Evidence map›Paper›PMID 35243375›Full record

ArticleSTAR protocols2022

Protocol for condition-dependent metabolite yield prediction using the TRIMER pipeline.

Puhua Niu, Maria J Soto, Byung-Jun Yoon, Edward R Dougherty, Francis J Alexander, Ian Blaby, Xiaoning Qian

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in STAR protocols, 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
–field-weighted citation impact
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. 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

7 authors.

Puhua NiuDepartment of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, USA.
Maria J SotoUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Byung-Jun YoonDepartment of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, USA.
Edward R DoughertyDepartment of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, USA.
Francis J AlexanderComputational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973, USA.
Ian BlabyUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Xiaoning QianDepartment of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, USA.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

This protocol explains the pipeline for condition-dependent metabolite yield prediction using Transcription Regulation Integrated with MEtabolic Regulation (TRIMER). TRIMER targets metabolic engineering applications via a hybrid model integrating transcription factor (TF)-gene regulatory network (TRN) with a Bayesian network (BN) inferred from transcriptomic expression data to effectively regulate metabolic reactions. For

Indexed as

Escherichia coliGene Regulatory NetworksBayes TheoremGene Expression RegulationSaccharomyces cerevisiaeTranscription FactorsTranscription FactorsBioinformaticsCell BiologyGene ExpressionMetabolismSystems biology

Identifiers

PMID35243375
PMCPMC8866898

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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.