Dr Partha Chattopadhyay

Biography

I am a Research Associate at the Victor Phillip Dahdaleh Heart & Lung Research Institute, University of Cambridge, exploring the molecular and cellular basis of atherosclerosis. My research focuses on building a spatio-temporal map of human coronary atherosclerosis using spatial transcriptomics and single-cell multiomics, bringing together experimental, clinical, and computational data to uncover key mechanisms driving coronary atherosclerosis, one of the leading causes of death worldwide.

I developed my expertise in single-cell multiomics, lncRNA biology, and repeat elements during my Ph.D. at the Institute of Genomics and Integrative Biology, Delhi, India. I have always been fascinated by how cells adapt and respond to their environment, particularly in the context of immune regulation and infectious diseases. My work combines high-dimensional data analysis with a systems biology approach to investigate these complex interactions.

Beyond the lab, I find inspiration in nature, especially through bird and landscape photography. Capturing the details of the natural world fuels my curiosity and appreciation for biological complexity—both in research and in life.

Publications

Key publications:

Soni, J., Mehta, P., Yadav, S., Chattopadhyay, P., & Pandey, R. (2025). Protocol for investigating intracellular microbial diversity using single-cell RNA-seq in immune cells of SARS-CoV-2-positive and recovered patients. STAR protocols, 6(1), 103546.
Mehta, P., Liu, C. S. C., Sinha, S., Mohite, R., Arora, S., Chattopadhyay, P., Budhiraja, S., ... & Pandey, R. (2024). Reduced protein-coding transcript diversity in severe dengue emphasises the role of alternative splicing. Life Science Alliance, 7(8).
Chattopadhyay, P^*., Mehta, P., Kanika, Mishra, P., Chen Liu, C. S., Tarai, B., Budhiraja, S., ... & Pandey, R. (2024). RNA editing in host lncRNAs as potential modulator in SARS-CoV-2 variants-host immune response dynamics. iScience, 27(6), 109846.
Chattopadhyay, P^†., Mehta, P^†., Soni, J., Tardalkar, K., Joshi, M., & Pandey, R. (2024). Cell-specific housekeeping role of lncRNAs in COVID-19-infected and recovered patients. NAR Genomics and Bioinformatics, 6(1), lqae023.
Soni, J^†., Chattopadhyay, P^†., Mehta, P., Mohite, R., Tardalkar, K., Joshi, M., & Pandey, R. (2024). Dynamics of Whole Transcriptome Analysis (WTA) and Surface markers expression (AbSeq) in Immune Cells of COVID-19 Patients and Recovered captured through Single Cell Genomics. Frontiers in medicine, 11, 1297001.
Mehta, P., Swaminathan, A., Yadav, A., Chattopadhyay, P., Shamim, U., & Pandey, R. (2024). Integrative genomics important to understand host-pathogen interactions. Briefings in functional genomics, 23(1), 1–14.
Mehta, P., Chattopadhyay, P., Mohite, R., D’Rozario, R., Bandopadhyay, P., Sarif, J., Ray, Y., ... & Pandey, R. (2024). Suppressed transcript diversity and immune response in COVID-19 ICU patients: a longitudinal study. Life Science Alliance, 7(1).
Yadav, S^†., Mehta, P^†., Soni, J^†., Chattopadhyay, P^†., Devi, P., Habyarimana, T., Tardalkar, K., ... & Pandey, R. (2023). Single-cell RNA-Seq reveals intracellular microbial diversity within immune cells during SARS-CoV-2 infection and recovery. iScience, 26(11), 108357.
Khare, K^†., Chattopadhyay, P^†., Devi, P., Mehta, P., Raina, A., Liu, C. S. C., Tardalkar, K., ... & Pandey, R. (2023). Dysregulated metal ion homeostasis underscores non-canonical function of CD8+ T cell during COVID-19. Frontiers in medicine, 10, 1282390.
Mehta, P^†., Chattopadhyay, P^†., Ravi, V., Tarai, B., Budhiraja, S., & Pandey, R. (2023). SARS-CoV-2 infection severity and mortality is modulated by repeat-mediated regulation of alternative splicing. Microbiology spectrum, 11(5), e0135123.
Singh, J., Anantharaj, A., Panwar, A., Rani, C., Bhardwaj, M., Kumar, P., Chattopadhyay, P., ... & Medigeshi, G. R. (2023). BA.1, BA.2 and BA.2.75 variants show comparable replication kinetics, reduced impact on epithelial barrier and elicit cross-neutralizing antibodies. PLoS Pathogens, 19(2), e1011196.
Chattopadhyay, P^†., Khare, K., Kumar, M., Mishra, P., Anand, A., Maurya, R., Gupta, R., ... & Pandey, R. (2022). Single-cell multiomics revealed the dynamics of antigen presentation, immune response and T cell activation in the COVID-19 positive and recovered individuals. Frontiers in Immunology, 13, 1034159.
Chattopadhyay, P^†., Mishra, P., Mehta, P., Soni, J., Gupta, R., Tarai, B., Budhiraja, S., ... & Pandey, R. (2022). Transcriptomic study reveals lncRNA-mediated downregulation of innate immune and inflammatory response in the SARS-CoV-2 vaccination breakthrough infections. Frontiers in Immunology, 13, 1035111.
Mehta, P., Ravi, V., Devi, P., Maurya, R., Parveen, S., Mishra, P., Yadav, A., ... Chattopadhyay, P., ... & Pandey, R. (2022). Mutational dynamics across VOCs in International travellers and Community transmission underscores importance of Spike-ACE2 interaction. Microbiological Research, 262, 127099.
Chattopadhyay, P^†., Mishra, P^†., Khare, K., Yadav, A., Mehta, P., Saifi, S., Swaminathan, A., ... & Pandey, R. (2022). LncRNAs harbouring regulatory motifs within repeat elements modulate immune response towards COVID-19 disease severity and clinical outcomes. Clinical and translational medicine, 12(7), e932.
Devi, P., Maurya, R., Mehta, P., Shamim, U., Yadav, A., Chattopadhyay, P., Kanakan, A., ... & Pandey, R. (2022). Increased Abundance of Achromobacter xylosoxidans and Bacillus cereus in Upper Airway Transcriptionally Active Microbiome of COVID-19 Mortality Patients Indicates Role of Co-Infections in Disease Severity and Outcome. Microbiology spectrum, 10(3), e0231121.
Maurya, R^†., Shamim, U^†., Chattopadhyay, P^†., Mehta, P., Mishra, P., Devi, P., Swaminathan, A., ... & Pandey, R. (2022). Human-host transcriptomic analysis reveals unique early innate immune responses in different sub-phenotypes of COVID-19. Clinical and translational medicine, 12(6), e856.
Maurya, R., Kanakan, A., Vasudevan, J. S., Chattopadhyay, P., & Pandey, R. (2022). Infection outcome needs two to tango: human host and the pathogen. Briefings in functional genomics, 21(2), 90–102.
Alle, S., Kanakan, A., Siddiqui, S., Garg, A., Karthikeyan, A., Mehta, P., Mishra, N., ... Chattopadhyay, P., ... & Priyakumar, U. D. (2022). COVID-19 Risk Stratification and Mortality Prediction in Hospitalized Indian Patients: Harnessing clinical data for public health benefits. Plos One, 17(3), e0264785.
Kanakan, A., Mehta, P., Devi, P., Saifi, S., Swaminathan, A., Maurya, R., Chattopadhyay, P., ... & Pandey, R. (2022). Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations? Frontiers in Microbiology, 13, 763169.
Kale, P., Gupta, E., Bihari, C., Patel, N., Rooge, S., Pandey, A., Bajpai, M., ... Chattopadhyay, P., ... & Sarin, S. K. (2021). Vaccine Breakthrough Infections by SARS-CoV-2 Variants after ChAdOx1 nCoV-19 Vaccination in Healthcare Workers. Vaccines, 10(1).
Bhat, S., Pandey, A., Kanakan, A., Maurya, R., Vasudevan, J. S., Devi, P., Chattopadhyay, P., ... & Pandey, R. (2021). Learning From Biological and Computational Machines: Importance of SARS-CoV-2 Genomic Surveillance, Mutations and Risk Stratification. Frontiers in cellular and infection microbiology, 11, 783961.
Sahni, S^†., Chattopadhyay, P^†., Khare, K., & Pandey, R. (2021). Single-Cell Genomics: Enabling the Functional Elucidation of Infectious Diseases in Multi-Cell Genomes. Pathogens (Basel, Switzerland), 10(11).
Mlcochova, P., Kemp, S. A., Dhar, M. S., Papa, G., Meng, B., Ferreira, I. A. T. M., Datir, R., ... Chattopadhyay, P., ... & Gupta, R. K. (2021). SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion. Nature, 599(7883), 114–119.
Sarif, J., Raychaudhuri, D., D’Rozario, R., Bandopadhyay, P., Singh, P., Mehta, P., Hoque, M. A., ... Chattopadhyay, P., ...& Ganguly, D. (2021). Plasma Gradient of Soluble Urokinase-Type Plasminogen Activator Receptor Is Linked to Pathogenic Plasma Proteome and Immune Transcriptome and Stratifies Outcomes in Severe COVID-19. Frontiers in Immunology, 12, 738093.
Mehta, P., Alle, S., Chaturvedi, A., Swaminathan, A., Saifi, S., Maurya, R., Chattopadhyay, P., ... & Pandey, R. (2021). Clinico-Genomic Analysis Reveals Mutations Associated with COVID-19 Disease Severity: Possible Modulation by RNA Structure. Pathogens, 10(9).
Devi, P^†., Khan, A^†., Chattopadhyay, P^†., Mehta, P., Sahni, S., Sharma, S., & Pandey, R. (2021). Co-infections as Modulators of Disease Outcome: Minor Players or Major Players? Frontiers in Microbiology, 12, 664386.
Mehta, P., Sahni, S., Siddiqui, S., Mishra, N., Sharma, P., Sharma, S., Tyagi, A., ...Chattopadhyay, P., ... & Pandey, R. (2021). Respiratory Co-Infections: Modulators of SARS-CoV-2 Patients’ Clinical Sub-Phenotype. Frontiers in Microbiology, 12, 653399.
Chattopadhyay, P^†., Srinivasa Vasudevan, J., & Pandey, R. (2021). Noncoding RNAs: modulators and modulatable players during infection-induced stress response. Briefings in functional genomics, 20(1), 28–41.

Other publications:

Chattopadhyay, P^†., Mehta, P., Maurya, R., Mishra, P., Kumari, M., Devi, P., Khare, K., ... & Pandey, R. (2023). Experimental repertoire to elucidate the functional landscape of host–pathogen interactome. Genomic surveillance and pandemic preparedness (pp. 227–266). Elsevier.
Saifi, S., Swaminathan, A., Devi, P., Chattopadhyay, P., Gupta, S., Garg, A., Saxena, S., ... & Pandey, R. (2023). A Tour-d’Horizon of microbiota therapeutics for metabolic disorders. Microbiome Therapeutics (pp. 231–253). Elsevier.
Khan, A^†., Chattopadhyay, P^†., Devi, P^†., & Pandey, R. (2022). Epigenetics of host–human gut microbiome interactions. Reference module in food science. Elsevier.
Devi, P^†., Khan, A^†., Chattopadhyay, P^†., Garg, A., & Pandey, R. (2021). Gut microbiota and the liver: interaction shaping interactome. Reference module in food science. Elsevier.