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
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
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
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)?
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
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
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
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
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
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
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
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
Typographical error in Materials and Methods (James Hane, 26 February 2013)
The first Materials and Methods sub-section, titled "Whole-genome comparisons", contains a typographical error. In the sentence which reads "Promer outputs were filtered for repetitive matches using the program 'delta-filter' (MUMmer 3.0) with the '-g' parameter."... the '-g' should be replaced with '-1'. Note: this parameter should be read as the numeral 'one', not a lowercase 'L'.
read full comment
error in formula 4 (Jo Vandesompele, 26 February 2013)
It only came recently to our attention that the factor (h-1) in the denominator of equation 4 misses a square root symbol. As such it should be sqrt(h-1).
read full comment
As a systematist, reading this paper made me feel like banging my head against a wall. I first saw a short article about it in Science Daily and laughed at the gross mischaracterization of Hymenoptera systematics portrayed there as typical of science journalism. Then I came here and was surprisedto find that they were largely verbatim quotes from the...
read full comment
Clearly a tutorial that has been missing for a long time, leaving many gloomy bioinformaticians in glamorous parties. The line I seem to have more success with lately is '.. DNA .. yes, so being able to tell whether you like or hate coriander, or have dry or wet earwax'.... If that fails, the male infertility GWAS is usually a hit.
read full comment
Wikipedia or database? (Peter Uetz, 25 September 2012)
Just a spontaneous thought: I wonder whether this project could or should be split up into a Wikipedia part (with all its advantages and disadvantages, but probably more advantages) and a database part. Wikipedia could fulfil the encyclopedic goal with images and human-readable text, essentially like mini-reviews. Everything else could go into various databases such as Uniprot, Intact, GEO etc. in order to provide a searchable dataset with links to all kinds of additional sources (PDB, PubMed...
read full comment
Note added in proof (Antonio Sarikas, 13 May 2011)
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.
read full comment
Change of corresponding author's e-mail address (Thomas Tilling, 24 February 2011)
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
read full comment
community and cloud computing (Dawn Field, 20 January 2011)
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.
Open software for biologists: from famine to feast Dawn Field1, Bela Tiwari1, Tim Booth1, Stewart Houten1, Dan Swan2, Nicolas Bertrand3...
read full comment
Speaking out for the humanities (Maureen O'Malley, 17 January 2011)
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...
read full comment
RSS
Latest comments
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
Genome sequencing reaches a new high. (Norman Doggett, 26 February 2013)
The Joint Genome Institute missed a perfect opportunity here. read full comment
Comment on: van Bakel et al. Genome Biology, 12:R102
Typographical error in Materials and Methods (James Hane, 26 February 2013)
The first Materials and Methods sub-section, titled "Whole-genome comparisons", contains a typographical error. In the sentence which reads "Promer outputs were filtered for repetitive matches using the program 'delta-filter' (MUMmer 3.0) with the '-g' parameter."... the '-g' should be replaced with '-1'. Note: this parameter should be read as the numeral 'one', not a lowercase 'L'. read full comment
Comment on: Hane et al. Genome Biology, 12:R45
error in formula 4 (Jo Vandesompele, 26 February 2013)
It only came recently to our attention that the factor (h-1) in the denominator of equation 4 misses a square root symbol. As such it should be sqrt(h-1). read full comment
Comment on: Hellemans et al. Genome Biology, 8:R19
hard to take... (Karl Magnacca, 26 February 2013)
As a systematist, reading this paper made me feel like banging my head against a wall. I first saw a short article about it in Science Daily and laughed at the gross mischaracterization of Hymenoptera systematics portrayed there as typical of science journalism. Then I came here and was surprisedto find that they were largely verbatim quotes from the... read full comment
Comment on: Ferreira et al. Genome Biology, 14:R20
long overdue (Ramneek Gupta, 07 February 2013)
Clearly a tutorial that has been missing for a long time, leaving many gloomy bioinformaticians in glamorous parties. The line I seem to have more success with lately is '.. DNA .. yes, so being able to tell whether you like or hate coriander, or have dry or wet earwax'.... If that fails, the male infertility GWAS is usually a hit. read full comment
Comment on: Oshlack Genome Biology, 14:104
Wikipedia or database? (Peter Uetz, 25 September 2012)
Just a spontaneous thought: I wonder whether this project could or should be split up into a Wikipedia part (with all its advantages and disadvantages, but probably more advantages) and a database part. Wikipedia could fulfil the encyclopedic goal with images and human-readable text, essentially like mini-reviews. Everything else could go into various databases such as Uniprot, Intact, GEO etc. in order to provide a searchable dataset with links to all kinds of additional sources (PDB, PubMed... read full comment
Comment on: Yusuf et al. Genome Biology, 13:R24
Note added in proof (Antonio Sarikas, 13 May 2011)
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. read full comment
Comment on: Sarikas et al. Genome Biology, 12:220
NHEJ Vs homologous recombination (Ronald Chalmers, 28 February 2011)
Quoting from the... read full comment
Comment on: Schaack et al. Genome Biology, 11:R46
Change of corresponding author's e-mail address (Thomas Tilling, 24 February 2011)
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 read full comment
Comment on: Wong et al. Genome Biology, 8:R72
community and cloud computing (Dawn Field, 20 January 2011)
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... read full comment
Comment on: Stein Genome Biology, 11:207
Speaking out for the humanities (Maureen O'Malley, 17 January 2011)
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... read full comment
Comment on: Petsko Genome Biology, 11:138