We recently published a method to normalize data that corrects for batch effects and allows for pooling of raw data across studies. In this post, I want to discuss more about the important (but potentially confusing) aspect of our method, where we add noise to the zeros before performing the normalization. I’ve gotten a few …
This is really fascinating: Source: Team discover how microbes survive clean rooms and contaminate spacecraft Hat tip to Elisabeth Bik for posting about this on Twitter So cool: microbes actually feed on the cleaning products. Also cool: undergraduates as authors. Team discover how microbes survive clean rooms and contaminate spacecraft https://t.co/ox4kMawHko — Elisabeth Bik (@MicrobiomDigest) June …
We started class by talking about how to interpret our PCR results by looking at gel images. The goal for the day was to prepare the samples that worked (ie had positive bands on gel) for submission for Sanger Sequencing. We had a brief discussion about why we need to clean up PCR products, how …
There can be points when running a CURE where there are tradeoffs between student learning and the best utilization of class time. In this case, we set-up and ran the PCR for the students ‘behind the scenes’ rather than using class time for them to do it themselves. These ‘black boxes’ can be detrimental to …
The structure of these two weeks involving pH growth curves and analysis was very similar to that of the previous two weeks (osmolarity). Before class, our student assistants performed dilution streaks (instead of the students) and prepared overnight cultures from those plates. The overnight cultures were used by the students for the pH growth curves. …
Twitter Logo: Wikimedia Commons Public Domain Thought this might be of interest to various folks. I made a Twitter moment regarding a discussion about microbial genome annotation methods. Microbial Genome Annotation Methods https://platform.twitter.com/widgets.js
So we recently had two problems with a common solution: #1, we hadn’t had a lab social function in awhile #2, we wanted to try using the MinION sequencer in a “field” setting, but weren’t quite ready to try it without electricity on hand. The obvious solution, have the entire lab over to my house …
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 …
So yesterday morning, Jonathan Eisen and myself headed down to Antioch, CA to sample a pilot wastewater treatment facility. In a couple of hours I went from knowing literally nothing about the process to having some handle on at least the latter stages. Pretty cool microbiology. As I understand the problem at hand, conventional wastewater …
Hotel pools and spas cause a third of pool-linked disease outbreaks Just a quick one here — From NBC: Here’s what’s in your pool this summer