Y.-Y. Liu

This paper develops a deep learning model to predict individual metabolite responses to dietary interventions based on gut microbiota composition, showing improved performance over traditional methods.

The paper investigates collective motion patterns in bird flocks and develops a model based on motion salience to explain hierarchy formation and swarm behavior.

This study introduces METRIC, a deep-learning method that uses gut microbiome data to correct random errors in self-reported dietary assessments, showing effectiveness in simulated and real-world datasets.

This paper introduces a deep learning framework to identify keystone species in microbial communities using synthetic and real microbiome data, finding taxa with high keystoneness show community specificity.

The paper predicts colonization outcomes of exogenous microbes in complex communities using a data-driven approach, validated with synthetic data and experimental tests.

This paper identifies conditions for feasibility in MacArthur's consumer-resource model and shows how system complexity and resource growth affect feasibility.

This paper introduces mNODE, a neural ODE-based method predicting metabolomic profiles from microbial composition, showing superior performance and interpretability across human and environmental microbiomes.

This study uses association rule mining to analyze the human gut microbiome, identifying higher-order microbial relationships and showing improved disease classification.

This study develops a computational pipeline combining metagenomics and metaproteomics to identify proteins' metabolic and ecological roles in gut microbiomes using simulated and real data.

This study investigates associations between emotions, emotion regulation, and the gut microbiome in women, finding links between emotional states and microbial diversity and pathways.

This study shows that existing microbial source tracking solvers fail to solve the MST problem when ecological dynamics, such as microbial interactions and priority effects, are present.

This study uses metagenome-assembled genomes to analyze the human microbiome's role in COVID-19, identifying gut microbiome signatures that distinguish cases from controls and predict disease progression.

This study examines how dietary fiber affects gut microbiome dynamics and SCFAs in mice, showing baseline-dependent responses and the importance of ecological modeling.

This study shows that gut microbiota signatures from young mice can predict healthy aging in older mice under calorie restriction.

The paper shows scaling laws in microbial dynamics are universal across habitats and driven by stochastic factors and inter-species interactions.

This study investigates how age-matching between fecal microbiota transplantation (FMT) donors and aged recipients affects microbiota establishment and resilience, finding that mismatched age may reduce resilience against inflammation.

The paper analyzes gut microbial dynamics in humans and mice, finding robust scaling laws, but cautions that these laws can be reproduced by randomized time series.

The paper investigates functional redundancy in the human microbiome by analyzing genomic content networks and developing a genome evolution model to explain their topological features.

This study identifies a conserved ubiquitin- and ESCRT-dependent pathway for degrading lysosomal membrane proteins in human and yeast cells.

The paper examines how temporal pH fluctuations affect nasal bacterial coexistence using experimental data and a mathematical model, finding that community composition is robust against pH changes.

This paper develops a theory linking colonization history to community composition, showing that community size, species connectivity, and growth rate variation influence the dominance of colonization history.

The paper uses DOA to analyze in vitro microbial communities, finding a negative correlation between dissimilarity and overlap in replicate habitats, suggesting potential for universal dynamics but not absolute universality.

The paper shows that TORC1 inactivation leads to vacuole membrane remodeling via ubiquitination and ESCRT-dependent microautophagy.

This study evaluates the in vitro and in vivo synergistic effects of linezolid and fosfomycin against vancomycin-susceptible and -resistant enterococci using a Galleria mellonella model.

The paper demonstrates that chasing triplets in predation can allow more consumer species to coexist than resources, overcoming the competitive exclusion principle.

This paper introduces a method to infer microbial ecological networks from steady-state data without assuming population dynamics models, validated on simulated and experimental datasets.

This study uses a population dynamics model to show that horizontal gene transfer affects microbial community stability and species coexistence by altering gene flux and direction.