4.6 Article

PyMiner: A method for metabolic pathway design based on the uniform similarity of substrate-product pairs and conditional search

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biotechnology & Applied Microbiology

Metabolic compartmentalization in yeast mitochondria: Burden and solution for squalene overproduction

Zhan-Tao Zhu et al.

Summary: Harnessing mitochondria for terpene biosynthesis is promising but can lead to metabolic burden and poor cell growth. Analysis shows toxicity from MVA pathway phosphorylated intermediates within mitochondria inhibits cellular functions. Combining cytoplasmic and mitochondrial engineering strategies can alleviate metabolic burden and enhance terpene production.

METABOLIC ENGINEERING (2021)

Review Biotechnology & Applied Microbiology

Recent Advances in Metabolic Engineering, Protein Engineering, and Transcriptome-Guided Insights Toward Synthetic Production of Taxol

Ishmael Mutanda et al.

Summary: Despite the wealth of information gained over the years on Taxol research, there are still supply issues to meet increasing clinical demand. Alternative production methods have drawbacks that cause supply shortages and high production costs. Developing biotechnological production platforms for Taxol is highly desired, but gaps in understanding of the biosynthetic pathway hinder progress.

FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY (2021)

Article Biochemical Research Methods

NICEpath: Finding metabolic pathways in large networks through atom-conserving substrate-product pairs

Jasmin Hafner et al.

Summary: This study proposes a method for extracting metabolic pathways from large biochemical networks by constructing searchable graph representations. By using weighted reactant-product pairs and efficient graph search algorithms, biologically relevant metabolic pathways can be extracted, improving navigation and pathway identification in big metabolic networks.

BIOINFORMATICS (2021)

Article Biochemistry & Molecular Biology

The MetaCyc database of metabolic pathways and enzymes - a 2019 update

Ron Caspi et al.

NUCLEIC ACIDS RESEARCH (2020)

Article Agriculture, Multidisciplinary

Metabolic Engineering of Saccharomyces cerevisiae To Overproduce Squalene

Tian Li et al.

JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY (2020)

Article Biochemical Research Methods

PATHcre8: A Tool That Facilitates the Searching for Heterologous Biosynthetic Routes

Olaa Motwalli et al.

ACS SYNTHETIC BIOLOGY (2020)

Article Biochemical Research Methods

De Novo Biosynthesis of Multiple Pinocembrin Derivatives in Saccharomyces cerevisiae

Xiaonan Liu et al.

ACS SYNTHETIC BIOLOGY (2020)

Article Biochemistry & Molecular Biology

Updates in Rhea: SPARQLing biochemical reaction data

Thierry Lombardot et al.

NUCLEIC ACIDS RESEARCH (2019)

Review Chemistry, Physical

A comprehensive metabolic map for production of bio-based chemicals

Sang Yup Lee et al.

NATURE CATALYSIS (2019)

Article Biotechnology & Applied Microbiology

RetroPath2.0: A retrosynthesis workflow for metabolic engineers

Baudoin Delepine et al.

METABOLIC ENGINEERING (2018)

Article Biotechnology & Applied Microbiology

Engineering de novo anthocyanin production in Saccharomyces cerevisiae

Mark Levisson et al.

MICROBIAL CELL FACTORIES (2018)

Article Biotechnology & Applied Microbiology

A modular metabolic engineering approach for the production of 1,2-propanediol from glycerol by Saccharomyces cerevisiae

Zia-ul Islam et al.

METABOLIC ENGINEERING (2017)

Article Multidisciplinary Sciences

A Method for Finding Metabolic Pathways Using Atomic Group Tracking

Yiran Huang et al.

PLOS ONE (2017)

Review Biotechnology & Applied Microbiology

A review of computational tools for design and reconstruction of metabolic pathways

Lin Wang et al.

SYNTHETIC AND SYSTEMS BIOTECHNOLOGY (2017)

Article Biochemistry & Molecular Biology

EcoSynther: A Customized Platform To Explore the Biosynthetic Potential in E. coli

Shaozhen Ding et al.

ACS CHEMICAL BIOLOGY (2017)

Review Biotechnology & Applied Microbiology

Metabolic engineering of Saccharomyces cerevisiae for 2,3-butanediol production

Soo-Jung Kim et al.

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2017)

Article Biochemistry & Molecular Biology

ChEBI in 2016: Improved services and an expanding collection of metabolites

Janna Hastings et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biochemistry & Molecular Biology

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

Zachary A. King et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biochemical Research Methods

Reaction Decoder Tool (RDT): extracting features from chemical reactions

Syed Asad Rahman et al.

BIOINFORMATICS (2016)

Article Biochemistry & Molecular Biology

MRE: a web tool to suggest foreign enzymes for the biosynthesis pathway design with competing endogenous reactions in mind

Hiroyuki Kuwahara et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biotechnology & Applied Microbiology

Metabolic Engineering of 3-Hydroxypropionic Acid Biosynthesis in Escherichia coli

Hun Su Chu et al.

BIOTECHNOLOGY AND BIOENGINEERING (2015)

Review Biotechnology & Applied Microbiology

Biocatalysis and biotransformation of resveratrol in microorganisms

Yan-Zhen Mei et al.

BIOTECHNOLOGY LETTERS (2015)

Article Biotechnology & Applied Microbiology

Biological synthesis of coumarins in Escherichia coli

So-Mi Yang et al.

MICROBIAL CELL FACTORIES (2015)

Article Biochemical Research Methods

Optimal metabolic route search based on atom mappings

Mario Latendresse et al.

BIOINFORMATICS (2014)

Review Microbiology

Semi-synthetic artemisinin: a model for the use of synthetic biology in pharmaceutical development

Chris J. Paddon et al.

NATURE REVIEWS MICROBIOLOGY (2014)

Article Biochemistry & Molecular Biology

Data, information, knowledge and principle: back to metabolism in KEGG

Minoru Kanehisa et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Biotechnology & Applied Microbiology

Biosynthesis of ethylene glycol in Escherichia coli

Huaiwei Liu et al.

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2013)

Article Mathematical & Computational Biology

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

Ali Ebrahim et al.

BMC SYSTEMS BIOLOGY (2013)

Article Biotechnology & Applied Microbiology

Systems metabolic engineering of Escherichia coli for production of the antitumor drugs violacein and deoxyviolacein

Andre L. Rodrigues et al.

METABOLIC ENGINEERING (2013)

Article Biotechnology & Applied Microbiology

Redesigning Escherichia coli Metabolism for Anaerobic Production of Isobutanol

Cong T. Trinh et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2011)

Article Biotechnology & Applied Microbiology

Metabolic Engineering of Escherichia coli for the Production of 1,2-Propanediol From Glycerol

James M. Clomburg et al.

BIOTECHNOLOGY AND BIOENGINEERING (2011)

Article Biotechnology & Applied Microbiology

Optimization of a heterologous pathway for the production of flavonoids from glucose

Christine Nicole S. Santos et al.

METABOLIC ENGINEERING (2011)

Article Biotechnology & Applied Microbiology

Optimization of a heterologous mevalonate pathway through the use of variant HMG-CoA reductases

Suzanne M. Ma et al.

METABOLIC ENGINEERING (2011)

Article Biotechnology & Applied Microbiology

What is flux balance analysis?

Jeffrey D. Orth et al.

NATURE BIOTECHNOLOGY (2010)

Article Biochemistry & Molecular Biology

FMM: a web server for metabolic pathway reconstruction and comparative analysis

Chih-Hung Chou et al.

NUCLEIC ACIDS RESEARCH (2009)

Article Biotechnology & Applied Microbiology

Metabolic engineering of taxadiene biosynthesis in yeast as a first step towards Taxol (Paclitaxel) production

Benedikt Engels et al.

METABOLIC ENGINEERING (2008)

Article Biotechnology & Applied Microbiology

Engineered synthetic pathway for isopropanol production in Escherichia coli

T. Hanai et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2007)

Article Biochemical Research Methods

Exploring the diversity of complex metabolic networks

V Hatzimanikatis et al.

BIOINFORMATICS (2005)

Article Biochemical Research Methods

Metabolic pathway analysis web service (Pathway Hunter Tool at CUBIC)

SA Rahman et al.

BIOINFORMATICS (2005)

Review Biochemical Research Methods

Metabolic engineering for the microbial production of 1,3-propanediol

CE Nakamura et al.

CURRENT OPINION IN BIOTECHNOLOGY (2003)

Article Biotechnology & Applied Microbiology

Benzene-free synthesis of adipic acid

W Niu et al.

BIOTECHNOLOGY PROGRESS (2002)