Dr. Manoj Kumar

Biography

Major Research Activities: Viral Bioinformatics/ Computational Biology/ Viral Genomics  Development of bioinformatics tools for RNAi (Antiviral siRNA, antiviral miRNA, Allele-specific siRNA, Genome wide-RNAi etc)  To develop in-silico resources for peptides (Antiviral peptides, anti-HIV peptides, Neuropeptides etc)  Prediction of potential vaccine /drug candidates for viruses  To develop prediction tools for Post Translational Modifications-PTMs  Development of in-silico tools for Quorum sensing / Bio-film phenomenon  Bioinformatics resources for CRISPR- an antiviral defense mechanism in prokaryotes  Annotation and analysis of the Next Generation Sequencing (NGS) data  Comparative and evolutionary genomics of important human viruses Past Research Work: Molecular Epidemiology (Epidemic/outbreak associated disease pathogens specially Viruses) I worked at Division of Biochemistry & Biotechnology, National Centre for Diseases Control (erstwhile: National Institute of Communicable Diseases) 22-Shamnath Marg, Delhi-110054, from 1996 to 2004. I have nine years experience in molecular characterization (Diagnosis, Strain differentiation, Drug resistance and Genotyping) of etiological pathogen involved in major EPIDEMICS/OUTBREAKS in INDIA under biosefety requirements (BSL-2/3) especially HIV, Dengue, influenza, Hepatitis, Polio, paramyxovirus, SARS, Yersinia pestis, Bacillus anthracis and M. tuberculosis etc. Selected list of Publications and Patents  * Corresponding Author Amit Kumar Gupta and Manoj Kumar*, HPVbase – a knowledgebase of viral integrations, methylation patterns and microRNAs aberrant expression: As potential biomarkers for Human papillomaviruses mediated carcinomas. Scientific Reports. 2015, 5, 12522; doi: 10.1038/srep12522. (Impact Factor 5.578) Karambir Kaur, Himani Tandon, Amit Kumar Gupta and Manoj Kumar*, CrisprGE: A central hub of CRISPR/Cas based genome editing. Database (Oxford). 2015. doi: 10.1093/database/bav055. (Impact Factor 4.457) Rajput A, Gupta AK, Kumar M*. Prediction and analysis of quorum sensing peptides based on sequence features. PLoS One. 2015 Mar 17;10(3):e0120066. doi: 10.1371/journal.pone.0120066. (Impact Factor 3.534) Qureshi A, Thakur N, Monga I, Thakur A, Kumar M*, VIRmiRNA: a comprehensive resource for experimentally validated viral miRNAs and their targets. Database (Oxford). 2014 Nov 7; 2014. doi: 10.1093/database/bau103. (Impact Factor 4.457) Qureshi A, Thakur N, Tandon H, Kumar M*, AVPdb: a database of experimentally validated antiviral peptides targeting medically important viruses. Nucleic Acids Res., 2014, 42 (D1), D1147-D1153 (Impact Factor 8.808) Qureshi A, Thakur N, Kumar M*, VIRsiRNApred: a web server for predicting inhibition efficacy of siRNAs targeting human viruses. Journal of translational medicine, 2013, 11 (1), 305 (Impact Factor 3.991) Qureshi A, Thakur N, Kumar M*, HIPdb: A database of experimentally validated HIV inhibiting peptides. PLoS ONE, 2013. 8(1): e54908. doi:10.1371/journal.pone.0054908. (Impact Factor 3.534) Thakur N, Qureshi A, Kumar M*, AVPpred: Collection and prediction of highly effective antiviral peptides. Nucleic Acids Res. 2012 Jul;40(Web Server issue):W199-204. Epub 2012 May 25. doi: 10.1093/nar/gks450. (Impact Factor 8.808) Thakur N, Qureshi A, Kumar M*, VIRsiRNAdb: a curated database of experimentally validated viral siRNA/shRNA. Nucleic Acids Res., 2012, 40(D1): D230-D236 doi:10.1093/nar/gkr1147. (Impact Factor 8.808) Tyagi A, Ahmed F, Thakur N, Sharma A, Raghava GPS and Kumar M*, HIVsirDB: A Database of HIV Inhibiting siRNAs. PLoS ONE, 2011, 6(10): e25917. doi:10.1371/journal.pone.0025917. (Impact Factor 3.534) Kumar M, Jain SK, Pasha ST, Chhatopadhyay D, Lal S and Rai A. Genomic diversity in the regulatory nef gene sequences in Indian isolates of HIV-1: emergence of a distinct subclade and predicted implications. AIDS Research and Human Retroviruses, 2006, 22(12), 1206-1219. (Impact Factor 2.705) Kumar M, Pasha ST, Mittal V, Rawat DS, Arya SC, Agarwal N, Bhattacharya D, Lal S and Rai A. Unusual emergence of guate98-like molecular subtype of DEN-3 during 2003 dengue outbreak in Delhi. Dengue Bulletins, 2004, 28, 161-167. (A WHO Publication) Dash, P.K., Parida, M.M., Saxena, P., Kumar M., Rai, A., Pasha, S.T. and Jana, A.M. Emergence and continued circulation of dengue-2 (genotype IV) virus strains in northern India. Journal of Medical Virology, 2004, 74, 314-322. (Impact Factor 2.373) Copyrights 11

Research Interest

My research interest is in viral bioinformatics and comparative/evolutionary genomics especially of human viruses namely HIV, Dengue, Influenza, Ebola, Hepatitis, HPV, EBV and Phages etc. Our lab involved in the development of prediction algorithms, web servers, databases and high throughput data analysis to solve biological problems. Also interested in wet lab validation of our bioinformatics predictions and NGS based viral genomics research work.