Zhaorong Ma, Ceyda Coruh and Michael J. Axtell (2010). Arabidopsis lyrata Small RNAs: Transient MIRNA and Small Interfering RNA Loci within the Arabidopsis Genus Plant Cell : 10.1105/tpc.110.073882
Here is an InBrief article about this paper and another paper by Fahlgren et al.
Nancy R. Hofmann (2010). MicroRNA Evolution in the Genus Arabidopsis Plant Cell : 10.1105/tpc.110.220411
However, the point to write about it is not to show off, but to make a list of corrections.
The study in this paper is data intensive, analysing hundreds of MIRNA genes at the same time. So it is easy to make mistakes. Or rather, I wasn’t careful enough… Anyway, when the proof of the article and supplementary data have been finalized, I spotted several errors due to bugs in my Python code (Don’t get it wrong, I won’t blame Python for that).
Unfortunately, unlike software industry, most scientific publications are final, black ink on white paper (or in Chinese, 白纸黑字). You can not publish a paper as a “Beta” version, and keep refining it as what Gmail did.
So below is the errata:
line 16, column E: 2:11845992-11846123 (+)
line 16, column H: scaffold_201452.1
line 16, column J: Single locus
line 16, column L: Yes
line 16, column N: Pass (all the above are concerning one MIRNA, aly-MIR157b, which was first mistakenly annotated as the same sequence as aly-MIR157a and then removed in the original study due to a bug in my code)
line 127, column N: Fail (basically it means aly-MIR832 actually FAILED MIRcheck)
Due to the change listed above, several numbers in the main text will have to change.
page 2, right column: “143 out of 157”, “143” should be “144”
page 2, right column: “A total of 154 A. lyrata MIRNA loci”, “154” should be “155”
page 2, right column: “Many of these loci (106)”, “106” should be “107”
page 3, right column: “between these 128 syntenic A. thaliana and A. lyrata loci (88 from MC families and 40 from LC families)”, “128” should be “129”, “88” should be “89”
Figure 1, 3 and 4 will change slightly, although the degree of change is difficult to detect by eye. The overall trends and results will not change.
I sincerely apologize for all these errors. If you spot other errors, please leave a comment.