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
Why present-day Plantae have no chlamydial symbionts? (Cesar Sanchez, 23 June 2008)
Excellent article. I very much enjoyed the detailed discussion of alternative hypotheses and phylogenies. I didn't know about the chlamydial role on plastid origin until I read a recent article confirming and expanding the results presented here:Moustafa A, Reyes-Prieto A, Bhattacharya D (2008) Chlamydiae Has Contributed at Least 55 Genes to Plantae with Predominantly Plastid Functions. PLoS ONE 3(5): e2205. doi:10.1371/journal.pone.0002205At the PLoS ONE site I have posted a comment/question (that of the title of the present comment), in case anybody can contribute to the discussion.
read full comment
An incorrect FACS plot for CD44 expression of mClone-3 was inadvertently used in the final version of the paper. This has now been corrected.
read full comment
Evidence for racial differences? (Peter Uetz, 10 December 2007)
Petsko claims that "we have the data to refute the claims that one race is superior and another inferior or that gender is linked to intellectual fitness". Do we? Where is that data? On the contrary, I think there is evidence showing that some races are superior to others. Look at the 100 m Olympic finalists, they are pretty much all black. This is good evidence that black athletes are superior to white ones. Maybe there is a similar imbalance for academics. Same for sex. Men are undoubtedly much better at crime than women (aren't 90% of all inmates male?). Am I a racist? Hopefully not - I am even in a bi-racial relationship. But it is undeniable that there are differences between different populations. This is biology.As long as these average differences are small (and they probably are)...
read full comment
I have to say I agree with Greg on this one. Many, many people heard Dr. Watson make disparaging remarks - particularly about women - over a very long time, yet none took him publicly to task (at least not that I have witnessed). I have had many female scientists say to me statements similar to "he got away with chauvinism for so long, it's surprising that this is what he was called on". Any of us (and particularly those famous scientists of the same era), who saw him talk and said nothing about such comments were enablers. Not only did we do a disservice to others in the audiences of talks who may have been offended, we did a disservice to Watson himself.
read full comment
Thanks for your open, honest, and insightful assessment of the situation and of human nature itself. In light of those who throughout history have risked or even given their lives in defense of worthy causes, the *least* we can do in the face of comments like Watson's is to speak up and do our scientific duty - demand logic and evidence.
read full comment
454 pyrosequencing C. elegans chromatin (Tom Owen-Hughes, 25 July 2007)
The article below describes the use of pyrosequencing to analyse chromatin structure in C.elegans. Johnson SM, Tan FJ, McCullough HL, Riordan DP, Fire AZ. Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin.Genome Res. 2006 Dec;16(12):1505-16. Epub 2006 Oct 12. Unfortunately I had not read this at the time I prepared this minireview. However, I do believe it deserves credit as perhaps the first application of pyrosequencing to analyse chromatin structure.
read full comment
Supra-genome vs. pangenome (David Ussery, 13 June 2007)
What is the difference between the "Supra-genome" mentioned in this article, and the "pangenome" first used to describe several sequenced Streptococcus agalactiae genomes, back in 2005? I can find the phrase "pan-genome" 16 times in PubMed, but "Supra-genome" is found only 3 times - once in this paper, and twice other by papers from the same group. Can't we reach an agreement on what to call all the combined genes in a set of sequenced genomes from the same species?Why should it be called "pan-genome" for Burkholderia, Campylobacter, E. coli, Streptococcus, and Vibrio, but for Haemophilus it is the "supra-genome"?
read full comment
Why Sotiriou2006 did not use Wang et al dataset (Pratyaksha Wirapati, 17 November 2006)
The authors wrote in the discussion:"Intriguingly though, the grade-derived signature was not validated in a large available cohort [11], raising doubts as to its wider applicability."The grade signature was not applied to Wang et al. cohort in the Sotirou 2006 paper because histologic grade data were not publicly available , and therefore the cohort can not be used to answer our main question. That is, figure 2 of Sotiriou et al. can not be produced without histologic grade information.The grade-index can be applied to this cohort, with hazard ratio 2.53 (1.62-3.94), under the cutoff that gives the same ratio of "poor" and "good" prognostic groups as that in figure 3b of this commented paper (Teschendorff et al.), in order to make the hazard ratios comparable. The HR above is similar to...
read full comment
Updates for ChIPOTle (Michael Buck, 31 October 2006)
ChIPOTle is continuing to be updated and enhanced; the latest version can be downloaded from http://www.bio.unc.edu/faculty/lieb/labpages/ChIPOTle/home.htm link.In addition, a PERL version of ChIPOTle is available at Perl-ChIPOTle. This version can be used with datasets too large for the Excel version (>65536 array elements).
read full comment
RSS
Latest comments
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
Why present-day Plantae have no chlamydial symbionts? (Cesar Sanchez, 23 June 2008)
Excellent article. I very much enjoyed the detailed discussion of alternative hypotheses and phylogenies. I didn't know about the chlamydial role on plastid origin until I read a recent article confirming and expanding the results presented here:Moustafa A, Reyes-Prieto A, Bhattacharya D (2008) Chlamydiae Has Contributed at Least 55 Genes to Plantae with Predominantly Plastid Functions. PLoS ONE 3(5): e2205. doi:10.1371/journal.pone.0002205At the PLoS ONE site I have posted a comment/question (that of the title of the present comment), in case anybody can contribute to the discussion. read full comment
Comment on: Huang et al. Genome Biology, 8:R99
Correction (Caroline Hering, 13 May 2008)
An incorrect FACS plot for CD44 expression of mClone-3 was inadvertently used in the final version of the paper. This has now been corrected. read full comment
Comment on: Ulloa-Montoya et al. Genome Biology, 8:R163
Evidence for racial differences? (Peter Uetz, 10 December 2007)
Petsko claims that "we have the data to refute the claims that one race is superior and another inferior or that gender is linked to intellectual fitness". Do we? Where is that data? On the contrary, I think there is evidence showing that some races are superior to others. Look at the 100 m Olympic finalists, they are pretty much all black. This is good evidence that black athletes are superior to white ones. Maybe there is a similar imbalance for academics. Same for sex. Men are undoubtedly much better at crime than women (aren't 90% of all inmates male?). Am I a racist? Hopefully not - I am even in a bi-racial relationship. But it is undeniable that there are differences between different populations. This is biology.As long as these average differences are small (and they probably are)... read full comment
Comment on: Petsko Genome Biology, 8:113
The (Roger Bumgarner, 10 December 2007)
I have to say I agree with Greg on this one. Many, many people heard Dr. Watson make disparaging remarks - particularly about women - over a very long time, yet none took him publicly to task (at least not that I have witnessed). I have had many female scientists say to me statements similar to "he got away with chauvinism for so long, it's surprising that this is what he was called on". Any of us (and particularly those famous scientists of the same era), who saw him talk and said nothing about such comments were enablers. Not only did we do a disservice to others in the audiences of talks who may have been offended, we did a disservice to Watson himself. read full comment
Comment on: Petsko Genome Biology, 8:113
Bravo! (Anne Carpenter, 10 December 2007)
Thanks for your open, honest, and insightful assessment of the situation and of human nature itself. In light of those who throughout history have risked or even given their lives in defense of worthy causes, the *least* we can do in the face of comments like Watson's is to speak up and do our scientific duty - demand logic and evidence. read full comment
Comment on: Petsko Genome Biology, 8:113
454 pyrosequencing C. elegans chromatin (Tom Owen-Hughes, 25 July 2007)
The article below describes the use of pyrosequencing to analyse chromatin structure in C.elegans. Johnson SM, Tan FJ, McCullough HL, Riordan DP, Fire AZ. Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin.Genome Res. 2006 Dec;16(12):1505-16. Epub 2006 Oct 12. Unfortunately I had not read this at the time I prepared this minireview. However, I do believe it deserves credit as perhaps the first application of pyrosequencing to analyse chromatin structure. read full comment
Comment on: Owen-Hughes et al. Genome Biology, 8:217
New URL for supplementary information (Paul Pavlidis, 12 July 2007)
The URL given in the article is no longer valid. Please use http://bioinformatics.ubc.ca/pavlidis/lab/mousebrain/. read full comment
Comment on: Pavlidis et al. Genome Biology, 2:research0042
Supra-genome vs. pangenome (David Ussery, 13 June 2007)
What is the difference between the "Supra-genome" mentioned in this article, and the "pangenome" first used to describe several sequenced Streptococcus agalactiae genomes, back in 2005? I can find the phrase "pan-genome" 16 times in PubMed, but "Supra-genome" is found only 3 times - once in this paper, and twice other by papers from the same group. Can't we reach an agreement on what to call all the combined genes in a set of sequenced genomes from the same species?Why should it be called "pan-genome" for Burkholderia, Campylobacter, E. coli, Streptococcus, and Vibrio, but for Haemophilus it is the "supra-genome"? read full comment
Comment on: Hogg et al. Genome Biology, 8:R103
Why Sotiriou2006 did not use Wang et al dataset (Pratyaksha Wirapati, 17 November 2006)
The authors wrote in the discussion:"Intriguingly though, the grade-derived signature was not validated in a large available cohort [11], raising doubts as to its wider applicability."The grade signature was not applied to Wang et al. cohort in the Sotirou 2006 paper because histologic grade data were not publicly available , and therefore the cohort can not be used to answer our main question. That is, figure 2 of Sotiriou et al. can not be produced without histologic grade information.The grade-index can be applied to this cohort, with hazard ratio 2.53 (1.62-3.94), under the cutoff that gives the same ratio of "poor" and "good" prognostic groups as that in figure 3b of this commented paper (Teschendorff et al.), in order to make the hazard ratios comparable. The HR above is similar to... read full comment
Comment on: Teschendorff et al. Genome Biology, 7:R101
Updates for ChIPOTle (Michael Buck, 31 October 2006)
ChIPOTle is continuing to be updated and enhanced; the latest version can be downloaded from http://www.bio.unc.edu/faculty/lieb/labpages/ChIPOTle/home.htm link.In addition, a PERL version of ChIPOTle is available at Perl-ChIPOTle. This version can be used with datasets too large for the Excel version (>65536 array elements). read full comment
Comment on: Buck et al. Genome Biology, 6:R97