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Overdispersion (Wolfgang Huber, 08 September 2014)

Dear Jean-Michel

apologies for the lack of citation, all I can say is that few papers manage to duly cite all relevant prior work, and that at the time of writing we must have assumed that in your case this was covered in one of the reviews or edgeR papers we... read full comment

Comment on: Anders et al. Genome Biology, 11:R106

A social media fire-storm (Mihai Pop, 08 September 2014)

This article caused a veritable social media fire-storm which raised some points that I would like to discuss in more detail... read full comment

Comment on: Hall Genome Biology, 15:424

Because competence is a better qualification for leadership than loud shouting (Wolfgang Huber, 04 August 2014)

Thanks to Neil for raising two important issues, although as any decent philosopher, he only gives us the questions, not the answers:

  1. How do we best define a scientist's real value to the community?
  2. Why are there some people that have a much bigger followership than 1. justifies, and do we want that?
Unsurprisingly, the answer to 1. is  more subtle than just WoK citations. As for 2., there are many frustrating examples in the world of science that mirror the Kardashian-Syria example, and it'll be good for us to be mindful about them.   read full comment

Comment on: Hall Genome Biology, 15:424

The Kardashian index... why should we care? (Madhu Singh, 31 July 2014)

First, I should congratulate the author for getting attention of the editors of Genome Biology to even get this 'paper' published.  Next, I should congratulate the editors for thinking 'out of the box' to accept this manuscript.  It will surely increase the traffic, even if the journal doesn't need a boost in its impact... read full comment

Comment on: Hall Genome Biology, 15:424

Response to comment "comparison with the epigenetic clock by Horvath 2013" (Wolfgang Wagner, 27 February 2014)

Steve Horwarth has compared the method described in this article (Weidner et al., PMID: 24490752) with his recently published age-predictor (Horvath 2013, PMID: 24138928). This comparison is very interesting and helpful. We are grateful for this... read full comment

Comment on: Weidner et al. Genome Biology, 15:R24

Comparison with the epigenetic clock by Horvath 2013 (Steve Horvath, 18 February 2014)

Weidener et al (2014) present an age predictor based on human blood methylation levels that only uses 3 CpGs. Last year, I published an age predictor (referred to as epigenetic clock) that works well in most human cells/tissues/organs (Horvath 2013, PMID: 24138928) but it makes use of 353 CpGs. Given that a sparse predictor has obvious practical advantages, readers may be interested in learning how the epigenetic clock compares to the predictor by Weidner et... read full comment

Comment on: Weidner et al. Genome Biology, 15:R24

Please check the human cofilin-1 and cofilin-2 protein sequences in figure 2 of this paper (Yi-Jang Lee, 17 January 2014)

Dear Sir   I recently read this review paper for some reference purpose, and unexpectedly found that the sequence of H. sapiens cof-1 and cof-2 proteins in the figure 2 seemed to be listed oppositely.  I checked the PDB and genebank and confirmed this potent flaw. Please check it out. Thank you! read full comment

Comment on: Maciver et al. Genome Biology, 3:reviews3007

Change of Institution (Jun Song, 23 December 2013)

I have moved from UCSF to University of Illinois, Urbana-Champaign. Please direct all inquiries to songj@illinois.edu read full comment

Comment on: Diaz et al. Genome Biology, 13:R98

Figures 2 and 3 have their captions and legends swapped (José María Fernández González, 16 December 2013)

Reading the manuscript, I have just realized Figures 2 and 3 have their captions and legends swapped read full comment

Comment on: Glass et al. Genome Biology, 14:R75

erratum in cancer tissues (Steve Horvath, 04 November 2013)

As the author of the article, I have to report a... read full comment

Comment on: Horvath Genome Biology, 14:R115

Table 2 erratum (Doron Betel, 04 November 2013)

There is a correction to table 2 that did not make it into the final version.
In the last row of table 2 called "Runtime for experiments with 3-5 replicates..." the values for edgeR and limmaVoom should be Seconds not Minutes.

For completeness, the following table is the runtime performance (in seconds) of six methods from DE analysis comparing the 5 replicates from groups A and B from the SEQC data.

DESeq | edgeR | PoissonSeq | limmaVoom | baySeq
user.self | 410.292 | 7.380 | 12.893 | 4.897 | 20.772
sys.self | 0.356 | 0.004 | 0.153 | 0.011 | 0.166
elapsed | 413.751 | 7.904 | 13.343 | 4.911 | 2028.279 read full comment

Comment on: Rapaport et al. Genome Biology, 14:R95

Data accessibility of Clonorchis sinensis genome (Xinbing Yu, 30 September 2013)

The genomic sequences in the paper are also available from GenBank [GenBank: BADR00000000.1]. Contigs, scaffolds and protein sequences are available under the NCBI Bioproject ID (PRJDA72781). Please contact Dr. Yu at yuxb@sysu.mail.edu.cn for more information. read full comment

Comment on: Wang et al. Genome Biology, 12:R107

NIH support (Ariel Fernandez, 03 September 2013)

The research reported was incorrectly stated to have been supported by NIH grant R01 GM072614 "Protein packing defects as functional markers and drug targets" (NIGMS, PI: Ariel Fernandez). The work is thematically unrelated to the NIH grant and did not receive any NIH support. The author apologizes for the mistake.
Ariel Fernandez read full comment

Comment on: Chen et al. Genome Biology, 9:R107

Error rate is random (Mauricio Carneiro, 30 August 2013)

Hi Ravi,

The key concept you are missing here is that the error (despite high at 14%) is random, therefore proportional coverage helps makes the error rate irrelevant, no error correction method is needed other than a good variant caller with a bayesian model (hint: GATK). read full comment

Comment on: Roberts et al. Genome Biology, 14:405

updated link (Jo Vandesompele, 19 August 2013)

URL in my comment from 2003 is no longer valid. The correct one should be http://medgen.ugent.be/~jvdesomp/genorm/ read full comment

Comment on: Vandesompele et al. Genome Biology, 3:research0034

multiplexed constructs (Jose L. Oliver, 22 July 2013)

Dear authors,

on page 10 of your paper you mention that you have `...identified 22 multiplexed constructs that drove GFP expression consistently at 24 hpf to at least one tissue (Figure 1d, Additional File 3). However, in Figure 1d you only labeled 6 of these constructs. Please, what are the labels of the remaining ones? Are they marked in some form on the excel file (additional file 3)?

Thanks in advance, sincerely,

Jose L. Oliver
University of Granada, Spain read full comment

Comment on: Smith et al. Genome Biology, 14:R72

Technical justification missing in the article (Ravi Shankar, 16 July 2013)

Well, the authors are correct that their is a huge apprehension in buying PacBio sequencers and they are surrounded by some negative publicity. However, this article appeared to be an academic attempt to bring PacBio sequencers in a good light. The entire article misses depth in dealing and really did not address a much technically to prove their points. If sequencing error is there with 14% or so, it is per base chance. Their error correction method is not convincing one, as they claim that they increase coverage to minimize the sequencing errors. This is not a right way and it can't remove innate errors per reads. It is like constituting jury of wrong people in majority, whose majority vote is counted to decide the point of agreement. So, these all jury members will finalize a sequence... read full comment

Comment on: Roberts et al. Genome Biology, 14:405

trxG regulators associated with highly expressed genes, not genome reorganization (Robert Cornman, 27 June 2013)

I do not believe these data should be interpreted as evidence that trxG regulation promotes the aggregation of target genes into physical clusters over evolutionary time. I believe the clustering reflects primarily tandem duplication of trxG-responsive genes. While the two mechanisms are not mutually exclusive, segmental duplication is a sufficient explanation founded on well studied phenomena, and can propagate both protein-coding sequences and cis-regulatory elements simultaneously. In contrast, I am unaware of a theoretical or empirical basis for arguing a fitness advantage of a clustered genotype over a dispersed genotype with respect to trxG targets.... read full comment

Comment on: Blanco et al. Genome Biology, 9:R134

EMu version 1.3 includes EMu-prepare (Andrej Fischer, 27 June 2013)

The new version of EMu includes a program to prepare the input files for an EMu analysis for generic mutation data sets. It can be found at the Sanger Institute software site. read full comment

Comment on: Fischer et al. Genome Biology, 14:R39

Inaccurate information in Table 1 (Nathaniel Street, 27 June 2013)

I would like to point out a factual inaccuracy in Table 1. The ConGenIE.org resource that hosts the Picea abies genome and associated expression visualisation tools is open with no restriction. The genome and resource is described in the open access paper by Nystedt et al. (2013). All data from the project is available in public access databases.

I would also point out that the PopGenIE.org resource does not only host draft genome assemblies of aspen species, it also includes a number of tools for exploring curated sets of public gene expression data. read full comment

Comment on: Neale et al. Genome Biology, 14:120

code on google (Christopher Lord, 27 June 2013)

we have now deposited the source code associated with this manuscript on

http://code.google.com/p/shalign/ read full comment

Comment on: Sims et al. Genome Biology, 12:R104

Acknowledgement of TCGA (Andrew Cosgrove, 04 June 2013)

We have been asked by the authors to provide the following acknowledgement:

The results published here are in whole or part based upon data generated
by The Cancer Genome Atlas pilot project established by the NCI and NHGRI
(Accession number: phs000178.v7p6). Information about TCGA and the
investigators and institutions who constitute the TCGA research network
can be found at http://cancergenome.nih.gov/ read full comment

Comment on: Bashashati et al. Genome Biology, 13:R124

Addendum - authorship of 'Photo 51' (Naomi Attar, 15 May 2013)

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... read full comment

Comment on: Attar Genome Biology, 14:402

Kudos! Great commentary on sequestration¿s impact on research! National media should talk about this and YOU should read it!!! (Leonardo Collado Torres, 03 May 2013)

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... read full comment

Comment on: Leek et al. Genome Biology, 14:109

Relative use of "sister group" (Toni Gabaldon, 12 March 2013)

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. read full comment

Comment on: Ferreira et al. Genome Biology, 14:R20