ArticleSystems and synthetic biology2010
The GeneOptimizer Algorithm: using a sliding window approach to cope with the vast sequence space in multiparameter DNA sequence optimization.
Article in Systems and synthetic biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 119 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
119 citing papers in PubMed, 208 citations in OpenAlex.
- Engineering mRNA-LNP Medicines for the Ageing Brain: Opportunities and Challenges for Neurodegenerative Diseases.Exploration (Beijing, China) · 2026Review
- Double-stranded DNA donors and CRISPR-Cas9 for universal correction of mutations causing cystic fibrosis in human airway cells.Molecular therapy. Nucleic acids · 2026Article
- A computational method to design broad-spectrum T cell-inducing vaccines applied to Betacoronaviruses.Cell reports methods · 2026Article
- EngineeringACS omega · 2026Article
- Genetically encoded manipulation of ATP/ADP ratio in human cells uncovers proteomic and physiological signatures of energy stress.Cell chemical biology · 2026Article
- Thermostable ancestors enabled evolutionary diversification of promiscuous chemical defence enzymes.The EMBO journal · 2026Article
- 2A peptides enable simplified discovery and heterologous production of fungal bioactive metabolites in Yarrowia lipolytica.Applied microbiology and biotechnology · 2026Article
- Genetically engineered lipases: advances in expression and upscaling for industrial applications.Archives of microbiology · 2026Review
- Pichia-CLM: A language model-based codon optimization pipeline forProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Recent Progress in Sequence Optimization of mRNA Vaccine: Biological Mechanism, Quantitative Metrics, and Computational Model.Bioinformatics and biology insights · 2026Review
- AI-powered mapping of tumor immunity for optimized mRNA vaccine engineering.Frontiers in oncology · 2026Review
- codonGPT: reinforcement learning on a generative language model enables scalable mRNA design.Nucleic acids research · 2025Article
- aPhyloGeo: a Python application for correlating genetic and climatic conditions.Bioinformatics (Oxford, England) · 2025Article
- Immunogenicity of a trivalent haemorrhagic fever vaccine candidate against Sudan virus, Marburg virus and Lassa virus in an mpox vaccine.The Journal of general virology · 2025Article
- Lipid nanoparticle-delivered IFNα2 activates Cxcl9 to increase T cell tumor recruitment to suppress lung metastasis.Journal for immunotherapy of cancer · 2025Article
- mRNA folding algorithms for structure and codon optimization.Briefings in bioinformatics · 2025Review
- Investigating the impact of synonymous gene recoding on a recombinantly expressed monoclonal antibody under different process parameters.Bioengineering & translational medicine · 2025Article
- Artificial intelligence-driven circRNA vaccine development: multimodal collaborative optimization and a new paradigm for biomedical applications.Briefings in bioinformatics · 2025Article
- Comparative Analysis of Codon Optimization Tools: Advancing toward a Multi-Criteria Framework for Synthetic Gene Design.Journal of microbiology and biotechnology · 2025Article
- A computationally designed antigen eliciting broad humoral responses against SARS-CoV-2 and related sarbecoviruses.Nature biomedical engineering · 2025Article
59 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
One of the main advantages of de novo gene synthesis is the fact that it frees the researcher from any limitations imposed by the use of natural templates. To make the most out of this opportunity, efficient algorithms are needed to calculate a coding sequence, combining different requirements, such as adapted codon usage or avoidance of restriction sites, in the best possible way. We present an algorithm where a "variation window" covering several amino acid positions slides along the coding sequence. Candidate sequences are built comprising the already optimized part of the complete sequence and all possible combinations of synonymous codons representing the amino acids within the window. The candidate sequences are assessed with a quality function, and the first codon of the best candidates' variation window is fixed. Subsequently the window is shifted by one codon position. As an example of a freely accessible software implementing the algorithm, we present the Mr. Gene web-application. Additionally two experimental applications of the algorithm are shown.
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.