Publications

Journal Articles

Verma N, Sharma T, Bhardwaj A*, Vemuluri VR*. Comparative genomics and characterization of a multidrug-resistant Acinetobacter baumannii VRL-M19 isolated from a crowded setting in India. Infect Genet Evol. 2024 January 3. doi:10.1016/j.meegid.2023.105549
Sharma T, Kumar R, Kalra JS, Singh S, Bhalla GS, Bhardwaj A*. Galaxy ASIST: A web-based platform for mapping and assessment of global standards of antimicrobial susceptibility: A case study in Acinetobacter baumannii genomes. Front Microbiol. 2023;13:1041847. 2023 Jan 27. doi:10.3389/fmicb.2022.1041847
Singh V, Pandey S, Bhardwaj A*. From the reference human genome to human pangenome: Premise, promise and challenge. Front Genet. 2022 Nov 10;13:1042550
Singh P, Ujjainiya R, Prakash S, et al. A machine learning-based approach to determine infection status in recipients of BBV152 (Covaxin) whole-virion inactivated SARS-CoV-2 vaccine for serological surveys. Comput Biol Med. 2022;146:105419. doi:10.1016/j.compbiomed.2022.105419
Kumar R, K Rajput N, Jolly B, Narwade A, Bhardwaj A*. MitoLink: A generic integrated web-based workflow system to evaluate genotype-phenotype correlations in human mitochondrial diseases: Observations from the GenomeAsia Pilot project. Mitochondrion. 2021 Sep 24;61:54-61
Kalra R, Tiwari D, Dkhar HK, Bhagyaraj E, Kumar R, Bhardwaj A, Gupta P. Host factors subverted by Mycobacterium tuberculosis: Potential targets for host directed therapy. Int Rev Immunol. 2021 Oct 22:1-28
Choudhury C, Bhardwaj A*. Hybrid dynamic pharmacophore models as effective tools to identify novel chemotypes for anti-TB inhibitor design: A case study with Mtb-DapB. Front. Chem. | doi: 10.3389/fchem.2020.596412. 2020 Oct 28.
McCormick EM, Lott MT, Dulik MC, Shen L, Attimonelli M, Vitale O, Karaa A, Bai R, Pineda-Alvarez DE, Singh LN, Stanley CM, Wong S, Bhardwaj A, Merkurjev D, Mao R, Sondheimer N, Zhang S, Procaccio V, Wallace DC, Gai X, Falk MJ. Specifications of the ACMG/AMP standards and guidelines for mitochondrial DNA variant interpretation. Hum Mutat. doi: 10.1002/humu.24107. 2020 Sep 9.
Bhardwaj A* et al. MtBrowse: An integrative genomics browser for human mitochondrial DNA. Mitochondrion. 2019 Feb 7.
Bhardwaj A*, et al. RepTB: A Gene Ontology based drug-repurposing approach for tuberculosis. J Cheminform. 2018, 21; 10 (1): 24.
Bhardwaj A et al. Assessing therapeutic potential of molecules: molecular property diagnostic suite for tuberculosis (MPDSTB). J. Chem Sci. 2017, 129 (5), 515-531.
Bhardwaj A* et al. dPABBs: A Novel in silico Approach for Predicting and Designing Antibiofilm Peptides. Sci. Rep. 2016, 25; 6: 21839.
Saraav I, Pandey K, Sharma M, Singh S, Dutta P, Bhardwaj A, Sharma S. Predicting promiscuous antigenic T cell epitopes of Mtb mymA operon proteins binding to MHC Class I and Class II molecules. Infection, Genetics and Evolution. 2016, 5; 44:182-189.
Bhardwaj A* et al. FROG - Fingerprinting Genomic Variation Ontology. PLoS One 2015, 10(8): e0134693.
Bhardwaj A* et al. Resources, Challenges and Way Forward in Rare Mitochondrial Diseases Research. F1000Research 2015, 4:70.
Pandey K, Sharma M, Saarava I, Singha S, Dutta P, Bhardwaj A, Sharma S. Analysis of the DosR Regulon Genes to Select Cytotoxic T Lymphocyte Epitope Specific Vaccine Candidates Using a Reverse Vaccinology Approach. Int J Mycobacteriol 2015.
Bhardwaj A* et al. BioPhytMol: A Drug Discovery Community Resource on Antimycobacterial Phytomolecules and Plant Extracts. J Cheminform 2014, 6 (1).
Bhardwaj A*. Investigating the Role of Site Specific Synonymous Variation in Disease Association Studies. Mitochondrion, 2014, 16(83), 8.
Vashisht R, Bhat AG, Kushwaha S, Bhardwaj A, OSDD Consortium, Brahmachari SK. Systems Level Mapping of Metabolic Complexity in Mycobacterium tuberculosis to Identify High-value Drug Targets. J Transl Med. 2014, 11; 12(1), 263.
Bhardwaj A* et al. Open Access Mycobacterium tuberculosis Clone Repository: a Community Resource by OSDD members. Current Science, 2013, 105 (10), 25.
Vashisht R, Bhardwaj A, OSDD Consortium, Brahmachari SK. Social networks to biological networks: systems biology of Mycobacterium tuberculosis. Mol. BioSyst. 2013, 9, 1584-1593.
Bhardwaj A* et al. MitoLSDB: A Comprehensive Resource to Study Genotype to Phenotype Correlations in Human Mitochondrial DNA Variations. PLoS One 2013, 8 (4), e60066.
Raghava GPS, Bhardwaj A et al. Open Source Software and Web Services for Designing Therapeutic Molecules. Current Topics in Medicinal Chemistry 2013, 13 (10), 1172-1191.
Bhardwaj A* et al. Crowd Sourcing a New Paradigm for Interactome Driven Drug Target Identification in Mycobacterium tuberculosis. PLoS One 2012; 7 (7), e39808.
Anand P, Sankaran S, Mukherjee S, Yeturu K, Laskowski R, Bhardwaj A, Bhagavat R; OSDD Consortium, Brahmachari SK, Chandra N. Structural Annotation of Mycobacterium tuberculosis Proteome. PLoS One. 2011; 6(10): e27044.
Bhardwaj A, Scaria V, Raghava GPS, Lynn AM, Chandra N, Banerjee S, Raghunandanan MV, Pandey V, Taneja B, Yadav J, Dash D, Bhattacharya J, Misra A, Kumar A, Ramachandran S, Thomas Z. Open Source Drug Discovery Consortium, Brahmachari SK, Open Source Drug Discovery- a new paradigm of collaborative research in Tuberculosis drug development. Tuberculosis, 2011 Sep; 91(5): 479-86.
Bhartiya D, Maini J, Sharma M, Joshi P, Laddha SV, Jalali S, Patowary A, Purkanti R, Lalwani M, Singh AR, Chauhan R, Singh N, Bhardwaj A, Scaria V, Sivasubbu S. FishMap Zv8 update-A Genomic Regulatory Map of Zebrafish. Zebrafish, 2010, 7(2), 179-80.
Bhardwaj A, Bhartiya D, Kumar N, Open Source Drug Discovery Consortium, Scaria V. TBrowse: an Integrative Genomics Map of Mycobacterium tuberculosis. Tuberculosis, 2009, 89, 386–387.
Bhardwaj A*, et al. MtSNPscore: A Combined Evidence Approach for Assessing Cumulative Impact of Mitochondrial Variations in Disease. BMC Bioinformatics, 2009, 10 (Suppl 8), S7.
Bhardwaj A. et al. Mycobacterium tuberculosis systems biology data in R, Biobytes, 2009, 5, 40-48.
Indian Genome Variation Consortium. Genetic landscape of the people of India: a canvas for disease gene exploration. J. Genet. 2008, 87, 3–20.
Bhardwaj A, Tiwari S. Evaluating the Association of Mitochondrial SNP Haplotypes with Disease Phenotypes using a Novel in silico Tool E-MIDAS. ICIT, 9th International Conference on Information Technology (ICIT'06), 2006, 17-20.

Science Translational Medicine Editor Choice Articles

Bhardwaj A*, Personalized cancer medicines. Sci. Transl. Med. 25 March 2015, 280ec48.
Bhardwaj A*, A molecular patch for DMD. Sci. Transl. Med. 11 Feb 2015, 7:274ec24.
Bhardwaj A*, Ctrl-Alt-Del: Host-Targeting Anti-Angiogenic Agents as Adjunct Therapy for Tuberculosis. Sci. Transl. Med. 24 Dec 2014 6:268ec218.
Bhardwaj A*, Cholesterol Therapy That’s Not Chopped Liver. Sci. Transl. Med. 12 Nov 2014 6:262ec193.
Bhardwaj A*, Synthetic Lethality: Drug Repurposing with a Difference. Sci. Transl. Med. 1 Oct 2014 6:256ec167.
Bhardwaj A*, Harnessing the Crowd for Neurology Research. Sci. Transl. Med. 20 Aug 2014 6:250ec141.
Bhardwaj A*, Dissecting the Enigma of Mycobacterium tuberculosis Pathogenesis. Sci. Transl. Med. 9 July 2014 6:244ec116.
Bhardwaj A*, Reactive Species Contribute to Antibiotic-Mediated Killing. Sci. Transl. Med. 28 May 2014 6:238ec92.
Bhardwaj A*, “Antigenomic” RNA as a Therapeutic Tool for Mitochondrial Diseases. Sci. Transl. Med. 16 April 2014 6:232ec66.

Book Chapters

Bhardwaj A* et al. Lipid biosynthetic pathways as potential drug targets for emerging mycobacterial pathogens, Biology of Mycobacterial Lipids, Elsevier 2021 .
Bhardwaj A* et al. Data-driven Systems Level Approaches for Drug Repurposing: Combating Drug Resistance in Priority Pathogens, 1st Edition, In Silico Drug Design-Repurposing Techniques and Methodologies, Elsevier 2019.
Bhardwaj A* et al. Mitochondrial Genomics- Emerging Paradigms and Challenges. Medical and Health Genomics, 1st Edition, Elsevier 2016.
Bhardwaj A et al. Software Platform for Metabolic Network Reconstruction of Mycobacterium tuberculosis. Springer - Systems Biology of Tuberculosis 2013, 21.
Bhardwaj A*, Scaria V, Thomas Z, Adayikkoth S, Open Source Drug Discovery Consortium, Brahmachari SK. Book chapter entitled “Collaborative tools to accelerate neglected diseases research” in the book “Collaborative Computational Technologies for Biomedical Research”. Wiley and Sons. May 2011.