R.  Samson, Shah, M., Yadav, R., Sarode, P., Rajput, V., Dastager, S. G., Dharne, M. S., and Khairnar, K., ?Metagenomic insights to understand transient influence of Yamuna River on taxonomic and functional aspects of bacterial and archaeal communities of River Ganges?, Science of the Total Environment, vol. 674, pp. 288-299, 2019.

R.  Yadav, Rajput, V., Gohil, K., Khairnar, K., and Dharne, M., ?Comprehensive metagenomic insights into a unique mass gathering and bathing event reveals transient influence on a riverine ecosystem?, Ecotoxicology and Environmental Safety, vol. 202, p. 110938, 2020.

R.  Samson, Rajput, V., Shah, M., Yadav, R., Sarode, P., Dastager, S. G., Dharne, M. S., and Khairnar, K., ?Deciphering taxonomic and functional diversity of fungi as potential bioindicators within confluence stretch of Ganges and Yamuna Rivers, impacted by anthropogenic activities?, Chemosphere, vol. 252, 2020.

J.  Chakraborty, Sapkale, V., Shah, M., Rajput, V., Mehetre, G., Agawane, S., Kamble, S., and Dharne, M., ?Metagenome sequencing to unveil microbial community composition and prevalence of antibiotic and metal resistance genes in hypersaline and hyperalkaline Lonar Lake, India?, Ecological Indicators, vol. 110, p. 105827, 2020.

K.  Gohil, Rajput, V., and Dharne, M., ?Pan-genomics of Ochrobactrum species from clinical and environmental origins reveals distinct populations and possible links?, Genomics, vol. 112, no. 5, pp. 3003-3012, 2020.

J.  Chakraborty, Sapkale, V., Rajput, V., Shah, M., Kamble, S., and Dharne, M., ?Shotgun metagenome guided exploration of anthropogenically driven resistomic hotspots within Lonar soda lake of India?, Ecotoxicology and Environmental Safety, vol. 194, p. 110443, 2020.

R.  Yadav, Rajput, V., and Dharne, M., ?Functional metagenomic landscape of polluted river reveals potential genes involved in degradation of xenobiotic pollutants?, Environmental Research, vol. 192, p. 110332, 2021.

R.  Yadav, Rajput, V., and Dharne, M., ?Metagenomic analysis of a mega-city river network reveals microbial compositional heterogeneity among urban and peri-urban river stretch?, Science of the Total Environment, vol. 783, p. 146960, 2021.

M.  Mohapatra, Yadav, R., Rajput, V., Dharne, M. S., and Rastogi, G., ?Metagenomic analysis reveals genetic insights on biogeochemical cycling, xenobiotic degradation, and stress resistance in mudflat microbiome?, Journal of Environmental Management, vol. 292, p. 112738, 2021.

V.  Rajput, Yadav, R., and Dharne, M. S., ?Metagenomic exploration reveals a differential patterning of antibiotic resistance genes in urban and peri-urban stretches of a riverine system?, Environmental Science and Pollution Research, vol. 28, no. 46, pp. 66477-66484, 2021.

J.  Chakraborty, Rajput, V., Sapkale, V., Kamble, S., and Dharne, M., ?Spatio-temporal resolution of taxonomic and functional microbiome of Lonar soda lake of India reveals metabolic potential for bioremediation?, Chemosphere, vol. 264, no. 2, p. 128574, 2021.

V. A.  Prabhu, Rajput, V., Yadav, R., Gohil, K., Dharne, M. S., Unnikrishnan, M. Kesavan, and Gorthi, S. Prasad, ?Gut microbiota dysbiosis in patients with intracranial sino-venous thrombosis and acute ischemic stroke in the young?, Annals of Indian Academy of Neurology, vol. 25, no. 5, p. 980+, 2022.

T.  Dharmadhikari, Rajput, V., Yadav, R., Boargaonkar, R., Patil, D., Kale, S., Kamble, S. P., Dastager, S. G., and Dharne, M. S., ?High throughput sequencing based direct detection of SARS-CoV-2 fragments in wastewater of Pune, West India?, Science of the Total Environment, vol. 807, p. 151038, 2022.

V.  Rajput, Samson, R., Yadav, R., Dastager, S., Khairnar, K., and Dharne, M., ?Metagenomic mining of Indian river confluence reveal functional microbial community with lignocelluloytic potential?, 3 Biotech, vol. 12, no. 6, p. 132, 2022.

V.  Rajput, Pramanik, R., Malik, V., Yadav, R., Samson, R., Kadam, P., Bhalerao, U., Tupekar, M., Deshpande, D., Shah, P., Shashidhara, L. S., Boargaonkar, R., Patil, D., Kale, S., Bhalerao, A., Jain, N., Kamble, S., Dastager, S., Karmodiya, K., and Dharne, M., ?Genomic surveillance reveals early detection and transition of delta to omicron lineages of SARS-CoV-2 variants in wastewater treatment plants of Pune, India?, Environmental Science and Pollution Research , vol. 30, no. 56, pp. 118976-118988, 2023.

R.  Samson, Rajput, V., Yadav, R., Shah, M., Dastager, S., Khairnar, K., and Dharne, M., ?Spatio-temporal variation of the microbiome and resistome repertoire along an anthropogenically dynamic segment of the Ganges River, India?, Science of the Total Environment, vol. 872, p. 162125, 2023.

V.  Rajput, Das, R., Pramanik, R., Nannaware, K., Sushma, Y., Taji, N., Rajput, V., Rajkhowa, R., Pacharne, P., Shah, P., Gogate, N., Sangwar, P., Bhalerao, A., Jain, N., Kamble, S., Dastager, S., Shashidhara, L. S., Karyakarte, R., and Dharne, M., ?Early detection of KP.2 SARS-CoV-2 variant using wastewater-based genomic surveillance in Pune, Maharashtra, India?, Journal of Travel Medicine, 2024.

H. V.  Dhondge, Barvkar, V. T., Dastager, S. G., Dharne, M. S., Rajput, V., Pable, A. A., Henry, R. J., and Nadaf, A. B., ?Genome sequencing and protein modeling unraveled the 2AP biosynthesis in Bacillus cereus DB25?, International Journal of Food Microbiology, vol. 413, p. 110600, 2024.

M.  Kaari, Manikkam, R., Joseph, J., Krishnan, S., Annamalai, K. Kumar, Khan, A., Rajput, V., Dastager, S. Gulam, Dharne, M. S., Umar, M., Venugopal, G., and Alexander, B., ?Integrated genomic and functional analysis of Streptomyces sp. UP1A-1 for bacterial wilt control and solanaceae yield increase?, Gene Reports, vol. 37, 2024.

R.  Pramanik, Rajput, V., Malik, V., Nannaware, K., Matra, S., Joshi, S., Kumar, S., Samson, R., Yadav, R. Kumar, Shah, P., Shashidhara, L. S., Dastager, S., Karmodiya, K., and Dharne, M., ?Long-term genomic surveillance of SARS-CoV-2 in campus wastewater depicts lineage trends and public health implications during and after omicron waves?, Environment & Health, vol. 3, no. 8, pp. 908?919, 2025.