So – just a quick post for now. More details to come. But I wanted to get a little bit about this out there. For a few years I have been teaching a mid-level course at UC Davis on “DNA sequencing based studies of microbial diversity’. The course has evolved over the years from a …
Just got an email pointing me to this White Paper on Figshare …… Seems like a worthy ambition and worth a look. Some key bits: Vision The rapid pace of scientific advancement presents a continuing challenge to effective life science education. The genomics revolution brings with it a unique challenge for the biology educator, as …
Just a quick post here about an upcoming anvi’o workshop at the Joint Genome Institute (JGI). While I’ve never used anvi’o myself, I know that people rave about it and the visualizations it produces look really cool. It can be used with metagenomic, genomic, and transcriptomic data. Information below copied from the workshop website. …
Why use Bracken instead of Kraken? by Jennifer Lu and Steven Salzberg Kraken is a very fast, accurate program for classifying metagenomic sequencing data. It takes a set of reads, contigs, or other DNA sequences and for assigns a taxonomic label (species, genus, etc.) to each one. Last year we discovered that some people were …
There is a whole issue of the Annals of the NY Academy of Sciences that may be of interest. The focus of the issue is on Antimicrobial Therapeutics Reviews. Some of the papers are freely available. These are Resistance diagnosis and the changing epidemiology of antibiotic resistance(pages 5–17) by David McAdams Resistance diagnosis and the changing …
Just got back from the Pacific Symposium in Biocomputing. The meeting had some aspects that may be of interest to various folks. Electronic proceedings of the meeting are here. I talked in a session on functional predictions. I was asked to do this at the last minute so I made my slides by hand. Here …
In January 2014 I wrote this post about “microbiome” sequencing services. I have gotten many outside requests for the following information — what places (companies, Universities, government agencies, etc) provide contract services for rRNA PCR and sequencing? Source: Request — Information on Places that do rRNA sequencing as a service — microBEnet: the microbiology of the …
The meeting page for the 21st Annual International Meeting on Microbial Genomes at Lake Arrowhead is now up. This has been one of my favorite meetings for many many years (full disclosure – I am now a co-organizer and have been for the last few meetings). Note – the meeting is NOT just about genomes – it …
This week in eLife, our lab published a study entitled Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis (NEC) development. Spearheaded by a talented Banfield Lab post-doc, Tali Raveh-Sadka, in collaboration with Michael Morowitz’s Lab, the study aimed to find the causative agent in an outbreak of NEC cases that …
Posted a request for help on Twitter but I thought it might be of interest to some other people so am also posting about it here. Basically what we (me and Lizzy Wilbanks in my lab) is to take some microbial genomes and to fully annotate all of the repeat elements and all of the …