Following a frequent request, here is a short video how to create your own Pubmed news feed. You simply need the Sage plugin for Firefox; then goto to Pubmed, create your personal RSS feed and import this URL into the bookmark category that Sage is looking for. Here is the show: Continue reading Any new paper? A video cast how to stay informed
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Detecting repoxygen infection
Doping rules are sometimes hard to understand. Sleeping in a low pressure chamber and training at high altitudes is allowed but taking epo is not – although net effects may be the same.
This might be a reason why some athletes are now trying to mimick more closely biology. Repoxygen is a viral vector known for some time that includes the human epo gene under control of a hypoxia control element. Clearly this drug has the potential to be used for doping (“Outlaw DNA“). Continue reading Detecting repoxygen infection
RNA genes – dark matter of human biology?
I currently hunting some transcripts of unknown function (see below), possibly a RNA gene? while it is difficult to locate any good annotation server. So far I tried RNAz based on a PNAS 2005 paper – another one was RNA Genie. Next step will be the new Gingeras paper that describes even a new class of RNA genes. Finally this may not even be a RNA at all but an alternative leading exon … Continue reading RNA genes – dark matter of human biology?
Question of the year in genetics
Nature genetics asked about 30 eminent scientists “What would you do if it became possibe to sequence the human genome for only $1,000?”. Unfortunately, this initiative has been launched 4 weeks too early as I believe some may have responded differentially if they could have a chance to read the ENCODE papers… The majority of scientists seems to follow the idea of Continue reading Question of the year in genetics
The world needs only five computers
The history of this quote is difficult to trace. cnet believes it is wrong to attribute it to IBM Chairman Thomas J. Watson. Continue reading The world needs only five computers
spickmich & meinprof
spickmich.de (for high school) and meinprof.de (for universities) are two large German portal sites that allow a rating of teachers and university professors.
Finally, now several German courts decided that online voting is legal – I wouldn´t believe that 20 years ago but think it will improve teacher student relationship if done in a responsible way.
Galaxy – a must have
Manipulating large SNP datasets has always been a hassle, a lot of cut & paste, quick & dirty database resorts and no documentation after all. Only by the last week, I learned form the ENCODE papers that there is now a web service that helps with all kind of these tasks. Check out Galaxy — a “must have”.
Design flaws plus delivery flaws equal faux conclusions
— the title of a letter in the most recent Journal of Allergy and Clinical Immunology. So there is no need to comment further studies in the same issue. Continue reading Design flaws plus delivery flaws equal faux conclusions
Food for thought
“Wer einmal aus dem Blechnapf frißt” (Fallada) – following my linux box post yesterday here is my lunch box for today. I think it is as good as the Japanese BentÅ box, isn´t it?
My linux box
When starting again analysis of pooled DNA samples – this time on the Affymetrix platform – I discovered not only the much improved “Genotyping Console” but also that my earlier Genepool binaries do not work anymore under VMWARE/Ubuntu. I therefore tried Continue reading My linux box
New DNA sequencing technologies
New DNA sequencing technologies & human genome variation, San Diego, HGVS Meeting (ASHG satellite). From the program
On the road to the € 1,000 human genome sequence, DNA sequencing technology is currently developing at an incredible speed. Although we are still far from the ultimate goal, DNA sequencing cost has already dropped close to the range of € 1,000 per 1 million nucleotides. These developments have tremendous consequences for the number of DNA variants that we will discover, both pathogenic and harmless. To get an up-to-date overview of the technologies behind this revolution, the HGVS has selected DNA sequencing technologies as this year’s special topic for its annual meeting. Speakers from the major players in the field have been invited to explain in detail the different technologies, their strong and weak points and to show some first innovative applications and results using the new sequencing power.
News about vitamin D’ficiency
“Normal vitamin D status despite of abundant sun exposure” would have been my title for a study in the JCEM this month. The authors, however, have choosen a different title: Continue reading News about vitamin D’ficiency
QQ plot
Do you wonder what QQ means? These are quantile – quantile plots that rank observed test statistics against expected test statistics. They allow a visual inspection of overdispersion due to population substructure or other sources of biases.
QQ plots have been recommended earlier, are now frequently used and available in the snpMatrix R package. Yea, yea.
Protected: ORMDL3 – what?
Can we meet on next Tuesday at 2 pm?
Answering this question always takes me 30 seconds – looking for my mobile and doing some pen strokes OR starting Outlook on the laptop and clicking to the desired week (BTW Sunbird is still in version 0.5). Finally I found a solution that gives me a chance for a response within 3 seconds. Continue reading Can we meet on next Tuesday at 2 pm?