Charles Plessy @charles_plessy@mastodon.technology

Freezing cells using #inkjet printing to encapsulate them in #microdroplets, which are then deposited on a glass slide cooled by liquid nitrogen: a recent article in #PNAS by Akiyama, …, and Kanda: “Cryoprotectant-free cryopreservation of mammalian cells by superflash freezing”, PNAS April 16, 2019 116 (16) 7738-7743; first published April 1, 2019 https://doi.org/10.1073/pnas.1808645116

Attending next week the BDR symposium 2019: “Control and Design of #Biosystems”, hosted by #RIKEN in #Kobe, #Japan. https://www2.bdr.riken.jp/sympo/2019/index.html

#OIST praised for its multidisciplinarity in #Nature Index Japan 2019: https://www.nature.com/articles/d41586-019-00830-6

Astonished by the speed and quality of the #dnafriend #DNA testing company. They really made my day. The only thing they are clearly doing wrong is to be on Twitter instead of Mastodon.

https://dnafriend.com/

More seriously, just make sure to use a disposable email address, etc., just in case, as their privacy policy mentions the possibility of collecting this data.

To everybody who writes a #CV: please to not use #antispam tricks in your #email address; this is the best way to lose opportunities.

"Beyond disciplines", a report of the Japanese Science and Technology agency (JST)'s Center for Research and Development Strategy has just been translated in English. It outlines 12 #transdisciplinary #research themes, and is an important tool to understand #Japan's scientific directions. https://www.jst.go.jp/crds/en/publications/CRDS-FY2018-RR-02_EN.html

The first #EMBO workshop in #Tokyo will be about #singlecell #biology and organised by my former colleagues from #RIKEN. 20 – 22 May 2019. More details at http://meetings.embo.org/event/19-single-cell-biology

Our manuscript describing the "C1 CAGE" method that we developed at #RIKEN to analyse gene expression (#transcriptome) of single cells on the #Fluidigm platform is finally published in Nature Communications (https://www.nature.com/articles/s41467-018-08126-5). The protocol itself has been already available for a couple of years directly on Fluidigm's website. Another method, not visible from the title, is also published in our manuscript: "color multiplexing" of single cells using live stains.

In “Programmable design of orthogonal #protein heterodimers”, Chen, ..., and Baker (University of Washington and others) have calculated and produced entirely artificial protein domains that make exclusive (”orthogonal”) pairs. In comparison, our #DNA has only two pairs, A:T and C:G. This is another big breakthrough in #synthetic biology Published this month in #Nature. https://doi.org/10.1038/s41586-018-0802-y

I am very excited to see the R's %>% pipe operator becoming first class in #Bioconductor thanks to the new plyrange package! See the paper of Lee, Cook and Lawrence (Genome Biology, 2019) for details. https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1597-8

#EMBO Press implements a Data Availability section in its #research articles. In addition to ease #data access for the reader, it also helps the publisher to make the information machine-readable behind the scenes. http://msb.embopress.org/content/14/12/e8783

Just found http://statcheck.io/, that will scan a PDF, DOCX or HTML-formatted document and tell if there are errors in the #statistics reported.

Sometimes I do not want to overwhelm or unfocus colleagues or collaborators with too many draft ideas at a time, but 15 years of professional experience have taught me that, in rare occasions, it is important to have a proof that I had a given idea independently, before somebody expressed it in a meeting. Thanks to the suggestion of our IT section, I am now exploring the use of #OpenTimestamps (https://opentimestamps.org) or #Woleet (https://woleet.io) for that purpose.

In the “nanoPARE” method for #transcriptome analysis, published in Genome Research by Schon & coll, (Gregor Mendel Institute, Austria), cDNAs get 5′ linkers by template-switching, and are then amplified in one library for 5′ ends and one for RNA-seq. As in similar methods, ~15% of the 5′ ends have extra Gs, which the authors use to mark transcription start sites (#TSS). Non-TSS peaks feature cleavage sites used for #miRNA analysis. https://doi.org/10.1101/gr.239202.118

A 3D-printed #cat tongue mimic and many other things published in #PNAS by researchers from the #Georgia Institute of Technology.

http://movie-usa.glencoesoftware.com/video/10.1073/pnas.1809544115/video-4

Cats use hollow papillae to wick saliva into fur. Alexis C. Noel and David L. Hu. PNAS December 4, 2018 115 (49) 12377-12382 https://doi.org/10.1073/pnas.1809544115

In #statistics #jargon, I always struggle to remember which is which between "type I" and "type II" errors (a.k.a. "alpha level" and "beta level"), because these names are so arbitrary. But I never fail to grasp the difference between "false positive" and "false negative", for the obvious reason that these terms are self-explanatory.

Wikipedia has a few words explaining why there is a difference between "type I error" and "false positive" despite being mathematically equal: https://en.wikipedia.org/wiki/False_positive_rate#Difference_from_%22type_I_error_rate%22_and_other_close_terms

#Bioconductor 3.8 was released today! Within it, the update of the CAGEr package (to analyse activity of gene promoters) brings a few bug fixes and new syntactic possibilities in the plotAnnot() function, using formula to express combinations of metadata. https://bioconductor.org/packages/3.8/bioc/html/CAGEr.html

Playing with yst (https://github.com/jgm/yst) for convertint #YAML to #Markdown.