Microbiome Bioinformatics Postdoctoral Scientist, Colorado State University

The Metcalf lab at Colorado State University is seeking a microbiome bioinformatics postdoctoral scientist. The scientist will analyze multi-omics data sets, including but not limited to: amplicon sequencing data, shotgun metagenomics data, and metabolomics data. Min. reqs. include: Ph.D. in bioinformatics, ecology, microbiology or similar field. Proficient in coding languages (Python preferred). Demonstrated knowledge of …

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 …

New tool of interest: GraftM: “a tool for scalable, phylogenetically informed classification of genes within metagenomes”

This could be of use to many people: Source: GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes | Nucleic Acids Research | Oxford Academic Large-scale metagenomic datasets enable the recovery of hundreds of population genomes from environmental samples. However, these genomes do not typically represent the full diversity of complex microbial …

An informative glimpse into the drug factory microbiome: Which bugs coexist with our drugs? The story behind the paper

The story behind: Toward the Drug Factory Microbiome: Microbial Community Variations in Antibiotic-Producing Clean Rooms (OMICS. 2018 Feb;22(2):133-144. doi: 10.1089/omi.2017.0091.) PMID: 28873001 [Preprint] It was in 2013, on my return to Cairo University after a couple of years as a visiting scientist at UCSD, that I met Amal for the first time. Amal was a fresh master’s …

Paper of possible interest: KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples

This may be of interest to people out there.  Source: KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples | mSystems Abstract: Microbiome analyses of low-biomass samples are challenging because of contamination and inefficiencies, leading many investigators to employ low-throughput methods with minimal controls. We developed a new automated protocol, KatharoSeq (from the Greek katharos [clean]), …

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 …