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.

Total Ph.Ds guided towards completion: 9

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

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.

Talks and Poster Presentations Delivered

1. "MiRNA: The "Little Master" of Gene Regulation", Indian Institute of Technology (IIT), Mandi. April 8, 2011.

2. "A MicroRNA target refinement method and tool", Indian Institute of Integrative Medicine, Jammu, June 26, 2009.

3. "AF-1: Finding Alus in Primate Genomes", Lecture Delivered at Faculty of Technology and Applied Mathematics, MS University, Baroda, Gujarat, 2008.

4. "Alu repeats as a caravan to regulatory house". Poster presented at BioTech 2004,India International Center, N. Delhi, 2004.

5. "Alu repeats as a caravan to regulatory house", A presentation during Celebration of 50 years of Triple Helix. Vigyan Bhawan, New Delhi. 2004. (Presentation given before Honorable President of India, Dr. APJ Kalam.)

6. "Strategies in Regulatory Elements Finding" at CeBiTech. The Bioinformatics Graduate School, Bielefeld, Germany. Research work presented on invitation from Beilefeld University, Germany (2003).

7. "Motif Finding and Statistics." at Informatics N. Delhi-2002.

8. "The HMM." at Informatics, N. Delhi-2002.

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 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, IHBT, CSIR, Palampur. (~~The first DBT, Government of India Sponsored Workshop on NGS in India~~)

Funded Project Grants Attracted:

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

2. Project titled "The Himalayan Centre for High-throughput Computational Biology (HiCHiCoB)", sanctioned for funding by the DBT, Government of India.
   

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

4. 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.
   

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

6. 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.
   

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

8. 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).
   

9. 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.
   

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

11. 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. miR-876-3p regulates glucose homeostasis and insulin sensitivity by targeting adiponectin.
   Journal of Endocrinology, 2 July 2018 Read accepted preprint 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*.
   

2. 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 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*.
   

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

4. 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*.
   

5. 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
   

6. 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.
   

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

8. 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*.
   

9. 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
   

10. 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*.
    

11. 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

12. A Deluge of Complex Repeats: The Solanum Genome. (Accepted at PLOS ONE)Mrigaya Mehra, Indu Gangwar, Ravi Shankar*.

13. 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

14. 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
    

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

16. 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.
    

17. 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.

18. 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

19. 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.
    

20. 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.
    

21. 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.
    

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

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

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

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

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

27. 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

28. 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

29. 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.

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