Y.-Y. Liu

Perception of Motion Salience Shapes the Emergence of Collective Motions

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

Microbiome-based correction for random errors in nutrient profiles derived from self-reported dietary assessments

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.

Data-driven prediction of colonization outcomes for complex microbial communities

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

Feasibility in MacArthur's Consumer-Resource Model

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

Identifying keystone species in microbial communities using deep learning

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.

Predicting metabolite response to dietary intervention using deep learning

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.

Predicting metabolomic profiles from microbial composition through neural ordinary differential equations

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.

Association Rule Mining of the Human Gut Microbiome

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

Pairing Metagenomics and Metaproteomics to Characterize Ecological Niches and Metabolic Essentiality of gut microbiomes

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.

Gut feelings: Associations of emotions and emotion regulation with the gut microbiome in women

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

Ecological Dynamics Imposes Fundamental Challenges in Microbial Source Tracking

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.

Dissecting the Role of the Human Microbiome in COVID-19 via Metagenome-assembled Genomes

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.

Ecological dynamics of the gut microbiome in response to dietary fiber

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

Gut Microbiota predicts Healthy Late-life Aging in Male Mice

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

Origins of Scaling Laws in Microbial Dynamics

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

Establishment and Resilience of Transplanted Gut Microbiota in Aged Mice

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.

Characterizing scaling laws in gut microbial dynamics from time series data: caution is warranted

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.

Deciphering Functional Redundancy in the Human Microbiome

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.

A conserved ubiquitin- and ESCRT-dependent pathway to regulate human lysosomal membrane proteins

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

Impact of temporal pH fluctuations on the coexistence of nasal bacteria

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.

The impact of colonization history on the composition of ecological systems

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.

Dissimilarity-Overlap Analysis of Replicate Enrichment Communities

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.

TORC1 regulates vacuole membrane composition through ubiquitin- and ESCRT-dependent microautophagy

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

Pharmacodynamics of linezolid-plus-fosfomycin against vancomycin-susceptible and -resistant enterococci in vitro and in vivo of a Galleria mellonella larval infection model

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.

Identifying sensor species to predict critical transitions in complex ecosystems

The paper develops a method to identify sensor species in ecosystems to predict critical transitions using network structure, validated on experimental lake data.

Controlling complex microbial communities: a network-based approach

This paper develops a network-based framework to control microbial communities by identifying driver species, validated on gut and sponge microbiota.

Overcome Competitive Exclusion in Ecosystems

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

Mapping the ecological networks of microbial communities

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.

Horizontal Gene Transfer Can Help Maintain the Equilibrium of Microbial Communities

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.