analysis with respect to microRNAs and development of related softwares and Servers", anctioned for funding by DBT.
• Project titled "Understanding plant-nematode interaction: Identification of plant and nematode genes involved in disease development", sanctioned for funding by Indian Council of Agricultural Research (ICAR).
• Project titled "Profiling and characterization of early phase differential mi-RNA(s) responsible for downstream development of insulin resistance in hMSC derived adipocytes", sanctioned for funding by DBT.
• National 12th Five Year Plan Project for Computational Biology,"GENESIS" (2012-2017).
• National 12th Five Year Plan Project for Epigenetics,"EpiHED" (2012-2017).

• PTF-Vac: Ab-initio discovery of plant transcription factors binding sites using deep co-learning encoders-decoders
  Sagar Gupta, Jyoti, Umesh Bhati, Veerbhan Kesarwani, Ravi Shankar*, bioRxiv, 2024
• Comprehensive analysis of computational approaches in plant transcription factors binding regions discovery
  Jyoti, Ritu, Sagar Gupta, Ravi Shankar*, Heliyon, 2024
• Genome wide identification of WUSHEL-related homeobox genes reveal their differential regulation during cold stress and in vitro organogenesis in Picrorhiza kurrooa
  Jhilmil Nath, Shubham Joshi, Sagar Gupta, Veerbhan Kesarwani, Ravi Shankar and Rohit Joshi*, In Vitro Cellular & Developmental Biology - Plant, 2024
• PTFSpot: deep co-learning on transcription factors and their binding regions attains impeccable universality in plants
  Sagar Gupta, Veerbhan Kesarwani, Umesh Bhati, Jyoti, Ravi Shankar*, Briefings in Bioinformatics, 2024
• Nutritional quality and microbial diversity of Chhurpe from different milk sources: An ethnic fermented food of high-altitude regions of the Western Himalayas
  Sahdev Choudhary^†, Kumari Shanu^†, Athrinandan S Hegde^†, Raman Kumar, Veerbhan Kesarwani, Ravi Shankar*, Sarita Devi*, Vidyashankar Srivatsan*, Discover Food, 2024
• Flavonoids from Aerial Parts of Cissampelos pareira L. as Antimalarial Agents: Computational Validation of Ethnopharmacological Relevance
  Patil Shivprasad Suresh^†, Veerbhan Kesarwani^†, Surekha Kumari, Ravi Shankar*, Upendra Sharma*, South African Journal of Botany, 2023
• miWords: Transformers based composite deep-learning for highly accurate discovery of pre-miRNA regions across plant genomes
  Sagar Gupta, Ravi Shankar*, Briefings in Bioinformatics, 2023
• Bisbenzylisoquinolines from Cissampelos pareira L. as Antimalarial Agents: Molecular Docking, Pharmacokinetics Analysis, and Molecular Dynamic Simulation Studies
  Patil Shivprasad Suresh^†, Veerbhan Kesarwani^†, Surekha Kumari, Ravi Shankar*, Upendra Sharma*, Computational Biology and Chemistry, 2023
• De novo transcriptome based insights into secondary metabolite biosynthesis in Malaxis acuminata (Jeevak) - A therapeutically important orchid
  Paromik Bhattacharyya^†, Tanvi Sharma^†, Abhinandan Yadav^†, Lucy Lalthafamkimi, Ritu, Mohit Kumar Swarnkar, Robin Joshi, Ravi Shankar*, Sanjay Kumar*, Frontiers in Plant Science, 2022
• Time-series RNA-Seq transcriptome profiling reveals novel insights about cold acclimation and de-acclimation processes in an evergreen shrub of high altitude
  Nikita Rathod^†, Prakash Kumar^†, Nandita Mehta, Mohit Kumar Swarnkar, Ravi Shankar*, Amit Chawla*, Scientific Reports, 2022
• DeepPlnc: Bi-modal Deep Learning for Highly Accurate Plant lncRNA Discovery
  Ritu^†, Sagar Gupta^†, Nitesh Kumar Sharma, Ravi Shankar*, Genomics, 2022
• RBPSpot: Learning on Appropriate Contextual Information for RBP Binding Sites Discovery
  Nitesh Kumar Sharma^†, Sagar Gupta, Ashwani Kumar, Prakash Kumar, Upendra Kumar Pradhan, Ravi Shankar*, iScience, 2021
• In-depth assembly of organ and development dissected Picrorhiza kurroa proteome map using mass spectrometry
  Manglesh Kumari^†, Upendra Kumar Pradhan, Robin Joshi, Ashwani Punia, Ravi Shankar, Rajiv Kumar*, BMC Plant Biology, 2021
• 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
• 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
• 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