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
The amazing lack of proper referencing in Bioinformatics and Biostatistics (Jean-Michel Claverie, 17 January 2011)
As an old timer, contributing to the field of computational biology since 1975 (the previous century! :-), I am amazed by the lack of proper reference to previous works by the current generation of bioinformaticians/biostatiticians. Most of them seem to believe that nothing existed before the Internet (1990), or even later. Take the example of this article: the authors apparently ignore that before the "RNA-Seq" era (a word that appeared in the context of the NGS approaches), we were sequencing "Expressed Sequences Tags" (ESTs) exactly for the same purpose, and with similar results. Of course, theoreticians developped the proper methods to analyze these data, methods that still apply...
read full comment
Response to Andreas Sundquist (Lincoln Stein, 28 September 2010)
I wish to thank Andreas Sundquist and colleagues for identifying a careless and significant error in my calculations of network transfer time for a 100 gigabyte sequencing file. I have repeated the calculation and confirm Sundquist's estimates.
read full comment
Hypomethylation may change Alu transcription level (Dajun Deng, 15 March 2010)
It is interesting that expessed Alu repeat may be a good reference for transcription normalization of target genes. However, it is well known that Alu elements in the human genome are hypomethylated in many cases such as cancer tissues and tissues exposed to cytotoxic chemicals and anoxic conditions. It is likely that transcription activity of Alu elements may change due to the hypomethylation, which might reduce the proposed normalization value of Alu transcripts. It will be useful if authors could exclude effect of the hypomethylation on Alu transcription.
read full comment
In the legend of Figure 3 parts (a) and (b) were incorrectly described as (a) CRLMM and (b) BRLMM in the final version of the paper. This has now been corrected.
read full comment
Separating racist judgement from scientific objectivism (John Copen, 30 July 2008)
There is no doubt there are both phenotypic and genotypic differences between individuals and between groups of similar individuals and groups of other similar individuals. But that really is the key, isn't it?The question is not are there differences, but what difference are we focusing on AND powerfully WHY. Racist judgement oozes like a sore from the WHY part of this question. Scientific objectivism must identify both WHAT and WHY and use WHY to explain away racist judgement. How so?Hierarchical assignment should not include a valuation such that it lends credibility to racist judgement. The existence of a hierarchy is not always objective as well, and is highly dependent upon the subjective determination of the value of a characteristic to an individual organism to survive, adapt, and...
read full comment
Data "waves" in SNP array data (Kylie Louise Gorringe, 01 July 2008)
We sometimes observe data "waves" in our Affy SNP array copy number data. It is inconsistent between samples or experimental batches and sometimes a second DNA prep or extra clean-up of the same sample removes the effect. It seems to be more common in whole-genome amplified DNA or DNA from limited sources (eg tumour biopsies). I'd be interested to know if anyone has identified why this occurs or has a solution for analysing tumor data.
read full comment
fighting back against anti-science legislatures (Steven Salzberg, 30 June 2008)
Greg, you make some excellent points - and I concur with your suggestion not to hold conferences in states that undermine the teaching of evolution. Another strategy we might consider - those of us in academia, that is - is announcing that we will downgrade applications for admission to our universities from students in states where evolution is not taught, or is taught badly. The quality of a student's education is a legitimate criterion for admission to university, and if a state wants to damage its own students by teaching pseudoscience, then the citizens of that state should be told that they are hurting the chances of their children to be admitted to college. Maybe that would wake up enough parents to stop the legislatures from passing any more of these backward-looking, anti-...
read full comment
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Latest comments
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
The amazing lack of proper referencing in Bioinformatics and Biostatistics (Jean-Michel Claverie, 17 January 2011)
As an old timer, contributing to the field of computational biology since 1975 (the previous century! :-), I am amazed by the lack of proper reference to previous works by the current generation of bioinformaticians/biostatiticians. Most of them seem to believe that nothing existed before the Internet (1990), or even later. Take the example of this article: the authors apparently ignore that before the "RNA-Seq" era (a word that appeared in the context of the NGS approaches), we were sequencing "Expressed Sequences Tags" (ESTs) exactly for the same purpose, and with similar results. Of course, theoreticians developped the proper methods to analyze these data, methods that still apply... read full comment
Comment on: Anders et al. Genome Biology, 11:R106
Response to Andreas Sundquist (Lincoln Stein, 28 September 2010)
I wish to thank Andreas Sundquist and colleagues for identifying a careless and significant error in my calculations of network transfer time for a 100 gigabyte sequencing file. I have repeated the calculation and confirm Sundquist's estimates. read full comment
Comment on: Stein Genome Biology, 11:207
Network transfer miscalculation (Andreas Sundquist, 05 August 2010)
Genome Biology ¿ Letter to... read full comment
Comment on: Stein Genome Biology, 11:207
Hypomethylation may change Alu transcription level (Dajun Deng, 15 March 2010)
It is interesting that expessed Alu repeat may be a good reference for transcription normalization of target genes. However, it is well known that Alu elements in the human genome are hypomethylated in many cases such as cancer tissues and tissues exposed to cytotoxic chemicals and anoxic conditions. It is likely that transcription activity of Alu elements may change due to the hypomethylation, which might reduce the proposed normalization value of Alu transcripts. It will be useful if authors could exclude effect of the hypomethylation on Alu transcription. read full comment
Comment on: Marullo et al. Genome Biology, 11:R9
The conference website (Jerzy Jurka, 23 April 2009)
More details about the conference, including the book of abstracts can be found on our website:
http://www.girinst.org/conference/Asilomar-2009/index.html read full comment
Comment on: Ivics Genome Biology, 10:306
Correction in Table I (Silvestro Conticello, 16 February 2009)
In the table the localization of APOBEC3A and APOBEC3B were inverted. This has now been corrected. read full comment
Comment on: Conticello Genome Biology, 9:229
Correction (Thanya Nirantasook, 14 August 2008)
In the legend of Figure 3 parts (a) and (b) were incorrectly described as (a) CRLMM and (b) BRLMM in the final version of the paper. This has now been corrected. read full comment
Comment on: Lin et al. Genome Biology, 9:R63
Separating racist judgement from scientific objectivism (John Copen, 30 July 2008)
There is no doubt there are both phenotypic and genotypic differences between individuals and between groups of similar individuals and groups of other similar individuals. But that really is the key, isn't it?The question is not are there differences, but what difference are we focusing on AND powerfully WHY. Racist judgement oozes like a sore from the WHY part of this question. Scientific objectivism must identify both WHAT and WHY and use WHY to explain away racist judgement. How so?Hierarchical assignment should not include a valuation such that it lends credibility to racist judgement. The existence of a hierarchy is not always objective as well, and is highly dependent upon the subjective determination of the value of a characteristic to an individual organism to survive, adapt, and... read full comment
Comment on: Lee et al. Genome Biology, 9:404
Data "waves" in SNP array data (Kylie Louise Gorringe, 01 July 2008)
We sometimes observe data "waves" in our Affy SNP array copy number data. It is inconsistent between samples or experimental batches and sometimes a second DNA prep or extra clean-up of the same sample removes the effect. It seems to be more common in whole-genome amplified DNA or DNA from limited sources (eg tumour biopsies). I'd be interested to know if anyone has identified why this occurs or has a solution for analysing tumor data. read full comment
Comment on: Marioni et al. Genome Biology, 8:R228
fighting back against anti-science legislatures (Steven Salzberg, 30 June 2008)
Greg, you make some excellent points - and I concur with your suggestion not to hold conferences in states that undermine the teaching of evolution. Another strategy we might consider - those of us in academia, that is - is announcing that we will downgrade applications for admission to our universities from students in states where evolution is not taught, or is taught badly. The quality of a student's education is a legitimate criterion for admission to university, and if a state wants to damage its own students by teaching pseudoscience, then the citizens of that state should be told that they are hurting the chances of their children to be admitted to college. Maybe that would wake up enough parents to stop the legislatures from passing any more of these backward-looking, anti-... read full comment
Comment on: Petsko Genome Biology, 9:106