positions open in " Information Science and ", " ", "Molecular and " and other areas at , the Institute of and Graduate University. Application deadline: April 30th. groups.oist.jp/facultyposition

Great to read advocacy the command-line in the scientific journal . By the way,

awk -F, '{ if ($4 > 50) print $0 }'

can be shortened to

awk -F, '$4 > 50''

Link to the article: nature.com/articles/d41586-021

“Guidance on software citation created by the community for the community”, a blog post about the work of the Implementation Working Group.


4-figures pre-prints show the ambition of their authors but their most important information in in the “supplemental” material.

I was reading about "hardware-agnostic" code in a research article. According to Wiktionary, "agnostic" comes from Greek and stands for "ignorant". But Wiktionary also tells us that "ignorant" comes from Latin (via French) and means "unknowing". If we would replace words from our such as "agnostic" with simpler words like "unknowing", would it make more accessible to all? I do not know.

The N704/S507 index pair considered harmful on MiSeq seqeuencers. 

Good catch from Hirose and colleagues, published in the journal "DNA research" this year. This particular combination of indexes might have partial self-complementarity that would be detrimental to cluster generation on DNA sequencers. academic.oup.com/dnaresearch/a

Our work on analysing the activity the of human papillomavirus () in patient samples using quantitative cDNA sequencing was finally published ! Our “” method focuses on the start (5′) sequences of the molecules to precisely locate the DNA regions that are active during HPV infection. It also easily discriminates between different HPV variants, allowing us to study co-infections. doi.org/10.1038/s41598-020-751

Relatives of rubella virus [found] in diverse mammals. 

Importantly, part of this discovery started as an effort to study in before the 2019 pandemic started. The other part of the discovery was made by studying sick animals in a . Published recently in Nature (doi.org/10.1038/s41586-020-281).

Biosynthesis of medicinal tropane alkaloids in yeast 

Some essential medicines still can only be extracted natural plants. This causes problems of supply chain and industrial . Srinivasan and Smolke, from Stanford University, published last month in Nature an engineered with no less than 34 modifications, that achieves the of hyoscyamine and scopolamine. They estimate that “sourcing sugar from sugarcane would require at least 10-fold less land”. nature.com/articles/s41586-020

We finished to assemble the of the local population of the dioica near on the island. We used sequencers and it allowed to assemble whole chromosomes into single contigs. Our preprint is available in : biorxiv.org/content/10.1101/20 Our results open the way to interesting comparisons with related populations, to better understand species in the .

20 years after reading the famous "Maniatis" book on molecular cloning, I read an actual article from him for the first time. 

The article demonstrates trans-splicing of nematode and trypanosome splice leaders in mammalian cells. (doi.org/10.1038/360692a0). "Trans-splicing" is the molecular basis for the gene structure in eukaryotic cells.

Receiving archives from your favourite funding agency with filenames encoded in Shift_JIS? Thanks to "Ask Ubuntu" I found out that "The Unarchiver" theunarchiver.com/ can convert them on the fly. askubuntu.com/questions/935022

Centromere-specific antibody-mediated karyotyping of Okinawan Oikopleura dioica suggests the presence of three chromosomes. 

Our latest work is now available before peer-review on . is the animal that we are studying at . Its is tiny and therefore its chromosomes are difficult to visualise. For that reason, we needed to make these experiments to confirm their number.

The Okinawa Institute of Science and Technology Graduate University hires to fight #COVID and develop #DNA sequencing technologies ! 

's DNA section hires one Testing and Sequencing Specialist and one R&D and Sequencing Specialist. is a very nice place to live, and has been relatively safe from covid with no cases for a month. And OISTs facilities are, in one word, fantastic.



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