Publications

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*Corresponding author
†Equal contribution
Papers published prior to 2015 that I had co-authored had the name Arunachalam R. Articles listed below with the names Ramaiah Arunachalam, and Arunachalam Ramaiah both refer to me alone.

2023
  • Garcia, G., Irudayam, J.I., Jeyachandran, A., Dubey, S., Chang, C., Castillo Cario, S., Price, N., Arumugam, S., Marquez, A.L., Shah, A., Fanaei, A., Chakravarty, N., Joshi, S., Sinha, S., French, S.W., Parcells, M., Ramaiah, A*. and Arumugaswami, V*. 2023. Innate immune pathway modulator screen identifies STING pathway activation as a strategy to inhibit multiple families of arbo and respiratory viruses. Cell Reports Medicine, 4: 101024. link 
  • Ramaiah, A†*., Khubbar, M†., Scott, S., Bauer, A., Lentz, J., Akinyemi, K., Skillman, A., Weiner, J., Balakrishnan, N. and Bhattacharyya, S. 2023. Implementation and evaluation of the Clear Dx platform for sequencing SARS-CoV-2 genomes in a Public Health Laboratory. Microbiology Spectrum, 11(2): e04957-22. link 
  • Ramaiah, A*., Khubbar, M., Bauer, A., Scott, S., Lentz, J., Akinyemi, K., Skillman, A., Weiner, J., Balakrishnan, N. and Bhattacharyya, S*. 2023. Genomic surveillance identifies SARS-CoV-2 transmission patterns in local university populations, Wisconsin, USA, 2020-2022. Microbial Genomics, 9(3): 000970. link
  • Contreras, D., Garcia, G., Jones, M.K., Martinez, L.E., Jayakarunakaran, A., Gangalapudi, V., Tang, J., Wu, Y., Zhao, J.J., Chen, Z., Ramaiah, A., Tsui, I., Kumar, A., Nielsen-Saines, K., Wang, S. and Arumugaswami, V*. 2023. Differential susceptibility of fetal retinal pigment epithelial cells, hiPSC-retinal stem cells, and retinal organoids to Zika virus infection. Viruses, 15(1): 142. pdf | link
2022
  • Garcia, G., Jeyachandran, A., Wang, Y., Irudayam, J.I., Cario, S.C., Sen, C., Li, S., Li, Y., Kumar, A., Nielsen-Saines, K., French, S.W., Shah, P.S., Marizono, K.., Gomperts, B, Deb, A., Ramaiah, A*., and Arumugaswami, V*. 2022. Hippo signaling pathway activation during SARS-CoV-2 infection contributes to host antiviral response. PLOS Biology, 20(11): e3001851. pdf | link
  • Chauhan, D., Chakravarty, N., Jeyachandran, A., Jayakarunakaran, A., Sinha, S., Mishra, R., Arumugaswami, V*. and Ramaiah, A*. 2022. In Silico genome analysis reveals the evolution and potential impact of SARS-CoV-2 Omicron structural changes on host immune evasion and antiviral therapeutics. Viruses, 14(11): 2461. pdf | link​
  • Wu, B†., Ramaiah, A†., Garcia Jr, G., Hasiakos, S., Arumugaswami, V*. and Srikanth, S*. 2022. ORAI1 limits SARS-CoV-2 infection by regulating tonic type I interferon signaling. The Journal of Immunology, 208(1): 74-84. pdf | link   
2021
  • 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 Jr, G*., Ramaiah, A*. and Arumugaswami, V*. 2021. Neurological pathophysiology of SARS-CoV-2 and pandemic potential RNA viruses: A comparative analysis. FEBS Letters, 595(23): 2854-2871. pdf | link
  • Mullen, P.J., Garcia, G., Purkayastha, A., Matulionis, N., Schmid, E.W., Momcilovic, M., Sen, C., Langerman, J., Ramaiah, A., Shackelford, D.B., Damoiseaux, R., French, S.W., Plath, K., Gomperts, B.N., Arumugaswami, V*. and Christofk, H.R*. 2021. SARS-CoV-2 infection rewires host cell metabolism and is potentially susceptible to mTORC1 inhibition. Nature Communications, 12, 1876. pdf | link 
  • Garcia Jr, 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*. 2021. Antiviral drug screen identifies DNA-damage response inhibitor as potent blocker of SARS-CoV-2 replication. Cell Reports, 108940. pdf | link
  • 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*. 2021. Hidden genomic features of an invasive malaria vector, Anopheles stephensi, revealed by a chromosome-level genome assembly. BMC Biology, 19, 28 link
2020
  • 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*. 2020. Efficient population modification gene-drive rescue system in the malaria mosquito Anopheles stephensi. Nature Communications, 11, 5553. pdf | link
  • Garcia Jr, 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*. 2020. 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. PMID: 32035058. pdf | link
  • Ramaiah, A* and Arumugaswami, V*. 2020. Insight into cross-species evolution of novel human coronavirus SARS-CoV-2 and defining immune determinants for vaccine development. bioRxiv, 925867. link
2019
  • Lopes de Carvalho, L., Blight-Linden, E., Ramaiah, A., Johnson, M.S. and Salminen, T.A*. 2019. Evolution and functional classification of mammalian copper amine oxidases. Molecular Phylogenetics and Evolution, 139, 106571. PMID: 31351182. pdf | link
  • Dasch, G.A*., Ramaiah, A., Holmes, Z.C., Zambrano, M.L. and Shirey, B.T. 2019. 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. pdf | link
  • 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*. 2019. Evidence for highly variable, region-specific patterns of T-cell epitope mutations accumulating in Mycobacterium tuberculosis strains. Frontiers in Immunology, 10: 195. PMID: 30814998. pdf | link
2018
  • Koralur, M.C., Ramaiah, A. and Dasch, G.A*. 2018. Detection and distribution of Sca autotransporter protein antigens in diverse isolates of Orientia tsutsugamushi. PLoS Neglected Tropical Diseases, 12(9): e0006784. PMID: 30235210. pdf
  • Rajeshkumar, S*., Venkatkumar, S., Ramaiah, A., Agarwal, H., Lakshmi, T. and Roopan, S.M*. 2018. 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. PMID: 30037558. pdf
  • Ramaiah, A., Koralur, M.C. and Dasch, G.A*. 2018. 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. PMID: 29698425. pdf
  • Ramaiah, A. and Dasch, G.A*. 2018. 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. PMID: 29599150. pdf
2017
  • Ramaiah, A., Dai, L., Contreras, D., Sinha, S., Sun, R. and Arumugaswami, V*. 2017. Comparative analysis of protein evolution in the genome of pre-epidemic and epidemic Zika virus. Infection, Genetics and Evolution, 51: 74-85. PMID: 28315476. pdf
  • Dasch, G.A*. and Ramaiah, A. 2017. 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. pdf
  • Ramaiah, A., Williams-Newkirk, A.J., Frace, M.A., Zambrano, M.L. and Dasch, G.A*. 2017. Evolution of the genomes of the Coxiella-like endosymbionts of ticks. Journal of the Mississippi Academy of Sciences, 62(1): 21. pdf
2016
  • Ramaiah, A., Contreras, D., Gangalapudi, V., Padhye, M.S., Tang, J. and Arumugaswami, V*. 2016. Dysregulation of long non-coding RNA (lncRNA) genes and predicted lncRNA-protein interactions during Zika virus infection. bioRxiv. DOI: http://dx.doi.org/10.1101/061788. pdf
  • Ramaiah, A†., Dai, L†., Contreras, D., Sinha, S., Sun, R*. and Arumugaswami, V*. 2016. Comparative analysis of protein evolution and RNA structural changes in the genome of pre-epidemic and epidemic Zika virus. bioRxiv. DOI: http://dx.doi.org/10.1101/050278. pdf
  • Ramaiah, A., Nayak, S., Rakshit, S., McGuire, A., Shanmugam, S., Chandrabose, J., Narayanan, S., Earl, A., Swaminathan, S. and Vyakarnam, A*. 2016. Evolutionary patterns of T cell epitopes in Mycobacterium tuberculosis strains isolated in India. International Journal of Infectious Diseases, 45, S1, 33. DOI: http://dx.doi.org/10.1016/j.ijid.2016.02.111. pdf
  • Ramaiah, A*. and Arumugaswami, V. 2016. Ebola virus evolves in human to minimize the detection by immune cells by accumulating adaptive mutations. VirusDisease, 27(2): 136-144. PMID: 27366764. pdf
2015
  • 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*. 2015. Profile of inflammation-associated genes during hepatic differentiation of human pluripotent stem cells. Data in Brief, 5: 871-878. PMID: 26702414. pdf
  • 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*. 2015. 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. PMID: 26313525. pdf
2014
  • Ramaiah, A*. 2014. Adaptive evolution of a novel avian-origin influenza A/H7N9 virus. Genomics, 104(6): 545-553. PMID: 25449177. pdf
2013
  • Ramaiah, A*. 2013. Detection of site-specific positive Darwinian selection on pandemic influenza A/H1N1 virus genome: integrative approaches. Genetica, 141(4-6): 143-155. PMID: 23529677. pdf
  • Blight-Linden, E., Ramaiah, A., Parkash V. and Salminen, T.A*. 2013. Structural comparison of the active site channels in rodent and primate vascular adhesion protein-1. Journal of Neural Transmission, 120(6): 947-950. PMID: 23328952. pdf
2012
  • Ramaiah, A., Paulkumar, K. and Annadurai, G*. 2012. Genetic ancestor of external antigens of pandemic Influenza A/H1N1 virus. Interdisciplinary Sciences: Computational Life Sciences, 4(4): 282-290. PMID: 23354817. pdf
  • Ramaiah, A., Senthilkumar, B., Senbagam, D., Selvamaleeshwaran, P. and Rajasekarapandian, M. 2012. Molecular phylogenetic approach for classification of Salmonella typhi. Research Journal of Microbiology, 7(1): 13-22. DOI: 10.3923/jm.2012.13.22. pdf
  • Ramaiah, A., Paulkumar, K. and Annadurai, G. 2012. Phylogenetic analysis of pandemic influenza A/H1N1 virus. Biologia, 67(1): 14-31. DOI: 10.2478/s11756-011-0163-6. pdf
2011
  • Paulkumar, K., Ramaiah, A. and Annadurai, G*. 2011. Biomedical applications of organically modified fluorescent labeled bioconjugated silica nanoparticles. International Journal of Nanotechnology, 8(8/9): 653-663. DOI: 10.1504/IJNT.2011.041436. pdf
  • Jayarajan, M., Ramaiah, A. and Annadurai, G*. 2011. 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. DOI: 10.3923/rjes.2011.434.443. pdf
  • Ramaiah, A. and Annadurai, G*. 2011. Nano-porous adsorbents from fruit peel waste for decolorization studies. Research Journal of Environmental Sciences, 5(4): 366-376. DOI: 10.3923/rjes.2011.366.376. pdf
  • Jayarajan, M., Ramaiah, A. and Annadurai, G*. 2011. Agricultural wastes of Jackfruit peel nano- porous adsorbent for removal of Rhodamine dye. Asian Journal of Applied Sciences, 4(3): 263-270. DOI: 10.3923/ajaps.2011.263.270. pdf
  • Ramaiah, A. and Annadurai, G*. 2011. Optimized response surface methodology for adsorption of dyestuff from aqueous solution. Journal of Environmental Science and Technology, 4(1): 65-72. DOI: 10.3923/jest.2011.65.72. pdf
  • Chakkaravarthy, V.M*., Ambrose, T., Vincent, S., Ramaiah, A., Paulraj, M.G., Ignacimuthu, S. and Annadurai, G. 2011. 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. DOI: 10.3923/je.2011.191.197. pdf
2010
  • Chakkaravarthy, V.M., Ramaiah, A., Vincent, S., Paulkumar, K. and Annadurai, G. 2010. Biodegradation of Tricalcium Phosphate by Phosphate Solubilizing Bacteria. Journal of Biological Sciences, 10(6): 531-535. pdf
  • George, J., Ramaiah, A., Paulkumar, K., Wesely, E.G., Shiburaj, S. and Annadurai, G. 2010. Characterization and phylogenetic analysis of cellulase producing Streptomyces noboritoensis SPKC1. Interdisciplinary Sciences: Computational Life Sciences, 2: 205-212. DOI: 10.1007/s12539-010-0069-y. PMID: 20640791. pdf
  • Malickbasha, M., Ramaiah, A., Senthilkumar, B., Rajasekarapandian, M. and Annadurai, G. 2010. Effect of OmpR gene mutation in expression of OmpC and OmpF of Salmonella typhi. Interdisciplinary Sciences: Computational Life Sciences, 2: 157-162. DOI: 10.1007/s12539-010-0067-0. PMID: 20640784. pdf
  • Amutha, M., Ramaiah, A., Umamaheswari, M., Usharamalakshmi, A., Ramakrishnan, S. and Annadurai, G. 2010. Medicinal use of Camellia sinensis on Lactose Intolerance. Journal of Biological Sciences, 10(2): 112-116. DOI: 10.3923/jbs.2010.112.116. pdf
  • Paulkumar, K., Ramaiah, A., Kameswaran, R., Ramanibai, R. and Annadurai, G. 2010. Anti-cancer effect of indirubin-3’-monoxime for human laryngeal carcinoma. International Journal of Cancer Research, 6(1): 27-34. DOI: 10.3923/ijcr.2010.27.34. pdf
  • Ramaiah, A., Wesely, E.G., George, J., Annadurai, G. 2010. Novel approaches for Identification of Streptomyces noboritoensis TBG-V20 with cellulase production. Current Research in Bacteriology, 3(1): 15-26. DOI: 10.3923/crb.2010.15.26. pdf
2009
  • Shalinimol, C.R., Ramaiah, A. and Annadurai, G*. 2009. Allocation and abundance of protozoa among soil aggregates. Journal of Biological Sciences, 9(7): 772-777. DOI: 10.3923/jbs.2009.772.777. pdf
  • Ramaiah, A., Paulkumar, K., Ranjitsingh, A.J.A. and Annadurai, G*. 2009. Environmental assessment due to air pollution near iron smelting industry. Journal of Environmental Science and Technology, 2(4): 179-186. DOI: 10.3923/jest.2009.179.186. pdf

In Preparation
  • ​​​Dasch, G.A*., Ramaiah, A. and Koralur, M.C. Genetic heterogeneity of the scaA-scaF cell surface antigen autotransporter genes of Orientia tsutsugamushi. In Preparation.
  • Ramaiah, A., Williams-Newkirk, A.J., Frace, M.A. and Dasch, G.A*. Genome deduction in Francisella tularensis, an endosymbiont of tick Dermacentor variabilis. In Preparation.
  • Ramaiah, A., Williams-Newkirk, A.J., Frace, M.A., Zambrano, M.L. and Dasch, G.A*. Genome evolution of Coxiella-like endosymbionts in the ticks, genera Rhipicephalus and Amblyomma. In Preparation.
  • ​Ramaiah, A., Holmes, Z.C. and Dasch, G.A*. Sequencing and annotation of Rickettsia plasmidomes obtained from tick metagenome data. In Preparation.
  • ​Ramaiah, A. and Dasch, G.A*. A quantitative genomic basis for species and sub-species in the genus Bartonella with new descriptions. In Preparation.
  • Ramaiah, A., Lydy, S., Rowe, L.A., Loparev, V.N., Knipe, K.M., Batra, D. and Dasch, G.A*. High quality complete genome sequences of four isolates of Bartonella carrionii. In Preparation.
  • Ramaiah, A., Rowe, L.A., Lydy, S., Batra, D., Knipe, K., Loparev, V.L., Hendrix, L. and Dasch, GA*. Complete genome sequences of two prototype stocks each of Bartonella bacilliformis KC583 (ATCC 35685T) and KC584 (ATCC 35686). In Preparation.
  • Dasch, G.A*., Holmes, Z.C., Shirey, B.T., Williams-Newkirk, A.J. and Ramaiah, A. Evaluation of mitochondrial genome sequences obtained with the Ion Torrent PGM from single Rhipicephalus, Amblyomma, and Dermacentor ticks. In Preparation.
  • ​Ramaiah, A†. and Dasch, G.A†,*. Diversity of the type-specific 56 kDa antigen of Orientia tsutsugamushi in the Asia-Pacific region and complexity and location of its potential CD4 T-cell epitopes. In Preparation.
  • Dubey, S†., Jeyachandran, A†., Irudayam, J.I., Chakravarty, N., Ramaiah, A*. and Arumugaswami, V*. Differential tropism and pathogenicity of hemorrhagic fever renal syndrome and cardiopulmonary syndrome causative Hantaviruses and antiviral agents. In Preparation.
  • Ramaiah, A., Chakraborty, M. and Emerson, J.J*. Improved assembly resolve the complexity of the Anopheles stephensi Y chromosome. In Preparation.