is an exciting question that will have a large disease relevance. I think this is not so much about cytogenetic abnormalities but the general understanding which genetic modules are recombining, e.g. are compatible in terms of function, and which need to be tight together. Continue reading How we are reshuffling our genome
The non-scientific world doesn’t have any problem to show failure. Have a look at
failblog.wordpress.com
www.doingitwrong.com
www.shipmentoffail.com
Why is failure of science Continue reading Fail!
A new paper in PLoS Biology highlights the duty to recontact you for whole-genome research on any stored sample Continue reading Duty to recontact you
Bruce Alberts, the new editor-in-chief of Science magazine, has in his March, 21 editorial a nice comment that I would like to highlight here
Scientists share a common way of reaching conclusions that is based not only on the evidence and logic, but also requires honesty, creativity, and openess to new ideas.
Struggling in an area where no (or only seldom) conclusions ar being reached, I agree Continue reading To be honest
The central limit theorem states that a sum of independent identically distributed random variables (lets say allele counts in genomewide association scans) of finite variance will be approximately normally distributed. Unfortunately the maximum of the distribution will not reflect the true value … or did I get it wrong?
I am currently playing with MACH and SNPMStat to impute marker based on public datasets. I do not have any opinion about the usefulness of this approach – largely due to the fact that ~10% of my allele coding is different to the public hapmap data. Continue reading How to impute marker genotypes
We probably all agree that a publication bias against negative studies will severely distorts our opinion. To repeat an earlier Nature letter
Why negatives should be viewed as positives … This filtering of results undoubtedly biases the information available to scientists (see, for example “Null and void” Nature 422, 554–555; 2003). And communication is at the heart of science.
Here is an email that I received from the editor Continue reading Bias against negative studies
Current RNA chip technology, although quite advanced, is usually limited to known transcripts. As rare transcripts (N=1 to 5) usually cannot be quantified, current chip technology is probably useless for building realistic virtual cells. Maybe there are there are other options? SAGE – serial analysis of gene expression – has been also around Continue reading SuperSAGE plus highly parallel sequencing
A nice study in Hum Genet by Eiberg hit the public press (and the blogosphere 1|2). Although I agree with most commentators that this is a sound study with a bit antiquity dust in the methods, I am unsure if I should believe the main conclusion of a founder mutation Continue reading Blue eyes
“Positively disruptive” – a new nature genetics editorial – makes a U turn of the opinion voiced only two months earlier – having at that time cautioned users of new consumer genomics services. The current editorial now reads like an advertisement for deCODEme or Navigenics. Continue reading Unnecessarily disruptive
While Nature magazine is preparing something about Darwin’s enduring legacy here is a piece from Darwin’s own writings
doubt always arises whether the convictions of man’s mind, which has been developed from the mind of the lower animals, are of any value or at all trustworthy. Would any one trust in the convictions of a monkey’s mind, if there are any convictions in such a mind?
which can be found in Continue reading Would any one trust in the convictions of a monkey’s mind?
A recent editorial in PLoS Biology was about “Sex, dose and equality“. I always had problems to understand X linked recessive disease and carrier status of a woman: If the random X inactivation would have been complete why are there not much more colorblind women? Obviously the second X is at least partially active as a rescue system. Continue reading X activity center
A recent study published in nature genetics study highlights a ß-defensin gene where increased copy numbers are related to psoriasis. The normal range is 2 – 12 copies with the risk increasing with each extra copy. I don´t know if the given explanation is really correct: more genomic copies lead to more RNA, lead to more antimicrobial peptide, lead to skin inflammation. Maybe there is an unknown intermediate step: more antimicrobial peptide -> induce other inflammtory interleukins -> skin inflammation.
In any case, Continue reading New psoriasis gene would have been missed by testing linkage only
Here is a proof of principle project that can be further adjusted to your own needs – a simple server script that can look up your most recent Zotero database entries and display them to the world. When run in a DOS or Linux box as ZoteroServer path/zotero.sqlite it will display the most recent entries to clients listening at localhost:8888. The code should be pretty straightforward and may be replaced with even other items.
ZoteroServer.pl
|wj_ZoteroServer.txt|
I started with the Khoury manuscript, replaced it with the Terwillinger book and are finally using this one.
It costs about 63$.