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Data visualization (Matthew Holden, 13 June 2015)

The global phylogenies displayed in Figure 3 have been loaded into the Microreact (microreact.org) application and can be viewed interactively: ST22: http://microreact.org/project/EyQY-i7L and ST239: http://microreact.org/project/NJ56s3QL read full comment

Comment on: Hsu et al. Genome Biology, 16:81

Thanks (Kevin Chen, 10 June 2015)

Hi Michael, thanks for the clarification. We weren't aware of this while writing the paper but will note it for the future. read full comment

Comment on: Song et al. Genome Biology, 16:33

Details of funding for this study (Louisa Flintoft, 21 May 2015)

Added on behalf of the authors: "This work was supported by Grant-in-Aid for Scientific Research (B) 22310117, Grant-in-Aid for Exploratory Research 23659050, from the Japan Society for the Promotion of Science, and Grant-in-Aid for Scientific Research on Innovative Areas 23125503 from the Ministry of Education, Culture, Sports, Science and Technology, Japan.  This research was also supported by CREST, JST, and by the Japan Society for the Promotion of Science (JSPS) through the “Funding Program for World-Leading Innovative R&D on Science and Technology (FIRST Program),” initiated by the Council for Science and Technology Policy (CSTP)."

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Comment on: Inoue et al. Genome Biology, 15:R63

In HGT how have foreign sequences entered the human genome? (Kevin Smith, 23 March 2015)

I suggest that the most likely route by which exogenous sequences have entered the human genome is via sperm-mediated gene transfer. I hypothesised about this possibility previously, if interested please see Smith K. The Role of Sperm-Mediated Gene Transfer in Genome Mutation and Evolution. Medical Hypotheses, 2002; 59(4): 433-437.     read full comment

Comment on: Crisp et al. Genome Biology, 16:50

Correction: Segway no longer needs a computer cluster (Michael Hoffman, 16 March 2015)

Minor correction: since the release of Segway 1.2.0 on 29 August 2014, Segway will run on standalone computers not attached to a cluster.
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Comment on: Song et al. Genome Biology, 16:33

Underlying mapping algorithm Batman still unpublished. (Alejandro Fernandez, 04 March 2015)

"After linker trimming, the tags are mapped to the corre-sponding reference genome using the Batman package (CTennakoon et al., manuscript submitted) with at most one mismatch."   I was unable to find references or any documentation regarding Batman, has this been documented? Does the tool work with BWA or Bowtie?    read full comment

Comment on: Li et al. Genome Biology, 11:R22

Author reply to comment of Martin Bachman (Colm Nestor, 16 February 2015)

Dear... read full comment

Comment on: Nestor et al. Genome Biology, 16:11

Global levels of 5hmC vs. proliferation (Martin Bachman, 10 February 2015)

The relationship between 5hmC levels and proliferation has already been described and explained in detail here: http://dx.doi.org/10.1038/NCHEM.2064 5hmC is restored on newly replicated DNA with a substantial time delay, and therefore in fast proliferating cells where a lot of new DNA is being synthesised, the global levels of 5hmC are diluted down.
Treatment with such high levels of Vitamin C (1 mM) will most certainly slow down proliferation and therefore partially restore levels of 5hmC. This also means that TET enzymes are still present and active in the cells, and their downregulation cannot be fully responsible for the observed "loss" of 5hmC upon placing primary cells in culture.

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Comment on: Nestor et al. Genome Biology, 16:11

Minor corrigendum regarding Figure 7 (Christopher Keeling, 03 February 2015)

In Figure 7, the labels DponCYP18A1 and DponCYP306A1 are switched.  Sorry for any confusion this may have caused. Chris Keeling, for the authors read full comment

Comment on: Keeling et al. Genome Biology, 14:R27

Important work in a very interesting paper. (Clement Kent, 02 February 2015)

Liu et al. use the power of whole genome sequencing of multiple haploid drones descending from the same queen to zoom in on where in the genome recombination events are happening. This paper is of special interest to social insect researchers because it suggests that the already high previous estimates of honeybee recombination rates may have been two-fold... read full comment

Comment on: Liu et al. Genome Biology, 16:15

One billion views for WEHI YouTube? (Neil Saunders, 02 January 2015)

The biomedical animations produced by the WEHI are terrific and popular, but I don't think they have amassed one billion YouTube views. That kind of number is reserved for South Korean pop stars. The current view count according to https://www.youtube.com/user/WEHImovies/about is 1 373 010. read full comment

Comment on: Khan et al. Genome Biology, 15:556

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