Research Profile:

• My current research focuses on identifying and analyzing non-coding RNAs to uncover their roles in molecular mechanisms linked to different diseases and disorders in diverse organisms. 

• Prior to this, I worked and gained experience in several areas of computational biology, including the identification and analysis of non-coding RNAs in plants, genome assembly and analysis, comparative genomics, transcriptomics, SNP genotyping, and developing standardized methodologies for computational analysis. 

• My PhD research centered on the comparative analysis of non-coding RNAs, such as miRNAs, tRFs, and circRNAs, which led to a growing interest in the study of non-coding RNAs. 

• I strongly believe in the importance of standardized and consistent practices when conducting comparative analyses and studies to address biological challenges across different kingdoms of life.

PhD Thesis

Thesis Title: Comparative analysis of non-coding RNAs (miRNAs, tRFs and circRNAs) of rice under salinity stress

Major Findings:

• Standardized methodologies, termed as miRPreM and tiRPreM, for the prediction of miRNAs and tRFs, respectively:

• Organism-specific reference genome • Presence in all the replicates • Normalized read count support • Perfect match search • At least   two tools with multiple runs for high-confidence prediction

• Demonstrated :

• The existence of species-specific miRNAs 

• Enhanced number of miRNAs (from published chickpea data)

• Prediction of tRFs from the sRNA data previously used for miRNA prediction only

Outcomes:

• First ever genome-specific study for the identification and analysis of miRNAs, tRFs and circRNAs under salinity stress

• First ever comparative study of miRNAs and tRFs from contrasting rice genotypes - IR29, Nonabokra and Oryza coarctata, under salinity stress at  reproductive stage

• Significant number of DE miRNAs , tRFs and circRNAs 

• Salt-stress related miRNA-mRNA-circRNA  and tRF-mRNA-circRNA modules to investigate

• Significant number of salinity stress responsive genes from salt-sensitive and salt-tolerant rice cultivars

Publications: 

1. Rawal, H.C., Ali, S., Mondal, T.K. miRPreM and tiRPreM: Improved methodologies for the prediction of miRNAs and tRNA-induced small non-coding RNAs for model and non-model organisms. Briefings in Bioinformatics. 23(1): bbab448b. doi: 10.1093/bib/bbab448 (2021)

2. Rawal, H.C., Ali, S., Mondal, T.K. Role of non-coding RNAs against salinity stress in Oryza species: Strategies and challenges in analyzing miRNAs, tRFs and circRNAs. International Journal of Biological Macromolecules. 242(3):125172. doi: 10.1016/j.ijbiomac.2023.125172. (2023).

Professional Services, Training and Other Experiences:

►Served as a judge for the Outstanding Graduate Researcher Award and the Research, Travel, and Materials Grant Program at the University of Nevada, Reno, evaluating and providing feedback for the 2024 and 2025 awardees.

►Trained Plant Genomics Scientists and Faculties in 21 days training on “Next Generation Sequencing and its Applications in Crop Sciences” conducted by ICAR-NRCPB, New Delhi under Centre for Advanced Faculty Training (CAFT) program in 2017, 2018, 2019 and 2022.

►UNIVERSITY OF TORONTO'S NON-CREDIT ONLINE Course on “An introduction to computer programming using Python”.

►Short Term course on “PHP & MySQL” from IT Brain Shapers, New Delhi, India.

Conference Presentation: 

Contributed Paper Presentation in International Conferences:

1. Hukam C. Rawal, N. K. Singh, T. R. Sharma. Computational Analysis of Antifungal-Pathogenesis related Proteins in Different Plant Species. International Conference on Statistics and Informatics in Agricultural Research, New Delhi, India, December 18-20, 2012.

Poster/Abstract Presentation in International Conferences: 

1. Hukam C. Rawal, Shakir Ali, Tapan Kumar Mondal. miRNAs, tRFs and circRNAs: a new team of regulatory non-coding RNAs in the fight against salinity stress in rice. International Conference on  Food and Nutritional Security (iFANS2023), NABI-CIAB, Mohali, India, January 6-9, 2023.

2. Hukam C. Rawal, Shakir Ali, Tapan Kumar Mondal.Identification and analysis of salt-stress responsive circRNAs from salt-susceptible and salt-tolerant rice genotypes. 43rd Annual Meeting of PTCA(I) & International Symposium on “Advances in Plant Biotechnology and Nutritional security” (APBNS-2022), New Delhi, India, April 28-30, 2022.

3. Hukam C. Rawal, Shakir Ali, Tapan Kumar Mondal. tRNA induced non-coding RNA Prediction Methodology (tiRPreM) for model and non-model organism. 3rd International Conference on “Global Initiative in Agricultural, Forestry and Applied Sciences for Food Security, Environmental Safety and Sustainable Development (GIAFAS-2021)”, Dehradun, India, October 17-18, 2021.

4. Hukam C. Rawal, Shakir Ali, Tapan Kumar Mondal. miRPreM : miRNA Prediction Methodology for model or non-model organism using Oryza coarctata, a wild rice as a case study. Bioinformatics: from Algorithms to Applications (BiATA) 2021 conference held virtually on July 12-15, 2021 at the Saint Petersburg State University, Russia. 

5. Hukam C. Rawal, Kanti Kiran, Himanshu Dubey, Rajdeep Jaswal, T. R. Sharma. Applications of PERL Scripts in Accelerating Genome Data Analysis. National Symposium on Germplasm to Genes: Harnessing Biotechnology for Food Security and Health, New Delhi, India, August 9-11, 2015.

6. Hukam C. Rawal, N. K. Singh, T. R. Sharma. CGPSA- Comparative Genomics Methodology for Phylogenetic and Synteny Analysis of gene families in different Plant species. 3rd World Congress on Biotechnology, Hyderabad, India, September 13-15, 2012.

7. Hukam C. Rawal, N.K. Singh, T.R. Sharma. Genome wide distribution and comparative analysis of plant defense response genes. International Conference on Plant Biotechnology for food security: New Frontiers, New Delhi, India, February 21-24, 2012.

8. Hukam C. Rawal, Pallavi Manral, Janesh Kumar, Tej P. Singh, Punit Kaur, 2007, Differentially Expressed Proteins in Multiple Sclerosis from Cerebrospinal Fluid: Identification, Analysis and Homology Modeling of Espin and Glypican. International Conference on Bioinformatics, (InCoB 2007), Hong Kong, August 27-30, 2007.  

Conferences\ Workshops\ Seminars attended: 

1. Two days workshop (online) on Analysing metagenomic assemblies using MGnify, conducted virtually at BiATA'21, the Saint Petersburg State University in Saint Petersburg, Russia, July 12-15, 2021. 

2. Interdisciplinary Science Conference on Recent Trends in Research in Biological Sciences, held at Jamia Millia Islamia, New Delhi, India, December 7, 2007.

3. Two Days Workshop on Recent Advances in Computational Biology and Structural Based Drug Designing, conducted at 3rd World Congress on Biotechnology, Hyderabad, India, September 13-15, 2012.