ArticleNucleic acids research2015
GenoLIB: a database of biological parts derived from a library of common plasmid features.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
12 citing papers in PubMed.
- When RNA goes off script: ensuring transcript fidelity in transgene expression.The EMBO journal · 2026Review
- Self-documenting plasmids.Trends in biotechnology · 2025Review
- Identifying widespread and recurrent variants of genetic parts to improve annotation of engineered DNA sequences.PloS one · 2024Article
- Engineered Living Hydrogels.Advanced materials (Deerfield Beach, Fla.) · 2022Review
- pLannotate: engineered plasmid annotation.Nucleic acids research · 2021Article
- Immunoinformatics-Based Designing of a Multi-Epitope Chimeric Vaccine From Multi-Domain Outer Surface Antigens ofFrontiers in immunology · 2021Article
- Rapid, robust plasmid verification by de novo assembly of short sequencing reads.Nucleic acids research · 2020Article
- Repository-based plasmid design.PloS one · 2020Article
- Prioritization of potential vaccine targets using comparative proteomics and designing of the chimeric multi-epitope vaccine against Pseudomonas aeruginosa.Scientific reports · 2019Article
- Optimizing DNA assembly based on statistical language modelling.Nucleic acids research · 2017Article
- Use of processed data to design an orderly logic gate to construct plasmids in GenoCAD.IET systems biology · 2017Article
- Rule-Based Design of Plant Expression Vectors Using GenoCAD.PloS one · 2015Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Synthetic biologists rely on databases of biological parts to design genetic devices and systems. The sequences and descriptions of genetic parts are often derived from features of previously described plasmids using ad hoc, error-prone and time-consuming curation processes because existing databases of plasmids and features are loosely organized. These databases often lack consistency in the way they identify and describe sequences. Furthermore, legacy bioinformatics file formats like GenBank do not provide enough information about the purpose of features. We have analyzed the annotations of a library of ∼2000 widely used plasmids to build a non-redundant database of plasmid features. We looked at the variability of plasmid features, their usage statistics and their distributions by feature type. We segmented the plasmid features by expression hosts. We derived a library of biological parts from the database of plasmid features. The library was formatted using the Synthetic Biology Open Language, an emerging standard developed to better organize libraries of genetic parts to facilitate synthetic biology workflows. As proof, the library was converted into GenoCAD grammar files to allow users to import and customize the library based on the needs of their research projects.
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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.