Evidence map›Paper›PMID 34762392›Full record

SynthesisACS synthetic biology2021

Patrick V Phaneuf, Daniel C Zielinski, James T Yurkovich, Josefin Johnsen, Richard Szubin, Lei Yang, Se Hyeuk Kim, Sebastian Schulz, Muyao Wu, Christopher Dalldorf and 4 more

Open access · greenAbstract readMeta-Analysis
In one paragraph

Synthesis in ACS synthetic biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers, 2 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
8citing papers in PubMed, 2 pooled it
1.9field-weighted citation impact, top 13% 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

8 citing papers in PubMed, 2 syntheses or guidelines pooled it, 15 citations in OpenAlex.

  1. Pooled it
  2. Pooled it
  3. Adaptive Laboratory Evolution inMicroorganisms · 2026
    Review
  4. Bacteria as living biosensors for DNA.Nature reviews bioengineering · 2026
    Article
  5. Article
  6. Article
  7. NAR genomics and bioinformatics · 2024
    Article
  8. 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

14 authors at 2 institutions in 3 countries.

Patrick V PhaneufBioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, California 92093, United States.
Daniel C ZielinskiDepartment of Bioengineering, University of California, San Diego, La Jolla, California 92093, United States.
James T YurkovichDepartment of Bioengineering, University of California, San Diego, La Jolla, California 92093, United States.
Josefin JohnsenNovo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark.
Richard SzubinDepartment of Bioengineering, University of California, San Diego, La Jolla, California 92093, United States.
Lei YangNovo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark.
Se Hyeuk KimNovo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark.
Sebastian SchulzNovo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark.
Muyao WuDepartment of Bioengineering, University of California, San Diego, La Jolla, California 92093, United States.
Christopher DalldorfDepartment of Bioengineering, University of California, San Diego, La Jolla, California 92093, United States.
Emre OzdemirNovo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark.
Rebecca M LennenNovo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark.
Bernhard O PalssonBioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, California 92093, United States.
Adam M FeistDepartment of Bioengineering, University of California, San Diego, La Jolla, California 92093, United States.ORCID 0000-0002-8630-4800
Novo Nordisk Foundation · DKUniversity of California San Diego · US

Funding

Systems Biology Approach to Redefine Susceptibility Testing and Treatment of MDR Pathogens in the Context of Host ImmunityU01AI124316 · NIAID · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI PALSSON, BERNHARD O · 2016 to 2020
$10.2M
NIAID NIH HHS U01 AI124316
6 · The paper itself

Abstract

Microbes are being engineered for an increasingly large and diverse set of applications. However, the designing of microbial genomes remains challenging due to the general complexity of biological systems. Adaptive Laboratory Evolution (ALE) leverages nature's problem-solving processes to generate optimized genotypes currently inaccessible to rational methods. The large amount of public ALE data now represents a new opportunity for data-driven strain design. This study describes how novel strain designs, or genome sequences not yet observed in ALE experiments or published designs, can be extracted from aggregated ALE data and demonstrates this by designing, building, and testing three novel

Indexed as

Escherichia coli K12Escherichia coli ProteinsEscherichia coliLaboratoriesMutationEscherichia coli Proteinsadaptive laboratory evolutiondata-driven strain designgenome design variablesmeta-analysismutation functional analysisstructural biology

Identifiers

PMID34762392
PMCPMC8870144
OpenAlexW3214728253

What Socratic 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 Socratic graph.