Evidence map›Paper›PMID 35089551›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2022

Tailoring Codon Usage to the Underlying Biology for Protein Expression Optimization.

Zahra Alirezaeizanjani, Jan-Hendrik Trösemeier, Christel Kamp, Sophia Rudorf

Abstract read
PubMed Publisher
In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
0.5field-weighted citation impact, top 47% of its field
1 · What the graph read from it

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed, 1 citations in OpenAlex.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

4 authors at 3 institutions in 1 country.

Zahra AlirezaeizanjaniMax Planck Institute of Colloids and Interfaces, Potsdam-Golm, Potsdam, Germany.
Jan-Hendrik TrösemeierDivision of Microbiology, Section Biostatistics, Paul Ehrlich Institute, Langen, Germany.
Christel KampDivision of Microbiology, Section Biostatistics, Paul Ehrlich Institute, Langen, Germany.
Sophia RudorfMax Planck Institute of Colloids and Interfaces, Potsdam-Golm, Potsdam, Germany. Sophia.Rudorf@mpikg.mpg.de.
Max Planck Institute of Colloids and Interfaces · DEGoethe University Frankfurt · DEPaul Ehrlich Institut · DE

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

For heterologous gene expression, codon optimization is required to enhance the quality and quantity of the protein product. Recently, we introduced the software tool OCTOPOS. This sequence optimizer combines a detailed mechanistic mathematical modeling of in vivo protein synthesis with a state-of-the-art machine learning algorithm to find the sequence that best serves a user's needs. Here, we briefly describe the algorithm and its implementation as well as its application in practice using OCTOPOS.

Indexed as

Codon UsageSoftwareAlgorithmsBiologyCodonCodonCodon optimizationHeterologous gene expressionmRNA translationOCTOPOSProtein synthesis

Identifiers

PMID35089551
OpenAlexW4210288688

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

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.