Why use Bracken instead of Kraken? by Jennifer Lu and Steven Salzberg Kraken is a very fast, accurate program for classifying metagenomic sequencing data. It takes a set of reads, contigs, or other DNA sequences and for assigns a taxonomic label (species, genus, etc.) to each one. Last year we discovered that some people were …
When I first started working in Dr. Jonathan Eisen’s lab my junior year of college, I was assigned a pretty open ended task. Swab something from the built environment and see what grows. This being the first time I was actually doing research, I was incredibly excited to go out and swab the world. My …
The Aerobiota of the Mauna Loa Observatory (MLO), Hawai’i project will fully characterize the fungal and bacterial communities captured over the last decade by air filters at the MLO on the island of Hawai’i, one of the most remote locations on earth. It might seem odd to call a weather station in a remote …
Last call for submissions of the ASM Agar Art Competition See American Society for Microbiology Submission Manager – Agar Art 2017 Submit a photo of your original, microbe- and agar-based art for the chance to win up to $485′ worth of prizes. Top submissions will be showcased online and in a gallery at the American Society …
Catching up after a couple of busy weeks. Microbes in the hospital Diversity changes of microbial communities into hospital surface environments – Rika Yano – Journal of Infection and Chemotherapy ($31.50) Previous works have demonstrated considerable variability in hospital cleanliness in Japan, suggesting that contamination is driven by factors that are currently poorly controlled. We undertook 16S …
(Thanks to Paula Olsiewski for passing on this information from the EPA) Dear Stakeholder, Consistent with Executive Order 13777, the U.S. Environmental Protection Agency’s (EPA) Office of Air and Radiation (OAR) is hosting a public teleconference on April 24, 2017, from 11:00 a.m. to 2:00 p.m. EDT to solicit input on specific air and radiation …
It seems to me that this is calling out for some large scale comparative microbial community study: Salt from icy roads is contaminating North America’s lakes – The Washington Post Basically, there is evidence that lakes throughout North America have seen a big increase in salt levels connected to salt used to try and deal …
Job posting of possible interest Source: Recruitment Details – UC Berkeley AP Recruit DESCRIPTION Bioinformatics and Biochemist Scientist, IGI Institute – University of California, Berkeley. The IGI Institute and the Department of Earth and Planetary Science at the University of California seek applications for a full time (100%) Associate Project Scientist, Step I – III, …
Of interest: Source: Alfred P. Sloan Foundation Award Fellowships to Study ISS Microbes | NASA Fellow: Melissa Dsouza, University of Auckland, New Zealand PI-Advisor: Kasthuri Venkateswaran, NASA Jet Propulsion Laboratory Investigating mechanisms for the acquisition and prevalence of antibiotic resistance genes in the ISS cultivable microbiome. Awarded by the NASA Space Biology Program. Fellow: Michael Lee, University of …
WTH is ILR? by Alex Washburne & Jamie Morton Jamie and I have penned a popularization of the isometric log-ratio transform with the intention to allow non-mathematicians to understand the intuition behind what it is, why we use it, and how different methods use the same tool in different ways. The full write-up is available …