Machine and deep learning meet genome-scale metabolic modeling

G Zampieri, S Vijayakumar, E Yaneske… - PLoS computational …, 2019 - journals.plos.org
Omic data analysis is steadily growing as a driver of basic and applied molecular biology
research. Core to the interpretation of complex and heterogeneous biological phenotypes …

Recent advances in machine learning applications in metabolic engineering

P Patra, BR Disha, P Kundu, M Das, A Ghosh - Biotechnology Advances, 2023 - Elsevier
Metabolic engineering encompasses several widely-used strategies, which currently hold a
high seat in the field of biotechnology when its potential is manifesting through a plethora of …

New applications of synthetic biology tools for cyanobacterial metabolic engineering

M Santos-Merino, AK Singh, DC Ducat - Frontiers in bioengineering …, 2019 - frontiersin.org
Cyanobacteria are promising microorganisms for sustainable biotechnologies, yet unlocking
their potential requires radical re-engineering and application of cutting-edge synthetic …

Systems biology approach for enhancing limonene yield by re-engineering Escherichia coli

JK Khanijou, YT Hee, CPM Scipion, X Chen… - npj Systems Biology …, 2024 - nature.com
Engineered microorganisms have emerged as viable alternatives for limonene production.
However, issues such as low enzyme abundance or activities, and regulatory …

Emerging species and genome editing tools: future prospects in cyanobacterial synthetic biology

GAR Gale, AA Schiavon Osorio, LA Mills, B Wang… - Microorganisms, 2019 - mdpi.com
Recent advances in synthetic biology and an emerging algal biotechnology market have
spurred a prolific increase in the availability of molecular tools for cyanobacterial research …

Next-generation genome-scale metabolic modeling through integration of regulatory mechanisms

CH Chung, DW Lin, A Eames, S Chandrasekaran - Metabolites, 2021 - mdpi.com
Genome-scale metabolic models (GEMs) are powerful tools for understanding metabolism
from a systems-level perspective. However, GEMs in their most basic form fail to account for …

OptRAM: In-silico strain design via integrative regulatory-metabolic network modeling

F Shen, R Sun, J Yao, J Li, Q Liu, ND Price… - PLoS computational …, 2019 - journals.plos.org
The ultimate goal of metabolic engineering is to produce desired compounds on an
industrial scale in a cost effective manner. To address challenges in metabolic engineering …

Synthesizing systems biology knowledge from omics using genome‐scale models

S Dahal, JT Yurkovich, H Xu, BO Palsson, L Yang - Proteomics, 2020 - Wiley Online Library
Omic technologies have enabled the complete readout of the molecular state of a cell at
different biological scales. In principle, the combination of multiple omic data types can …

Seeing the wood for the trees: a forest of methods for optimization and omic-network integration in metabolic modelling

S Vijayakumar, M Conway, P Lió… - Briefings in …, 2018 - academic.oup.com
Metabolic modelling has entered a mature phase with dozens of methods and software
implementations available to the practitioner and the theoretician. It is not easy for a …

Biomedical applications of genome-scale metabolic network reconstructions of human pathogens

LJ Dunphy, JA Papin - Current opinion in biotechnology, 2018 - Elsevier
Highlights•Genome-scale metabolic network reconstructions capture human pathogen
phenotypes.•Reconstructions can explore relationships between drug resistance and …