Last week I had the opportunity to present a lecture on the history of DNA sequencing in Jonathan Eisen’s EVE 161 Microbial Phylogenomics course. This lecture uses Elaine Mardis’ excellent review papers on the next generation sequencing methods as a guide (and required reading). You can see videos of both Dr. Mardis and Dr. Eisen presenting lectures on this topic. …
“All right, but apart from the sanitation, medicine, education, wine, public order, irrigation, roads, the fresh water system and public health, what have the Romans ever done for us?” from Monty Python’s Life of Brian When they conquered large parts of Europa and the Mediterranean in the 1st-3rd centuries AD, the Romans brought a lot of …
This month the QIIME development group is starting the transition from prototyping to developing QIIME 2. To mark this transition and to follow up on my recent blog post, Toward QIIME 2, I put together a demo video that illustrates the end point of one of our QIIME 2 prototypes, q2d2, which you can find …
I made a Storify summary of the Tweets from a workshop at the Pacific Symposium on Biocomputing that I attended on Tuesday on Computational Microbiology (with a big focus on microbiomes). [<a href="//storify.com/phylogenomics/psb16-session-on-microbiomes” target=”_blank”>View the story “#PSB16 session on computational microbiome #microbiomes ” on Storify]
Our food comes into contact with a lot of different materials and machines before it reaches our plates. The agriculture industry tries hard to ensure proper food safety by testing random representative samples of each batch of produce or food product before sending it out for distribution. They cannot send out the batch until they …
MicroBEnet community, I’m now entering the 5th month of sampling for my MoBE postdoctoral fellowship [see https://microbe.net/2014/10/29/microbiomes-and-the-athletic-arena-indoor-track-facility-microbiome-in-conjunction-with-salivary-and-nostril-microbiomes-of-indooroutdoor-runners/] and want to begin compiling the pertinent physical building-centric metadata (not for the individual samples, that I have as ongoing) for my project. Below is the list that I currently have, but if the community feels that there are other …
Happy New Year to you all! Here are some interesting new papers that I found over the holidays. Floors Rapid assemblage of diverse environmental fungal communities on public restroom floors – Jennifer Fouquier – Indoor Air An increasing proportion of humanity lives in urban environments where they spend most of their lives indoors. Recent molecular studies …
Here are my notes from day 3 of the Mothur Workshop that is taught by Pat Schloss (pdschloss at gmail.com) at a hotel that is conveniently located near the Detroit airport. Of all of the bioinformatic workshops I have attended, this group of students was my favorite so far. We had a lot of fun …
The list of things that are sterile is shrinking as DNA sequencing methods become more sensitive and are able to pick up microbial signals in even the sparsest environments. A news article in the Times discusses research on the microbiome of the human womb and the fact that it is not actually as sterile as …
Here are my notes from day 2 of the Mothur workshop taught by Pat Schloss (pdschloss at gmail.com) in December 2015. For those who are interested in learning to use Mothur for microbiome studies, Pat will be teaching another one in February. Mothur is better for bacterial characterization than eukaryotes because the sequences are aligned before OTU clustering. This …