Literature DB >> 21278369

Case studies in reproducibility.

Torsten Hothorn1, Friedrich Leisch.   

Abstract

Reproducible research is a concept of providing access to data and software along with published scientific findings. By means of some case studies from different disciplines, we will illustrate reasons why readers should be given the possibility to look at the data and software independently from the authors of the original publication. We report results of a survey comprising 100 papers recently published in Bioinformatics. The main finding is that authors of this journal share a culture of making data available. However, the number of papers where source code for simulation studies or analyzes is available is still rather limited.

Mesh:

Year:  2011        PMID: 21278369     DOI: 10.1093/bib/bbq084

Source DB:  PubMed          Journal:  Brief Bioinform        ISSN: 1467-5463            Impact factor:   11.622


  19 in total

1.  Reproducible Research Using Biomodels.

Authors:  Pedro Mendes
Journal:  Bull Math Biol       Date:  2018-09-06       Impact factor: 1.758

2.  Performance reproducibility index for classification.

Authors:  Mohammadmahdi R Yousefi; Edward R Dougherty
Journal:  Bioinformatics       Date:  2012-09-06       Impact factor: 6.937

3.  Increasing value and reducing waste: addressing inaccessible research.

Authors:  An-Wen Chan; Fujian Song; Andrew Vickers; Tom Jefferson; Kay Dickersin; Peter C Gøtzsche; Harlan M Krumholz; Davina Ghersi; H Bart van der Worp
Journal:  Lancet       Date:  2014-01-08       Impact factor: 79.321

Review 4.  Particle tracking in drug and gene delivery research: State-of-the-art applications and methods.

Authors:  Benjamin S Schuster; Laura M Ensign; Daniel B Allan; Jung Soo Suk; Justin Hanes
Journal:  Adv Drug Deliv Rev       Date:  2015-04-07       Impact factor: 15.470

5.  Reproducibility of computational workflows is automated using continuous analysis.

Authors:  Brett K Beaulieu-Jones; Casey S Greene
Journal:  Nat Biotechnol       Date:  2017-03-13       Impact factor: 54.908

6.  YAMP: a containerized workflow enabling reproducibility in metagenomics research.

Authors:  Alessia Visconti; Tiphaine C Martin; Mario Falchi
Journal:  Gigascience       Date:  2018-07-01       Impact factor: 6.524

7.  Reproducible probe-level analysis of the Affymetrix Exon 1.0 ST array with R/Bioconductor.

Authors:  Maria Rodrigo-Domingo; Rasmus Waagepetersen; Julie Støve Bødker; Steffen Falgreen; Malene Krag Kjeldsen; Hans Erik Johnsen; Karen Dybkær; Martin Bøgsted
Journal:  Brief Bioinform       Date:  2014-07       Impact factor: 11.622

8.  Increasing value and reducing waste in research design, conduct, and analysis.

Authors:  John P A Ioannidis; Sander Greenland; Mark A Hlatky; Muin J Khoury; Malcolm R Macleod; David Moher; Kenneth F Schulz; Robert Tibshirani
Journal:  Lancet       Date:  2014-01-08       Impact factor: 79.321

9.  Sequencing and Reconstructing Helminth Mitochondrial Genomes Directly from Genomic Next-Generation Sequencing Data.

Authors:  Nikola Palevich; Paul Haydon Maclean
Journal:  Methods Mol Biol       Date:  2021

10.  Where in the genome are we? A cautionary tale of database use in genomics research.

Authors:  Laura K Vaughan; Vinodh Srinivasasainagendra
Journal:  Front Genet       Date:  2013-03-21       Impact factor: 4.599

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