Research Articles
ECMpy for Automated ecGEMs: A Step-by-Step Workflow for Accelerating Metabolic Network Analysis in Biomedical Research
This article provides a comprehensive guide to using ECMpy, a powerful Python-based workflow for constructing Enzyme-Constrained Genome-Scale Metabolic Models (ecGEMs).
E. coli vs. S. cerevisiae: Choosing the Optimal Microbial Host for Heterologous Natural Product Synthesis
This article provides a comprehensive, comparative analysis of Escherichia coli and Saccharomyces cerevisiae as heterologous hosts for the biosynthesis of high-value natural products.
Dynamic Flux Balance Analysis (dFBA): Modeling Transient Metabolism for Biomedical Breakthroughs
This article provides a comprehensive guide to Dynamic Flux Balance Analysis (dFBA), a critical computational framework for modeling metabolism in unsteady state conditions.
DreaMS vs SIRIUS: Comprehensive Performance Comparison for Mass Spectra Annotation in Drug Discovery
This article provides a detailed comparative analysis of DreaMS (Data-driven and Rule-based Exact Annotation of Mass Spectra) and SIRIUS, two leading computational platforms for annotating metabolites from LC-MS/MS data.
DreaMS: How Transformer Models are Revolutionizing MS/MS Spectra Interpretation for Biomarker and Drug Discovery
This article explores the DreaMS transformer model, a cutting-edge deep learning framework designed for the interpretation of tandem mass spectrometry (MS/MS) spectra.
Redundancy in Metabolic Flux Analysis: From Core Concepts to Cutting-Edge Applications in Biomedical Research
This article provides a comprehensive overview of redundancy in metabolic flux analysis (MFA) for researchers and drug development professionals.
Taming the Tail: Advanced Statistical Strategies for Non-Normal Metabolomics Data
This article provides a comprehensive guide for metabolomics researchers and pharmaceutical scientists on addressing the pervasive challenge of skewed data distributions in statistical analysis.
Beyond the Optimum: Mastering Alternate Flux Solutions in FBA for Robust Metabolic Modeling
This article provides a comprehensive guide to alternate optimal solutions (AOS) in Flux Balance Analysis (FBA) for researchers and drug development professionals.
Building a Robust Data-Adaptive Filtering Pipeline: A Step-by-Step Guide for LC-MS Metabolomics
This article provides a comprehensive guide for researchers developing or optimizing data filtering pipelines for liquid chromatography-mass spectrometry (LC-MS) metabolomics.
Beyond the Noise: A Cross-Platform Guide to Optimal Metabolomics Data Filtering for Biomarker Discovery
This comprehensive review addresses the critical challenge of data filtering in cross-platform metabolomics studies, which is essential for robust biomarker identification and clinical translation.