Joint species distribution models (JSDMs) are central to biodiversity forecasting and conservation decision-making. As ecological datasets grow in size, dimensionality, and spatio-temporal resolution, there is a need for flexible yet scalable JSDMs t... read more
Peripheral artery disease (PAD) is a complex vascular disorder characterized by heterogeneous molecular mechanisms and incomplete functional annotation, limiting systematic biomarker discovery. Network-based learning approaches provide a powerful fra... read more
Prediction of conformational B-cell epitopes is critical for vaccine design, immunotherapy, and antibody engineering. To date, several host-independent computational methods have been developed for predicting antibody-interacting residues in antigen ... read more
By resolving cell-type compositions from multi-cellular spatial measurements, deconvolution is central to resolving the cellular landscape of complex tissues. Existing deconvolution methods fit continuous expression values and are therefore sensitive... read more
In task-oriented teams, long-term coordination among specialized roles may contribute to shared patterns of cognition and behavior, yet little is known about how such experience is reflected in brain functional organization. Here, we examined whether... read more
Selecting the correct mouse gene to model a human disease phenotype is critical for translational research, yet sequence-based orthology can fail when genes have been lost, duplicated, or functionally rewired between species. Here we present BRIDGE (... read more
Convolutional Neural Networks (CNNs) have become increasingly prominent in biodiversity monitoring due to their strong performance in accurately detecting species from sound recordings, overcoming some limitations of traditional methods such as point... read more
Rapid and accurate prediction of protein-ligand bindings is essential for drug discovery. While generative AI has driven rapid advancements in structure-based approaches, sequence-based methods remain significantly faster and more cost-effective. Her... read more
Explainable machine learning (ML) methods are gaining increasing attention in environmental and ecological research for their ability to reveal relationships between environmental drivers and population dynamics. However, there remain questions on th... read more
Constraint-based metabolic modeling is a powerful way to study the mechanistic basis of cellular states and disease, but its effective use demands substantial computational expertise and careful coordination of multi-step analyses. We developed MechA... read more
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