I am a post-doctoral researcher at Marine Biological Laboratory, The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, studying microbial ecology under the supervision of Mitchell L. Sogin with my computer science background. My e-mail address is a.murat.eren at gmail (PGP Key).
I develop algorithms to make sense of high-throughput sequencing data and better understand the diversity of bacteria in nature mostly through 16S rRNA gene amplicons. Even though I enjoy working with bacterial samples from many different habitats, I am mostly focused on human microbiome.
Oligotyping is a novel method that may be useful in the domain of microbial ecology to answer some specific questions. The method makes it possible to decompose very closely related taxa based on high-throughput sequencing analysis of phylogenetically informative genes amplified from environmental samples (such as 16S rRNA gene). I’ve been playing with the idea and the implementation during my Ph.D.
I recently started maintaining a blog on oligotyping for people who might be interested: http://oligotyping.org/
Fall in love with some activity, and do it! Nobody ever figures out what life is all about, and it doesn’t matter. Explore the world. Nearly everything is really interesting if you go into it deeply enough. Work as hard and as much as you want to on the things you like to do the best. Don’t think about what you want to be, but what you want to do. Keep up some kind of a minimum with other things so that society doesn’t stop you from doing anything at all.
Yes! Fall in love with some activity. Fall in love with some people, too. Don’t ever let the society intimidate you. Be the honey badger. Eat cobra.
This is where I am originally from (more photos):
In a parallel universe I am still a shepherd on these mountains.
I have a bunch of Staphlococcus aureus guys on my arm:
Here is the story of it:
When I was a researcher analyzing molecular signal data from nano-pore experiments at the Research Institute of Children’s Hospital in New Orleans, I met Michael J. Ferris, a professor in microbiology at Louisiana State University, and ended up helping him to solve one of the ‘microbial ecology’ problems he was dealing with that required serious computational aid.
I didn’t really know much about microbiology or microbial ecology when I met him, but while I was trying to help him with his problem, I started to learn about the fascinating universe of microbial beings (who govern the nutrient cycle on the planet, form much of our planets biomass, harbor our bodies with numbers we could not comprehend, can communicate intensively, form biofilms for healthier communities, show altruistic and social behaviors, and get organized and do things together –maybe way better than us, in most cases).
The more I learned, the more attached I felt and it didn’t take much time to realize that I wanted to be a microbial ecologist more than a computer scientist. Soon after the serendipitous encounter with Dr. Ferris, I changed my research focus and started working with bacterial populations and their ecology from the perspective of the human microbiome. I was quite concerned at the beginning with the almost-impossible-to-address diversity of bacteria, but after a while I became comfortable with the idea that we may never be able to cover the entire diversity of bacteria, or understand their distribution patterns completely (and this, after almost two years since I started working with microbial populations, gives me an interesting eudemonia).
One day I asked a friend of mine, Kevin Simpson, who was a post-doctoral researcher in Children’s Hospital, whether he would like to draw some bacteria, protozoa and maybe other microbial beings for me to use in one of my upcoming presentations. He did. When I saw his drawings, I remember myself thinking that no one could have portrayed Staphlococcus aureus any better than the way Kevin portrayed them. Even though most people know S. aureus due to the hospital-acquired infections caused by methicillin-resistant strains, S. aureus actually is a commensal resident of healthy human skin flora and most of the time they mind their own business (probably chilling around just like those smiling guys on my arm).
If you are interested to know more about the most diverse clade of life and our interrelationship with them, you might want to read this -now quite dated- article by Carl Zimmer: “How Microbes Defend and Define Us“.