metagenomics

"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

I just love this title! It's nerdy and cute, all at the same time. I read about this in www.researchblogging.org and had to check out the paper and blog write up from The Beagle Project (BTW: some of you may be interested in knowing that The Beagle Project is not a blog about dogs.) The paper describes a class where students from Marseilles University investigate the function of unidentified genes from a ... 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

Ribosomes are molecular machines that build new proteins. This process of synthesizing a protein is also known as translation. Many antibiotics prevent translation by binding to ribosomal RNA. In the class that I'm teaching, we're going to be looking at ribosome structures to see if the polymorphisms that we find in the sequences of 16S ribosomal RNA are related antibiotic resistance. This is related to our ... Read more

Okay OpenOffice fans, show me what you can do. Earlier this week, I wrote about my challenges with a bug in Microsoft Excel that only appears on Windows computers. Since I use a Mac, I didn't know about the bug when I wrote the assignment and I only found out about it after all but one of my students turned in assignment results with nonsensical pie graphs. So, I asked what other instructors do with software that behaves differently on different computing platforms. I never did hear from ... Read more

Do different kinds of biomes (forest vs. creek) support different kinds of bacteria? Or do we find the same amounts of each genus wherever we look? Those are the questions that we'll answer in this last video. We're going to use pivot tables and count all the genera that live in each biome. Then, we'll make pie graphs so that we can have a visual picture of which bacteria live in each environment. The parts of this series are: I. Downloading the data from iFinch and preparing it ... Read more

This is third video in our series on analyzing the DNA sequences that came from bacteria on the JHU campus. In this video, we use a pivot table to count all the different types of bacteria that students found in 2004 and we make a pie graph to visualize the different numbers of each genus. The parts of this series are: I. Downloading the data from iFinch and preparing it for analysis. (this is the video below) (We split the data from one column into three). II. ... Read more

What do you do after you've used DNA sequencing to identify the bacteria, viruses, or other organisms in the environment? What's the next step? This four part video series covers those next steps. In this part, we learn that a surprisingly large portion of bioinformatics, or any type of informatics is concerned with fixing data entry errors and spelling mistakes. The parts of this series are: I. Downloading the data from iFinch and preparing it for analysis. (this is the ... Read more

For the past few years, I've been collaborating with a friend, Dr. Rebecca Pearlman, who teaches introductory biology at the Johns Hopkins University. Her students isolate bacteria from different environments on campus, use PCR to amplify the 16S ribosomal RNA genes, send the samples to the JHU core lab for sequencing, and use blastn to identify what they found. Every year, I collect the data from her students' experiments. Then, in the bioinformatics classes I teach, we work with the chromatograms and other data to see what we can find. This is the first part of a four part video series ... Read more