Evidence map›Paper›PMID 29188184›Full record

ArticleMetabolic engineering communications2017

UP Finder: A COBRA toolbox extension for identifying gene overexpression strategies for targeted overproduction.

Xi Wang, Liang Yu, Shulin Chen

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Metabolic engineering communications, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
0.1field-weighted citation impact, top 49% 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

2 citing papers in PubMed, 11 citations in OpenAlex.

  1. Article
  2. Review
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

3 authors at 1 institution in 1 country.

Xi WangDepartment of Biological Systems Engineering, Washington State University, Pullman, WA 99164, USA.
Liang YuDepartment of Biological Systems Engineering, Washington State University, Pullman, WA 99164, USA.
Shulin ChenDepartment of Biological Systems Engineering, Washington State University, Pullman, WA 99164, USA.
Washington State University · US

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Overexpression of key genes is a basic strategy for overproducing target products via metabolic engineering. Traditionally, identifying those key genes/pathways largely relies on the knowledge of biochemistry and bioinformatics. In this study, a modeling tool named UP Finder was developed to facilitate the rapid identification of gene overexpression strategies. It was based on the COBRA toolbox under MATLAB environment. All the key gene/pathway targets are identified in one click after simply loading a Systems Biology Markup Language model and specifying a metabolite as the targeted product. The outputs are also quantitatively ranked to show the preference for determining overexpression strategies in pathway design. Analysis examples for overproducing lycopene precursor in

Indexed as

COBRA toolboxGene overexpression strategyMetabolic engineeringRational pathway designTargeted overproduction

Identifiers

PMID29188184
PMCPMC5699525
OpenAlexW2747884407

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.