Ujjwal Neogi

My research has established an integrated systems virology framework that connects mechanistic virus-host biology to clinically relevant biomarkers, stratification tools, and therapeutic hypotheses. Across multiple viral infections and experimental systems, my work has delivered the following main results:

1)    Systems-level definition of virus–host immunometabolic programs that shape disease severity and viral control

A central outcome of my research is the demonstration that host immunometabolic states are not merely correlates of infection but functional determinants of disease trajectories. By integrating transcriptomics, proteomics, metabolomics, immunophenotyping, and network-based modeling, we have identified reproducible metabolic and immune-response signatures linked to (i) severe disease, (ii) recovery trajectories, and (iii) durable viral control. This has provided a quantitative basis for understanding how energy metabolism, innate immune programming, and inflammatory set points jointly influence pathogenesis across infections. (Appelberg et al 2020, Emerg Microbes Infect, Krishnan et al 2021, Mol Cell Proteomics, Ambikan et al 2022, Cell Systems, Ambikan et al 2023, Proc Natl Acad Sci USA, Capendale et al 2024, Nat Commun)

2)    Genome-scale metabolic modeling as a translational engine for virology

We extensively use of genome-scale metabolic models (GEMs) and constraint-based analyses in high-impact virology settings to uncover host metabolic vulnerabilities that viruses exploit. By combining host transcriptomics and metabolomics with viral context (including viral biomass/replication demands where applicable), my work has generated testable hypotheses on metabolic dependencies that can be targeted therapeutically. It has helped move virology from descriptive profiling to predictive, mechanism-oriented modeling. (Ambikan et al 2022, Life Sci Alliance, Ambikan et al 2022, Cell Systems, Ambikan et al 2023, Proc Natl Acad Sci USA.)

3)    HIV persistence and long-term ART: identification of immunometabolic risk states and mechanistic consequences

Using deeply phenotyped cohorts and multi-omics integration, my completed work has clarified that long-term treated HIV infection can retain a distinct immunometabolic impairment, including network-level metabolic “at-risk” profiles, dysregulated myeloid and monocyte function, and signatures consistent with biological aging acceleration, despite virological suppression. These findings provide a mechanistic basis for patient stratification and for designing interventions aimed at reducing chronic inflammation, comorbidity risk, and potentially the permissive environment for reservoir persistence (Mikaealoff et al 2025, Adv Sci, Mikaealoff et al 2024 Aging Cell, Svensson Akusjärvi et al 2023, AIDS).

4)    High-resolution characterization of emerging and high-consequence viral infections (SARS-CoV-2, CCHFV, dengue)

My research has delivered multi-omics maps of host responses in high-biosafety, pathogen-focused contexts, including systems-level temporal immune–metabolic profiling of Crimean-Congo hemorrhagic fever virus infection, and tissue- and variant-dependent metabolic reprogramming and inflammatory signaling in SARS-CoV-2 models. In dengue, my work has contributed predictive frameworks (e.g., cytokine dynamics) relevant to severity and public-health interpretation. Collectively, these outcomes strengthen preparedness by providing transferable analytical strategies that can be rapidly adapted to future viral threats. (Ambikan et al 2022, Cell Systems, Ambikan et al 2023, Proc Natl Acad Sci USA, Bhatt et al 2024, Virus Res)

5)   Neuroinfection and organoid-based infection biology: mechanistic links between infection, immunometabolism, and neuropathology

A major completed line of work established human brain organoids and related models as powerful platforms for dissecting viral neuropathogenesis. This includes demonstrating that disease-relevant outcomes may be driven less by neurotropism alone and more by host innate inflammatory and immunometabolic disruptions, and identifying mechanisms (including excitotoxicity-related pathways) that connect infection-induced metabolic perturbations to neural injury phenotypes. These findings open concrete routes for diagnostic biomarker discovery and therapeutic targeting in neurotropic viral disease. (Mikaealoff et al 2025, Adv Sci, Capendale et al 2024, Nat Commun, Capendale et al 2025, Cell Mol Life Sci).

I want to integrate teaching at the level of bachelor's, master's, and doctoral studies in virology and system biology by participating in lectures, seminars, and practical courses. Depending on the teaching modules already available, I could provide teaching in molecular and clinical virology, emerging and re-emerging infectious diseases, system biology in infectious diseases, diagnostic virology, and molecular virology. I have already taught RNA viruses, molecular epidemiology of emerging and re-emerging viruses, diagnostics microbiology, and application of omics in infectious diseases. Apart from that, I aim to teach the concept of immune aging in infectious diseases. Finally, I also aim to provide training for projects, as well as bachelor's and master's students, by hosting them in my laboratory for short-term research projects in the wet lab and dry lab. Apart from that, I aim to supervise doctoral students and postdoc fellows.

Manipal Institute of Virology, Karnataka, India (Since 2021): Master's in Clinical Virology, MIV610 Virological Technology, MIV512 Emerging and Re-emerging viruses. MIV509/511: Systematic Virology. (Lecture, Assignments, Seminar, Exam, 60h every semester). MIV512 received an average rating of 4.8 out of 5 from the students.

Karolinska Institute, Stockholm, Sweden (Since 2015): First Cycle: Integrated Biomedical Laboratory Science (1BA127), Microbiology 2 (1BA061), Microbial pathogenesis (2TL008), Microbiology - Methodology and Diagnostics (1BA124), Microbial pathogenesis (2TL062). Second Cycle: Infection Biology (1BA124) Stockholm University, Third Cycle: Graduate School in Molecular Medicine for Clinicians (Lectures, Seminar, Practical, Laboratory).