R. S.  Coyne, Hannick, L., Shanmugam, D., Hostetler, J. B., Brami, D., Joardar, V. S., Johnson, J., Radune, D., Singh, I., Badger, J. H., Kumar, U., Saier, M., Wang, Y., Cai, H., Gu, J., Mather, M. W., Vaidya, A. B., Wilkes, D. E., Rajagopalan, V., Asai, D. J., Pearson, C. G., Findly, R. C., Dickerson, H. W., Wu, M., Martens, C., Van de Peer, Y., Roos, D. S., Cassidy-Hanley, D. M., and Clark, T. G., ?Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control?, Genome Biology, vol. 12, no. 10, p. Article Number: R100, 2011.

A. James Reid, Vermont, S. J., Cotton, J. A., Harris, D., Hill-Cawthorne, G. A., Koenen-Waisman, S., Latham, S. M., Mourier, T., Norton, R., Quail, M. A., Sanders, M., Shanmugam, D., Sohal, A., Wasmuth, J. D., Brunk, B., Grigg, M. E., Howard, J. C., Parkinson, J., Roos, D. S., Trees, A. J., Berriman, M., Pain, A., and Wastling, J. M., ?Comparative genomics of the apicomplexan parasites toxoplasma gondii and neospora caninum: coccidia differing in host range and transmission strategy?, Plos Pathogens, vol. 8, no. 3, 2012.

M. P.  Magarinos, Carmona, S. J., Crowther, G. J., Ralph, S. A., Roos, D. S., Shanmugam, D., and Van Voorhis, W. C., ?TDR Targets: a chemogenomics resource for neglected diseases?, Nucleic Acids Research, vol. 40, no. D1, pp. D1118-D1127, 2012.

Y. H.  Woo, Ansari, H., Otto, T. D., Klinger, C. M., Kolisko, M., Michalek, J., Saxena, A., Shanmugam, D., Tayyrov, A., Veluchamy, A., Ali, S., Bernal, A., del Campo, J., Cihlar, J., Flegontov, P., Gornik, S. G., Hajduskova, E., Horak, A., Janouskovec, J., Katris, N. J., Mast, F. D., Miranda-Saavedra, D., Mourier, T., Naeem, R., Nair, M., Panigrahi, A. K., Rawlings, N. D., Padron-Regalado, E., Ramaprasad, A., Samad, N., Tomcala, A., Wilkes, J., Neafsey, D. E., Doerig, C., Bowler, C., Keeling, P. J., Roos, D. S., Dacks, J. B., Templeton, T. J., Waller, R. F., Lukes, J., Obornik, M., and Pain, A., ?Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites?, Elife, vol. 4, p. Article Number: e06974, 2015.

K. B.  Batkulwar, Bansode, S. B., Patil, G. V., Godbole, R. K., Kazi, R. S., Chinnathambi, S., Shanmugam, D., and Kulkarni, M. J., ?Investigation of phosphoproteome in RAGE signaling?, Proteomics, vol. 15, no. 2-3, pp. 245-259, 2015.

I. Q. H.  Phan, Davies, D. R., Moretti, N. Silvio, Shanmugam, D., Cestari, I., Anupama, A., Fairman, J. W., Edwards, T. E., Stuart, K., Schenkman, S., and Myler, P. J., ?Iron superoxide dismutases in eukaryotic pathogens: new insights from apicomplexa and trypanosoma structures?, Acta Crystallographica Section F-Structural Biology Communications, vol. 71, pp. 615-621, 2015.

A. A.  Chinchansure, Arkile, M. A., Shukla, A., Shanmugam, D., Sarkar, D., and Joshi, S. P., ?Leucas mollissima, a source of bioactive compounds with antimalarial and antimycobacterium activities?, Planta Medica Letter, vol. 2, no. 1, pp. e35-e38, 2015.

J. D.  Lykins, Filippova, E. V., Halavaty, A. S., Minasov, G., Zhou, Y., Dubrovska, I., Flores, K. J., Shuvalova, L. A., Ruan, J., Bissati, K. El, Dovgin, S., Roberts, C. W., Woods, S., Moulton, J. D., Moulton, H., Mcphillie, M. J., Muench, S. P., Fishwick, C. W. G., Sabini, E., Shanmugam, D., Roos, D. S., Mcleod, R., Anderson, W. F., and Ngo, H. M., ?CSGID solves structures and identifies phenotypes for five enzymes in toxoplasma gondii?, Frontiers in Cellular and Infection Microbiology, vol. 8, 2018.

P. R.  Athawale, Jachak, G., Shukla, A., Shanmugam, D., and Reddy, S., ?Efforts to access the potent antitrypanosomal marine natural product janadolide: synthesis of des- tert -butyl janadolide and its biological evaluation?, ACS Omega, 2018.

R.  Shivapurkar, Hingamire, T., Kulkarni, A. S., Rajamohanan, P. R., D. Reddy, S., and Shanmugam, D., ?Evaluating antimalarial efficacy by tracking glycolysis in Plasmodium falciparum using NMR spectroscopy?, Scientific Reports, vol.  8, 2018.

A.  Shukla, Olszewski, K. L., Llinas, M., Rommereim, L. M., Fox, B. A., Bzik, D. J., Xia, D., Wastling, J., Beiting, D., Roos, D. S., and Shanmugam, D., ? Glycolysis is important for optimal asexual growth and formation of mature tissue cysts by Toxoplasma gondii?, International Journal for Parasitology , vol. 48, no. 12, pp. 955-968, 2018.

R.  Salunke, Mourier, T., Banerjee, M., Pain, A., and Shanmugam, D., ?Highly diverged novel subunit composition of apicomplexan F-type ATP synthase identified from Toxoplasma gondii?, Plos Biology, vol. 16, no. 7, p. e2006128, 2018.

P.  Das, Babbar, P., Malhotra, N., Sharma, M., Jachak, G. R., Gonnade, R. G., Shanmugam, D., Harlos, K., Yogavel, M., Sharma, A., and D. Reddy, S., ?Specific stereoisomeric conformations determine the drug potency of cladosporin scaffold against malarial parasite?, Journal of Medicinal Chemistry, vol. 61, no. 13, pp. 5664-5678, 2018.

G.  Subramanian, ?Targeted phenotypic screening in plasmodium falciparum and toxoplasma gondii reveals novel modes of action of medicines for malaria venture malaria box molecules?, mSphere, vol. 3, no. 1, pp.  e00534-17, 2018.

B.  Subramani, Shantamurthy, C. D., Maru, P., Belekar, M. A., Mardhekar, S., Shanmugam, D., and Kikkeri, R., ?Demystifying a hexuronic acid ligand that recognizes Toxoplasma gondii and blocks its invasion into host cells?, Organic & Biomolecular Chemistry, vol. 17, no. 18, pp. 4535-4542, 2019.

A. A.  Betgiri, Jadhav, S. N., Pawde, M., Shukla, A., Mote, C., Pawar, P. D., Shanmugam, D., and Kundu, K., ?Mitochondrial cytochrome oxidase C subunit III (cox3) gene as a sensitive and specific target for molecular detection of Babesia gibsoni infection in dogs?, Experimental Parasitology, vol. 206, p. 107771, 2019.

A. D.  Bendre, Suresh, C. G., Shanmugam, D., and Ramasamy, S., ?Structural insights into the unique inhibitory mechanism of Kunitz type trypsin inhibitor from Cicer arietinum L. Vol. 37?, Journal of Biomolecular Structure & Dynamics, vol. 37, no. 10, pp. 2669-2677, 2019.

G.  Subramanian, Belekar, M. A., Shukla, A., Tong, J. Xin, Sinha, A., Chu, T. T. T., Kulkarni, A. S., Preiser, P. R., D. Reddy, S., Tan, K. S. W., Shanmugam, D., and Chandramohanadas, R., ?Targeted phenotypic screening in plasmodium falciparum and toxoplasma gondii reveals novel modes of action of medicines for malaria venture malaria box molecules (vol 3, e00534-17, 2018)?, MSphere, vol. 4, no. 2, pp. e00159-19, 2019.

A. Kumar Sahu, Said, M. S., Hingamire, T., Gaur, M., Khan, A., Shanmugam, D., Barvkar, V. T., Dharne, M. S., Bharde, A. A., and Dastager, S. G., ?Approach to nigericin derivatives and their therapeutic potential?, RSC Advances, vol. 10, no. 70, pp. 43085-43091, 2020.

K.  Verma, Saxena, K., Donaka, R., Chaphalkar, A., Rai, M. Kumar, Shukla, A., Zaidi, Z., Dandage, R., Shanmugam, D., and Chakraborty, K., ?Distinct metabolic states of a cell guide alternate fates of mutational buffering through altered proteostasis?, Nature Communications, vol. 11, no. 1, p. 2926, 2020.

L. Uran Landaburu, Berenstein, A. J., Videla, S., Maru, P., Shanmugam, D., Chernomoretz, A., and Aguero, F., ?TDR Targets 6: driving drug discovery for human pathogens through intensive chemogenomic data integration?, Nucleic Acids Research, vol. 48, no. D1, pp. D992-D1005, 2020.

A. Tanala Patra, Hingamire, T., Belekar, M. A., Xiong, A., Subramanian, G., Bozdech, Z., Preiser, P., Shanmugam, D., and Chandramohanadas, R., ?Whole-cell phenotypic screening of medicines for malaria venture pathogen box identifies specific inhibitors of plasmodium falciparum late-stage development and egress?, Antimicrobial Agents and Chemotherapy, vol. 64, no. 5, pp. e01802-19, 2020.

R. Lochana Panchangam, Rao, R. Nishanth, Balamurali, M. Motilal, Hingamire, T. B., Shanmugam, D., Manickam, V., and Chanda, K., ?Antitumor effects of Ir(III)-2H-indazole complexes for triple negative breast cancer?, Inorganic Chemistry, vol. 60, no. 23, pp. 17593-17607, 2021.

M. K.  Singh, Jayarajan, R., Varshney, S., Upadrasta, S., Singh, A., Yadav, R., Scaria, V., Sengupta, S., Shanmugam, D., Shalimar,, Sivasubbu, S., Gandotra, S., and Sachidanandan, C., ?Chronic systemic exposure to IL6 leads to deregulation of glycolysis and fat accumulation in the zebrafish liver?, Biochimica ET Biophysica Acta-Molecular and Cell Biology of Lipids, vol. 1866, no. 5, p. 158905, 2021.

J.  Behari, Borkar, P., Vindu, A., Dandewad, V., Upadrasta, S., Shanmugam, D., and Seshadri, V., ?Conserved RNA binding activity of phosphatidyl inositol 5-phosphate 4-kinase (PIP4K2A)?, Frontiers in Molecular Biosciences, vol. 8, p. 631281, 2021.

S.  M. Dar, Dholakia, B. B., Kulkarni, A. P., Oak, P. S., Shanmugam, D., Gupta, V. S., and Giri, A. P., ?Influence of domestication on specialized metabolic pathways in fruit crops?, Planta, vol. 253, no. 2, p. 61, 2021.

G. R.  Jachak, Elizebath, D., Shukla, A., Shanmugam, D., and D. Reddy, S., ?Synthesis and biological evaluation of hoshionolactam-based compounds?, European Journal of Organic Chemistry, vol. 2021, no. 15, pp. 2212-2218, 2021.

R.  Godbole, Gaur, A., Nayar, P., Kiruthiga, K., D'Costa, P., Manchanda, R., Khilari, A., Shanmugam, D., Muglikar, K. D., and Kundu, K., ?Case report: a fatal case of babesiosis in a splenectomized male patient from Western India?, American Journal of Tropical Medicine and Hygiene, vol. 106, no. 5, pp. 1421-1425, 2022.

A.  Prabhu, Shanmugam, D., and Gadgil, M., ?Engineering nucleotide sugar synthesis pathways for independent and simultaneous modulation of N-glycan galactosylation and fucosylation in CHO cells?, Metabolic Engineering, vol. 74, pp. 61-71, 2022.

J.  Chhibber-Goel, Shukla, A., Shanmugam, D., and Sharma, A., ?Profiling of metabolic alterations in mice infected with malaria parasites via high-resolution metabolomics?, Molecular and Biochemical Parasitology, vol. 252, p. 111525, 2022.

M.  Kaushik, Hoti, S. L., Saxena, J. Kumar, Hingamire, T., Shanmugam, D., Joshi, R. K., Metgud, S. C., Ungar, B., Singh, I., and Hegde, H. V., ?Antimalarial activity of anacardium occidentale leaf extracts against plasmodium falciparum transketolase (PfTK)?, Acta Parasitologica, vol. 68, no. 4, pp. 832-841, 2023.

C. L.  Meena, Hingamire, T., Gupta, T., Deshmukh, B., Karmodiya, K., Joshi, R., Shanmugam, D., and Sanjayan, G. J., ?Histidinal-based potent antimalarial agents?, ChemMedChem, vol. 18, no. 9, 2023.

A. H.  Chaurasiya, Khilari, A. A., Kazi, R., Jaiswal, M. R., Bhoite, G. M., Padwal, M. K., Momin, A. A., Shanmugam, D., and Kulkarni, M. J., ?Nanopore sequencing of RAGE gene polymorphisms and their association with type 2 diabetes?, ACS Omega, vol. 8, no. 29, pp. 25727-25738, 2023.

D.  Niveditha, Khan, S., Khilari, A., Nadkarni, S., Bhalerao, U., Kadam, P., Yadav, R., Kanekar, J. B., Shah, N., Likhitkar, B., Sawant, R., Thakur, S., Tupekar, M., Nagar, D., Rao, A. G., Jagtap, R., Jogi, S., Belekar, M., Pathak, M., Shah, P., Ranade, S., Phadke, N., Das, R., Joshi, S., Karyakarte, R., Ghose, A., Kadoo, N., Shashidhara, L. S., Monteiro, J. Merwin, Shanmugam, D., Raghunathan, A., and Karmodiya, K., ?Tale of two waves: Delineating diverse genomic and transmission landscapes driving the COVID-19 pandemic in Pune, India?, Journal of Infection and Public Health, vol. 16, no. 8, pp. 1290-1300, 2023.

V. D.  Navale, Yadav, R., Khilari, A., Dharne, M., Shanmugam, D., and Vamkudoth, K. Rao, ?Dietary supplementation of lactococcus lactis subsp. lactis BIONCL17752 on growth performance, and gut microbiota of broiler chickens?, Probiotics and Antimicrobial Proteins, 2024.

D.  Purkayastha, Pandit, K., Upadrasta, S., Khilari, A., Shanmugam, D., and Karmodiya, K., ?32nd National Congress of Parasitology, Pune: bringing together India's parasitologists?, Trends in Parasitology, vol. 41, no. 1, pp. 1-7, 2025.

M.  Bajpai, Khilari, A., Likhitkar, B., Musale, P., Jadhav, S., Dhanikachalam, V., Kakramkar, P., Bhave, K., Swaminathan, M., Joshi, S., and Shanmugam, D., ?Detection and variant characterization of lumpy skin disease virus from dairy cattle in India?, Virus Evolution, vol. 11, no. 1, p. veaf090, 2025.

J. M.  Bhagat, Khilari, A. A., Shanmugam, D., and Patankar, M., ?Expanding the Egbenema horizon: Novel species discovery in India and first complete genome assembly of the genus?, Algal Research-Biomass Biofuels and Bioproducts, vol. 90, p. 104256, 2025.

P.  Musale, Khilari, A., Gade, R., Dhanikachalam, V., Jadhav, S., Bajpai, M., Turakani, B., Joshi, A., Prajapati, A., Srivastava, A., Swaminathan, M., Joshi, S., and Shanmugam, D., ?Identification of genetic variations linked to buparvaquone resistance in Theileria annulata infecting dairy cattle in India?, Plos One, vol. 20, no. 7, p. e0326243, 2025.

A. - H.  Emwas, Zacharias, H. U., Alborghetti, M. Rodrigo, Gowda, G. A. Nagana, Raftery, D., Mckay, R. T., Chang, C. -ke, Saccenti, E., Gronwald, W., Schuchardt, S., Leiminger, R., Merzaban, J., Madhoun, N. Y., Iqbal, M., Alsiary, R. A., Shivapurkar, R., Pain, A., Shanmugam, D., Ryan, D., Roy, R., Schirra, H. Joachim, Morris, V., Zeri, A. Carolina, Alahmari, F., Kaddurah-Daouk, R., Salek, R. M., LeVatte, M., Berjanskii, M., Lee, B., and Wishart, D. S., ?Recommendations for sample selection, collection and preparation for NMR-based metabolomics studies of blood?, Metabolomics, vol. 21, no. 3, p. 66, 2025.

A.  Khilari, Sharma, S., Bajpai, M., K. Viswan, A., Chaturvedi, R., Mirdha, B. R., Rahi, M., Sharma, A., and Shanmugam, D., ?Targeted genomic surveillance unveils genetic variations linked to regional malaria drug resistance dynamics in India?, Open Forum Infectious Diseases, vol. 13, no. 3, p. ofag106, 2026.

G.  Kumari, Kumar, A., Muduli, R., Das, M., Bhowmik, P., Singha, B., Namdeo, A., Dcosta, C., Wadhwa, N., Maras, J. Singh, Kundu, R., Gupta, N., Anand, R., Shanmugam, D., and Majumdar, T., ??-catenin-driven innate and metabolic reprograming in macrophages fuel T-cell-dependent inflammation in Toxoplasma gondii infection: implications for therapeutic intervention?, Cell Death & Disease, vol. 17, no. 1, p. 568, 2026.