Most Cited Bioinformatics Articles (Why none before 2011)?

Most Cited Bioinformatics Articles (Why none before 2011)?

From Bioinformatics journal (h/t: @genetics_blog).

Top three are:

Cytoscape 2.8: new features for data integration and network visualization

[The variant call format and VCFtools

Scaffolding pre-assembled contigs using SSPACE

Interestingly, none of the highly cited papers was published in journal before

  1. We do not understand why it is so. Is there a cutoff in their list, or do researchers not like to cite any paper before 2011? Sometimes, those old and ‘rejected’ papers turn out to be much better than ones considered ‘hot’. Here is a good example from Daniel Lemire’s google plus page:


Daniel Lemire

1:17 PM (edited) - Public

I’m a little bit proud of this:

” To our knowledge, there is only one paper that offers a plausible speedup based on a tighter lower boundLemire (2009) suggests a mean speedup of about 1.4 based on a tighter bound. These results are reproducible, and testing on more general data sets we obtained similar results (…) “ (Wang et al. 2013,

If you read Wang et al., you will notice that some of the denounced papers (those that are not reproducible) appeared in top-tier conferences. My own paper could not appear in such conferences because I did not claim 10x improvements or other spectacular gains.

Which paper do you prefer? A paper reporting a 1.4x gain that you can reproduce, or one that reports a 100x gain that you can’t reproduce?

My original article is at and my software at

In the meanwhile, the frustration level among researchers regarding journal access is rising very high (please click on image to get a better view):


Written by M. //