Genome Biology - Latest Comments

Addendum - authorship of 'Photo 51'

Naomi Attar — 2013-05-15T16:27:35Z

In this article, I (the author) followed multiple sources in referring to 'Photo 51' as the work of Rosalind Franklin. However, medical geneticist Jim Lupski raised a query about the accuracy of the attribution, having received correspondence from Jim Watson which mentioned in passing that Ray Gosling had taken the photo.

I put the query to Gosling, who confirms that he was indeed 'Photo 51' photographer:
'It was part of the program that Rosalind and I were carrying out to check the effect of the humidity on the crystallization of DNA. This was the 51st of that program, and I was the one who took that particular diffraction pattern.'

Thanks to Jim Lupski for bringing the inaccuracy to my attention, to Ray Gosling for providing further information, and to Jim Watson for confirming that this was his understanding of events.

Kudos! Great commentary on sequestration¿s impact on research! National media should talk about this and YOU should read it!!!

Leonardo Collado Torres — 2013-05-03T17:27:10Z

I have greatly enjoyed reading this commentary by Leek and Salzberg and find it a must read for anyone. I am not talking just researchers and those involved in science, but the general public. I wrote my comments with this in mind at Fellgernon Bit and would love to see the national media commenting Leek and Salzberg's point of view.

I do have to emphasize that this is a commentary that should be read by the general public and is important for them to have access to it. Thus, while Genome Biology offers 30 day free trial accounts, I hope that an exception can be made and offer give this commentary open-access like it is done for research articles. I understand that Genome Biology has to survive too, so maybe a quick donation drive can be made or something like that.

Relative use of "sister group"

Toni Gabaldon — 2013-03-12T10:35:10Z

We use the term "sister group" in its relative sense.

The use of the term "sister group" in phylogenetics is generally used in relation only to the taxa/lineages represented in the analysis, denoting as sister group the closest relative only among the groups included in the analysis. That is In the general case, two groups are sister groups if they share their most recent ancestral node among those in the phylogenetic tree. This differs from the use of the term by systematicists which tend to include all known lineages and define sister-group as the closest clade, but this use is also relative to what lineages are known/considered. Note that the impossibility to know all extinct lineages precludes us from using "sister group" in absolute terms.

Genome sequencing reaches a new high.

Norman Doggett — 2013-02-26T16:43:51Z

The Joint Genome Institute missed a perfect opportunity here.

Typographical error in Materials and Methods

James Hane — 2013-02-26T16:43:26Z

The first Materials and Methods sub-section, titled "Whole-genome comparisons", contains a typographical error. In the sentence which reads "Promer outputs were filtered for repetitive matches using the program 'delta-filter' (MUMmer 3.0) with the '-g' parameter."... the '-g' should be replaced with '-1'. Note: this parameter should be read as the numeral 'one', not a lowercase 'L'.

error in formula 4

Jo Vandesompele — 2013-02-26T16:42:12Z

It only came recently to our attention that the factor (h-1) in the denominator of equation 4 misses a square root symbol. As such it should be sqrt(h-1).

hard to take...

Karl Magnacca — 2013-02-26T16:41:33Z

As a systematist, reading this paper made me feel like banging my head against a wall. I first saw a short article about it in Science Daily and laughed at the gross mischaracterization of Hymenoptera systematics portrayed there as typical of science journalism. Then I came here and was surprisedto find that they were largely verbatim quotes from the paper.

To list a few: Aculeata contains much more than just Vespoidea, including Apoidea (aka Sphecoidea) and Chrysidoidea. Vespoidea contains much more than just Vespidae and Formicidae; while it may be subject to change (possibly excluding ants), it will not be dropped due to paraphyly but restricted to the closest relatives of Vespidae (given the earlier phylogenetic results, some serious revision is likely in order, but exactly what is very unclear). The placement of bees within Apoidea as sister to Crabronidae and Sphecidae (other groups of wasps, in case you're not familiar with them) is incontrovertible. No matter how many genes you have, you cannot draw any kind of sweeping conclusions from two conflicting trees with an extremely shallow node.

It's extremely disappointing that not only the authors but the reviewers failed to notice the lack of taxonomic understanding evidenced here.

long overdue

Ramneek Gupta — 2013-02-07T10:04:31Z

Clearly a tutorial that has been missing for a long time, leaving many gloomy bioinformaticians in glamorous parties. The line I seem to have more success with lately is '.. DNA .. yes, so being able to tell whether you like or hate coriander, or have dry or wet earwax'.... If that fails, the male infertility GWAS is usually a hit.

Wikipedia or database?

Peter Uetz — 2012-09-25T16:38:18Z

Just a spontaneous thought: I wonder whether this project could or should be split up into a Wikipedia part (with all its advantages and disadvantages, but probably more advantages) and a database part. Wikipedia could fulfil the encyclopedic goal with images and human-readable text, essentially like mini-reviews. Everything else could go into various databases such as Uniprot, Intact, GEO etc. in order to provide a searchable dataset with links to all kinds of additional sources (PDB, PubMed etc.).

Maybe more functionality is coming, but right now the search function seems to be quite limited (e.g. no search for tissue-specific transcription factors).

An overview article of all TFs would be nice too (similar to Vaquerizas et al. 2009, Nat Rev Genet 10: 253), especially if it were kept up-to-date. On the other hand, printed peer-reviewed mini-reviews are nice, but they are out of days after a few years and then need to be rewritten. Why not just keep your database up to date, or make it more widely available through Wikipedia?

Note added in proof

Antonio Sarikas — 2011-05-13T14:49:46Z

Recently, Pei et al. reported that deletion of the Parc (Cul9) gene in Mus musculus resulted in spontanous tumor development.

Pei XH, Bai F, Li Z, Smith MD, Whitewolf G, Jin R, Xiong Y. Cytoplasmic CUL9/PARC Ubiquitin Ligase Is a Tumor Suppressor and Promotes p53-Dependent Apoptosis.
Cancer Res. 2011; 71: 2969-77.