Qingzhen Hou

MNetClass: A Control-Free Microbial Network Clustering Framework for Identifying Central Subcommunities Across Ecological Niches

MNetClass identifies central microbial subcommunities across ecological niches without control samples, outperforming existing methods in accuracy and predictive power.

Towards a Better Understanding of Batch Effects in Spatial Transcriptomics: Definition and Method Evaluation

The paper defines batch effects in spatial transcriptomics and evaluates methods for batch correction across different integration scenarios.

Enzyme stability-activity trade-off: new insights from protein stability weaknesses and evolutionary conservation

The paper identifies a stability-activity trade-off in enzymes, showing oscillatory patterns of stability strengths and weaknesses around catalytic sites and their evolutionary conservation.

Genome-scale enzymatic reaction prediction by variational graph autoencoders

The paper introduces MPI-VGAE, a framework for predicting metabolite-protein interactions across organisms, showing improved performance in reconstructing metabolic pathways and disease-specific networks.

SeRenDIP-CE: Sequence-based Interface Prediction for Conformational Epitopes

The paper introduces SeRenDIP-CE, a sequence-based method for predicting conformational epitopes, achieving better performance than existing predictors on an antibody-antigen structure.

SWOTein: A structure-based approach to predict stability Strengths and Weaknesses of prOTEINs

SWOTein predicts stability strengths and weaknesses in proteins using statistical energy functions, showing agreement with experimental data and identifying functional regions.

SOLart: a structure-based method to predict protein solubility and aggregation

SOLart predicts protein solubility using structure-based features, achieving high correlation with experimental values and outperforming existing predictors.

A comprehensive computational study of amino acid interactions in membrane proteins

This study develops new energy functions to analyze amino acid interactions in membrane proteins, revealing differences in stability contributions between transmembrane and extramembrane regions.