4.8 Article

Organizing genome engineering for the gigabase scale

Related references

Note: Only part of the references are listed.
Article Multidisciplinary Sciences

Total synthesis of Escherichia coli with a recoded genome

Julius Fredens et al.

NATURE (2019)

Letter Biotechnology & Applied Microbiology

The Kipoi repository accelerates community exchange and reuse of predictive models for genomics

Ziga Avsec et al.

NATURE BIOTECHNOLOGY (2019)

Article Biochemistry & Molecular Biology

WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs

Yuxing Liao et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biochemical Research Methods

Synthetic Bistability and Differentiation in Yeast

Yaoyu Yang et al.

ACS SYNTHETIC BIOLOGY (2019)

Editorial Material Multidisciplinary Sciences

Technological challenges and milestones for writing genomes

Nili Ostrov et al.

SCIENCE (2019)

Article Biochemistry & Molecular Biology

Ensembl 2019

Fiona Cunningham et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Mathematical & Computational Biology

ModelBricks-modules for reproducible modeling improving model annotation and provenance

Ann E. Cowan et al.

NPJ SYSTEMS BIOLOGY AND APPLICATIONS (2019)

Article Biochemical Research Methods

The BioCyc collection of microbial genomes and metabolic pathways

Peter D. Karp et al.

BRIEFINGS IN BIOINFORMATICS (2019)

Article Biochemistry & Molecular Biology

BioModels: expanding horizons to include more modelling approaches and formats

Mihai Glont et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Biochemistry & Molecular Biology

RefSeq: an update on prokaryotic genome annotation and curation

Daniel H. Haft et al.

NUCLEIC ACIDS RESEARCH (2018)

Review Biochemical Research Methods

Emerging whole-cell modeling principles and methods

Arthur P. Goldberg et al.

CURRENT OPINION IN BIOTECHNOLOGY (2018)

Article Biochemistry & Molecular Biology

From plant metabolic engineering to plant synthetic biology: The evolution of the design/build/test/learn cycle

Benjamin Pouvreau et al.

PLANT SCIENCE (2018)

Article Multidisciplinary Sciences

Quantification of bacterial fluorescence using independent calibrants

Jacob Beal et al.

PLOS ONE (2018)

Article Biochemical Research Methods

SynBioHub: A Standards-Enabled Design Repository for Synthetic Biology

James Alastair McLaughlin et al.

ACS SYNTHETIC BIOLOGY (2018)

Article Biology

OpenWorm: overview and recent advances in integrative biological simulation of Caenorhabditis elegans

Gopal P. Sarma et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2018)

Editorial Material Biotechnology & Applied Microbiology

Opening options for material transfer

Linda Kahl et al.

NATURE BIOTECHNOLOGY (2018)

Article Biochemistry & Molecular Biology

FAIRDOMHub: a repository and collaboration environment for sharing systems biology research

Katherine Wolstencroft et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Biochemistry & Molecular Biology

The Human Phenotype Ontology in 2017

Sebastian Koehler et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Biochemical Research Methods

Streamlining the Design-to-Build Transition with Build-Optimization Software Tools

Ernst Oberortner et al.

ACS SYNTHETIC BIOLOGY (2017)

Letter Biotechnology & Applied Microbiology

Nextflow enables reproducible computational workflows

Paolo Di Tommaso et al.

NATURE BIOTECHNOLOGY (2017)

Letter Biotechnology & Applied Microbiology

iML1515, a knowledgebase that computes Escherichia coli traits

Jonathan M. Monk et al.

NATURE BIOTECHNOLOGY (2017)

Letter Biotechnology & Applied Microbiology

Toil enables reproducible, open source, big biomedical data analyses

John Vivian et al.

NATURE BIOTECHNOLOGY (2017)

Review Genetics & Heredity

Beyond editing to writing large genomes

Raj Chari et al.

NATURE REVIEWS GENETICS (2017)

Article Biochemistry & Molecular Biology

Large-scale recoding of a bacterial genome by iterative recombineering of synthetic DNA

Yu Heng Lau et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Multidisciplinary Sciences

Design of a synthetic yeast genome

Sarah M. Richardson et al.

SCIENCE (2017)

Article Cell Biology

Synthetic DNA Synthesis and Assembly: Putting the Synthetic in Synthetic Biology

Randall A. Hughes et al.

COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY (2017)

Review Biochemistry & Molecular Biology

Needs and opportunities in bio-design automation: four areas for focus

Evan Appleton et al.

CURRENT OPINION IN CHEMICAL BIOLOGY (2017)

Review Biochemistry & Molecular Biology

A standard-enabled workflow for synthetic biology

Chris J. Myers et al.

BIOCHEMICAL SOCIETY TRANSACTIONS (2017)

Editorial Material Biotechnology & Applied Microbiology

Synthesis aided design: The biological design-build-test engineering paradigm?

Ryan T. Gill et al.

BIOTECHNOLOGY AND BIOENGINEERING (2016)

Article Biochemistry & Molecular Biology

The International Nucleotide Sequence Database Collaboration

Guy Cochrane et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biochemistry & Molecular Biology

DNA data bank of Japan (DDBJ) progress report

Jun Mashima et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biochemistry & Molecular Biology

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

Nuala A. O'Leary et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biochemistry & Molecular Biology

Ensembl Genomes 2016: more genomes, more complexity

Paul Julian Kersey et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Endocrinology & Metabolism

Recon 2.2: from reconstruction to model of human metabolism

Neil Swainston et al.

METABOLOMICS (2016)

Article Multidisciplinary Sciences

Design, synthesis, and testing toward a 57-codon genome

Nili Ostrov et al.

SCIENCE (2016)

Article Multidisciplinary Sciences

Design and synthesis of a minimal bacterial genome

Clyde A. Hutchison et al.

SCIENCE (2016)

Editorial Material Multidisciplinary Sciences

The Genome Project-Write

Jef D. Boeke et al.

SCIENCE (2016)

Article Multidisciplinary Sciences

Genetic circuit design automation

Alec A. K. Nielsen et al.

SCIENCE (2016)

Review Biotechnology & Applied Microbiology

Harnessing QbD, Programming Languages, and Automation for Reproducible Biology

Michael I. Sadowski et al.

TRENDS IN BIOTECHNOLOGY (2016)

Article Biochemical Research Methods

An Implementation-Focused Bio/Algorithmic Workflow for Synthetic Biology

Angel Goni-Moreno et al.

ACS SYNTHETIC BIOLOGY (2016)

Article Biochemical Research Methods

Sharing Structure and Function in Biological Design with SBOL 2.0

Nicholas Roehner et al.

ACS SYNTHETIC BIOLOGY (2016)

Article Biochemical Research Methods

A Converter from the Systems Biology Markup Language to the Synthetic Biology Open Language

Tramy Nguyen et al.

ACS SYNTHETIC BIOLOGY (2016)

Article Multidisciplinary Sciences

Comment: The FAIR Guiding Principles for scientific data management and stewardship

Mark D. Wilkinson et al.

SCIENTIFIC DATA (2016)

Article Multidisciplinary Sciences

General calibration of microbial growth in microplate readers

Keiran Stevenson et al.

SCIENTIFIC REPORTS (2016)

Review Biochemical Research Methods

Next-generation genome-scale models for metabolic engineering

Zachary A. King et al.

CURRENT OPINION IN BIOTECHNOLOGY (2015)

Article Biochemical Research Methods

Generating Systems Biology Markup Language Models from the Synthetic Biology Open Language

Nicholas Roehner et al.

ACS SYNTHETIC BIOLOGY (2015)

Article Biotechnology & Applied Microbiology

Promoting coordinated development of community-based information standards for modeling in biology: the COMBINE initiative

Michael Hucka et al.

FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY (2015)

Article Biochemical Research Methods

COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project

Frank T. Bergmann et al.

BMC BIOINFORMATICS (2014)

Article Microbiology

An ontology for microbial phenotypes

Marcus C. Chibucos et al.

BMC MICROBIOLOGY (2014)

Article Neurosciences

Model exchange with the NeuroML model database

Sharon M Crook et al.

BMC NEUROSCIENCE (2014)

Review Biochemical Research Methods

Narrowing the gap between the promise and reality of polyketide synthases as a synthetic biology platform

Sean Poust et al.

CURRENT OPINION IN BIOTECHNOLOGY (2014)

Review Biochemical Research Methods

Large-scale de novo DNA synthesis: technologies and applications

Sriram Kosuri et al.

NATURE METHODS (2014)

Article Biochemistry & Molecular Biology

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

Ross Overbeek et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Multidisciplinary Sciences

Total Synthesis of a Functional Designer Eukaryotic Chromosome

Narayana Annaluru et al.

SCIENCE (2014)

Article Genetics & Heredity

Choice of transcripts and software has a large effect on variant annotation

Davis J. McCarthy et al.

GENOME MEDICINE (2014)

Review Biochemical Research Methods

Model selection in systems and synthetic biology

Paul Kirk et al.

CURRENT OPINION IN BIOTECHNOLOGY (2013)

Review Biochemistry & Molecular Biology

Genome-scale engineering for systems and synthetic biology

Kevin M. Esvelt et al.

MOLECULAR SYSTEMS BIOLOGY (2013)

Article Chemistry, Applied

Metabolic Engineering: Past and Future

Benjamin M. Woolston et al.

Annual Review of Chemical and Biomolecular Engineering (2013)

Article Biochemistry & Molecular Biology

A Whole-Cell Computational Model Predicts Phenotype from Genotype

Jonathan R. Karr et al.

Review Automation & Control Systems

Trends in laboratory information management system

Poonam J. Prasad et al.

CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS (2012)

Article Genetics & Heredity

Three Ontologies to Define Phenotype Measurement Data

Mary Shimoyama et al.

Frontiers in Genetics (2012)

Article Biochemical Research Methods

RightField: embedding ontology annotation in spreadsheets

Katy Wolstencroft et al.

BIOINFORMATICS (2011)

Article Biochemical Research Methods

The Physiome Model Repository 2

Tommy Yu et al.

BIOINFORMATICS (2011)

Article Cell Biology

DNA assembly for synthetic biology: from parts to pathways and beyond

Tom Ellis et al.

INTEGRATIVE BIOLOGY (2011)

Article Biochemistry & Molecular Biology

Controlled vocabularies and semantics in systems biology

Melanie Courtot et al.

MOLECULAR SYSTEMS BIOLOGY (2011)

Article Multidisciplinary Sciences

Synthetic chromosome arms function in yeast and generate phenotypic diversity by design

Jessica S. Dymond et al.

NATURE (2011)

Article Multidisciplinary Sciences

A Modular Cloning System for Standardized Assembly of Multigene Constructs

Ernst Weber et al.

PLOS ONE (2011)

Article Biochemical Research Methods

Standard virtual biological parts: a repository of modular modeling components for synthetic biology

M. T. Cooling et al.

BIOINFORMATICS (2010)

Article Biochemical Research Methods

Modeling sample variables with an Experimental Factor Ontology

James Malone et al.

BIOINFORMATICS (2010)

Article Biochemistry & Molecular Biology

The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants

Peter J. A. Cock et al.

NUCLEIC ACIDS RESEARCH (2010)

Article Biochemistry & Molecular Biology

myExperiment: a repository and social network for the sharing of bioinformatics workflows

Carole A. Goble et al.

NUCLEIC ACIDS RESEARCH (2010)

Article Multidisciplinary Sciences

Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome

Daniel G. Gibson et al.

SCIENCE (2010)

Article Biotechnology & Applied Microbiology

A standard variation file format for human genome sequences

Martin G. Reese et al.

GENOME BIOLOGY (2010)

Article Biochemical Research Methods

Enzymatic assembly of DNA molecules up to several hundred kilobases

Daniel G. Gibson et al.

NATURE METHODS (2009)

Article Biochemical Research Methods

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

Da Wei Huang et al.

NATURE PROTOCOLS (2009)

Review Cell Biology

The second wave of synthetic biology: from modules to systems

Priscilla E. M. Purnick et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2009)

Article Biochemistry & Molecular Biology

Metabolic flux analysis and metabolic engineering of microorganisms

Hyun Uk Kim et al.

MOLECULAR BIOSYSTEMS (2008)

Article Biotechnology & Applied Microbiology

Metabolic engineering of Saccharomyces cerevisiae for the production of n-butanol

Eric J. Steen et al.

MICROBIAL CELL FACTORIES (2008)

Article Multidisciplinary Sciences

Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome

Daniel G. Gibson et al.

SCIENCE (2008)

Article Biotechnology & Applied Microbiology

The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration

Barry Smith et al.

NATURE BIOTECHNOLOGY (2007)

Article Biochemical Research Methods

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

Alan Villalobos et al.

BMC BIOINFORMATICS (2006)

Article Biotechnology & Applied Microbiology

The Sequence Ontology: a tool for the unification of genome annotations

K Eilbeck et al.

GENOME BIOLOGY (2005)

Article Multidisciplinary Sciences

Accurate multiplex gene synthesis from programmable DNA microchips

JD Tian et al.

NATURE (2004)

Article Multidisciplinary Sciences

Total synthesis of long DNA sequences: Synthesis of a contiguous 32-kb polyketide synthase gene cluster

SJ Kodumal et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)