BE microbiome as biosensors

  Hi MoBE blog, I just wanted to share a piece that I recently wrote for a Special Issue on the journal Microbial Biotechnology. The Special issue presents a collection articles about “The contribution of microbial biotechnology to sustainable development goals”, and the title of my article is “Microbial communities as biosensors for monitoring urban …

Worth a look: new paper on “The application of project-based learning in bioinformatics training”

  This new paper in PLOS Computational. Biology may be of interest: : The application of project-based learning in bioinformatics training by Emery LR and Morgan SL. Although many out there may already be doing projects based learning for bioinformatics, many others are not.  This paper discusses how the authors added a projects component to an existing course …

New standards recommendations on minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

Of possible interest – a new paper (on which I am a coauthor) on standards for minimum information about single cell genomes and genomes assembled from metagenomes.  See link below: Source: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea : Nature Biotechnology : Nature Research  

Full-length #16S rRNA #nanopore sequencing of dog #skin microbiota

We are a research group working on Genetics in a Vet School and closely collaborating with veterinary clinicians and dermatologists. We moved from specific pathogens, such as Leishmania, to specific commensals such as Demodex… and finally ended studying the whole: the skin microbiota on healthy dogs. Vets are always wondering why there are differences among …

Everyone should read this piece by Ed Yong: Norm Pace Blew The Door Off The Microbial World

There is a wonderful tribute to Norm Pace in the Atlantic by Ed Yong. Norm Pace truly did blow the door off the microbial world. Source: Norm Pace Blew The Door Off The Microbial World – The Atlantic Lots of good stuff in there about Pace and his career.  See for example this: Pace also …

Could be interesting: The Metagenomics MVP Challenge v1.0

Source: NIST Challenge — CosmosID – Exploring the Universe of Microbes This could be interesting.  NIST & COSMOS ID and ABRF are conducting a metagenomic sequencing methods challenge. From their site: When using metagenomic methods to assess the content of a complex microbial sample, there are many steps in the measurement process where bias might …

WTH is ILR?

WTH is ILR? by Alex Washburne & Jamie Morton Jamie and I have penned a popularization of the isometric log-ratio transform with the intention to allow non-mathematicians to understand the intuition behind what it is, why we use it, and how different methods use the same tool in different ways. The full write-up is available …