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Gautam, Sakshi and Thakur, Anamika and Rajput, Akanksha and Kumar, Manoj (2023) Anti-Dengue: A Machine Learning-Assisted Prediction of Small Molecule Antivirals against Dengue Virus and Implications in Drug Repurposing. VIRUSES-BASEL, 16 (1).
Mukhopadhyay, A and Choudhury, Shubham and Kumar, Manoj (2023) Metaviromic analyses of DNA virus community from sediments of the N-Choe stream, North India. Virus Research, 330.
Gupta, Amit and Kumar, Manoj (2023) An integrative approach toward identification and analysis of therapeutic targets involved in HPV pathogenesis with a focus on carcinomas. Cancer Biomarkers , 36 (1). pp. 32-52.
Thakur, Anamika and Kumar, Manoj (2022) AntiVIRmiR: A repository of host antiviral miRNAs and their expression along with experimentally validated viral miRNAs and their targets. FRONTIERS IN GENETICS, 13.
Rajput, Akanksha and Bhamare, Kailash T. and Thakur, Anamika and Kumar, Manoj (2022) Biofilm-i: A Platform for Predicting Biofilm Inhibitors Using Quantitative Structure-Relationship (QSAR) Based Regression Models to Curb Antibiotic Resistance. MOLECULES, 27 (15).
Gupta, Amit Kumar and Kumar, Manoj (2022) Benchmarking and Assessment of Eight De Novo Genome Assemblers on Viral Next-Generation Sequencing Data, Including the SARS-CoV-2. OMICS: A Journal of Integrative Biology, 26 (7).
Kamboj, Sakshi and Rajput, Akanksha and Rastogi, Amber and Thakur, Anamika and Kumar, Manoj (2022) Targeting non-structural proteins of Hepatitis C virus for predicting repurposed drugs using QSAR and machine learning approaches. Computational and Structural Biology , 20. pp. 3422-3438.
Randhawa, Vinay and Pathania, Shivalika and Kumar, Manoj (2022) Computational Identification of Potential Multitarget Inhibitors of Nipah Virus by Molecular Docking and Molecular Dynamics. Microorganisms, 10 (6).
Patidar , Anil and Malhotra, Himanshu and Chaudhary, Surbhi and Kumar, Manoj and Dilawari, Rahul and Chaubey, Gaurav Kumar and Dhiman, Asmita and Modanwal , Radheshyam and Talukdar, Sharmila and Raje , Chaaya Iyengar and Raje, Manoj (2022) Host glyceraldehyde-3-phosphate dehydrogenase-mediated iron acquisition is hijacked by intraphagosomal Mycobacterium tuberculosis. Cellular and Molecular Life Sciences , 79 (1).
Randhawa, Vinay and Kumar, Manoj (2021) An integrated network analysis approach to identify potential key genes, transcription factors, and microRNAs regulating human hematopoietic stem cell aging. MOLECULAR OMICS. pp. 967-984.
Rajput, Akanksha and Thakur, Anamika and Rastogi, Amber and Choudhury, Shubham and Kumar, Manoj (2021) Computational identification of repurposed drugs against viruses causing epidemics and pandemics via drug-target network analysis. COMPUTERS IN BIOLOGY AND MEDICINE, 136.
Rajput, Akanksha and Kumar, Manoj (2021) Anti-Ebola: an initiative to predict Ebola virus inhibitors through machine learning. MOLECULAR DIVERSITY.
Randhawa, Vinay and Kumar, Manoj (2021) Analysis of aging-related protein interactome and cross-network module comparisons across tissues provide new insights into aging. COMPUTATIONAL BIOLOGY AND CHEMISTRY, 92.
Rajput, Akanksha and Thakur, Anamika and Mukhopadhyay, Adhip and Kamboj, Sakshi and Rastogi, Amber and Gautam, Sakshi and Jassal, Harvinder and Kumar, Manoj (2021) Prediction of repurposed drugs for Coronaviruses using artificial intelligence and machine learning. COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL, 19. pp. 3133-3148.
Kumar, Narender and Gupta, Amit Kumar and Sudan, Sarabjeet Kour and Pal, Deepika and Randhawa, Vinay and Sahni, Girish and Mayilraj, Shanmugam and Kumar, Manoj (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 (Larchmont, N.Y.). ISSN 1931-8448
Rajput, Akanksha and Kumar, Archit and Megha, Kirti and Thakur, Anamika and Kumar, Manoj (2021) DrugRepV: a compendium of repurposed drugs and chemicals targeting epidemic and pandemic viruses. Briefings in Bioinformatics, 22 (2). pp. 1076-1084. ISSN 1467-5463
Pathania, Shivalika and Randhawa, Vinay and Kumar, Manoj (2019) Identifying potential entry inhibitors for emerging Nipah virus by molecular docking and chemical-protein interaction network. Journal of biomolecular structure & dynamics. pp. 1-18. ISSN 1538-0254
Rajput, Akanksha and Kumar, Archit and Kumar, Manoj (2019) Computational Identification of Inhibitors Using QSAR Approach Against Nipah Virus. Frontiers in pharmacology, 10. p. 71. ISSN 1663-9812
Chauhan, Anoop Singh and Kumar, Manoj and Chaudhary, Surbhi and Dhiman, Asmita and Patidar, Anil and Jakhar, Priyanka and Jaswal, Pallavi and Sharma, Kapil and Sheokand, Navdeep and Malhotra, Himanshu and Raje, Chaaya Iyengar and Raje, Manoj (2019) Trafficking of a multifunctional protein by endosomal micro-autophagy: linking two independent unconventional secretory pathways. FASEB journal : official publication of the Federation of American Societies for Experimental Biology. fj201802102R. ISSN 1530-6860
Monga, Isha and Kumar, Manoj (2019) Computational Resources for Prediction and Analysis of Functional miRNA and Their Targetome. Methods in molecular biology (Clifton, N.J.), 1912. pp. 215-250. ISSN 1940-6029
Malhotra, Himanshu and Kumar, Manoj and Chauhan, Anoop Singh and Dhiman, Asmita and Chaudhary, Surbhi and Patidar, Anil and Jaiswal, Pallavi and Sharma, Kapil and Sheokand, Navdeep and Raje, Chaaya Iyengar and Raje, Manoj (2019) Moonlighting Protein Glyceraldehyde-3-Phosphate Dehydrogenase: A Cellular Rapid-Response Molecule for Maintenance of Iron Homeostasis in Hypoxia. Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology, 52 (3). pp. 517-531. ISSN 1421-9778
Rajput, Akanksha and Kumar, Manoj (2018) Anti-flavi: A Web Platform to Predict Inhibitors of Using QSAR and Peptidomimetic Approaches. Frontiers in microbiology, 9. p. 3121. ISSN 1664-302X
Showkat, Ahmad and Kumar, Manoj (2018) saRNAdb: Resource of Small Activating RNAs for Up-regulating the Gene Expression. Journal of molecular biology, 430 (15). pp. 2212-2218. ISSN 1089-8638
Qureshi, Abid and Rajput, Akanksha and Kaur, Gazaldeep and Kumar, Manoj (2018) HIVprotI: an integrated web based platform for prediction and design of HIV proteins inhibitors. Journal of Cheminformatics, 10 (1). ISSN 1758-2946
Rajput, Akanksha and Thakur, Anamika and Sharma, Shivangi and Kumar, Manoj (2018) aBiofilm: a resource of anti-biofilm agents and their potential implications in targeting antibiotic drug resistance. Nucleic Acids Research, 46 (D1). D894-D900. ISSN 0305-1048
Monga, Isha and Qureshi, Abid and Thakur, Nishant and Gupta, Amit Kumar and Kumar, Manoj (2017) ASPsiRNA: A Resource of ASP-siRNAs Having Therapeutic Potential for Human Genetic Disorders and Algorithm for Prediction of Their Inhibitory Efficacy. G3 (Bethesda, Md.), 7 (9). pp. 2931-2943. ISSN 2160-1836
Rajput, Akanksha and Kumar, Manoj (2017) Computational Exploration of Putative LuxR Solos in Archaea and Their Functional Implications in Quorum Sensing. Frontiers in Microbiology, 8. ISSN 1664-302X
Rajput, Akanksha and Kumar, Manoj (2017) In silico analyses of conservational, functional and phylogenetic distribution of the LuxI and LuxR homologs in Gram-positive bacteria. Scientific Reports, 7 (1). ISSN 2045-2322
Chauhan, Anoop Singh and Kumar, Manoj and Chaudhary, Surbhi and Patidar, Anil and Dhiman, Asmita and Sheokand, Navdeep and Malhotra, Himanshu and Raje, Chaaya Iyengar and Raje, Manoj (2017) Moonlighting glycolytic protein glyceraldehyde-3-phosphate dehydrogenase (GAPDH): an evolutionarily conserved plasminogen receptor on mammalian cells. The FASEB Journal, 31 (6). pp. 2638-2648. ISSN 0892-6638
Thakur, A and Qureshi, Abid and Kumar, Manoj (2017) vhfRNAi: a web-platform for analysis of host genes involved in viral infections discovered by genome wide RNAi screens. Molecular BioSystems, 13 (7). pp. 1377-1387. ISSN 1742-206X
Dar, Showkat Ahmad and Gupta, Amit Kumar and Thakur, Anamika and Kumar, Manoj (2016) SMEpred workbench: a web server for predicting efficacy of chemically modified siRNAs. RNA biology. ISSN 1555-8584
Thakur, Anamika and Rajput, Akanksha and Kumar, Manoj (2016) MSLVP: prediction of multiple subcellular localization of viral proteins using a support vector machine. Molecular bioSystems, 12 (8). pp. 2572-86. ISSN 1742-2051
Malhotra, Himanshu and Sheokand, Navdeep and Kumar, Santosh and Chauhan, Anoop S and Kumar, Manoj and Jakhar, Priyanka and Boradia, Vishant M and Raje, Chaaya I and Raje, Manoj (2016) Exosomes: Tunable Nano Vehicles for Macromolecular Delivery of Transferrin and Lactoferrin to Specific Intracellular Compartment. Journal of biomedical nanotechnology, 12 (5). pp. 1101-14. ISSN 1550-7033
Sheokand, Navdeep and Malhotra, Himanshu and Chauhan, Anoop Singh and Kumar, Manoj and Chaudhary, Surbhi and Patidar, Anil and Boradia, Vishant Mahendra and Raje, Chaaya Iyengar and Raje, Manoj (2016) Reverse overshot water-wheel retroendocytosis of Apo Transferrin extrudes cellular iron. Journal of cell science, 129. pp. 843-53. ISSN 1477-9137
Rajput, Akanksha and Kaur, Karambir and Kumar, Manoj (2016) SigMol: repertoire of quorum sensing signaling molecules in prokaryotes. Nucleic acids research, 44 (D1). D634-9. ISSN 1362-4962
Khan, Mohd Shoaib and Gupta, Amit Kumar and Kumar, Manoj (2016) ViralEpi v1.0: a high-throughput spectrum of viral epigenomic methylation profiles from diverse diseases. Epigenomics, 8 (1). pp. 67-75. ISSN 1750-192X
Qureshi, Abid and Kaur, Gazaldeep and Kumar, Manoj (2016) AVCpred: an integrated web server for prediction and design of antiviral compounds. Chemical Biology & Drug Design, 89 (1). pp. 74-83. ISSN 17470277
Boradia, Vishant Mahendra and Patil, Pravinkumar and Agnihotri, Anushri and Kumar, Ajay and Rajwadi, Kalpesh Kumar and Sahu, Ankit and Bhagath, Naveen and Sheokand, Navdeep and Kumar, Manoj and Malhotra, Himanshu and Patkar, Rachita and Hasan, Navi and Raje, Manoj and Raje, Chaaya Iyengar (2016) Mycobacterium tuberculosis H37Ra: a surrogate for the expression of conserved, multimeric proteins of M.tb H37Rv. Microbial cell factories, 15 (1). p. 140. ISSN 1475-2859
Gupta, Amit Kumar and Kaur, Karambir and Rajput, Akanksha and Dhanda, Sandeep Kumar and Sehgal, Manika and Khan, Md Shoaib and Monga, Isha and Dar, Showkat Ahmad and Singh, Sandeep and Nagpal, Gandharva and Usmani, Salman Sadullah and Thakur, Anamika and Kaur, Gazaldeep and Sharma, Shivangi and Bhardwaj, Aman and Qureshi, Abid and Raghava, G.P.S. and Kumar, Manoj (2016) ZikaVR: An Integrated Zika Virus Resource for Genomics, Proteomics, Phylogenetic and Therapeutic Analysis. Scientific reports, 6. p. 32713. ISSN 2045-2322
Kaur, Karambir and Gupta, Amit Kumar and Rajput, Akanksha and Kumar, Manoj (2016) ge-CRISPR - An integrated pipeline for the prediction and analysis of sgRNAs genome editing efficiency for CRISPR/Cas system. Scientific reports, 6. p. 30870. ISSN 2045-2322
Dar, Showkat Ahmad and Thakur, Anamika and Qureshi, Abid and Kumar, Manoj (2016) siRNAmod: A database of experimentally validated chemically modified siRNAs. Scientific reports, 6. p. 20031. ISSN 2045-2322
Qureshi, Abid and Tandon, Himani and Kumar, Manoj (2015) AVP-IC50 Pred: Multiple machine learning techniques-based prediction of peptide antiviral activity in terms of half maximal inhibitory concentration (IC50 ). Biopolymers, 104 (6). pp. 753-63. ISSN 1097-0282
Kaur, Karambir and Tandon, Himani and Gupta, Amit Kumar and Kumar, Manoj (2015) CrisprGE: a central hub of CRISPR/Cas-based genome editing. Database : the journal of biological databases and curation, 2015. ISSN 1758-0463
Gupta, Amit Kumar and Kumar, Manoj (2015) HPVbase--a knowledgebase of viral integrations, methylation patterns and microRNAs aberrant expression: As potential biomarkers for Human papillomaviruses mediated carcinomas. Scientific reports, 5. p. 12522. ISSN 2045-2322
Rajput, Akanksha and Gupta, Amit Kumar and Kumar, Manoj (2015) Prediction and analysis of quorum sensing peptides based on sequence features. PloS one, 10 (3). e0120066. ISSN 1932-6203
Qureshi, Abid and Thakur, Nishant and Tandon, Himani and Kumar, Manoj (2014) AVPdb: a database of experimentally validated antiviral peptides targeting medically important viruses. Nucleic acids research, 42 (Databa). D1147-53. ISSN 1362-4962
Qureshi, Abid and Thakur, Nishant and Monga, Isha and Thakur, Anamika and Kumar, Manoj (2014) VIRmiRNA: a comprehensive resource for experimentally validated viral miRNAs and their targets. Database : the journal of biological databases and curation, 2014. ISSN 1758-0463
Qureshi, Abid and Thakur, Nishant and Kumar, Manoj (2013) VIRsiRNApred: a web server for predicting inhibition efficacy of siRNAs targeting human viruses. Journal of translational medicine, 11. p. 305. ISSN 1479-5876
Qureshi, Abid and Thakur, Nishant and Kumar, Manoj (2013) HIPdb: A Database of Experimentally Validated HIV Inhibiting Peptides. PloS one, 8 (1). e54908. ISSN 1932-6203
Thakur, Nishant and Qureshi, Abid and Kumar, Manoj (2012) AVPpred: collection and prediction of highly effective antiviral peptides. Nucleic acids research, 40 (Web Se). W199-204. ISSN 1362-4962
Thakur, Nishant and Qureshi, Abid and Kumar, Manoj (2012) VIRsiRNAdb: a curated database of experimentally validated viral siRNA/shRNA. Nucleic acids research, 40. D230-6. ISSN 1362-4962
Tyagi, Atul and Ahmed, Firoz and Thakur, Nishant and Sharma, Arun and Raghava, G.P.S. and Kumar, Manoj (2011) HIVsirDB: A Database of HIV Inhibiting siRNAs. PloS one, 6 (10). e25917. ISSN 1932-6203
Kukreti, Himani and Mittal, Veena and Chaudhary, Artee and Rautela, Rajendra Singh and Kumar, Manoj and Chauhan, Sheetal and Bhat, Sunil and Chhabra, Mala and Bhattacharya, Dipesh and Pasha, Syed Tazeen and Kumar, Devinder and Gomber, Sunil and Lal, Shiv and Rai, Arvind (2010) Continued persistence of a single genotype of dengue virus type-3 (DENV-3) in Delhi, India since its re-emergence over the last decade. Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi, 43 (1). pp. 53-61. ISSN 1995-9133
Kumar, Manoj and Jain, Swatantra Kumar and Pasha, S.T and Chattopadhaya, Debasish and Lal, Shiv and Rai, Arvind (2006) Genomic diversity in the regulatory nef gene sequences in Indian isolates of HIV type 1: emergence of a distinct subclade and predicted implications. AIDS research and human retroviruses, 22 (12). pp. 1206-19. ISSN 0889-2229
Dash, Paban Kumar and Parida, Man Mohan and Saxena, Parag and Kumar, Manoj and Rai, Arvind and Pasha, S.T and Jana, Asha Mukul (2004) Emergence and continued circulation of dengue-2 (genotype IV) virus strains in northern India. Journal of medical virology, 74 (2). pp. 314-22. ISSN 0146-6615
Kumar, Manoj and Pasha, S.T and Mittal, V. and Arya, S.C. and Agrawal, N. and Bhattacharya, D. and Shiv, Lal and Rai, Arvind (2004) Unusual emergence of guate98-like molecular subtype of DEN-3 during 2003 dengue outbreak in Delhi. Dengue Bulletin, 28. pp. 457-461.
Kumar, Manoj and Rajput, Akanksha (2018) Phylogenomics and Evolutionary Perspective of Quorum Sensing Regulators (LuxI/LuxR) in Prokaryotes. In: Quorum Sensing and its Biotechnological Applications. Springer, Singapore, pp. 61-70.
Rajput, Akanksha and Kumar, Manoj (2018) Anti-biofilm Peptides: A New Class of Quorum Quenchers and Their Prospective Therapeutic Applications. In: Biotechnological Applications of Quorum Sensing Inhibitors. Springer, Singapore, pp. 87-110.
