I am currently working as Project Associate-II at Bioinformatics Centre and Virology Unit, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India. I have recently finished doctoral training (Ph.D. thesis submitted, November 2020) as a DST-INSPIRE Fellow at CSIR-IMTECH, Chandigarh, India, under the supervision of Dr. Manoj Kumar, Principal Scientist and Head Virology Unit. I have completed a Master of Science (M.Sc.) in Bioinformatics from Manipal Life Sciences Centre (MLSC), Manipal University, Karnataka, in 2012 with the distinction (First Rank). I have done graduation (B.Sc. Bioinformatics, Biotechnology, Computer science) from Devi Ahilya Vishwavidyalaya (DAVV), Indore (M.P.), in 2009.
As a part of research work, I have completed several independent and collaborative projects successfully focusing on the development of computational web resources, machine learning prediction algorithms, HPV and carcinoma, viromics, NGS, and metagenomics.
Google Scholar:https://scholar.google.com/citations?user=DLKvqVsAAAAJ
ORCID iD: https://orcid.org/0000-0002-8395-1201
Narender Kumar#, Amit Kumar Gupta#, Sarabjeet Kour Sudan#, Deepika Pal, Vinay Randhawa, Girish Sahni, Shanmugam Mayilraj* and Manoj Kumar*. (2021) Abundance and diversity of phages, microbial taxa and antibiotic resistance genes in the sediments of the river Ganges through metagenomic approach. Microbial Drug Resistance. (Impact Factor-2.5)
Amit Kumar Gupta and Manoj Kumar*. (2020) HPVomics: an integrated resource for the human papillomavirus epitome and therapeutics. Genomics 112 (6) 4853-4862. (Impact Factor-6.205)
Amit Kumar Gupta#, Md. Shoaib Khan#, Shubham Choudhury#, Adhip Mukhopadhyay#, Sakshi#, Amber Rastogi#, Anamika Thakur, Pallawi Kumari, Manmeet Kaur, Shalu, Chanchal Saini, Vandna Sapehia, Barkha, Pradeep Kumar Patel, Kailash T. Bhamare and Manoj Kumar*. (2020) CoronaVR: A Computational Resource and Analysis of Epitopes and Therapeutics for Severe Acute Respiratory Syndrome Coronavirus-2. Front Microbiol. 2020; 11: 1858. (Impact Factor-4.235)
Amit Kumar Gupta, Archit Kumar, Akanksha Rajput, Karambir Kaur, Anamika Thakur, Showkat Ahmed Dar, Kirti Megha and Manoj Kumar*. (2020) NipahVR: multi-targeted putative therapeutics and epitome resource for the nipah virus. Database, Volume 2020, baz159. (Impact Factor-2.593)
Isha Monga, Abid Qureshi, Nishant Thakur, Amit Kumar Gupta, and Manoj Kumar*. (2017) ASPsiRNA: A Resource of ASP-siRNAs Having Therapeutic Potential for Human Genetic Disorders and Algorithm for Prediction of Their Inhibitory Efficacy. G3: Genes, Genomes, Genetics 7 (9), 2931-2943. (Impact Factor-2.742)
Showkat Ahmad Dar, Amit Kumar Gupta, Anamika Thakur, and Manoj Kumar*. (2016) SMEpred workbench: A web server for predicting efficacy of chemically modified siRNAs. RNA biology 13 (11), 1144-1151. (Impact Factor-4.076)
Karambir Kaur#, Amit Kumar Gupta#, Akanksha Rajput#, and Manoj Kumar*. (2016) ge-CRISPR - An integrated pipeline for the prediction and analysis of sgRNAs genome editing efficiency for CRISPR/Cas system. Sci. Rep. 6, 30870. (Impact Factor-5.228)
Amit Kumar Gupta#, Karambir Kaur#, Akanksha Rajput#, Sandeep Kumar Dhanda#, Manika Sehgal#, Md Shoaib Khan#, Isha Monga, Showkat Ahmad Dar, Sandeep Singh, Gandharva Nagpal, Salman Sadullah Usmani, Anamika Thakur, Gazaldeep Kaur, Shivangi Sharma, Aman Bhardwaj, Abid Qureshi, Gajendra Pal Singh Raghava, and Manoj Kumar*. (2016) ZikaVR: An Integrated Zika Virus Resource for Genomics, Proteomics, Phylogenetic and Therapeutic Analysis. Sci. Rep. 6, 32713. (Impact Factor-5.228)
Amit Kumar Gupta and Manoj Kumar*. (2015) HPVbase- a knowledgebase of viral integrations, methylation patterns and microRNAs aberrant expression: As potential biomarkers for Human papillomaviruses mediated carcinomas. Sci. Rep. 5, 12522. (Impact Factor-5.578)
Md Shoaib Khan#, Amit Kumar Gupta# and Manoj Kumar*. (2015) ViralEpi v1.0: a high-throughput spectrum of viral epigenomic methylation profiles from diverse diseases. Epigenomics: 67-75. (Impact Factor-4.044)
Karambir Kaur, Himani Tandon, Amit Kumar Gupta and Manoj Kumar*. (2015) CrisprGE: a central hub of CRISPR/Cas-based genome editing. Database (Oxford), bav055. (Impact Factor-2.627)
Akanksha Rajput, Amit Kumar Gupta and Manoj Kumar*. (2015) Prediction and Analysis of Quorum Sensing Peptides Based on Sequence Features. PLoS ONE 10(3): e0120066. (Impact Factor-3.057)
Amit Kumar Gupta and Manoj Kumar*. Multi-omics approach towards identification and analysis of therapeutic targets involved in HPV pathogenesis with special focus on carcinomas: Implication in drug repurposing.
Amit Kumar Gupta and Manoj Kumar*. Benchmarking of de novo genome assemblers on the viral next generation sequencing (NGS) data.
Amit Kumar Gupta and Manoj Kumar*. VIRpipe: an integrated pipeline for rapid virus identification and discovery from the clinical and environmental metagenomic samples.
Md Shoaib Khan, Amit Kumar Gupta and Manoj Kumar*. TcellEpi: Prediction of immunogenic and non-immunogenic CD8+ T-cell and CD4+ T-cell epitopes.
Md Shoaib Khan, Amit Kumar Gupta and Manoj Kumar*. BcellEpi: Prediction of linear B-cell epitopes from viruses, bacteria and altered-self.
Amit Kumar Gupta and Manoj Kumar*. Landscape of HPV mediated events as potential biomarkers in diverse carcinomas. Proceedings of VIROCON 2015, XXIV National Conference of Indian Virological Society (IVS) at NEIGRIHMS, Shillong, India
Amit Kumar Gupta and Manoj Kumar*. HPV integration associated genome-wide disruption –A functional and network analysis. Proceedings of NextGen Genomics, Biology and Bioinformatics and Technologies (NGBT) International Conference 2016 organized by SciGenom Research Foundation (SGRF) at Cochin, India
Amit Kumar Gupta and Manoj Kumar*. Pilot study to evaluate the effect of different sequencing platforms and virus species on genome assembly quality. IMTechCon: An Industry- Academia meet, 2017, at CSIR-Institute of Microbial Technology, Chandigarh, India
Md Shoaib Khan, Amit Kumar Gupta and Manoj Kumar*. Comparative analysis of immunogenic viral epitopes with altered-self and bacterial epitopes restricted by HLA-A26/B8: Therapeutic implication for viruses. Proceedings of VIROCON 2015, XXIV National Conference of Indian Virological Society (IVS) at NEIGRIHMS, Shillong, India
Md Shoaib Khan, Amit Kumar Gupta and Manoj Kumar*. Prediction and analysis of viral and bacterial MHC class II immunogenic and non-immunogenic epitopes restricted to human host. INTERVIROCON 2018, International Conference of Virology, Global Viral Epidemics: A Challenging Threat, PGIMER, Chandigarh, India
#Equal contribution, *Corresponding authors