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 is working as an Assistant professor in Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala since 2019.
• He has completed his Ph.D. degree in Life Sciences, from National Centre for Biological Sciences, Bangalore; Tata Institute of Fundamental Research, A Deemed University, Mumbai.
• His research work involves NGS based understanding of genome and transcriptome of medicinal plants to understand the societal importance of the selected secondary metabolites.
• He has also worked on computational approaches to understand protein sequence-structure-function relationships.
• He uses machine-learning approaches such as Support Vector Machines (SVM), Random Forest (RF) for the classification of biological data to infer their biological 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

Publication

SCI papers:

1. 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
2. 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
3. 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. Pharmacogenomics, 25(7), 299–314. https://doi.org/10.1080/14622416.2024.2355864
4. 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
5. 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 Pathology, 130, 102237. https://doi.org/10.1016/j.pmpp.2024.102237
6. 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
7. 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 Dynamics, 42(15), 7715-7729. 10.1080/07391102.2023.2241543
8. Singh, A., & Upadhyay, A. K. (2022). Identification and annotation of peptide allergens in prunus dulcis. International Journal of Peptide Research and Therapeutics, 28(6), 157. https://doi.org/10.1007/s10989-022-10468-0
9. 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 Biotechnology, 20(1), 140. 10.1186/s43141-022-00415-3
10. Bhatia, A., Upadhyay, A. K., & Sharma, S. (2023). miRNAs are now starring in “No Time to Die: Overcoming the chemoresistance in cancer”. IUBMB life, 75(3), 238-256. https://doi.org/10.1002/iub.2652
11. 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. Molecules, 27(9), 2748. 10.3390/molecules27092748
12. 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 Bioinformatics, 11, 1-10. https://doi.org/10.1007/s13721-021-00339-x
13. 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 Acids, 54(3), 411-419. https://doi.org/10.1007/s00726-022-03138-4
14. 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
15. 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. Lett, 26(1), 2195-2206. 10.25083/rbl/26.1/2195.2206
16. 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 Brief, 30, 105416. 10.1016/j.dib.2020.105416
17. 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 Therapeutics, 26(1), 85-91. https://doi.org/10.1007/s10989-019-09818-2
18. 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 Bioinformatics, 16(6), 766-773. https://doi.org/10.2174/1574893615999200831144028
19. 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. MethodsX, 7, 101053. 10.1016/j.mex.2020.101053
20. 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). Genomics, 112(1), 621-628. 10.1016/j.ygeno.2019.04.014
21. 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 insights, 13, 1177932218821362. 10.1177/1177932218821362
22. 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 genomics, 20, 1-12. https://doi.org/10.1186/s12864-019-6354-1
23. 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 genetics, 98(1), 18.
24. 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 Research, 73(9).
25. 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 Research, 73(9).
26. 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 Research, 73(7).
27. Upadhyay, A. K., & Sowdhamini, R. (2016). Genome-wide prediction and analysis of 3D-domain swapped proteins in the human genome from sequence information. Plos one, 11(7), e0159627.
28. 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 biology, 15, 1-20.
29. 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. Database, 2014, bau026.

Non-SCI paper:

1. Singh, A., Garg, S., & Upadhyay, A. K*. (2023). Identification and analysis of allergens in edible mushroom (Agaricus bisporus). Materials Today: Proceedings.
2. 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 RESEARCH, 17(1), BC06-BC10.
3. Singh, B., Jan, S., Kumar Upadhyay, A*., & Raj Sharma, N. (2023). In silico investigation for drug-like pharmacophores against food allergen profilins. Allergo Journal International, 32(2), 38-46. https://doi.org/10.1007/s40629-022-00222-9
4. 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. BioTechnologia, 103(1), 53.
5. 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.
6. 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 Technology, 13(4), 1744-1746.
7. 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 Research, 12(2), 282-285.
8. 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.
9. Karnwal, A., Bhardwaj, V., Dohroo, A., Upadhyay, A. K., & Bala, R., (2018). Effect of microbial surfactants on heavy metal polluted wastewater. Pollut. Res, 37, 39-46.
10. Noomansiddique, M., & Upadhyay, A K.: Short report on d-endotoxins of bacillus thuringiensis (bt) as future bio-insecticide.
11. 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. Sci, 20, S200-S204.
12. 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 Technology, 11(11), 5205-5211.
13. Bansal, A., & Upadhyay, A. K. (2017). Genome-wide identification and analysis of putative Rhomboid Gene enhancers in multiple Drosophila species. Immunome Res, 13(143), 2.
14. 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 Upadhyay, R Sowdhamini, Virupaksh 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 Research, 83(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 Research, 83(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 Dynamics, 33(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. Blood, 122(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

List of Master’s students

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.