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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

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