Here is another take home item of the recent EMGS 2011 meeting at the King’s College. Located in the apse there are 5 topics as originally conceived by Gilbert Scott: Christ in the carpenter’s shop, Christ and the lawyers, Christ healing the sick, Christ teaching the people and The Cruxification. While that may all be appropriate for today’s Sunday Continue reading The DNA window at the King’s College Chapel at the Strand
A longstanding wish has become true – a useful graphical interface for R. While recent versions still had major problems on my Mac, the most recent nightly build works as expected, thanks Josh!
I have been reading now many times in nature genetics that a few newly found SNPs explain about half of the attributable risk by genes while I fear that this probably mixes up different epidemiological concepts.
The population attributable risk is usually defined as the reduction in incidence that would be observed if the population were entirely unexposed. This cannot be meant as I don’t know of any genetic study examining incidence so far. Continue reading 50% of all disease genes found, really?
A recent article on WPA hacking using the Amzon EC2 cloud computing facility let me wonder whether there couldn’t be more useful projects. For example gene-gene interaction testing would be nice – indeed somebody has already setup a possibility to use R: Robert Grossman, director at the Informatics at the Institute for Genomics and Systems Biology. Great, many thanks!
What’s even better, a
… 60 Genomes dataset can be found here, as part of the public data that Bionimbus makes available to researchers. With the Bionimbus Community Cloud, the data is available via both the commodity Internet, as well as via high performance research networks, such as the National LambdaRail and Internet2 … If you are a member of the Bionimbus Community Cloud, then you don’t need to download the data but can compute over the data directly with Bionimbus. Currently, we are not making the Bionimbus Cloud generally available, but expect to do so beginning in approximately June, 2011.
A new study in the AJRCCM shows that eosinophils are dispensable for allergic remodeling and immunity Continue reading I am confused but on a higher level
Some fascinating new paper at PLoS ONE
Placebo treatment can significantly influence subjective symptoms. However, it is widely believed that response to placebo requires concealment or deception […] Placebos administered without deception may be an effective treatment for [irritable bowel symptoms]
I have no idea, how this is working…
I have just subscribed to the junkchart RSS feed that I found during the preparation of my forthcoming talk about data visualization. Well, and here is another spin-off – a picture how wordle sees this blog’ front page
The new connectome website has some unusual (artistic) brain pictures that look so much “outward bound”. Although the neuronal direction is well-known for decades, the pictures there are so impressive that I moving that blog entry even in the Science + Theology section, yea, yea.
I need live circos plotting for an upcoming seminar next year.
After installing the most recent xcode, a new macports and a fresh GD library, I issued on the command prompt
sudo port selfupdate
sudo port install gd2
which perl
sudo perl -MCPAN -e shell
cpan> install MD5
cpan> install YAML
cpan> install CPAN
cpan> reload cpan
cpan> install Clone
cpan> install GD
cpan> install GD::Polyline Continue reading OSX 10.6, Macports, GD and finally Circos
It seems that I am not alone here to think that the hygiene hypothesis has thrown back allergy research for 20 years – despite the desperate attempts of journalists and scientists. Here is an an excerpt of Hygiene hypothesis: wanted—dead or alive
When it comes down to all, the best evidence to prove or dispute the hygiene hypothesis will probably come from ongoing and future randomized trials of interventions, e.g. treatment with probiotics and microbial products, that have been developed in the light of the hygiene hypothesis. In the mean time, we must prepare ourselves to face the results of these trials as well as of other types of evidence. It is a possibility that it may turn out that the hygiene hypothesis is more dead than alive, or at the least needs another revision.
We just published the largest study so far of human serum cytokines providing for the first time reference values.
In this study we investigated serum samples from 944 individuals of 218 asthma-affected families by a multiplex, microsphere based system detecting at high sensitivity eleven asthma associated mediators: eotaxin (CCL11), granulocyte macrophage stimulating factor (GM-CSF), interferon gamma (IFNγ), interleukin-4 (IL-4), IL-5, IL-8, IL-10, IL-12 (p40), IL-13, IL-17 and tumor necrosis factor alpha (TNFα). Continue reading The largest study so far on serum cytokines
I always thought that all the interest in epidemiology & biobanking is a rather new development.
But that needs some correction as I just heard about the Virchow study of 1874 at planet-wissen. Continue reading Virchow Study 1874
During a correspondence with a colleague about the validity of genotyping rare variants I became aware of a paper in Science that I missed initially. It is about genetic signatures in longevity:
Using these data, we built a genetic model that includes 150 single-nucleotide polymorphisms (SNPs) and found that it could predict EL with 77% accuracy in an independent set of centenarians and controls.
That’s an extremely difficult enterprise given our recent results of the heritability of life span. But that’s not the point, reading now the editorial expression of concern by Bruce Alberts.
In their study, Sebastiani et al. used a number of different genotyping platforms and neglected to perform data quality-control steps, which resulted in their reporting several false-positive single-nucleotide polymorphism (SNP) associations. In particular, one of the platforms used in their work, the Illumina 610-Quad array, has been shown in unpublished studies by other investigators to produce artifactual genotype data at a subset of SNPs.
No idea, what’s bad with the Illumina Continue reading What’s wrong with these genotypes?
I have made several attempts here to estimate the number of somatic mutations: 3,93 mutations / Mb(2007), the long fuse (2007), about the cancer the legacy (2010) or 1/day in the life of a mutation (2010) but the best summary now comes from the 1000 genomes
From the two trios, we directly estimate the rate of de novo germline base substitution mutations to be approximately 10^-8 per base pair per generation.
along with the fact that
on average, each person is found to carry approximately 250 to 300 loss-of-function variants in annotated genes and 50 to 100 variants previously implicated in inherited disorders.
which raises some doubts that these 50 to 100 have only been implicated but not proven…