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 …

Assistant Professor in Soil Microbiomics

Assistant Professor Position in Soil  Microbiomics with a 75% research, 25% teaching appointment. The Department of Ecosystem Science and Management seeks candidates interested in conducting research to understand the distribution, composition, diversity, and functional impact of microbial communities in soil-plant habitats. We seek individuals with diverse interests in soil microbiomes and in teaching related courses. …

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 …

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 …