Dr. Atul Kumar Upadhyay

Associate Professor

Specialization

Computational Biology, Genomics and Plant Biotechnology

Email

atul.upadhyay@thapar.edu; Date of Joining: 25-07-2019

Specialization

Computational Biology, Genomics and Plant Biotechnology

Email

atul.upadhyay@thapar.edu; Date of Joining: 25-07-2019

Google Scholar:

https://scholar.google.co.in/citations?user=Zu1b2NUAAAAJ&hl=en

LinkedIn:

https://www.linkedin.com/in/atul-kumar-upadhyay-6977b617/?originalSubdomain=in

Biography

  • Dr. Atul Kumar Upadhyay has been serving as an Associate Professor in the Department of Biotechnology at the Thapar Institute of Engineering and Technology, Patiala. (2026 to Cont..)
  • Served as an Assistant Professor in the Department of Biotechnology at the Thapar Institute of Engineering and Technology, Patiala. (2019 to 2026).
  • Worked as an Assistant Professor at Lovely Professional University, Ludhiana, Punjab (2016-2019).
  • He has completed his Ph.D. degree in Life Sciences from the National Centre for Biological Sciences, Bangalore, and the Tata Institute of Fundamental Research, a deemed university in Mumbai (2010 - 2016).
  • His research work involves NGS based understanding of genome and transcriptome of medicinal plants to understand the societal importance of the selected secondary metabolites and food allergy.
  • He has also worked on computational approaches to understand protein sequence-structure-function relationships.
  • He employs machine-learning approaches and Artificial Intelligence (AI) algorithms to classify biological data and infer their functions.

Education

  • Ph.D. Life Sciences, National Centre for Biological Sciences, Bangalore, India (2015)
  • M. Sc (Agri.) Plant Biotechnology, University of Agricultural Sciences, Dharwad, India (2010)
  • B. Sc. Agri. (Honors.), Chandra Shekhar Azad University of Agriculture & Technology, Kanpur, India (2007)

Teaching Interests

  • Bioinformatics
  • Genomics and proteomics
  • Plant Biotechnology
  • Molecular Biology
  • Bio-computing

Research Interest

  •  Genomics-driven understanding of Plant systems, Food allergy
  • Cancer genomics and cure
  • Computational approaches for DNA and Protein sequence-structure-function relationships 

Projects

S. No. 

Year

Project Title

Role

Funding Agency

Funding

1.

2026 to 2028

Synthesis and Functionalization of MXene-Based Biosensors for Comprehensive Allergen/Toxin Detection: Integrating Computational Prediction and Advanced Nanomaterials

Principal Investigator (PI)

ACT Centre, TIET

₹11.50 Lakhs

2.

2026 to 2028

AI-Powered Cheminformatics Pipeline for Discovering Neuroprotective Bioactive Compounds from Endophytic Fungal Metabolomes

Co-Principal Investigator (Co-PI)

TIET–UQ Centre of Excellence (CoDSaI)

₹9.90 Lakhs

3.

2020 to 2022

Genome and Transcriptome Enabled Identification of Novel Food Allergens and Decoding Their Possible Role in Human Diseases

Principal Investigator (PI)

TIET Seed Money Grant

₹4.50 Lakhs

Publication

SCI papers:

  1. Prasad, D., Mohanty, D., Qadri, O.S., Handa, V. and Upadhyay, A.K. (2026), Insights into amino acid usage patterns among allergenic and non-allergenic proteins to develop biomarkers for early detection of food-allergenic proteins. J Sci Food Agric, 106: 2380-2387. https://doi.org/10.1002/jsfa.70345
  2. Basu, T., Upadhyay, A.K. In silico approaches to identify therapeutic drug targets against COVID-19: a detailed review with a case study. In Silico Pharmacol. 13, 162 (2025). https://doi.org/10.1007/s40203-025-00447-w
  3. Pandey, A., Kumar Upadhyay, A. Machine Learning Prediction of 3D Domain Swapping Proteins in Medicinal Plants. J. Vis. Exp. (222), e68519, doi:10.3791/68519 (2025).
  4. Bhatia, A., Upadhyay, A. K., & Sharma, S. (2025). Deciphering the structural dynamics of Argonaute (AGO)-mediated gene silencing of miR-21-5p, miR-221-3p, miR-126-3p, miR-34a-5p and their role as potential biomarkers in lung cancer. Nucleosides, Nucleotides & Nucleic Acids, 1–34. https://doi.org/10.1080/15257770.2025.2535749 
  5. Gujjar, R. S., Kumar, R., Goswami, S. K., Tiwari, R. K., Kumar, A., Kumari, M., Singh, S. P., Kumar, R., Lal, M. K., Upadhyay, A. K., & Atta, K. Approaches to enhance bioethanol production from sugarcane biomass by manipulating the lignin content. Biofuels, Bioproducts and Biorefining. https://doi.org/10.1002/bbb.70018
  6. Bhatia, A., Upadhyay, A. K., Garg, K., Chopra, V., & Sharma, S. (2025). Analyzing the role of genetic variants in microRNAs and its role as a modulator towards Chronic Obstructive Pulmonary disease (COPD) susceptibility in North Indian population. Gene952, 149413.
  7. Chugh, R., Handa, V., & Upadhyay, A. K. (2025). In silico identification and structural insight of allergens in Pleurotus ostreatus. Journal of the science of food and agriculture.
  8. Puneet, Singh, R., Bhardwaj, V., Upadhyay A. K., et al. Haptoglobin Polymorphisms: Translational Insights and Regenerative Potential in Disease Management. Regen. Eng. Transl. Med. (2025). https://doi.org/10.1007/s40883-025-00391-3
  9. Satapathy, B. S., Zafar, A., Warsi, M. H., Behera, S., Mohanty, D. I., Mujtaba, M. A., Upadhyay A. K,... & Khalid, M. (2025). Luliconazole–niacinamide lipid nanocarrier laden gel for enhanced treatment of vaginal candidiasis: in vitro, ex vivo, in silico and preclinical insights. RSC advances15(8), 5665-5680.
  10. Basu, T., Singh, A., G, Vanishree., Patial, VU,. Tiwari, JK,. Gujjar, RS,. Upadhyay, A. K*. Comparative Transcriptome Analysis of Potato (Solanum tuberosum L.) Tubers at Different Developmental Stages of the Cryopreserved Germplasm. Potato Res. (2025). https://doi.org/10.1007/s11540-024-09843-9
  11. Gujjar, R.S., Joshi, D., Goswami, S.K. Kumar R, Singh A, Upadhyay, A. K. Unravelling the proteome of Saccharum officinarum cv. BO91 for novel defense-related proteins during C. falcatum infection. Acta Physiol Plant 47, 20 (2025). https://doi.org/10.1007/s11738-025-03766-9
  12. Gujjar, R. S., Supaibulwatana, K., Srivastava, S., & Upadhyay, A. K. (2024). Regulation of stress-responsive transcription factors of rice by CPPU, a synthetic cytokinin, during water deficit stress at protein level. Cereal Research Communications, 1-17. https://doi.org/10.1007/s42976-024-00540-4
  13. Patel, S. K., Vikram, A., Pathania, D., Chugh, R., Gaur, P., Prajapati, G., Upadhyay, A. K.  ... & Dwivedi, A. (2024). Allergic Potential & Molecular Mechanism of Skin Sensitization of Cinnamaldehyde Under Environmental UVB Exposure. Chemosphere, 143508. https://doi.org/10.1016/j.chemosphere.2024.143508
  14. Bhatia, A., Upadhyay, A. K*., & Sharma, S. (2024). Screening and analysis of single nucleotide polymorphism in the 3′-UTR microRNA target regions and its implications for lung tumorigenesis. Pharmacogenomics25(7), 299–314. https://doi.org/10.1080/14622416.2024.2355864
  15. Vikram, A., Patel, S. K., Singh, A., Pathania, D., Ray, R. S., Upadhyay, A. K., & Dwivedi, A. (2024). Natural Autophagy Activators: A Promising Strategy for Combating Photoaging. Phytomedicine, 155508. https://doi.org/10.1016/j.phymed.2024.155508
  16. Gujjar, R. S., Kumar, R., Goswami, S. K., Srivastava, S., & Upadhyay, A. K. (2024). Colletotrichum falcatum influences sucrose accumulation in sugarcane stalks by modulating the expression of SPS, SPP, SuSy, and invertases. Physiological and Molecular Plant Pathology130, 102237. https://doi.org/10.1016/j.pmpp.2024.102237
  17. Sheoran, S., Arora, S., Basu, T., Negi, S., Subbarao, N., Upadhyay, A. K, ... & Vuree, S. (2023). In silico analysis of Diosmetin as an effective chemopreventive agent against prostate cancer: Molecular docking, validation, dynamic simulation and pharmacokinetic prediction-based studies. Journal of Biomolecular Structure and Dynamics, 1-13. 10.1080/07391102.2023.2250451
  18. Basu, T., & Upadhyay, A. K. (2024). In silico study of novel alpha tocopheroids as effective inhibitors of aldo-keto reductase 1c3 (AKR1C3) enzyme. Journal of Biomolecular Structure and Dynamics42(15), 7715-7729. 10.1080/07391102.2023.2241543
  19. Singh, A., & Upadhyay, A. K. (2022). Identification and annotation of peptide allergens in prunus dulcis. International Journal of Peptide Research and Therapeutics28(6), 157. https://doi.org/10.1007/s10989-022-10468-0
  20. Akhtar, N., Singh, A., Upadhyay, A. K., & Mannan, M. A. U. (2022). Design of a multi-epitope vaccine against the pathogenic fungi Candida tropicalis using an in silico approach. Journal of Genetic Engineering and Biotechnology20(1), 140. 10.1186/s43141-022-00415-3
  21. Bhatia, A., Upadhyay, A. K., & Sharma, S. (2023). miRNAs are now starring in “No Time to Die: Overcoming the chemoresistance in cancer”. IUBMB life75(3), 238-256. https://doi.org/10.1002/iub.2652
  22. Mohanty, D., Zafar, A., Jafar, M., Upadhyay, A. K., Haque, M. A., Gupta, J. K., ... & Ansari, M. J. (2022). Development, in-vitro characterization and preclinical evaluation of esomeprazole-encapsulated proniosomal formulation for the enhancement of anti-ulcer activity. Molecules27(9), 2748. 10.3390/molecules27092748
  23. Joshi, A., Ray, N. M., Singh, J., Upadhyay, A. K., & Kaushik, V. (2022). T-cell epitope-based vaccine designing against Orthohantavirus: a causative agent of deadly cardio-pulmonary disease. Network Modeling Analysis in Health Informatics and Bioinformatics11, 1-10. https://doi.org/10.1007/s13721-021-00339-x
  24. Singh, B., Ahanathapillai, V., Sharma, N. R., Jan, S., Roy, A., & Upadhyay, A. K. (2021). Structural insights into the amino acid usage variations in the profilin gene family. Amino Acids54(3), 411-419. https://doi.org/10.1007/s00726-022-03138-4
  25. Singh, S. K., Upadhyay, A. K., & Reddy, M. S. (2022): Screening of potent drug inhibitors against SARS-CoV-2 RNA polymerase: an in silico approach. 3 Biotech 2021; 11: 93. 10.1007/s13205-020-02610-w
  26. Sachan, R. S. K., Upadhyay, A. K., Dohroo, A., & Karnwal, A. (2021). An Upsurge of the novel sub-acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic: A systematic review. Roman. Biotechnol. Lett26(1), 2195-2206. 10.25083/rbl/26.1/2195.2206
  27. Shafi, K. M., Joshi, A. G., Meenakshi, I., Pasha, S. N., Harini, K., Mahita, J., Upadhyay AK... & Sowdhamini, R. (2020). Dataset for the combined transcriptome assembly of M. oleifera and functional annotation. Data in Brief30, 105416. 10.1016/j.dib.2020.105416
  28. Sharma, P., Kaur, R., Upadhyay, A. K., & Kaushik, V. (2020). In-silico prediction of peptide based vaccine against Zika virus. International Journal of Peptide Research and Therapeutics26(1), 85-91. https://doi.org/10.1007/s10989-019-09818-2
  29. Aglawe, S. B., Verma, A. K., & Upadhyay, A. K. (2021). Bioinformatics tools and databases for genomics-assisted breeding and population genetics of plants: a review. Current Bioinformatics16(6), 766-773. https://doi.org/10.2174/1574893615999200831144028
  30. Joshi, A. G., Harini, K., Meenakshi, I., Shafi, K. M., Pasha, S. N., Mahita, J., Upadhya A. K. & Sowdhamini, R. (2020). A knowledge-driven protocol for prediction of proteins of interest with an emphasis on biosynthetic pathways. MethodsX7, 101053. 10.1016/j.mex.2020.101053
  31. Pasha, S. N., Shafi, K. M., Joshi, A. G., Meenakshi, I., Harini, K., Mahita, J., Upadhyay A. K. & Sowdhamini, R. (2020). The transcriptome enables the identification of candidate genes behind medicinal value of Drumstick tree (Moringa oleifera). Genomics112(1), 621-628. 10.1016/j.ygeno.2019.04.014
  32. Upadhyay, A. K., & Sowdhamini, R. (2019). Genome-wide analysis of domain-swap predicted products in the genome of anti-stress medicinal plant: Ocimum tenuiflorum. Bioinformatics and biology insights13, 1177932218821362. 10.1177/1177932218821362
  33. Gurung, P. D., Upadhyay, A. K., Bhardwaj, P. K., Sowdhamini, R., & Ramakrishnan, U. (2019). Transcriptome analysis reveals plasticity in gene regulation due to environmental cues in Primula sikkimensis, a high altitude plant species. BMC genomics20, 1-12. https://doi.org/10.1186/s12864-019-6354-1
  34. Sharma, G., Upadhyay, A. K., Biradar, H., Sonia, & Hittalmani, S. (2019). OsNAC-like transcription factor involved in regulating seed-storage protein content at different stages of grain filling in rice under aerobic conditions. Journal of genetics98(1), 18.
  35. Upadhyay, A. K., Tripathi, S., Mannan, M. A. U., Deb, Y., Katagi, R., & Singh, C. (2017). Molecular modeling and analysis of key proteins in cytokinin mediated leaf senescence of wheat. PONTE International Journal of Science and Research73(9).
  36. Mannan, M. A. U., Dhial, S., Lall, S., Singh, J., & Upadhyay, A. K. (2017). Hypertension and Genetic Polymorphism of ACE and ADD1 gene in North Indian Population. PONTE International Journal of Science and Research73(7).
  37. Upadhyay, A. K., & Sowdhamini, R. (2016). Genome-wide prediction and analysis of 3D-domain swapped proteins in the human genome from sequence information. Plos one11(7), e0159627.
  38. Upadhyay, A. K., Chacko, A. R., Gandhimathi, A., Ghosh, P., Harini, K., Joseph, A. P., ... & Sowdhamini, R. (2015). Genome sequencing of herb Tulsi (Ocimum tenuiflorum) unravels key genes behind its strong medicinal properties. BMC plant biology15, 1-20.
  39. Joseph, A. P., Shingate, P., Upadhyay, A. K., & Sowdhamini, R. (2014). 3PFDB+: improved search protocol and update for the identification of representatives of protein sequence domain families. Database2014, bau026.

Non-SCI paper:

  1. Puneet, Singh, R., Bhardwaj, V. et al. Haptoglobin Polymorphisms: Translational Insights and Regenerative Potential in Disease Management. Regen. Eng. Transl. Med. 12, 91–104 (2026). https://doi.org/10.1007/s40883-025-00391-3
  2. Chugh, R., Yadvi Sandhir, Gujjar, R.S. et al. Exploring the potential cross-reactivity of allergenic proteins from Anacardium occidentale using in-silico approaches. J Proteins Proteom 17, 73–87 (2026). https://doi.org/10.1007/s42485-025-00202-x
  3. Singh, A., Garg, S., & Upadhyay, A. K*. (2023). Identification and analysis of allergens in edible mushroom (Agaricus bisporus). Materials Today: Proceedings.
  4. Puneet, Upadhyay, A. K., Kaur, M., & Singh, R. D. (2023). Assessment of Haptoglobin 2-2 Genotype in Type 2 Diabetes and Cardiovascular Patients in North Indian Population: A Case-control Study. JOURNAL OF CLINICAL AND DIAGNOSTIC RESEARCH17(1), BC06-BC10.
  5. Singh, B., Jan, S., Kumar Upadhyay, A*., & Raj Sharma, N. (2023). In silico investigation for drug-like pharmacophores against food allergen profilins. Allergo Journal International32(2), 38-46. https://doi.org/10.1007/s40629-022-00222-9
  6. Akhtar, N., Verma, H., Silkari, O. M., Upadhyay, A. K., Kaushik, V., & Mannan, M. A. U. (2022). Drummondin E and Flinderole B are potential inhibitors of RNA-dependent RNA polymerase of SARS-CoV-2: an in silico study. BioTechnologia103(1), 53.
  7. Singh, B., Upadhyay, A. K., Al-Tawaha, T. W., Al-Tawaha, A. R., & Sirajuddin, S. N. (2020, April). Biofertilizer as a tool for soil fertility management in changing climate. In IOP Conference Series: Earth and Environmental Science (Vol. 492, No. 1, p. 012158). IOP Publishing.
  8. Singh, H., Siddique, N., & Upadhyay, A. K. (2020). Genome-wide Identification and Annotation of metabolite producing Gene Clusters in Rice Genome. Research Journal of Pharmacy and Technology13(4), 1744-1746.
  9. Sharma, K., Akhtar, N., Upadhyay, A. K., & Mannan, M. A. (2020). Efficacy of Trichoderma harzianum, a biocontrol agent for controlling opportunistic fungal pathogens. Journal of Pharmaceutical Sciences and Research12(2), 282-285.
  10. Bansal, A., Sharma, N. R., Upadhyay, A. K., Kaushik, S., & Thomas, T. G. (2019). Evaluation of Carvacrol and its Receptor (Ubiquinone-c-reductase) as a Potential Anti-malarial Drug. Journal of Communicable Diseases (E-ISSN: 2581-351X & P-ISSN: 0019-5138)51(4), 16-20.
  11. Karnwal, A., Bhardwaj, V., Dohroo, A., Upadhyay, A. K., & Bala, R., (2018). Effect of microbial surfactants on heavy metal polluted wastewater. Pollut. Res37, 39-46.
  12. Noomansiddique, M., & Upadhyay, A K.: Short report on d-endotoxins of bacillus thuringiensis (bt) as future bio-insecticide.
  13. Akhtar, N., Karnwal, A., Upadhyay, A. K., Paul, S., & Mannan, M. A. U. (2018). Saccharomyces cerevisiae bio-ethanol production, a sustainable energy alternative. Asian J. Microbiol. Biotechnol. Environ. Sci20, S200-S204.
  14. Mohanty, D., Jhansi, M., Bakshi, V., Haque, A., Swapna, S., Sahoo, C. K., & Upadhyay, A. K. (2018). Niosomes: A Novel Trend in Drug Delivery. Research Journal of Pharmacy and Technology11(11), 5205-5211.
  15. Bansal, A., & Upadhyay, A. K. (2017). Genome-wide identification and analysis of putative Rhomboid Gene enhancers in multiple Drosophila species. Immunome Res13(143), 2.
  16. M Sunitha, P Ghosh, & Upadhyay, A. K.,.…R Sowdhamini: Draft Genome of Cissus quadrangularis to Elucidate the Medicinal Values. (2015). Journal of Herbal Medicine, 2(1).

Book chapters:

  1. Kumari, V., Kumawat, P., Rajput, S. S., Choudhary, S., Sharma, R., Upadhyay, A. K., ... & Sharma, M. (2024). Allele Mining: Potential Tool for Accelerated Crop Breeding. In Smart Breeding (pp. 243-260). Apple Academic Press.
  2. Basu, T., Chugh, R., Gujjar, R. S., & Upadhyay, A. K*. (2023). Approaches for In Silico Validation of Safety (Toxicity) Data for Cosmetics. In Skin 3-D Models and Cosmetics Toxicity (pp. 187-210). Singapore: Springer Nature Singapore.
  3. Singh, B., Mohanty, D., & Upadhyay, A. K*. (2023). Impact of Genomics in Improvement of Rice Bean Production and Productivity: An Orphan Crop. In Genomics of Plant–Pathogen Interaction and the Stress Response (pp. 64-73). CRC Press.
  4. Singh, B., Karnwal, A., Tripathi, A., & Upadhyay, A. K*. (2021). Food allergens and related computational biology approaches: a requisite for a healthy life. Bioinformatics for agriculture: High-throughput approaches, 145-160.
  5. Singh, B., Mohanty, D., Bakshi, V., Gujjar, R. S., & Upadhyay, A. K*. (2021). The distinction of omics in amelioration of food crops nutritional value. Bioinformatics for agriculture: High-throughput approaches, 85-99.
  6. Singh, B., Malhotra, H., Kumar, D., Mujtaba, S. F., & Upadhyay, A. K*. (2019). Understanding cellular and molecular events of skin aging and cancer: An integrative perspective. Skin Aging & Cancer: Ambient UV-R Exposure, 11-28.
  7. Hazra, D., & Upadhyay, A. K*. (2018). Computational Tools and Databases of Microbes and Its Bioprospecting for Sustainable Development. Microbial Bioprospecting for Sustainable Development, 385-397.
  8. Upadhyay, A. K., & Sharma, G. (2018). Computational Approaches to Understand the Genome and Protein Sequences of Fungi. Fungi and their Role in Sustainable Development: Current Perspectives, 635-649.
  9. Singh, B., Mohanty, D., & Upadhyay, A. K. (2020). Computational approach to understand fungal secondary metabolites and responsible biological molecules. In New and Future Developments in Microbial Biotechnology and Bioengineering (pp. 105-114). Elsevier.
  10. Sharma, G., Sonia, & Upadhyay, A. K. (2020). Quantitative Genetics and the Genetic Basis for Polyphenolics Trait in Plants. Plant Phenolics in Sustainable Agriculture: Volume 1, 501-515.
  11. Shingate, p., Upadhyay, A. K., Raghavender, U., & Sowdhamini, R. (2013). Identification and conformational analysis of hinge regions in proteins that undergo domain swapping. In Biomolecular Forms and Functions: A Celebration of 50 Years of the Ramachandran Map (pp. 320-332).

Books as Editor:

  1. Pant, A. B., Dwivedi, A., Ray, R. S., Tripathi, A., Upadhyay, A. K., & Poojan, S. (Eds.). (2023). Skin 3-D Models and Cosmetics Toxicity. Springer.
  2. Atul Kumar UpadhyayR SowdhaminiVirupaksh U. Patil (Eds) (2021): Bioinformatics for agriculture: High-throughput approaches. Springer.

SCI/Scopus indexed conference papers/abstract:

  1. Sheoran, S., Arora, S., Basu, T., Subbarao, N., Upadhyay, A. K., & Vuree, S. (2023). Assessment of polyphenolic secondary metabolites and small molecules against the xenobiotic metabolic and cell cycle regulatory proteins in prostate cancer. Cancer Research83(7_Supplement), 5342-5342.
  2. Arora, S., Sheoran, S., Basu, T., Subbarao, N., Upadhyay, A. K., & Vuree, S. (2023). Evaluating the screened polyphenolics molecules as potential chemosensitizers against the oncogenic signalling proteins in lung cancer. Cancer Research83(7_Supplement), 5343-5343.
  3. Shingate, P., Upadhyay, A., Khader, S., & Sowdhamini, R. (2015). 172 Computational analysis and prediction of proteins that undergo domain swapping. Journal of Biomolecular Structure and Dynamics33(sup1), 112-113.
  4. Chacko, A. R., Patil, S., Srivastava, S., Arya, D., Upadhayay, A., Nagrajan, A., ... & Sowdhamini, R. (2014, September). A longitudinal study to examine the exome of a good responder CML patient under imatinib at diagnosis and under remission. In FEBS JOURNAL (Vol. 281, pp. 89-89). 111 RIVER ST, HOBOKEN 07030-5774, NJ USA: WILEY-BLACKWELL.
  5. Chacko, A., Patil, S., Upadhayay, A., Arya, D., Nagrajan, A., Khatri, R., ... & Behl, R. (2013). A high throughput exome sequencing approach to analyse events within a good responder CML patient under imatinib at diagnosis and under remission. Blood122(21), 5161.
  6. Chacko, A., Patil, S., Upadhyay, A., Nagrajan, A., Khatri, R., Arya, D., ... & Ramanathan, S. (2013, June). Creation of a resource group on" genomics in the clinic in low resource settings": an example using a longitudinal study of a cml case. In haematologica (vol. 98, pp. 549-549). Via giuseppe belli 4, 27100 pavia, italy: ferrata storti foundation.
  7. Chacko, A. R., Patil, S., Upadhayay, A. K., Nagrajan, A., Khatri, R., Arya, D., ... & Ross, C. (2013, May). A bioinformatics pipeline for sequence to structure: A case study with a Cml patient undergoing treatment with imatinib. In 2013 Biomedical Sciences and Engineering Conference (BSEC) (pp. 1-4). IEEE.
  8. Khanna, D., Kaushik, V., & Upadhyay, A. K. (2018, October). Genome-wide prediction and analysis of siRNA as potential antiviral agent against Hepatitis-C virus. In 2018 International Conference on Bioinformatics and Systems Biology (BSB) (pp. 1-4). IEEE.

List of PhD students

S. No.

Name of Student

Registration No.

Year

Title Of PhD

Status

1. Divya Mohan 902500010 2025 Comparative Evaluation of Solvent-Based MXene Nano-Priming Strategies for Modulating Germination, Photosynthetic Performance, and Antioxidant Defense in Lettuce (Lactuca sativa L.) under Controlled Soilless Cultivation Ongoing
2. Rasman Kaur 902500014 2025

Investigation Of Molecular Interactions Of Aptamer With Allergen Using Functionalized Mxene

Ongoing
3. Ishita 902500025 2025

An Integrative Multi-Omics Framework for Decoding Epithelial Barrier Dysfunction in Food Allergy

Ongoing
4. Devvrat Prasad

902400002

2024

Analysis of Processing Induced Changes in Tree Nut Proteins through Computational and Experimental Approaches

Ongoing
5.

Rashi Chugh

9021000011

2021

Identification of putative allergens in edible varieties of Oyster mushroom using genomic and transcriptomic data.

Ongoing

6.

Aakanksha Pandey

902000008

2020

Investigation of 3-D domain-swapped proteins and their function in medicinal plants.

Ongoing

7.

Amardeep Singh

901903003

2019

Efficient discovery of transcription factor binding sites in DNA sequences.

Ongoing

8. Tanmayee Basu 902000006 2020 Genome and transcriptome-enabled identification and validation of secondary metabolite-producing biosynthetic gene clusters of medicinal plants.  Submitted 
9.

Puneet

11512761

2024

Association of haptoglobin gene polymorphism in diabetes and cardiovascular disease in north Indian population

Completed

10.

Bhupender Singh

11617871

2023

Genome-wide prediction and expression analysis of food allergens

Completed

11.

Anmol Bhatia

902000011

2020

Single nucleotide polymorphism in microRNA genes and their association with lung disorders.

Completed

 

List of Master’s students

S.No. Name of student Title of the thesis M.Sc./ M.Tech Year Supervisor/Co-supervisor Completed/Ongoing  

1.

Tanmay Bist
(6024040026)

Genomic and Functional Analysis of FLG and IL13 Variants Implicated in Allergic Disease Susceptibility

M.Tech

2026

Supervisor

Completed

 

2. 

Ritish Kamboj
(3024010034)

Rational Design and In Silico Optimization of DNA Aptamers Targeting Ricin B-Chain for Biosensor Applications Using Integrated Molecular Docking, Dynamics, and AI-Guided Approaches 

MSC

2026

Supervisor

Completed

 

2.

Shubhkarandeep Singh Judge
(3024010041)

Analyzing Genomic Variations in IL4 and IL13 Genes Associated with Food Allergy Genetics

MSC

2026

Supervisor

Completed

 

3.

Priyanka Yadav
(302301010)

Identification and analysis of putative allergens in Edible mushroom (Agaricus bisporus)

MSC

2025

Supervisor

 

Completed

 

 

4.

Ishita
(602304004)

A Droplet Digital Polymerase Chain Reaction (ddPCR) Approach for Sensitive and Non-Invasive Detection of Fetal Genetic Abnormalities

M.Tech

2025

Supervisor

 

Completed

 

 

5.

Devrat Prasad (302201015)

Insights of amino acid usage patterns among allergenic and non-allergenic proteins

MSC

2024

Supervisor

Completed

 

6.

Ayushi Gupta (302201003)

Identification of Anti-Allergic Natural compounds through in-situ methods and Docking

MSC

2024

Supervisor

Completed

 

7.

Shivangi Jain (602204017)

Novel natural compounds targeting human histamine H1 receptor for
6anti-allergic therapy.

M.Tech

2024

Supervisor

Completed

 

8.

Avneet Kaur (302101005)

Genome analysis of Murraya koenigii to study the expression of genes involved in secondary metabolite production

M.Sc.

2023

Supervisor

Completed

 

9.

Rishika Konsal (3021011019)

Role of sensitization in the development of anti HLA antibodies in solid organ transplant

M.Sc.

2023

Co-Supervisor

Completed

 

10.

Yadvir (602104019)

Identification and structural insights of allergens in Anacardium occidentale

M. Tech

2023

Supervisor

Completed

 

11.

Soumi Biswas (602104014)

Probing the molecular diversity of symbiodinium species associated with corals in the intertidal reef habitat

M. Tech

2023

Co-Supervisor

Completed

 

12.

Chandni (302001004)

Identification and comparative analysis of Seed storage proteins in sequenced cereal genomes.

M.Sc.

2022

Supervisor

Completed

 

13.

Payal Singh Kashyap

(602004016)

Genome-wide analysis of 3D-Domain swapped predicted proteins in Sesamum indicum.

M. Tech

2022

Supervisor

Completed

 

14.

Eva Rathi (602004007)

Virtual screening of natural compounds as interleukin-6 inhibitors to cure Covid-19

M. Tech

2022

Supervisor

Completed

 

Seminars and training

  • Conducted a national workshop on “Next Generation Sequencing (NGS) data analysis” 30-31 March 2018, Lovely Professional University, Punjab.
  • Participated in 5 days of training on “Effective Teaching” conducted by the National Institute of Technical Teachers Training Research, Chandigarh, 12 – 16 February 20018.
  • Participated in a one-day workshop on “Big Data in Genomics” 4th  February 2017 at IIIT Delhi.
  • Oral presentation in the “Bioinformatics workshop, SHIASTS, Allahabad”
  • Poster presentation in the “Plant Genome Evolution Conference 2015” Amsterdam, The Netherlands, 6th to 8th September 2015.
  • Participated in the “International Conference on Biomolecular Forms and Functions (ICBFF)” J. N. Tata Auditorium, IISC, Bangalore, India, 8-11th January 2013.
  • Attended “The Highlights of 16th Congress of EHA”, Bangalore, 4 - 6th November 2011.
  • Participated in the “National Workshop on Next Generation Sequencing (NGS) data analysis” IBAB, Bangalore, India, 3rd - 5th September 2011.
  • Participated in the workshop on “Protein Structure, Function and Folding” IISC, Bangalore, 20-24th  December 2010.
  • Attended an intensive Rural Awareness Work Experience (RAWE) course from 03-07-2005 to 30-12-2006 in the village, Nangapur, Uttar Pradesh, India.
  • Attended two days “Peer-educator training under universities talk AIDS program” sponsored by the Government of India, Ministry of youth affairs and sports.

Achievements

  • Cleared All India entrance for graduate studies, ICAR, India, 2003-2007.
  • Gold medalist in B.Sc. (Agri.) Honors from the college of agriculture, CSA University, Kanpur.
  • Qualified in JNU combined entrance examination for admission to M.Sc. (Agri.) Biotechnology, DBT, 2007-2009.
  • Qualified in the National Eligibility Test (NET) by ICAR in September 2010 in major discipline “Basic Plant Sciences” and eligible for Lecturer/Assistant professor. This certificate is recognized by the “University Grant Commission” (UGC) and “Council for Scientific and Industrial Research” (CSIR), India.
  • Qualified “National Centre for Biological Sciences, TIFR” entrance exam, 2010-11 leading to the award of JRF and SRF for the entire period of Ph.D. (5 Yrs.)
  • Participated as a player in the 7th  All India Inter Agriculture University sports and games meet, 2005- 06.
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