ArticleNature methods2014
Interactive assembly algorithms for molecular cloning.
Article in Nature methods, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
What it found
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Who cites it
19 citing papers in PubMed.
- Minimum-Cost Synthetic Genome Planning: An Algorithmic Framework.Computational and structural biotechnology journal · 2026Article
- The design and engineering of synthetic genomes.Nature reviews. Genetics · 2025Review
- A framework to efficiently describe and share reproducible DNA materials and construction protocols.Nature communications · 2022Article
- Aquarium: open-source laboratory software for design, execution and data management.Synthetic biology (Oxford, England) · 2021Article
- GEDpm-cg: Genome Editing Automated Design Platform for Point Mutation Construction inFrontiers in bioengineering and biotechnology · 2021Article
- Design and assembly of DNA molecules using multi-objective optimization.Synthetic biology (Oxford, England) · 2021Article
- The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering.Frontiers in bioengineering and biotechnology · 2020Article
- Deep learning to predict the lab-of-origin of engineered DNA.Nature communications · 2018Article
- Automated Robotic Liquid Handling Assembly of Modular DNA Devices.Journal of visualized experiments : JoVE · 2017Article
- Engineering biological systems using automated biofoundries.Metabolic engineering · 2017Review
- Large-scale design of robust genetic circuits with multiple inputs and outputs for mammalian cells.Nature biotechnology · 2017Article
- Design Automation in Synthetic Biology.Cold Spring Harbor perspectives in biology · 2017Review
- Registry in a tube: multiplexed pools of retrievable parts for genetic design space exploration.Nucleic acids research · 2017Article
- Synthetic biology to access and expand nature's chemical diversity.Nature reviews. Microbiology · 2016Review
- An innovative platform for quick and flexible joining of assorted DNA fragments.Scientific reports · 2016Article
- Algorithmic co-optimization of genetic constructs and growth conditions: application to 6-ACA, a potential nylon-6 precursor.Nucleic acids research · 2015Article
- Bricks and blueprints: methods and standards for DNA assembly.Nature reviews. Molecular cell biology · 2015Review
- Pydna: a simulation and documentation tool for DNA assembly strategies using python.BMC bioinformatics · 2015Article
- Systems and synthetic biology approaches to alter plant cell walls and reduce biomass recalcitrance.Plant biotechnology journal · 2014Review
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Molecular biologists routinely clone genetic constructs from DNA segments and formulate plans to assemble them. However, manual assembly planning is complex, error prone and not scalable. We address this problem with an algorithm-driven DNA assembly planning software tool suite called Raven (http://www.ravencad.org/) that produces optimized assembly plans and allows users to apply experimental outcomes to redesign assembly plans interactively. We used Raven to calculate assembly plans for thousands of variants of five types of genetic constructs, as well as hundreds of constructs of variable size and complexity from the literature. Finally, we experimentally validated a subset of these assembly plans by reconstructing four recombinase-based 'genetic counter' constructs and two 'repressilator' constructs. We demonstrate that Raven's solutions are significantly better than unoptimized solutions at small and large scales and that Raven's assembly instructions are experimentally valid.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.