Dr. Arunachalam Ramaiah
Director
Pathogen Genomics Center of Excellence

​Dr. Arunachalam Ramaiah is a Group Leader (Lead Bioinformatician) at the City of Milwaukee Health Department (MHD). Before joining MHD, he was a Faculty (Senior Scientist) at the Tata Institute for Genetics and Society, Bangalore. Dr. Ramaiah did his postdoctoral research at the Indian Institute of Science, India (IISc), Centers for Disease Control and Prevention, USA (CDC), Stanford University School of Medicine, USA, and the University of California, Irvine/ UCSD, USA. Dr. Ramaiah received his PhD in Bioinformatics jointly from the Manonmaniam Sundaranar University, India, and Abo Akademi University, Finland. He is a recipient of the prestigious ‘ISID New Investigator Award – 2016’ from the International Society for Infectious Diseases (ISID), USA, for his research on T-cell epitope evolution in Mycobacterium tuberculosis strains from India. He is also a recipient of highly competitive APHL-CDC Bioinformatics Postdoctoral Fellowship and Finnish Government Scholarship. In 2022, Dr. Ramaiah has been elected as a Fellow of Royal Society for Public Health and member of Royal Society for Biology, UK. He is a life member of ISID and American Society for Rickettsiology. He is one of the two leads, who have assembled and annotated a ground-breaking new reference genome for the Asian Malaria mosquito Anopheles stephensi and discovered thousands of new gold-standard genes vital for targeting pathogen transmission and immunity. His lab research at MHD, focuses on studying the genomic epidemiology of the SARS-CoV-2, transmission patterns, and studying the RNA viruses (i.e. SARS-CoV-2, Zika virus, Influenza virus) evolution and viral molecular and immunological interactions with their host.

Dr. Ramaiah is an Academic Editor in PLoS ONE, Review Editor in Frontiers in Microbiology, Frontiers in Genetics and Frontiers in Ecology and Evolution journals, and also a reviewer for more than ten international peer-reviewed journals. Dr. Ramaiah is a member of the International Society for Infectious Diseases, Infectious Diseases Society of America, International Society for Computational Biology, American Society for Microbiology, and American Society for Rickettsiology. He has 12 years of academic experiences gained from leading Institutions in India, Finland and USA and has made academic visits to several countries. He received 25 awards/fellowships/recognitions from both national and International organizations.

Selected Publications:
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Innate immune modulator screen identifies STING pathway activation as a strategy to inhibit multiple families of arbo and respiratory viruses. Cell Reports Medicine, 2023
Comparative analysis of molecular pathogenic mechanisms and antiviral development targeting old and new world hantaviruses. pre-print, 2023
Implementation and evaluation of the Clear Dx platform for sequencing SARS-CoV-2 genomes in a Public Health Laboratory. Microbiology Spectrum, 2023 
Genomic surveillance identifies SARS-CoV-2 transmission patterns in local university populations, Wisconsin, USA, 2020-2022. Microbial Genomics, 2023
Hippo signaling pathway activation during SARS-CoV-2 infection contributes to host antiviral response. PLOS Biology, 2022 
ORAI1 limits SARS-CoV-2 infection by regulating tonic type I interferon signaling. The Journal of Immunology, 2022
Hidden genomic features of an invasive malaria vector, Anopheles stephensi, revealed by a chromosome-level genome assembly. BMC Biology, 2021
SARS-CoV-2 infection rewires host cell metabolism and is potentially susceptible to mTORC1 inhibition, Nature Communications, 2021
Antiviral drug screen identifies DNA-damage response inhibitor as potent blocker of SARS-CoV-2 replication. Cell Reports, 2021
Efficient population modification gene-drive rescue system in the malaria mosquito Anopheles stephensi. Nature Communications, 2020
Use of the Ion Torrent PGM for determining the genomic sequences of Francisella and Coxiella-like endosymbionts and Rickettsia directly from hard ticks. Contemporary Acarology, 2019
Evidence for highly variable, region-specific patterns of T-cell epitope mutations accumulating in Mycobacterium tuberculosis strains. Frontiers in Immunology, 2019
Complexity of type-specific 56 kDa antigen CD4 T-cell epitopes of Orientia tsutsugamushi strains causing Scrub typhus in India. PLoS ONE, 2018
Comparative analysis of protein evolution in the genome of pre-epidemic and epidemic Zika virus. Infection, Genetics and Evolution, 2017
Adaptive evolution of a novel avian-origin influenza A/H7N9 virus. Genomics, 2014
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