Hi.
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.
I graduated from the University of New Orleans in 2011, where my research interests shifted from machine learning to the study of microbial communities and their ecology.
During my Ph.D., I studied the human microbiome and microbial diversity, and developed tools and methods to facilitate microbial community analyses based on 16S rRNA gene-tag sequences. I also studied channel current cheminformatics and single-molecule analyses with α-hemolysin based nanopore experiments for the first 3 years of my Ph.D.
I am a GNU and open-source advocate, and an open-science / open-access supporter, and I am proud to be one of the developers of Pardus Linux.
Finally, here is my LinkedIn profile, and the public GitHub repository I recently started using to keep track of some of the bioinformatics tools I develop. Also my Ph.D. dissertation is available here.
Oligotyping
Oligotyping is a young method that may be useful in the domain of microbial ecology to answer some specific questions. I’ve been playing with the idea and the implementation during my Ph.D.
It’s aim is to allow researchers (who are working with 16S ribosomal RNA gene tag sequences to generate microbial community profiles of environmental samples) to decompose and investigate hidden types within their libraries. I recently started maintaining a blog on oligotyping for people who might be interested at http://oligotyping.org/.
Photography
Photography is something I do passionately. You can see some of my photography here. I also have a photography blog in Turkish.
If you are here because you need a photographer, please send me an e-mail. I am an open minded photographer who likes to experiment, and try different things. I am not doing photography for money, and you can’t hire me. However, if you have an interesting idea/project I might like to give it a try. If you are a non-profit organization and in need of a photographer for any purpose, please let me know. I have a crush on NPO’s and I would be glad to try to help. TFP requests are welcome depending on the project, as well. You may send your e-mails to a.murat.eren/gmail.
Tattoo
This is my Science Tatto Emporium-reject tattoo (smiley):
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 helped 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 are governing the nutrient cycle on this planet, forming much of our planet’s biomass, harboring our bodies with numbers we could not comprehend, and who can communicate intensively, form strong biofilms for healthier communities, show altruistic and social behaviors, and get organized and do things together –maybe way better than us, in some cases).
The more I learned, the more attached I felt. It didn’t take much time to realize that I wanted to be a microbial ecologist more than a computer scientist. Soon after this 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 their 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 them 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, if 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 representation, I remember myself thinking that no one could have portrayed Staphlococcus aureus any better than that: 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 Kevin drew).
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 article by Carl Zimmer: “How Microbes Defend and Define Us“.
