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Charles Plessy

Adiconis and co. published an analysis in Nature Methods showing that CAGE is the best method for 5'-end RNA-. It is a nice benchmark with overall a strong design.

Our method was also tested and performed poorly in the hands of the authors. However, they used 7.5 μg of total as starting material, which is totally out of the range that we designed nanoCAGE for. Therefore, I have posted a response on explaining that fact.

When BLT is about beads and transposases and not bacon and tomatoes Show more

Needing a new laptop at work that can run Office, I was tempted to try again after more than a decade on OSX, because I am quite curious about the windows for Linux. Unfortunately, the laptop that I wanted to buy was only available in Japanese, and despite we are in 2018 it seems that MS still sells "single-language pack" systems were English can not be installed. Thus, I am going for a Mac instead. And of course running on my main desktop. Sorry MS, you must do better!

Poster flash talks in conferences: nice idea, but it takes precious time, so I was unsure if it was worth doing it, but recently I realised that it is an excellent opportunity to show videos, which obviously can not be on the posters (at least for the moment...).

Ranting on about authors who did not seem to check that their introduction was still up to date before submitting their paper:

High-throughput homologous recombination mutagenesis in yeast with libraries of plasmids providing the DNA template for recombination and expressing a guide RNA for inducing the recombination with a CRISPR-Cas9 break: 3 papers in last week's issue of Nature Biotechnology.

This year's application call for faculty positions at (Okinawa Institute of Science and Technology) is out ! Deadline: August 31st.

Transparency on scientific instruments Show more

"Preproducibility", a new word to foster reproducible research. Show more

With long-lasting human biological materials, such as stem cells, initial donor is necessary but not sufficient, write Boers & Bredenoord in Nature Cell Biology.

The authors underline that donors need to be informed about the future governance of the biomedical projects to which they contribute. This in line with the initiative to create a code of for health research in the wake of EU's General Data Protection Regulation (). code-of-conduct-for-health-res

Now I am fully convinced that the 5′ #RNA cap is reverse-transcribed. Show more

I will be moving to (Okinawa Institute of Science and Technology) on August 1st, to join the Luscombe laboratory (Genomics and Regulatory Systems Unit). Expect more posts on marine creatures, although my core activities will still revolve around nucleic acids, genetic programs and free software.

The article also states: "Use of a software product incorporating such open source license requirements in a medical device may increase the risk that the medical device is disapproved by regulatory bodies due to being tamper-prone or otherwise unsafe."

Is that or did that happen at least once in the past ?

Bio-IT World published an article entitled "Open Source Pitfalls At The Biotechnology-High Technology Crossover" by Paul Liu (May 14, 2018)

In very brief, it reminds to people new to the field that open source softwares have licenses that vary in what they permit, and that one needs to be careful when combining software with different licenses. Key recommendations: monitoring, documentation, anticipation.

Major update of the CAGEr package for bioinformatics analysis of transcription start sites. Show more

Just registered to the European Research Night organised by and in on May 24.

The theme is "Open Science's Impact on Research Careers".

"Re-elected as Debian Project Leader", by Chris Lamb

Interesting... when replying to content-warning (CW) posts, the CW is sticky and has to be removed manually.

#Nanopore #protein #sequencing comes closer! Show more