The Computational Virology Core develops and applies computational, statistical and bioinformatic approaches to support research across the AIDS and Cancer Virus Program, including studies of viral dynamics, evolution and responses to therapeutic and other experimental interventions.
The core collaborates closely with the AIDS and Cancer Virus Program’s experimental sections and cores on study design, analysis and interpretation. Many studies involve longitudinal or multidimensional measurements, while others use emerging assays or experimental systems that call for methods tailored to the biological question.
Much of our work centers on HIV and simian immunodeficiency virus (SIV). We also focus on Kaposi sarcoma-associated herpesvirus (KSHV), with an emphasis on analyzing its complex genome and developing methods to resolve genomic features that are difficult to capture with standard approaches.
The core also contributes computational expertise to collaborative studies of HIV co-infections, including tuberculosis.
Computational expertise tailored to the biological question
Many biological processes cannot be observed directly. Experiments may capture changes over time, differences among anatomical sites or responses to an intervention, but computational and statistical approaches are often needed to infer the underlying dynamics and connect those observations to the biological question.
The same is true when the experimental technology itself is new. Emerging assays can generate measurements that do not fit established pipelines, making it important to develop the analysis alongside the experiment so that each can inform the other as the assay is refined and validated.
Modeling and analysis embedded in experimental virology
The Computational Virology Core works closely with experimental teams from study design through analysis and interpretation. Projects often involve large, heterogeneous datasets generated by very different experimental approaches, requiring models, quality-control methods and analytical approaches adapted or developed to fit the study.
Analyzing genetic data for diverse studies
Several current SIV/HIV studies across the AIDS and Cancer Virus Program use genetically barcoded virus to address questions about viral origins, population dynamics and selection. The core develops approaches for analyzing these data, including methods that use tissue-associated barcodes to identify likely sources of virus during early infection, after treatment interruption and in semen.
In separate studies, longitudinal barcoded viral sequence data are used to follow individual lineages over time and quantify population bottlenecks and changes in lineage composition during natural infection and under experimental interventions.
Other current work focuses on emerging assays and experimental systems. This includes analysis for CRISPR/Cas-based and other integration-site assays, genome assembly and analysis of the structurally complex KSHV genome, and RNA-seq analysis supporting the development and characterization of artificial thymic organoid systems.
We also analyze immunohistochemistry and imaging-derived cell-level measurements, including cellular phenotypes and activation markers during HIV/SIV infection including with co-infection of other pathogens, including tuberculosis.
Our capabilities and specializations
Quantitative modeling and statistical inference
We develop and apply models and statistical methods for longitudinal, population-level, spatial and intervention-based studies, with an emphasis on extracting biological information that is not directly observable from individual measurements.
Bioinformatics and data analysis
We analyze a range of biological data, from viral sequence and genomic data to transcriptomic, tissue-based, and imaging-derived measurements, selecting and adapting methods to the scientific question and study design. Across our modeling and analysis work, we also use current AI-assisted and agentic tools to support computational development, testing, documentation and reproducible workflows.
Methods for emerging assays and experimental approaches
For assays and experimental systems that are not well served by existing pipelines, we develop approaches for data processing, quality control, statistical analysis and interpretation in collaboration with the teams developing and applying those methods.