It's been exciting to see the progress in getting the Theobroma cacao genome sequenced and off to the databases.
But....
I've toured the Theo chocolate factory twice now, and there's a crucial piece in the story that appears to be missing.
... Read more
"Digital biology," as I use the phrase, refers to the idea of using digital information for doing biology. This digital information comes from multiple sources such as DNA sequences, protein sequences, DNA hybridization, molecular structures, analytical chemistry, biomarkers, images, GIS, and more. We obtain this information either from experiments or from a wide variety of databases and we work with this information using several kinds of bioinformatics tools.
The reason I'm calling this field "digital biology" and not "bioinformatics" (even though I typically use the terms ... Read more
Hey students: if you are looking for a summer internship in marine metagenomics and you can get your application together before June 16th, Jonathan Eisen posted information about an open position on his blog.
It also looks like he's looking for post-docs (see the side bar on the right of this page.)Read more
Have you ever wondered what kinds of viruses can be found in human waste?
Mya Breitbart and team have been sequencing nucleic acids from fecal samples in order to find out. You might expect that we'd find viruses that infect humans or viruses that infect the bacteria in our gut.
I wouldn't have expected to learn the result that they found.
A large number, 60% of the viral DNA sequences were from unknown viruses. That's not a surprise. The surprise came when they looked at the RNA viruses.
Instead, the viral sequences most often came from a plant pathogen ... Read more
I'm in Berkeley right now at the annual Bio-Link Summer Fellows forum. We're getting to hear talks from people in the biotech industry, listen to enthusiastic instructors describe their biotech programs and ideas, and try out new educational materials.
Yesterday, two speakers (Damon Tighe and Jason Baumohl) from the Joint Genome Institute in Walnut Creek, CA, gave a fun talk about DNA sequencing and sequence assembly.
They also showed some very nice Flash animations, made by Damon Tighe, at the JGI, that illustrate how DNA sequencing is done ... Read more
We have lots of DNA samples from bacteria that were isolated from dirt. Now it's time to our own metagenomics project and figure out what they are. Our class project is on a much smaller scale than the honeybee metagenomics project that I wrote about yesterday, but we're using many of the same principles.
The general process is this:
1. We sort the chromatogram data to identify good data and separate it from bad data. Informatics can help you determine if data is
A few years ago, the General Biology students at the Johns Hopkins University began to interrogate the unseen world. During this semester-long project, they study the ecosystems of the Homewood campus, and engage in novel research by exploring the microbial ecosystems in different sections of the campus. Biology lab students gather environmental samples from different campus ... Read more
A few years ago, the General Biology students at the Johns Hopkins University began to interrogate the unseen world. During this semester-long project, they study the ecosystems of the Homewood campus, and engage in novel research by exploring the microbial ecosystems in different sections of the campus. Biology lab students gather environmental samples from different campus ... 