Literature DB >> 33710326

A research parasite's perspective on establishing a baseline to avoid errors in secondary analyses.

Ayush T Raman1,2.   

Abstract

To enhance reproducibility in scientific research, more and more datasets are becoming publicly available so that researchers can perform secondary analyses to investigate questions the original scientists had not posited. This increases the return on investment for the NIH and other funding bodies. These datasets, however, are not perfect, and a better understanding of the assumptions that shaped them is required. The 2020 Junior Research Parasite Award recognized our work that showed that the signal-to-noise ratio in a particular dataset had not been investigated, leading to an erroneous conclusion in the original research. In this commentary, I share the process that led to the identification of the problem and hopefully provide useful lessons for other research parasites.
© The Author(s) 2021. Published by Oxford University Press GigaScience.

Entities:  

Year:  2021        PMID: 33710326      PMCID: PMC7953484          DOI: 10.1093/gigascience/giab015

Source DB:  PubMed          Journal:  Gigascience        ISSN: 2047-217X            Impact factor:   6.524


  10 in total

1.  Gene length matters in neurons.

Authors:  Mark J Zylka; Jeremy M Simon; Benjamin D Philpot
Journal:  Neuron       Date:  2015-04-22       Impact factor: 17.173

2.  Opinion: Reproducible research can still be wrong: adopting a prevention approach.

Authors:  Jeffrey T Leek; Roger D Peng
Journal:  Proc Natl Acad Sci U S A       Date:  2015-02-10       Impact factor: 11.205

Review 3.  Power failure: why small sample size undermines the reliability of neuroscience.

Authors:  Katherine S Button; John P A Ioannidis; Claire Mokrysz; Brian A Nosek; Jonathan Flint; Emma S J Robinson; Marcus R Munafò
Journal:  Nat Rev Neurosci       Date:  2013-04-10       Impact factor: 34.870

4.  1,500 scientists lift the lid on reproducibility.

Authors:  Monya Baker
Journal:  Nature       Date:  2016-05-26       Impact factor: 49.962

5.  Celebrating parasites.

Authors:  Casey S Greene; Lana X Garmire; Jack A Gilbert; Marylyn D Ritchie; Lawrence E Hunter
Journal:  Nat Genet       Date:  2017-03-30       Impact factor: 38.330

6.  A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium.

Authors: 
Journal:  Nat Biotechnol       Date:  2014-08-24       Impact factor: 54.908

7.  Apparent bias toward long gene misregulation in MeCP2 syndromes disappears after controlling for baseline variations.

Authors:  Ayush T Raman; Amy E Pohodich; Ying-Wooi Wan; Hari Krishna Yalamanchili; William E Lowry; Huda Y Zoghbi; Zhandong Liu
Journal:  Nat Commun       Date:  2018-08-13       Impact factor: 14.919

8.  Disruption of DNA-methylation-dependent long gene repression in Rett syndrome.

Authors:  Harrison W Gabel; Benyam Kinde; Hume Stroud; Caitlin S Gilbert; David A Harmin; Nathaniel R Kastan; Martin Hemberg; Daniel H Ebert; Michael E Greenberg
Journal:  Nature       Date:  2015-03-11       Impact factor: 49.962

9.  Data detectives, self-love, and humility: a research parasite's perspective.

Authors:  Claire Duvallet
Journal:  Gigascience       Date:  2020-01-01       Impact factor: 6.524

  10 in total

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