Computational tools for the synthetic design of biochemical pathways (Q37977830)

26 August 2017

Computational tools for the synthetic design of biochemical pathways (English)

1 reference

26 August 2017

Renske van Raaphorst

2

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Marnix H Medema

object named as

Marnix H Medema

series ordinal

1

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Eriko Takano

object named as

Eriko Takano

series ordinal

3

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Rainer Breitling

object named as

Rainer Breitling

series ordinal

4

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language of work or name

English

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publication date

23 January 2012

1 reference

Nature Reviews Microbiology

26 August 2017

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26 August 2017

10

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26 August 2017

3

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26 August 2017

191-202

1 reference

https://scigraph.springernature.com/pub.10.1038/nrmicro2717

26 August 2017

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cites work

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Enzyme mechanism as a kinetic control element for designing synthetic biofuel pathways

31 March 2020

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Synthetic biology: applications come of age

31 March 2020

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Exploiting plug-and-play synthetic biology for drug discovery and production in microorganisms

31 March 2020

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Natural products version 2.0: connecting genes to molecules.

31 March 2020

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Engineered synthetic pathway for isopropanol production in Escherichia coli

31 March 2020

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Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels

31 March 2020

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https://api.crossref.org/works/10.1038%2FNRMICRO2717

Engineered biosynthesis of bacterial aromatic polyketides in Escherichia coli

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

Redesign, synthesis and functional expression of the 6-deoxyerythronolide B polyketide synthase gene cluster.

31 March 2020

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https://api.crossref.org/works/10.1038%2FNRMICRO2717

Isoprenoid pathway optimization for Taxol precursor overproduction in Escherichia coli

31 March 2020

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https://api.crossref.org/works/10.1038%2FNRMICRO2717

De novo biosynthetic pathways: rational design of microbial chemical factories

31 March 2020

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https://api.crossref.org/works/10.1038%2FNRMICRO2717

Synthetic metabolism: engineering biology at the protein and pathway scales.

31 March 2020

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Toward design-based engineering of industrial microbes

31 March 2020

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https://api.crossref.org/works/10.1038%2FNRMICRO2717

Constructing de novo biosynthetic pathways for chemical synthesis inside living cells

31 March 2020

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31 March 2020

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https://api.crossref.org/works/10.1038%2FNRMICRO2717

Engineering a mevalonate pathway in Escherichia coli for production of terpenoids

31 March 2020

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https://api.crossref.org/works/10.1038%2FNRMICRO2717

Production of the antimalarial drug precursor artemisinic acid in engineered yeast

31 March 2020

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https://api.crossref.org/works/10.1038%2FNRMICRO2717

Engineering Escherichia coli for production of functionalized terpenoids using plant P450s

31 March 2020

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https://api.crossref.org/works/10.1038%2FNRMICRO2717

Reconstruction of biochemical networks in microorganisms

31 March 2020

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https://api.crossref.org/works/10.1038%2FNRMICRO2717

Computational methods for protein sequence comparison and search

31 March 2020

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https://api.crossref.org/works/10.1038%2FNRMICRO2717

Computational design tools for synthetic biology

31 March 2020

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https://api.crossref.org/works/10.1038%2FNRMICRO2717

OptStrain: a computational framework for redesign of microbial production systems.

31 March 2020

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https://api.crossref.org/works/10.1038%2FNRMICRO2717

PathMiner: predicting metabolic pathways by heuristic search

31 March 2020

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https://api.crossref.org/works/10.1038%2FNRMICRO2717

Microbial pathway prediction: a functional group approach

31 March 2020

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https://api.crossref.org/works/10.1038%2FNRMICRO2717

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

31 March 2020

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https://api.crossref.org/works/10.1038%2FNRMICRO2717

Exploring the diversity of complex metabolic networks.

31 March 2020

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https://api.crossref.org/works/10.1038%2FNRMICRO2717

Biosynthesis: is it time to go retro?

31 March 2020

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https://api.crossref.org/works/10.1038%2FNRMICRO2717

DESHARKY: automatic design of metabolic pathways for optimal cell growth.

31 March 2020

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https://api.crossref.org/works/10.1038%2FNRMICRO2717

Prediction of novel synthetic pathways for the production of desired chemicals

31 March 2020

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https://api.crossref.org/works/10.1038%2FNRMICRO2717

A retrosynthetic biology approach to metabolic pathway design for therapeutic production

31 March 2020

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https://api.crossref.org/works/10.1038%2FNRMICRO2717

Extreme pathway lengths and reaction participation in genome-scale metabolic networks

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

Group contribution method for thermodynamic analysis of complex metabolic networks

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

New surveyor tools for charting microbial metabolic maps.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

OptFlux: an open-source software platform for in silico metabolic engineering

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

Encoding multiple unnatural amino acids via evolution of a quadruplet-decoding ribosome

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

Reengineering orthogonally selective riboswitches

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

De novo generation of mutually orthogonal aminoacyl-tRNA synthetase/tRNA pairs.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

Synthesis of orthogonal transcription-translation networks

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

Evolved orthogonal ribosomes enhance the efficiency of synthetic genetic code expansion.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

Genome-scale models of bacterial metabolism: reconstruction and applications

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

Genome-scale models of microbial cells: evaluating the consequences of constraints

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

Applications of genome-scale metabolic reconstructions

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

Toward metabolic phenomics: analysis of genomic data using flux balances

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

What is flux balance analysis?

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

Analysis of optimality in natural and perturbed metabolic networks

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

Improved vanillin production in baker's yeast through in silico design

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

Enhancing sesquiterpene production in Saccharomyces cerevisiae through in silico driven metabolic engineering.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

Thermodynamics-based metabolic flux analysis

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

SurreyFBA: a command line tool and graphics user interface for constraint-based modeling of genome-scale metabolic reaction networks

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

CycSim--an online tool for exploring and experimenting with genome-scale metabolic models

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

BioMet Toolbox: genome-wide analysis of metabolism

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

In silico feasibility of novel biodegradation pathways for 1,2,4-trichlorobenzene.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

High-throughput generation, optimization and analysis of genome-scale metabolic models

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

Comparative genome-scale metabolic modeling of actinomycetes: The topology of essential core metabolism

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

GLAMM: Genome-Linked Application for Metabolic Maps

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

Standard biological parts knowledgebase

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

Refinement and standardization of synthetic biological parts and devices

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

The Pfam protein families database

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

SMART 6: recent updates and new developments

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

PAR-3D: a server to predict protein active site residues.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

SitesIdentify: a protein functional site prediction tool

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

Resurrecting ancient genes: experimental analysis of extinct molecules

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

Simple and accurate estimation of ancestral protein sequences

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

Combining structure and sequence information allows automated prediction of substrate specificities within enzyme families

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

NRPSpredictor2--a web server for predicting NRPS adenylation domain specificity

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

Gene context analysis in the Integrated Microbial Genomes (IMG) data management system

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

OPTIMIZER: a web server for optimizing the codon usage of DNA sequences

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

GeneDesign 3.0 is an updated synthetic biology toolkit

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

Gene Designer: a synthetic biology tool for constructing artificial DNA segments

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

31 March 2020

Writing DNA with GenoCAD

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

Synthetic biology: understanding biological design from synthetic circuits

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

Robust multicellular computing using genetically encoded NOR gates and chemical 'wires'.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

SynBioSS designer: a web-based tool for the automated generation of kinetic models for synthetic biological constructs

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

BioNetCAD: design, simulation and experimental validation of synthetic biochemical networks

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

Automated design of synthetic ribosome binding sites to control protein expression

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

The ribosome binding site calculator.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

RBSDesigner: software for designing synthetic ribosome binding sites that yields a desired level of protein expression.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

DNAWorks: an automated method for designing oligonucleotides for PCR-based gene synthesis

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

TmPrime: fast, flexible oligonucleotide design software for gene synthesis

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

High-fidelity gene synthesis by retrieval of sequence-verified DNA identified using high-throughput pyrosequencing

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

Parallel on-chip gene synthesis and application to optimization of protein expression.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

First heterologous reconstruction of a complete functional fungal biosynthetic multigene cluster.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

Five hard truths for synthetic biology

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

Computational strategies for metabolite identification in metabolomics

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

Chemical Similarity Searching

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

Mechanisms and evolution of control logic in prokaryotic transcriptional regulation.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

A generic approach to identify Transcription Factor-specific operator motifs; Inferences for LacI-family mediated regulation in Lactobacillus plantarum WCFS1.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

Fundamental relationship between operon organization and gene expression

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

Spatial organization of the flow of genetic information in bacteria

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

A novel semi-biosynthetic route for artemisinin production using engineered substrate-promiscuous P450(BM3).

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

Metabolic engineering of the E. coli L-phenylalanine pathway for the production of D-phenylglycine (D-Phg).

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

Synthesis of methyl halides from biomass using engineered microbes

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

Engineering microbial biofuel tolerance and export using efflux pumps

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

The Unusual Origin of the Polymerase Chain Reaction

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

Basic local alignment search tool

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

Whole-genome random sequencing and assembly of Haemophilus influenzae Rd

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

KEGG: kyoto encyclopedia of genes and genomes

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

Finding metabolic pathways using atom tracking

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

The KEGG databases at GenomeNet

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

CLONEQC: lightweight sequence verification for synthetic biology

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

TinkerCell: modular CAD tool for synthetic biology

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

Asmparts: assembly of biological model parts.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2717

Discovery and analysis of novel metabolic pathways for the biosynthesis of industrial chemicals: 3-hydroxypropanoate

31 March 2020

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22266781

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A new generation of homology search tools based on probabilistic inference

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22266781

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

The unusual origin of the polymerase chain reaction

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22266781

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1038/NRMICRO2717

1 reference

26 August 2017

1 reference

PubMed ID

22266781