Evidence map›Paper›PMID 35524128›Full record

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

High-Throughput, High-Precision Colony Phenotyping with Pyphe.

Stephan Kamrad, Jürg Bähler, Markus Ralser

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 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing 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

3 citing papers in PubMed.

  1. Article
  2. Article
  3. 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

3 authors.

Stephan KamradDepartment of Genetics, Evolution and Environment, Institute of Healthy Ageing, University College London, London, UK.
Jürg BählerDepartment of Genetics, Evolution and Environment, Institute of Healthy Ageing, University College London, London, UK.
Markus RalserMolecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK. markus.ralser@charite.de.

Funding

Cancer Research UKMedical Research CouncilWellcome Trust 200829/Z/16/ZWellcome Trust FC001134
6 · The paper itself

Abstract

Colony fitness screens are powerful approaches for functional genomics and genetics. This protocol describes experimental and computational procedures for assaying the fitness of thousands of microbial strains in numerous conditions in parallel. Data analysis is based on pyphe, an all-in-one bioinformatics toolbox for scanning, image analysis, data normalization, and interpretation. We describe a standard protocol where endpoint colony areas are used as fitness proxy and two variations on this, one using colony growth curves and one using colony viability staining with phloxine B. Different strategies for experimental design, normalization and quality control are discussed. Using these approaches, it is possible to collect hundreds of thousands of data points, with low technical noise levels around 5%, in an experiment typically lasting 2 weeks or less.

Indexed as

GenomicsImage Processing, Computer-AssistedPhenotypeCell viabilityColonyFitnessFunctional genomicsGrowth curveLarge-scale phenotypingMicrobiologyPhenomicsPython softwareScreen

Identifiers

PMID35524128

What Socratic 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 Socratic graph.