ArticleNucleic acids research2014
MODEST: a web-based design tool for oligonucleotide-mediated genome engineering and recombineering.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
38 citing papers in PubMed.
- Adaptation-coupled CRISPRi identifies antibiotic-sensitizing genes leading to a novel plasmid selection marker.Nucleic acids research · 2026Article
- Fine modulation of carbon flow in central carbon metabolism via ribosome-binding site modification inMetabolic engineering communications · 2026Article
- Sequential Phage Delivery Can Outperform Cocktails by Delaying Cross-Resistance Evolution.Viruses · 2026Article
- Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications.Chemical reviews · 2026Review
- Combinatorial mutagenesis of N-terminal sequences reveals unexpected and expanded stability determinants of thebioRxiv : the preprint server for biology · 2025Article
- Convergent evolution of antibiotic resistance mechanisms between pyrrolobenzodiazepines and albicidin in multidrug resistant Klebsiella pneumoniae.npj antimicrobials and resistance · 2025Article
- The design and engineering of synthetic genomes.Nature reviews. Genetics · 2025Review
- Unraveling N-Terminal Proteoform Interactomes via Multiplexed Recombineering in Salmonella.Methods in molecular biology (Clifton, N.J.) · 2025Article
- ORBIT for E. coli: kilobase-scale oligonucleotide recombineering at high throughput and high efficiency.Nucleic acids research · 2024Article
- Unpredictability of the Fitness Effects of Antimicrobial Resistance Mutations Across Environments in Escherichia coli.Molecular biology and evolution · 2024Article
- Proteins à la carte: riboproteogenomic exploration of bacterial N-terminal proteoform expression.mBio · 2024Article
- Genotype-by-environment interactions govern fitness changes associated with adaptive mutations in two-component response systems.Frontiers in genetics · 2024Article
- Reporting off-target effects of recombinant engineering using the pORTMAGE system.Journal of microbiological methods · 2023Article
- Recombineering in Non-Model Bacteria.Current protocols · 2022Article
- Efficient Bacterial Genome Engineering throughout the Central Dogma Using the Dual-Selection MarkerACS synthetic biology · 2022Article
- Article
- Article
- Evolutionary repair reveals an unexpected role of the tRNA modification m1G37 in aminoacylation.Nucleic acids research · 2021Article
- Article
- A standardized genome architecture for bacterial synthetic biology (SEGA).Nature communications · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
Recombineering and multiplex automated genome engineering (MAGE) offer the possibility to rapidly modify multiple genomic or plasmid sites at high efficiencies. This enables efficient creation of genetic variants including both single mutants with specifically targeted modifications as well as combinatorial cell libraries. Manual design of oligonucleotides for these approaches can be tedious, time-consuming, and may not be practical for larger projects targeting many genomic sites. At present, the change from a desired phenotype (e.g. altered expression of a specific protein) to a designed MAGE oligo, which confers the corresponding genetic change, is performed manually. To address these challenges, we have developed the MAGE Oligo Design Tool (MODEST). This web-based tool allows designing of MAGE oligos for (i) tuning translation rates by modifying the ribosomal binding site, (ii) generating translational gene knockouts and (iii) introducing other coding or non-coding mutations, including amino acid substitutions, insertions, deletions and point mutations. The tool automatically designs oligos based on desired genotypic or phenotypic changes defined by the user, which can be used for high efficiency recombineering and MAGE. MODEST is available for free and is open to all users at http://modest.biosustain.dtu.dk.
Indexed as
Identifiers
What OpenQuestion holds
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.