Computational tools for the synthetic design of biochemical pathways

Constructing de Novo Biosynthetic Pathways for Chemical Synthesis inside Living Cells

(2011) Amy M. Weeks et al.   BIOCHEMISTRY

A retrosynthetic biology approach to metabolic pathway design for therapeutic production

(2011) Pablo Carbonell et al.   BMC Systems Biology

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

(2011) Mohammad Tauqeer Alam et al.   FEBS LETTERS

Engineering microbial biofuel tolerance and export using efflux pumps

(2011) M. J. Dunlop et al.   Molecular Systems Biology

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

(2011) Jiayuan Quan et al.   NATURE BIOTECHNOLOGY

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

(2011) Brooks B Bond-Watts et al.   Nature Chemical Biology

GLAMM: Genome-Linked Application for Metabolic Maps

(2011) J. T. Bates et al.   NUCLEIC ACIDS RESEARCH

NRPSpredictor2—a web server for predicting NRPS adenylation domain specificity

(2011) Marc Röttig et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Marnix H. Medema et al.   NUCLEIC ACIDS RESEARCH

Standard Biological Parts Knowledgebase

(2011) Michal Galdzicki et al.   PLoS One

Fundamental relationship between operon organization and gene expression

(2011) H. N. Lim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2010) A. Gevorgyan et al.   BIOINFORMATICS

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

(2010) Stéphanie Rialle et al.   BIOINFORMATICS

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

(2010) D. Na et al.   BIOINFORMATICS

Finding metabolic pathways using atom tracking

(2010) Allison P. Heath et al.   BIOINFORMATICS

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

(2010) Stacey D Finley et al.   BMC Systems Biology

Prediction of novel synthetic pathways for the production of desired chemicals

(2010) Ayoun Cho et al.   BMC Systems Biology

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

(2010) Isabel Rocha et al.   BMC Systems Biology

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

(2010) E. Weeding et al.   BRIEFINGS IN BIOINFORMATICS

First Heterologous Reconstruction of a Complete Functional Fungal Biosynthetic Multigene Cluster

(2010) Mary N. Heneghan et al.   CHEMBIOCHEM

Toward design-based engineering of industrial microbes

(2010) Keith EJ Tyo et al.   CURRENT OPINION IN MICROBIOLOGY

De NovoGeneration of Mutually Orthogonal Aminoacyl-tRNA Synthetase/tRNA Pairs

(2010) Heinz Neumann et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Natural Products Version 2.0: Connecting Genes to Molecules

(2010) Christopher T. Walsh et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

(2010) Ana Brochado et al.   Microbial Cell Factories

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

(2010) Heinz Neumann et al.   NATURE

Robust multicellular computing using genetically encoded NOR gates and chemical ‘wires’

(2010) Alvin Tamsir et al.   NATURE

Five hard truths for synthetic biology

(2010) Roberta Kwok   NATURE

Microbial production of fatty-acid-derived fuels and chemicals from plant biomass

(2010) Eric J. Steen et al.   NATURE

Spatial organization of the flow of genetic information in bacteria

(2010) Paula Montero Llopis et al.   NATURE

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

(2010) Mark Matzas et al.   NATURE BIOTECHNOLOGY

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

(2010) Sriram Kosuri et al.   NATURE BIOTECHNOLOGY

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

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

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

(2010) Polly M Fordyce et al.   NATURE BIOTECHNOLOGY

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

Biosynthesis: Is it time to go retro?

(2010) Brian O Bachmann   Nature Chemical Biology

Synthetic biology: applications come of age

(2010) Ahmad S. Khalil et al.   NATURE REVIEWS GENETICS

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

(2010) Marnix H. Medema et al.   NATURE REVIEWS MICROBIOLOGY

GeneDesign 3.0 is an updated synthetic biology toolkit

(2010) Sarah M. Richardson et al.   NUCLEIC ACIDS RESEARCH

CLONEQC: lightweight sequence verification for synthetic biology

(2010) Pablo A. Lee et al.   NUCLEIC ACIDS RESEARCH

BioMet Toolbox: genome-wide analysis of metabolism

(2010) M. Cvijovic et al.   NUCLEIC ACIDS RESEARCH

Reengineering orthogonally selective riboswitches

(2010) N. Dixon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Isoprenoid Pathway Optimization for Taxol Precursor Overproduction in Escherichia coli

(2010) P. K. Ajikumar et al.   SCIENCE

DREAMS of metabolism

(2010) Keng Cher Soh et al.   TRENDS IN BIOTECHNOLOGY

Combining Structure and Sequence Information Allows Automated Prediction of Substrate Specificities within Enzyme Families

(2010) Marc Röttig et al.   PLoS Computational Biology

A Novel Semi-biosynthetic Route for Artemisinin Production Using Engineered Substrate-Promiscuous P450BM3

(2009) Jeffrey A. Dietrich et al.   ACS Chemical Biology

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

(2009) F. Le Fevre et al.   BIOINFORMATICS

SitesIdentify: a protein functional site prediction tool

(2009) Tracey Bray et al.   BMC BIOINFORMATICS

Synthetic Metabolism: Engineering Biology at the Protein and Pathway Scales

(2009) Collin H. Martin et al.   CHEMISTRY & BIOLOGY

Computational design tools for synthetic biology

(2009) Mario A Marchisio et al.   CURRENT OPINION IN BIOTECHNOLOGY

Synthesis of Methyl Halides from Biomass Using Engineered Microbes

(2009) Travis S. Bayer et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

(2009) Mohammad A. Asadollahi et al.   METABOLIC ENGINEERING

Mechanisms and Evolution of Control Logic in Prokaryotic Transcriptional Regulation

(2009) S. A. F. T. van Hijum et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Applications of genome-scale metabolic reconstructions

(2009) Matthew A Oberhardt et al.   Molecular Systems Biology

Automated design of synthetic ribosome binding sites to control protein expression

(2009) Howard M Salis et al.   NATURE BIOTECHNOLOGY

TmPrime: fast, flexible oligonucleotide design software for gene synthesis

(2009) Marcus Bode et al.   NUCLEIC ACIDS RESEARCH

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

(2009) Chih-Hung Chou et al.   NUCLEIC ACIDS RESEARCH

Writing DNA with GenoCADTM

(2009) M. J. Czar et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2009) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Gene Context Analysis in the Integrated Microbial Genomes (IMG) Data Management System

(2009) Konstantinos Mavromatis et al.   PLoS One

Synthesis of orthogonal transcription-translation networks

(2009) W. An et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Computational strategies for metabolite identification in metabolomics

(2009) David S Wishart   Bioanalysis

TinkerCell: modular CAD tool for synthetic biology

(2009) Deepak Chandran et al.   Journal of Biological Engineering

DESHARKY: automatic design of metabolic pathways for optimal cell growth

(2008) Guillermo Rodrigo et al.   BIOINFORMATICS

Group Contribution Method for Thermodynamic Analysis of Complex Metabolic Networks

(2008) Matthew D. Jankowski et al.   BIOPHYSICAL JOURNAL

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

(2008) Christof Francke et al.   BMC GENOMICS

De novo biosynthetic pathways: rational design of microbial chemical factories

(2008) Kristala L Jones Prather et al.   CURRENT OPINION IN BIOTECHNOLOGY

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

(2008) Shota Atsumi et al.   NATURE

Refinement and standardization of synthetic biological parts and devices

(2008) Barry Canton et al.   NATURE BIOTECHNOLOGY

Reconstruction of biochemical networks in microorganisms

(2008) Adam M. Feist et al.   NATURE REVIEWS MICROBIOLOGY

SMART 6: recent updates and new developments

(2008) I. Letunic et al.   NUCLEIC ACIDS RESEARCH

Engineered biosynthesis of bacterial aromatic polyketides in Escherichia coli

(2008) W. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

New surveyor tools for charting microbial metabolic maps

(2007) Rainer Breitling et al.   NATURE REVIEWS MICROBIOLOGY