I helped write a blog post explaining how Artsy hires engineers: artsy.github.io/blog/2019/01/2

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 to analyse gene expression () of single cells on the platform is finally published in Nature Communications (nature.com/articles/s41467-018). 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 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 has only two pairs, A:T and C:G. This is another big breakthrough in biology Published this month in . doi.org/10.1038/s41586-018-080

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 thanks to the new plyrange package! See the paper of Lee, Cook and Lawrence (Genome Biology, 2019) for details. genomebiology.biomedcentral.co

Press implements a Data Availability section in its articles. In addition to ease access for the reader, it also helps the publisher to make the information machine-readable behind the scenes. msb.embopress.org/content/14/1

Just found statcheck.io/, that will scan a PDF, DOCX or HTML-formatted document and tell if there are errors in the 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.org) or (woleet.io) for that purpose.

TSS and RNA-seq data in a single experiment. Show more

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


Cats use hollow papillae to wick saliva into fur. Alexis C. Noel and David L. Hu. PNAS December 4, 2018 115 (49) 12377-12382 doi.org/10.1073/pnas.180954411

In , 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: en.wikipedia.org/wiki/False_po

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. bioconductor.org/packages/3.8/

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

A new cap structure published by Munir, Banerjee and Shuman (Sloan-Kettering Institute, New York) in (academic.oup.com/nar/article/4). 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

First use of the technique in 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, linkinghub.elsevier.com/retrie

Journée Francophone de la Recherche à 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 event.

With all due respect for the contribution of to , I would like to stop using "et al." in . (en.wikipedia.org/wiki/List_of_). 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

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