Research
Interpretable models for complex biology.
Selected projects in cancer epigenomics, single-cell analysis, and the tumor-associated microbiome—each with its own question, approach, and research outputs.
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2026 · Preprint 2025 · Published 2020 · Published
Recovering tumor-intrinsic DNA methylation signals from bulk cancer epigenomes
MONTE estimates tumor purity and corrects DNA methylation at single-CpG resolution, recovering tumor-intrinsic regulatory signals from bulk cancer samples.
Cancer epigenomicsDNA methylationTumor purity
Disentangling condition-specific signals from complex sequencing data
ALPINE separates condition-associated structure from shared and confounding variation while directly prioritizing genes linked to the condition of interest.
Single-cell RNA-seqInterpretable NMFBatch correction
Profiling the cancer-associated microbiome from small RNA sequencing data
An analytical framework recovers microbial signals from host microRNA sequencing data to study microbiome–tumor relationships when direct microbial sampling is unavailable.
Cancer microbiomeSmall RNA sequencingColorectal cancer