Computational Biology, Genomics and Plant Biotechnology
Dr. Atul Kumar Upadhyay is working as Assistant professor in Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala since 2019. He completed his PhD 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 classification of biological data to infer their biological functions.
- PhD 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. (Honrs.), Chandra Shekhar Azad University of Agriculture & Technology, Kanpur, India (2007)
- Genomics and proteomics
- Plant Biotechnology
- Molecular Biology
- 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
- Atul K Upadhyay, et al., 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 (IF: 4.8)
- 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.
- 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. (IF: 2.8)
- Pasha SN, Shafi M, Joshi A, Meenakshi, Harini K, Mahita J, Sanjeevan RS, Karpe SD, Ghosh P, Nitesh S, Gandhimathi A, Mathew OK, Prasanna Sh, Malini M, Mutt E, Ravooru N, Rao RM, Shingate PN, Sukhwal A, Sunitha MS, Upadhyaya AK, Vinekar RS, Sowdhamini R: 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. (IF: 3.1)
- 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, DOI: 10.1007/s10989-019-09818-2. (IF: 1.6)
- Sharma G, Upadhyay AK et al., 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: https://doi.org/10.1007/s12041-019-1066-5. (IF: 1.2)
- 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. (IF: 4.4)
- 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). (IF: 11.8)
- 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).
Book chapter and review articles
- Prashant Shingate, Atul K Upadhyay, U S Raghavender and R. Sowdhamini: Identification and conformational analysis of hinge regions in proteins that undergo domain swapping. 01/2013.
- 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, 2018.
- Dipannita Hazra and Atul K Upadhyay: Computational tools and databases of microbes and its bioprospecting for sustainable development, SPRINGER, 2018.
- 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,  2018.
- 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.
Conference papers and abstracts
- 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.
- 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.
- 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
- 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
- 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.
Seminars, workshops and training courses
- Conducted a national workshop on “Next Generation Sequencing (NGS) data analysis” 30-31 March 2018, Lovely Professional University, Punjab.
- Participated in 5 days training on “Effective Teaching” conducted by National Institute of Technical Teachers Training Research, Chandigarh, 12 – 16 February 20018.
- Participated in 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 village, Nangapur, Uttar Pradesh, India
Achievements, Awards and Recognitions
- Cleared All India entrance for graduate studies, ICAR, India, 2003-2007.
- Gold medalist in B.Sc. (Agri.) Honors from 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 “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 PhD (5 Yrs.)
- Participated as a player in the 7th All India Inter Agriculture University sports and games meet, 2005- 06.