Speed fluctuations of bacterial replisomes. I am co-author in this preprint. In this work, three units joined their forces to produce experimental data of abundance in exponentially growing Escherichia coli, and to formulate a that permits to infer the of replisomes from the DNA abundance distribution. Big congratulations to my colleagues Deepak and Simone who lead that work.

Just gave a presentation on R packaging this morning in a mini-course at . Our slides are here: github.com/Rafael-Ayala/R-pack

RTF-EXPAR: Isothermal and exponential detection of the SARS-CoV-2 RNA under 10 minutes. 

In today, an article from the University of , using the BstNI enzyme to nick a oligonucleotide annealed to the of the SARS-CoV-2 (causing ) produce the trigger for detection under 10 min with an exponential amplification system called . pnas.org/content/118/35/e21003

Call for applications for the Interdisciplinary Postdoctoral Scholar Fellowship Program at OIST. 

The Scholar (IPSF) program provides a unique opportunity to advance researchers' academic careers by conducting full-time research and training at the Institute for and (). Follow this link to apply: apply.interfolio.com/75577

Co-first, equal authorship is great ! 

Scientists are being judged – and too much – on their publication list, and on their contribution to these publications. Often, there is more than one person who was essential to the work.

I disagree with the negative image given to co-first authorship in this career feature article in the Nature journal. Co-first authorship is a win, not a loss. Employers who consider shared authorship as lessening someone's contribution are wrong. nature.com/articles/d41586-021

positions open in " Information Science and ", " ", "Molecular and " and other areas at , the Institute of and Graduate University. Application deadline: April 30th. groups.oist.jp/facultyposition

Great to read advocacy the command-line in the scientific journal . By the way,

awk -F, '{ if ($4 > 50) print $0 }'

can be shortened to

awk -F, '$4 > 50''

Link to the article: nature.com/articles/d41586-021

“Guidance on software citation created by the community for the community”, a blog post about the work of the Implementation Working Group.


4-figures pre-prints show the ambition of their authors but their most important information in in the “supplemental” material.

I was reading about "hardware-agnostic" code in a research article. According to Wiktionary, "agnostic" comes from Greek and stands for "ignorant". But Wiktionary also tells us that "ignorant" comes from Latin (via French) and means "unknowing". If we would replace words from our such as "agnostic" with simpler words like "unknowing", would it make more accessible to all? I do not know.

The N704/S507 index pair considered harmful on MiSeq seqeuencers. 

Good catch from Hirose and colleagues, published in the journal "DNA research" this year. This particular combination of indexes might have partial self-complementarity that would be detrimental to cluster generation on DNA sequencers. academic.oup.com/dnaresearch/a

Our work on analysing the activity the of human papillomavirus () in patient samples using quantitative cDNA sequencing was finally published ! Our “” method focuses on the start (5′) sequences of the molecules to precisely locate the DNA regions that are active during HPV infection. It also easily discriminates between different HPV variants, allowing us to study co-infections. doi.org/10.1038/s41598-020-751

Relatives of rubella virus [found] in diverse mammals. 

Importantly, part of this discovery started as an effort to study in before the 2019 pandemic started. The other part of the discovery was made by studying sick animals in a . Published recently in Nature (doi.org/10.1038/s41586-020-281).

Biosynthesis of medicinal tropane alkaloids in yeast 

Some essential medicines still can only be extracted natural plants. This causes problems of supply chain and industrial . Srinivasan and Smolke, from Stanford University, published last month in Nature an engineered with no less than 34 modifications, that achieves the of hyoscyamine and scopolamine. They estimate that “sourcing sugar from sugarcane would require at least 10-fold less land”. nature.com/articles/s41586-020

We finished to assemble the of the local population of the dioica near on the island. We used sequencers and it allowed to assemble whole chromosomes into single contigs. Our preprint is available in : biorxiv.org/content/10.1101/20 Our results open the way to interesting comparisons with related populations, to better understand species in the .

Show older
Mastodon for Tech Folks

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!