Genome Biology - Latest Comments

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.

NHEJ Vs homologous recombination

Ronald Chalmers — 2011-02-28T14:07:48Z

Quoting from the intro:

"Although, DNA transposons are generally not thought to exhibit replicative gains when mobilized, for members of subclass 1, copy number can increase due to homologue-dependent DNA repair after excision at homozygous loci, which can result in the reconstitution of a TE in the donor location and, therefore, replicative gain."

My understanding is slightly different from this. Class 2 DNA transposons become amplified by two mechanisms operating during S phase of the cell cycle. Following excision, the empty donor site is restored to a filled donor site by homologous recombination with the sister chromosome (ie. the product of replication). Furthermore, if the transposon excises behind one replication fork and inserts in front of another fork, it makes further copy number gains.

In some organisms the repair of double strand breaks by homologous recombination is restricted to S phase. During the rest of the cell cycle non homologous end joining predominates. There is therefore very little scope for replicative gains by homologous repair from the homolog. I do not know if this is true in daphnia, but it probably is.

English and Jones 1995 did some nice work in this area with the Ac/Ds system in maize.

Change of corresponding author's e-mail address

Thomas Tilling — 2011-02-24T14:50:44Z

Please note that the corresponding author's e-mail address and affiliation have changed.
The new e-mail address is:
t.tilling@uke.uni-hamburg.de
The new affiliation is:
Universitätsklinikum Hamburg-Eppendorf
Campus Forschung - Dermatologie
N 27
Martinistrasse 52
D-20246 Hamburg
Germany

community and cloud computing

Dawn Field — 2011-01-20T15:05:02Z

Great paper and love the idea of the genomic informatics world as an ecosystem. Yes, it will certainly change and perhaps the biggest benefit will be more of a chance to share expertise/tools/data. The cloud should help naturally support collaboration and community-led projects. For example, great to see JCVI Cloud Bio-Linux cited - we provide NEBC Bio-Linux* upon which the cloud image is built: http://nebc.nox.ac.uk/biolinux.html Very happy to see our project/packages being put into the cloud by a third party. This is the vision of the new ecosystem.

* Nature Biotechnology 24, 801 - 803 (2006)
doi:10.1038/nbt0706-801

Open software for biologists: from famine to feast
Dawn Field1, Bela Tiwari1, Tim Booth1, Stewart Houten1, Dan Swan2, Nicolas Bertrand3 & Milo Thurston1

Abstract
Developing and deploying specialized computing systems for specific research communities is achievable, cost effective and has wide-ranging benefits.

Speaking out for the humanities

Maureen O'Malley — 2011-01-17T14:03:35Z

As a philosopher of biology, I wish to offer thanks for this editorial and its inclusive scope (literature, arts, humanities, social sciences). While it is addressed to a specific situation in the US, the argument holds across the world, including the UK, where a similar climate prevails. Education is structured differently here (someone learning about biology from an undergraduate level onwards need never encounter any subject outside biology again), but the same caveats about fickle fashions, shallow knowledge bases, and the unpredictability of sources of scientific inspiration still apply. It is unusual for a scientist to speak out so strongly for the arts and humanities, and very encouraging to see that valuable insights from such a range of disciplines can be put to work on the pages of a prominent scientific journal. A collaborative goal for endangered and non-endangered disciplines might be to devise and foster teaching practices that go beyond a traditional 'two cultures' perspective in education. Programmes along these lines exist in North America, Europe and further afield. If the argument of the editorial is correct, and I think it is, it is in everyone¿s interests to support such programmes before the extinction of stand-alone arts and humanities departments.

The amazing lack of proper referencing in Bioinformatics and Biostatistics

Jean-Michel Claverie — 2011-01-17T14:00:19Z

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.

Response to Andreas Sundquist

Lincoln Stein — 2010-09-28T16:24:55Z

I wish to thank Andreas Sundquist and colleagues for identifying a careless and significant error in my calculations of network transfer time for a 100 gigabyte sequencing file. I have repeated the calculation and confirm Sundquist's estimates.

Network transfer miscalculation

Andreas Sundquist — 2010-08-05T17:06:24Z

Genome Biology ¿ Letter to Editor

Dear Editor,

Lincoln Stein's excellent article on Cloud Computing in the latest issue of Genome Biology is a timely and insightful analysis of the promise of cloud computing for bioinformatics. As founders of a cloud-based DNA sequence analysis service, DNAnexus.com, we wholeheartedly agree that cloud bioinformatics is here to stay, as it translates cost-effectiveness and scalability into real-world time and resource savings for anyone dealing with large genomics datasets.

A key parameter for the viability of the cloud model for bioinformatics, for academic and commercial efforts alike, is whether standard networks are fast enough to support the upload of the large data files produced by sequencing machines. Dr. Stein's calculations suggest that network speeds are the major obstacle to widespread adoption. He states:

"For genomics, the biggest obstacle to moving to the cloud may well be network bandwidth. A typical research institution will have network bandwidth of about a gigabit/second (roughly 125 megabytes/second). On a good day this will support sustained transfer rates of 5 to 10 megabytes/second across the internet. Transferring a 100 gigabyte next-generation sequencing data file across such a link will take about a week in the best case."

We were struck by these numbers. For us, uploading a 1 gigabyte file, which corresponds to a typical single-lane fastq file from an Illumina GAIIx machine, takes little more than a minute. That 100 gigabytes should take a week seemed inconsistent with our first-hand experience. Indeed, upon further examination, we noticed that the calculations are off by a factor of about 60. To keep with the quoted example, transferring a 100 gigabyte next-generation sequencing data file across a network that supports real speeds of 10 megabytes per second will take 10,000 seconds, or about 3 hours, which is about 1/60 of a week.

In our experience, network speed is the first issue potential users mention, usually in a skeptical way, when they learn about DNAnexus. We hope that our clarification, in the context of Dr. Stein's article, will help to dissipate this skepticism by making users realize that bandwidth is not an issue in most settings, where a modest number of sequencing machines feed data over a standard network.

Sincerely,

Andreas Sundquist, Principal Founder and CEO, DNAnexus
Serafim Batzoglou, Co-founder, DNAnexus, and Associate Professor of Computer Science, Stanford University
Arend Sidow, Co-founder, DNAnexus, and Associate Professor of Pathology and of Genetics, Stanford University

Hypomethylation may change Alu transcription level

Dajun Deng — 2010-03-15T15:49:25Z

It is interesting that expessed Alu repeat may be a good reference for transcription normalization of target genes. However, it is well known that Alu elements in the human genome are hypomethylated in many cases such as cancer tissues and tissues exposed to cytotoxic chemicals and anoxic conditions. It is likely that transcription activity of Alu elements may change due to the hypomethylation, which might reduce the proposed normalization value of Alu transcripts. It will be useful if authors could exclude effect of the hypomethylation on Alu transcription.

The conference website

Jerzy Jurka — 2009-04-23T09:28:15Z

More details about the conference, including the book of abstracts can be found on our website:

http://www.girinst.org/conference/Asilomar-2009/index.html