Definitions of viruses (Edward Rybicki, 18 April 2013)
A great piece of work - and since I met Dr van Etten in 1982 in Lincoln, after he and co-workers discovered the first PCBV, something I've been waiting quite a long time to see!
I especially like the comment "...which suggests that the recently acquired genes originate from a still largely un-sequenced reservoir of genomes, possibly other unknown viruses that infect the same hosts.", as it meshes really well with what I have been telling students for while now:
"A virus is an infectious acellular entity composed of compatible genomic components derived from a pool of genetic elements." read full comment
Comment on: Jeanniard et al. BMC Genomics, 14:158
Can it really achieve globin switching in vitro within one-phase system? (Wentian Wang, 10 March 2013)
see below read full comment
Comment on: Li et al. BMC Genomics, 13:153
Are assembled data available (Mark Blaxter, 08 March 2013)
I have been unable to access the SRA accession for this report, and wonder if the assemblies are also to be made available? read full comment
Comment on: Xi et al. BMC Genomics, 13:227
Corrected expression values in supplementary tables (Matthias Erwin Futschik, 06 August 2012)
The original supplementary tables 2-5 of this article contained some entries, which were given as date instead as a number (caused by automatic formating in Excel). These entries were corrected in the revised supplementary tables, that can be found at our web-page. read full comment
Comment on: Russ et al. BMC Genomics, 11:305
Incorrect reference for Bland and Altman (Jacob Hurst, 06 August 2012)
<p>The correct reference is given below. <br/> <br/>J MARTIN BLAND and DOUGLAS G ALTMAN <br/>Misleading Statistics: Errors in Textbooks, Software and Manuals <br/>Int. J. Epidemiol. (1988) 17(2): 245-247 doi:10.1093/ije/17.2.245 <br/> <br/><a href='http://ije.oxfordjournals.org/content/17/2.toc'>Here is a link to the journal</a></p> read full comment
Comment on: McIntyre et al. BMC Genomics, 12:293
Brief comparison to Roberts et al. (Jonathan Dreyfuss, 06 August 2012)
<p>I hope you enjoy our article and welcome any... read full comment
Comment on: Dreyfuss et al. BMC Genomics, 13:340
There is a typo (Yuan Zhou, 25 July 2012)
There is a typo in the Table 1, where the protein number of Arabidopsis genome should be 27,169. We regret the confusion caused by this typo. read full comment
Comment on: Zhou et al. BMC Genomics, 12:632
Streptomyces genomics (hang wu, 25 July 2012)
<p>Comparative streptomyces genomics was also described in the published manuscript.</p> read full comment
Comment on: Wu et al. BMC Genomics, 13:337
Correction to error in the caption of Figure 5 (Ainhoa Ruiz-Aracama, 04 July 2012)
The authors reported that the caption of Figure 5 was incorrect in the originally published version. The correct caption is:... read full comment
Comment on: Ruiz-Aracama et al. BMC Genomics, 12:251
Web access to Haloarchaeal Protein Clusters (Shiladitya DasSarma, 17 May 2012)
Comment on: Capes et al. BMC Genomics, 13:39
erratum concerning Figure 3 (Marc Robinson-Rechavi, 17 May 2012)
A mistake escaped our attention while correcting the proofs, for which we apologize.
The caption of figure 3B should not be: ("B) immune system co-module containing lymph node and thymus", but rather should be: "(B) co-module containing liver and kidney". read full comment
Comment on: Piasecka et al. BMC Genomics, 13:124
Diverse buffers for dosage imbalances (Ariel Fernandez, 17 May 2012)
Expression divergence due to subfunctionalization, the focus of this contribution, is one of various regulatory mechanisms to buffer the effects of dosage imbalance resulting from gene duplication. There are other processes operating at the post-transcriptional regulatory level (protein oligomerization, micro-RNA suppressive control, post-translational modifications, etc.) that may serve as alternative buffers to mitigate the effects of dosage imbalance (A. Fernández and J. Chen, Genome Research 19, 2185-92, 2009). For this reason, we postulate two broad but distinctive distributions corresponding to two qualitatively different buffering regimes that are apparent in the plots of Fig. 1: One regime, in which genes exclusively or nearly exclusively resort to expression divergence as a buffer... read full comment
Comment on: Fernández et al. BMC Genomics, 12:604
Post publication attention (Jing Tu, 27 March 2012)
It has been brought to our attention post publication that we omitted reference to a previously reported method of paired tagging.... read full comment
Comment on: Tu et al. BMC Genomics, 13:43
Typographical error in Table 1 (James Hane, 24 January 2012)
In the fourth line of Table 1 (beginning "CpT"), the 3rd and 4th columns ("ApA ApG") should instead read ("ApG ApA"). read full comment
Comment on: Hane et al. BMC Genomics, 11:655
Correction of Figure 4B (Maria Jose Lopez-Barragan, 23 January 2012)
The ID numbers of the genes and isoforms shown in Figure 4B are MAL7P1.157, MAL7P1.157a and MAL7P1.157b, instead of MAL7P1.175, MAL7P1.175a and MAL7P1.175b, respectively. read full comment
Comment on: López-Barragán et al. BMC Genomics, 12:587
Update information (Ganggang Guo, 29 November 2011)
We've noticed that the link of maize WebFPC database link has changed, and some of the neareast markers of maize ARFs are inconsistent with its BAC location in Table 1. The updated information are as follows:
a. The new link of WebFPC ( http://www.genome.arizona.edu/fpc/maize/WebFPC/) in the 4th part of Methods paragraph;
b. The updated Table 1 is too large to post here, please contact the author when you need, we will email it to you as soon as possible. read full comment
Comment on: Xing et al. BMC Genomics, 12:178
New Address (Yannick Wurm, 24 November 2011)
Comment on: Wurm et al. BMC Genomics, 10:5
RefGenes is made Open Access (Philip Zimmermann, 24 November 2011)
The RefGenes tool has now been made fully Open Access and has a new website with useful information for the user such as a tutorial and examples. RefGenes can be started directly at www.refgenes.org.
read full comment
Comment on: Hruz et al. BMC Genomics, 12:156
query regarding this software (Mamoonah Chaudhry, 18 October 2011)
one of my friend referred this article to me as i was aiming to do allele specific PCR. i found this software very useful.As i am trying to design primers using this software, maximum Tm difference is quite confusing, as far as my knowledge is concerned, it should be not more than 5 degree c. whenever i try to change it in software, it designs no primers. please give me your email address for direct contact or please help me in this regard.
thanks read full comment
Comment on: Wangkumhang et al. BMC Genomics, 8:275
New data link (Esther Black, 18 October 2011)
The microarray data associated with this manuscript can now be found with the GEO accession number GSE31625.
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE31625 read full comment
Comment on: Balko et al. BMC Genomics, 7:289
Serious Concerns (Jared Decker, 18 October 2011)
I have serious concerns about the statistical methods used in this paper. With the recent advances in statistical methods for genome-wide association studies, I am troubled that the authors did not account for pedigree relationships between cows in the study. For an overview of different methods available to correct for cryptic relatedness see Nat Rev Genet. 2010 Jul;11(7):459-63.; J Dairy Sci. 2008 Nov;91(11):4414-23.; and Am J Hum Genet. 2011 Jan 7;88(1):76-82..
Furthermore, I am concerned that the authors used PTA values without deregressing the... read full comment
Comment on: Cole et al. BMC Genomics, 12:408
Using Newbler 2.5 (or 2.6) with -cdna and -utr (Sujai Kumar, 19 September 2011)
For transcriptome data, Newbler has had a -cdna option since version 2.3 that makes "isotigs" and "isogroups".
However, since version 2.5(p1), there has been a -urt option as well which is recommended as a way of recovering low coverage transcripts (documented in detail in the manual for version 2.6) - and that is why we recommended using Newbler 2.5 with the -urt option in our paper.
We have been recommending Newbler 2.5 to our collaborators. I have heard of other researchers saying Newbler 2.5 (and now 2.6) didn't work as well as we said it would. However, in all those cases, the -urt option had not been used either.
So we are trying to figure out if some researchers are getting poorer results with Newbler despite using the -urt option, in which case we... read full comment
Comment on: Kumar et al. BMC Genomics, 11:571
Related Algorithms (Jared Roach, 19 September 2011)
The calling schema of parent sibling tracing (Additional File 1B) shows some common heritage with algorithms such as those discussed in these two sources:
Shih MC, Whittemore AS. Allele-sharing among affected relatives:non-parametric methods for identifying genes. Stat Methods Med Res. 2001 Feb;10(1):27-55. Review. PubMed PMID: 11329690
Roach JC, Glusman G, Smit AF, Huff CD, Hubley R, Shannon PT, Rowen L, Pant KP, Goodman N, Bamshad M, Shendure J, Drmanac R, Jorde LB, Hood L, Galas DJ. Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science. 2010 Apr 30;328(5978):636-9. Epub 2010 Mar 10. PubMed PMID: 20220176; PubMed Central PMCID: PMC3037280.
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Comment on: Lee et al. BMC Genomics, 12:434
Some typographical errors in my article (Xudong Wu, 27 June 2011)
List of typographical errors
B.1.1 in the third sentence: "is pervasive in animals" should be "is pervasive in the human genome"
B.3.2 in the second sentence: "included a third set of" should be "used the set of"
B.3.3 in last sentence:"p-values < 1.7E-289 for the four datasets" should be "p-values ≤ 1.7E-289, two-tailed" read full comment
Comment on: Wu et al. BMC Genomics, 12:244
Some errors in my article (Genyi Li, 10 June 2011)
List of Errors:
B.4.3 in the last sentence: "," should be "."
B.6.2 :1.25 GB should be 1.28 GB .
B.8.2 in last sentence: '(http://hordeum.oscs.montana.edu/genographer/)'
should be removed.
B.11.1 in the first sentence: "243"should be 241
B.16.1 in the second sentence: "and unique Solexa sequence paired-end
sequences" should be ' and unique Solexa paired-end sequences'.
read full comment
Comment on: Li et al. BMC Genomics, 12:249