Hukam C. Rawal, Ph.D.
Post-doctoral Fellow (Bioinformatics) (2023-2025), University of Nevada, Reno, Nevada, US
Ph.D. (Bioinformatics) (2023), Jamia Hamdard, New Delhi, India
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Most Recent Publications:
Plank H.B., Zhang X., Rawal H.C., Yu J., Zhou C., Chen Q., and Zhou T., Dissecting the small RNA code of inflammatory bowel disease. Molecular Medicine (accepted).
Shi, J., Zhang, X., Cai, C., Liu, S., Yu, J., James, E., Liu, L., Emery, B., McMurray, M., Torres-Arce, E., Rawal, H.C., Ramsay, J., Kunisaki, J., Zhou, C., Milstone, D.S., Patti, M.E., Yang, X., Jenkins, T., Quinlan, A.R.. Cairns, B.R., Schimmel, P., Hotaling, J.M., Aston, K,I., Zhou, T., Chen, Q. Conserved shifts in sperm small non-coding RNA profiles during mouse and human aging. The EMBO Journal (in press).
Li, X., Hernandez, R., Zhang, X., Tang, S., Yuan, X., Wu, J., Pham, K., Rawal, H.C., Heinrich, E.C., Zhang, S., Chen, Q., Zhou, T., Zhou, C. A cholesterol-responsive hepatic tRNA-derived small RNA regulates cholesterol homeostasis and atherosclerosis development. Nature Communications. 16(1): 11043 (2025). doi: 10.1038/s41467-025-67387-z
Rawal, H.C., Pal, R.K., Mondal, T.K. Identification and characterization of tissue- and stress-specific circular RNAs (circRNAs) of tea to generate the largest tea circRNAs data repository. Scientific Reports. 15(1): 36999 (2025). doi: 10.1038/s41598-025-94480-6
Rawal, H.C., Chen, Q., Zhou, T. FUSION: a family-level integration approach for robust differential analysis of small non-coding RNAs. Bioinformatics. 41(10): btaf526 (2025). doi: 10.1093/bioinformatics/btaf526
A research fellow with over 17 years’ experience in Bioinformatics based research covering the areas of comparative genomics, non-coding RNAs analysis, genome assembly and analysis, transcriptomics, SNP genotyping, developing standardized methodologies for computational analysis, analyzing/presenting the data, and writing scientific reports/articles.
Research Interest:
Research Interest:
Analysis of non-coding RNAs, Comparative genomics, Data mining and bioinformatics data analysis, Genome assembly and analysis.
Education:
Education:
Ph.D. (Bioinformatics) (2023), Jamia Hamdard, New Delhi, India
M.Sc. Bioinformatics (2007), Jamia Millia Islamia, New Delhi, India
B.Sc. Life Sciences (2005), University of Delhi, New Delhi, India
Professional Experience:
Professional Experience:
Post-doctoral Fellow (Bioinformatics) at Physiology and Cell Biology Department, School of Medicine, University of Nevada, Reno, Nevada, US (November 2023 - October 2025).
Principal Project Associate at ICAR-National Institute for Plant Biotechnology (NIPB), New Delhi, India in a DBT-funded project (January 2022 - October 2023).
Bioinformatics Research Associate at ICAR-NIPB, New Delhi, India in an NTRF-funded project on “Tea genome sequencing” (March 2020 - October 2021).
Research Associate in various ICAR or DBT-funded projects at ICAR-NIPB, New Delhi, India (March 2013 - February 2020).
Senior Research Fellow in an ICAR-funded project on “Bioinformatics and Comparative Genomics” at ICAR-NIPB, New Delhi, India (January 2010 - March 2013).
Research Intern at CSIR - Intellectual Property Management Division (IPMD), New Delhi, India (July 2008 - January 2010).
Bioinformatics Research Trainee at Biomedical Informatics Centre, Department of Biophysics, AIIMS, New Delhi, India (July 2007 - July 2008).
Research Profile:
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.
Thesis Title: Comparative analysis of non-coding RNAs (miRNAs, tRFs and circRNAs) of rice under salinity stress
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).
Peer Review Experience:
Peer Review Experience:
Reviewed manuscripts for the following journals:
Genomics
BMC Genomics
Scientific Reports
Frontiers in Genetics
Frontiers in Plant Science
Molecular Biology Reports
Industrial Crops and Products
Functional & Integrative Genomics
Environmental and Experimental Botany
International Journal of Biological Macromolecules
Physiological and Molecular Plant Pathology
Plant Physiology and Biochemistry
Microbiological Research
BMC Plant Biology
Brain Disorders
Plant Methods
Plant Science
Plant Stress
Genetica
Heliyon
Professional Services, Training and Other Experiences:
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.
Awards and Honors:
Awards and Honors:
Best poster presentation award in International Symposium on “Advances in Plant Biotechnology and Nutritional Security” (APBNS-2022), New Delhi, India, April 28-30, 2022
Best poster presentation award in 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.
GATE 2009
CSIR Diamond Jubilee Research Interns Award 2008-2010
Conference Presentation:
Conference Presentation:
Contributed Paper Presentation in International Conferences:
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:
Hukam C. Rawal, Qi Chen, Tong Zhou. Improving differential expression analysis of sncRNAs through family-level integration in paired samples. International Conference on Intelligent Biology and Medicine (ICIBM 2025), Columbus, OH, USA, August 3-5, 2025.
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.
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.
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.
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.
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.
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.
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.
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:
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.
Interdisciplinary Science Conference on Recent Trends in Research in Biological Sciences, held at Jamia Millia Islamia, New Delhi, India, December 7, 2007.
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.
Figures from my Published Work
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