My Mentors

Prof. Mitali Mukerji [Ph.D Guide]

Dr. Jerzy Jurka [At GIRI, California]

Prof. Alok Bhattacharya [Teacher at JNU]

Area of Interest

https://scbb.ihbt.res.in/SCBB_dept/Research_Area.php

Education

• Schooling: Kendriya Vidyalaya, Kankerbaugh, Patna, 1994


• B.Sc from University of Delhi, 1997


• M.Sc Biochemistry, Jamia Hamdard, New Delhi, 1999


• Post Graduate Advanced Diploma in Bioinformatics, JNU, New Delhi 2001


• Ph.D Bioinformatics/Biotechnology, IGIB, CSIR, Delhi, 2006.

Professional and Research Experience

• Researcher at Genetic Information Research Institute (GIRI), Mountain View, California, USA, 2007.


• Main Bioinformatician, BIOBASE International (Transfac fame), Bangalore, 2008.


• Faculty in Bioinformatics, Indian Institute of Advanced Research, Gandhinagar, Gujarat, 2009.


• Scientist, Biotechnology Division, CSIR-Institute of Himalyan Bioresources Technology, Palampur, H.P., India, 2010-2014.


• Senior Scientist, Biotechnology Division, CSIR-Institute of Himalyan Bioresources Technology, Palampur, H.P., India, 2014-2018.


• Principal Scientist, Biotechnology Division, CSIR-Institute of Himalyan Bioresources Technology, Palampur, H.P., India, 2018-2023.


• Senior Principal Scientist, Biotechnology Division, CSIR-Institute of Himalyan Bioresources Technology, Palampur, H.P., India, Since 2023.

Total Ph.Ds guided towards completion: 10

1. Dr. Ashwani Jha

2. Dr. Mrigaya Mehra

3. Dr. Vandana Chawla

4. Dr. Indu Gangwar

5. Dr. Ganesh Panzade

6. Dr. Ajay Kumar

7. Dr. Nitesh Kumar Sharma

8. Dr. Upendra Kumar Pradhan

9. Dr. Prakash Kumar

10. Dr. Ritu

Fellowships and Recognition

GATE qualified
CSIR-NET qualified
DBT fellowship
Hewlett-Packard fellowship
NIH, USA project fellow
DST/SERB Young Scientist Fast Track Grant Award.
Member, Board of Examiners, Central University of Bihar.
INSA-Australian Academy of Science Visiting Scientist Fellowship, 2012-13.
Visiting faculty and CDC committee member, Central University of Himachal Pradesh.
UGC ENCORE Faculty for University of Jammu.

Academic Referee/Reviewer for Journals/Publishers

Nucleic Acids Research
FEBS
RNA (Cold Spring Harbor Lab Publication)
Nature Scientific Reports
BMC Bioinformatics
Bioinformatics
CRC Press
BMC Genomics
Genomics, Proteomics and Bioinformatics
Genome
PLOS ONE
Genomics (Elsevier)
DATABASE (Oxford)
Plant Molecular Biology
Journal of Biosciences
Journal of Genetics
Molecular Breeding
PeerJ

Refree for National and International Grant Funding Agencies

• Reviewer for DFG, a National Funding agency of Germany.


• Reviewer for Department of Biotechnology (DBT), Government of India.


• Reviewer for Department of Science & Technology (DST), Government of India.

Course Director and Organizer

• National Bioinformatics Workshop on "The Bioinformatics of Next Generation Sequencing" June 17-18, 2010, CSIR-IHBT, Palampur. (~~The first DBT, Government of India Sponsored Workshop on NGS in India~~)


• National Bioinformatics Workshop on "Deep Bioinformatics Boot Camp", August 28-30, 2023, CSIR-IHBT, Palampur.
  


• National Bioinformatics Workshop on "Deep Bioinformatics Boot Camp - Season 2", February 18-21, 2025, CSIR-IHBT, Palampur.
  

Funded Project Grants Attracted:

1. 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.
   

2. Project titled "National Network Project of CSIR-IHBT, Palampur ", sanctioned for funding by the DBT, Government of India.
   

3. Project titled "The Himalayan Centre for High-throughput Computational Biology (HiCHiCoB) - BIC at CSIR-IHBT, Palampur (HP) ", sanctioned for funding by the DBT, Government of India.
   

4. Project titled "iPRESS: Integrated Plant REgulomics Software & Server", sanctioned for funding by the CSIR, India.
   

5. 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.
   

6. Project titled "Epigenetic and transcriptional regulation by small RNAs: a computational approach", sanctioned for funding by the Department of Science and Technology.
   

7. 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.
   

8. Project titled "Regulatory system Analysis with respect to microRNAs and development of related softwares and Servers", sanctioned for funding by DBT.
   

9. 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).
   

10. 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.
    

11. National 12th Five Year Plan Project for Computational Biology, "GENESIS" (2012-2017).

12. National 12th Five Year Plan Project for Epigenetics, "EpiHED" (2012-2017).

* Besides these projects, Co-PI in several other projects, funded by DBT and CSIR.

Selected Publications: (Full updated list available at Google Scholar link: Updated Publication )

† Equally contributed
* Corresponding Author

1. Perform search in Google Scholar Citations

1. Conference Poster: Decoding stress specific transcriptional regulation by causality aware Graph-Transformer deep learning
   Umesh Bhati, Akanksha Sharma, Sagar Gupta, Anchit Kumar, Upendra Kumar Pradhan, Ravi Shankar*,
   22nd Horizons in Molecular Biology Symposium, Max Planck Institute for Multidisciplinary Sciences, Gottingen, Germany, 2025 Find the conference poster here
   

2. Conference Poster: Decoding Plant TF-DNA Interactions Using PTFSpot and PTF-Vac: A Universal and Data-Independent Deep Learning Approach
   Sagar Gupta, Jyoti, Umesh Bhati, Veerbhan Kesarwani, Akanksha Sharma, Ravi Shankar*,
   22nd Horizons in Molecular Biology Symposium, Max Planck Institute for Multidisciplinary Sciences, Gottingen, Germany, 2025 Find the conference poster here
   

3. Genome-wide identification, characterization, and expression pattern analysis of the glyoxalase gene family in Phyllostachys pubescens during abiotic stresses
   Anita Kumari^†, Umesh Bhati^†, Ravi Shankar, Sudesh Kumar Yadav, Sudhir Kumar Sopory, Rohit Joshi*,
   BMC Plant Biology, 2025 Read the research article here
   

4. PTF-Vāc: An explainable and generative deep co-learning encoders-decoders system for ab-initio discovery of plant transcription factor binding sites
   Sagar Gupta, Jyoti, Umesh Bhati, Veerbhan Kesarwani, Akanksha Sharma, Ravi Shankar*,
   Plant Communications, 2025 Read the research article here
   

5. Conference Poster: The Genomics Armoury @ The Himalayan Centre for High-throughput Computational Biology
   Sagar Gupta, Umesh Bhati, Jyoti, Veerbhan Kesarwani, Akanksha Sharma, Anchit Kumar, Ravi Shankar*,
   Genomics India Conference, IISc, Bengaluru, 2025 Find the conference poster here
   

6. Deep-Learning on condition specific expression profiles reveal critical cytosines in gene regulation
   Veerbhan Kesarwani, Anchit Kumar, Akanksha Sharma, Sagar Gupta, Ravi Shankar*,
   bioRxiv, 2025 Read the research article here
   

7. Chemoinformatics exploration of synthetically accessible N-heterocycles: uncovering new antifungal lead candidates
   Shiv Shankar Gupta, Veerbhan Kesarwani, Ravi Shankar*, Upendra Sharma*,
   In Silico Pharmacology, 2025 Read the research article here
   

8. Transcriptional landscape illustrates the diversified adaptation of medicinal plants to multifactorial stress combinations linked with high altitude
   Manglesh Kumari, Prakash Kumar, Vishal Saini, Rohit Joshi, Ravi Shankar*, Rajiv Kumar*,
   Planta, 2025 Read the research article here
   

9. Decoding stress specific transcriptional regulation by causality aware Graph-Transformer deep learning
   Umesh Bhati, Akanksha Sharma, Sagar Gupta, Anchit Kumar, Upendra Kumar Pradhan, Ravi Shankar*,
   Current Plant Biology, 2025 Read the research article here
   

10. DMRU: Generative Deep-Learning to unravel condition specific cytosine methylation in plants
    Sagar Gupta, Anchit Kumar, Veerbhan Kesarwani, Umesh Bhati, Ravi Shankar*,
    Briefings in Bioinformatics (Accepted), 2025 Read the research article here
    

11. Comprehensive analysis of computational approaches in plant transcription factors binding regions discovery
    Jyoti, Ritu, Sagar Gupta, Ravi Shankar*,
    Heliyon, 2024 Read the research article here
    

12. 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 Read the research article here
    

13. 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 Read the research article here
    

14. 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 Read the research article here

15. 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 Read the research article here
    

16. 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 Read the research article here
    

17. 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 Read the research article here
    

18. 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 Read the research article here
    

19. 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 Read the research article here
    

20. DeepPlnc: Bi-modal Deep Learning for Highly Accurate Plant lncRNA Discovery
    Ritu^†, Sagar Gupta^†, Nitesh Kumar Sharma, Ravi Shankar*,
    Genomics, 2022 Read the research article here
    

21. 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 Read the research article here
    

22. 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 Read the research article here
    

23. 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 the research article here
    

24. 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 the research article here
    

25. 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 the research article here
    

26. Comparative transcriptome analysis of Rheum australe, an endangered medicinal herb, growing 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 the research article here
    

27. The dynamic aspects of RNA regulation (book chapter)
    Ravi Shankar*
    RNA-Based Regulation in Human Health and Disease, 2020 Read book here
    

28. 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, 2019 Read the research article here
    

29. Regulation of color transition in purple tea (Camellia sinensis)
    Manglesh Kumari, Shweta Thakur, Ajay Kumar, Robin Joshi, Prakash Kumar, Ravi Shankar & Rajiv Kumar
    Planta, 18 December 2019 Read the research article here
    

30. 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 Read the research article here
    

31. miR-876-3p regulates glucose homeostasis and insulin sensitivity by targeting adiponectin.
    Journal of Endocrinology, 2 July 2018 Read the research article here
    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*.
    

32. Transcriptome and Co-Expression Network Analyses Identify Key Genes Regulating Nitrogen Use Efficiency in Brassica juncea L.
    Scientific Reports, 2018;doi:10.1038/s41598-018-25826-6 Read the research article here
    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*.
    

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

34. Comparative Transcriptome Analysis of Chinary, Assamica and Cambod tea (Camellia sinensis) Types during Development and Seasonal Variation using RNA-seq Technology.
    Scientific Reports, 2016
    Ajay Kumar^†, Vandna Chawla^†, Eshita Sharma, Pallavi Mahajan, Ravi Shankar* and Sudesh Yadav*.
    

35. Genome-wide regulatory dynamics of G-Quadruplexes in human malaria parasite Plasmodium falciparum.
    Genomics, Oct 2016
    Deeksha Bhartiya^†, Vandna Chawla^†, Sourav Ghosh, Ravi Shankar, Niti Kumar
    

36. Transcriptome Analysis Reveals Candidate Genes involved in Blister Blight defense in Tea (Camellia sinensis (L) Kuntze).
    Scientific Reports, Jul 2016
    Kuldip Jayaswall, Pallavi Mahajan, Gagandeep Singh, Rajni Parmar, Romit Seth, Aparnashree Raina , Mohit k Swarnkar, Anil Singh, Ravi Shankar, Ram K Sharma.
    

37. Identifying wrong assemblies in de novo short read primary sequence assembly contigs.
    Journal Of Biosciences, September 2016
    Vandna Chawla, Rajnish Kumar and Ravi Shankar*.
    

38. Global de novo protein-protein interactome elucidates interactions of drought responsive proteins in horsegram (Macrotyloma uniflorum).
    Journal of proteome research; May 10, 2016
    Bhardwaj Jyoti^†, Gangwar Indu^†, Panzade Ganesh, Ravi Shankar*, Kumar Sudesh*.
    

39. Transcriptome analysis of stem wood of Nothapodytes nimmoniana (Graham) Mabb. identifies genes associated with biosynthesis of camptothecin, an anti-carcinogenic molecule.
    J Bioscience, Mar 2016
    Manjunath BL, Singh HR, Ravikanth G, Karaba NN, Shankar R, Kumar S, Uma Shankeer R
    

40. A legion of potential regulatory sRNAs exists beyond the typical microRNAs microcosm.
    (Nucleic Acids Research[NAR]), 2015
    Ashwani Jha, Ganesh Panzade, Rajesh Pandey and Ravi Shankar*.
    

41. 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

42. A Deluge of Complex Repeats: The Solanum Genome.
    PLOS ONE, 2015
    Mrigaya Mehra, Indu Gangwar, Ravi Shankar*.

43. 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

44. 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
    

45. miRNAting control of DNA methylation. Ashwani Jha and Ravi Shankar*. J biosci. 39 365-380.
    

46. 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.
    

47. Transcriptome sequencing of rhizome tissue of Sinopodophyllum hexandrum at two temperatures.
    A Kumari^†, HR Singh^†, A Jha, MK Swarnkar, R Shankar*, S Kumar*.
    BMC Genomics, 15 (1), 871.

48. 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

49. 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.
    

50. miR-BAG: Bagging Based Identification of MicroRNA Precursors.
    Ashwani Jha^†, Rohit Chauhan^†, Mrigaya Mehra^†, Heikham Russiachand Singh, Ravi Shankar* PLOS ONE 2012 7(9): e45782. doi:10.1371/journal.pone.0045782.
    

51. De novo sequencing and characterization of Picrorhiza kurrooa transcriptome at two temperatures showed major transcriptome adjustments.
    Parul Gahlan^†, Heikham Russiachand Singh^†, Ravi Shankar¹*, Niharika Sharma, Anita Kumari, Vandna Chawla, Paramvir Singh Ahuja, Sanjay Kumar²*.
    BMC Genomics, 13:126, March, 2012.
    

52. Employing machine learning for reliable miRNA target identificaiton in plants.
    Ashwani Jha and Ravi Shankar*.
    BMC Genomics,12:636, December, 2011.

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

54. EGLN1 involvement in high-altitude adaptation revealed through genetic analysis of extreme constitution types defined in Ayurveda.
    Aggarwal et al.
    PNAS, 107, 44, 2010

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

56. Flanking region sequence information to improve microRNA target prediction.
    Journal of Biosciences, Springer, 35(1), March 2010, 105-118
    Russiachand Heikham and Ravi Shankar*.

57. Involvement of repeats in non-random genomic divergence in 5' upstream regions of Human and Chimpanzee genes of different biological processes.
    HUGO's 13th international meeting on the Human Genome.
    The HUGO Journal (Genomic Medicine) (2008) 2:401-413.
    Chaurasia A, Shankar R, Mukerji M

58. Non-random genomic divergence in repetitive sequences of human and chimpanzee in genes of different functional categories.
    Mol Genet Genomics.2007 Apr;277(4):441-55.
    Shankar R, Chaurasia A, Ghosh B, Chekmenev D, Cheremushkin E, Kel A, Mukerji M

59. Evolution and distribution of RNA polymerase II regulatory sites from RNA polymerase III dependant mobile Alu elements.
    BMC Evolutionary Biology, BMC Evol Biol. 2004 Oct 4;4(1):37
    Shankar R, Grover D, Brahmachari S K, Mukerji M.

60. Repbase Reports. 2006, Vol. 6, Issue 10.
    Shankar R & Jerzy Jurka.