Research Articles
A Comprehensive Flux Balance Analysis (FBA) Protocol for E. coli: From Foundational Concepts to Advanced Applications in Biomedical Research
This article provides a comprehensive guide for researchers and scientists on implementing Flux Balance Analysis (FBA) for E.
Beyond Cutting: The CRISPR-Cas9 Toolkit for Precision Metabolic Pathway Engineering
This article provides a comprehensive overview of the expanding CRISPR-Cas9 toolkit for metabolic pathway engineering, moving beyond simple gene knockouts to include transcriptional control, epigenetic editing, and base editing.
Synthetic Biology and Metabolic Engineering: Principles and Practices for Next-Generation Bioproduction
This article provides a comprehensive guide to the principles of synthetic biology for metabolic engineers in research and drug development.
Stoichiometric vs. Kinetic Metabolic Modeling: A Comprehensive Guide for Biomedical Research and Drug Development
This article provides a systematic comparison of stoichiometric and kinetic modeling approaches for analyzing cellular metabolism, tailored for researchers and drug development professionals.
Dynamic Metabolic Engineering: Revolutionizing Bioproduction with Smart Cellular Control
Dynamic metabolic engineering represents a paradigm shift from static genetic modification to the design of autonomous, self-regulating microbial cell factories.
Strategic Host Organism Selection for Microbial Cell Factories: A Comprehensive Guide for Biomanufacturing and Drug Development
Selecting the optimal microbial host is a critical, multi-factorial decision that determines the success of biomanufacturing processes for pharmaceuticals and chemicals.
Accelerating Bioprocesses: The DBTL Cycle in Modern Metabolic Engineering
This article provides a comprehensive overview of the Design-Build-Test-Learn (DBTL) cycle, a foundational framework in metabolic engineering for developing microbial cell factories.
Genome-Scale Metabolic Model Reconstruction: A Comprehensive Guide from Foundations to Biomedical Applications
Genome-scale metabolic models (GEMs) provide powerful computational frameworks for systems-level metabolic studies by describing gene-protein-reaction associations across entire metabolic genes.
Flux Balance Analysis: A Beginner's Guide to Metabolic Modeling for Biomedical Research
This guide provides a comprehensive introduction to Flux Balance Analysis (FBA), a cornerstone computational method in systems biology and metabolic engineering.
Stoichiometric Inconsistency and Network Gaps: From Detection to Resolution in Metabolic Models
This article explores the critical challenge of stoichiometric inconsistencies in genome-scale metabolic models (GEMs) and their role in creating network gaps that impair predictive accuracy. Aimed at researchers, scientists, and drug development professionals, it details how these structural errors arise, their impact on flux balance analysis, and the computational methods—from established algorithms like fastGapFill to emerging deep learning tools like CHESHIRE—used to detect and resolve them. The content further covers troubleshooting techniques for error isolation, the validation of gap-filling solutions, and the implications of robust, stoichiometrically consistent models for advancing biomedical research and therapeutic discovery.