Dr. Atul Kumar Upadhyay
Computational Biology, Genomics and Plant Biotechnology
Computational Biology, Genomics and Plant Biotechnology
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).
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.
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.
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
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
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.
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
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.
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
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.
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
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.
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.
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  2017; DOI: 10.21506/j.ponte.2017.9.11
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.
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  07/2017; DOI: 10.21506/j.ponte.2017.7.32
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.
Nancy Bhura and Atul K Upadhyay*: Overview of a typical next generation sequencing (NGS) project. IJSSR, 2017, 42(2): 190-195.
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.
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).
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
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.
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).
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
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.
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
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.
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.
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.
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.
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.
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.
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.
Dipannita Hazra and Atul K Upadhyay*: Computational tools and databases of microbes and its bioprospecting for sustainable development, SPRINGER, 2018.