Prasad Padmanabhan

Research Interests:

My research focuses on understanding how molecular, environmental, and socioeconomic factors influence infectious disease transmission, host–pathogen interactions, and disease dynamics by integrating molecular biology, vector biology, bioinformatics, and advanced statistical modeling. I am particularly interested in understanding how climate variability and environmental changes influence pathogen transmission, disease emergence, and severity.

A major component of my research involves investigating vector-borne infectious diseases using experimental and computational approaches. I work with mosquito infection models to study vector competence, viral transmission dynamics, and mosquito–virus interactions through mosquito rearing, experimental infections, tissue dissections, cell culture, molecular assays, and viral quantification. These experimental studies are complemented by quantitative approaches to identify biological and environmental factors influencing arboviral transmission.

I apply statistical approaches to integrate epidemiological, climate, environmental, and socioeconomic datasets to investigate infectious disease dynamics. My recent work on the Thermal Mismatch Hypothesis demonstrates how integrating diverse datasets can improve our understanding of climate-sensitive infectious diseases and help predict disease risk under changing environmental conditions.

I also analyze high-dimensional biological datasets using bioinformatics approaches. My research includes developing reproducible workflows for single-cell and bulk transcriptomic analyses to identify transcriptional changes and interpret their biological significance. By integrating genomic, epidemiological, and environmental data, my goal is to uncover the complex interactions between pathogens, hosts, vectors, and environmental factors that shape infectious disease outcomes.

Overall, my research integrates molecular biology, vector biology, genomics, bioinformatics, epidemiology, and quantitative modeling to understand infectious disease biology across multiple biological scales. By combining experimental and computational approaches, I aim to improve infectious disease surveillance, develop predictive models for disease emergence, and contribute to evidence-based strategies for disease prevention and global public health.

Biography:

• Assistant Research Professor, Department of Biological Science, University of Notre Dame IN. 2023-Present
• Staff scientist, University of Notre Dame, South Bend, IN, USA. 2020-2023
• Research Associate, Laval University, Quebec. 2015-2020
• Post-doctorate fellow, Harvard T.H Chan School of Public Health. 2012-2015
• Post-doctorate fellow, Laval University, Quebec. 2007-2012

Education:

• Ph.D (Molecular Biology and Biochemistry of Infectious Diseases, Jawaharlal Nehru University, New Delhi, India)
• M.S. in Biochemistry, Manipal Academy of Higher Education, Karnataka, India)

Recent Papers:

• Md. Suhail Alam*, Padmanabhan PK*, Ryan McArdle, Alejandro Lopez-Ramirez, Arpitha Mysore Rajashekara, James Knopp, Gabriela Kim, Maria Virginia Centeo, Apkar Vania Apkarian, Vivek Swarup, Kasturi Haldar. Chronic HDACi emends microglial differentiation and neurological disease in a mouse model of intellectual disability. bioRxiv preprint, 2025 May 07 doi: https://doi.org/10.1101/2025.05.01.651719 *Equal contributions
• Alejandro Lopez-Ramirez, Adviti Bali, Md Suhail Alam, PadmanabhanPK, Shaun Calhoun, Caroline Bickerton, Ana Flores-Mireles, Kasturi Haldar. Gene therapy prevents disease and death from non-ketotic hyperglycinemia. bioRxiv, 2025 May 13, https://www.biorxiv.org/content/10.1101/2025.03.26.645560v2
• Mukherjee A, Crochetière MÈ, Sergerie A, Amiar S, Thompson LA, Ebrahimzadeh Z, Gagnon D, Lauruol F, Bourgeois A, Galaup T, Roucheray S, Hallée S, Padmanabhan PK, Stahelin RV, Dacks JB, Richard D. A Phosphoinositide-Binding Protein Acts in the Trafficking Pathway of Hemoglobin in the Malaria Parasite Plasmodium falciparum. mBio. 2022 Jan 18;13(1): e0323921. doi: 10.1128/mbio.03239-21.
• Padmanabhan PK, Ferreira GR, Zghidi-Abouzid O, Oliveira C, Dumas C, Mariz FC, Papadopoulou B.,Genetic depletion of the RNA helicase DDX3 leads to impaired elongation of translating ribosomes triggering co-translational quality control of newly synthesized polypeptides. Nucleic Acids Res. 2021 Sep 20;49(16):9459-9478. doi: 10.1093/nar/gkab667.
• Aguiar BG, Dumas C, Maaroufi H, Padmanabhan PK, Papadopoulou B. The AAA + ATPase valosincontaining protein (VCP)/p97/Cdc48 interaction network in Leishmania. Sci Rep. 2020 Aug 4;10(1):13135. doi: 0.1038/s41598-020-70010-4.
• Bhattacharya A, Bigot S, Padmanabhan PK, Mukherjee A, Coelho A, Leprohon P, Papadopoulou B, Ouellette M. New insights in the mode of action of anti-leishmanial drugs by using chemical mutagenesis screens coupled to next-generation sequencing. Microb Cell. 2020 Jan 21;7(2):59-61. doi: 10.15698/mic2020.02.708
• Bhattacharya A, Leprohon P, Bigot S, Padmanabhan PK, Mukherjee A, Roy G, Gingras H, Mestdagh A, Papadopoulou B, Ouellette M. Coupling chemical mutagenesis to next generation sequencing for the identification of drug resistance mutations in Leishmania. Nature Commuication. 2019 Dec 9;10(1):5627. doi: 10.1038/s41467-019-13344-6.
• Guedes Aguiar B, Padmanabhan PK, Dumas C, Papadopoulou B.Valosin-containing protein VCP/p97 is essential for the intracellular development of Leishmania and its survival under heat stress. Cell Microbiol. 2018 Oct;20(10):e12867. doi: 10.1111/cmi.12867.
• Hiva Azizi, Tatiany P. Romão, Karen Santos Charret, Padmanabhan PK, Osvaldo P. de Melo Neto, Michaela Müller-McNicoll, Barbara Papadopoulou.RNA secondary structure and nucleotide composition of the conserved hallmark sequence of Leishmania SIDER2 retroposons are essential for endonucleolytic cleavage and mRNA degradation. PLoS One, Jul 13, 2017.
• Padmanabhan PK, Zghidi-Abouzid O, Samant M, Dumas C, Aguiar BG, Estaquier J, Papadopoulou B. DDX3 DEAD-box RNA helicase plays a central role in mitochondrial protein quality control in Leishmania. Cell Death Diseases, Oct 13, 2016.
• Mantel PY, Hjelmqvist D, Walch M, Kharoubi-Hess S, Nilsson S, Ravel D, Ribeiro M, Grüring C, Ma S, Padmanabhan PK, Trachtenberg A, Ankarklev J, Brancucci NM, Huttenhower C, Duraisingh MT, Ghiran I, Kuo WP, Filgueira L, Martinelli R, Marti M. Infected erythrocyte-derived extracellular vesicles alter vascular function via regulatory Ago2-miRNA complexes in malaria. Nature Communications, Oct 10, 2016.
• Yuan Li, Sheena Shah-Simpson, Kwame Okrah, A. Trey Belew, Jungmin Choi, Kacey L. Caradonna, Padmanabhan PK, David M. Ndegwa, M. Ramzi Temanni, Héctor Corrada Bravo, Najib M. El-Sayed, Barbara A. Burleigh.Transcriptome Remodeling in Trypanosoma cruzi and Human Cells during Intracellular Infection. PLoS Pathog. 2016 Apr 5;12(4):e1005511. doi: 10.1371/journal.ppat.1005511. eCollection 2016 Apr