Category Archives: Genetics

Genetics

PDF rename based on Zotero entry

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Here is a tool that will automatically rename the most recently downloaded PDF with the most recently entered Zotero entry. You may call it directly from the browser by setting a link in the toolbar to file:///c:/system/test.000 while setting the file association for 000 in the Content tab to the location of ZoteroRename.exe.

ZoteroRename.zip includes the source perl script including a compiled windows version.
|wj_ZoteroRename.txt|

 

CC-BY-NC Science Surf accessed 21.12.2025
Genetics

Don’t ask for salary

Here is what the University of Cologne published recently

An der Medizinischen Fakultät der Universität zu Köln ist unter den Voraussetzungen des § 36 des Hochschulfreiheitsgesetzes des Landes Nordrhein-Westfalen baldmöglichst eine W 2-Professur für Theorie und Ethik des Gesundheitsmanagements zu besetzen. Die Bewerbung setzt voraus, dass sich die Bewerberin / der Bewerber gleichzeitig bei der DFG um eine Heisenberg-Professur bewirbt. Die Berufung erfolgt dann vorbehaltlich der Bewilligung der Heisenberg-Professur nach den Richtlinien der Deutschen Forschungsgemeinschaft. Eine Zwischenevaluierung nach drei Jahren ist vorgesehen und entscheidend für die Üernahme in den Etat der Hochschule nach fünf Jahren.

It says that can try to get a salary from the German Science Association which will be honored in turn by a position at the medical faculty. When writing this post I did a typing error, writing slavery instead of salary, yea, yea.

 

CC-BY-NC Science Surf accessed 21.12.2025
Genetics

Outlook calendar export

It should be quite easy to export Outlook appointments into .ics format and let third party applications like phpicalendar stitch these snippets together into a coherent view. Unfortunately older Outlook versions are not supporting ics export. After several frustrating attempts (installing VB macros that are buggy and software like freemical that misses important fields) I finally wrote my own exporter that includes also a category filter as otherwise too may entries will have to be parsed by phpicalendar.

ol2ics.zip includes the source perl script including a compiled windows version.
|wj_olics.txt|

The ics file may then be uploaded to the phpicalendar directory using a wput call like
wput –reupload my.ics ftp://name:password@domain.de/calendar/my.ics

 

CC-BY-NC Science Surf accessed 21.12.2025
Genetics, Software

Annotation of regulatory sequences is largely insufficient

Of a proven set of regulatory regions in zebrafish, computer programs find only between 29% and 61% of the true motifs. This does not come very much unexpected given the vast array of data shown by the Encode project. It even relates to the most basic question: What is a gene?

The more expert scientists become in molecular genetics, the less easy it is to be sure about what, if anything, a gene actually is.

iwith at least 5772 21U-RNAs? So – if I am sitting on the other side of the table when you are being examined don’t talk about junk DNA anymore, yea, yea.

 

CC-BY-NC Science Surf accessed 21.12.2025
Genetics, Software

Anonymizing genetic data

I have currently a paper under submission at the EJHG that covers ethical issues of genetic testing. One of the key messages is that genetic data are not anonymous if having simply stripped of names.
A story in a completely different field confirms my fears. According to a NYT article

Last October, Netflix, the online movie rental service, announced that it would award $1 million to the first person or team who can devise a system that is 10 percent more accurate than the company’s current system for recommending movies that customers would like.

but things turned worse by an article of Narayanan und Shmatikov Continue reading Anonymizing genetic data →

 

CC-BY-NC Science Surf accessed 21.12.2025
Genetics, Software

Genome explained

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You may want to read the full story at Public Rambling (fiction), the NYT article of Amy Harmon (fact) or the “Peepshow” article of Marco Evers (fact) and come back here afterwards.
The recent advances in genome sequencing (and typing) has left us with an enormous amount of data. Although technology has been available for a couple of years knowledge exploded only recently, where people now may decide to participate in a genome study or even have their genes tested on their own costs at DeCodeMe, 23andme, Navigenics or other personal genome service provider.
The main question is, what do these data really mean for us? Should we start an Open Source Project Genome Explained to collect the necessary annotation rules and provide a platform to apply these rules to local data? The data mode may be quite simple: Continue reading Genome explained →

 

CC-BY-NC Science Surf accessed 21.12.2025
Allergy, Genetics

Best allergy paper 2007

The end of the year 2007 is approaching very fast. I can already vote for the best allergy paper in 2007 – it is a paper from Vienna by Victoria Leb about the molecular and functional analysis of the Ambrosia antigen T cell receptor. They have been able to isolate and transfer alpha (TRAV17-TRAJ45) and beta chain (TRBV18,TRBD1 and TRBJ2-7) TCR chains into Jurkat cells and even other human blood lymphocytes with convicing evidence that the infected cells were Ambrosia Art V1 reactive.
This opens brand new perspectives for developing a truely allergic TCR transgenic mouse that can be easily challenged and desensitized. It may even allow immediate testing of a variety of substance (and constructs) to ultimately cure allergy. My favorite is to feed DCs with antigen coupled to a T cell suicide program on succesfull antigen presentation.

 

CC-BY-NC Science Surf accessed 21.12.2025
Genetics

How to get closer to the target

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Attending last week another Illumina sequencer course, I still have the question how to enrich the target sequence. A colleague calling me this morning (thanks TB!) had a pointer to a new nature methods editorial covering three different methods- a 100-mer capture probe for each exon sized segment with the need of extremely deep resequencing and two other methods using direct hybridization of segments onto commercially oligo arrays. Aren´t there any other protocols?

 

CC-BY-NC Science Surf accessed 21.12.2025