Arunachalam Ramaiah

Arunachalam Ramaiah
Senior Scientist
arunachalam@tigs.res.in

Education

• Ph.D in Bioinformatics jointly from Manonmaniam Sundaranar University, India, and Abo Akademi University, Finland, 2012

Experience

• TIGS Visiting Scientist, University of California, Irvine, and University of California, San Diego, USA, 2019-2021
• Senior Postdoctoral Scholar, Stanford University School of Medicine, USA, 2018-2019
• APHL-CDC Bioinformatics Postdoctoral Fellow, Centers for Disease Control and Prevention, USA, 2016-2018
• Postdoctoral Research Associate / Research Scientist, Indian Institute of Science, Bangalore, 2014-2016
• Visiting Researcher, Manonmaniam Sundaranar University, India, 2013-2014
• CIMO Fellow, Abo Akademi University, Finland, 2011-2012
• UGC Project Fellow, Manonmaniam Sundaranar University, India, 2009-2011

Expertise

• Bioinformatics
• Host-pathogen interactions
• Metagenomics, Evolutionary genomics
• Computational immunology

Areas of interest

Genome evolution of RNA viruses, including SARS-CoV-2, and host molecular and immunological responses to these viruses, evolution of immune genes and Y chromosome of Malaria mosquito Anopheles stephensi

Honors and Awards

• Alumni Achiever Award, Sri Paramakalyani College Alumni Association, India, 2016
• ISID New Investigator Award, International Society for Infectious Diseases (ISID) (17 th ICID), USA, 2016
• Young Scientist Award, Science and Engineering Research Board (SERB), Department of Science and Technology, India, 2014
• Finnish Government Scholarship, Centre for International Mobility, Finland, 2011-2012

Publications

• Wu, B., Ramaiah, A., Garcia, G., Hasiakos, S., Arumugaswami, V*. and Srikanth, S*. ORAI1 limits SARS-CoV-2 infection by regulating tonic type I interferon signaling. The Journal of Immunology, 208(1): 74-84. 2022
• Chakravarty, N., Senthilnathan, T., Paiola, S., Gyani, P., Cario, S.C., Urena, E., Jeysankar, A., Jeysankar, P., Ignatius Irudayam, J., Natesan Subramanian, S., Lavretsky, H., Joshi, S., Garcia, G*., Ramaiah, A*. and Arumugaswami, V*. Neurological pathophysiology of SARS-CoV-2 and pandemic potential RNA viruses: A comparative analysis. FEBS Letters, 595(23): 2854-2871, 2021.
• Mullen, P.J., Garcia, G., Purkayastha, A., Schmid, E.W., Langerman, J., Momcilovic, M., Matulionis, N., Ramaiah, A., Shackelford, D.B., Damoiseaux, R., French, S.W., Plath, K., Gomperts, B.N., Arumugaswami, V*. and Christofk, H.R*. SARS-CoV-2 infection rewires host cell metabolism and is potentially susceptible to mTORC1 inhibition. Nature Communications, 12: 1876, 2021.
• Garcia, G., Sharma, A., Ramaiah, A., Sen, C., Purkayastha, A., Kohn, D.B., Parcells, M.S., Beck, S., Kim, H., Bakowski, M.A., Kirkpatrick, M.G., Riva, L., Wolff, K.C., Han, B., Yuen, C., Ulmert, D., Purbey, P.K., Scumpia, P., Beutler, N., Rogers, T.F., Chatterjee, A.K., Gabriel, G., Bartenschlager, R., Gomperts, B., Svendsen, C.N., Betz, U.A.K*., Damoiseaux, R.D*. and Arumugaswami, V. Antiviral drug screen identifies DNA-damage response inhibitor as potent blocker of SARS-CoV-2 replication. Cell Reports, 108940, 2021.
• Chakraborty, M., Ramaiah, A., Adolfi, A., Halas, P., Kaduskar, B., Ngo, L.T., Jayaprasad, S., Paul, K., Whadgar, S., Srinivasan, S., Subramani, S., Bier, E., James, A.A. and Emerson, J.J. Hidden genomic features of an invasive malaria vector, Anopheles stephensi, revealed by a chromosome-level genome assembly. BMC Biology, 19: 28, 2021.
• Adolfi, A., Gantz, V.M., Jasinskiene, N., Lee, H-F., Hwang, K., Terradas, G., Bulger, E.A., Ramaiah, A., Bennett, J.B., Emerson, J.J., Marshall, J.M., Bier, E. and James, A.A. Efficient population modification gene-drive rescue system in the malaria mosquito Anopheles stephensi. Nature Communications, 11: 5553, 2020.
• Garcia, G., Paul, S., Beshara, S., Ramanujan, K., Ramaiah, A., Nielsen-Saines, K., Li, M.M.H., French, S.W., Morizono, K., Kumar, A. and Arumugaswami, V. Hippo signaling pathway has a critical role in Zika virus replication and in the pathogenesis of neuroinflammation. The American Journal of Pathology, 190(4): 844-861, 2020.
• Lopes de Carvalho, L., Blight-Linden, E., Ramaiah, A., Johnson, M.S. and Salminen, T.A. Evolution and functional classification of mammalian copper amine oxidases. Molecular Phylogenetics and Evolution, 13: 106571, 2019.
• Ramaiah, A., Nayak, S., Rakshit, S., Manson, A.L., Abeel, T., Shanmugam, S., Sahoo, P.N., Jesuraj, A., Sundaramurthi, J.C., Narayanan, S., D’Souza, G., Hoegen, P., Ottenhoff, T.H.M., Swaminathan, S., Earl, A. and Vyakarnam, A. Evidence for highly variable, region-specific patterns of T-cell epitope mutations accumulating in Mycobacterium tuberculosis strains. Frontiers in Immunology, 10: 195, 2019.
• Koralur, M.C., Ramaiah, A. and Dasch, G.A. Detection and distribution of Sca autotransporter protein antigens in diverse isolates of Orientia tsutsugamushi. PLoS Neglected Tropical Diseases, 12(9): e0006784, 2018.
• Rajeshkumar, S., Venkatkumar, S., Ramaiah, A., Agarwal, H., Lakshmi, T. and Roopan, S.M. Biosynthesis of Zinc oxide nanoparticles using Mangifera indica leaves and evaluation of their antioxidant and cytotoxic properties in lung cancer (A549) cells. Enzyme and Microbial Technology, 117: 91-95, 2018.
• Ramaiah, A., Koralur, M.C. and Dasch, G.A. Complexity of type-specific 56 kDa antigen CD4 T-cell epitopes of Orientia tsutsugamushi strains causing Scrub typhus in India. PLoS ONE, 13(4): e0196240, 2018.
• Ramaiah, A. and Dasch, G.A. Genome sequence of Coxiella-like endosymbiont strain CLE-RmD, a bacterial agent in the cattle tick, (Rhipicephalus microplus) Deutsch strain. Genome Announcements, 6(13): e00003-18, 2018.
• Ramaiah, A., Dai, L., Contreras, D., Sinha, S., Sun, R*. and Arumugaswami, V. Comparative analysis of protein evolution in the genome of pre-epidemic and epidemic Zika virus. Infection, Genetics and Evolution, 51: 74-85, 2017.
• Ramaiah, A. and Arumugaswami, V. Ebola virus evolves in human to minimize the detection by immune cells by accumulating adaptive mutations. Virus Disease, 27(2): 136-144, 2016.
• Irudayam, J.I., Contreras, D., Spurka, L., Ren, S., Kanagavel, V., Ramaiah, A., Annamalai, A., French, S.W., Klein, A.S., Funari, V. and Arumugaswami, V. Profile of inflammation-associated genes during hepatic differentiation of human pluripotent stem cells. Data in Brief, 5: 871-878, 2015.
• Irudayam, J.I., Contreras, D., Spurka, L., Subramanian, A., Allen, J., Ren, S., Kanagavel, V., Nguyen, Q., Ramaiah, A., Kalidas, R., French, S.W., Klein, A.S., Funari, V. and Arumugaswami, V. Characterization of Type I Interferon pathway during Hepatic differentiation of human pluripotent stem cells and hepatitis C virus infection. Stem Cell Research, 15(2): 354-364, 2015.
• Ramaiah, A. Adaptive evolution of a novel avian-origin influenza A/H7N9 virus. Genomics, 104(6): 545-553, 2014.
• Ramaiah, A. Detection of site-specific positive Darwinian selection on pandemic influenza A/H1N1 virus genome: integrative approaches. Genetica, 141(4-6): 143-155, 2013.
• Blight-Linden, E., Ramaiah, A., Parkash V. and Salminen, T.A. Structural comparison of the active site channels in rodent and primate vascular adhesion protein-1. Journal of Neural Transmission, 120(6): 947-950, 2013.
• Ramaiah, A., Paulkumar, K. and Annadurai, G. Genetic ancestor of external antigens of pandemic Influenza A/H1N1 virus. Interdisciplinary Sciences: Computational Life Sciences, 4(4): 282-290, 2012.
• Ramaiah, A., Senthilkumar, B., Senbagam, D., Selvamaleeshwaran, P. and Rajasekarapandian, M. Molecular phylogenetic approach for classification of Salmonella typhi. Research Journal of Microbiology, 7(1): 13-22, 2012.
• Ramaiah, A., Paulkumar, K. and Annadurai, G. Phylogenetic analysis of pandemic influenza A/H1N1 virus. Biologia, 67(1): 14-31, 2012.
• Paulkumar, K., Ramaiah, A. and Annadurai, G. Biomedical applications of organically modified fluorescent labeled bioconjugated silica nanoparticles. International Journal of Nanotechnology, 8(8/9): 653-663, 2011.
• Jayarajan, M., Ramaiah, A. and Annadurai, G. Use of low cost nano-porous materials of Pomelo fruit peels wastes in removal of textile dye. Research Journal of Environmental Sciences, 5(5): 434-443, 2011.
• Ramaiah, A. and Annadurai, G. Nano-porous adsorbents from fruit peel waste for decolorization studies. Research Journal of Environmental Sciences, 5(4): 366-376, 2011.
• Jayarajan, M., Ramaiah, A. and Annadurai, G. Agricultural wastes of Jackfruit peel nano- porous adsorbent for removal of Rhodamine dye. Asian Journal of Applied Sciences, 4(3): 263-270, 2011.
• Ramaiah, A. and Annadurai, G. Optimized response surface methodology for adsorption of dyestuff from aqueous solution. Journal of Environmental Science and Technology, 4(1): 65-72, 2011.
• Chakkaravarthy, V.M., Ambrose, T., Vincent, S., Ramaiah, A., Paulraj, M.G., Ignacimuthu, S. and Annadurai, G. Bioefficacy of Azadirachta Indica (A. Juss) and Datura metel (Linn.) leaves extracts in controlling Culex quinquefasciatus (Diptera: Culicidae). Journal of Entomology, 8(2): 191-197, 2011.
• Chakkaravarthy, V.M., Ramaiah, A., Vincent, S., Paulkumar, K. and Annadurai, G. Biodegradation of Tricalcium Phosphate by Phosphate Solubilizing Bacteria. Journal of Biological Sciences, 10(6): 531-535, 2010.
• George, J., Ramaiah, A., Paulkumar, K., Wesely, E.G., Shiburaj, S. and Annadurai, G. Characterization and phylogenetic analysis of cellulase producing Streptomyces noboritoensis SPKC1. Interdisciplinary Sciences: Computational Life Sciences, 2: 205-212, 2010.
• Malickbasha, M., Ramaiah, A., Senthilkumar, B., Rajasekarapandian, M. and Annadurai, G. Effect of OmpR gene mutation in expression of OmpC and OmpF of Salmonella typhi. Interdisciplinary Sciences: Computational Life Sciences, 2: 157-162, 2010.
• Amutha, M., Ramaiah, A., Umamaheswari, M., Usharamalakshmi, A., Ramakrishnan, S. and Annadurai, G. Medicinal use of Camellia sinensis on Lactose Intolerance. Journal of Biological Sciences, 10(2): 112-116, 2010.
• Paulkumar, K., Ramaiah, A., Kameswaran, R., Ramanibai, R. and Annadurai, G. Anti-cancer effect of indirubin-3’-monoxime for human laryngeal carcinoma. International Journal of Cancer Research, 6(1): 27-34, 2010.
• Ramaiah, A., Wesely, E.G., George, J., Annadurai, G. Novel approaches for Identification of Streptomyces noboritoensis TBG-V20 with cellulase production. Current Research in Bacteriology, 3(1): 15-26, 2010.
• Shalinimol, C.R., Ramaiah, A. and Annadurai, G. Allocation and abundance of protozoa among soil aggregates. Journal of Biological Sciences, 9(7): 772-777, 2009.
• Ramaiah, A., Paulkumar, K., Ranjitsingh, A.J.A. and Annadurai, G. Environmental assessment due to air pollution near iron smelting industry. Journal of Environmental Science and Technology, 2(4): 179-186, 2009.

Proceedings

• Dasch, G.A. and Ramaiah, A. Challenges and advances in the metagenomic and microbiome characterization of bacteria in clinical and arthropod vector samples. Journal of the Mississippi Academy of Sciences, 62(1): 18-19, 2017.
• Ramaiah, A., Williams-Newkirk, A.J., Frace, M.A., Zambrano, M.L. and Dasch, G.A. Evolution of the genomes of the Coxiella-like endosymbionts of ticks. Journal of the Mississippi Academy of Sciences, 62(1): 21, 2017.
• Ramaiah, A., Nayak, S., Rakshit, S., McGuire, A., Shanmugam, S., Chandrabose, J., Narayanan, S., Earl, A., Swaminathan, S. and Vyakarnam, A. Evolutionary patterns of T cell epitopes in Mycobacterium tuberculosis strains isolated in India. International Journal of Infectious Diseases, 45, S1, 33, 2016. (IF: 3.62)

Book Chapters

• Dasch, G.A*., Ramaiah, A., Holmes, Z.C., Zambrano, M.L. and Shirey, B.T. Use of the Ion Torrent PGM for determining the genomic sequences of Francisella and Coxiella-like endosymbionts and Rickettsia directly from hard ticks. In: Skvarla M., Ochoa R., Verle Rodrigues J., Hutcheson H. (eds). Springer, Cham. Contemporary Acarology, 1-35, 2019.