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
A new #RNA cap structure published by Munir, Banerjee and Shuman (Sloan-Kettering Institute, New York) in #NAR (https://academic.oup.com/nar/article/46/18/9617/5092737). All is in the title: « NAD+-dependent synthesis of a 5′-phospho-ADP-ribosylated RNA/DNA cap by RNA 2′-phosphotransferase Tpt1 »
The Open Material Transfer Agreement Show more
The Open #MTA was announced in this week's issue of Nature Biotechnology. Its goal is to promote and ease the exchange of research materials under the same spirit as #opensource software. This is one more step towards #openscience. See https://biobricks.org/open-material-transfer-agreement/ and https://www.openplant.org/openmta/
First use of the #CRISPR #Cas9 technique in #Oikopleura dioica, where double-strand breaks induce microdeletions when flanked by microhomology regions, because of the absence of the canonical non-homologous end-joining pathway. Deng, Henriet and Chourrout, 2018, Sars International Centre for Marine Molecular Biology, University of Bergen, Norway, https://linkinghub.elsevier.com/retrieve/pii/S0960-9822(18)31132-1
Journée Francophone de la Recherche à #Tôkyô le 12 décembre 2018. Inscriptions : 1er novembre 2018 (contributions) / 03 décembre 2018 (auditeurs).
The best French-speaking symposium in Japan! Joke apart, it leverages the modest but significant size of our linguistic community to make a truly #multidisciplinary event.
With all due respect for the contribution of #Latin to #science, I would like to stop using "et al." in #bibliography. (https://en.wikipedia.org/wiki/List_of_Latin_phrases_(E)#et_alii). This complicated way to say "and collaborators" is only a small obstacle for newcomers, but why keeping it in our digital age where a few extra characters will not cost precious ink and parchment anymore? I will probably go for "and coll." when not needing to follow an established style, unless there is a better alternative?
Xdrop: targeted sequencing of long DNA molecules from low input samples using droplet sorting. Show more
Article on #bioRxiv by Madsen, ..., and Mikkelsen (Samplix, Denmark). Enrichment by encapsulating #DNA fragments in double-emulsion #droplets, detecting the target by hydrolysis probe PCR, sorting the fluorescent droplets and amplifying their content by isothermal strand-displacement, and finally sequencing. When enriching for #HPV DNA in HeLa genomes, 5 to 10% of the reads were on target. https://doi.org/10.1101/409086
Researcher at OIST, Okinawa, Japan — Debian Developer. My private account is @charles_plessy on framapiaf.org.
This Mastodon instance is for people interested in technology. Discussions aren't limited to technology, because tech folks shouldn't be limited to technology either!
Hosting costs are largely covered by our generous supporters on Patreon – thanks for all the help!