Differential expression analysis for sequence count data

The amazing lack of proper referencing in Bioinformatics and Biostatistics

Jean-Michel Claverie   (2011-01-17 14:00)  CNRS

As an old timer, contributing to the field of computational biology since 1975 (the previous century! :-), I am amazed by the lack of proper reference to previous works by the current generation of bioinformaticians/biostatiticians. Most of them seem to believe that nothing existed before the Internet (1990), or even later. Take the example of this article: the authors apparently ignore that before the "RNA-Seq" era (a word that appeared in the context of the NGS approaches), we were sequencing "Expressed Sequences Tags" (ESTs) exactly for the same purpose, and with similar results. Of course, theoreticians developped the proper methods to analyze these data, methods that still apply today. It is thus amazing that NONE of those widely used approaches are cited in this "modern work". And this is not by lack of visibility. For instance, the approach that I developed with my colleague Stephane Audic in 1997 (The significance of digital gene expression profiles. Genome Res 1997 7:986-95. - PMID:9331369) has been cited 500 times and is still averaging more than 40 citations per year. But this is just one example, and many highly used methods are similarly ignored. I believe it is also the responsability of the reviewers, and of the editors, to ensure that what was considered an ethical behavior not so long ago, continues to be enforced in this booming field.

Competing interests

None declared (except that I am citing one of my
own article, for the sake of demonstration).

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