Understanding the properties of microbial ecosystems has taken on new importance for explaining the role of bacteria in human health, or for developing efficient environmental resource management strategies.
Research on microbial communities gain more and more attention with the increasing availability of next-generation sequencing technologies, and requires the use of greater computational resources as DNA datasets grow ever larger. On the other hand, extracting biologically meaningful signals from complex and inherently noisy datasets is not straightforward, and new analytical paradigms are required to meet the dramatic increase in the rate of data acquisition.
My research at the MBL revolves around the development of efficient algorithms that translate ‘the complex’ into ‘the comprehensible’ while making the biology main source of inspiration.
Selected Publications ^
Eren AM, et al. (2014). “Minimum entropy decomposition: Unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences“. The ISME Journal.
Eren AM, et al. (2014). “Oligotyping analysis of the human oral microbiome“. PNAS.
Eren AM, et al. (2013). “Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene data“. Methods in Ecology and Evolution.
Eren AM, et al. (2014). “A single genus in the gut microbiome reflects host preference and specificity”. The ISME Journal.
Eren AM, et al. (2011). ”Exploring the diversity of Gardnerella vaginalis through subtle nucleotide variation”. PLoS ONE.
Eren AM, et al. (2013). ”A Filtering Method to Generate High Quality Short Reads Using Illumina Paired-End Technology“. PLoS ONE.
Eren AM, et al. (2013). “DRISEE overestimates errors in metagenomic sequencing data“. Briefings in Bioinformatics.
McLellan SL and Eren AM (2014). “Discovering new indicators of fecal pollution“. Trends in Microbiology.
A full list can be seen in my Mendeley profile.
Research Interests ^
Human microbiome. Diverse assemblage of bacteria that harbor all surfaces of the human body makes us great environments to study ecological questions, and to develop a better understanding of the function of bacterial communities from a public health perspective. I study human vaginal, gastrointestinal and oral communities to find associations between microbial community structures and health and disease states of their hosts.
Marker gene anlayses. Marker genes amplified from environmental samples are indispensable tools for deep and detailed characterization of microbial population structures, including very rare members they harbor. The 16S rRNA gene has been historically a very useful gene to target and over the years we have generated tremendous amount of data. I develop tools that allow researchers to partition their high-throughput sequencing datasets into highly resolved and ecologically relevant units.
Metagenomics. Although marker genes are indispensable for the characterization of the community structure, they cannot answer questions about these communities regarding what they are capable of doing with respect to their total genomic content with confidence. Although there are challenges, metagenomic approaches that utilize shotgun sequencing of environmental DNA is key to understand the overall functional potential of microbial communities and I am interested in working with metagenomics datasets to look for answers marker gene analyses cannot provide.
Quality Filtering. Adequate quality filtering of raw sequences is a critical aspect of all studies that rely on next-generation high-througput sequencing data. I develop and maintain tools and methods to perform quality filtering on raw reads generated by massively-parallel sequencing platforms.
Oligotyping. Oligotyping is a computational method that aims to 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). For more information, please visit http://oligotyping.org.
Illumina Utilities Library. With its paired-end technology, throughput, and affordability, Illumina sequencing platforms are widely used in many fields of biological sciences. I started developing the Illumina Utils library to facilitate the application of standard operations (such as quality filtering and merging partially overlapping reads) on raw sequencing results to prepare datasets for downstream analyses. Illumina utils is a core component of the sequencing operations in the MBL. Please visit https://github.com/meren/illumina-utils more information and the source code.
BLAST Filtering Pipeline. Depending on the experimental design, partitioning reads in a metagenomic dataset into a finite number of bins may be a useful first step (such as removing host-associated DNA given the host genome, or binning the viral reads for a separate analysis given the database of viral genomes). BLAST filtering pipeline uses a very flexible configuration format that allows its user to define a chain of filters, each of which performs on the input data provided by the previous filter. It can exploit Sun Grid Engine and distribute individual processes. Please visit https://github.com/meren/BLAST-filtering-pipeline for the source code. If you think BLAST Filtering Pipeline is what you need, please get in touch with me and I may be able to help you to set it up.
|2011-2013||Post-Doctoral Training, Marine Biological Laboratory
Supervised by Dr. Mitchell L. Sogin.
|2007-2011||Ph.D., University of New Orleans
Supervised by Michael J. Ferris (Microbial Ecology), Christopher M. Taylor (Computer Science).
|1998-2002||B.S., Canakkale Onsekiz Mart Universitesi, Turkey.|