Machine learning applications for mass spectrometry-based metabolomics

UW Liebal, ANT Phan, M Sudhakar, K Raman… - Metabolites, 2020 - mdpi.com
The metabolome of an organism depends on environmental factors and intracellular
regulation and provides information about the physiological conditions. Metabolomics helps …

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 …

Systems biology and multi-omics integration: viewpoints from the metabolomics research community

FR Pinu, DJ Beale, AM Paten, K Kouremenos… - Metabolites, 2019 - mdpi.com
The use of multiple omics techniques (ie, genomics, transcriptomics, proteomics, and
metabolomics) is becoming increasingly popular in all facets of life science. Omics …

[HTML][HTML] A machine learning approach to predict metabolic pathway dynamics from time-series multiomics data

Z Costello, HG Martin - NPJ systems biology and applications, 2018 - nature.com
New synthetic biology capabilities hold the promise of dramatically improving our ability to
engineer biological systems. However, a fundamental hurdle in realizing this potential is our …

Systems biology of metabolism

J Nielsen - Annual review of biochemistry, 2017 - annualreviews.org
Metabolism is highly complex and involves thousands of different connected reactions; it is
therefore necessary to use mathematical models for holistic studies. The use of …

Barriers and opportunities in bio-based production of hydrocarbons

YJ Zhou, EJ Kerkhoven, J Nielsen - Nature Energy, 2018 - nature.com
Global climate change caused by the accumulation of greenhouse gases (GHGs) has
caused concerns regarding the continued reliance on fossil fuels as our primary energy …

Microbial production of limonene and its derivatives: Achievements and perspectives

Y Ren, S Liu, G Jin, X Yang, YJ Zhou - Biotechnology Advances, 2020 - Elsevier
Limonene and its derivatives have great market potential with diverse applications in food,
pharmaceuticals, cosmetics, etc. Commercial production of limonene and its derivatives …

Engineering biological systems using automated biofoundries

R Chao, S Mishra, T Si, H Zhao - Metabolic Engineering, 2017 - Elsevier
Engineered biological systems such as genetic circuits and microbial cell factories have
promised to solve many challenges in the modern society. However, the artisanal processes …

[HTML][HTML] Systems biology approaches integrated with artificial intelligence for optimized metabolic engineering

M Helmy, D Smith, K Selvarajoo - Metabolic engineering communications, 2020 - Elsevier
Metabolic engineering aims to maximize the production of bio-economically important
substances (compounds, enzymes, or other proteins) through the optimization of the …

Integrated analysis of isopentenyl pyrophosphate (IPP) toxicity in isoprenoid-producing Escherichia coli

KW George, MG Thompson, J Kim, EEK Baidoo… - Metabolic …, 2018 - Elsevier
Isopentenyl pyrophosphate (IPP) toxicity presents a challenge in engineered microbial
systems since its formation is unavoidable in terpene biosynthesis. In this work, we develop …