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Genetics

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 →

 

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Genetics

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? →

 

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Genetics, Philosophy

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 →

 

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Uncategorized

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.

 

CC-BY-NC Science Surf accessed 10.11.2025
Genetics, Software

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”.

galaxy.png

 

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Uncategorized

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.

 

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Noteworthy

I do not wish to donate organs after death

True or not, there are reports about sale of human organs from prisoners in China (link1, link2) and India (link3). I do not want to be involved in a business where life is being prolonged until multi organ explanation and death being defined by ever changing arbitrary criteria.

I have also a deeply rooted belief about the integrity of the human body – there is natural barrier against organ transplantation both from an immunological and psychological side (cannibalism is a taboo in every human culture). So, I would like to ask doctors in the emergency room to work hard to save my life (as I did also for many years rescuing other lifes).

In case, you want to read more on that topic, please go to an excellent essay in the TAZ. Many other physicians will share my belief, that donation of organs should remain an individual decision.

 

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Genetics, Software

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.
qqplot1.png

 

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Software

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? →

 

CC-BY-NC Science Surf accessed 10.11.2025