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
#OIST praised for its multidisciplinarity in #Nature Index Japan 2019: https://www.nature.com/articles/d41586-019-00830-6
"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
I helped write a blog post explaining how Artsy hires engineers: http://artsy.github.io/blog/2019/01/23/artsy-engineering-hiring/
Engineering hiring is really broken, generally, and while our approach isn't perfect for every team, it's a source of strength for us.
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
GitHub is now offering unlimited private repos for the "free" tier, s/th to keep in mind. My previously "academic" tier has apparenly been converted to "Pro".
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
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.
TSS and RNA-seq data in a single experiment. Show more
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
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
Researcher at OIST, Okinawa, Japan — Debian Developer. My private account is @charles_plessy on framapiaf.org.
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