Dr. Atul Kumar Upadhyay

Assistant Professor


Computational Biology, Genomics and Plant Biotechnology




Computational Biology, Genomics and Plant Biotechnology



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  • 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.


  • 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

  • Genome and transcriptome enabled understanding of pathways of secondary metabolite producing genes.
  • Next-Generation Sequencing data analysis of different biological samples such as microbes, humans and plant/crops.
  • Computational approaches for DNA and Protein sequence-structure-function relationships


  1. Singh S.K, Upadhyay A.K, and Reddy M.S: Screening of potent drug inhibitors against SARS-CoV-2 RNA polymerase: an in silico approach: 3 Biotech 11, 93 (2021).

  2. R. S. K. Sachan, A. K. Upadhyay, A. Dohroo, and A. Karnwal: An Upsurge of the novel sub-acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic: A systematic review. Rom Biotechnol Lett 26 (1), 2195-2206.

  3. Adwait G. Joshi, K. Harini, Iyer Meenakshi, K. Mohamed Shafi, Shaik Naseer Pasha, Jarjapu Mahita, Radha Sivarajan Sajeevan, Snehal D. Karpe, Pritha Ghosh, Sathyanarayanan Nitish, A. Gandhimathi, Oommen K. Mathew, Subramanian Hari Prasanna, Manoharan Malini, Eshita Mutt, Mahantesha Naika, Nithin Ravooru, Rajas M. Rao, Prashant N. Shingate, Anshul Sukhwal, Margaret S. Sunitha, Atul K. Upadhyay, Rithvik S. Vinekar, Ramanathan Sowdhamini: A knowledge-driven protocol for prediction of proteins of interest with an emphasis on biosynthetic pathways, MethodsX, 7: 2020,https://doi.org/10.1016/j.mex.2020.101053.

  4. Supriya Babasaheb Aglawe*, Amit Kumar Verma and Atul Kumar Upadhyay*, “Bioinformatics tools and Databases for Genomics-assisted Breeding and Population Genetics of Plants: A Review”, Current Bioinformatics (2020) 15: 1. https://doi.org/10.2174/1574893615999200831144028

  5. Shaik Naseer Pasha, K. Mohamed Shafi, Adwait G. Joshi, Iyer Meenakshi, K. Harini, Jarjapu Mahita, Radha Sivarajan Sajeevan, Snehal D. Karpe, Pritha Ghosh, Sathyanarayanan Nitish, A. Gandhimathi, Oommen K. Mathew, Subramanian Hari Prasanna, Manoharan Malini, Eshita Mutt, Mahantesha Naika, Nithin Ravooru, Rajas M. Rao, Prashant N. Shingate, Anshul Sukhwal, Margaret S. Sunitha, Atul K. Upadhyay, Rithvik S. Vinekar, Ramanathan Sowdhamini: Dataset for the combined transcriptome assembly of M. oleifera and functional annotation. Data in Brief, Vol. 30, 2020 DOI: 10.1016/j.dib.2020.105416

  6. Parul Sharma, Rajbir Kaur, Atul Kumar Upadhyay and Vikas Kaushik: In-Silico Prediction of Peptide Based Vaccine Against Zika Virus, International Journal of Peptide Research and Therapeutics 2020, DOI: 10.1007/s10989-019-09818-2.

  7. Priya Darshini Gurung, Atul Kumar Upadhyay, Pardeep Kumar Bhardwaj, Ramanathan Sowdhamini and Uma Ramakrishnan: Transcriptome analysis reveals plasticity in gene regulation due to environmental cues in Primula sikkimensis, a high altitude plant species. BMC Genomics 12/2019

  8. Bansal A, Sharma NR,  Upadhyay  AK,  Kaushik  S, Thomas TG. Evaluation of Carvacrol and its Receptor (Ubiquinone-c-reductase) as a Potential Anti-malarial Drug. J Commun Dis 2019; 51(4): 16-20.

  9. Sharma G, Upadhyay AK, Biradar H, Sonia, Hittalmani S: 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, 03/2019

  10. Atul K Upadhyay and R Sowdhamini: Genome-wide analysis of domain-swap predicted products in the genome of anti-stress medicinal plant: Ocimum tenuiflorum: Bioinformatics and Biology Insights, 2019/01, DOI: 10.1177/1177932218821362.

  11. Shaik Naseer Pasha, K. Mohamed Shafi, Adwait G. Joshi, Iyer Meenakshi, K. Harini, Jarjapu Mahita, Radha Sivarajan Sajeevan, Snehal D. Karpe, Pritha Ghosh, Sathyanarayanan Nitish, A. Gandhimathi, Oommen K. Mathew, Subramanian Hari Prasanna, Manoharan Malini, Eshita Mutt, Mahantesha Naika, Nithin Ravooru, Rajas M. Rao, Prashant N. Shingate, Anshul Sukhwal, Margaret S. Sunitha, Atul K. Upadhyay, Rithvik S. Vinekar, Ramanathan Sowdhamini: The transcriptome enables the identification of candidate genes behind medicinal value of Drumstick tree (Moringa oleifera). Genomics 04/2019: Doi.org/10.1016/j.ygeno.2019.04.014

  12. Dibyalochan Mohanty, M. Jhansi, Dr. Vasudha Bakshi, M. Akiful Haque, Swapna S, Chinmaya Keshari Sahoo, and Atul K Upadhyay: Niosomes: A Novel Trend in Drug Delivery: Research J. Pharm. and Tech. 11(12): December 2018.

  13. Arun Karnawal, Vaishali Bharadwaj, Aradhana Dohroo, Atul K Upadhyay, Ritu Bala: Effect of microbial surfactants on heavy metal polluted wastewater: Pollution Research (37) 2018/5.

  14. Shashank Tripathi, M. Amin-ul Mannan, Yamini Deb, Rajkumar Katag, Chandrakant Singh and Atul K Upadhyay*: Molecular modeling and analysis of key protein in Cytokinin mediated leaf senescence of wheat: Ponte Academic Journal, 73 [9] 2017; DOI: 10.21506/j.ponte.2017.9.11

  15. Bansal A, Upadhyay AK* (2017) Genome-Wide Identification and Analysis of Putative Rhomboid Gene Enhancers in Multiple Drosophila Species. Immunome Res 13: 143. doi: 10.4172/17457580.1000143.

  16. M. Amin-ul Mannan, Shikha Dhial, Sahiba Lall, Jasdeep Singh, Atul K Upadhyay: Hypertension and genetic polymorphism of ace and add1 gene in north Indian population. Ponte Academic Journal [73] 07/2017; DOI:  10.21506/j.ponte.2017.7.32 

  17. Nooman Siddique, M. Amin-ul Mannana and Atul K Upadhyay*: A Short Report on Delta-Endotoxins of Bacillus thuringiensis (Bt) as Future Bio-Insecticide, Asian Journal of Microbiology, Biotechnology and Environmental science, [1] 2018.  

  18. Akhtara N, Karnawal A, Upadhyay AK, Paulab S and Mannan A, (2018) Saccharomyces cerevisiae bio-ethanol production, a sustainable energy alternative. Asian Journal of Microbiology, Biotechnology and Environmental science 20 (2018): 202-206.

  19. Nancy Bhura and Atul K Upadhyay*: Overview of a typical next generation sequencing (NGS) project. IJSSR, 2017, 42(2): 190-195.

  20. Atul Kumar Upadhyay, Ramanathan Sowdhamini: Genome-Wide Prediction and Analysis of 3D-Domain Swapped Proteins in the Human Genome from Sequence Information. PLoS ONE 07/2016; 11(7). DOI: 10.1371/journal.pone.0159627.

  21. A Gandhimathi, Margaret Sunitha, Atul Kumar Upadhyay et al.: Draft Genome of Cissus quadrangularis to Elucidate the Medicinal Values. Journal of Herbal Medicine 01/2016; 2(1).

  22. Upadhyay AK, Chacko AR, Gandhimathi A, Ghosh P, Harini K, Joseph AP, Joshi AG, Karpe SD, Kaushik S, Kuravadi N, Lingu CS, Mahita J, Malarini R, Malhotra S, Malini M, Mathew OK, Mutt E, Naika M, Nitish S, Pasha SN, Raghavender US, Rajamani A, Shilpa S, Shingate PN, Singh HR, Sukhwal A, Sunitha MS, Sumathi M, Ramaswamy S, Gowda M, Sowdhamini R: Genome sequencing of herb Tulsi (Ocimum tenuiflorum) unravels key genes behind its strong medicinal properties. BMC Plant Biology 08/2015, 15(212). DOI: 10.1186/s12870-015-0562-x

  23. Agnel P Joseph, Prashant Shingate, Atul K Upadhyay, R Sowdhamini: 3PFDB+: improved search protocol and update for the identification of representatives of protein sequence domain families. Database The Journal of Biological Databases and Curation 01/2014; 2014. DOI: 10.1093/database/bau026.

  24. Anita Chacko, Shankarrao Patil, Atul K Upadhayay, et.al., A High Throughput Exome Sequencing Approach to Analyse Events Within a Good Responder CML Patient Under Imatinib At Diagnosis and Under Remission. Blood 10/2013; 122(21).

  25. Singh H, Nooman S, and Upadhyay AK: Genome-wide identification and annotation of metabolite producing gene clusters in rice genome. Research Journal of Pharmacy and Technology, 13(4): 1744-1746, DOI: 10.5958/0974-360X.202.00314.5

  26. Atul Kumar Upadhyay: Genome and transcriptome identification of novel food allergens with their possible roles in human diseases. National Symp NSTPB2020, TIFAC-CORE /TIET, Patiala Punjab, 2020.

  27. Anita Rachel Chacko, Shankarrao Patil, Atul K Upadhayay, Ashwat Nagrajan, Rakesh Khatri, Deepak Arya, Sudhir Krishna, R Sowdhamini: A Bioinformatics Pipeline For Sequence To Structure: A Case Study With A Cml Patient Undergoing Treatment With Imatinib *. IEEE; 05/2013.

  28. Divya Khanna, Vikas Kaushik and Atul K Upadhyay*: Genome-wide prediction and analysis of siRNA as potential antiviral agent against Hepatitis-C: IEEE, 2018, BSBE Conference, DOI: 10.1109/BSB.2018.8770691.

  29. Prashant Shingate, Atul K Upadhyay, Shameer Khader, Ramanathan Sowdhamini: Computational analysis and prediction of proteins that undergo domain swapping. Journal of Biomolecular structure & dynamics; 05/2015

  30. A R Chacko, S Patil, S Srivastava, D Arya, A K Upadhayay, A Nagrajan, C Ross, S Krishna, R Sowdhamini: A longitudinal study to examine the exome of a good responder CML patient under imatinib at diagnosis and under remission. FEBS-EMBO; 09/2014

  31. A Chacko, S Patil, Atul K Upadhyay, A Nagrajan, R Khatri, D Arya, S Krishna, C Ross, S Ramanathan: creation of a resource group on "genomics in the clinic in low resource settings” an example using a longitudinal study of a cml case. EHA, Stockholm, Sweden; 06/2013

  32. Bhupender Singh, Dibyalochan Mohanty and Atul Kumar Upadhyay: Computational approach to understand fungal secondary metabolites and responsible biological molecules, New and Future Developments in Microbial Biotechnology and Bioengineering, Elsevier, 2020, Pages 105-114, https://doi.org/10.1016/B978-0-12-821008-6.00011-6.

  33. Sharma G., Sonia, Upadhyay A.K. (2020) Quantitative Genetics and the Genetic Basis for Polyphenolics Trait in Plants. In: Lone R., Shuab R., Kamili A. (eds) Plant Phenolics in Sustainable Agriculture. Springer, Singapore. https://doi.org/10.1007/978-981-15-4890-1_21.

  34. B Singh, AK Upadhyay, TW Al-Tawaha, AR Al-Tawaha, SN Sirajuddin: Biofertilizer as a tool for soil fertility management in changing climate. Vol 492: 2020, IOP Publishing.

  35. Sujata MauryaVaishali, Chandel Sibi, Raj Sibi, Raj Show, Atul Kumar Upadhyay, Dhruv Kuma: Omics in cancer: from diagnostics to therapeutics. Vol 20, 2020, Recent Trends in ‘Computational Omics, Nova Science Publishers, Inc.

  36. B Singh, H Malhotra, D Kumar, S F Mujtaba and A K Upadhyay*: Understanding Cellular and Molecular Events of Skin Aging and Cancer: An Intergrative Prespective, Skin Aging & Cancer. SPRINGER, Singapore, 2019.

  37. Prashant Shingate, Atul K Upadhyay, U S Raghavender, R. Sowdhamini: Identification and conformational analysis of hinge regions in proteins that undergo domain swapping. 01/2013.

  38. Atul K Upadhyay* and Gaurav Sharma: Computational approaches to understand the genome and protein sequences of fungi. Fungi and their Role in Sustainable Development: Current Perspectives, SPRINGER, Singapore, 2018.

  39. Dipannita Hazra and Atul K Upadhyay*: Computational tools and databases of microbes and its bioprospecting for sustainable development, SPRINGER, 2018.

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.


  • 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.