Evidence map›Paper›PMID 27211860›Full record

ArticleCell systems2016

Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow.

Elizabeth Brunk, Kevin W George, Jorge Alonso-Gutierrez, Mitchell Thompson, Edward Baidoo, George Wang, Christopher J Petzold, Douglas McCloskey, Jonathan Monk, Laurence Yang and 8 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell systems, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.

0numbers the graph read from it
0cells of the map it votes in
33citing 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

33 citing papers in PubMed.

  1. Article
  2. Article
  3. Metabolic modeling of host-microbe interactions.Computational and structural biotechnology journal · 2025
    Review
  4. Review
  5. Review
  6. Review
  7. Article
  8. Exploring synergies between plant metabolic modelling and machine learning.Computational and structural biotechnology journal · 2022
    Review
  9. Article
  10. Article
  11. Omics-Driven Biotechnology for Industrial Applications.Frontiers in bioengineering and biotechnology · 2021
    Review
  12. Article
  13. Review
  14. Review
  15. Article
  16. Review
  17. Article
  18. Review
  19. The era of big data: Genome-scale modelling meets machine learning.Computational and structural biotechnology journal · 2020
    Review
  20. Review
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

18 authors.

Elizabeth BrunkJoint Bioenergy Institute (JBEI), 5885 Hollis Street, Emeryville, CA 94608, USA; Department of Bioengineering, University of California, San Diego, San Diego, CA 92093, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Kevin W GeorgeJoint Bioenergy Institute (JBEI), 5885 Hollis Street, Emeryville, CA 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Jorge Alonso-GutierrezJoint Bioenergy Institute (JBEI), 5885 Hollis Street, Emeryville, CA 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Mitchell ThompsonJoint Bioenergy Institute (JBEI), 5885 Hollis Street, Emeryville, CA 94608, USA; Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
Edward BaidooJoint Bioenergy Institute (JBEI), 5885 Hollis Street, Emeryville, CA 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
George WangJoint Bioenergy Institute (JBEI), 5885 Hollis Street, Emeryville, CA 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Christopher J PetzoldJoint Bioenergy Institute (JBEI), 5885 Hollis Street, Emeryville, CA 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Douglas McCloskeyDepartment of Bioengineering, University of California, San Diego, San Diego, CA 92093, USA.
Jonathan MonkDepartment of Bioengineering, University of California, San Diego, San Diego, CA 92093, USA.
Laurence YangDepartment of Bioengineering, University of California, San Diego, San Diego, CA 92093, USA.
Edward J O'BrienDepartment of Bioengineering, University of California, San Diego, San Diego, CA 92093, USA.
Tanveer S BatthJoint Bioenergy Institute (JBEI), 5885 Hollis Street, Emeryville, CA 94608, USA.
Hector Garcia MartinJoint Bioenergy Institute (JBEI), 5885 Hollis Street, Emeryville, CA 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Adam FeistDepartment of Bioengineering, University of California, San Diego, San Diego, CA 92093, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Paul D AdamsJoint Bioenergy Institute (JBEI), 5885 Hollis Street, Emeryville, CA 94608, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Jay D KeaslingJoint Bioenergy Institute (JBEI), 5885 Hollis Street, Emeryville, CA 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970 Horsholm, Denmark; Department of Chemical & Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA.
Bernhard O PalssonDepartment of Bioengineering, University of California, San Diego, San Diego, CA 92093, USA; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970 Horsholm, Denmark. Electronic address: palsson@eng.ucsd.edu.
Taek Soon LeeJoint Bioenergy Institute (JBEI), 5885 Hollis Street, Emeryville, CA 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Electronic address: tslee@lbl.gov.

Funding

GENOMICALLY BASED MODELS FOR ANTIBIOTIC DEVELOPMENTR01GM057089 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI PALSSON, BERNHARD O · 1998 to 2021
$6.9M
NIGMS NIH HHS R01 GM057089
6 · The paper itself

Abstract

Understanding the complex interactions that occur between heterologous and native biochemical pathways represents a major challenge in metabolic engineering and synthetic biology. We present a workflow that integrates metabolomics, proteomics, and genome-scale models of Escherichia coli metabolism to study the effects of introducing a heterologous pathway into a microbial host. This workflow incorporates complementary approaches from computational systems biology, metabolic engineering, and synthetic biology; provides molecular insight into how the host organism microenvironment changes due to pathway engineering; and demonstrates how biological mechanisms underlying strain variation can be exploited as an engineering strategy to increase product yield. As a proof of concept, we present the analysis of eight engineered strains producing three biofuels: isopentenol, limonene, and bisabolene. Application of this workflow identified the roles of candidate genes, pathways, and biochemical reactions in observed experimental phenomena and facilitated the construction of a mutant strain with improved productivity. The contributed workflow is available as an open-source tool in the form of iPython notebooks.

Indexed as

Escherichia coliBiofuelsComputational BiologyEscherichia coli ProteinsMetabolic EngineeringModels, BiologicalSynthetic BiologyWorkflowBiofuelsEscherichia coli Proteins

Identifiers

PMID27211860
PMCPMC4882250

What OpenQuestion holds

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Registered trials

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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.