Charles Plessy @charles_plessy@mastodon.technology

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.

I am looking for a simple template system for producing #HTML or #Markdown pages using input data serialised in simple tab-separated, #YAML files, or anything else that can be simply edited by non-programmers. The conversion would run through a git hook. Any suggestion ?

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 #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).

http://www.sciencescope.org/jfr-2018-journee-francophone-de-la-recherche-2018/

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?

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