Academic Projects
scTEQuant: viral & transposable-element quantification
Bayesian quantification · single-cell & bulk RNA-seq
A next-generation Bayesian pipeline for locus-specific viral and transposable-element quantification from single-cell and bulk RNA-seq, developed with AI-assisted tooling and benchmarked head-to-head against established methods.
- Locus-specific quantification at transcriptional-unit resolution across bulk, single-cell, and spatial RNA-seq
- Improves quantification accuracy for repetitive and virus-derived loci
- Built for direct application to EBV and HIV-1 transcriptional profiling
Viral influence on immune cells in EBV+ and EBV/HIV lymphoma
Host-pathogen immunology · viral latency & reactivation
Asking how viruses alter immune cell function and drive its dysregulation, by resolving EBV lytic-versus-latency programs and HIV-1 transcription alongside host gene expression at single-cell resolution across a cohort of EBV+ lymphoma patients, including EBV/HIV co-infected cases.
- Links viral programs to changes in immune cell state and function in the tumor and its microenvironment
- Antiviral immunology: how innate sensing and adaptive immune pressure shape EBV and HIV-1 reservoirs, and which immune states permit or suppress reactivation
- Characterizes consequences of co-infection in immunocompromised hosts
- Applies scTEQuant to jointly quantify host, EBV, and HIV-1 transcription
Quantification of transposable element expression in healthy and virus-infected samples
HERVs · locus-specific quantification
Co-developed Stellarscope, a bioinformatic tool to quantify locus-specific expression of transposable element sequences, and published the first single-cell atlas of TE and HERV expression across the human immune system.
- Resolves individual HERV loci rather than family-level aggregates
- Links HERV expression patterns to specific immune cell identities and states
- SARS-CoV-2 induces expression of specific HERV loci, even in comparison to related viruses (SARS-CoV and MERS-CoV)
- Locus-level HERV expression can tell lymphoma subtypes apart
- Foundation for downstream work on HERVs in immune surveillance, tolerance, and autoimmune disease
Independent Projects
Cracking the Glycan Shield
HIV-1 broadly neutralizing antibodies · glycan shield · viral escape
An AI-driven pipeline that maps where six antibodies can and cannot get through HIV's glycan shield, and models how the virus escapes the ones that do. Published as a full interactive report with five companion explorers.
- Coverage Explorer: antibody combinations checked against 525 real viruses
- Full-Density Glycan Shield: complete Man9 glycans modeled on the 5FYJ trimer in 3D
- Sampling Blind Spot and Origin Network: why sequencing depth hides independent escape events