Thinking about microbial quantity and function

One of the hurdles in linking microbial ecology with building science has been incorporating quantitative information about the microorganisms encountered in indoor environments, mainly because the standard high-throughput amplicon approach for community analysis is semi-quantitative, at best. Over the summer, there was a Twitter conversation related to this topic. My take-away from this (what I view …

Call for Proposals: 2019 FICUS JGI-NERSC-KBase Biological Data Science

Of potential interest: Source: FICUS JGI-NERSC-KBase – DOE Joint Genome Institute I am copying some of the announcement below: The Biological Data Science call will enable users to perform state-of-the-art computational research to explore the wealth of genomic and metagenomic data generated worldwide and translate sequence information into biological discovery. Users will have access to …

Paper of interest: Predicting antibiotic resistance from full genome sequences 

This preprint seems like it may be of interest to folks: Precise prediction of antibiotic resistance in Escherichia coli from full genome sequences | bioRxiv Basically, the authors showed that, using a machine learning approach, they can quite accurately predict antibiotic resistance in E. coli from whole genome data. The emergence of microbial antibiotic resistance …

A microbial sequencing discussion course built around a paper and a blog post

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 …

Postdoc Opportunity for Computational Microbial Ecologist in Seattle

  The Gibbons group at the Institute for Systems Biology (ISB) is seeking a computationally-oriented Postdoctoral Fellow with interests in microbial ecology, evolution, and human health. The successful applicant will work with an interdisciplinary team of microbiologists, systems biologists, bioinformaticians, and clinical researchers to:  Integrate and analyze multi-omic data from Arivale as part of the …

Help wanted: looking for a recent (post 2012) #openaccess review on molecular phylogenetic methods

I am getting ready for my “EVE161” class on Sequence based studies of the diversity of microbes.  For more about past versions of the class see here: https://www.microbe.net/eve161/. Anyway – I am working on the reading for the class and I am looking for a good, recent, open access review of molecular phylogenetic methods.  Any recommendations …