Adrien Osakwe

Single-cell gene programs define subtype identity and metastatic trajectories in renal cell carcinoma

This study identifies 59 gene expression programs in RCC that reveal subtype identity and metastatic trajectories, including a metastatic signature linked to poor clinical outcomes.

scTimeBench: A streamlined benchmarking platform for single-cell time-series analysis

scTimeBench benchmarks single-cell time-series analysis methods across forecast accuracy, embedding coherence, and lineage fidelity using eight datasets from four species.

GFETM: Genome Foundation-based Embedded Topic Model for scATAC-seq Modeling

GFETM improves scATAC-seq modeling by integrating genome foundation model embeddings, revealing cell-state specific TF activity and kidney diabetes epigenomic signatures.

InSTaPath: Integrating Spatial Transcriptomics and histoPathology Images via Multimodal Topic Learning

InSTaPath integrates spatial transcriptomics and histopathology images using multimodal topic learning to improve spatial domain identification and uncover gene-morphology relationships.

SpaTM: Topic Models for Inferring Spatially Informed Transcriptional Programs

SpaTM is a topic modeling framework for spatial transcriptomics data that supports both annotation-guided and annotation-free analysis, showing competitiveness in spatial label prediction and clustering.

Transcriptional Reprogramming of Skeletal Muscle Stem Cells by the Niche Environment

This study shows that the niche environment significantly influences skeletal muscle stem cell transcriptional activity, with some age-related changes being reversible through exposure to a young niche.