We’d like to first thank Jon for the opportunity to discuss our work in this forum. We recently published a study investigating direct functional annotation of short metagenomic reads that stemmed from protocol development for our lab. Jon invited us to write a blog post on the subject, and we thought it would be a …
We recently submitted a paper to biorxiv on the estimation of average genome size from shotgun metagenomics data and it’s application to the human microbiome (http://biorxiv.org/content/biorxiv/early/2014/09/11/009001.full.pdf). It is currently undergoing peer review. This study was motivated by the troubling observation that many universal single-copy genes appear to vary significantly across metagenomes. How can this be? …
Some interesting things in this post from Kelly Rae Chi at the Scientist: Metagenomics Mash-Up. It includes a discussion of metagenomics generally and then some metagenomic tools including MEGAN5, Kraken, MG-RAST, Metavir, and HI-C. The section on HI-C discusses the work of Chris Beitel in my lab. If you are doing metagenomic analysis or considering it or …
Another really interesting microbial diversity paper in mBio. This one is from Josh Neufeld and colleagues: Multisubstrate Isotope Labeling and Metagenomic Analysis of Active Soil Bacterial Communities. The key thing they did is summarized in their abstract: We incubated samples from three disparate Canadian soils (tundra, temperate rainforest, and agricultural) with five native carbon (12C) or …
Will be headed to this meeting organized by IBM next week: Almaden Institute 2014: Sequence the City -Metagenomics in the Era of Big Data. Not 100% sure where the whole thing is going but IBM has become interested in the informatics and big data aspects of the microbial ecology of urban & built environments. And …
Professor Jane Carlton, the director of the NYU Center for Genomics and Systems Biology, is leading a team of scientists to study the metagenome of New York City. They have begun a pilot study of the microbial populations on one dollar bills, and they have begun to sample different sewage lines in all five boroughs. In …
Postdoctoral Position in Environmental Metagenomics, Norman Pace Lab, Boulder, CO Available September 1, 2012, three years appointment, NIH salary grades. A three-year Research Associate position is available for participation with a team studying the microbial metagenomics of municipal water distribution systems. Although seemingly a mundane setting, little is known about the microbiology of municipal drinking …
Here are the slides I plan to use for my talk in a little bit at Indoor Air 2011 Eisen #microBEnet #IndoorAir2011http://static.slidesharecdn.com/swf/ssplayer2.swf?doc=eisen-indoorair2011-110609092812-phpapp02&stripped_title=eisen-microbenet-indoorair2011&userName=phylogenomics View more presentations from Jonathan Eisen.
Data collection and annotation are critical parts of all aspects of science. However, it’s not always clear what data to collect. For example, say you go out in the field and harvest a plant for an experiment. You might note the time of day, the weather conditions, other nearby plants, the soil temperature, the presence …
For those interested in microbial diversity and/or metagenomics there are two volumes that are coming out soon that are of interest: Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches. Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats Edited by Frans J. de Bruijn these two volumes are the most comprehensive coverage …