Joon‐Yong Lee

Coupling Flux Balance Analysis with Reactive Transport Modeling through Machine Learning for Rapid and Stable Simulation of Microbial Metabolic Switching

The paper develops an ANN-based reduced-order model to accelerate FBA integration with RTMs, enabling efficient simulation of microbial metabolic switching in Shewanella oneidensis.

Uncovering hidden members and functions of the soil microbiome using de novo metaproteomics

This paper introduces a de novo metaproteomics pipeline using a deep learning model to identify soil microbiome composition and functions without relying on metagenomic data.

Representing Organic Matter Thermodynamics in Biogeochemical Reactions via Substrate-Explicit Modeling

This paper introduces a new biogeochemical modeling approach that explicitly represents organic matter thermodynamics to improve predictions of microbial degradation processes and their environmental impacts.

A generalizable method for false-discovery rate estimation in mass spectrometry-based lipidomics

This paper introduces a generalizable method for estimating false discovery rates in mass spectrometry-based lipidomics to enable automated data analysis.

Blazing Signature Filter: a library for fast pairwise similarity comparisons

The paper introduces BSF, a fast pairwise similarity algorithm that filters unproductive comparisons to enable efficient data mining.