badcode.bib

%% badcode.bib
%% List of examples where errors in research software have resulted in retractions or public issues

@article{ChangSummary,
  author  = {Greg Miller}, 
  title   = {A Scientist's Nightmare: Software Problem Leads to Five Retractions},
  journal = {Science},
  year    = 2006,
  number  = 5807,
  pages   = {1856-1857},
  month   = 12,
  note    = {Summary of the fallout of the Chang retraction in protein crystallography caused by data analysis program flipping two columns}, 
  volume  = 314
  doi = {10.1126/science.314.5807.1856},
  url = {http://dx.doi.org/10.1126/science.314.5807.1856}
}

@article{Jobb2015,
  doi = {10.1186/s12862-015-0513-z},
  url = {http://dx.doi.org/10.1186/s12862-015-0513-z},
  year  = {2015},
  month = {nov},
  publisher = {Springer Science $\mathplus$ Business Media},
  volume = {15},
  number = {1},
  author = {Gangolf Jobb and Arndt von Haeseler and Korbinian Strimmer},
  title = {Retraction Note: {TREEFINDER}: a powerful graphical analysis environment for molecular phylogenetics},
  journal = {{BMC} Evol Biol},
  note = {Retraction because of limitations placed by author on use of {TREEFINDER} software}
}

@article{Callaway2016,
  doi = {10.1038/nature.2016.19258},
  url = {http://dx.doi.org/10.1038/nature.2016.19258},
  year  = {2016},
  month = {jan},
  publisher = {Nature Publishing Group},
  author = {Ewen Callaway},
  title = {Error found in study of first ancient African genome},
  journal = {Nature},
  note = {Overview of retraction of high profile migration paper due to bioinformatics binning pipeline error}
}

@techreport{Herndon2013,
  url          = {http://www.peri.umass.edu/236/hash/31e2ff374b6377b2ddec04deaa6388b1/publication/566/},
  year         = {2013},
  month        = {apr},
  author       = {Thomas Herndon and Michael Ash and Robert Pollin}, 
  title        = {Does High Public Debt Consistently Stifle Economic Growth? A Critique of Reinhart and Rogoff},
  institution  = {Political Economy Research Institute},
  number       = 322,
  address      = {Gordon Hall, 418 N. Pleasant St., Suite A, Amherst, MA 01002 },
  note         = {Replication study showing that Excel coding errors, selective exclusion of available data, and unconventional weighting of summary statistics lead to serious errors that inaccurately represent the relationship between public debt and GDP growth}
}

@article{Ferrari2013,
  doi = {10.1126/science.1231815},
  url = {http://dx.doi.org/10.1126/science.1231815},
  year  = {2013},
  month = {apr},
  publisher = {American Association for the Advancement of Science ({AAAS})},
  volume = {340},
  number = {6130},
  pages = {273--273},
  author = {F. Ferrari and Y. L. Jung and P. V. Kharchenko and A. Plachetka and A. A. Alekseyenko and M. I. Kuroda and P. J. Park},
  title = {Comment on "Drosophila Dosage Compensation Involves Enhanced Pol {II} Recruitment to Male X-Linked Promoters"},
  journal = {Science},
  note = {An incorrect normalization step in a calculation by Conrad et al. produced results that are wrong by three orders of magnitude}
}

% TODO: Early access version published ahead of print publication - revise citation when published 
@unpublished{fMRIfalsepositive,
  author  = {Anders Eklund and Thomas E. Nichols and Hans Knutssona}, 
  title   = {Cluster failure: Why fMRI inferences for spatial extent have inflated false-positive rates},
  journal = {Proc. Natl. Acad. Sci. USA},
  year    = 2016,
  month   = 5,
  note    = {Study identifying very high false positive rates in data from fMRI studies analysed by common software packages}, 
  doi = {10.1073/pnas.1602413113},
  url = {http://dx.doi.org/10.1073/pnas.1602413113}
}

@misc{ToyotaAcceleration,
  year={2013},
  month={November 7},
  title={Toyota Unintended Acceleration and the Big Bowl of ``Spaghetti'' Code},
  author={{Safety Research \& Strategies, Inc.}},
  journal={Vehicle and Product Safety},
  url={http://www.safetyresearch.net/blog/articles/toyota-unintended-acceleration-and-big-bowl-“spaghetti”-code#.V4D1FDwtiKQ.twitter},
  note={Blog saying that Toyota's software engineering process and the source code for the 2005 Toyota Camry were defective and dangerous and riddled with bugs and gaps in its failsafes that led to the root cause of a crash in Oklahoma},
}